https://wiki.geneontology.org/api.php?action=feedcontributions&user=Valwood&feedformat=atomGO Wiki - User contributions [en]2024-03-29T01:46:45ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Ontology_meeting_2023-07-17&diff=85612Ontology meeting 2023-07-172023-07-15T07:19:58Z<p>Valwood: Created page with " Suggested item. Further improving the efficiency of term obsoletion. These small tweeks: 1. When we create the annotation files, 4 files are not created and we need to look at them all to see if they have any contents. Is it possible to not create the file if there are no annotations? 2. We still need to create a lot of tickets for the obsoletion, and then do the e-mail. Can we think of any other ways to streamline further?"</p>
<hr />
<div><br />
Suggested item. Further improving the efficiency of term obsoletion.<br />
These small tweeks:<br />
1. When we create the annotation files, 4 files are not created and we need to look at them all to see if they have any contents. Is it possible to not create the file if there are no annotations?<br />
2. We still need to create a lot of tickets for the obsoletion, and then do the e-mail. Can we think of any other ways to streamline further?</div>Valwoodhttps://wiki.geneontology.org/index.php?title=Variant_annotation&diff=82964Variant annotation2022-08-17T11:54:31Z<p>Valwood: /* Schizosaccharomyces pombe */</p>
<hr />
<div>[[Category:Reference Genome]]<br />
This page describes the different ways in which GOC annotation generators deal with alternate spliceforms. See also [[Annotation_of_Alternate_Spliceforms]]<br />
<br />
==Arabidopsis thaliana==<br />
<br />
We annotate splice variant specific information when available. Our INTERPRO2GO- and TargetP- based IEA annotations are splice variant specific, if one of the proteins that is encoded by the locus does not have a domain that the other/s do, this one does not get that annotation. I think that there are very few experimental annotations that we have that are splice variant specific.* <br />
<br />
* '''CONFIRMED''': gene-associations/gene_association.tair.gz has only ''gene'' in col12 -- CJM<br />
* '''NOTE''': we hope to transition to having more that one DB_Object_Type in the next month or so --Tanya<br />
<br />
==Caenorhabditis elegans==<br />
<br />
We are starting to see a few examples of isoform-specific functions and/or localization in the C. elegans literature. In the cases where we can confidently match the isoform to a Wormpep protein identifier (e.g., WP:CE25075), then we make the annotation specifically to that isoform. If, from the paper, we can't determine the specific isoform used, then by default we make the annotation to all of the protein isoforms.<br />
<br />
* '''CONFIRMED''' -- CJM (see also [[Annotation_of_Alternate_Spliceforms]])<br />
<br />
==Danio rerio==<br />
We almost never have enough info to curate to the level of a splice variant. Our annotations are applied at the level of the gene.<br />
<br />
==Dictyostelium discoideum==<br />
<br />
So far we only have a few genes and publications that described splice variants, and the papers never described different functions for the different variants. Hence, we currently don't capture annotations to different variants of gene products.<br />
<br />
==Drosophila melanogaster==<br />
<br />
At the moment we attach all GO terms to genes. We are in the process of figuring out how to move to change our curation method to annotating proteins. In the meantime we make an internal note for papers that describe isoform specific info so that we can revisit these.<br />
<br />
==Escherichia coli==<br />
<br />
==Gallus gallus==<br />
<br />
We are using UniProtKB accession IDs wherever possible and this allows us to annotate specific isoforms if required.<br />
<br />
==Homo sapiens==<br />
<br />
The human group annotates to UniProtKB accessions. When a paper provides isoform-specific information, then this data can be captured using the appropriate UniProt isoid. E.g. Q4VCS5-1, Q4VCS5-2.<br />
When isoform-specific information is not provided then the top-level UniProt accession number is only annotated to, e.g. Q4VCS5.<br />
<br />
* Chris - the above may reflect how this is captured internally, but this is not reflected in the GAF<br />
* Emily - this information *is* exported in the UniProt file, however due to a production bug, isoid annotations are not getting into the species-specific files. This is being rectified.<br />
<br />
==Mus musculus==<br />
<br />
For each annotation, MGI has a "notes field" that is not available to the public. That note has a structure as follows:<br />
<br />
evidence:<br />
anatomy:<br />
cell type:<br />
gene product:<br />
qualifier:<br />
target:<br />
external ref:<br />
text:<br />
<br />
If a paper actually specifies a specific isoform, the appropriate refseq is entered into the "gene_product" field<br />
<br />
eg, For the annotation of MGI:1341722,Kcnh2,to GO:0005886, plasma membrane,by IDA, the field would look like:<br />
<br />
gene_product:SPKW:O35219-1<br />
<br />
We presently only have about 300 of these with experimental evidence codes, annotated after the adoption of the structured notes. So QC has to be done for some. Annotations done prior to that will not have any entry, as we had no way of capturing the data.<br />
We are looking at ways to "back annotate" by identifying having multiple isoforms identified in references that have been used for GO annotation at MGI.<br />
<br />
* NOTE: See [[Annotation_of_Alternate_Spliceforms]] for more on MGI method --CJM<br />
<br />
==Rattus norvegicus==<br />
<br />
There are not too many splice variants currently in the database. Those that are have their own DB:ID, get the symbol of the parent gene with underscore vnumber followed by variant of symbol in parentheses with symbol hyperlinked to the report page of the parent gene. Example:geneX_v1 (variant of geneX). The variants can also be accessed from the top level gene. The variants may have some mapping, sequence, other external database links, if applicable. They seldom have annotations. It may happen that the information in the literature allows for annotation of the splice variants but that is rather rare.<br />
<br />
* '''CONFIRMED''': GAF has gene and protein in col12. Protein annotations are to a mixture of ENSEMBL and UNIPROT IDs<br />
<br />
==Saccharomyces cerevisiae==<br />
<br />
We have very few documented cases of splicing or processing variants, and our database structure currently cannot display variant gene product forms. So, we do not at this time annotate variants. We annotate only one gene product per gene. We are working on a database restructure so that we can represent different variants, but it has not yet been implemented.<br />
<br />
==Schizosaccharomyces pombe==<br />
<br />
Pending</div>Valwoodhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2021-04-20&diff=80117Annotation Conf. Call 2021-04-202021-04-20T15:16:02Z<p>Valwood: /* Attendance */</p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== GOC Meetings, Other Announcements ==<br />
<br />
=== May Consortium Meeting ===<br />
* Virtual Consortium Meeting -Tuesday May 4th - Friday May 7th (note shift forward by one day)<br />
* [https://www.eventbrite.com/e/gene-ontology-main-meeting-remote-tickets-150240357955 Registration]<br />
** [https://docs.google.com/document/d/1QVruWj797NOHJgs06859Hy3WvsL504H5XcTEwSiGqUQ/edit Agenda/Minutes] - review topics for breakout groups and/or workshops<br />
* Group presentations:<br />
** Organize around topics<br />
*** Community Curation and Automated Approaches<br />
*** GO Annotation of Host-Pathogen Interactions<br />
<br />
=== GO-CAM Office Hours ===<br />
* [https://docs.google.com/document/d/1_ZIasvb0hhmJ1teEQ-wegvPob5T74-JeV4UGcZn_evE Agenda]<br />
<br />
=== Noctua Outages ===<br />
* Weekend of April 23rd (this coming weekend)<br />
** Planned LBL outages<br />
<br />
== GAF 2.2 ==<br />
* Waiting for an official release<br />
* Some issues along the way have prevented a public release<br />
* Snapshot ran on Sunday, April 18th<br />
* One meeting workshop - [https://docs.google.com/spreadsheets/d/1JTvDVpggXgpsmCpHHdurqM6NxiTGK4LXkxdQr66jf48 capturing metadata] about annotation file flow, gene product-to-term relations, group contacts<br />
<br />
= Attendance =<br />
* On call: Birgit, Chris, David, Dustin, Edith, Giulia, Harold, Helen, Kimberly, Li, Malcolm, Mary K, Midori, Pascale, Penelope, Petra, Raymond, Rob, Robert, Ruth, Seth, Stacia, Stan, Suzi, Val<br />
<br />
[[Category:Annotation Working Group]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2019-11-26&diff=76857Annotation Conf. Call 2019-11-262019-11-26T16:28:14Z<p>Valwood: /* Minutes */</p>
<hr />
<div>= Agenda =<br />
== Progress Reports ==<br />
*Reminder: due mid-December<br />
*Annotation Group [https://docs.google.com/document/d/15HObk9-uPxYrgHaOK6RKKCbGJybnOrdoIr4JtkUTdjM Template]<br />
*GO will generate annotation stats<br />
<br />
== Pipeline Reports ==<br />
*Continue to check these as more rules are implemented<br />
*Question about pipeline for 'do not annotate' to external2go groups, e.g. InterPro<br />
**https://github.com/geneontology/go-annotation/issues/1748<br />
*Question about [https://github.com/geneontology/go-site/blob/master/metadata/rules/gorule-0000015.md gorule0000015 - Dual species taxon check]<br />
**Should defense responses to bacteria, for example, be considered GO:0044419 : interspecies interaction between organisms<br />
<br />
==Noctua Form 2.0 Demo==<br />
*Demonstration of the newly redesigned Noctua curation form<br />
*[https://docs.google.com/document/d/1DZu25YKdH_D3Ics5BSmyvN8IGfGlTcCcwQ4HzviZeWM/edit#heading=h.e6msjvy4rdk9 User Guide]<br />
*[https://geneontology.github.io/noctua-form/ Draft User Guide with short video]<br />
<br />
== Upcoming Meetings ==<br />
*Pathways2GO - NYU, December 2nd-4th<br />
*Alliance F2F and SAB - Cambridge, MA, December 9th - 12th<br />
<br />
= Minutes =<br />
*Present: Dave F, David H, Edith, Giulia, Harold, Karen, Kimberly, Laurent-Philippe, Leonore, Michele, Niels, Pascale, Patrick, Penelope, Petra, Seth, Shur-Jen, Stacia, Stan, Suzi A, Val<br />
<br />
== activated_by annotation extensions ==<br />
*Petra suggested we look at some specific examples that may not be immediately amenable to re-annotating with an MF 'binding' term<br />
*Pascale will create a ticket in go-annotation so we can track discussion in the ticket<br />
<br />
[[Category:Annotation Working Group]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=761372019 Berkeley GOC Meeting Logistics2019-09-08T09:22:44Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351| Eventbrite]--pay online with credit or debit card or Paypal<br />
** $130 registration fee covers coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner on Oct 9 (not including alcoholic beverages). It does NOT cover any expenses for the User Meeting or the SAB meeting.<br />
* Please also fill in the fields in the [[#Attendees | Attendees list]] at the bottom of this page.<br />
** If you don't have edit permission as a GO member, you can instead fill out [https://bit.ly/2019GOBerkeley this signup form].<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics SAB Meeting], UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley).<br />
* Note that food and beverages at the User Meeting are not covered by the GOC meeting registration fee--you are responsible for paying for your own food and beverages during the User Meeting.<br />
<br />
=SAB Meeting=<br />
* SAB Meeting: Friday, October 11 (time TBA) in [https://goo.gl/maps/kFG8EPBBjWJnuy6EA Stanley Hall] on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
Scroll down to the "Getting around" section for more info.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the Potter Street meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/event-reservations/reservation-link.mi?id=1563407776453&key=GRP&app=resvlink| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the Potter Street meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the Potter Street meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the Potter Street meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
= Getting around / To do / Local activities =<br />
<br />
The organizers have lived in the area for a very long time. If you have *any* questions, do not hesitate to reach out to us and let us make your stay in the Bay Area more more pleasant.<br />
<br />
== Getting around ==<br />
<br />
The LBL Potter Street site is located near a highway in a mixed business park and light industrial area.<br />
<br />
=== Walking ===<br />
<br />
Walking from the Emeryville hotel (Four Points Sheraton) to the meeting site is doable, but not necessarily a "pleasant" walk. It takes about half an hour.<br />
<br />
Walking from downtown is not advised and would take about an hour.<br />
<br />
=== By car (inc. "rideshare") ===<br />
<br />
If you are driving to the GO meeting, parking should not be an issue--while there will be no on-site parking, there is usually plenty of on-street parking in the surrounding area if you can walk a little. If you intend on driving, contact Seth or Nomi for details.<br />
<br />
The are usually plenty of Lyfts and Ubers in the area. The downtown area is about 10-12 minutes away.<br />
<br />
=== By public transportation ===<br />
<br />
==== From downtown ====<br />
<br />
===== LBL shuttle =====<br />
<br />
There is a fairly frequent LBL shuttle that directly connects downtown Berkeley area and the Potter Street site:<br />
<br />
https://commute.lbl.gov/resource/shuttle-buses/maps-routes-schedules/potter-st-jbei-route/<br />
<br />
You will need to show an LBL guest pass to board this shuttle. We can provide these on request--contact Seth or Nomi. The shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
===== Bus (AC Transit) =====<br />
<br />
There is also a bus that departs from near downtown and the Durant hotel and has a stop quite near the Potter Street site:<br />
<br />
http://www.actransit.org/maps/schedule_results.php?quick_line=36&Go=Go<br />
<br />
==== From Emeryville ====<br />
<br />
While it does not run directly by the hotel, one would need to walk a little and cross a bridge over the tracks, there is a free public shuttle that runs from near the hotel to near the Potter Street site: The Emery Go-round ():<br />
<br />
https://www.emerygoround.com/standard-service.html<br />
<br />
=== Biking and scootering ===<br />
<br />
The are is fairly well served by various "last mile" solutions.<br />
<br />
Rental bikes (now Lyft, previously Ford GoBikes) are available at various locations (https://member.baywheels.com/map/), including downtown Berkeley and near the meeting site (next to the Berkeley Bowl grocery store).<br />
<br />
==Food and drinks==<br />
<br />
=== Overview ===<br />
<br />
Downtown Berkeley has lots of places to eat. The LBL Potter Street location is much more limited for cafes and restaurants, but there is a large supermarket with a cafe (Berkeley Bowl) a few blocks away. Ubereats and the like are always an option for people wanting more variety and many of the organizers will have vehicles and may be doing various errands about town anyways, if there is something in particular you want or need.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==Exercise==<br />
<br />
For people interested in hitting the gym or swimming, the UC Berkeley recreational facilities are open to the general public with day passes:<br />
<br />
https://recsports.berkeley.edu/day-passes/<br />
<br />
The main rec facility and pool location is a short walk from downtown Berkeley. Several of the satellite pools have reduced day pass rates.<br />
<br />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 9, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 10, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
If you're staying around until Friday, there's an optional expedition on Thursday evening (see above).<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Nash Hotel<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
|<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not yet booked<br />
| Yes<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| <br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Alex Ignatchenko<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jeff De Pons<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| George Georghiou<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| <br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Valerie Wood<br />
| Cambridge<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airb&b<br />
| Yes<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Malcolm Fisher (Xenbase) will attend remotely.<br />
<br />
Li Ni (MGI) will attend remotely.<br />
<br />
Birgit Meldal (EBI Complex Portal) - remotely if required (need to see schedule) / manageable (I'm +8 hours)<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=761362019 Berkeley GOC Meeting Logistics2019-09-08T09:22:16Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351| Eventbrite]--pay online with credit or debit card or Paypal<br />
** $130 registration fee covers coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner on Oct 9 (not including alcoholic beverages). It does NOT cover any expenses for the User Meeting or the SAB meeting.<br />
* Please also fill in the fields in the [[#Attendees | Attendees list]] at the bottom of this page.<br />
** If you don't have edit permission as a GO member, you can instead fill out [https://bit.ly/2019GOBerkeley this signup form].<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics SAB Meeting], UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley).<br />
* Note that food and beverages at the User Meeting are not covered by the GOC meeting registration fee--you are responsible for paying for your own food and beverages during the User Meeting.<br />
<br />
=SAB Meeting=<br />
* SAB Meeting: Friday, October 11 (time TBA) in [https://goo.gl/maps/kFG8EPBBjWJnuy6EA Stanley Hall] on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
Scroll down to the "Getting around" section for more info.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the Potter Street meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/event-reservations/reservation-link.mi?id=1563407776453&key=GRP&app=resvlink| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the Potter Street meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the Potter Street meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the Potter Street meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
= Getting around / To do / Local activities =<br />
<br />
The organizers have lived in the area for a very long time. If you have *any* questions, do not hesitate to reach out to us and let us make your stay in the Bay Area more more pleasant.<br />
<br />
== Getting around ==<br />
<br />
The LBL Potter Street site is located near a highway in a mixed business park and light industrial area.<br />
<br />
=== Walking ===<br />
<br />
Walking from the Emeryville hotel (Four Points Sheraton) to the meeting site is doable, but not necessarily a "pleasant" walk. It takes about half an hour.<br />
<br />
Walking from downtown is not advised and would take about an hour.<br />
<br />
=== By car (inc. "rideshare") ===<br />
<br />
If you are driving to the GO meeting, parking should not be an issue--while there will be no on-site parking, there is usually plenty of on-street parking in the surrounding area if you can walk a little. If you intend on driving, contact Seth or Nomi for details.<br />
<br />
The are usually plenty of Lyfts and Ubers in the area. The downtown area is about 10-12 minutes away.<br />
<br />
=== By public transportation ===<br />
<br />
==== From downtown ====<br />
<br />
===== LBL shuttle =====<br />
<br />
There is a fairly frequent LBL shuttle that directly connects downtown Berkeley area and the Potter Street site:<br />
<br />
https://commute.lbl.gov/resource/shuttle-buses/maps-routes-schedules/potter-st-jbei-route/<br />
<br />
You will need to show an LBL guest pass to board this shuttle. We can provide these on request--contact Seth or Nomi. The shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
===== Bus (AC Transit) =====<br />
<br />
There is also a bus that departs from near downtown and the Durant hotel and has a stop quite near the Potter Street site:<br />
<br />
http://www.actransit.org/maps/schedule_results.php?quick_line=36&Go=Go<br />
<br />
==== From Emeryville ====<br />
<br />
While it does not run directly by the hotel, one would need to walk a little and cross a bridge over the tracks, there is a free public shuttle that runs from near the hotel to near the Potter Street site: The Emery Go-round ():<br />
<br />
https://www.emerygoround.com/standard-service.html<br />
<br />
=== Biking and scootering ===<br />
<br />
The are is fairly well served by various "last mile" solutions.<br />
<br />
Rental bikes (now Lyft, previously Ford GoBikes) are available at various locations (https://member.baywheels.com/map/), including downtown Berkeley and near the meeting site (next to the Berkeley Bowl grocery store).<br />
<br />
==Food and drinks==<br />
<br />
=== Overview ===<br />
<br />
Downtown Berkeley has lots of places to eat. The LBL Potter Street location is much more limited for cafes and restaurants, but there is a large supermarket with a cafe (Berkeley Bowl) a few blocks away. Ubereats and the like are always an option for people wanting more variety and many of the organizers will have vehicles and may be doing various errands about town anyways, if there is something in particular you want or need.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==Exercise==<br />
<br />
For people interested in hitting the gym or swimming, the UC Berkeley recreational facilities are open to the general public with day passes:<br />
<br />
https://recsports.berkeley.edu/day-passes/<br />
<br />
The main rec facility and pool location is a short walk from downtown Berkeley. Several of the satellite pools have reduced day pass rates.<br />
<br />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 9, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 10, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
If you're staying around until Friday, there's an optional expedition on Thursday evening (see above).<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Nash Hotel<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
|<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not yet booked<br />
| Yes<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| <br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Alex Ignatchenko<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jeff De Pons<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| George Georghiou<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| <br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Valerie Wood<br />
| Cambridge<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Malcolm Fisher (Xenbase) will attend remotely.<br />
<br />
Li Ni (MGI) will attend remotely.<br />
<br />
Birgit Meldal (EBI Complex Portal) - remotely if required (need to see schedule) / manageable (I'm +8 hours)<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=761352019 Berkeley GOC Meeting Logistics2019-09-08T09:21:31Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Berkeley, October 7-10, 2019=<br />
<br />
* Location: [https://goo.gl/maps/cfabKMyCSPZmFkFf7| 717 Potter Street, Berkeley, CA]<br />
<br />
==Registration==<br />
* Via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351| Eventbrite]--pay online with credit or debit card or Paypal<br />
** $130 registration fee covers coffee & snacks for the 2.5-day GOC meeting, as well as 2 lunches and the Consortium dinner on Oct 9 (not including alcoholic beverages). It does NOT cover any expenses for the User Meeting or the SAB meeting.<br />
* Please also fill in the fields in the [[#Attendees | Attendees list]] at the bottom of this page.<br />
** If you don't have edit permission as a GO member, you can instead fill out [https://bit.ly/2019GOBerkeley this signup form].<br />
<br />
==Overall schedule== <br />
*Monday, October 7: User Meeting (8:30am-5pm)<br />
*Tuesday-Thursday October 8-10: GOC Meeting (8:30am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11 (time TBA): [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics SAB Meeting], UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley).<br />
* Note that food and beverages at the User Meeting are not covered by the GOC meeting registration fee--you are responsible for paying for your own food and beverages during the User Meeting.<br />
<br />
=SAB Meeting=<br />
* SAB Meeting: Friday, October 11 (time TBA) in [https://goo.gl/maps/kFG8EPBBjWJnuy6EA Stanley Hall] on the UC Berkeley campus. Logistics [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| here].<br />
* SAB dinner: Thursday, October 10, 7pm: place TBD<br />
<br />
=Arriving=<br />
<br />
The closest airports are San Francisco (SFO) and Oakland (OAK). From either of those, you can take BART to Berkeley and get a taxi/Lyft/Uber from the Ashby BART station.<br />
<br />
Scroll down to the "Getting around" section for more info.<br />
<br />
=Hotels=<br />
These are listed in increasing order by price. The Four Points by Sheraton is the only one that's walking distance (1.4 miles) from the meeting location; the others are downtown, a short drive away. [https://docs.google.com/document/d/1DaSiBXlW6gjH840h9kdC3FVbuVuetqglcsgrDvB7maE/edit| This map] shows the relative locations of the hotels.<br />
<br />
For travel to our building, we will arrange for attendees to have access to the LBNL Potter St. shuttle to our building from downtown Berkeley.<br />
<br />
===[http://downtownberkeleyinn.com/| Downtown Berkeley Inn]===<br />
* '''Address''': 2001 Bancroft Way, Berkeley (2.4 miles from the Potter Street meeting location)<br />
* '''Phone''': (510) 843-4043<br />
* '''Rate''': LBNL rate is $129/night (normal rate $139/night).<br />
* '''How to book''': Phone (don't book online) and ask for “LBL” or “Gene Ontology” room block.<br />
** 10 rooms reserved--we may be able to get more if needed.<br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': Very basic, but adequate.<br />
* '''Advantages''': Cheapest option. Fairly close to downtown Berkeley.<br />
<br />
===[https://www.marriott.com/event-reservations/reservation-link.mi?id=1563407776453&key=GRP&app=resvlink| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the Potter Street meeting location),<br />
* '''Phone''': 1-800-325-3535<br />
* '''Rate''': $175/night (single or double) block rate for “Gene Ontology / GO meeting”.<br />
* '''How to book''': Book using this link: https://www.marriott.com/events/start.mi?id=1563407776453&key=GRP or call 1-800-325-3535 and ask for the “Gene Ontology” room block. <br />
** Check in as early as Oct 6; check out as late as Oct 12.<br />
** Last day to get the group rate: September 6, 2019.<br />
* '''Description''': A normal hotel. Has an outdoor pool and a fitness center.<br />
* '''Advantages''': Closest hotel to meeting location.<br />
<br />
===[https://www.graduatehotels.com/berkeley/| The Graduate] (formerly the Hotel Durant)===<br />
* '''Address''': 2600 Durant Ave, Berkeley (2.9 miles from the Potter Street meeting location)<br />
* '''Phone''': 510-845-8981<br />
* '''Rate''': Average of $210/night for a room with one queen.<br />
* '''How to book''': No special rates; you can book [https://www.graduatehotels.com/berkeley| online]<br />
* '''Description''': No pool or fitness center. More distinctive than the similarly-priced Hotel Shattuck Plaza. A recent article about The Graduate noted, "Berkeley's quirky counterculture is represented by bong-shaped lamps in the guestrooms and a restroom urinal painted with the logo and colors of Stanford, Cal-Berkeley’s arch-rival." Known for having made a brief appearance in the movie of the same name.<br />
* '''Advantages''': Near UC Campus and Telegraph Avenue, a colorful if slightly sketchy part of Berkeley.<br />
<br />
===[http://www.hotelshattuckplaza.com| Hotel Shattuck Plaza]===<br />
* '''Address''': 2086 Allston Way, Berkeley (2.5 miles from the Potter Street meeting location)<br />
* '''Phone''': 866-466-9199<br />
* '''Rate''': UC Berkeley rate: $215/night. Same price for double or single. <br />
* '''How to book''': You will need to phone and ask for the UC Berkeley rate--not available online.<br />
* '''Description''': A more upscale hotel than the previous three, it was completely remodeled a few years ago. Has a fitness center but no pool.<br />
* '''Advantages''': Right in the heart of downtown Berkeley, near BART, Potter St. shuttle, and many world-class restaurants<br />
<br />
= Getting around / To do / Local activities =<br />
<br />
The organizers have lived in the area for a very long time. If you have *any* questions, do not hesitate to reach out to us and let us make your stay in the Bay Area more more pleasant.<br />
<br />
== Getting around ==<br />
<br />
The LBL Potter Street site is located near a highway in a mixed business park and light industrial area.<br />
<br />
=== Walking ===<br />
<br />
Walking from the Emeryville hotel (Four Points Sheraton) to the meeting site is doable, but not necessarily a "pleasant" walk. It takes about half an hour.<br />
<br />
Walking from downtown is not advised and would take about an hour.<br />
<br />
=== By car (inc. "rideshare") ===<br />
<br />
If you are driving to the GO meeting, parking should not be an issue--while there will be no on-site parking, there is usually plenty of on-street parking in the surrounding area if you can walk a little. If you intend on driving, contact Seth or Nomi for details.<br />
<br />
The are usually plenty of Lyfts and Ubers in the area. The downtown area is about 10-12 minutes away.<br />
<br />
=== By public transportation ===<br />
<br />
==== From downtown ====<br />
<br />
===== LBL shuttle =====<br />
<br />
There is a fairly frequent LBL shuttle that directly connects downtown Berkeley area and the Potter Street site:<br />
<br />
https://commute.lbl.gov/resource/shuttle-buses/maps-routes-schedules/potter-st-jbei-route/<br />
<br />
You will need to show an LBL guest pass to board this shuttle. We can provide these on request--contact Seth or Nomi. The shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
===== Bus (AC Transit) =====<br />
<br />
There is also a bus that departs from near downtown and the Durant hotel and has a stop quite near the Potter Street site:<br />
<br />
http://www.actransit.org/maps/schedule_results.php?quick_line=36&Go=Go<br />
<br />
==== From Emeryville ====<br />
<br />
While it does not run directly by the hotel, one would need to walk a little and cross a bridge over the tracks, there is a free public shuttle that runs from near the hotel to near the Potter Street site: The Emery Go-round ():<br />
<br />
https://www.emerygoround.com/standard-service.html<br />
<br />
=== Biking and scootering ===<br />
<br />
The are is fairly well served by various "last mile" solutions.<br />
<br />
Rental bikes (now Lyft, previously Ford GoBikes) are available at various locations (https://member.baywheels.com/map/), including downtown Berkeley and near the meeting site (next to the Berkeley Bowl grocery store).<br />
<br />
==Food and drinks==<br />
<br />
=== Overview ===<br />
<br />
Downtown Berkeley has lots of places to eat. The LBL Potter Street location is much more limited for cafes and restaurants, but there is a large supermarket with a cafe (Berkeley Bowl) a few blocks away. Ubereats and the like are always an option for people wanting more variety and many of the organizers will have vehicles and may be doing various errands about town anyways, if there is something in particular you want or need.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==Exercise==<br />
<br />
For people interested in hitting the gym or swimming, the UC Berkeley recreational facilities are open to the general public with day passes:<br />
<br />
https://recsports.berkeley.edu/day-passes/<br />
<br />
The main rec facility and pool location is a short walk from downtown Berkeley. Several of the satellite pools have reduced day pass rates.<br />
<br />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 9, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 10, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
If you're staying around until Friday, there's an optional expedition on Thursday evening (see above).<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Nash Hotel<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
|<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not yet booked<br />
| Yes<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| <br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| Yes<br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Alex Ignatchenko<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Jeff De Pons<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| George Georghiou<br />
| EBI<br />
| Yes<br />
| Yes<br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| <br />
|-<br />
| Anushya Muruganujan<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Valerie Wood<br />
| Cambridge<br />
| Yes<br />
| Yes<br />
| Yes<br />
| No<br />
| Yes<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Malcolm Fisher (Xenbase) will attend remotely.<br />
<br />
Li Ni (MGI) will attend remotely.<br />
<br />
Birgit Meldal (EBI Complex Portal) - remotely if required (need to see schedule) / manageable (I'm +8 hours)<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=734842019 Cambridge GOC Meeting Logistics2019-03-27T08:30:40Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* '''Deadline:''' Thursday March 28th, or until full (max 50 people)<br />
<br />
==Consortium dinner==<br />
Thursday 11th April at [http://www.unicen.cam.ac.uk/riverside-restaurant The Riverside Restaurant], University Centre, Granta Pl, Cambridge CB2 1RU (same venue as the meeting).<br />
<br />
==Planned Schedule== <br />
*9am-5pm Thursday April 11th<br />
**New item! Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
*9am-5pm Friday April 12th<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
|-<br />
| Rob Finn<br />
| InterPro<br />
| Friday p.m. only<br />
| <br />
|-<br />
| Lorne Richardson<br />
| InterPro<br />
| Friday p.m. only<br />
| <br />
|-<br />
| Colin Logie<br />
| Radboud Institute for Molecular Life Sciences<br />
| Thursday only<br />
| TBC<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 13th March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=734062019 Cambridge GOC Meeting Logistics2019-03-21T11:01:32Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* '''Deadline:''' Thursday March 28th, or until full (max 50 people)<br />
<br />
==Consortium dinner==<br />
Thursday 11th April at [http://www.unicen.cam.ac.uk/riverside-restaurant The Riverside Restaurant], University Centre, Granta Pl, Cambridge CB2 1RU (same venue as the meeting).<br />
<br />
==Planned Schedule== <br />
*9am-5pm Thursday April 11th<br />
**New item! Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
*9am-5pm Friday April 12th<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
|-<br />
| Rob Finn<br />
| InterPro<br />
| Friday p.m. only<br />
| <br />
|-<br />
| Lorne Richardson<br />
| InterPro<br />
| Friday p.m. only<br />
| <br />
|-<br />
| Colin Logie<br />
| Radboud Institute for Molecular Life Sciences<br />
| Yes<br />
| TBC<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 13th March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=734052019 Cambridge GOC Meeting Logistics2019-03-21T11:00:38Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* '''Deadline:''' Thursday March 28th, or until full (max 50 people)<br />
<br />
==Consortium dinner==<br />
Thursday 11th April at [http://www.unicen.cam.ac.uk/riverside-restaurant The Riverside Restaurant], University Centre, Granta Pl, Cambridge CB2 1RU (same venue as the meeting).<br />
<br />
==Planned Schedule== <br />
*9am-5pm Thursday April 11th<br />
**New item! Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
*9am-5pm Friday April 12th<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
|-<br />
| Rob Finn<br />
| InterPro<br />
| <br />
| <br />
|-<br />
| Lorne Richardson<br />
| InterPro<br />
| <br />
| <br />
|-<br />
| Colin Logie<br />
| Radboud Institute for Molecular Life Sciences<br />
| Yes<br />
| TBC<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 13th March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=734042019 Cambridge GOC Meeting Logistics2019-03-21T10:59:42Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* '''Deadline:''' Thursday March 28th, or until full (max 50 people)<br />
<br />
==Consortium dinner==<br />
Thursday 11th April at [http://www.unicen.cam.ac.uk/riverside-restaurant The Riverside Restaurant], University Centre, Granta Pl, Cambridge CB2 1RU (same venue as the meeting).<br />
<br />
==Planned Schedule== <br />
*9am-5pm Thursday April 11th<br />
**New item! Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
*9am-5pm Friday April 12th<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
-<br />
| Rob Finn<br />
| InterPro<br />
| <br />
| <br />
-<br />
| Lorne Richardson<br />
| InterPro<br />
| <br />
| <br />
-<br />
| Colin Logie<br />
| Radboud Institute for Molecular Life Sciences<br />
| Yes<br />
| TBC<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 13th March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=734032019 Cambridge GOC Meeting Logistics2019-03-21T10:58:18Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* '''Deadline:''' Thursday March 28th, or until full (max 50 people)<br />
<br />
==Consortium dinner==<br />
Thursday 11th April at [http://www.unicen.cam.ac.uk/riverside-restaurant The Riverside Restaurant], University Centre, Granta Pl, Cambridge CB2 1RU (same venue as the meeting).<br />
<br />
==Planned Schedule== <br />
*9am-5pm Thursday April 11th<br />
**New item! Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
*9am-5pm Friday April 12th<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
-<br />
| Colin Logie<br />
| Radboud Institute for Molecular Life Sciences<br />
| Yes<br />
| TBC<br />
-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 13th March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=734022019 Cambridge GOC Meeting Logistics2019-03-21T10:57:29Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* '''Deadline:''' Thursday March 28th, or until full (max 50 people)<br />
<br />
==Consortium dinner==<br />
Thursday 11th April at [http://www.unicen.cam.ac.uk/riverside-restaurant The Riverside Restaurant], University Centre, Granta Pl, Cambridge CB2 1RU (same venue as the meeting).<br />
<br />
==Planned Schedule== <br />
*9am-5pm Thursday April 11th<br />
**New item! Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
*9am-5pm Friday April 12th<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
-<br />
| Colin Logie<br />
| Radboud Institute for Molecular Life Sciences<br />
| Yes<br />
| TBC<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 13th March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=734012019 Cambridge GOC Meeting Logistics2019-03-21T10:57:03Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Fee: '''£65''' with dinner, or £35 for the meeting only<br />
* Link to [https://onlinesales.admin.cam.ac.uk/conferences-and-events/biochemistry/go-consortium-meeting/go-consortium-meeting-april-2019 pay by credit or debit card]<br />
* '''Note that this is also the sign-up for dinner on Thursday evening'''<br />
* '''Deadline:''' Thursday March 28th, or until full (max 50 people)<br />
<br />
==Consortium dinner==<br />
Thursday 11th April at [http://www.unicen.cam.ac.uk/riverside-restaurant The Riverside Restaurant], University Centre, Granta Pl, Cambridge CB2 1RU (same venue as the meeting).<br />
<br />
==Planned Schedule== <br />
*9am-5pm Thursday April 11th<br />
**New item! Dinner Thursday evening at [http://www.unicen.cam.ac.uk/riverside-restaurant Riverside Restaurant] in the University Centre<br />
*9am-5pm Friday April 12th<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings.<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Michele Magrane<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Mike Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Felix Gondwe<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Alexander Diehl<br />
| University at Buffalo<br />
| Yes<br />
| Yes<br />
|-<br />
| Nick Brown<br />
| FlyBase<br />
| Yes<br />
| No<br />
-<br />
| Colin Logie<br />
| Radboud Institute for Molecular Life Sciences<br />
| Yes<br />
| TBC<br />
}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 13th March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: just across the green from the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam. Not to be confused with The Mill (see below).<br />
<br />
*[https://www.themillpubcambridge.com/ The Mill]: cosy pub nearly adjacent to the meeting venue, with a good selection of beer and food. Not to be confused with Millworks (see above).<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=729342019 Cambridge GOC Meeting Logistics2019-02-21T16:06:14Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
<br />
==Planned Schedule== <br />
*9am-5pm Thursday April 11th<br />
*9am-5pm Friday April 12th<br />
*Note: 2 days only.<br />
*We'll be running to a pretty tight schedule - many people will have already have been at the Biocurator Conference plus pre-meeting meetings. If you would like to arrange a focus group on the Saturday, please let Val or Helen know).<br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|MIke Cherry<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| No<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<br />
| Yes<br />
| No<br />
|-<br />
| Pascale Gaudet<br />
| SIB/USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
| Peter D'Eustachio<br />
| NYUMC / Reactome<br />
| Yes<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
| Tremayne Mushayahama<br />
| USC<br />
| Yes<br />
| TBD<br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br/><br />
Mary Dolan (Jackson Lab) will attend remotely<br />
<br/><br />
Tom Hayman (RGD) will attend remotely<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th).<br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
** Breakfast included (there will be no breakfast provided at the meeting).<br />
<br />
*<b>Discounted booking ends 1st March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: really close to the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam.<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=728422019 Cambridge GOC Meeting Logistics2019-02-11T21:09:48Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
<br />
==Planned Schedule== <br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| TBD<br />
|-<br />
|Sandra Orchard<br />
|EBI (UniProt/GOA/IntAct/Complex Portal)<br />
|Yes<br />
|No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
| Paul Sternberg<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th). <br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
<br />
*<b>Discounted booking ends 1st March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: really close to the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam.<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=728392019 Cambridge GOC Meeting Logistics2019-02-11T19:36:13Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
<br />
==Planned Schedule== <br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| TBD<br />
|-<br />
|Sandra Orchard<br />
|EBI (UniProt/GOA/IntAct/Complex Portal)<br />
|Yes<br />
|No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Alayne Cuzick<br />
| PHI-base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th). <br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
<br />
*<b>Discounted booking ends 1st March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: really close to the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam.<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=728382019 Cambridge GOC Meeting Logistics2019-02-11T19:35:26Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
<br />
==Planned Schedule== <br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Alex Ignatchenko<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| George Georghiou<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Sandra Orchard<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Maria Martin<br />
| EBI (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Suzi Aleksander<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Stacia Engel<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| TBD<br />
|-<br />
|Sandra Orchard<br />
|EBI (UniProt/GOA/IntAct/Complex Portal)<br />
|Yes<br />
|No<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| TBD<br />
|-<br />
| Alayne Cuzick<br />
| Phi-Base<br />
| Thursday a.m only<br />
| No <br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th). <br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
<br />
*<b>Discounted booking ends 1st March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: really close to the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam.<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=728152019 Cambridge GOC Meeting Logistics2019-02-09T10:10:18Z<p>Valwood: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
<br />
==Planned Schedule== <br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|-<br />
| David Hill<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Gaurab Mukherjee<br />
| Jackson Lab<br />
| Yes<br />
| No<br />
|-<br />
| Alan Bridge<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Anne Morgat<br />
| SIB (UniProt / Rhea)<br />
| Yes<br />
| TBC<br />
|-<br />
| Lionel Breuza<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Marc Feuermann<br />
| SIB (UniProt)<br />
| Yes<br />
| TBC<br />
|-<br />
| Patrick Masson<br />
| SIB (UniProt / ViralZone)<br />
| Yes<br />
| TBC<br />
|-<br />
|Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
|Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
|-<br />
|Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
|-<br />
|Ruth Lovering<br />
| UCL<br />
| Yes<br />
| No<br />
|-<br />
|Suvarna Nadendla<br />
| ECO (Instit for Genome Sci)<br />
| Yes<br />
| No<br />
|-<br />
|Antonia Lock<br />
| PomBase (Cambridge)<br />
| First day only<br />
| No<br />
|-<br />
|Malcolm Fisher<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Christina James-Zorn<br />
| Xenbase (CCHMC)<br />
| Yes<br />
| No<br />
|-<br />
|Petra Fey<br />
| dictyBase<br />
| Yes<br />
| TBD<br />
|-<br />
|Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| TBD<br />
|-<br />
| Achchuthan Shanmugasundram<br />
| FungiDB<br />
| Yes<br />
| -<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
Nomi Harris (LBNL)--it will be difficult for me to attend remotely due to the 8-hour time difference.<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
*[http://eventsathilton.com/show/5c38d22f917ce83a55fb2adb BOOK] discounted accommodation at the [https://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree Hotel] for the nights of the 10th-12th April (checkout 13th). <br />
** Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 10 seconds from venue, overlooks the river)<br />
**£186.00 per room per night based on single occupancy<br />
**£196.00 per room per night for double occupancy<br />
<br />
*<b>Discounted booking ends 1st March 2019 and rooms block booking will be released.</b><br />
<br />
<br />
*If you wish to book something else, here are some other options:<br />
**[https://www.accorhotels.com/gb/hotel-8548-ibis-cambridge-central-station/index.shtml Ibis Cambridge Central Station.] 2 Station Square, CB1 2GA Cambrige. Tel: +44 (0) 1223 320960. Prices range from ~£80-£150/night. Approx. 30 minute walk to meeting venue. <br />
**[http://www.thetamburlaine.co.uk/ Tamburlaine Hotel.] 27-29 Station Rd, Cambridge CB1 2FB, UK. Tel: +44 (0) 1223792888. ~£150-240/night. Approx. 30 minute walk to meeting venue.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 10 min walk from the meeting venue. Approx. £200/night.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631. 10 min walk from the meeting venue. email: reservations.cambridge@sjhotels.co.uk. Approx. £160/night.<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier.<br />
*[http://www.themillworks.co.uk/ Millworks]: really close to the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam.<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=726162019 Cambridge GOC Meeting Logistics2019-01-10T17:59:42Z<p>Valwood: </p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
<br />
==Planned Schedule== <br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, the dinner (Tuesday), so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
|-<br />
|}<br />
<br />
NOT attending (please indicate if you will attend remotely):<br />
<br />
<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
<br />
To follow<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier. Please keep in mind that, since the meeting will be in the first week of the University term, you may have some trouble in getting tables in some places.<br />
<br />
*[http://www.themillworks.co.uk/ Millworks]: really close to the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam.<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=726152019 Cambridge GOC Meeting Logistics2019-01-10T17:57:35Z<p>Valwood: </p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
==Consortium dinner ==<br />
<br />
<br />
==Planned Schedule== <br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, the dinner (Tuesday), so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
|-<br />
|}<br />
<br />
NOT attending (please indicate if you will attend remotely):<br />
<br />
<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
<br />
To follow<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier. Please keep in mind that, since the meeting will be in the first week of the University term, you may have some trouble in getting tables in some places.<br />
<br />
*[http://www.themillworks.co.uk/ Millworks]: really close to the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam.<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=726142019 Cambridge GOC Meeting Logistics2019-01-10T17:55:18Z<p>Valwood: Created page with "=GOC Meeting, Cambridge , XXXX, 2019= * Location: ** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room. ==Registration== * Please register at: XXXXXXX..."</p>
<hr />
<div>=GOC Meeting, Cambridge , XXXX, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
==Consortium dinner ==<br />
<br />
<br />
==Planned Schedule== <br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, the dinner (Tuesday), so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
|-<br />
|}<br />
<br />
NOT attending (please indicate if you will attend remotely):<br />
<br />
<br />
<br />
= Group Photo =<br />
<br />
<br />
<br />
=Remote Attendance=<br />
<br />
Please join us via Zoom.<br />
<br />
* https://stanford.zoom.us/j/976175422<br />
<br />
* iPhone one-tap (US Toll): +18333021536,,976175422# or +16507249799,,976175422#<br />
*Telephone:<br />
** +1 650 724 9799 (US, Canada, Caribbean Toll) or +1 833 302 1536 (US, Canada, Caribbean Toll Free).<br />
** UK toll free +44 (0) 80 0031 5717.<br />
** Switzerland toll free +41 800 002 622<br />
<br />
* Meeting ID: 976 175 422<br />
<br />
=Accommodations=<br />
<br />
To follow<br />
<br />
=Food and drinks=<br />
<br />
In Cambridge there are many restaurants, of many kinds. In fact, it can get really difficult to pick one! Here are some suggestions, to make your life a bit easier. Please keep in mind that, since the meeting will be in the first week of the University term, you may have some trouble in getting tables in some places.<br />
<br />
*[http://www.themillworks.co.uk/ Millworks]: really close to the meeting venue. They define themselves as "an eclectic modern brasserie". You can get good food while being close to the river Cam.<br />
<br />
*[http://www.anchorcambridge.com/ The Anchor]: also close to the meeting venue, serving traditional British pub grub. Pink Floyd had their first gigs in this pub. If you are lucky you can get a table with a nice view over the river.<br />
<br />
*[http://vedanta-cambridge.co.uk/ Vedanta]: very good Indian restaurant on Regent street, but small, so it's good to book in advance!<br />
<br />
*[http://www.thehouseauthenticthai.com/cambridge/home.html The House]: a good and cheap Thai restaurant, again on Regent Street.<br />
<br />
*[http://www.eagle-cambridge.co.uk/ The Eagle]: the pub where Francis Crick announced on February 28th, 1953 that he and James Watson had "discovered the secret of life" (the structure of the DNA).<br />
<br />
*[http://www.aromi.co.uk/ Aromi]: in case you want to have a slice of Italian pizza and a good coffee, maybe together with some Sicilian cannoli or some ice cream. There are two Aromi restaurants in the city centre, very close to each other, and they sell different products. They are both usually very busy!<br />
<br />
*[http://www.sticksnsushi.co.uk/restaurants/cambridge.html Sticks'n'sushi]: Japanese restaurant in the city centre, with nice sushi and a cool atmosphere. A bit on the pricey side.<br />
<br />
*[https://www.iguanas.co.uk/restaurants/cambridge Las Iguanas]: Latin American restaurant on Quayside with a vibrant atmosphere. Always with a 2-for-1 cocktail offer, in case you just want to go there for drinks. It does get a bit noisy with loud music, so not great if you look for something quiet.<br />
<br />
*[https://thaikhun.co.uk/ Thaikhun]: in case you still want to stay in the Quayside area, this is a good Thai restaurant, still with an interesting vibe, but quieter<br />
<br />
*[http://www.sixcambridge.co.uk/ Six]: if the weather is good, you can get a nice view of Cambridge, either from the rooftop bar, or from the restaurant that is on the floor right under the bar (so, unlike the bar, it's covered).<br />
<br />
What constitutes a good coffee is of course really subjective, but here are some suggestions in case you are desperate:<br />
<br />
*[http://www.aromi.co.uk/ Aromi]<br />
*[https://caffenero.com/uk/en/ Caffé Nero]<br />
*[http://www.savinos.co.uk/contactUs.php Savino's]<br />
*[http://www.fitzbillies.com/ Fitzbillies] (also good for an afternoon tea)<br />
*[http://hotnumberscoffee.co.uk/land Hot Numbers] [https://www.google.co.uk/maps/place/Hot+Numbers+Coffee/@52.1992715,0.121472,15z/data=!4m8!1m2!2m1!1sHot+Numbers,+Unit+6+Dale's+Brewery,+Gwydir+Street,+Cambridge,,+,+,+gb!3m4!1s0x47d870988d4c481b:0xc97ca0e02fb73288!8m2!3d52.1984856!4d0.1219986 Map]<br />
*If you prefer, we also have a few [https://www.starbucks.co.uk/store-locator?map=52.204051,0.121294,15z Starbucks] in Cambridge!<br />
<br />
= Local activities =<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=Consortium_Meetings_and_Workshops&diff=72613Consortium Meetings and Workshops2019-01-10T17:50:16Z<p>Valwood: /* 2019 */</p>
<hr />
<div><br />
=2019=<br />
<br />
*GOC meeting - Cambridge, UK April 11th - 12th (right after ISB meeting)<br />
** [[2019 Cambridge GOC Meeting Logistics]]<br />
** [[2019 Cambridge GOC Meeting Agenda]]<br />
<br />
=2018=<br />
* [[2018 Ontology Editors' GH ticket Meeting]]<br />
* [[2018 USC Noctua developers meeting]]<br />
* [[2018 Berkeley GO Docathon]]<br />
* [[2018 Berkeley GO-Dev April Hackathon]]<br />
* [[2018 Berkeley GO-Dev July Hackathon]]<br />
*GOC meeting - New York (NYU) May 12-14<br />
** [[2018 NYU GOC Meeting Logistics]]<br />
** [[2018 NYU GOC Meeting Agenda]]<br />
** [[2018 NYU SAB Meeting Logistics]]<br />
** [[2018 NYU SAB Meeting Agenda]]<br />
*[[2018 August USC Developers Meeting]]<br />
*20th anniversary GOC meeting to be held in Montreal October 17-19, 2018<br />
** [[2018 Montreal GOC Meeting Logistics]]<br />
** [[2018 Montreal GOC Meeting Agenda]]<br />
** [[2018 Montreal GOC users workshop]]<br />
* [[Geneva ontology editors meeting- Dec 10-13, 2018 - Logistics]] <br />
** Agenda: https://docs.google.com/document/d/1ixnmDZ75cFFdGN9H6CY5hyRkoPrCn6MvZVmERo_--Rw/edit<br />
<br />
=2017=<br />
<br />
* [[2017 November Berkeley Noctua Developers Meeting]]<br />
* GOC Meeting, Cambridge, UK, October 2-4, 2017<br />
** [[2017 Cambridge GOC Meeting Logistics]]<br />
** [[2017 Cambridge GOC Meeting Agenda]]<br />
** [[2017 Cambridge GOC Signalling Workshop]]<br />
* GOC GO Editors Workshop II, Berkeley, Aug 15-17<br />
**[[2017 Berkeley GO Editors Workshop II]]<br />
* GOC Meeting, Corvallis, Oregon, June 1-3 (plus workshops June 4-5), 2017<br />
** Logistics: https://sites.google.com/view/goc2017<br />
** [[2017 Corvallis GOC Meeting Agenda]]<br />
* GOC Protege Training Meeting Feb. 22, 23, and 24<br />
**[[Protege-OWL_Berkeley_Training_Logistics]]<br />
**Agenda: https://github.com/geneontology/protege-tutorial<br />
**Example tickets<br />
*** Adding a term: https://github.com/geneontology/go-ontology/issues/12996<br />
*** Obsoleting terms: https://github.com/geneontology/go-ontology/issues/12923<br />
*** Adding a term to a slim: https://github.com/geneontology/go-ontology/issues/13031<br />
*** Adding a taxon restriction:<br />
*** Merging terms https://github.com/geneontology/go-ontology/issues/12782<br />
<br />
=2016=<br />
* GOC Meeting, Los Angeles, November 4-6, 2016<br />
** [[2016 Los Angeles GOC Meeting Logistics]] <br />
** [[2016 Los Angeles GOC Meeting Agenda]]<br />
* Hinxton LEGO/Noctua Training, Hinxton, August 31 - September 02, 2016<br />
** [[2016 Hinxton LEGO/Noctua Training Logistics]] <br />
** [[2016 Hinxton LEGO/Noctua Training Agenda]]<br />
* GOC Meeting, Geneva, Switzerland, April 15-16, 2016<br />
** [[2016 Geneva GOC Meeting Logistics]] <br />
** [[2016 Geneva GOC Meeting Agenda]]<br />
<br />
=2015=<br />
* LEGO Jamboree, Geneva, Switzerland, December 8-10, 2015<br />
** [[2015 LEGO Jamboree Logistics]]<br />
* GOC Meeting, Washington, DC, August 30 - September 2, 2015<br />
** [[2015 Washington DC GOC Meeting Logistics]] <br />
** [[2015 Washington DC GOC Meeting Agenda]]<br />
** [[2015 Washington DC GOC Meeting Minutes]] <br />
** [[2015 Washington DC GOC Symposium Agenda]] <br />
** [[2015 Washington DC GOC Scientific Advisory Board Meeting Agenda]]<br />
* GOC All Hands Teleconference, April 1, 2015 <br />
** [[April 2015 GOC Teleconference Agenda and Logistics]]<br />
** [[April 2015 GOC Teleconference Minutes]]<br />
<br />
=2014=<br />
* GOC Meeting, Barcelona, October 13-15, 2014<br />
** [[2014 Barcelona Meeting Logistics]]<br />
** [[2014_Barcelona GOC Meeting_Agenda]]<br />
** [https://docs.google.com/document/d/1NonH97s8xEpDdx6DfonKPKI_RdHbbG-yft85UZtUmF0/edit#heading=h.2hxg96gzn5xe 2014 Barcelona Meeting Minutes]<br />
* PAINT Jamboree, Stanford CA, July 28-31, 2014<br />
** [[PAINT 2014 Summer Jamboree Kickoff Meeting Logistics]]<br />
* GOC Meeting, College Station, TX, March 16-17, 2014<br />
** [[2014 College Station Logistics]] <br />
** [[2014 College Station GOC Meeting Agenda]]<br />
<br />
=2013=<br />
* GOC Meeting, Bar Harbor, Maine, October (3), 4-6, 2013<br />
** [[2013 Bar Harbor Logistics]] <br />
** [[2013 Bar Harbor GOC Meeting Agenda]] <br />
** [[2013 GO Challenge]]<br />
* GOC Meeting, Cambridge, UK, April 11 - 13, 2013<br />
** [[2013 Cambridge Logistics]]<br />
** [[2013 Cambridge GOC Meeting Agenda]]<br />
** [[2013 Cambridge GOC Scientific Advisory Board Meeting Agenda]]<br />
* [http://www.ebi.ac.uk/biocuration2013/ BioCurator]<br />
* [[Ontology_workshop_Jan_2013]]<br />
<br />
=2012=<br />
*PAINT Training meeting, Stanford, Dec 10-13 2012<br />
** [[2012 PAINT workshop Logistics]] | [[2012 PAINT]] <br />
* GOC Meeting, Caltech, Pasadena, October 7 - 9, 2012<br />
** [[2012 Caltech GOC Meeting Logistics]] - [http://wiki.geneontology.org/index.php/2012_GOC_Meeting_Caltech 2012 Caltech GOC Meeting Agenda]<br />
* CAT Meeting, Caltech<br />
** [http://wiki.geneontology.org/index.php/Common_Annotation_Framework_Specification#Working_Meeting.2C_Caltech.2C_June_4th-8th.2C_2012 CAT meeting]<br />
* GOC Annotation Meeting, Stanford University, 26-28th February 2012<br />
** [[2012 Stanford Annotation Meeting Logistics]] - [http://wiki.geneontology.org/index.php/2012_Annotation_Meeting_Stanford 2012 Annotation Meeting Agenda]<br />
* [[Hinxton OBO-Edit/Protege 4 workshop Jan 2012 | Protege/OWL workshop]], Hinxton, UK, 30-31st Jan 2012<br />
<br />
=2011=<br />
* GOC meeting, University College London, 7-9th November 2011<br />
** [[2011 UCL Meeting Logistics]] - [[2011 UCL Meeting Agenda]]<br />
<br />
* GOC meeting, University of Southern California, 19-21st May 2011<br />
** [[2011 USC Meeting Logistics]] <br />
** [[2011 USC Meeting Agenda]]<br />
** [[2011 USC Meeting Action Items]]<br />
** [[File:minutes_LA2011.pdf]] <br />
<br />
* UCL GO [http://www.ucl.ac.uk/cardiovasculargeneontology/Outreach/Annotation_Workshops Annotation workshop] London, 6-7th April 2011<br />
<br />
=2010=<br />
* The Jackson Laboratory, Bar Harbor, Maine, GOC Sept 7-9, 2010<br />
** [[2010 Bar Harbor Minutes]]<br />
<br />
* GO annotation camp, Centre Médical Universitaire (CMU) Geneva, Switzerland, June 16-18 2010<br />
** [[2010 GO camp Meeting Logistics]] <br />
** [[2010_GO_camp_Meeting_Agenda]]<br />
** [http://wiki.geneontology.org/index.php/Talk:2010_GO_camp_Meeting_Agenda GO camp Meeting Minutes]<br />
* GO Reference Genome Meeting Bar Harbor May 20-21, 2010 <br />
** Ref Genome May 2010 minutes [[RefG_Bar_Harbor_May_20-21_2010]]<br />
* GO Reference Genome Princeton April 12-13, 2010 <br />
** Ref Genome April 2010 minutes [[RefG_Princeton_April_12-13_2010]]<br />
* Leland Stanford Jr. University, Stanford, California, GOC March 30-31 & SAB April 1, 2010<br />
** [[2010 Stanford Meeting Minutes]]<br />
<br />
=2009=<br />
* [[Cambridge GO Consortium Meeting | Cambridge Combined GO Consortium and SAB Meeting]] Jesus College, Cambridge, UK, September 23-25, 2009<br />
** [[2009 Cambridge Meeting Logistics]] <br />
** [[GOC Meeting Minutes September 2009|GOC Meeting Minutes September 2009]]<br />
* [[Oregon GO Consortium Meeting]] Eugene, Oregon, March 30, 31, 2009 <br />
** [[2009_Oregon_Meeting_Logistics|2009 Oregon Meeting Logistics]]<br />
* [[Oregon Reference Genomes Meeting]] Eugene, Oregon, April 1, 2009<br />
** [[2009_Oregon_Meeting_Logistics|2009 Oregon Meeting Logistics]]<br />
* Heart development workshop : [[Heart_Development_workshop_(Archived)]]<br />
** [[Minutes_Heart_Development_workshop]]<br />
<br />
=2008=<br />
* [[20th GO Consortium Meeting]] Montreal, October 21-22, 2008 -- '''[[October 2008 Meeting Logistics]]'''<br />
** [[20th_GO_Consortium_Meeting_Minutes | 20th GO Consortium Meeting minutes]]<br />
* [[Oct 2008 SAB Meeting]] Montreal, October 23, 2008 -- '''[[October 2008 Meeting Logistics]]'''<br />
<br />
* [[SLC GO Reference Genome Project Meeting]], April 20-21, 2008 Univ. of Utah, Salt Lake City, Utah<br />
** [[Reference Genome Meeting Minutes April 2008|Reference Genome Meeting Minutes April 2008]]<br />
** [[April 2008 Meeting logistics summary]]<br />
* [[GO Field Trip]], Afternoon of April 21, 2008: Antelope Island<br />
** [[wildlife and birds seen]] - List of Birds and Mammals<br />
* [[SLC GO Consortium Meeting]], April 22-23, 2008 Univ of Utah, Salt Lake City, Utah Photo:[[http://www.geneontology.org/photo_GO_SaltLakeCity.shtml]]<br />
** [[SLC GO Consortium Meeting Minutes April 2008|SLC GO Consortium Meeting Meeting Minutes April 2008]]<br />
** [[April 2008 Meeting logistics summary]]<br />
* Please [[http://gocwiki.geneontology.org/index.php/Register#Registration_for_April_2008_GO_Meetings_at_University_of_Utah.2C_SLC Register]] for one or both meetings.<br />
<br />
=2007=<br />
*[[GO Reference Genome Meeting]], Sept 26-27th, 2007 Princeton, New Jersey<br />
** [[Reference Genome minutes|Reference Genome minutes]]<br />
** [[September 2007 Meeting logistics summary]]<br />
*[[GO 3rd Advisors Meeting]], September 25th, 2007 Princeton, New Jersey<br />
** [[SAB minutes|Minutes from SAB]]<br />
** [[September 2007 Meeting logistics summary]]<br />
* [[GO 18th Consortium Meeting]], September 23-24th, 2007 Princeton, New Jersey. Photo:[[http://www.geneontology.org/images/photo_GOC_20070923.jpg]]<br />
** [[GO 18th Consortium Meeting Minutes Day 1|Draft Minutes Day 1]]<br />
** [[GO 18th Consortium Meeting Minutes Day 2|Draft Minutes Day 2]]<br />
** [[GO 18th Consortium Meeting Action Items ]]<br />
** [[Outstanding Action Items from 17th GOC Meeting, Cambridge UK]]<br />
** [[September 2007 Meeting logistics summary]]<br />
*[[GO Consortium Meeting 2007]], January 7-10th, 2007 Cambridge UK Photo:[[http://www.geneontology.org/photo_GO_JesusCollege.shtml]], Minutes:[[http://www.geneontology.org/meeting/minutes/20070108_Cambridge.doc]]<br />
*[[GO Advisors Meeting]], September 7th, 2006 Seattle Washington<br />
*Third Annotation Camp, July 10-14th, 2006 Stanford University. Photo:[[http://www.geneontology.org/photo_GO_Annotation_Camp_20060714.shtml]], Minutes:[[http://www.geneontology.org/meeting/minutes/20060710_GOannotCamp_Stanford.pdf]]<br />
----<br />
<br />
=Progress Reports for GOC Meetings=<br />
#Meeting Progress Reports 2011<br />
## [[Meeting_Progress_Reports_November_2011]]<br />
## [[Meeting_Progress_Reports_May_2011]]<br />
#Meeting Progress Reports 2010<br />
## [[Meeting_Progress_Reports_September_2010]]<br />
## [[Meeting_Progress_Reports_March_2010]]<br />
#Meeting Progress Reports 2009<br />
##[[Meeting_Progress_Reports_September_2009]]<br />
##[[Meeting_Progress_Reports_March_2009]]<br />
##[[Meeting_Progress_Reports_September_2009]]<br />
#Meeting Progress Reports 2008<br />
##[[Meeting_Progress_Report_April_2008]]<br />
##[[Meeting Progress Reports October 2008]]<br />
#[[Converting .doc or .docx to Wiki]]<br />
<br />
=Progress Report Templates=<br />
# [[MOD template]] (wiki)<br />
# [[Ontology Development template]]<br />
# [[Outreach and Advocacy report template]]<br />
# [[SO progress report template]]<br />
<br />
=Publications, tutorials, talks, posters=<br />
# [[Publications, tutorials, talks, posters]]<br />
<br />
<br />
[[Category:Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=717942018 Montreal GOC Meeting Agenda2018-10-16T15:38:30Z<p>Valwood: /* Representing complete proteomes in GO (added by Val, as suggested by Chris) */</p>
<hr />
<div>=Agenda moved to https://docs.google.com/document/d/16KMJRn-Vqf4yRsXAR1KYlwYvPob1tRTQbq2cEs6IJNY/edit#heading=h.uxqb7a8gufke=<br />
<br />
<br />
<br />
<br />
<br />
-----<br />
==This below is out of date== <br />
<br />
=Wednesday Morning=<br />
Paul<br />
Project status, main accomplishments and discussion topics for the meeting<br />
<br />
==New Pipeline & new pipeline documentation==<br />
'''Kimberly'''<br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Report monthly PAINT updates and GAF file generation QC (Huaiyu/Dustin) https://github.com/orgs/geneontology/projects/23<br />
* Plan for migrating to GPAD (Kimberly)<br />
** Reports from each group<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs: https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see https://github.com/geneontology/go-site/issues/791<br />
<br />
* Fate of external2go mappings (Chris): https://github.com/geneontology/go-docs/pull/27#issuecomment-426311327<br />
<br />
==Differences between old releases and new releases== <br />
Seth ? <br />
* Now releasing as a bundle <br />
* Implications for various groups- including other distributors of GO data (QuickGO, NCBI)<br />
* Improves (or just enables!) reproducibility<br />
<br />
==GO rules update and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
** Status taxon checks (https://github.com/geneontology/go-site/issues/660 and https://github.com/geneontology/go-site/issues/758)<br />
* New Error reports: http://snapshot.geneontology.org/reports/gorule-report.html (daily)<br />
<br />
== GO-CAM and Noctua ==<br />
https://github.com/orgs/geneontology/projects/19<br />
=== Noctua 1.1 release ===<br />
Kimberly<br />
*Updates on progress towards the 1.1 release<br />
**Bug fixes<br />
**New features<br />
**Groundwork for future releases<br />
=== Annotation review form ===<br />
Treymane<br />
=== GO-CAM integration with other pathway resources ===<br />
Ben<br />
*Reactome<br />
=== Roadmap for next Noctua release ===<br />
Kimberly<br />
* Integrating all (more) genomes in GOC<br />
<br />
==AmiGO update==<br />
Seth https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe/Suzi A: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
* future plans<br />
<br />
==Annotation==<br />
===Gene Product to terms relations===<br />
https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
===PAINT tickets===<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
===QC group report===<br />
* Add topics (report on progress)<br />
<br />
====How to blacklist papers====<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO/comment, including retracted papers<br />
* Centralized paper tracking system<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
** protein complex x binding: how does that impact 'colocalizes with protein complex x'? <br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
<br />
===GO subsets update===<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
Val: proposed new generic slim (15 minutes)<br />
<br />
==Defining redundant information==<br />
(Chris)<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files.<br />
There are tickets that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris''' <br />
<br />
Use cases for 'redundant', non-experimental annotation<br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
<br />
What data to present to which users<br />
<br />
Examples (different types of redundancy):<br />
* TAS http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177 (13 annotations to the same activity and 10 to the same component by TAS)<br />
* Exact duplicates by GOC function-process pipeline<br />
* Identical annotation by different groups (rare)<br />
<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
3. What to do about READThroughs from Ensembl (MED17 as an example)<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
{{strike| https://github.com/geneontology/helpdesk/issues/161}} closed moved to https://github.com/geneontology/go-site/issues/819 (this ticket is just a general question about which dataset we use)<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475 (vw I don' understand the issues in this ticket any more, so not included in summary)<br />
* https://github.com/geneontology/helpdesk/issues/144 CHTF8, included as example<br />
* https://github.com/geneontology/go-annotation/issues/2082 SLC35A4, MOCS2 includedas examples<br />
* https://github.com/geneontology/go-annotation/issues/2081 ignore this one<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
==ChEBI ontology (as suggested by Gareth Owen)==<br />
<br />
1) Would the GOC be interested in simplifying the ChEBI Ontology?<br />
<br />
Over the last year or so, we have been working on allowing individual users to 'personalise' the ChEBI Ontology, by choosing terms in the ontology that they don't wish to see (in effect, reducing the number of levels between the name of a molecule at one end and "chemical entity" at the other).<br />
This has to be done term by term, but we have also been working with the Ontology Lookup Service to enable this type of process to be automated.<br />
<br />
2) There are a few GO-submitted issues in the ChEBI issue tracker on GitHub that could benefit from discussion (though I suspect that a discussion of a few people during a break may be more useful than involving everybody ia a separate part of the agenda?)<br />
<br />
3) From a ChEBI point of view, a lot of effort goes in to building and maintaining the ChEBI ontology, but we would like to understand how the ChEBI ontology is then actually used (perhaps as part of GO) to tackle real problems. While we know that a number of ontologies (including GO!) make use of lots of ChEBI terms, we would be very interested in how the ontologies are actually being used in tools, applications, etc. in the 'real' world.<br />
<br />
4) Give a broad perspective of ChEBI, how it links to other resources e.g. via UniChem and key applications e.g. in metabolomics.<br />
<br />
=Breakout sessions topics=<br />
#Specifications for next version of GPAD/GPI<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=717862018 Montreal GOC Meeting Agenda2018-10-16T14:35:38Z<p>Valwood: /* Representing complete proteomes in GO (added by Val, as suggested by Chris) */</p>
<hr />
<div>=Agenda moved to https://docs.google.com/document/d/16KMJRn-Vqf4yRsXAR1KYlwYvPob1tRTQbq2cEs6IJNY/edit#heading=h.uxqb7a8gufke=<br />
<br />
<br />
<br />
<br />
<br />
-----<br />
==This below is out of date== <br />
<br />
=Wednesday Morning=<br />
Paul<br />
Project status, main accomplishments and discussion topics for the meeting<br />
<br />
==New Pipeline & new pipeline documentation==<br />
'''Kimberly'''<br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Report monthly PAINT updates and GAF file generation QC (Huaiyu/Dustin) https://github.com/orgs/geneontology/projects/23<br />
* Plan for migrating to GPAD (Kimberly)<br />
** Reports from each group<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs: https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see https://github.com/geneontology/go-site/issues/791<br />
<br />
* Fate of external2go mappings (Chris): https://github.com/geneontology/go-docs/pull/27#issuecomment-426311327<br />
<br />
==Differences between old releases and new releases== <br />
Seth ? <br />
* Now releasing as a bundle <br />
* Implications for various groups- including other distributors of GO data (QuickGO, NCBI)<br />
* Improves (or just enables!) reproducibility<br />
<br />
==GO rules update and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
** Status taxon checks (https://github.com/geneontology/go-site/issues/660 and https://github.com/geneontology/go-site/issues/758)<br />
* New Error reports: http://snapshot.geneontology.org/reports/gorule-report.html (daily)<br />
<br />
== GO-CAM and Noctua ==<br />
https://github.com/orgs/geneontology/projects/19<br />
=== Noctua 1.1 release ===<br />
Kimberly<br />
*Updates on progress towards the 1.1 release<br />
**Bug fixes<br />
**New features<br />
**Groundwork for future releases<br />
=== Annotation review form ===<br />
Treymane<br />
=== GO-CAM integration with other pathway resources ===<br />
Ben<br />
*Reactome<br />
=== Roadmap for next Noctua release ===<br />
Kimberly<br />
* Integrating all (more) genomes in GOC<br />
<br />
==AmiGO update==<br />
Seth https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe/Suzi A: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
* future plans<br />
<br />
==Annotation==<br />
===Gene Product to terms relations===<br />
https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
===PAINT tickets===<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
===QC group report===<br />
* Add topics (report on progress)<br />
<br />
====How to blacklist papers====<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO/comment, including retracted papers<br />
* Centralized paper tracking system<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
** protein complex x binding: how does that impact 'colocalizes with protein complex x'? <br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
<br />
===GO subsets update===<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
Val: proposed new generic slim (15 minutes)<br />
<br />
==Defining redundant information==<br />
(Chris)<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files.<br />
There are tickets that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris''' <br />
<br />
Use cases for 'redundant', non-experimental annotation<br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
<br />
What data to present to which users<br />
<br />
Examples (different types of redundancy):<br />
* TAS http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177 (13 annotations to the same activity and 10 to the same component by TAS)<br />
* Exact duplicates by GOC function-process pipeline<br />
* Identical annotation by different groups (rare)<br />
<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
3. What to do about READThroughs from Ensembl (MED17 as an example)<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
{{strike| https://github.com/geneontology/helpdesk/issues/161}} closed moved to https://github.com/geneontology/go-site/issues/819 (this ticket is just a general question about which dataset we use)<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475 (vw I don' understand the issues in this ticket any more, so not included in summary)<br />
* https://github.com/geneontology/helpdesk/issues/144 CHTF8, included as example<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
==ChEBI ontology (as suggested by Gareth Owen)==<br />
<br />
1) Would the GOC be interested in simplifying the ChEBI Ontology?<br />
<br />
Over the last year or so, we have been working on allowing individual users to 'personalise' the ChEBI Ontology, by choosing terms in the ontology that they don't wish to see (in effect, reducing the number of levels between the name of a molecule at one end and "chemical entity" at the other).<br />
This has to be done term by term, but we have also been working with the Ontology Lookup Service to enable this type of process to be automated.<br />
<br />
2) There are a few GO-submitted issues in the ChEBI issue tracker on GitHub that could benefit from discussion (though I suspect that a discussion of a few people during a break may be more useful than involving everybody ia a separate part of the agenda?)<br />
<br />
3) From a ChEBI point of view, a lot of effort goes in to building and maintaining the ChEBI ontology, but we would like to understand how the ChEBI ontology is then actually used (perhaps as part of GO) to tackle real problems. While we know that a number of ontologies (including GO!) make use of lots of ChEBI terms, we would be very interested in how the ontologies are actually being used in tools, applications, etc. in the 'real' world.<br />
<br />
4) Give a broad perspective of ChEBI, how it links to other resources e.g. via UniChem and key applications e.g. in metabolomics.<br />
<br />
=Breakout sessions topics=<br />
#Specifications for next version of GPAD/GPI<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=717822018 Montreal GOC Meeting Agenda2018-10-16T13:57:46Z<p>Valwood: /* Representing complete proteomes in GO (added by Val, as suggested by Chris) */</p>
<hr />
<div>=Agenda moved to https://docs.google.com/document/d/16KMJRn-Vqf4yRsXAR1KYlwYvPob1tRTQbq2cEs6IJNY/edit#heading=h.uxqb7a8gufke=<br />
<br />
<br />
<br />
<br />
<br />
-----<br />
==This below is out of date== <br />
<br />
=Wednesday Morning=<br />
Paul<br />
Project status, main accomplishments and discussion topics for the meeting<br />
<br />
==New Pipeline & new pipeline documentation==<br />
'''Kimberly'''<br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Report monthly PAINT updates and GAF file generation QC (Huaiyu/Dustin) https://github.com/orgs/geneontology/projects/23<br />
* Plan for migrating to GPAD (Kimberly)<br />
** Reports from each group<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs: https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see https://github.com/geneontology/go-site/issues/791<br />
<br />
* Fate of external2go mappings (Chris): https://github.com/geneontology/go-docs/pull/27#issuecomment-426311327<br />
<br />
==Differences between old releases and new releases== <br />
Seth ? <br />
* Now releasing as a bundle <br />
* Implications for various groups- including other distributors of GO data (QuickGO, NCBI)<br />
* Improves (or just enables!) reproducibility<br />
<br />
==GO rules update and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
** Status taxon checks (https://github.com/geneontology/go-site/issues/660 and https://github.com/geneontology/go-site/issues/758)<br />
* New Error reports: http://snapshot.geneontology.org/reports/gorule-report.html (daily)<br />
<br />
== GO-CAM and Noctua ==<br />
https://github.com/orgs/geneontology/projects/19<br />
=== Noctua 1.1 release ===<br />
Kimberly<br />
*Updates on progress towards the 1.1 release<br />
**Bug fixes<br />
**New features<br />
**Groundwork for future releases<br />
=== Annotation review form ===<br />
Treymane<br />
=== GO-CAM integration with other pathway resources ===<br />
Ben<br />
*Reactome<br />
=== Roadmap for next Noctua release ===<br />
Kimberly<br />
* Integrating all (more) genomes in GOC<br />
<br />
==AmiGO update==<br />
Seth https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe/Suzi A: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
* future plans<br />
<br />
==Annotation==<br />
===Gene Product to terms relations===<br />
https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
===PAINT tickets===<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
===QC group report===<br />
* Add topics (report on progress)<br />
<br />
====How to blacklist papers====<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO/comment, including retracted papers<br />
* Centralized paper tracking system<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
** protein complex x binding: how does that impact 'colocalizes with protein complex x'? <br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
<br />
===GO subsets update===<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
Val: proposed new generic slim (15 minutes)<br />
<br />
==Defining redundant information==<br />
(Chris)<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files.<br />
There are tickets that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris''' <br />
<br />
Use cases for 'redundant', non-experimental annotation<br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
<br />
What data to present to which users<br />
<br />
Examples (different types of redundancy):<br />
* TAS http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177 (13 annotations to the same activity and 10 to the same component by TAS)<br />
* Exact duplicates by GOC function-process pipeline<br />
* Identical annotation by different groups (rare)<br />
<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
3. What to do about READThroughs from Ensembl (MED17 as an example)<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
{{strike| https://github.com/geneontology/helpdesk/issues/161}} closed moved to https://github.com/geneontology/go-site/issues/819 (this ticket is just a general question about which dataset we use)<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475 (vw I don' understand the issues in this ticket any more, so not included in summary)<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
==ChEBI ontology (as suggested by Gareth Owen)==<br />
<br />
1) Would the GOC be interested in simplifying the ChEBI Ontology?<br />
<br />
Over the last year or so, we have been working on allowing individual users to 'personalise' the ChEBI Ontology, by choosing terms in the ontology that they don't wish to see (in effect, reducing the number of levels between the name of a molecule at one end and "chemical entity" at the other).<br />
This has to be done term by term, but we have also been working with the Ontology Lookup Service to enable this type of process to be automated.<br />
<br />
2) There are a few GO-submitted issues in the ChEBI issue tracker on GitHub that could benefit from discussion (though I suspect that a discussion of a few people during a break may be more useful than involving everybody ia a separate part of the agenda?)<br />
<br />
3) From a ChEBI point of view, a lot of effort goes in to building and maintaining the ChEBI ontology, but we would like to understand how the ChEBI ontology is then actually used (perhaps as part of GO) to tackle real problems. While we know that a number of ontologies (including GO!) make use of lots of ChEBI terms, we would be very interested in how the ontologies are actually being used in tools, applications, etc. in the 'real' world.<br />
<br />
4) Give a broad perspective of ChEBI, how it links to other resources e.g. via UniChem and key applications e.g. in metabolomics.<br />
<br />
=Breakout sessions topics=<br />
#Specifications for next version of GPAD/GPI<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=717772018 Montreal GOC Meeting Agenda2018-10-16T13:40:11Z<p>Valwood: /* Representing complete proteomes in GO (added by Val, as suggested by Chris) */</p>
<hr />
<div>=Agenda moved to https://docs.google.com/document/d/16KMJRn-Vqf4yRsXAR1KYlwYvPob1tRTQbq2cEs6IJNY/edit#heading=h.uxqb7a8gufke=<br />
<br />
<br />
<br />
<br />
<br />
-----<br />
==This below is out of date== <br />
<br />
=Wednesday Morning=<br />
Paul<br />
Project status, main accomplishments and discussion topics for the meeting<br />
<br />
==New Pipeline & new pipeline documentation==<br />
'''Kimberly'''<br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Report monthly PAINT updates and GAF file generation QC (Huaiyu/Dustin) https://github.com/orgs/geneontology/projects/23<br />
* Plan for migrating to GPAD (Kimberly)<br />
** Reports from each group<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs: https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see https://github.com/geneontology/go-site/issues/791<br />
<br />
* Fate of external2go mappings (Chris): https://github.com/geneontology/go-docs/pull/27#issuecomment-426311327<br />
<br />
==Differences between old releases and new releases== <br />
Seth ? <br />
* Now releasing as a bundle <br />
* Implications for various groups- including other distributors of GO data (QuickGO, NCBI)<br />
* Improves (or just enables!) reproducibility<br />
<br />
==GO rules update and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
** Status taxon checks (https://github.com/geneontology/go-site/issues/660 and https://github.com/geneontology/go-site/issues/758)<br />
* New Error reports: http://snapshot.geneontology.org/reports/gorule-report.html (daily)<br />
<br />
== GO-CAM and Noctua ==<br />
https://github.com/orgs/geneontology/projects/19<br />
=== Noctua 1.1 release ===<br />
Kimberly<br />
*Updates on progress towards the 1.1 release<br />
**Bug fixes<br />
**New features<br />
**Groundwork for future releases<br />
=== Annotation review form ===<br />
Treymane<br />
=== GO-CAM integration with other pathway resources ===<br />
Ben<br />
*Reactome<br />
=== Roadmap for next Noctua release ===<br />
Kimberly<br />
* Integrating all (more) genomes in GOC<br />
<br />
==AmiGO update==<br />
Seth https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe/Suzi A: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
* future plans<br />
<br />
==Annotation==<br />
===Gene Product to terms relations===<br />
https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
===PAINT tickets===<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
===QC group report===<br />
* Add topics (report on progress)<br />
<br />
====How to blacklist papers====<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO/comment, including retracted papers<br />
* Centralized paper tracking system<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
** protein complex x binding: how does that impact 'colocalizes with protein complex x'? <br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
<br />
===GO subsets update===<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
Val: proposed new generic slim (15 minutes)<br />
<br />
==Defining redundant information==<br />
(Chris)<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files.<br />
There are tickets that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris''' <br />
<br />
Use cases for 'redundant', non-experimental annotation<br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
<br />
What data to present to which users<br />
<br />
Examples (different types of redundancy):<br />
* TAS http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177 (13 annotations to the same activity and 10 to the same component by TAS)<br />
* Exact duplicates by GOC function-process pipeline<br />
* Identical annotation by different groups (rare)<br />
<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
3. What to do about READThroughs from Ensembl (MED17 as an example)<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
{{strike| https://github.com/geneontology/helpdesk/issues/161}} closed moved to https://github.com/geneontology/go-site/issues/819 (this ticket is just a general question about which dataset we use)<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
==ChEBI ontology (as suggested by Gareth Owen)==<br />
<br />
1) Would the GOC be interested in simplifying the ChEBI Ontology?<br />
<br />
Over the last year or so, we have been working on allowing individual users to 'personalise' the ChEBI Ontology, by choosing terms in the ontology that they don't wish to see (in effect, reducing the number of levels between the name of a molecule at one end and "chemical entity" at the other).<br />
This has to be done term by term, but we have also been working with the Ontology Lookup Service to enable this type of process to be automated.<br />
<br />
2) There are a few GO-submitted issues in the ChEBI issue tracker on GitHub that could benefit from discussion (though I suspect that a discussion of a few people during a break may be more useful than involving everybody ia a separate part of the agenda?)<br />
<br />
3) From a ChEBI point of view, a lot of effort goes in to building and maintaining the ChEBI ontology, but we would like to understand how the ChEBI ontology is then actually used (perhaps as part of GO) to tackle real problems. While we know that a number of ontologies (including GO!) make use of lots of ChEBI terms, we would be very interested in how the ontologies are actually being used in tools, applications, etc. in the 'real' world.<br />
<br />
4) Give a broad perspective of ChEBI, how it links to other resources e.g. via UniChem and key applications e.g. in metabolomics.<br />
<br />
=Breakout sessions topics=<br />
#Specifications for next version of GPAD/GPI<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=717762018 Montreal GOC Meeting Agenda2018-10-16T13:38:38Z<p>Valwood: /* Representing complete proteomes in GO (added by Val, as suggested by Chris) */</p>
<hr />
<div>=Agenda moved to https://docs.google.com/document/d/16KMJRn-Vqf4yRsXAR1KYlwYvPob1tRTQbq2cEs6IJNY/edit#heading=h.uxqb7a8gufke=<br />
<br />
<br />
<br />
<br />
<br />
-----<br />
==This below is out of date== <br />
<br />
=Wednesday Morning=<br />
Paul<br />
Project status, main accomplishments and discussion topics for the meeting<br />
<br />
==New Pipeline & new pipeline documentation==<br />
'''Kimberly'''<br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Report monthly PAINT updates and GAF file generation QC (Huaiyu/Dustin) https://github.com/orgs/geneontology/projects/23<br />
* Plan for migrating to GPAD (Kimberly)<br />
** Reports from each group<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs: https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see https://github.com/geneontology/go-site/issues/791<br />
<br />
* Fate of external2go mappings (Chris): https://github.com/geneontology/go-docs/pull/27#issuecomment-426311327<br />
<br />
==Differences between old releases and new releases== <br />
Seth ? <br />
* Now releasing as a bundle <br />
* Implications for various groups- including other distributors of GO data (QuickGO, NCBI)<br />
* Improves (or just enables!) reproducibility<br />
<br />
==GO rules update and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
** Status taxon checks (https://github.com/geneontology/go-site/issues/660 and https://github.com/geneontology/go-site/issues/758)<br />
* New Error reports: http://snapshot.geneontology.org/reports/gorule-report.html (daily)<br />
<br />
== GO-CAM and Noctua ==<br />
https://github.com/orgs/geneontology/projects/19<br />
=== Noctua 1.1 release ===<br />
Kimberly<br />
*Updates on progress towards the 1.1 release<br />
**Bug fixes<br />
**New features<br />
**Groundwork for future releases<br />
=== Annotation review form ===<br />
Treymane<br />
=== GO-CAM integration with other pathway resources ===<br />
Ben<br />
*Reactome<br />
=== Roadmap for next Noctua release ===<br />
Kimberly<br />
* Integrating all (more) genomes in GOC<br />
<br />
==AmiGO update==<br />
Seth https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe/Suzi A: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
* future plans<br />
<br />
==Annotation==<br />
===Gene Product to terms relations===<br />
https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
===PAINT tickets===<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
===QC group report===<br />
* Add topics (report on progress)<br />
<br />
====How to blacklist papers====<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO/comment, including retracted papers<br />
* Centralized paper tracking system<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
** protein complex x binding: how does that impact 'colocalizes with protein complex x'? <br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
<br />
===GO subsets update===<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
Val: proposed new generic slim (15 minutes)<br />
<br />
==Defining redundant information==<br />
(Chris)<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files.<br />
There are tickets that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris''' <br />
<br />
Use cases for 'redundant', non-experimental annotation<br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
<br />
What data to present to which users<br />
<br />
Examples (different types of redundancy):<br />
* TAS http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177 (13 annotations to the same activity and 10 to the same component by TAS)<br />
* Exact duplicates by GOC function-process pipeline<br />
* Identical annotation by different groups (rare)<br />
<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
3. What to do about READThroughs from Ensembl (MED17 as an example)<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
{{strike|https://github.com/geneontology/helpdesk/issues/161}} closed moved to https://github.com/geneontology/go-site/issues/819 (this ticket is just a general question about which dataset we use)<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
==ChEBI ontology (as suggested by Gareth Owen)==<br />
<br />
1) Would the GOC be interested in simplifying the ChEBI Ontology?<br />
<br />
Over the last year or so, we have been working on allowing individual users to 'personalise' the ChEBI Ontology, by choosing terms in the ontology that they don't wish to see (in effect, reducing the number of levels between the name of a molecule at one end and "chemical entity" at the other).<br />
This has to be done term by term, but we have also been working with the Ontology Lookup Service to enable this type of process to be automated.<br />
<br />
2) There are a few GO-submitted issues in the ChEBI issue tracker on GitHub that could benefit from discussion (though I suspect that a discussion of a few people during a break may be more useful than involving everybody ia a separate part of the agenda?)<br />
<br />
3) From a ChEBI point of view, a lot of effort goes in to building and maintaining the ChEBI ontology, but we would like to understand how the ChEBI ontology is then actually used (perhaps as part of GO) to tackle real problems. While we know that a number of ontologies (including GO!) make use of lots of ChEBI terms, we would be very interested in how the ontologies are actually being used in tools, applications, etc. in the 'real' world.<br />
<br />
4) Give a broad perspective of ChEBI, how it links to other resources e.g. via UniChem and key applications e.g. in metabolomics.<br />
<br />
=Breakout sessions topics=<br />
#Specifications for next version of GPAD/GPI<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=717752018 Montreal GOC Meeting Agenda2018-10-16T13:37:13Z<p>Valwood: /* Representing complete proteomes in GO (added by Val, as suggested by Chris) */</p>
<hr />
<div>=Agenda moved to https://docs.google.com/document/d/16KMJRn-Vqf4yRsXAR1KYlwYvPob1tRTQbq2cEs6IJNY/edit#heading=h.uxqb7a8gufke=<br />
<br />
<br />
<br />
<br />
<br />
-----<br />
==This below is out of date== <br />
<br />
=Wednesday Morning=<br />
Paul<br />
Project status, main accomplishments and discussion topics for the meeting<br />
<br />
==New Pipeline & new pipeline documentation==<br />
'''Kimberly'''<br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Report monthly PAINT updates and GAF file generation QC (Huaiyu/Dustin) https://github.com/orgs/geneontology/projects/23<br />
* Plan for migrating to GPAD (Kimberly)<br />
** Reports from each group<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs: https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see https://github.com/geneontology/go-site/issues/791<br />
<br />
* Fate of external2go mappings (Chris): https://github.com/geneontology/go-docs/pull/27#issuecomment-426311327<br />
<br />
==Differences between old releases and new releases== <br />
Seth ? <br />
* Now releasing as a bundle <br />
* Implications for various groups- including other distributors of GO data (QuickGO, NCBI)<br />
* Improves (or just enables!) reproducibility<br />
<br />
==GO rules update and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
** Status taxon checks (https://github.com/geneontology/go-site/issues/660 and https://github.com/geneontology/go-site/issues/758)<br />
* New Error reports: http://snapshot.geneontology.org/reports/gorule-report.html (daily)<br />
<br />
== GO-CAM and Noctua ==<br />
https://github.com/orgs/geneontology/projects/19<br />
=== Noctua 1.1 release ===<br />
Kimberly<br />
*Updates on progress towards the 1.1 release<br />
**Bug fixes<br />
**New features<br />
**Groundwork for future releases<br />
=== Annotation review form ===<br />
Treymane<br />
=== GO-CAM integration with other pathway resources ===<br />
Ben<br />
*Reactome<br />
=== Roadmap for next Noctua release ===<br />
Kimberly<br />
* Integrating all (more) genomes in GOC<br />
<br />
==AmiGO update==<br />
Seth https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe/Suzi A: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
* future plans<br />
<br />
==Annotation==<br />
===Gene Product to terms relations===<br />
https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
===PAINT tickets===<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
===QC group report===<br />
* Add topics (report on progress)<br />
<br />
====How to blacklist papers====<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO/comment, including retracted papers<br />
* Centralized paper tracking system<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
** protein complex x binding: how does that impact 'colocalizes with protein complex x'? <br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
<br />
===GO subsets update===<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
Val: proposed new generic slim (15 minutes)<br />
<br />
==Defining redundant information==<br />
(Chris)<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files.<br />
There are tickets that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris''' <br />
<br />
Use cases for 'redundant', non-experimental annotation<br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
<br />
What data to present to which users<br />
<br />
Examples (different types of redundancy):<br />
* TAS http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177 (13 annotations to the same activity and 10 to the same component by TAS)<br />
* Exact duplicates by GOC function-process pipeline<br />
* Identical annotation by different groups (rare)<br />
<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
3. What to do about READThroughs from Ensembl (MED17 as an example)<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
{{https://github.com/geneontology/helpdesk/issues/161}} closed moved to https://github.com/geneontology/go-site/issues/819 (this ticket is just a general question about which dataset we use)<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
==ChEBI ontology (as suggested by Gareth Owen)==<br />
<br />
1) Would the GOC be interested in simplifying the ChEBI Ontology?<br />
<br />
Over the last year or so, we have been working on allowing individual users to 'personalise' the ChEBI Ontology, by choosing terms in the ontology that they don't wish to see (in effect, reducing the number of levels between the name of a molecule at one end and "chemical entity" at the other).<br />
This has to be done term by term, but we have also been working with the Ontology Lookup Service to enable this type of process to be automated.<br />
<br />
2) There are a few GO-submitted issues in the ChEBI issue tracker on GitHub that could benefit from discussion (though I suspect that a discussion of a few people during a break may be more useful than involving everybody ia a separate part of the agenda?)<br />
<br />
3) From a ChEBI point of view, a lot of effort goes in to building and maintaining the ChEBI ontology, but we would like to understand how the ChEBI ontology is then actually used (perhaps as part of GO) to tackle real problems. While we know that a number of ontologies (including GO!) make use of lots of ChEBI terms, we would be very interested in how the ontologies are actually being used in tools, applications, etc. in the 'real' world.<br />
<br />
4) Give a broad perspective of ChEBI, how it links to other resources e.g. via UniChem and key applications e.g. in metabolomics.<br />
<br />
=Breakout sessions topics=<br />
#Specifications for next version of GPAD/GPI<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=717742018 Montreal GOC Meeting Agenda2018-10-16T13:36:25Z<p>Valwood: /* Representing complete proteomes in GO (added by Val, as suggested by Chris) */</p>
<hr />
<div>=Agenda moved to https://docs.google.com/document/d/16KMJRn-Vqf4yRsXAR1KYlwYvPob1tRTQbq2cEs6IJNY/edit#heading=h.uxqb7a8gufke=<br />
<br />
<br />
<br />
<br />
<br />
-----<br />
==This below is out of date== <br />
<br />
=Wednesday Morning=<br />
Paul<br />
Project status, main accomplishments and discussion topics for the meeting<br />
<br />
==New Pipeline & new pipeline documentation==<br />
'''Kimberly'''<br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Report monthly PAINT updates and GAF file generation QC (Huaiyu/Dustin) https://github.com/orgs/geneontology/projects/23<br />
* Plan for migrating to GPAD (Kimberly)<br />
** Reports from each group<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs: https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see https://github.com/geneontology/go-site/issues/791<br />
<br />
* Fate of external2go mappings (Chris): https://github.com/geneontology/go-docs/pull/27#issuecomment-426311327<br />
<br />
==Differences between old releases and new releases== <br />
Seth ? <br />
* Now releasing as a bundle <br />
* Implications for various groups- including other distributors of GO data (QuickGO, NCBI)<br />
* Improves (or just enables!) reproducibility<br />
<br />
==GO rules update and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
** Status taxon checks (https://github.com/geneontology/go-site/issues/660 and https://github.com/geneontology/go-site/issues/758)<br />
* New Error reports: http://snapshot.geneontology.org/reports/gorule-report.html (daily)<br />
<br />
== GO-CAM and Noctua ==<br />
https://github.com/orgs/geneontology/projects/19<br />
=== Noctua 1.1 release ===<br />
Kimberly<br />
*Updates on progress towards the 1.1 release<br />
**Bug fixes<br />
**New features<br />
**Groundwork for future releases<br />
=== Annotation review form ===<br />
Treymane<br />
=== GO-CAM integration with other pathway resources ===<br />
Ben<br />
*Reactome<br />
=== Roadmap for next Noctua release ===<br />
Kimberly<br />
* Integrating all (more) genomes in GOC<br />
<br />
==AmiGO update==<br />
Seth https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe/Suzi A: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
* future plans<br />
<br />
==Annotation==<br />
===Gene Product to terms relations===<br />
https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
===PAINT tickets===<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
===QC group report===<br />
* Add topics (report on progress)<br />
<br />
====How to blacklist papers====<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO/comment, including retracted papers<br />
* Centralized paper tracking system<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
** protein complex x binding: how does that impact 'colocalizes with protein complex x'? <br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
<br />
===GO subsets update===<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
Val: proposed new generic slim (15 minutes)<br />
<br />
==Defining redundant information==<br />
(Chris)<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files.<br />
There are tickets that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris''' <br />
<br />
Use cases for 'redundant', non-experimental annotation<br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
<br />
What data to present to which users<br />
<br />
Examples (different types of redundancy):<br />
* TAS http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177 (13 annotations to the same activity and 10 to the same component by TAS)<br />
* Exact duplicates by GOC function-process pipeline<br />
* Identical annotation by different groups (rare)<br />
<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
3. What to do about READThroughs from Ensembl (MED17 as an example)<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
~https://github.com/geneontology/helpdesk/issues/161~ closed moved to https://github.com/geneontology/go-site/issues/819 (this ticket is just a general question about which dataset we use)<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
==ChEBI ontology (as suggested by Gareth Owen)==<br />
<br />
1) Would the GOC be interested in simplifying the ChEBI Ontology?<br />
<br />
Over the last year or so, we have been working on allowing individual users to 'personalise' the ChEBI Ontology, by choosing terms in the ontology that they don't wish to see (in effect, reducing the number of levels between the name of a molecule at one end and "chemical entity" at the other).<br />
This has to be done term by term, but we have also been working with the Ontology Lookup Service to enable this type of process to be automated.<br />
<br />
2) There are a few GO-submitted issues in the ChEBI issue tracker on GitHub that could benefit from discussion (though I suspect that a discussion of a few people during a break may be more useful than involving everybody ia a separate part of the agenda?)<br />
<br />
3) From a ChEBI point of view, a lot of effort goes in to building and maintaining the ChEBI ontology, but we would like to understand how the ChEBI ontology is then actually used (perhaps as part of GO) to tackle real problems. While we know that a number of ontologies (including GO!) make use of lots of ChEBI terms, we would be very interested in how the ontologies are actually being used in tools, applications, etc. in the 'real' world.<br />
<br />
4) Give a broad perspective of ChEBI, how it links to other resources e.g. via UniChem and key applications e.g. in metabolomics.<br />
<br />
=Breakout sessions topics=<br />
#Specifications for next version of GPAD/GPI<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=717732018 Montreal GOC Meeting Agenda2018-10-16T13:36:11Z<p>Valwood: /* Representing complete proteomes in GO (added by Val, as suggested by Chris) */</p>
<hr />
<div>=Agenda moved to https://docs.google.com/document/d/16KMJRn-Vqf4yRsXAR1KYlwYvPob1tRTQbq2cEs6IJNY/edit#heading=h.uxqb7a8gufke=<br />
<br />
<br />
<br />
<br />
<br />
-----<br />
==This below is out of date== <br />
<br />
=Wednesday Morning=<br />
Paul<br />
Project status, main accomplishments and discussion topics for the meeting<br />
<br />
==New Pipeline & new pipeline documentation==<br />
'''Kimberly'''<br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Report monthly PAINT updates and GAF file generation QC (Huaiyu/Dustin) https://github.com/orgs/geneontology/projects/23<br />
* Plan for migrating to GPAD (Kimberly)<br />
** Reports from each group<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs: https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see https://github.com/geneontology/go-site/issues/791<br />
<br />
* Fate of external2go mappings (Chris): https://github.com/geneontology/go-docs/pull/27#issuecomment-426311327<br />
<br />
==Differences between old releases and new releases== <br />
Seth ? <br />
* Now releasing as a bundle <br />
* Implications for various groups- including other distributors of GO data (QuickGO, NCBI)<br />
* Improves (or just enables!) reproducibility<br />
<br />
==GO rules update and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
** Status taxon checks (https://github.com/geneontology/go-site/issues/660 and https://github.com/geneontology/go-site/issues/758)<br />
* New Error reports: http://snapshot.geneontology.org/reports/gorule-report.html (daily)<br />
<br />
== GO-CAM and Noctua ==<br />
https://github.com/orgs/geneontology/projects/19<br />
=== Noctua 1.1 release ===<br />
Kimberly<br />
*Updates on progress towards the 1.1 release<br />
**Bug fixes<br />
**New features<br />
**Groundwork for future releases<br />
=== Annotation review form ===<br />
Treymane<br />
=== GO-CAM integration with other pathway resources ===<br />
Ben<br />
*Reactome<br />
=== Roadmap for next Noctua release ===<br />
Kimberly<br />
* Integrating all (more) genomes in GOC<br />
<br />
==AmiGO update==<br />
Seth https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe/Suzi A: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
* future plans<br />
<br />
==Annotation==<br />
===Gene Product to terms relations===<br />
https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
===PAINT tickets===<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
===QC group report===<br />
* Add topics (report on progress)<br />
<br />
====How to blacklist papers====<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO/comment, including retracted papers<br />
* Centralized paper tracking system<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
** protein complex x binding: how does that impact 'colocalizes with protein complex x'? <br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
<br />
===GO subsets update===<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
Val: proposed new generic slim (15 minutes)<br />
<br />
==Defining redundant information==<br />
(Chris)<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files.<br />
There are tickets that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris''' <br />
<br />
Use cases for 'redundant', non-experimental annotation<br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
<br />
What data to present to which users<br />
<br />
Examples (different types of redundancy):<br />
* TAS http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177 (13 annotations to the same activity and 10 to the same component by TAS)<br />
* Exact duplicates by GOC function-process pipeline<br />
* Identical annotation by different groups (rare)<br />
<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
3. What to do about READThroughs from Ensembl (MED17 as an example)<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
~* https://github.com/geneontology/helpdesk/issues/161~ closed moved to https://github.com/geneontology/go-site/issues/819 (this ticket is just a general question about which dataset we use)<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
==ChEBI ontology (as suggested by Gareth Owen)==<br />
<br />
1) Would the GOC be interested in simplifying the ChEBI Ontology?<br />
<br />
Over the last year or so, we have been working on allowing individual users to 'personalise' the ChEBI Ontology, by choosing terms in the ontology that they don't wish to see (in effect, reducing the number of levels between the name of a molecule at one end and "chemical entity" at the other).<br />
This has to be done term by term, but we have also been working with the Ontology Lookup Service to enable this type of process to be automated.<br />
<br />
2) There are a few GO-submitted issues in the ChEBI issue tracker on GitHub that could benefit from discussion (though I suspect that a discussion of a few people during a break may be more useful than involving everybody ia a separate part of the agenda?)<br />
<br />
3) From a ChEBI point of view, a lot of effort goes in to building and maintaining the ChEBI ontology, but we would like to understand how the ChEBI ontology is then actually used (perhaps as part of GO) to tackle real problems. While we know that a number of ontologies (including GO!) make use of lots of ChEBI terms, we would be very interested in how the ontologies are actually being used in tools, applications, etc. in the 'real' world.<br />
<br />
4) Give a broad perspective of ChEBI, how it links to other resources e.g. via UniChem and key applications e.g. in metabolomics.<br />
<br />
=Breakout sessions topics=<br />
#Specifications for next version of GPAD/GPI<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=716922018 Montreal GOC Meeting Agenda2018-10-07T13:54:03Z<p>Valwood: /* Handling redundant information */</p>
<hr />
<div>=Montreal meeting Topics=<br />
<br />
=Intro=<br />
Paul<br />
Project status, main accomplishments and discussion topics for the meeting<br />
<br />
==New Pipeline & new pipeline documentation==<br />
'''Kimberly'''<br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Report monthly PAINT updates and GAF file generation QC (Huaiyu/Dustin) https://github.com/orgs/geneontology/projects/23<br />
* Plan for migrating to GPAD (Kimberly)<br />
** Reports from each group<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs: https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see https://github.com/geneontology/go-site/issues/791<br />
<br />
* Fate of external2go mappings (Chris): https://github.com/geneontology/go-docs/pull/27#issuecomment-426311327<br />
<br />
==Differences between old releases and new releases== <br />
Seth ? <br />
* Now releasing as a bundle <br />
* Implications for various groups- including other distributors of GO data (QuickGO, NCBI)<br />
* Improves (or just enables!) reproducibility<br />
<br />
==GO rules update and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
** Status taxon checks (https://github.com/geneontology/go-site/issues/660 and https://github.com/geneontology/go-site/issues/758)<br />
* New Error reports: http://snapshot.geneontology.org/reports/gorule-report.html (daily)<br />
<br />
== GO-CAM and Noctua ==<br />
https://github.com/orgs/geneontology/projects/19<br />
=== Noctua 1.1 release ===<br />
Kimberly<br />
*Updates on progress towards the 1.1 release<br />
**Bug fixes<br />
**New features<br />
**Groundwork for future releases<br />
=== Annotation review form ===<br />
Treymane<br />
=== GO-CAM integration with other pathway resources ===<br />
Ben<br />
*Reactome<br />
=== Roadmap for next Noctua release ===<br />
Kimberly<br />
* Integrating all (more) genomes in GOC<br />
<br />
==AmiGO update==<br />
Seth https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe/Suzi A: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
* future plans<br />
<br />
==Annotation==<br />
===Gene Product to terms relations===<br />
https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
===PAINT tickets===<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
===QC group report===<br />
* Add topics (report on progress)<br />
<br />
====How to blacklist papers====<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO/comment, including retracted papers<br />
* Centralized paper tracking system<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
** protein complex x binding: how does that impact 'colocalizes with protein complex x'? <br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
<br />
===GO subsets update===<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
==Handling redundant information==<br />
(Chris)<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files.<br />
There are tickets that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris''' <br />
<br />
Discussion points: Is redundant, non-experimental annotation ever useful? <br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
<br />
Examples (different types of redundancy):<br />
* TAS http://amigo.geneontology.org/amigo/gene_product/UniProtKB:P05177 (13 annotations to the same activity and 10 to the same component by TAS)<br />
* Exact duplicates by GOC function-process pipeline<br />
* Identical annotation by different groups (rare)<br />
<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
3. What to do about READThroughs from Ensembl (MED17 as an example)<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
* https://github.com/geneontology/helpdesk/issues/161<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
==ChEBI ontology (as suggested by Gareth Owen)==<br />
<br />
1) Would the GOC be interested in simplifying the ChEBI Ontology?<br />
<br />
Over the last year or so, we have been working on allowing individual users to 'personalise' the ChEBI Ontology, by choosing terms in the ontology that they don't wish to see (in effect, reducing the number of levels between the name of a molecule at one end and "chemical entity" at the other).<br />
This has to be done term by term, but we have also been working with the Ontology Lookup Service to enable this type of process to be automated.<br />
<br />
2) There are a few GO-submitted issues in the ChEBI issue tracker on GitHub that could benefit from discussion (though I suspect that a discussion of a few people during a break may be more useful than involving everybody ia a separate part of the agenda?)<br />
<br />
3) From a ChEBI point of view, a lot of effort goes in to building and maintaining the ChEBI ontology, but we would like to understand how the ChEBI ontology is then actually used (perhaps as part of GO) to tackle real problems. While we know that a number of ontologies (including GO!) make use of lots of ChEBI terms, we would be very interested in how the ontologies are actually being used in tools, applications, etc. in the 'real' world.<br />
<br />
4) Give a broad perspective of ChEBI, how it links to other resources e.g. via UniChem and key applications e.g. in metabolomics.<br />
<br />
=Breakout sessions topics=<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=QCQA_next_call&diff=71679QCQA next call2018-10-05T13:29:50Z<p>Valwood: /* Discussion: Annotation redundancy - non-experimental annotations */</p>
<hr />
<div>=Preparing for GOC meeting =<br />
<br />
=Annotation redundancy - non-experimental annotations=<br />
**Can we come up with a proposal for the Montreal meeting?<br />
**http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda#Handling_redundant_information<br />
<br />
==Discussion: Annotation redundancy - non-experimental annotations==<br />
* We need to define what constitutes a redundant information, WRT to sources, evidences and references<br />
* There is a ticket that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris'''<br />
* https://github.com/geneontology/go-annotation/issues/2060<br />
* https://github.com/geneontology/go-annotation/issues/1879<br />
<br />
Different types of redundancy<br />
* identical experimental annotations from different sources https://github.com/geneontology/go-annotation/issues/1404<br />
* inferred and IEA, ISO, ISM, IBA annotations when EXP exist<br />
* Redundant inferred annotations from GOC F-P links pipeline e.g. https://github.com/geneontology/go-site/issues/576<br />
* TAS /NAS (special case)<br />
<br />
There is no use case for users of MODs and AMiGO to see automated annotations when EXP annotations are present.<br />
If somebody wants a complete set of annotations from a mapping resource these could be made available separately.<br />
<br />
==New error reports - status==<br />
http://snapshot.geneontology.org/reports/gorule-report.html<br />
https://github.com/geneontology/go-site/issues/709<br />
<br />
=How to blacklist papers=<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO<br />
<br />
= Update: Unmaintained annotation sets=<br />
https://github.com/geneontology/go-annotation/issues/1724#issuecomment-390136730<br />
* '''AI: check status with Tony - Unmaintained annotation sets'''<br />
<br />
TIGR, JCVI, PAMGO ISS annotations: Michelle: <br />
The ISS annotations from at least TIGR (and should be also JCVI and PAMGO) were all manual. They were either matches to HMMs or based on pairwise alignments. We used IEA for any annotations that were automatic from our pipeline and not reviewed. I assume JCVI continued that process after I left - at least until they stopped using their pipeline and shifted completely to using the NCBI PGAP tool (prokaryotic genome annotation pipeline).<br />
I think we (and hopefully PAMGO) were pretty good about using the GO_REFs to indicate whether it was HMM or pairwise. The problem with replacing our HMM annotations with InterPro2GO mappings is that we made much more specific annotations based on HMMs than what the InterPro mappings often do. I'd hate to lose those but I understand your desire to keep the annotations current.<br />
<br />
= Reported from the previous meeting =<br />
* GO-CAM QC plan<br />
** including SynGO, > 90 % of the production models<br />
<br />
<br />
=To revisit later= <br />
==SPKW hierarchy - at odds with transitivity as found in GO ontology?==<br />
**https://github.com/geneontology/go-annotation/issues/2036<br />
**emailed Chris, Seth about help with querying the GO database for non-redundant SPKW-based annotations (2018-08-16)<br />
** Kimberly: WB looking into the information added by SPKW in WormBase. From that evaluation we can perhaps decide whether we want to keep them. <br />
<br />
<br />
<br />
[[Category:Quality Control]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=QCQA_next_call&diff=71678QCQA next call2018-10-05T13:29:35Z<p>Valwood: /* Discussion: Annotation redundancy - non-experimental annotations */</p>
<hr />
<div>=Preparing for GOC meeting =<br />
<br />
=Annotation redundancy - non-experimental annotations=<br />
**Can we come up with a proposal for the Montreal meeting?<br />
**http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda#Handling_redundant_information<br />
<br />
==Discussion: Annotation redundancy - non-experimental annotations==<br />
* We need to define what constitutes a redundant information, WRT to sources, evidences and references<br />
* There is a ticket that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris'''<br />
* https://github.com/geneontology/go-annotation/issues/2060<br />
* https://github.com/geneontology/go-annotation/issues/1879<br />
<br />
Different types of redundancy<br />
* identical experimental annotations from different sources https://github.com/geneontology/go-annotation/issues/1404<br />
* inferred and IEA, ISO, ISM, IBA annotations when EXP exist<br />
* Redundant inferred annotations from GOC F-P links pipeline<br />
e.g. https://github.com/geneontology/go-site/issues/576<br />
* TAS /NAS (special case)<br />
<br />
There is no use case for users of MODs and AMiGO to see automated annotations when EXP annotations are present.<br />
If somebody wants a complete set of annotations from a mapping resource these could be made available separately.<br />
<br />
==New error reports - status==<br />
http://snapshot.geneontology.org/reports/gorule-report.html<br />
https://github.com/geneontology/go-site/issues/709<br />
<br />
=How to blacklist papers=<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO<br />
<br />
= Update: Unmaintained annotation sets=<br />
https://github.com/geneontology/go-annotation/issues/1724#issuecomment-390136730<br />
* '''AI: check status with Tony - Unmaintained annotation sets'''<br />
<br />
TIGR, JCVI, PAMGO ISS annotations: Michelle: <br />
The ISS annotations from at least TIGR (and should be also JCVI and PAMGO) were all manual. They were either matches to HMMs or based on pairwise alignments. We used IEA for any annotations that were automatic from our pipeline and not reviewed. I assume JCVI continued that process after I left - at least until they stopped using their pipeline and shifted completely to using the NCBI PGAP tool (prokaryotic genome annotation pipeline).<br />
I think we (and hopefully PAMGO) were pretty good about using the GO_REFs to indicate whether it was HMM or pairwise. The problem with replacing our HMM annotations with InterPro2GO mappings is that we made much more specific annotations based on HMMs than what the InterPro mappings often do. I'd hate to lose those but I understand your desire to keep the annotations current.<br />
<br />
= Reported from the previous meeting =<br />
* GO-CAM QC plan<br />
** including SynGO, > 90 % of the production models<br />
<br />
<br />
=To revisit later= <br />
==SPKW hierarchy - at odds with transitivity as found in GO ontology?==<br />
**https://github.com/geneontology/go-annotation/issues/2036<br />
**emailed Chris, Seth about help with querying the GO database for non-redundant SPKW-based annotations (2018-08-16)<br />
** Kimberly: WB looking into the information added by SPKW in WormBase. From that evaluation we can perhaps decide whether we want to keep them. <br />
<br />
<br />
<br />
[[Category:Quality Control]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=QCQA_next_call&diff=71677QCQA next call2018-10-05T13:29:22Z<p>Valwood: /* Discussion: Annotation redundancy - non-experimental annotations */</p>
<hr />
<div>=Preparing for GOC meeting =<br />
<br />
=Annotation redundancy - non-experimental annotations=<br />
**Can we come up with a proposal for the Montreal meeting?<br />
**http://wiki.geneontology.org/index.php/2018_Montreal_GOC_Meeting_Agenda#Handling_redundant_information<br />
<br />
==Discussion: Annotation redundancy - non-experimental annotations==<br />
* We need to define what constitutes a redundant information, WRT to sources, evidences and references<br />
* There is a ticket that explains the strategy that will be taken for this: see https://github.com/geneontology/amigo/issues/43 and https://github.com/geneontology/amigo/issues/440<br />
* '''AI: Rules for flagging redundant annotations need to be documented - Chris'''<br />
* https://github.com/geneontology/go-annotation/issues/2060<br />
* https://github.com/geneontology/go-annotation/issues/1879<br />
<br />
Different types of redundancy<br />
* identical experimental annotations from different sources https://github.com/geneontology/go-annotation/issues/1404<br />
* inferred and IEA, ISO, ISM, IBA annotations when EXP exist<br />
* Redundant inferred annotations from GOC F-P links pipeline<br />
* e.g. https://github.com/geneontology/go-site/issues/576<br />
* TAS /NAS (special case)<br />
<br />
There is no use case for users of MODs and AMiGO to see automated annotations when EXP annotations are present.<br />
If somebody wants a complete set of annotations from a mapping resource these could be made available separately.<br />
<br />
==New error reports - status==<br />
http://snapshot.geneontology.org/reports/gorule-report.html<br />
https://github.com/geneontology/go-site/issues/709<br />
<br />
=How to blacklist papers=<br />
Pascale <br />
* List/form template of excluded papers or combinations of PMID/Gene/GO<br />
<br />
= Update: Unmaintained annotation sets=<br />
https://github.com/geneontology/go-annotation/issues/1724#issuecomment-390136730<br />
* '''AI: check status with Tony - Unmaintained annotation sets'''<br />
<br />
TIGR, JCVI, PAMGO ISS annotations: Michelle: <br />
The ISS annotations from at least TIGR (and should be also JCVI and PAMGO) were all manual. They were either matches to HMMs or based on pairwise alignments. We used IEA for any annotations that were automatic from our pipeline and not reviewed. I assume JCVI continued that process after I left - at least until they stopped using their pipeline and shifted completely to using the NCBI PGAP tool (prokaryotic genome annotation pipeline).<br />
I think we (and hopefully PAMGO) were pretty good about using the GO_REFs to indicate whether it was HMM or pairwise. The problem with replacing our HMM annotations with InterPro2GO mappings is that we made much more specific annotations based on HMMs than what the InterPro mappings often do. I'd hate to lose those but I understand your desire to keep the annotations current.<br />
<br />
= Reported from the previous meeting =<br />
* GO-CAM QC plan<br />
** including SynGO, > 90 % of the production models<br />
<br />
<br />
=To revisit later= <br />
==SPKW hierarchy - at odds with transitivity as found in GO ontology?==<br />
**https://github.com/geneontology/go-annotation/issues/2036<br />
**emailed Chris, Seth about help with querying the GO database for non-redundant SPKW-based annotations (2018-08-16)<br />
** Kimberly: WB looking into the information added by SPKW in WormBase. From that evaluation we can perhaps decide whether we want to keep them. <br />
<br />
<br />
<br />
[[Category:Quality Control]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=715962018 Montreal GOC Meeting Agenda2018-10-01T19:06:26Z<p>Valwood: /* Representing complete proteomes in GO (added by Val, as suggested by Chris) */</p>
<hr />
<div>=Montreal meeting Milestones=<br />
<br />
<br />
==New Pipeline & new pipeline documentation==<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Announcement: plan for migrating to GPAD (Seth)<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs : <br />
https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see <br />
https://github.com/geneontology/go-site/issues/791<br />
<br />
==GO rules update, pipeline and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports: http://snapshot.geneontology.org/reports/gorule-report.html<br />
<br />
<br />
==PAINT pipeline update==<br />
===PAINT GAF file generation QC===<br />
Huaiyu and Pascale<br />
https://github.com/orgs/geneontology/projects/23<br />
<br />
(can we do this at the same time as pipeline -- cjm?)<br />
<br />
== GO-CAM and Noctua ==<br />
Kimberly Seth, Ben, Tremayne, Laurent-Phillipe<br />
https://github.com/orgs/geneontology/projects/19<br />
=== Noctua 1.1 release ===<br />
*Updates on progress towards the 1.1 release<br />
**Bug fixes<br />
**New features<br />
**Groundwork for future releases<br />
=== GO-CAM integration with other pathway resources ===<br />
*Reactome<br />
=== Roadmap for next release ===<br />
<br />
==AmiGO update==<br />
https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe, Suzanna, Suzi, etc: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
<br />
==GO subsets update==<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
==PAINT tickets==<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
==Annotation==<br />
* Gene Product to terms relations: https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
==Handling redundant information==<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files. <br />
<br />
Discussion points: Is redundant, non-experimental annotation ever useful? <br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
3. What to do about READThroughs from Ensembl (MED17 as an example)<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
* https://github.com/geneontology/helpdesk/issues/161<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
=Breakout sessions topics=<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=715502018 Montreal GOC Meeting Agenda2018-09-28T10:30:28Z<p>Valwood: /* Representing complete proteomes in GO (added by Val) */</p>
<hr />
<div>=Montreal meeting Milestones=<br />
<br />
<br />
==New Pipeline & new pipeline documentation==<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
* Announcement: plan for migrating to GPAD (Seth)<br />
<br />
'''Information points:'''<br />
* Manage migration of consortium members to use explicit snapshot PURLs : <br />
https://github.com/geneontology/go-site/issues/783 <br />
<br />
* Excluding MOD-specific refs from the GO database: see <br />
https://github.com/geneontology/go-site/issues/791<br />
<br />
==GO rules update, pipeline and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports: http://snapshot.geneontology.org/reports/gorule-report.html<br />
<br />
<br />
==PAINT pipeline update==<br />
===PAINT GAF file generation QC===<br />
Huaiyu and Pascale<br />
https://github.com/orgs/geneontology/projects/23<br />
<br />
(can we do this at the same time as pipeline -- cjm?)<br />
<br />
==Noctua 1.1==<br />
Kimberly Seth, etc<br />
https://github.com/orgs/geneontology/projects/19<br />
<br />
==AmiGO update==<br />
https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe, Suzanna, Suzi, etc: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
<br />
==GO subsets update==<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
==PAINT tickets==<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
==Annotation==<br />
* Gene Product to terms relations: https://github.com/orgs/geneontology/projects/13 (Kimberley, Dustin)<br />
Suggestions: <br />
* Resources for Annotation Review? Is reviewing a priority compared to creating new annotations?<br />
* Signaling 2017 update<br />
* ECM reviews<br />
* Transcription reviews<br />
* Transcription guidelines: https://docs.google.com/presentation/d/1hOBMnpHbGyKsOJi-Ah3xhAavzOg2RgM4AXRdGbF8A6M/edit#slide=id.p1<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
* All synapse tickets are closed <br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
==Handling redundant information==<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files. <br />
<br />
Discussion points: Is redundant, non-experimental annotation ever useful? <br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val, as suggested by Chris)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
* https://github.com/geneontology/helpdesk/issues/161<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
=Breakout sessions topics=<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#Modeling transcription in GO-CAMs<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=714782018 Montreal GOC Meeting Agenda2018-09-25T05:18:14Z<p>Valwood: /* Representing complete proteomes in GO (added by Val) */</p>
<hr />
<div>=Montreal meeting Milestones=<br />
<br />
<br />
==New Pipeline & new pipeline documentation==<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
'''Information points:'''<br />
Manage migration of consortium members to use explicit snapshot PURLs : <br />
* https://github.com/geneontology/go-site/issues/783 <br />
<br />
==GO rules update, pipeline and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
==PAINT pipeline update==<br />
===PAINT GAF file generation QC===<br />
Huaiyu and Pascale<br />
https://github.com/orgs/geneontology/projects/23<br />
<br />
==Noctua 1.1==<br />
Kimberly Seth, etc<br />
https://github.com/orgs/geneontology/projects/19<br />
<br />
==AmiGO update==<br />
https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe, Suzanna, Suzi, etc: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
<br />
==GO subsets update==<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
==PAINT tickets==<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
==Annotation==<br />
* Gene Product to terms relations: https://github.com/orgs/geneontology/projects/13<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: x involved in y, X protein binding, protein complex x binding etc<br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
<br />
<br />
===Binding and Protein complexes===<br />
Kimberly<br />
* Should these be separate branches of GO ? <br />
See (among other tickets) https://github.com/geneontology/go-annotation/issues/1940<br />
<br />
* Proposal to convert all protein binding terms from IPI and a target in the 'with' field to IDA and a has_input.<br />
<br />
==Handling redundant information==<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files. <br />
<br />
Discussion points: Is redundant, non-experimental annotation ever useful? <br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
* https://github.com/geneontology/helpdesk/issues/161<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
=Breakout sessions topics=<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=714522018 Montreal GOC Meeting Agenda2018-09-23T14:58:59Z<p>Valwood: /* Representing complete proteomes in GO (added by Val) */</p>
<hr />
<div>=Montreal meeting Milestones=<br />
<br />
<br />
==New Pipeline & new pipeline documentation==<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
'''Information points:'''<br />
Manage migration of consortium members to use explicit snapshot PURLs : <br />
* https://github.com/geneontology/go-site/issues/783 <br />
<br />
==GO rules update, pipeline and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
==PAINT pipeline update==<br />
===PAINT GAF file generation QC===<br />
Huaiyu and Pascale<br />
https://github.com/orgs/geneontology/projects/23<br />
<br />
==Noctua 1.1==<br />
Kimberly Seth, etc<br />
https://github.com/orgs/geneontology/projects/19<br />
<br />
==AmiGO update==<br />
https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe, Suzanna, Suzi, etc: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
<br />
==GO subsets update==<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
==PAINT tickets==<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
==Annotation==<br />
* Gene Product to terms relations: https://github.com/orgs/geneontology/projects/13<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: X protein binding, protein complex x binding, etc<br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
<br />
==Handling redundant information==<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files. <br />
<br />
Discussion points: Is redundant, non-experimental annotation ever useful? <br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
Overview.<br />
Nobody seems really sure what happens. I'll document what I think happens here and then run it by others to confirm<br />
<br />
1. GO uses<br />
https://www.ebi.ac.uk/reference_proteomes to define the set of human IDs uniquely. This is also used by Panther.<br />
This reference proteome set represents each HGNC ID uniquely.<br />
This causes issues when 2 proteins are encoded by the a loci described by a single HGNC name.<br />
<br />
2. UniProt has other versions of reference proteome (I asked UniProt helpdesk about this).<br />
<br />
Questions<br />
<br />
How do changes in the reference proteome in-between releases affect GO? i.e What happens to new or revised IDs if they are used in GO annotations, but are not represented in the reference proteome?<br />
<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
=Breakout sessions topics=<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=714512018 Montreal GOC Meeting Agenda2018-09-23T14:51:33Z<p>Valwood: /* Representing complete proteomes in GO (added by Val) */</p>
<hr />
<div>=Montreal meeting Milestones=<br />
<br />
<br />
==New Pipeline & new pipeline documentation==<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
'''Information points:'''<br />
Manage migration of consortium members to use explicit snapshot PURLs : <br />
* https://github.com/geneontology/go-site/issues/783 <br />
<br />
==GO rules update, pipeline and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
==PAINT pipeline update==<br />
===PAINT GAF file generation QC===<br />
Huaiyu and Pascale<br />
https://github.com/orgs/geneontology/projects/23<br />
<br />
==Noctua 1.1==<br />
Kimberly Seth, etc<br />
https://github.com/orgs/geneontology/projects/19<br />
<br />
==AmiGO update==<br />
https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe, Suzanna, Suzi, etc: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
<br />
==GO subsets update==<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
==PAINT tickets==<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
==Annotation==<br />
* Gene Product to terms relations: https://github.com/orgs/geneontology/projects/13<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: X protein binding, protein complex x binding, etc<br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
<br />
==Handling redundant information==<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files. <br />
<br />
Discussion points: Is redundant, non-experimental annotation ever useful? <br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
* https://github.com/geneontology/go-site/issues/816<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
=Breakout sessions topics=<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=714502018 Montreal GOC Meeting Agenda2018-09-23T14:50:26Z<p>Valwood: /* Representing complete proteomes in GO (added by Val) */</p>
<hr />
<div>=Montreal meeting Milestones=<br />
<br />
<br />
==New Pipeline & new pipeline documentation==<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
* https://github.com/orgs/geneontology/projects/15<br />
* http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
'''Information points:'''<br />
Manage migration of consortium members to use explicit snapshot PURLs : <br />
* https://github.com/geneontology/go-site/issues/783 <br />
<br />
==GO rules update, pipeline and error reports==<br />
Eric & Pascale<br />
* https://github.com/orgs/geneontology/projects/20<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
==PAINT pipeline update==<br />
===PAINT GAF file generation QC===<br />
Huaiyu and Pascale<br />
https://github.com/orgs/geneontology/projects/23<br />
<br />
==Noctua 1.1==<br />
Kimberly Seth, etc<br />
https://github.com/orgs/geneontology/projects/19<br />
<br />
==AmiGO update==<br />
https://github.com/orgs/geneontology/projects/21<br />
<br />
==GO website migration==<br />
Laurent-Philippe, Suzanna, Suzi, etc: https://github.com/orgs/geneontology/projects/22<br />
<br />
==Ontology and Annotation documentation update==<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier to find old discussions<br />
<br />
==GO subsets update==<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
==PAINT tickets==<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
==Annotation==<br />
* Gene Product to terms relations: https://github.com/orgs/geneontology/projects/13<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
==Ontology==<br />
Suggestions: <br />
* MF refactor including transcription: https://github.com/orgs/geneontology/projects/25<br />
* ECM update<br />
* Stop creating and start merging precomposed terms: X protein binding, protein complex x binding, etc<br />
* Pathways2GO: https://github.com/orgs/geneontology/projects/24<br />
* Ontology maintenance: https://github.com/orgs/geneontology/projects/14<br />
<br />
==Handling redundant information==<br />
* Define redundant information: <br />
In AmiGO, we should be able to improve the display by removing redundant information. <br />
That information may be useful for certain purposes, so we should provide it in files. We could also provide the 'core set' ('stringent set') in some version of files. <br />
<br />
Discussion points: Is redundant, non-experimental annotation ever useful? <br />
* Are there any use cases where people have used these annotations for some type of analysis?<br />
* Some pipelines (InterPro2GO, SPKW, PAINT, F-P links), sometimes provide data that is already captured experimentally, and some groups would like the redundancy reduced. <br />
* Should all GOC members be handling redundancy in the same way?<br />
* If redundant, non-experimental annotations are present and are going to be removed, at what point in the pipeline should they be filtered, e.g. annotation file production by GOC, annotation file processing by MODs, website display?<br />
* If we filter annotations files, should we then also provide two annotation files for users, one complete and one filtered? <br />
*[https://github.com/geneontology/go-annotation/issues/2042#issuecomment-412964090 Doubled up IBA+EXP annotations (from Karen Christie)]<br />
* [https://github.com/geneontology/go-site/issues/767 Issue with GOC inference file (i) incorrect aspect reported]<br />
*'''Proposal:'''<br />
<br />
=New topics=<br />
<br />
==Representing complete proteomes in GO (added by Val)==<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* https://github.com/geneontology/helpdesk/issues/144<br />
* https://github.com/geneontology/go-annotation/issues/2082<br />
* https://github.com/geneontology/go-annotation/issues/2081<br />
<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper)<br />
<br />
=Breakout sessions topics=<br />
# Guidelines for submitting annotations to GO - for example Ivan Erill also had an idea to ask the organizers of the Phage Meeting to provide an option for abstract submissions to include author-generated GO annotations. What would our guidelines be ? <br />
# GO Slims - review Alliance slim with latest stats from Mary Dolan. Does the goslim_agr need any updates?<br />
#'Response to' workshop (similar to the signaling WS)<br />
#Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
=Product owners/tech leads discussion - lunch Thursday=<br />
* Small debrief session: Lessons learned, suggestions for improvements, next face-2-face meeting<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=707702018 Montreal GOC Meeting Agenda2018-08-10T12:46:35Z<p>Valwood: /* Representing complete proteomes in GO (added by Val) */</p>
<hr />
<div>= AGENDA=<br />
<br />
<br />
==Milestones to be met for the Montreal meeting==<br />
<br />
===GO rules update, pipeline and error reports===<br />
Eric & Pascale<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
===Pipeline documentation===<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
<br />
====Ontology and Annotation documentation update====<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier t find old discussions<br />
<br />
===GO website migration===<br />
Laurent-Philippe, SuziA, etc<br />
<br />
===Noctua 1.1===<br />
Kimberly Seth, etc<br />
<br />
===PAINT===<br />
====PAINT GAF file generation QC====<br />
Huaiyu and Pascale<br />
<br />
====PAINT tickets====<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
====Annotation====<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
<br />
====Ontology====<br />
Suggestions: <br />
* MF refactor update, including transcription<br />
* ECM update<br />
<br />
<br />
====GO subsets update====<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
== Suggestions for topics Fall 2018==<br />
===Carried over from May 2018===<br />
*'Response to' workshop (similar to the signaling WS)<br />
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
<br />
===New topics===<br />
<br />
====Representing complete proteomes in GO (added by Val)====<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
https://github.com/geneontology/helpdesk/issues/144<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper) <br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=707542018 Montreal GOC Meeting Agenda2018-08-10T04:18:51Z<p>Valwood: /* Representing complete proteomes (added by Val) */</p>
<hr />
<div>= AGENDA=<br />
<br />
<br />
==Milestones to be met for the Montreal meeting==<br />
<br />
===GO rules update, pipeline and error reports===<br />
Eric & Pascale<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
===Pipeline documentation===<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
<br />
====Ontology and Annotation documentation update====<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier t find old discussions<br />
<br />
===GO website migration===<br />
Laurent-Philippe, SuziA, etc<br />
<br />
===Noctua 1.1===<br />
Kimberly Seth, etc<br />
<br />
===PAINT===<br />
====PAINT GAF file generation QC====<br />
Huaiyu and Pascale<br />
<br />
====PAINT tickets====<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
====Annotation====<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
<br />
====Ontology====<br />
Suggestions: <br />
* MF refactor update, including transcription<br />
* ECM update<br />
<br />
<br />
====GO subsets update====<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
== Suggestions for topics Fall 2018==<br />
===Carried over from May 2018===<br />
*'Response to' workshop (similar to the signaling WS)<br />
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
<br />
===New topics===<br />
<br />
====Representing complete proteomes in GO (added by Val)====<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper) <br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=707532018 Montreal GOC Meeting Agenda2018-08-10T04:18:13Z<p>Valwood: /* Representing complete proteomes (added by Val) */</p>
<hr />
<div>= AGENDA=<br />
<br />
<br />
==Milestones to be met for the Montreal meeting==<br />
<br />
===GO rules update, pipeline and error reports===<br />
Eric & Pascale<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
===Pipeline documentation===<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
<br />
====Ontology and Annotation documentation update====<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier t find old discussions<br />
<br />
===GO website migration===<br />
Laurent-Philippe, SuziA, etc<br />
<br />
===Noctua 1.1===<br />
Kimberly Seth, etc<br />
<br />
===PAINT===<br />
====PAINT GAF file generation QC====<br />
Huaiyu and Pascale<br />
<br />
====PAINT tickets====<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
====Annotation====<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
<br />
====Ontology====<br />
Suggestions: <br />
* MF refactor update, including transcription<br />
* ECM update<br />
<br />
<br />
====GO subsets update====<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
== Suggestions for topics Fall 2018==<br />
===Carried over from May 2018===<br />
*'Response to' workshop (similar to the signaling WS)<br />
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
<br />
===New topics===<br />
<br />
====Representing complete proteomes (added by Val)====<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper) <br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=707522018 Montreal GOC Meeting Agenda2018-08-10T04:17:55Z<p>Valwood: /* Representing complete proteomes (added by Val) */</p>
<hr />
<div>= AGENDA=<br />
<br />
<br />
==Milestones to be met for the Montreal meeting==<br />
<br />
===GO rules update, pipeline and error reports===<br />
Eric & Pascale<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
===Pipeline documentation===<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
<br />
====Ontology and Annotation documentation update====<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier t find old discussions<br />
<br />
===GO website migration===<br />
Laurent-Philippe, SuziA, etc<br />
<br />
===Noctua 1.1===<br />
Kimberly Seth, etc<br />
<br />
===PAINT===<br />
====PAINT GAF file generation QC====<br />
Huaiyu and Pascale<br />
<br />
====PAINT tickets====<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
====Annotation====<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
<br />
====Ontology====<br />
Suggestions: <br />
* MF refactor update, including transcription<br />
* ECM update<br />
<br />
<br />
====GO subsets update====<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
== Suggestions for topics Fall 2018==<br />
===Carried over from May 2018===<br />
*'Response to' workshop (similar to the signaling WS)<br />
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
<br />
===New topics===<br />
<br />
====Representing complete proteomes (added by Val)====<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? <br />
Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper) <br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=707512018 Montreal GOC Meeting Agenda2018-08-10T04:17:18Z<p>Valwood: /* Representing complete proteomes (added by Val) */</p>
<hr />
<div>= AGENDA=<br />
<br />
<br />
==Milestones to be met for the Montreal meeting==<br />
<br />
===GO rules update, pipeline and error reports===<br />
Eric & Pascale<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
===Pipeline documentation===<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
<br />
====Ontology and Annotation documentation update====<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier t find old discussions<br />
<br />
===GO website migration===<br />
Laurent-Philippe, SuziA, etc<br />
<br />
===Noctua 1.1===<br />
Kimberly Seth, etc<br />
<br />
===PAINT===<br />
====PAINT GAF file generation QC====<br />
Huaiyu and Pascale<br />
<br />
====PAINT tickets====<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
====Annotation====<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
<br />
====Ontology====<br />
Suggestions: <br />
* MF refactor update, including transcription<br />
* ECM update<br />
<br />
<br />
====GO subsets update====<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
== Suggestions for topics Fall 2018==<br />
===Carried over from May 2018===<br />
*'Response to' workshop (similar to the signaling WS)<br />
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
<br />
===New topics===<br />
<br />
====Representing complete proteomes (added by Val)====<br />
<br />
Datasets (obtaining/maintaining complete datasets with unique identifiers)<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
Annotation<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? <br />
Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper) <br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=707502018 Montreal GOC Meeting Agenda2018-08-10T04:16:25Z<p>Valwood: /* Representing complete proteomes (added by Val) */</p>
<hr />
<div>= AGENDA=<br />
<br />
<br />
==Milestones to be met for the Montreal meeting==<br />
<br />
===GO rules update, pipeline and error reports===<br />
Eric & Pascale<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
===Pipeline documentation===<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
<br />
====Ontology and Annotation documentation update====<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier t find old discussions<br />
<br />
===GO website migration===<br />
Laurent-Philippe, SuziA, etc<br />
<br />
===Noctua 1.1===<br />
Kimberly Seth, etc<br />
<br />
===PAINT===<br />
====PAINT GAF file generation QC====<br />
Huaiyu and Pascale<br />
<br />
====PAINT tickets====<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
====Annotation====<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
<br />
====Ontology====<br />
Suggestions: <br />
* MF refactor update, including transcription<br />
* ECM update<br />
<br />
<br />
====GO subsets update====<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
== Suggestions for topics Fall 2018==<br />
===Carried over from May 2018===<br />
*'Response to' workshop (similar to the signaling WS)<br />
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
<br />
===New topics===<br />
<br />
====Representing complete proteomes (added by Val)====<br />
<br />
* =====Datasets (obtaining/maintaining complete datasets with unique identifiers)=====<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
=====Annotation=====<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? <br />
Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper) <br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=707492018 Montreal GOC Meeting Agenda2018-08-10T04:15:51Z<p>Valwood: /* Annotation */</p>
<hr />
<div>= AGENDA=<br />
<br />
<br />
==Milestones to be met for the Montreal meeting==<br />
<br />
===GO rules update, pipeline and error reports===<br />
Eric & Pascale<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
===Pipeline documentation===<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
<br />
====Ontology and Annotation documentation update====<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier t find old discussions<br />
<br />
===GO website migration===<br />
Laurent-Philippe, SuziA, etc<br />
<br />
===Noctua 1.1===<br />
Kimberly Seth, etc<br />
<br />
===PAINT===<br />
====PAINT GAF file generation QC====<br />
Huaiyu and Pascale<br />
<br />
====PAINT tickets====<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
====Annotation====<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
<br />
====Ontology====<br />
Suggestions: <br />
* MF refactor update, including transcription<br />
* ECM update<br />
<br />
<br />
====GO subsets update====<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
== Suggestions for topics Fall 2018==<br />
===Carried over from May 2018===<br />
*'Response to' workshop (similar to the signaling WS)<br />
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
<br />
===New topics===<br />
<br />
====Representing complete proteomes (added by Val)====<br />
<br />
=====Datasets (obtaining/maintaining complete datasets with unique identifiers)=====<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
=====Annotation=====<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? <br />
Establish the difference between: <br />
* (1) "not in the GO database (not found); <br />
* (2) "unknown" (ND), <br />
* (3) "unannotated" (no ND, and no annotation in Aspect of interest) <br />
(difference can be established using the complete known protein ID set for your organism and GO term mapper https://go.princeton.edu/cgi-bin/GOTermMapper) <br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=707482018 Montreal GOC Meeting Agenda2018-08-10T04:13:54Z<p>Valwood: /* Suggestions for topics Fall 2018 */</p>
<hr />
<div>= AGENDA=<br />
<br />
<br />
==Milestones to be met for the Montreal meeting==<br />
<br />
===GO rules update, pipeline and error reports===<br />
Eric & Pascale<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
===Pipeline documentation===<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
<br />
====Ontology and Annotation documentation update====<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier t find old discussions<br />
<br />
===GO website migration===<br />
Laurent-Philippe, SuziA, etc<br />
<br />
===Noctua 1.1===<br />
Kimberly Seth, etc<br />
<br />
===PAINT===<br />
====PAINT GAF file generation QC====<br />
Huaiyu and Pascale<br />
<br />
====PAINT tickets====<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
====Annotation====<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
<br />
====Ontology====<br />
Suggestions: <br />
* MF refactor update, including transcription<br />
* ECM update<br />
<br />
<br />
====GO subsets update====<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
== Suggestions for topics Fall 2018==<br />
===Carried over from May 2018===<br />
*'Response to' workshop (similar to the signaling WS)<br />
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
<br />
===New topics===<br />
<br />
====Representing complete proteomes (added by Val)====<br />
<br />
=====Datasets (obtaining/maintaining complete datasets with unique identifiers)=====<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
=====Annotation=====<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? If anyone is interested, there is a very quick/easy way to establish the difference between: (1) "not in the GO database (not found); (2) "unknown" (ND), and (3) "unannotated" (no ND, and no annotation in Aspect of interest) for your organisms proteins using the complete known protein ID set for your organism and the GO term mapper tool https://go.princeton.edu/cgi-bin/GOTermMapper (GOTermMapper provides these numbers as part of the output so that the slim set results can be interpreted correctly). <br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwoodhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Agenda&diff=707472018 Montreal GOC Meeting Agenda2018-08-10T04:12:58Z<p>Valwood: /* New topics */</p>
<hr />
<div>= AGENDA=<br />
<br />
<br />
==Milestones to be met for the Montreal meeting==<br />
<br />
===GO rules update, pipeline and error reports===<br />
Eric & Pascale<br />
* Documentation of rules: Which annotation validation rules are currently implemented? https://github.com/geneontology/go-annotation/issues/1928<br />
* Current rules status & future priorities<br />
* For MODs: where to find reports<br />
<br />
===Pipeline documentation===<br />
Kimberly, Pascale, Chris, Seth, etc <br />
Must be completed (as much as possible) and announced<br />
http://wiki.geneontology.org/index.php/Release_Pipeline<br />
<br />
<br />
====Ontology and Annotation documentation update====<br />
David, Kimberly and Pascale<br />
(random thoughts: <br />
* Ontology: mention the creation of 'projects' in GH where we moved old projects, so that its' easier t find old discussions<br />
<br />
===GO website migration===<br />
Laurent-Philippe, SuziA, etc<br />
<br />
===Noctua 1.1===<br />
Kimberly Seth, etc<br />
<br />
===PAINT===<br />
====PAINT GAF file generation QC====<br />
Huaiyu and Pascale<br />
<br />
====PAINT tickets====<br />
Marc & Pascale<br />
https://github.com/geneontology/go-annotation/labels/PAINT%20annotation<br />
<br />
====Annotation====<br />
Suggestions: <br />
* Signaling 2017 update<br />
* Transcription reviews<br />
* ECM reviews<br />
<br />
<br />
====Ontology====<br />
Suggestions: <br />
* MF refactor update, including transcription<br />
* ECM update<br />
<br />
<br />
====GO subsets update====<br />
Pascale: <br />
* Deprecated a number of unused/unmaintained subsets <br />
* Show subset yaml files and how they are used<br />
* Each subset needs a maintainer<br />
<br />
== Suggestions for topics Fall 2018==<br />
===Carried over from May 2018===<br />
*'Response to' workshop (similar to the signaling WS)<br />
* Use cases: Should we add this to the agenda? What would be a productive way of discussing this topic? https://docs.google.com/document/d/104m4jUNjPH9pCpskg8E29Zm2pLHhPFmKyIFLa9l_EOQ/edit<br />
<br />
<br />
===New topics===<br />
<br />
===Representing complete proteomes (added by Val)===<br />
<br />
===Datasets (obtaining/maintaining complete datasets with unique identifiers)===<br />
<br />
* https://github.com/geneontology/go-site/issues/756<br />
* https://github.com/geneontology/amigo/issues/475<br />
* What does reference proteome mean, why we have duplicates for pufferfish, and why it includes unreviewed proteins? See https://docs.google.com/document/d/1l4hZw_ZTor8RoTjYTNS4FtGAba4HZrewmjccrSXJ9Hs/edit<br />
* https://github.com/pantherdb/Helpdesk/issues/1<br />
<br />
===Annotation===<br />
* Which organisms other than cerevisiae and pombe have looked at all protein coding genes for the availability/possibility of GO annotation? If anyone is interested, there is a very quick/easy way to establish the difference between: (1) "not in the GO database (not found); (2) "unknown" (ND), and (3) "unannotated" (no ND, and no annotation in Aspect of interest) for your organisms proteins using the complete known protein ID set for your organism and the GO term mapper tool https://go.princeton.edu/cgi-bin/GOTermMapper (GOTermMapper provides these numbers as part of the output so that the slim set results can be interpreted correctly). <br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Valwood