https://wiki.geneontology.org/api.php?action=feedcontributions&user=TanyaB&feedformat=atomGO Wiki - User contributions [en]2024-03-29T06:02:55ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Ontology_meeting_2023-10-16&diff=86129Ontology meeting 2023-10-162023-10-16T16:03:28Z<p>TanyaB: </p>
<hr />
<div>* '''Group members:''' Pascale, Raymond, Edith, Val, Steven, Jim, Tanya, Kimberly, Peter, Chris, Paul<br />
* '''Present:'''<br />
* '''Regrets:''' Tanya<br />
<br />
=Discussion points=<br />
<br />
==Protégé 5.6.3==<br />
* Won't install, there is a bug. <br />
* Everyone will need to switch at the same time, please wait for green light<br />
<br />
==Cryptic Travis errors==<br />
Added a new wiki page: <br />
[[Interpretation_of_Travis_checks_errors]]<br />
<br />
<br />
==Switching from has in/output to has primary in/output==<br />
* '''TBC''' OK to merge, in the sense that the inferences are no worse than current and no equivalent terms are being created<br />
* Need decision on relation to use for [https://github.com/geneontology/go-ontology/issues/26217 receptor activity] <br />
<br />
==[https://github.com/geneontology/go-ontology/issues/25933 Cell to cell signaling terms]==<br />
Request was to <br />
* Replace "epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification GO:0060802, with epiblast cell-extraembryonic ectoderm cell signaling (Single EXP to PMID:14511481) <br />
* Replace "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation GO:0021937, with: cerebellar Purkinje cell-granule cell precursor cell signaling (def: Any process that mediates the transfer of information from Purkinje cells to granule cell precursors.) ([https://amigo.geneontology.org/amigo/term/GO:0021937 9 EXP])<br />
* <br />
Some example terms: <br />
* neuron-glial cell signaling<br />
* epithelial-mesenchymal cell signaling<br />
* mesenchymal-epithelial cell signaling<br />
* astrocyte-dopaminergic neuron signaling<br />
* ectoderm and mesoderm interaction<br />
* mesodermal-endodermal cell signaling<br />
* glial cell-neuron signaling<br />
<br />
There are also terms for which the cells signaling to each other are not specified: <br />
* cell-cell signaling involved in amphid sensory organ development<br />
* cell-cell signaling involved in cardiac conduction<br />
* cell-cell signaling involved in cell fate commitment<br />
* cell-cell signaling involved in kidney development<br />
* cell-cell signaling involved in lung development<br />
etc<br />
<br />
* The question is, is 'cell x to cell y' signaling a biological process relevant for GO? <br />
* '''Issues: '''<br />
** orthogonal to other signaling pathways<br />
** For example: neuron-glial cell signaling is defined as "Cell-cell signaling that mediates the transfer of information from a neuron to a glial cell. This signaling has been shown to be mediated by various molecules released by different types of neurons, e.g. glutamate, gamma-amino butyric acid (GABA), noradrenaline, acetylcholine, dopamine and adenosine."<br />
*** ''acetylcholine receptor signaling pathway'' is not a child of cell-cell signaling<br />
*** ''dopamine receptor signaling pathway'' is a has_part child, with the relation 'has part 'synaptic transmission, dopaminergic'<br />
*** We dont have ''noradrenaline signaling'', but we have ''synaptic transmission, noradrenergic''<br />
*** >> but none of these are linked to neuron-glial cell signaling, which is probably OK, since these pathways may be taking place in various cell types<br />
*** >>> '''It seems these terms are BPs that contain CC information, and this information should be captured with 'occurs in' '''<br />
<br />
* Terms are not much used: <br />
** cell-cell signaling involved in cell fate commitment 9 EXP<br />
** epithelial-mesenchymal cell signaling 4 EXP<br />
** glutamate secretion, neurotransmission 4 EXP<br />
** mesenchymal-epithelial cell signaling 4 EXP<br />
** mesodermal-endodermal cell signaling 2 EXP<br />
** neuron-glial cell signaling 5 EXP<br />
<br />
* '''Chris's slides: [https://docs.google.com/presentation/d/1q7PE8VGRGYWyohbLMwpiYpd6dnCJQVuomyzsK5dC9bc/edit#slide=id.p Decomposition of macro biological processes in GO]'''<br />
<br />
[[Category:Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2021-04-20&diff=80121Annotation Conf. Call 2021-04-202021-04-20T17:18:47Z<p>TanyaB: /* 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 />
** [https://drive.google.com/drive/folders/1vdyOPtR91L0u5y6XYuwOd71LRt6xZXKS Data Flow Spreadsheet Directory]<br />
<br />
= Attendance =<br />
* On call: Birgit, Chris, David, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Karen, Kimberly, Li, Malcolm, Mary K, Midori, Pascale, Penelope, Petra, Raymond, Rob, Robert, Ruth, Seth, Stacia, Stan, Suzi, Tanya, Val<br />
<br />
[[Category:Annotation Working Group]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2020-04-21&diff=78091Annotation Conf. Call 2020-04-212020-04-21T15:38:37Z<p>TanyaB: /* Attendance */</p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== GOC Meeting - May 2020 ==<br />
* Paris consortium meeting scheduled for May 12th - 14th will be held virtually<br />
* Please keep the dates open<br />
* We are planning for shorter days ( ~4 hrs ?) to accommodate all time zones as best as possible<br />
* [https://docs.google.com/document/d/1DTBCxib8aRwyw5IWLbYRHtPLCnmcbjUNAV1gwj_2hlo Please suggest agenda items]<br />
* Users meeting - May 11th<br />
<br />
== ChEBI Roles in the Ontology ==<br />
* Update on reasoning over roles (Karen)<br />
<br />
== File Formats ==<br />
<br />
=== Proposed GAF Update, GAF 2.2 ===<br />
* Started documentation/FAQ for community<br />
* GAF 2.1 will continue to be produced and supported by the GOC into the foreseeable future<br />
* However, we are proposing an incremental update to the GAF to allow for use of the full set of gp2term relations<br />
* Proposed set of allowed relations is in this github ticket: https://github.com/geneontology/go-annotation/issues/2917<br />
** This would be the same set of gp2term relations used in the GPAD, the main difference is that they are in the same column as negation and when both apply they are pipe-separted<br />
** Default gp2term relations:<br />
*** Molecular Function: enables<br />
*** Cellular Component: located_in<br />
*** Biological Process: individual groups decide based on annotation practice<br />
*Why do this?<br />
** The expanded set of gp2term relations is available in annotation tools, e.g. Noctua and Protein2GO, but by not including them in the GAF, we don't give the GOC, or users, any mechanism to filter specific sets of annotations for GAFs and subsequent analyses. Making this change will allow GO and groups to do this.<br />
<br />
=== GPAD/GPI 2.0 Specifications ===<br />
*Review specs on github: https://github.com/geneontology/go-annotation/edit/master/specs/gpad-gpi-2-0.md<br />
<br />
*github ticket for comments: https://github.com/geneontology/go-annotation/issues/2864<br />
<br />
*Questions/Comments<br />
**We need guidelines for how to represent proteins ids or accessions shared by multiple gene products, e.g. histones. [Stacia]<br />
<br />
*Response:<br />
**Groups should work with UniProt or internally to disambiguate protein records that refer to multiple genes, i.e. generate gene-centric protein entries in UniProt<br />
**In the interim, we are proposing that protein entries that correspond to the product of multiple genes be included as a single entry in the gpi, with one name chosen as a symbol, and other names listed as synonyms. All parent gene ids will be listed in the 'Encoded_By' field.<br />
<br />
=== Deadlines ===<br />
*Groups have asked by what date they need to produce these new files.<br />
** Alliance members that will be migrating to Noctua, will need to use the gpad/gpi 2.0 file format for the data ingest.<br />
** Otherwise, GO will continue to consume and produce GAF for the foreseeable future, but note that gpad/gpi is a richer and more robust file format and is preferred for data exchange within the GOC.<br />
** For GAF 2.2, the software group will need some time to prepare the pipeline and other software (e.g. AmiGO) and we will also want to announce this change to the community, so there will be some lead time here (exact TBD).<br />
<br />
== Annotation Expertise ==<br />
* Consistency in use of gene-product-to-term relations is an ongoing concern<br />
* Previous conference call we discussed soliciting ideas from groups about how to leverage expertise in specific areas of biology or curation to help achieve consistent representation in our annotations<br />
* Follow-up<br />
** In what areas of the BP branch do curators have expertise?<br />
*** Also look at Annual Reviews? Organism-specific 'book's, e.g. WormBook?<br />
** Discuss in more detail at May meeting to begin formulating a plan and more concrete deliverables, e.g. GO-CAM templates, curation guidelines?<br />
<br />
= Attendance =<br />
* On call: David, Dmitry, Dustin, Edith, Giulia, Harold, Helen, Judy, Karen, Kimberly, Li, Malcolm, Midori, Pascale, Patrick, Petra, Prita, Rob, Sabrina, Seth, Stacia, Stan, Suzi, Tanya, Val<br />
<br />
[[Category:Annotation Working Group]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2020-04-06&diff=77984Ontology meeting 2020-04-062020-04-06T16:35:38Z<p>TanyaB: /* More on Roles */</p>
<hr />
<div>= Conference Line =<br />
See calendar for details<br />
<br />
On call: <br />
<br />
= Agenda =<br />
<br />
==More on Roles==<br />
Karen has asked for some discussion.<br />
<br />
<br />
T: Practical question: new and old curators will have to remember that they need to annotate to ‘xenobiotic %’ and ‘chemical x %’ to get both - how can we make this easier? term-specific annotation guidance in Noctua? <br />
<br />
<br />
D: One practical solution would be to always use the xenobiotic term when it is appropriate. If you then specify the chemical and the logical refs for the chemicals are in place, we will automatically infer the correct chemical hierarchy. logica defs. The chemical would be annotated in a way the annotation extensions are used now, only in Noctua. So xenobiotic catabolic process and has_primary_input cocaine would also resolve to cocaine catabolic process. No need to double annotate if they logical refs are carefully thought out. <br />
<br />
==Other Business==<br />
https://github.com/geneontology/go-ontology/projects/1<br />
<br />
<br />
<br />
====Minutes should be recorded on individual tickets and in individual projects====<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2020-04-06&diff=77983Ontology meeting 2020-04-062020-04-06T16:35:25Z<p>TanyaB: /* More on Roles */</p>
<hr />
<div>= Conference Line =<br />
See calendar for details<br />
<br />
On call: <br />
<br />
= Agenda =<br />
<br />
==More on Roles==<br />
Karen has asked for some discussion.<br />
<br />
<br />
T: Practical question: new and old curators will have to remember that they need to annotate to ‘xenobiotic %’ and ‘chemical x %’ to get both - how can we make this easier? term-specific annotation guidance in Noctua? <br />
D: One practical solution would be to always use the xenobiotic term when it is appropriate. If you then specify the chemical and the logical refs for the chemicals are in place, we will automatically infer the correct chemical hierarchy. logica defs. The chemical would be annotated in a way the annotation extensions are used now, only in Noctua. So xenobiotic catabolic process and has_primary_input cocaine would also resolve to cocaine catabolic process. No need to double annotate if they logical refs are carefully thought out. <br />
<br />
==Other Business==<br />
https://github.com/geneontology/go-ontology/projects/1<br />
<br />
<br />
<br />
====Minutes should be recorded on individual tickets and in individual projects====<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Ontology]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=763142019 Berkeley GOC Meeting Logistics2019-10-01T00:57:12Z<p>TanyaB: /* 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 />
* [[2019_Berkeley_GOC_Meeting_Agenda]]<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 />
<br />
==Overall schedule== <br />
*Monday, October 7: [https://docs.google.com/document/d/1YBCEeSl1MKPvtRNAMGBGcOZqdZl3wlbwWC1nuDnccqE/edit# User Meeting (9:00am-5pm)]<br />
*Tuesday-Thursday October 8-10: GOC Meeting (9am-5pm first 2 days, 9am-12:30pm third day)<br />
*Friday, October 11, 9am-3pm: [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics SAB Meeting], 717 Potter room 248. (SAB dinner will be Thursday, Oct 10 at 7:30pm.)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, at [https://www.google.com/maps/dir/717+Potter+St,+Berkeley,+CA+94710-2722,+USA/Stella+Nonna,+1407+San+Pablo+Ave,+Berkeley,+CA+94702/@37.857716,-122.2988811,14.76z/data=!4m14!4m13!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!1m5!1m1!1s0x80857ecf3c1a4765:0xec53c8ef10026f6f!2m2!1d-122.294867!2d37.878534!3e0 Stella Nonna (1407 San Pablo Ave., Berkeley)]<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, 9am-3pm, 717 Potter St., room 248<br />
* [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics SAB meeting logistics]<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 and fill out the [http://bit.ly/2019GOCBerkeleyTransportation form] so we can submit for site access in the week before the meeting.<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 and fill out the [http://bit.ly/2019GOCBerkeleyTransportation form] so we can submit for site access in the week before the meeting. 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 (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, and a taco truck even closer. Ubereats and the like are always an option for people wanting more variety.<br />
<br />
Seth will be happy to talk nearly endlessly about local restaurant, bar, and tea/cafe opportunities.<br />
<br />
==== Official and unofficial GOC dinners ====<br />
<br />
Tuesday, October 8, 5:30pm: [http://www.rottencitypizza.com/#board Rotten City Pizza], located walking distance between Potter Street and Emeryville. Beer, wine, cider, pizza, pool & darts. Pay your own way.<br />
<br />
Wednesday, October 9, 6pm: '''GOC meeting dinner''', [https://www.google.com/maps/dir/717+Potter+St,+Berkeley,+CA+94710-2722,+USA/Stella+Nonna,+1407+San+Pablo+Ave,+Berkeley,+CA+94702/@37.857716,-122.2988811,14.76z/data=!4m14!4m13!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!1m5!1m1!1s0x80857ecf3c1a4765:0xec53c8ef10026f6f!2m2!1d-122.294867!2d37.878534!3e0 Stella Nonna (1407 San Pablo Ave., Berkeley)]. Covered by registration fee.<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 Thursday, Oct 10, we will organize an optional hike in Tilden Park with plenty of Bay views.<br />
<br />
That evening, if there is interest, 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, some people may want to take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] (advance reservations required) and get dinner in the San Francisco Ferry Building.<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! (If you don't have edit permission, you can instead fill out [https://bit.ly/2019GOBerkeley this signup form].)<br />
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 />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Nomi Harris<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 />
| Reactome / NYULMC<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<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 />
| Four Points<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 />
| Yes<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| No<br />
| No<br />
| N/A<br />
| Yes<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 />
| Yes<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| Yes<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 />
| Berkeley Inn<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 />
| Yes<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Berkeley Inn <br />
| Yes<br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hotel Shattuck Plaza<br />
| Yes<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hotel Shattuck Plaza<br />
| Yes<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 />
| Yes<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 />
| Felix Gondwe<br />
| SGD, Stanford<br />
| Yes<br />
| Yes <br />
| No<br />
| N/A<br />
| Yes<br />
|-<br />
| Patrick Masson<br />
| SIB<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Paul Sternberg<br />
| Caltech<br />
| ?<br />
| ?<br />
| ?<br />
| Four Points?<br />
| not yet<br />
|-<br />
| Bill Duncan<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Joanna Argasinska<br />
| SGD, Stanford<br />
| Yes<br />
| Yes <br />
| No<br />
| Hotel Shattuck Plaza<br />
| Yes <br />
|-<br />
| Peifen Zhang<br />
| Phoenix Bioinformatics<br />
| No<br />
| No<br />
| Yes<br />
| <br />
| -<br />
|-<br />
| <br />
| <br />
| <br />
| <br />
|<br />
| <br />
| <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 />
Stacia Engel (SGD) not attending - son on Fall Break so we're doing family stuff<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=760092019 Berkeley GOC Meeting Logistics2019-08-20T15:07:31Z<p>TanyaB: /* 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)<br />
* Please also fill in the fields in the Attendees list at the bottom of this page. If you don't have edit permission, 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): 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). More details soon.<br />
<br />
=SAB Meeting=<br />
* Meeting: Friday, October 11 (time TBA) in 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 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/hotels/travel/sfofp-four-points-san-francisco-bay-bridge/| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the 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 />
** 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''': 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 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 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 />
= 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 />
=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 />
|<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 />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| TBD<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<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 />
|<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| TBD<br />
|<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 />
| Maybe<br />
| Maybe<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=759632019 Berkeley GOC Meeting Logistics2019-08-15T15:56:54Z<p>TanyaB: /* 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)<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): 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). More details soon.<br />
<br />
=SAB Meeting=<br />
* Meeting: Friday, October 11 (time TBA) in 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 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/hotels/travel/sfofp-four-points-san-francisco-bay-bridge/| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the 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 />
** 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''': 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 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 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 />
==== 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 />
=== Biking ===<br />
Rental bikes are available in various locations, 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 />
= 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 />
=Attendees=<br />
Please add yourself to the table if you plan to attend!<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 />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| TBD<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Maybe<br />
| Yes<br />
| N/A<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| Maybe<br />
| Maybe<br />
| N/A<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| N/A<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=759422019 Berkeley GOC Meeting Logistics2019-08-13T18:06:36Z<p>TanyaB: /* 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)<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): 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). More details soon.<br />
<br />
=SAB Meeting=<br />
* Meeting: Friday, October 11 (time TBA) in 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 />
=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 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/hotels/travel/sfofp-four-points-san-francisco-bay-bridge/| Four Points by Sheraton Bay Bridge]===<br />
* '''Address''': 1603 Powell Street, Emeryville (1.4 miles from the 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 />
** 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''': 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 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 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 />
=Attendees=<br />
Please add yourself to the table if you plan to attend!<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 />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
| Jim Balhoff<br />
| RENCI<br />
| Yes<br />
| Yes<br />
| No<br />
| TBD<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase, GO - Caltech<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Maybe<br />
| Maybe<br />
| N/A<br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<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 />
==== 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. As well, the shuttle is often a 15-person van, so large groups may need to split up at peak times.<br />
<br />
If you are planning to use this shuttle, you will need to make sure that you have the appropriate LBL guest pass.<br />
<br />
==== 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 />
==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 />
= 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 />
[[Category: GO Consortium Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=728542019 Cambridge GOC Meeting Logistics2019-02-12T16:11:17Z<p>TanyaB: /* 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 />
| 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 />
| 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 />
| TBD<br />
|-<br />
| Eva Huala<br />
| TAIR/Phoenix<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 />
= 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>TanyaBhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2018-10-22&diff=71843Ontology meeting 2018-10-222018-10-22T17:09:19Z<p>TanyaB: /* TermGenie Replacment */</p>
<hr />
<div>= Conference Line =<br />
<br />
*Zoom: https://stanford.zoom.us/j/828418143<br />
<br />
= Agenda =<br />
<br />
==Meetings==<br />
<br />
===Ontology Developers' workshop===<br />
[[Fall 2018 ontology editors meeting - potential agenda topics]]<br />
* Airfare from BGR to Geneva searched on Monday Oct 22. Main cabin on American $1379, leaving from Boston is the same. <br />
<br />
===Montreal GOC Meeting===<br />
*Recap of the Montreal Meeting<br />
<br />
<br />
= Minutes =<br />
*On call: Barbara, Ben, Chris, David, Harold, Jim, Kimberly, Pascale, Paul, Peter, Tanya<br />
<br />
== Geneva Meeting ==<br />
*December 10th - 13th, 2018<br />
*Send flight requests to Lourdes<br />
<br />
== Taxon Constraints ==<br />
*https://github.com/geneontology/go-ontology/pull/16508<br />
*Will no longer be managed in Protege<br />
*Will be managed similarly to imports<br />
*There will be a tsv file to edit<br />
*Once edited, the taxon constraints will need to be added by regenerating the imported file.<br />
*Inferred taxon constraints are not visible over the ontology in Protege.<br />
*Would it also be useful, for each term, to list from what terms a term in the ontology inherits its taxon constraints?<br />
*'''AI: Update the documentation on editing the taxon constraints file.'''<br />
<br />
== TermGenie Replacment ==<br />
*Could the INCA tool be used for at least some of the functionality?<br />
*For example, X metabolic process-type terms?<br />
*Will explore possible replacement workflows<br />
*Tanya promises not to bring up this topic again<br />
<br />
[[Category: Ontology]]<br />
[[Category: Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Ontology_Editors_Daily_Workflow&diff=71724Ontology Editors Daily Workflow2018-10-12T15:25:47Z<p>TanyaB: /* Deleting the branch */</p>
<hr />
<div>==Updating the local copy of the ontology with ‘git pull’==<br />
<br />
<br />
* Navigate to the ontology directory of go-ontology: cd repos/go-ontology/src/ontology.<br />
* If the terminal window is not configured to display the branch name, type <code>git status</code><br />
<br />
You will see:<br />
* On branch [master] [or the name of the branch you are on]<br />
Your branch is up-to-date with 'origin/master'.<br />
<br />
* If you’re not in the master branch, type: <code>git checkout master</code><br />
* From the master branch, type: <code>git pull</code> . This will update your master branch, with the files that are most current on GitHub, bringing in and merging any changes that were made since you last pulled the repository using the command git pull. You will see something like this:<br />
~/repos/go-ontology(master) $ git pull<br />
remote: Counting objects: 26, done.<br />
remote: Compressing objects: 100% (26/26), done.<br />
remote: Total 26 (delta 12), reused 0 (delta 0), pack-reused 0<br />
Unpacking objects: 100% (26/26), done.<br />
From https://github.com/geneontology/go-ontology<br />
580c01d..7225e89 master -> origin/master<br />
* [new branch] issue#13029 -> origin/issue#13029<br />
Updating 580c01d..7225e89<br />
Fast-forward<br />
src/ontology/go-edit.obo | 39 ++++++++++++++++++++++++---------------<br />
1 file changed, 24 insertions(+), 15 deletions(-)<br />
~/repos/go-ontology(master) $<br />
<br />
==Creating a new working branch with ‘git checkout’==<br />
<br />
*'''You should never work on the master branch.''' When starting to work on a ticket, you should create a new branch of the repository to edit the ontology file.<br />
*'''Make sure you are on the master branch before creating a new branch.''' If the terminal window is not configured to display the branch name, type <code>git status</code> to check which is the active branch. If necessary, go to master by typing <code>git checkout master</code>.<br />
*'''Create a new branch''': type: <code>git checkout -b branch_name</code> in the terminal window. <br />
*'''Naming branches''': we recommend using the string ‘issue-‘ followed by the issue number. For instance, for this issue in the tracker: https://github.com/geneontology/go-ontology/issues/13390, you would create a branch as follows: <code>git checkout -b issue-13390</code>. Typing this command will automatically put you in the new branch. You will see this message in your terminal window:<br />
~/repos/go-ontology/src/ontology(master) $ git checkout -b issue-13390<br />
Switched to a new branch 'issue-13390'<br />
~/repos/go-ontology/src/ontology(issue-13390) $<br />
<br />
==Continuing work on an existing working branch and dealing with conflicts==<br />
* If the terminal window is not configured to display the branch name, type: <code>git status</code> to check which is the active branch. If necessary, go to master by typing <code>git checkout master</code>.<br />
* Update master by typing <code>git pull</code><br />
*'''To list existing local branches''': type <code>git branch -l</code><br />
* From the master branch, '''switch to your branch''' by typing <code>git checkout [branch name]</code><br />
* '''Update the working branch with respect to the current version of the ontology''' ('''OPTIONAL''') by typing <code>git pull origin master</code><br />
** This step is optional because it is not necessary to work on the current version of the ontology. <br />
** Usually, changes in the working branch will be synchronized with master when you merge the pull request.<br />
** When you run the 'git pull origin master' command, 3 things can happen: <br />
<ul><br />
<ol><br />
<li>'''All is OK''': No action needed. You will get a message that the branch is 'Already up to date', followed by the normal prompt in your terminal window.</li><br />
~/repos/go-ontology (issue-14892)]$ git pull origin master <br />
From https://github.com/geneontology/go-ontology<br />
* branch master -> FETCH_HEAD<br />
Already up to date.<br />
~/repos/go-ontology (issue-14892)]$<br />
<br />
<li>'''Some changes have been imported that need to be merged into your branch:''' You may get a message requesting that you merge the master branch into your branch ''(note that 'merge' is a type of 'commit')''. Git opens a text editor window (dependent on how which text editor is set up by default; instructions here are for the vi Editor; https://www.ccsf.edu/Pub/Fac/vi.html) with the following comment: <br />
<pre><br />
Merge branch 'master' of https://github.com/geneontology/go-ontology into issue-16057<br />
# Please enter a commit message to explain why this merge is necessary,<br />
# especially if it merges an updated upstream into a topic branch.<br />
#<br />
# Lines starting with '#' will be ignored, and an empty message aborts<br />
# the commit.<br />
</pre><br />
In the vi editor:<br />
# Type <code>i</code> (for 'insert'). This will put your cursor in the first line ("Merge branch...") and allow you to edit. <br />
# Type the comment (for example, 'merged master') <br />
# Exit: type <code>esp</code>, then <code>:q!</code> to save changes and quit (q= quit, ! = save). You will get a message in the terminal that looks like this, followed by the normal prompt in your terminal window: <br />
<pre><br />
Auto-merging src/ontology/go-edit.obo<br />
Merge made by the 'recursive' strategy.<br />
src/ontology/go-edit.obo | 117 +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++---------------------<br />
src/ontology/subsets/gosubset_prok.yaml | 2 +-<br />
src/ontology/subsets/mf_needs_review.yaml | 5 ++---<br />
3 files changed, 95 insertions(+), 29 deletions(-) <br />
</pre><br />
</li> <br />
: This merges and commit the merged branch (master + your branch).<br />
:4. Type <code>git push origin mybranch</code> to push your changes to the remote repository.<br />
<li>'''There are conflicts that prevent git from merging'''<br />
* In some cases, in particular when there are inconsistencies between your branch and master, (for example when new terms have been created since your branch was last updated, or terms were merged or obsoleted), this step is necessary. These problems are usually reported by the Travis checks.<br />
* Sometimes when you do git pull origin master, the branch is found by git to have conflicts with master, which will lead to an error message in the terminal window (see next section).<br />
* The version of the ontology in the local branch may be in conflict with master. In this case, the terminal will return a message that looks like this (for a branch named 'mybranch'): <br />
<pre><br />
Switched to branch 'mybranch'<br />
~/repos/go-ontology/src/ontology (mybranch)]$ git pull origin master <br />
From https://github.com/geneontology/go-ontology<br />
* branch master -> FETCH_HEAD<br />
Auto-merging src/ontology/go-edit.obo<br />
CONFLICT (content): Merge conflict in src/ontology/go-edit.obo<br />
Automatic merge failed; fix conflicts and then commit the result.<br />
~/repos/go-ontology/src/ontology (mybranch|MERGING)]$<br />
</pre><br />
* The problem with conflicts is that you cannot switch to another branch until they are resolved. <br />
<br />
* '''NOTE: This is a delicate operation. Ask someone to review the changes if you have any doubts.'''<br />
<br />
* To fix conflicts: <br />
** Open the go-edit.obo file using your favorite text editor. <br />
** Conflicts will be within tags like <br />
<pre><br />
<<<<<<< HEAD<br />
...<br />
>>>>>>> hash number<br />
<br />
For example: <br />
<br />
<<<<<<< HEAD<br />
=======<br />
id: GO:0019836<br />
name: hemolysis by symbiont of host erythrocytes<br />
namespace: biological_process<br />
def: "The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in the host organism by a symbiont. The host is defined as the larger of the organisms involved in a symbiotic interaction." [GOC:add, UniProtKB-KW:KW-0354]<br />
synonym: "haemolysis in host" EXACT []<br />
synonym: "hemolysin activity" RELATED []<br />
synonym: "hemolysis by symbiont of host RBCs" EXACT [CL:0000232]<br />
synonym: "hemolysis by symbiont of host red blood cells" EXACT [CL:0000232]<br />
synonym: "regulation of cytolysis of host cells by symbiont" EXACT [GOC:dph, GOC:tb]<br />
is_a: GO:0001897 ! cytolysis by symbiont of host cells<br />
is_a: GO:0052331 ! hemolysis in other organism involved in symbiotic interaction<br />
[Term]<br />
>>>>>>> e3d0e5afcd225e02722423ef17d2b2fa669a33f3<br />
</pre><br />
* ''Usually'', what is within the <code><<<<<<< HEAD</code> and <code>>>>>>>> hash</code>, can be deleted. <br />
* Save your changes. <br />
* Commit by typing <code>git commit -i * -m 'fixed conflict' go-edit.obo</code><br />
* Do a <code>git diff master</code> to make sure that the changes you have made are correct ('git diff' only will not do because you have already committed).<br />
* If you have any doubt about the changes, delete the branch and start the work over. To do this, type <code>git checkout master</code> and delete the branch by typing, <code>git branch -d mybranch</code>. <br />
*'''If the branch is never pushed to origin, there is no impact of the main go-edit.obo file.''' <br />
* If the changes are as expected, you can go ahead with the [http://wiki.geneontology.org/index.php/Ontology_Editors_Daily_Workflow#Push push] and the further steps.<br />
<br />
==Loading, navigating and saving the Ontology in Protégé==<br />
<br />
* Before launching Protégé, make sure you are in the correct branch. To check the active branch, type <code>git status</code><br />
* '''Open the go-edit.obo file:''' Click on the ‘File’ pulldown. The first time, you will have to navigate to repos/go-ontology/src/ontology. Once you have worked on the file, it will show up in the menu under ‘Open’/’Recent’.<br />
* Click on the ‘Classes’ tab.<br />
* '''Searching:''' Use the search box on the upper right to search for a term in the ontology. Wait for autocomplete to work in the pop-up window.<br />
* '''Viewing a term:''' Double-click on the term. This will reveal the term in the ‘Class hierarchy’ window after a few seconds.<br />
* '''Launching the reasoner:''' To see the term in the ‘Class hierarchy’ (inferred) window, you will need to run the ‘ELK reasoner’. Go to menu: <code>‘Reasoner’ > select ELK 0.4.3</code>, then click ‘Start reasoner’. Close the various pop-up warnings about the ELK reasoner. You will now see the terms in the inferred hierarchy.<br />
* After modification of the ontology, '''synchronize the reasoner'''. Go to menu: <code>‘Reasoner’ > ‘ Synchronize reasoner’</code><br />
** '''NOTE:''' The only changes that the reasoner will detect are those impacting the ontology structure: changes in equivalence axioms, subclasses, merges, obsoletions, new terms.<br />
*'''Saving:''' Use <code>File > Save</code> to save your changes.<br />
<br />
==Committing, pushing and merging your changes to the repository==<br />
<br />
===Reviewing changes===<br />
Changes made to the ontology can be viewed by typing in the terminal window: <code>git diff</code>. <br />
If there are changes that have already been committed, the full changes in the active branch relative to master can be viewed by typing <code>git diff master</code>.<br />
<br />
[[File:Git-diff-terminal window.png|center|1000px|Git diff in the mac terminal window]]<br />
<br />
===Committing changes to the local branch=== <br />
Changes can be committed by typing <code>git commit -m ‘Meaningful message Fixes #ticketnumber’ go-edit.obo</code>. <br />
The message ('-m') must be in either single or double quotes. <br />
* For example: <code>git commit -m ‘hepatic stellate cell migration and contraction and regulation terms. Fixes #13390’ go-edit.obo</code> <br />
<br />
* This will ''commit'' the saved changes to the go-edit.obo file in your active branch. The terminal window will show something like:<br />
<br />
~/repos/go-ontology/src/ontology(issue-13390) $ git commit -m 'Added hepatic stellate cell migration and contraction and regulation terms. Fixes #13390' go-edit.obo</code><br />
[issue-13390 dec9df0] Added hepatic stellate cell migration and contraction and regulation terms. Fixes #13390<br />
1 file changed, 79 insertions(+)</code><br />
~/repos/go-ontology/src/ontology(issue-13390) $ </code><br />
<br />
* '''NOTES''' <br />
**The word ‘fixes’ is a magic word in GitHub; when used in combination with the ticket number, it will automatically close the ticket ''(in the go-ontology repo; if you are working on a ticket from a different repo the command will still go to the go-ontology repo and close a ticket there)''. In the above example, when the file is merged in GitHub, it will close issue number 13390. Learn more on this GitHub Help Documentation page about [https://help.github.com/articles/closing-issues-using-keywords/ Closing issues using keywords].<br />
**‘Fixes’ is case-insensitive.<br />
**If you don’t want to close the ticket, just refer to the ticket # without the word ‘Fixes’. The commit will be associated with the correct ticket but the ticket will remain open.<br />
**It is also possible to type a longer message than allowed when using the ‘-m’ argument; to do this, skip the -m, and a vi window (on mac) will open in which an unlimited description may be typed.<br />
<br />
===Pushing working branch to origin=== <br />
To add your branch to the remote repository, type: <code>git push origin mynewbranch.</code><br />
<br />
Example: <code>git push origin issue-13390</code> <br />
<br />
* '''TIP:''' Once you have pushed your changes to the repository, they are available for everyone to see, so at this stage you can ask for feedback.<br />
<br />
===Creating a Pull Request for your branch===<br />
* In your browser, return to the [https://github.com/geneontology/go-ontology GO Ontology repository on GitHub].<br />
* Navigate to the tab labeled as ‘Code’ https://github.com/geneontology/go-ontology/code. You will see your commit listed at the top of the page in a light yellow box. If you don’t see it, click either on the ‘Branches’ link or on the 'branches' pull down menu to reveal it in the list (see screenshot).<br />
<br />
[[File:View-branches.png|center|550px|How to view branches]]<br />
====Compare (last sanity check before pull request)====<br />
Click the green button <code>Compare & Pull request</code> on the right (see screenshot below). This will allow you to open a Pull Request, and determine if there are conflicts between your branch and master (if there are no conflicts, there will be a green check mark and the text 'Able to merge'. <br />
<br />
[[File:Compare and PR.png|center|750px|How to initiate a pull request]]<br />
<br />
The diff for your file is at the bottom of the page. Examine it as a sanity check.<br />
[[File:GH-diff.png|center|750px|Git diff]]<br />
<br />
====Open the pull request====<br />
Click the green button <code>Create pull request</code> (see screenshot below). This will start to compare your branch with master and initiate the Travis checks to find potential errors in your branch (for example: missing IDs, missing references for definitions, is_a incomplete, logical errors). <br />
<br />
[[File:Open-PR.jpg|center|750px|How to open a pull request]]<br />
<br />
====Request a review (optional)====<br />
You may now add comments and ask a colleague to review your pull request by selecting a reviewer in the ‘Reviewers’ list (e.g. @superuser1). The reviewer will be notified. Since the pull request is also a GitHub issue, the reviewer’s comments will show up in the comments section of the pull request, similarly to any other issue filed on the tracker.<br />
<br />
===Automated checks===<br />
* Wait for the Travis checks to complete (this can take a few minutes; see screenshot). <br />
<br />
[[File:Travis-checks.jpg|center|750px|Travis checks]]<br />
<br />
* If the Travis checks fail, you will see a red <code>x</code> at the left of each of the checks. Go back to your local branch, correct the reported errors, commit them to the branch, and push to origin. The Travis checks will then start automatically (since the pull request has already been generated).<br />
<br />
[[File:Travis-Fail.png|center|750px|Travis Fail]]<br />
<br />
* If the Travis checks pass, you will see a green check mark at the left of each of the checks.<br />
[[File:Travis-Success.png|center|750px|Travis success]]<br />
<br />
<br />
===Merging the Pull Request===<br />
'''When (and only when!) the Travis checks are successful''' and if you're ready to integrate the changes in the main ontology file, merge the pull request, by clicking on the green <code>Merge pull request</code> button.<br />
* '''Note that the reviewer should go ahead and merge the pull request''' if s/he agrees with the changes.<br />
* Confirming the merge will close the ticket if you have used the word ‘fixes’ in your commit comment. <br />
<br />
[[File:Merge-PR.jpg|center|750px|How to merge a pull request]]<br />
<br />
* You can now safely delete the branch, both in the repository and in your local repository.<br />
<br />
====Deleting the branch====<br />
* Delete your branch on the repository using the button on the right of the successful merge message.<br />
<br />
* You may also delete the working branch on your local copy. Note that this step is optional. However, if you wish to delete branches on your local machine, in your terminal window:<br />
** Go back to the master branch by typing <code>git checkout master</code>.<br />
** Update your local copy of the repository by typing <code>git pull origin master</code><br />
** Delete the branch by typing <code>git branch -d workingbranchname</code><br />
** Example: <code>git branch -d issue-13390</code><br />
<br />
== Review Status ==<br />
<br />
Last reviewed: August 8, 2018<br />
<br />
[http://wiki.geneontology.org/index.php/Ontology_Editing_Guide Back to: Ontology Editing Guide]<br />
<br />
[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2018_Montreal_GOC_Meeting_Logistics&diff=709072018 Montreal GOC Meeting Logistics2018-08-20T16:10:01Z<p>TanyaB: /* Attendees */</p>
<hr />
<div><br />
=Start and end of meeting=<br />
* Main meeting starts on: Wednesday October 17, 8h30 AM<br />
* Meeting ends on Friday October 19th, 4 PM <br />
<br />
=Registration fee=<br />
To be announced <br />
<br />
=Meeting site=<br />
'''Université du Québec à Montreal (UQAM), Pavillon Président-Kennedy'''<br />
* 201 Avenue du Président-Kennedy, Montréal, QC H2X 3Y7<br />
* Location: https://goo.gl/V1ZrsJ<br />
<br />
=Call-in information=<br />
To be announced<br />
<br />
=Travel=<br />
<br />
<br />
<br />
=Accommodations=<br />
<br />
Two options: Delta Hotel and Hotel Zero1<br />
<br />
==1) Delta Hotel Montreal==<br />
* https://www.marriott.com/hotels/travel/yuldb-delta-hotels-montreal/<br />
* '''Address:''' 475 President-Kennedy Avenue, Montreal, QC H3A 1J7<br />
* '''Directions to meeting venue:''' https://goo.gl/ha8fay<br />
* '''Phone:''' 1 (514) 286-1986<br />
* '''Reservation:''' Call Marriott Reservations at 1 (844) 860-3753 or use this link: <br />
https://www.marriott.com/meeting-event-hotels/group-corporate-travel/groupCorp.mi?resLinkData=UQAM%20GO%20Meeting%202018^yuldb`q78q78z`188.00`CAD`false`4`10/15/18`10/21/18`9/18/18&app=resvlink&stop_mobi=yes<br />
<br />
** Book under: UQAM GO Meeting 2018<br />
** All reservations must be guaranteed with a major credit card.<br />
* '''Rate available until Tuesday, September 18, 2018'''. <br />
* '''Cancellation policy''': Individual reservations may be cancelled up until 48 hours local time prior to arrival with no penalty. Cancellations received after this time will be subject to one night’s room & tax, applied to the credit card used to guarantee the reservation.<br />
* '''Rates for October 16th-19th (rates are valid from Oct 15th to the 20th (checkout on the 21st))'''<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Room Type <br />
! Daily rate (excl tax)<br />
! Daily rate (incl tax; estimate)<br />
|-<br />
| Single/Double<br />
| CAN $188<br />
| CAN $222<br />
|-<br />
| Triple<br />
| CAN $208 <br />
| CAN $246<br />
|-<br />
| Quad<br />
| CAN $228<br />
| CAN $270<br />
|-<br />
|}<br />
<br />
<br />
'''Rate includes: '''<br />
* Free WiFi in room (+ wires) and WiFi in all public areas<br />
* Breakfast not included<br />
* Gym<br />
* Parking available: On-site parking: CAN $ 26.50 daily; Valet parking: CAN $32 daily<br />
<br />
==2) Hotel Zero1 Montreal== <br />
* http://www.zero1-mtl.com/en/default.html<br />
* '''Address:''' 1 RenéLévesque Est Montréal QC H2X 3Z5<br />
* '''Directions to meeting venue:''' https://goo.gl/1BkxYh<br />
* '''Phone:''' 1 (514) 871-9696 / 1 (855) 301-0001<br />
* '''Reservation:''' Call the hotel at 1 (514) 871-9696 / 1 (855) 301-0001<br />
** Book under: GO meeting at UQAM<br />
** All reservations must be guaranteed with a major credit card.<br />
* '''Rate available until September 1st, 2018'''. <br />
* '''Cancellation policy''': Inform the hotel in writing 48 hours prior to arrival date. If no notice is received, a penalty of one night (including all taxes) will be charged on the credit card on file (no show). <br />
* Upon arrival of the participant at the hotel, a deposit corresponding to the total accommodation fees (including taxes) + a security deposit will be due. <br />
* '''Rates for October 16th-19th (rates are valid from Oct 13th to the 24th)'''<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Room Type <br />
! Daily rate (excl tax)<br />
! Daily rate (incl tax; estimate)<br />
|-<br />
| "Pop room" - 1 queen bed <br />
| CAN $169<br />
| CAN $200<br />
|-<br />
|}<br />
<br />
'''Rate includes: '''<br />
* Free WiFi in room and all public areas<br />
* Free local calls<br />
* Shower only<br />
* Gym (seems small)<br />
* American buffet breakfast included at the Z Tapas Lounge<br />
* Valet service available for CAN $28.00/day + applicable taxes.<br />
<br />
=Food=<br />
* World-famous Montreal bagels: [http://www.stviateurbagel.com/ St. Viateur] and [https://fairmountbagel.com/ Fairmount Bagel] (both opened 24 hours, in case you need a 3 am warm snack)<br />
* World-famous Montreal smoked meat: [http://www.schwartzsdeli.com/ Schwartzs Deli]<br />
* Poutine: [http://labanquise.com/ La Banquise] (opened 24h) and [https://www.yelp.ca/biz/chez-claudette-montr%C3%A9al Chez Claudette] (opened 24h Thu-Sat)<br />
* Croissants and Kouign-Amann: [https://www.yelp.ca/biz/au-kouign-amann-montr%C3%A9al-2 Au Kouign-Amann]<br />
* [http://dieuduciel.com/en/ Dieu du Ciel] microbrewery <br />
* [http://saintbock.com/ Saint Bock] microbrewery<br />
* [http://www.brasseriebenelux.com/ Benelux] artisanal brewery<br />
<br />
=Bicycling and walking / running=<br />
* The venue is less than 1 km away from [https://goo.gl/v5fyYq Parc Mont Royal], great for walking and running (and biking if you like small hills)<br />
* [https://goo.gl/maps/6kscfTfshhw Parc La Fontaine]<br />
* [https://www.yelp.ca/search?cflt=bikerentals&find_loc=Montreal%2C+QC Bike rental] places<br />
* If you have an afternoon, rent a bike or roller blades in the Old port and bike the Canal Lachine<br />
<br />
=To do and see=<br />
* [https://www.quartierdesspectacles.com/en/ Quartier des spectacles] (the venue is right in that neighborhood)<br />
* Rue [http://www.ruesaintdenis.ca/en/ Saint-Denis]<br />
* Boulevard [http://boulevardsaintlaurent.com/en/ Saint-Laurent] ("La Main")<br />
* [https://localfoodtours.com/montreal/10-things-to-do-in-the-mile-end-montreal/ Mile End neighbourhood] (a couple of km North/East of the venue; very trendy right now)<br />
* [http://www.oldportofmontreal.com/ Old port]<br />
* [https://www.mtl.org/en/explore/neighbourhoods/old-montreal Old Montreal]<br />
* [https://www.marchespublics-mtl.com/en/marches/jean-talon-market/ Jean Talon Market]<br />
* [https://www.marchespublics-mtl.com/en/marches/atwater-market/ Atwater Market]<br />
* [https://www.saint-joseph.org/en/ Saint Joseph's Oratory] of Mount Royal<br />
* [https://www.basiliquenotredame.ca/en Notre-Dame Basilica]<br />
* [http://espacepourlavie.ca/en/botanical-garden Botanical Garden]<br />
* [https://www.mbam.qc.ca/en/ Montreal Museum of Fine Arts]<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, and the dinner, so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
! Attend the GOC dinner (Thursday 18th)? <br />
! Food restrictions<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GO Central<br />
| Yes<br />
| <br />
|-<br />
| Val Wood<br />
| PomBase<br />
| Yes<br />
| <br />
|-<br />
| Suzanna Lewis<br />
| BBOP/LBNL<br />
| Yes<br />
| <br />
|-<br />
| Seth Carbon<br />
| BBOP/LBNL<br />
| Yes<br />
| <br />
|-<br />
| David Hill (leaving early 10/19)<br />
| GOC/MGI<br />
| Yes? Yes :)<br />
|<br />
|-<br />
| Harold Drabkin<br />
| MGI/GO/PRO<br />
| Yes<br />
|<br />
|-<br />
| Mary Dolan<br />
| MGI/GO<br />
| Yes<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Yes<br />
| Vegetarian preferred<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
|<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
|<br />
|--<br />
| Tony Sawford<br />
| EBI<br />
| Yes<br />
| <br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
|-<br />
| Alex Ignachenko<br />
| EBI<br />
| Yes<br />
| <br />
|--<br />
| Sandra Orchard<br />
| EBI<br />
| Yes<br />
| <br />
|--<br />
| Maria Martin<br />
| EBI<br />
| Yes<br />
| <br />
|--<br />
| Laurent-Philippe Albou<br />
| USC / LBNL<br />
| Yes<br />
| <br />
|--<br />
| Debby Siegele<br />
| TAMU<br />
| Yes<br />
|<br />
|--<br />
| Sandy LaBonte<br />
| TAMU<br />
| Yes<br />
|<br />
|--<br />
| Jim Hu<br />
| TAMU<br />
| Yes<br />
|<br />
|--<br />
| Tanya Berardini<br />
| TAIR/Phoenix<br />
| Yes<br />
|<br />
|--<br />
<br />
|<br />
<br />
=Remote attendees=<br />
If you plan to attend remotely, please sign up here and indicate the sessions you are likely to attend:<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
|-<br />
|}<br />
<br />
[[Category: GO Consortium Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Logistics&diff=683692018 NYU GOC Meeting Logistics2018-04-02T16:19:51Z<p>TanyaB: /* Attendees */</p>
<hr />
<div>More details will be available in the next few weeks. Meanwhile, here is some information to help you make travel arrangements. The meeting will start first thing on Saturday May 12 (so plan to arrive on Friday) and will end on Monday May 14 early enough in the afternoon to allow people to get to the airport for overnight flights to Europe.<br><br>See you in May!<br />
<br />
==Registration fee==<br />
Amount and payment details to be determined, but we hope to keep the amount low and find a convenient way to pay.<br />
<br />
==Meeting site==<br />
Translational Research Building, 227 East 30th Street, in the Murray Hill neighborhood of Manhattan. You'll need an official ID (passport, driver's license) to get into the building; the meeting room is immediately on your left at street level.<br />
<br />
=Travel=<br />
Kennedy and Newark Airports both are workable for long-distance flights; Kennedy is somewhat more convenient. LaGuardia Airport is closest to Manhattan but is accessible only by taxi or ride-sharing, or by incredibly inconvenient public transportation.<br />
==[https://www.jfkairport.com/#/ Kennedy Airport] details==<br />
You can get into Manhattan by taxi (up to four people can share a cab for a flat fare plus tolls and tip), or ride-sharing (Uber, Lyft, etc.), or by public transportation, which is fast (about an hour) and cheap ($7.75 per person). Here's how to do it: follow the signs in the terminal to the [https://www.jfkairport.com/#/to-from-airport/air-train AirTrain]. Take an AirTrain to Jamaica. To get off the AirTrain platform, you'll need to buy a MetroCard from a vending machine. If you'll be using the card only to travel to and from the airport, put $15.50 on the card; more if you'll be using the subway to get around New York ($2.75 per ride). Once you're off the AirTrain platform in Jamaica, follow the signs past the Jamaica Long Island Train station (overpass) to an elevator to the subway. Swipe your card again to get into the subway, and take an "E" train in the direction of Manhattan / World Trade Center. At Lexington Avenue / 53rd Street, get off the "E" train and follow the signs to transfer to a "6" train going downtown to Brooklyn Bridge / City Hall. Ride two stops to 33rd Street. Go up to the street (Park Avenue South), walk on Park Avenue South to 37th Street, turn left, walk one block to Lexington Avenue, and the Shelburne Hotel will be on your left on the far side of the street. If you're less adventurous, you can instead take the Long Island Railroad train from Jamaica to Penn Station (buy ticket from vending machine before getting on the train), and walk from Penn Station to the hotel.<br />
==[https://www.newarkairport.com/#/ Newark Airport] details==<br />
You can get into Manhattan by taxi or ride-sharing, or by public transportation, which takes longer and costs more than it does from Kennedy but is still reliable. Follow signs in the terminal to the [https://www.newarkairport.com/#/to-from-airport/air-train air-train]. There's only one choice; it takes you to the Newark Airport Station for Amtrak and New Jersey Transit. From a vending machine, get a combined one-way ticket that will allow you to get off the air-train platform and on to a New Jersey Transit train into New York Penn Station. (Amtrak trains are much more expensive and, for this trip, hardly faster.)<br />
<br />
==[http://laguardiaairport.com/ LaGuardia Airport] details==<br />
There is no good public transportation from LaGuardia Airport into Manhattan. Use a taxi (up to four people can share for the same fare) or ride-sharing service.<br />
<br />
==By train==<br />
Amtrak Northeast Corridor trains (Boston - New York - Washington) all stop at Penn Station as do the Long Island Railroad train from Kennedy / Jamaica or the New Jersey transit train from Newark. To get from Penn Station to the hotel, follow signs inside the station to 7th Avenue. You'll go up a long flight of stairs or escalator to leave the station and come upon a taxi queue. Take a taxi to the hotel or cross 7th Avenue and walk away from the station on 32nd Street until you get to Lexington Avenue, then turn left and walk to 37th Street to get to the hotel (0.8 mile, about 20 minutes per Google).<br />
<br />
==By car==<br />
Try not to. Manhattan is incredibly congested (average speed achieved by cars on weekdays is 4.7 miles per hour) and parking anywhere near the meeting site is incredibly expensive.<br />
<br />
=Accommodations=<br />
New York is a large, busy city with many hotels but mid-May is a popular time (graduation week for many local universities). We have a block of rooms at the [[media:Shelburne Hotel Brochure.pdf | Shelburne NYC]] (a 10 minute half-mile walk from the meeting venue, comfortable, and very convenient to public transportation). They will only hold rooms until April 6, so book early. Rooms have been reserved for arrival on Friday May 11 and departure on Monday May 14 or Tuesday May 15. You can book a room online [https://gc.synxis.com/rez.aspx?Hotel=10146&Chain=5158&Dest=NYC&shell=2014GCF&group=1805NYUMEDI here] or by phone at 866-233-4642 - identify yourself as part of the GO Consortium (NYU Medical) Room Block to guarantee the special rate. The room rate is $289 nightly ($249 + taxes), a very good rate for a room with free WiFi and private bath.<br />
<br />
*'''note: people should book at this hotel rather than at a separate one since we have a block booking'''<br />
<br />
*'''note: if you have any difficulty making your hotel booking, contact Peter D'E (deustp01@med.nyu.edu) immediately for help'''<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting, and the dinner (Sunday), so we can get a headcount estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name <br />
! Organization <br />
! Attend the GOC meeting? <br />
! Attend the GOC dinner? <br />
<br />
<br />
<br />
|-<br />
| Tony Sawford<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| George Georghiou<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Michele Magrane<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Penelope Garmiri<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Maria Martin<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Alex Ignatchenko<br />
| EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| GO@LBNL<br />
| Yes<br />
| Yes<br />
|-<br />
| David Hill<br />
| MGI/GOC<br />
| Yes<br />
| No<br />
|-<br />
|Judy Blake<br />
| MGI/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Mary Dolan<br />
| MGI/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Li NI<br />
| MGI/GOC<br />
| Yes (Saturday and Sunday)<br />
| No<br />
|-<br />
|Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
|Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
|Stacia Engel<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|Mike Cherry<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|Suzi Aleksander<br />
| SGD Stanford<br />
| Yes<br />
| Yes<br />
|-<br />
|Helen Attrill<br />
| FlyBase, Cambridge UK<br />
| Yes<br />
| Yes<br />
|-<br />
|Kimberly Van Auken<br />
|WormBase, Caltech<br />
|Yes<br />
|Yes<br />
|-<br />
|Sandra Orchard<br />
|EMBL-EBI<br />
|Yes<br />
|No<br />
|-<br />
|Petra Fey<br />
|dictyBase, Northwestern<br />
|Yes<br />
|Yes<br />
|-<br />
|Ruth Lovering<br />
|University College London<br />
|Yes<br />
|Yes<br />
|-<br />
|Benjamin Good<br />
|LBNL<br />
|Yes<br />
|Yes<br />
|-<br />
|Chris Mungall<br />
|LBNL<br />
|Yes<br />
|Yes<br />
|-<br />
|Tom Hayman<br />
|RGD<br />
|Yes<br />
|Yes<br />
|-<br />
|Jim Balhoff<br />
|RENCI<br />
|Yes<br />
|Yes<br />
|-|-<br />
|Sabrina Toro<br />
|ZFIN<br />
|Yes<br />
|No<br />
|-<br />
|Michelle Giglio<br />
|IGS at U MD School of Medicine<br />
|Yes (Sunday and Monday)<br />
|Yes<br />
|-<br />
|Suvvi Nadendla<br />
|IGS at U MD School of Medicine<br />
|Yes<br />
|No<br />
|-<br />
|Becky Tauber<br />
|IGS at U MD School of Medicine<br />
|Yes<br />
|<br />
|-<br />
|Debby Siegele<br />
|Texas A&M University<br />
|Yes<br />
|Yes<br />
|-<br />
|Jim Hu<br />
|Texas A&M University<br />
|Yes<br />
|Yes<br />
|-<br />
|}<br />
<br />
If you plan to attend remotely, please sign up here and indicate the sessions you are likely to attend:<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Saturday AM<br />
! Saturday PM<br />
! Sunday AM<br />
! Sunday PM<br />
! Monday AM<br />
|-<br />
| Birgit Meldal<br />
| EBI<br />
| no<br />
| no<br />
| no<br />
| maybe<br />
| maybe<br />
|-<br />
| Li Ni<br />
| MGI<br />
| no<br />
| no<br />
| no<br />
| no<br />
| yes<br />
|-<br />
| Tanya Berardini<br />
| TAIR<br />
| no<br />
| no<br />
| no<br />
| no<br />
| yes<br />
|-<br />
|}<br />
<br />
AM sessions will start at approximately 9 AM EDT / 2 PM BST / 6 AM PDT; PM sessions will start at approximately 2 PM EDT / 7 PM BST / 11 AM PDT.<br />
<br />
[[Category: GO Consortium Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2018-01-09&diff=66349Annotation Conf. Call 2018-01-092018-01-09T17:02:57Z<p>TanyaB: /* Minutes */</p>
<hr />
<div>= Meeting URL =<br />
*https://stanford.zoom.us/j/976175422<br />
<br />
= Agenda =<br />
==Review of Cambridge meeting action items and milestones for 2018-05 GOC meeting in NYC==<br />
In geneontology/go-annotation on github, there is a Milestone '2018-05 GOC meeting'<br />
<br />
==Requests for Proposals==<br />
<br />
====Protein Complexes Working Group====<br />
*[https://github.com/geneontology/go-annotation/issues/1662 Inferring MF annotations for complex members]<br />
*[https://github.com/geneontology/go-annotation/issues/1650 Proposal for guidelines for using contributes_to]<br />
*[https://github.com/geneontology/go-annotation/issues/1500 should we really use "colocalizes_with" with cc complex terms]<br />
*[https://github.com/geneontology/go-annotation/issues/1661 Protein complex representation in Noctua]<br />
*[https://github.com/geneontology/go-ontology/issues/14375 Do we have to hard-code CC complex terms to MF and BP relationships in the ontology?]<br />
**Working group established, one meeting in late November<br />
**Next meeting?<br />
*Updates from Birgit:<br />
**Latest: I have to design a user survey to answer some of the open questions from our call. It's on my to-do list for this month.<br />
**Other discussion points rely on us finishing the complex IDs. Our developers were rather stretched this autumn so it's taking a little longer than expected but they are back on it and it's really close!<br />
<br />
====Annotation Relations - Cellular Component====<br />
*[https://github.com/geneontology/go-annotation/issues/1500 should we really use "colocalizes_with" with cc complex terms]<br />
*[https://github.com/geneontology/go-annotation/issues/1639 Relations to describe gene product - component annotation]<br />
*Draft proposal (Kimberly) - need input from Chris on RO<br />
**Relations between gene products and organelles/locations<br />
**Relations between gene products and macromolecular complexes<br />
<br />
====Annotation Relations - Biological Process====<br />
*[https://github.com/geneontology/go-annotation/issues/1517 New qualifiers for biological processes - including how to deal with legacy annotations]<br />
<br />
====Cellular Component Annotations for Transmembrane Proteins====<br />
[https://github.com/geneontology/go-annotation/issues/1621 https://github.com/geneontology/go-annotation/issues/1621]<br />
<br />
====InterPro2GO Pipeline====<br />
*[https://github.com/geneontology/go-annotation/issues/1653 InterPro2GO pipeline]<br />
**Need to establish a working group here<br />
<br />
====Engaging External Experts====<br />
*[https://github.com/geneontology/go-annotation/issues/1652 Recommendations and guidelines for next time we engage an external group of experts]<br />
**Need to have a working group or responsible persons here, too<br />
<br />
==Annotation Review==<br />
====HTP Annotations====<br />
*[https://github.com/geneontology/go-annotation/issues/1655 Review HTP annotations]<br />
**[https://drive.google.com/drive/u/0/folders/0BwxQUKMmvm0kRTlSNmNmZV9aTHc HTP_Guidelines_condensed_version]<br />
***Forward genetic screens - may need further clarification and examples of what is/is not high throughput<br />
*[https://github.com/geneontology/go-annotation/issues/1654 HTP-types will not be allowed as evidence for ISS+ISO]<br />
**Set date for meeting to discuss ISS/ISO transfer from HTP to be discussed in Feb.<br />
<br />
====Signaling Workshop====<br />
In geneontology/go-annotation on github, there is a label 'GO workshop signaling 2017'<br />
====General Signaling Issues====<br />
*[https://github.com/geneontology/go-annotation/issues/1713 Review annotation to 'receptor ligand activity' (GO:0048018)]<br />
*[https://github.com/geneontology/go-ontology/issues/13912 MP cell surface receptor signaling pathway]<br />
<br />
====Ca2+ Signaling - Fertilization====<br />
*[https://github.com/geneontology/go-ontology/issues/13980 Revision of relationship of GO:0060468 (prevention of polyspermy) and GO:0060471 ( cortical granule exocytosis)]<br />
<br />
====GPCR-mediated cAMP Signaling====<br />
*[https://github.com/geneontology/go-annotation/issues/1712 Review annotations to 'cAMP biosynthetic process']<br />
*[https://github.com/geneontology/go-annotation/issues/1691 Review annotation for GPCR]<br />
*[https://github.com/geneontology/go-ontology/issues/14733 NTR: regulation terms for adenylate cyclase-activating adrenergic receptor signaling pathway]<br />
*[https://github.com/geneontology/go-ontology/issues/14718 cAMP biosynthetic process - merges & obsoletion]<br />
*[https://github.com/geneontology/go-ontology/issues/13903 GO:0007189 adenylate cyclase-activating G-protein coupled receptor signaling pathway... missing parent]<br />
<br />
====JAK/STAT Signaling Pathway====<br />
====MAPK Cascade====<br />
*[https://github.com/geneontology/go-ontology/issues/14676 How to name specific MAPK pathways]<br />
<br />
====Canonical Wnt Signaling Pathway====<br />
*[https://github.com/geneontology/go-annotation/issues/1736 PAINT:PTN000226268 Wnt signaling pathway to positive regulation of... ]<br />
*[https://github.com/geneontology/go-annotation/issues/1714 Review annotations to beta catenin]<br />
*[https://github.com/geneontology/go-annotation/issues/1696 PANTHER:PTN000139394: remove wnt binding annotation to smoothened receptors]<br />
*https://github.com/geneontology/go-ontology/issues/14275 NTR: “receptor ligand agonist activity” and “receptor ligand antagonist activity”]<br />
<br />
==GO-CAM and Noctua==<br />
*No call tomorrow<br />
*Software team has been working on the priority issues for Noctua 1.0 release<br />
*[https://github.com/geneontology/go-annotation/issues/1651 QC for Noctua models]<br />
<br />
==Protein2GO Reports==<br />
*Protein2GO users please remember to check the monthly reports and work on updating/fixing flagged annotations<br />
<br />
==Two Working Meetings==<br />
*January 22nd - 26th: Docathon at Berkeley<br />
*February 12 - 16th: Ontology GitHub jamboree in Denver<br />
<br />
= Minutes =<br />
*On call: David H, Eric, George, Harold, Helen, Karen, Kimberly, Li, Liz, Pascale, Paul T., Petra, Rachael, Rob, Sabrina, Sage, Sandra, Stacia, Stan, Suzi, Tanya, Tom, Val<br />
<br />
<br />
<br />
<br />
[[Category:Annotation Working Group]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66225TAIR December 20172017-12-22T20:09:17Z<p>TanyaB: /* 5. Other Highlights */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding (ended Feb. 28, 2017).<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/16 = 12/31/2016 and 12/17 = 12/22/2017.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 24546 ||23902 ||+ 644 || 16197 || 15707 ||+ 490 || 57194 ||56832|| + 362 ||<br />
|-<br />
| IEA || 5591 || 5441 || + 150 || 7848 || 8603 || - 755 || 1045 || 966 || + 79 ||<br />
|-<br />
| ND ||7708 || 7921 || - 213 || 4645|| 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9862 || 9646 || + 216 || 8604 || 8417 || + 187 || 23557 || 23529 || + 28 ||<br />
|-<br />
| IEA || 4876 || 4785 || + 91 || 5897 || 66112 || - 639 || 972 || 899 || + 73 ||<br />
|-<br />
| ND || 7708 || 7921 || - 231 || 4645 || 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from GOC<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 12 new GO terms using Protege (id: GO:0090730 through id: GO:0090741) and 8 new GO terms through TermGenie before that service was discontinued.<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
*attended the GO Ontology Editing workshop in Berkeley in August 2017<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui Li participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66224TAIR December 20172017-12-22T19:53:42Z<p>TanyaB: /* 5. Other Highlights */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding (ended Feb. 28, 2017).<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/16 = 12/31/2016 and 12/17 = 12/22/2017.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 24546 ||23902 ||+ 644 || 16197 || 15707 ||+ 490 || 57194 ||56832|| + 362 ||<br />
|-<br />
| IEA || 5591 || 5441 || + 150 || 7848 || 8603 || - 755 || 1045 || 966 || + 79 ||<br />
|-<br />
| ND ||7708 || 7921 || - 213 || 4645|| 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9862 || 9646 || + 216 || 8604 || 8417 || + 187 || 23557 || 23529 || + 28 ||<br />
|-<br />
| IEA || 4876 || 4785 || + 91 || 5897 || 66112 || - 639 || 972 || 899 || + 73 ||<br />
|-<br />
| ND || 7708 || 7921 || - 231 || 4645 || 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from GOC<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 12 new GO terms using Protege (id: GO:0090730 through id: GO:0090741) and 8 new GO terms through TermGenie before that service was discontinued.<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
*attended the GO Ontology Editing workshop in Berkeley in August 2017<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66223TAIR December 20172017-12-22T19:51:29Z<p>TanyaB: /* 3. Methods and strategies for annotation */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding (ended Feb. 28, 2017).<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/16 = 12/31/2016 and 12/17 = 12/22/2017.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 24546 ||23902 ||+ 644 || 16197 || 15707 ||+ 490 || 57194 ||56832|| + 362 ||<br />
|-<br />
| IEA || 5591 || 5441 || + 150 || 7848 || 8603 || - 755 || 1045 || 966 || + 79 ||<br />
|-<br />
| ND ||7708 || 7921 || - 213 || 4645|| 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9862 || 9646 || + 216 || 8604 || 8417 || + 187 || 23557 || 23529 || + 28 ||<br />
|-<br />
| IEA || 4876 || 4785 || + 91 || 5897 || 66112 || - 639 || 972 || 899 || + 73 ||<br />
|-<br />
| ND || 7708 || 7921 || - 231 || 4645 || 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from GOC<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 12 new GO terms using Protege (id: GO:0090730 through id: GO:0090741) and 8 new GO terms through TermGenie before that service was discontinued.<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66222TAIR December 20172017-12-22T19:49:25Z<p>TanyaB: /* TAIR, The Arabidopsis Information Resource, December 2017 */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding (ended Feb. 28, 2017).<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/16 = 12/31/2016 and 12/17 = 12/22/2017.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 24546 ||23902 ||+ 644 || 16197 || 15707 ||+ 490 || 57194 ||56832|| + 362 ||<br />
|-<br />
| IEA || 5591 || 5441 || + 150 || 7848 || 8603 || - 755 || 1045 || 966 || + 79 ||<br />
|-<br />
| ND ||7708 || 7921 || - 213 || 4645|| 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9862 || 9646 || + 216 || 8604 || 8417 || + 187 || 23557 || 23529 || + 28 ||<br />
|-<br />
| IEA || 4876 || 4785 || + 91 || 5897 || 66112 || - 639 || 972 || 899 || + 73 ||<br />
|-<br />
| ND || 7708 || 7921 || - 231 || 4645 || 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 12 new GO terms using Protege (id: GO:0090730 through id: GO:0090741) and 8 new GO terms through TermGenie before that service was discontinued.<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66221TAIR December 20172017-12-22T19:48:00Z<p>TanyaB: /* 2. Annotation progress */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
****IN PROGRESS**<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/16 = 12/31/2016 and 12/17 = 12/22/2017.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 24546 ||23902 ||+ 644 || 16197 || 15707 ||+ 490 || 57194 ||56832|| + 362 ||<br />
|-<br />
| IEA || 5591 || 5441 || + 150 || 7848 || 8603 || - 755 || 1045 || 966 || + 79 ||<br />
|-<br />
| ND ||7708 || 7921 || - 213 || 4645|| 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9862 || 9646 || + 216 || 8604 || 8417 || + 187 || 23557 || 23529 || + 28 ||<br />
|-<br />
| IEA || 4876 || 4785 || + 91 || 5897 || 66112 || - 639 || 972 || 899 || + 73 ||<br />
|-<br />
| ND || 7708 || 7921 || - 231 || 4645 || 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 12 new GO terms using Protege (id: GO:0090730 through id: GO:0090741) and 8 new GO terms through TermGenie before that service was discontinued.<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66220TAIR December 20172017-12-22T19:31:09Z<p>TanyaB: /* 2. Annotation progress */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
****IN PROGRESS**<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/16 = 12/31/2016 and 12/17 = 12/22/2017.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 24546 ||23902 ||+ 644 || 16197 || 15707 ||+ 490 || 57194 ||56832|| + 362 ||<br />
|-<br />
| IEA || 5591 || 5441 || + 150 || 7848 || 8603 || - 755 || 1045 || 966 || + 79 ||<br />
|-<br />
| ND ||7708 || 7921 || - 213 || 4645|| 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9862 || 9646 || + 216 || 8604 || 8417 || + 187 || 23557 || 23810 || -253 ||<br />
|-<br />
| IEA || 4876 || 4785 || + 91 || 5897 || 66112 || - 639 || 972 || 899 || + 73 ||<br />
|-<br />
| ND || 7708 || 7921 || - 231 || 4645 || 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 12 new GO terms using Protege (id: GO:0090730 through id: GO:0090741) and 8 new GO terms through TermGenie before that service was discontinued.<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66219TAIR December 20172017-12-22T19:25:44Z<p>TanyaB: /* 2. Annotation progress */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
****IN PROGRESS**<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 24546 ||23902 ||+ 644 || 16197 || 15707 ||+ 490 || 57194 ||56832|| + 362 ||<br />
|-<br />
| IEA || 5591 || 5441 || + 150 || 7848 || 8603 || - 755 || 1045 || 966 || + 79 ||<br />
|-<br />
| ND ||7708 || 7921 || - 213 || 4645|| 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9862 || 9646 || + 216 || 8604 || 8417 || + 187 || 23557 || 23810 || -253 ||<br />
|-<br />
| IEA || 4876 || 4785 || + 91 || 5897 || 66112 || - 639 || 972 || 899 || + 73 ||<br />
|-<br />
| ND || 7708 || 7921 || - 231 || 4645 || 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 12 new GO terms using Protege (id: GO:0090730 through id: GO:0090741) and 8 new GO terms through TermGenie before that service was discontinued.<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66218TAIR December 20172017-12-22T19:21:02Z<p>TanyaB: /* 2. Annotation progress */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
****IN PROGRESS**<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 24546 ||23902 ||+ 644 || 16197 || 15707 ||+ 490 || 57194 ||56832|| + 362 ||<br />
|-<br />
| IEA || 5591 || 5441 || + 150 || 7848 || 8603 || - 755 || 1045 || 966 || + 79 ||<br />
|-<br />
| ND ||7708 || 7921 || - 213 || 4645|| 4753 || - 108 || 4036 || 4053 || - 17 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| || 9646 || - || || 8417 || + || || 23810 || + ||<br />
|-<br />
| IEA || || 4785 || - || || 66112 || - || || 899 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 12 new GO terms using Protege (id: GO:0090730 through id: GO:0090741) and 8 new GO terms through TermGenie before that service was discontinued.<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2016&diff=66217TAIR December 20162017-12-22T18:47:10Z<p>TanyaB: /* 2. Annotation progress */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2016 ==<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini (0.35 FTE), Donghui Li (0.3 FTE), Leonore Reiser (0.5 FTE)<br />
<br />
The total number of FTE working on GOC tasks is 1.15.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 22786 ||23902 ||+ 1116 ||14584 || 15707 ||+ 1123 || 56339 ||56832|| + 493 ||<br />
|-<br />
| IEA || 5689 || 5441 || - 248 ||9236 || 8603 || - 633 || 1354 || 966 || - 388 ||<br />
|-<br />
| ND ||8106 || 7921 || - 185 || 4861|| 4753 || - 108 || 4065|| 4053 || - 12 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9730 || 9646 || - 84 || 8020 || 8417 || + 397 ||23782 || 23810 || + 28 ||<br />
|-<br />
| IEA || 4593 || 4785 || - 192 || 6574 || 6536 || - 38 || 1224 || 899 || - 325 ||<br />
|-<br />
| ND ||8106 || 7921 || - 185 || 4861|| 4753 || - 108 || 4065|| 4053 || - 12||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. INTERPRO2GO-based IEA annotations from UniProtKB<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
Donghui, Leonore, and Tanya review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2016 GO 2016 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Berardini TZ, Li D, Muller R, Strait EM, Li Q, Mezheritsky Y, Vetushko A, Huala E.<br />
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. Database (Oxford). 2016 Mar 17;2016. pii: baw018. doi: 10.1093/database/baw018.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Donghui Li, TAIR: A Sustainable Community Resource for Arabidopsis Research, International Conference on Arabidopsis Research (ICAR 2016), GyeongJu, Korea<br />
<br />
Tanya Berardini, Using biological ontologies to accelerate progress in plant biology research, ASPB Plant Biology Annual Meeting, 2016, Minneapolis, MN<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participates in the rota for GitHub (formerly Sourceforge) requests (4 total people in rota, one week at a time, biweekly conference call)<br />
*participates in the rota for the gatekeeper for the TermGenie requests (4 total people in rota, one week at a time)<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
* '''PAINT annotation'''<br />
<br />
Donghui Li does PAINT-based annotation. <br />
*attends PAINT annotation conference calls<br />
*curated 40 families.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui Li participate in manning the GO helpdesk. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66216TAIR December 20172017-12-22T18:03:35Z<p>TanyaB: /* 5. Other Highlights */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
****IN PROGRESS**<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| ||23902 ||+ || || 15707 ||+ || ||56832|| + ||<br />
|-<br />
| IEA || || 5441 || - || || 8603 || - || || 966 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| || 9646 || - || || 8417 || + || || 23810 || + ||<br />
|-<br />
| IEA || || 4785 || - || || 66112 || - || || 899 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 12 new GO terms using Protege (id: GO:0090730 through id: GO:0090741) and 8 new GO terms through TermGenie before that service was discontinued.<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66215TAIR December 20172017-12-22T17:52:02Z<p>TanyaB: /* 4. Presentations and publications */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
****IN PROGRESS**<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| ||23902 ||+ || || 15707 ||+ || ||56832|| + ||<br />
|-<br />
| IEA || || 5441 || - || || 8603 || - || || 966 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| || 9646 || - || || 8417 || + || || 23810 || + ||<br />
|-<br />
| IEA || || 4785 || - || || 66112 || - || || 899 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
*FIX*<br />
<br />
Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub (formerly Sourceforge) requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66214TAIR December 20172017-12-22T17:51:37Z<p>TanyaB: /* 4. Presentations and publications */</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
****IN PROGRESS**<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| ||23902 ||+ || || 15707 ||+ || ||56832|| + ||<br />
|-<br />
| IEA || || 5441 || - || || 8603 || - || || 966 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| || 9646 || - || || 8417 || + || || 23810 || + ||<br />
|-<br />
| IEA || || 4785 || - || || 66112 || - || || 899 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2017 GO 2017 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
Tanya Berardini and Leonore Reiser, Introduction to TAIR Resources, Workshop sponsored by Stanford University Science library, November 2017. Stanford, CA<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
*FIX*<br />
<br />
Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub (formerly Sourceforge) requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66213TAIR December 20172017-12-22T17:43:14Z<p>TanyaB: </p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
****IN PROGRESS**<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| ||23902 ||+ || || 15707 ||+ || ||56832|| + ||<br />
|-<br />
| IEA || || 5441 || - || || 8603 || - || || 966 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| || 9646 || - || || 8417 || + || || 23810 || + ||<br />
|-<br />
| IEA || || 4785 || - || || 66112 || - || || 899 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2017 GO 2017 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
*FIX*<br />
<br />
Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub (formerly Sourceforge) requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
*participates in the Protein Complexes Working Group conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
Tanya Berardini performs QC review of TAIR annotations as issues with particular terms or evidence codes are brought up by the consortium.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66212TAIR December 20172017-12-22T17:40:32Z<p>TanyaB: </p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
****IN PROGRESS**<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| ||23902 ||+ || || 15707 ||+ || ||56832|| + ||<br />
|-<br />
| IEA || || 5441 || - || || 8603 || - || || 966 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| || 9646 || - || || 8417 || + || || 23810 || + ||<br />
|-<br />
| IEA || || 4785 || - || || 66112 || - || || 899 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2017 GO 2017 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
*FIX*<br />
<br />
Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participated in the rota for GitHub (formerly Sourceforge) requests until the end of Feb. 2017<br />
*participated in the rota for the gatekeeper for the TermGenie requests until the end of Feb. 2017<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui participated in manning the GO helpdesk for one week each in January 2017. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2017&diff=66211TAIR December 20172017-12-22T17:37:09Z<p>TanyaB: Created page with " == TAIR, The Arabidopsis Information Resource, December 2017 == ****IN PROGRESS** === 1. Staff working on GOC tasks === Tanya Berardini, Leonore Reiser, (Donghui Li left..."</p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2017 ==<br />
<br />
****IN PROGRESS**<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini, Leonore Reiser, (Donghui Li left the project in July 2017)<br />
<br />
TAIR no longer receives GO funding.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| ||23902 ||+ || || 15707 ||+ || ||56832|| + ||<br />
|-<br />
| IEA || || 5441 || - || || 8603 || - || || 966 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/17)<br />
! BP (12/16)<br />
! change<br />
! MF (12/17)<br />
! MF (12/16)<br />
! change<br />
! CC (12/17)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| || 9646 || - || || 8417 || + || || 23810 || + ||<br />
|-<br />
| IEA || || 4785 || - || || 66112 || - || || 899 || - ||<br />
|-<br />
| ND || || 7921 || - || || 4753 || - || || 4053 || - ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. IEA annotations based on various methods from the GOA group<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
TAIR curators review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2017 GO 2017 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Subramaniam S, Li D, Huala E. Using the Arabidopsis Information Resource (TAIR) to Find Information About Arabidopsis Genes. Curr Protoc Bioinformatics. 2017 Dec 8;60:1.11.1-1.11.45. doi: 10.1002/cpbi.36.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Eva Huala and Shabari Subramaniam, New Tools and Data at TAIR, 2017 International Conference on Arabidopsis Research (ICAR), St. Louis, MO<br />
<br />
Leonore Reiser, The Arabidopsis Information Resource: A curated reference resource for translational plant biology. 2017 Annual Meeting of the American Society for Plant Biology (ASPB), Honolulu, HI<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
*FIX*<br />
<br />
Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
*FIX<br />
<br />
Tanya Berardini:<br />
*participates in the rota for GitHub (formerly Sourceforge) requests (4 total people in rota, one week at a time, biweekly conference call)<br />
*participates in the rota for the gatekeeper for the TermGenie requests (4 total people in rota, one week at a time)<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
* '''PAINT annotation'''<br />
<br />
Donghui Li does PAINT-based annotation. <br />
*attends PAINT annotation conference calls<br />
*curated 40 families.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui Li participate in manning the GO helpdesk. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2017-11-20&diff=65846Ontology meeting 2017-11-202017-11-20T18:16:37Z<p>TanyaB: </p>
<hr />
<div>= Conference Line =<br />
<br />
*Zoom: https://stanford.zoom.us/j/828418143<br />
<br />
= Agenda =<br />
== Documentation on Asserted Parents ==<br />
*Deleting asserted parents was already included in the section on [https://github.com/geneontology/go-ontology/blob/master/docs/CreateNewTerm.md CreateNewTerm].<br />
*Does it need to be somewhere else?<br />
*Is it not clear enough?<br />
==GH project link==<br />
https://github.com/geneontology/go-ontology/projects/1<br />
<br />
== Editors Discussion ==<br />
*cellular component assembly vs biogenesis vs morphogenesis - any guidelines for deciding when to instantiate which terms?<br />
**[https://github.com/geneontology/go-ontology/issues/14579 GO:0043683 type IV pilus biogenesis parentage]<br />
**[https://github.com/geneontology/go-ontology/issues/14469 NTR: Type I pilus biogenesis]<br />
**[https://github.com/geneontology/go-ontology/issues/14540 OTR/NTR: not all synaptic vesicle endocytosis is clathrin-mediated]<br />
***See towards the end of the thread on synaptic vesicle formation is_a cellular component organization<br />
*design patterns<br />
**[https://github.com/geneontology/go-ontology/issues/14494 update equivalence axiom for GO:0015165 - pyrimidine nucleotide-sugar transmembrane transporter activity]<br />
<br />
= Minutes =<br />
*On call: Barbara, Chris, Harold, Jim, Judy, Karen, Kimberly, Pascale, Tanya<br />
<br />
== Documentation on Asserted Parents ==<br />
suggestion: move remove asserted parent info to its own section and link from relevant places, like create new term and review existing terms<br />
<br />
== Editors Discussion ==<br />
*cellular component assembly vs biogenesis vs morphogenesis - any guidelines for deciding when to instantiate which terms?<br />
<br />
creation of ribosome biogenesis term set a precedent for the creation of other cellular component biogenesis terms – some of which are not really biogenesis as the definition implies, but rather just plain old assembly - differences between biogenesis and assembly and synonyms – need to look at synonyms too<br />
<br />
KMV will look at biogenesis terms more carefully and see if we really think that we need them or just retain CCorganization and just have assembly/disassembly/maintainance/morphogenesis as child terms and no biogenesis. <br />
<br />
What about annotations? Besides GO-CAM model solution, perhaps add annot extension to indicate inputs for genes that are annotated to things like ribosome biogenesis<br />
<br />
KMV will talk more with Jim about specifics of having the different pili in GO and how to classify them.<br />
<br />
<br />
<br />
<br />
<br />
<br />
[[Category: Ontology]]<br />
[[Category: Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2017-09-26&diff=65274Annotation Conf. Call 2017-09-262017-09-26T15:54:42Z<p>TanyaB: </p>
<hr />
<div>= Meeting URL =<br />
*https://stanford.zoom.us/j/976175422<br />
<br />
= Agenda =<br />
== Review Cambridge Consortium Meeting Logistics and Agenda ==<br />
*http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Meeting_Logistics<br />
*http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Meeting_Agenda<br />
<br />
== Update on Signaling Project ==<br />
*[http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Signalling_Workshop Workshop, Sunday, October 1st]<br />
**Please update the [http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Signalling_Workshop#Attendees Attendees table]<br />
*[http://wiki.geneontology.org/index.php/Signalling_Workshop_Agenda Agenda Page]<br />
**Need volunteers for minutes - one topic/person<br />
*Presenters - please add all relevant docs, spreadsheets, slides to [https://drive.google.com/drive/u/0/folders/0B7bEr6HANSlGQmlCYm5VRHNMNW8 Signaling Project folder] on GO's Google Drive<br />
*Ca2+ signaling in mammalian fertilization<br />
*GPCR<br />
*Jak/Stat<br />
*MAPK<br />
*Wnt<br />
<br />
== Reminder ==<br />
*GO-CAM/Noctua call tomorrow at 8am PST<br />
*https://stanford.zoom.us/j/679970729<br />
<br />
= Minutes = <br />
*On call: Chris, David H., Edith, George, Giulia, Harold, Helen, Jim, Karen, Li, Midori, Paul T., Penelope, Petra, Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Tanya, Terry, Val<br />
<br />
*Reviewed consortium meeting logistics<br />
**Please bring your registration fee (120 GBP) in cash<br />
*We like to have working group meetings<br />
**When? Maybe not the first thing in the schedule<br />
**Scheduling can be tricky when there's overlap<br />
**Would be good to schedule these for when remote participants (e.g. US West Coast) can attend<br />
**If working groups don't include all attendees, what will those people do during that time?<br />
*Would it be worthwhile to have a session on the GO Handbook?<br />
**Yes, this might be a good way to start the meeting<br />
*For discussion of relations and qualifiers<br />
**Need an introductory presentation to frame the discussion<br />
*Proteoform discussion will be moved to an annotation call since Harold and Li will not be at the Cambridge meeting<br />
*Workshop suggestions - please claim ownership so we can make plans!<br />
**Follow-up from signaling workshop would be good here<br />
<br />
<br />
<br />
<br />
[[Category: Annotation Working Group]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=650792017 Cambridge GOC Meeting Logistics2017-09-06T14:53:28Z<p>TanyaB: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
*7:30pm, Tuesday 3rd October at [http://www.galleriacambridge.co.uk/ The Galleria Restaurant], 33 Bridge St, Cambridge CB2 1UW<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<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 (detailes at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
==Meeting Dinner==<br />
* Dinner will be on Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, 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 />
! Are you planning to attend the GOC dinner<br />
! Are you planning to bring a poster? (indicate number)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes, 3 perhaps 4<br />
|-<br />
| Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Chris Mungall<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Seth Carbon<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Eric Douglass<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Nick Brown<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| No<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-UniProt, GOA, IntAct<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| No<br />
|<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mary Dolan<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Paul Thomas<br />
| GOC/USC<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| GOC/neXtProt <br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Shur-Jen Wang<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes, w/Liz, (1) signaling<br />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes, w/Shur-Jen, (1)<br />
|-<br />
| Kimberly Van Auken<br />
| WB/Caltech<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
|Michele Magrane <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Tony Sawford <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Penelope Garmiri <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alice Shypitsyna <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|George Georghiou <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alex Ignatchenko <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Maria Martin <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Alan Bridge <br />
|SIB<br />
|Yes <br />
|Yes <br />
| Yes (1) <br />
|- <br />
|Marc Feuermann <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Patrick Masson <br />
|SIB<br />
|Yes <br />
|Yes <br />
|<br />
|- <br />
|Sylvain Poux <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|<br />
|- <br />
|Jacky Hayles <br />
|PomBase<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Huaiyu Mi<br />
|USC<br />
|Yes <br />
|Yes<br />
|<br />
|- <br />
|Astrid Laegreid<br />
|NTNU<br />
|Yes<br />
|Yes<br />
|No<br />
|<br />
|-<br />
|Marcio Luis Acencio<br />
|NTNU<br />
|Yes<br />
|Yes<br />
|Yes (1)<br />
|<br />
|-<br />
|Susan Tweedie (pending confirmation)<br />
| HGNC<br />
|Yes<br />
|Yes<br />
|Yes (1)<br />
|<br />
|}<br />
<br />
NOT attending (please indicate if you will attend remotely):<br />
<br />
Peter D'Eustachio<br /><br />
Doug Howe <br><br />
TAIR representative (Attending remotely)<br><br />
Harold Drabkin (Attending remotely)<br />
<br />
==Accommodations==<br />
*Cambridge is a small, busy city and accommodation is limited. Please book early, as the beginning of October is drop-off time for the students and lots of worried-looking parents will be in town.<br />
<br />
<br />
*We have a block allocation of rooms at The Royal Hotel (5-10 min walk from the meeting venue). They will only hold until the 1st August, so book early! The allocation is from the Sunday 1st-Thurs 5th. After this date the rooms will not be held but can still be booked at the discounted rate. There are an extra 10 rooms allocated for 30th September for those attending the signalling workshop.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631, email: reservations.cambridge@sjhotels.co.uk<br />
**The special room rate for the The Royal Cambridge Hotel cannot be accessed via the hotel website. Please contact the hotel directly via email or phone.<br />
** To book phone +44 (0)1223 351631 or e-mail reservations.cambridge@sjhotels.co.uk. To get the discount rate, please quote CAMB63710<br />
** Rates:<br />
*** twin/double room - £160 per room per night included breakfast and VAT<br />
*** single room - £130 per person per night included breakfast and VAT<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. Quote University of Cambridge code LCCUNI to get a discounted rate (~£210-£220/night). Approx. 30 minute walk to meeting venue.<br />
**[http://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree by Hilton.] Granta Place Mill Lane, Cambridge, CB2 1RT, United Kingdom TEL: +44 (0) 1223 259988. Located opposite the meeting venue, but has some building work going on at the moment and is on the more expensive side.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 5-10 min walk from the meeting venue. Approx. £200/night.<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=650782017 Cambridge GOC Meeting Logistics2017-09-06T14:52:08Z<p>TanyaB: </p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
*7:30pm, Tuesday 3rd October at [http://www.galleriacambridge.co.uk/ The Galleria Restaurant], 33 Bridge St, Cambridge CB2 1UW<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<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 (detailes at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
==Meeting Dinner==<br />
* Dinner will be on Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, 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 />
! Are you planning to attend the GOC dinner<br />
! Are you planning to bring a poster? (indicate number)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes, 3 perhaps 4<br />
|-<br />
| Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Chris Mungall<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Seth Carbon<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Eric Douglass<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Nick Brown<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| No<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-UniProt, GOA, IntAct<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| No<br />
|<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mary Dolan<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Paul Thomas<br />
| GOC/USC<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| GOC/neXtProt <br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Shur-Jen Wang<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes, w/Liz, (1) signaling<br />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes, w/Shur-Jen, (1)<br />
|-<br />
| Kimberly Van Auken<br />
| WB/Caltech<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
|Michele Magrane <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Tony Sawford <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Penelope Garmiri <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alice Shypitsyna <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|George Georghiou <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alex Ignatchenko <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Maria Martin <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Alan Bridge <br />
|SIB<br />
|Yes <br />
|Yes <br />
| Yes (1) <br />
|- <br />
|Marc Feuermann <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Patrick Masson <br />
|SIB<br />
|Yes <br />
|Yes <br />
|<br />
|- <br />
|Sylvain Poux <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|<br />
|- <br />
|Jacky Hayles <br />
|PomBase<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Huaiyu Mi<br />
|USC<br />
|Yes <br />
|Yes<br />
|<br />
|- <br />
|Astrid Laegreid<br />
|NTNU<br />
|Yes<br />
|Yes<br />
|No<br />
|<br />
|-<br />
|Marcio Luis Acencio<br />
|NTNU<br />
|Yes<br />
|Yes<br />
|Yes (1)<br />
|<br />
|-<br />
|Susan Tweedie (pending confirmation)<br />
| HGNC<br />
|Yes<br />
|Yes<br />
|Yes (1)<br />
|<br />
|}<br />
<br />
NOT attending (please indicate if you will attend remotely):<br />
<br />
Peter D'Eustachio<br /><br />
Doug Howe <br><br />
TAIR representative <br><br />
Harold Drabkin (Attending remotely)<br />
<br />
==Accommodations==<br />
*Cambridge is a small, busy city and accommodation is limited. Please book early, as the beginning of October is drop-off time for the students and lots of worried-looking parents will be in town.<br />
<br />
<br />
*We have a block allocation of rooms at The Royal Hotel (5-10 min walk from the meeting venue). They will only hold until the 1st August, so book early! The allocation is from the Sunday 1st-Thurs 5th. After this date the rooms will not be held but can still be booked at the discounted rate. There are an extra 10 rooms allocated for 30th September for those attending the signalling workshop.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631, email: reservations.cambridge@sjhotels.co.uk<br />
**The special room rate for the The Royal Cambridge Hotel cannot be accessed via the hotel website. Please contact the hotel directly via email or phone.<br />
** To book phone +44 (0)1223 351631 or e-mail reservations.cambridge@sjhotels.co.uk. To get the discount rate, please quote CAMB63710<br />
** Rates:<br />
*** twin/double room - £160 per room per night included breakfast and VAT<br />
*** single room - £130 per person per night included breakfast and VAT<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. Quote University of Cambridge code LCCUNI to get a discounted rate (~£210-£220/night). Approx. 30 minute walk to meeting venue.<br />
**[http://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree by Hilton.] Granta Place Mill Lane, Cambridge, CB2 1RT, United Kingdom TEL: +44 (0) 1223 259988. Located opposite the meeting venue, but has some building work going on at the moment and is on the more expensive side.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 5-10 min walk from the meeting venue. Approx. £200/night.<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=648562017 Cambridge GOC Meeting Logistics2017-08-21T19:49:58Z<p>TanyaB: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
To be added<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<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 (detailes at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
==Meeting Dinner==<br />
* Dinner will be on Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, 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 />
! Are you planning to attend the GOC dinner<br />
! Are you planning to bring a poster? (indicate number)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes, 3 perhaps 4<br />
|-<br />
| Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Chris Mungall<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Seth Carbon<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Eric Douglass<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Moni Munoz-Torres<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Nick Brown<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-UniProt, GOA, IntAct<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| No<br />
|<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mary Dolan<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paul Thomas<br />
| GOC/USC<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| GOC/neXtProt <br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Shur-Jen Wang<br />
| RGD<br />
| Yes<br />
| Yes<br />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Maybe<br />
|-<br />
| Kimberly Van Auken<br />
| WB/Caltech<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
|Michele Magrane <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Tony Sawford <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Penelope Garmiri <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alice Shypitsyna <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|George Georghiou <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alex Ignatchenko <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Maria Martin <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Alan Bridge <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Marc Feuermann <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Patrick Masson <br />
|SIB<br />
|Yes <br />
|Yes <br />
|<br />
|- <br />
|Sylvain Poux <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Jacky Hayles <br />
|PomBase<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Huaiyu Mi<br />
|USC<br />
|Yes <br />
|Yes<br />
| <br />
|}<br />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<br /><br />
Doug Howe <br><br />
TAIR representative<br />
<br />
==Accommodations==<br />
*Cambridge is a small, busy city and accommodation is limited. Please book early, as the beginning of October is drop-off time for the students and lots of worried-looking parents will be in town.<br />
<br />
<br />
*We have a block allocation of rooms at The Royal Hotel (5-10 min walk from the meeting venue). They will only hold until the 1st August, so book early! The allocation is from the Sunday 1st-Thurs 5th. There are an extra 10 rooms allocated for 30th September for those attending the signalling workshop.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631, email: reservations.cambridge@sjhotels.co.uk<br />
**The special room rate for the The Royal Cambridge Hotel cannot be accessed via the hotel website. Please contact the hotel directly via email or phone.<br />
** To book phone +44 (0)1223 351631 or e-mail reservations.cambridge@sjhotels.co.uk. To get the discount rate, please quote CAMB63710<br />
** Rates:<br />
*** twin/double room - £160 per room per night included breakfast and VAT<br />
*** single room - £130 per person per night included breakfast and VAT<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. Quote University of Cambridge code LCCUNI to get a discounted rate (~£210-£220/night). Approx. 30 minute walk to meeting venue.<br />
**[http://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree by Hilton.] Granta Place Mill Lane, Cambridge, CB2 1RT, United Kingdom TEL: +44 (0) 1223 259988. Located opposite the meeting venue, but has some building work going on at the moment and is on the more expensive side.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 5-10 min walk from the meeting venue. Approx. £200/night.<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=648552017 Cambridge GOC Meeting Logistics2017-08-21T19:49:36Z<p>TanyaB: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , October 2-4, 2017=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre]<br />
<br />
<br />
==Registration==<br />
* Please register at: <br />
<br />
==Consortium dinner ==<br />
<br />
To be added<br />
<br />
==Planned Schedule== <br />
<br />
* '''Monday October 2nd''': <br />
:* Meeting will run from 9am to 5pm. <br />
<br />
*'''Tuesday October 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday October 4th''': <br />
:* Meeting will run from 9am to 1pm.<br />
:* Optional break out groups may follow.<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 (detailes at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
==Meeting Dinner==<br />
* Dinner will be on Tuesday evening<br />
<br />
==Attendees==<br />
Please add your name to the table if you intend to attend the meeting, the dinner, 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 />
! Are you planning to attend the GOC dinner<br />
! Are you planning to bring a poster? (indicate number)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
| Yes, 3 perhaps 4<br />
|-<br />
| Midori Harris<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Chris Mungall<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Seth Carbon<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Eric Douglass<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Moni Munoz-Torres<br />
| BBOP (LBNL)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Nick Brown<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
| Sandra Orchard<br />
| EBI-UniProt, GOA, IntAct<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| No<br />
|<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mary Dolan<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Paul Thomas<br />
| GOC/USC<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Pascale Gaudet<br />
| GOC/neXtProt <br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Shur-Jen Wang<br />
| RGD<br />
| Yes<br />
| Yes<br />
| <br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Maybe<br />
|-<br />
| Kimberly Van Auken<br />
| WB/Caltech<br />
| Yes<br />
| Yes<br />
| Yes (1)<br />
|-<br />
|Michele Magrane <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Tony Sawford <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Penelope Garmiri <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alice Shypitsyna <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|George Georghiou <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Alex Ignatchenko <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Maria Martin <br />
|EBI-UniProt, GOA <br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Alan Bridge <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Marc Feuermann <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Patrick Masson <br />
|SIB<br />
|Yes <br />
|Yes <br />
|<br />
|- <br />
|Sylvain Poux <br />
|SIB<br />
|Yes <br />
|Yes <br />
| <br />
<br />
|- <br />
|Jacky Hayles <br />
|PomBase<br />
|Yes <br />
|Yes <br />
| <br />
|- <br />
|Huaiyu Mi<br />
|USC<br />
|Yes <br />
|Yes<br />
| <br />
|}<br />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<br /><br />
Doug Howe<br />
TAIR representative<br />
<br />
==Accommodations==<br />
*Cambridge is a small, busy city and accommodation is limited. Please book early, as the beginning of October is drop-off time for the students and lots of worried-looking parents will be in town.<br />
<br />
<br />
*We have a block allocation of rooms at The Royal Hotel (5-10 min walk from the meeting venue). They will only hold until the 1st August, so book early! The allocation is from the Sunday 1st-Thurs 5th. There are an extra 10 rooms allocated for 30th September for those attending the signalling workshop.<br />
**[https://www.theroyalcambridgehotel.co.uk/ Royal Cambridge Hotel.] Trumpington Street, Cambridge CB2 1PY. Tel: +44 (0)1223 351631, email: reservations.cambridge@sjhotels.co.uk<br />
**The special room rate for the The Royal Cambridge Hotel cannot be accessed via the hotel website. Please contact the hotel directly via email or phone.<br />
** To book phone +44 (0)1223 351631 or e-mail reservations.cambridge@sjhotels.co.uk. To get the discount rate, please quote CAMB63710<br />
** Rates:<br />
*** twin/double room - £160 per room per night included breakfast and VAT<br />
*** single room - £130 per person per night included breakfast and VAT<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. Quote University of Cambridge code LCCUNI to get a discounted rate (~£210-£220/night). Approx. 30 minute walk to meeting venue.<br />
**[http://doubletree3.hilton.com/en/hotels/united-kingdom/doubletree-by-hilton-hotel-cambridge-city-centre-STNCBDI/index.html?WT.mc_id=zELWAKN0EMEA1DT2DMH3LocalSearch4DGGenericx6STNCBDI Double Tree by Hilton.] Granta Place Mill Lane, Cambridge, CB2 1RT, United Kingdom TEL: +44 (0) 1223 259988. Located opposite the meeting venue, but has some building work going on at the moment and is on the more expensive side.<br />
**[https://www.hotelduvin.com/locations/cambridge/ Hotel du Vin.] 15-19 Trumpington Street, Cambridge CB2 1QA. Tel: +44 (0) 1223 227330. 5-10 min walk from the meeting venue. Approx. £200/night.<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2017_Berkeley_GO_Editors_Workshop_II&diff=648292017 Berkeley GO Editors Workshop II2017-08-16T16:49:24Z<p>TanyaB: /* Tuesday 15th */</p>
<hr />
<div><br />
= Agenda (Draft) =<br />
<br />
== Tuesday 15th ==<br />
<br />
Note: Jim may have a hard time calling in on wed afternoon, tue better, so we may rearrange to accomodate<br />
<br />
=== Tue Morning 9am-12pm ===<br />
<br />
* Intro, goals (Chris)<br />
* Advanced OWL Tutorial (Chris, DOS)<br />
** Work through exercises: https://github.com/geneontology/protege-tutorial<br />
*** Disjoint classes<br />
*** Imports<br />
** Improving the tutorial for others<br />
* Advanced concepts<br />
** GCIs (General Class Inclusion)<br />
** Hidden GCIs<br />
** How to write good logical definitions<br />
<br />
=== Tue Afternoon 1pm-5pm ===<br />
<br />
sparkly swirly things<br />
<br />
* SPARQL (Eric, Chris)<br />
* SWRL (DavidOS)<br />
<br />
How to do cool stuff on the command line<br />
<br />
* [https://github.com/ontodev/robot ROBOT] tutorial<br />
** Setup (Eric)<br />
** Commands (Chris)<br />
* You'll love Makefiles. No, really you will<br />
** Makefile concepts<br />
** Overview of the GO makefile<br />
<br />
Pipes and stuff<br />
<br />
* Pipelines and Continuous Integration (Chris, Seth, Eric)<br />
** Travis deep dive<br />
** How to figure out WTF went wrong with your pull request<br />
** Jenkins Release pipeline (Seth)<br />
<br />
== Wednesday 16th ==<br />
<br />
=== Wed Morning 9am-12pm ===<br />
<br />
DOSDPs, yaml, INCA is the new TermGenie<br />
<br />
* [https://github.com/geneontology/go-ontology/issues/13692 TermGenie Replacement]<br />
** [https://docs.google.com/presentation/d/17hXXSWBiqP4mg0c3MX_vIO5OgwVvfa2b8i-sqoUMY9c/edit?usp=sharing Plan Overview] (Chris)<br />
** yaml design pattern overview (Nicole V, David OS)<br />
** INCAForm demo (Nicole V)<br />
* Exercises<br />
** Add a new term in INCAForm<br />
** Make a new design pattern<br />
* Discussion<br />
** Reusing templates in Noctua<br />
** Getting stricter about accepting compositional terms<br />
<br />
Planning for the future<br />
<br />
* Protege and WebProtege (Tentative) (Matt H)<br />
* Discussion: What would an ideal ontology development environment be like?<br />
<br />
=== Wed Afternoon 1pm-5pm ===<br />
<br />
* RO<br />
** Overview (DavidOS, Chris)<br />
*** Gene product to class relations (KVA)<br />
** Exercise: making an RO pull request<br />
** GORel (for extensions) (DavidOS)<br />
** Discussion<br />
*** retiring GORel<br />
** Documentathon: documenting RO for curators<br />
** ABox Ontologies (DavidOS)<br />
* Noctua<br />
** Ontology-based QC of Noctua (Chris)<br />
** The Arachne reasoner (Chris, or Jim if he can call in)<br />
** Debugging using the explanation panel<br />
** Table Mode demo (Dan) 4pm<br />
<br />
=== Wed Evening: Party! (or at least dinner together) ===<br />
<br />
*Where: [https://goo.gl/maps/UsbWRZLMFMy 2 Biehs Court, Oakland, CA 94618]<br />
*When: Wednesday, August 16 (whenever the meeting closes down and you get over there)<br />
*Ideas for what you'd like to eat? And drink?<br />
<br />
== Thursday 17th ==<br />
<br />
=== Morning 9am-12pm ===<br />
<br />
Ontology Content<br />
<br />
* Problematic GitHub tickets/mini Projects, backlog<br />
** Pascale: https://github.com/geneontology/go-ontology/issues/13731 <br />
**Kimberly [https://github.com/geneontology/go-ontology/issues/13944 #13944 protein quality control]<br />
**Kimberly [https://github.com/geneontology/go-ontology/issues/12272 #12272 receptor agonist activity]<br />
***Receptor agonist activity is being classified as a 'signal transducer activity' but the annotation documentation says that ligands cannot be annotated to 'signal transducer activity'<br />
* Update on status of Molecular Function re-factor<br />
* Review the accumulated use cases for GO from ontology ticket #13606. Discuss how we can continue to best meet the needs of our various communities.<br />
* Review all documentation of SOPs for ontology editors.<br />
<br />
=== Afternoon 1pm-5pm ===<br />
<br />
* Improving editors documentation<br />
* Goals for signaling workshop<br />
**Design templates for MFs for signaling pathway components<br />
***Ligands, e.g. Wnt, EGFs, Delta/Serrate<br />
***Receptors<br />
***Downstream cascade components, e.g. protein kinases, scaffolds<br />
***Transcription factors<br />
<br />
== Topics ==<br />
<br />
=== Fundamentals ===<br />
<br />
* Understanding OWL reasoning. A practical sessions with problem solving exercises, covering:<br />
** Equivalent Class, SubClass; Relations: Characteristics, disjoints, hierarchy, chains, domain and range; GCIs; advanced querying; explanations.<br />
* Understanding the current GO relation set. (A practical session with problem solving exercises + aim to develop better doc)<br />
* The art of designing robust equivalence axioms & design patterns ( editors would like more guidelines on how to construct these.)<br />
<br />
=== Infrastructure ===<br />
<br />
* Design pattern infrastructure<br />
* Pipelines and how they run, both imports and file output. Starting jobs with ROBOT.<br />
* Build failures<br />
** Document the various fail messages and how to correct the issues.<br />
* Ontology work for GO-CAM<br />
** QC-checking property chains and relations that will be used for GPAD generation<br />
** Removing the part_of o regulates chains--- Do we want to instantiate all of the current inferences before removal?<br />
**How will design patterns be implemented in Noctua?<br />
***What design patterns should have priority for Noctua?<br />
<br />
= Logistics =<br />
<br />
== Accommodations ==<br />
<br />
* http://www.fourpointssanfranciscobaybridge.com/<br />
<br />
Getting there:<br />
<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/MacArthur+BART+Station,+40th+Street,+Oakland,+CA/@37.8346259,-122.2866117,15z/am=t/data=!3m1!5s0x80857e0870dbdd83:0x571df460c4d9d3cb!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857de2a98ae50d:0xc5fce433b2157d9f!2m2!1d-122.267047!2d37.8290643!3e3 shuttle from MacArthur BART]<br />
<br />
Taxis also available from either MacArthur or Ashby<br />
<br />
== Parking ==<br />
<br />
We will try to reserve as many spots outside the front entrance as we can. Look for spots that say "GO meeting". if you see one, take it.<br />
<br />
If there is none available, don't worry. Park temporarily and grab a parking pass from the person at the gate, you can then park in the garage:<br />
<br />
* http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/<br />
<br />
== Meeting Location ==<br />
<br />
[http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/ Berkeley Lab, Aquatic Park Offices]<br />
<br />
Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley<br />
Physical address: 717 Potter Street, Berkeley, CA 94710<br />
<br />
Meeting room: room 181<br />
<br />
=== Travel between hotel and meeting ===<br />
<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8448697,-122.3011831,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e2 Walk, 1.3 miles]<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8450306,-122.3024045,15z/am=t/data=!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e3 Free Hollis Shuttle ]<br />
* Taxi/Lyft/Uber<br />
<br />
Aim to be at the lab for 9am<br />
<br />
<br />
<br />
== Participants ==<br />
<br />
{| {{Prettytable}}<br />
|-<br />
! Name<br />
! Organization<br />
! Comments<br />
|-<br />
| David Hill<br />
| Jackson Laboratory<br />
| <br />
|<br />
|-<br />
|Harold Drabkin<br />
| Jackson Laboratory<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| Caltech<br />
| Arriving SFO Monday, 8/14, 5:03PM<br />
|-<br />
| Pascale Gaudet<br />
| SIB Swiss Institute of Bioinformatics<br />
| <br />
|-<br />
| David Osumi-Sutherland<br />
| EBI<br />
| <br />
|-<br />
| Karen Christie<br />
| Jackson Laboratory<br />
| <br />
|-<br />
| Tanya Berardini<br />
| TAIR/Phoenix<br />
| <br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
|<br />
|-<br />
| Nicole Vasilevsky<br />
| OHSU<br />
|<br />
|-<br />
| Matt Horridge <br />
| Stanford<br />
|<br />
|-<br />
| Donghui Li<br />
| CZI<br />
| wed only?<br />
|-<br />
|}<br />
<br />
LBL:<br />
<br />
* Chris Mungall<br />
* Eric Douglass<br />
* Monica Munoz-Torres<br />
* Seth Carbon<br />
* Suzi Lewis<br />
<br />
<br />
[[Category:Meetings]]<br />
[[Category:Protege]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2017_Berkeley_GO_Editors_Workshop_II&diff=645572017 Berkeley GO Editors Workshop II2017-07-19T23:59:24Z<p>TanyaB: /* Participants */</p>
<hr />
<div>= Agenda (Draft) =<br />
<br />
== Topics ==<br />
<br />
=== Fundamentals ===<br />
* Understanding OWL reasoning. A practical sessions with problem solving exercises, covering:<br />
* Equivalent Class, SubClass; Relations: Characteristics, hierarchy, chains, domain and range; GCIs; advanced querying; explanations.<br />
* Understanding the current GO relation set. (A practical session with problem solving exercises + aim to develop better doc)<br />
* The art of designing robust equivalence axioms & design patterns ( editors would like more guidelines on how to construct these.)<br />
<br />
=== Infrastructure ===<br />
* Design pattern infrastructure<br />
* Pipelines and how they run, both imports and file output. Starting jobs with ROBOT.<br />
* Build failures<br />
* Document the various fail messages and how to correct the issues.<br />
<br />
=== Content ===<br />
* Problematic GitHub tickets/mini Projects<br />
** Pascale: #13731 <br />
* Review the accumulated use cases for GO from ontology ticket #13606. Discuss how we can continue to best meet the needs of our various communities.<br />
<br />
= Logistics =<br />
<br />
== Accommodations ==<br />
<br />
* http://www.fourpointssanfranciscobaybridge.com/<br />
<br />
Getting there:<br />
<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/MacArthur+BART+Station,+40th+Street,+Oakland,+CA/@37.8346259,-122.2866117,15z/am=t/data=!3m1!5s0x80857e0870dbdd83:0x571df460c4d9d3cb!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857de2a98ae50d:0xc5fce433b2157d9f!2m2!1d-122.267047!2d37.8290643!3e3 shuttle from MacArthur BART]<br />
<br />
Taxis also available from either MacArthur or Ashby<br />
<br />
== Meeting Location ==<br />
<br />
[http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/ Berkeley Lab, Aquatic Park Offices]<br />
<br />
Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley<br />
Physical address: 717 Potter Street, Berkeley, CA 94710<br />
<br />
Meeting room: room 181<br />
<br />
=== Travel between hotel and meeting ===<br />
<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8448697,-122.3011831,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e2 Walk, 1.3 miles]<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8450306,-122.3024045,15z/am=t/data=!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e3 Free Hollis Shuttle ]<br />
* Taxi/Lyft/Uber<br />
<br />
Aim to be at the lab for 9am<br />
<br />
== Participants ==<br />
<br />
{| {{Prettytable}}<br />
|-<br />
! Name<br />
! Organization<br />
! Comments<br />
|-<br />
| David Hill<br />
| Jackson Laboratory<br />
| <br />
|<br />
|-<br />
|Harold Drabkin<br />
| Jackson Laboratory<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| Caltech<br />
| Arriving SFO Monday, 8/14, 5:03PM<br />
|-<br />
| Pascale Gaudet<br />
| SIB Swiss Institute of Bioinformatics<br />
| <br />
|-<br />
| David Osumi-Sutherland<br />
| EBI<br />
| <br />
|-<br />
| Karen Christie<br />
| Jackson Laboratory<br />
| <br />
|-<br />
| Tanya Berardini<br />
| TAIR/Phoenix<br />
| <br />
|-<br />
|}<br />
<br />
LBL:<br />
<br />
* Chris Mungall<br />
* Eric Douglass<br />
* Monica Munoz-Torres<br />
* Seth Carbon<br />
<br />
[[Category:Meetings]]<br />
[[Category:Protege]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Signalling_Workshop&diff=644852017 Cambridge GOC Signalling Workshop2017-07-14T18:59:22Z<p>TanyaB: /* Attendees */</p>
<hr />
<div>==Planned Schedule== <br />
<br />
* '''Sunday October 1st''': <br />
:* Meeting will run from 9am to 5:00pm.<br />
<br />
==Agenda==<br />
<br />
[[Signalling Workshop Agenda ]]<br />
<br />
==Minutes and useful links==<br />
<br />
*[https://docs.google.com/document/d/1wCzCkPL9ft20ZP5XnTn8IQAcxoFEduaBmzVWKN0hbU0/edit?usp=sharing google minutes] Signaling workshop hopefully this link will enable everyone to edit the doc<br />
<br />
*[http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2017-06-27 27June17 annotation call minutes]<br />
<br />
*[http://www.geneontology.org/page/go-annotation-conventions#ligand Annotation Conventions - General Ligand-Receptor Pathway]<br />
<br />
*[http://wiki.geneontology.org/index.php/Signaling Ontology signaling project started 2009]<br />
<br />
==Items agreed==<br />
Hopefully no further discussion required:<br />
# All signaling ontology terms should have a defined start and end - work on the ontology is required<br />
# GO-CAM models will be created to present clear views of what is part of a pathway, what regulates the pathway, and what is causally upstream of the pathway<br />
# The Cambridge meeting will focus on a selection of specific pathways<br />
# Annotation conference calls will spend some time looking at these<br />
<br />
==Pre-meeting github tickets==<br />
<br />
[https://github.com/geneontology/go-annotation/projects/4 signaling project at GitHub]<br />
<br />
==Attendees==<br />
Please add your name to the table and indicate if you intend to participate in the pre-meeting discussions<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Participate in pre-meeting discussions<br />
! Request funding for Saturday night hotel accommodation near meeting<br />
! Interested in attending Sunday 1st October<br />
<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| Yes<br />
| Maybe?<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Sandra Orchard<br />
| EBI-UniProt/GOA/IntAct<br />
| <br />
| No<br />
| Yes<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| <br />
| Yes<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| <br />
| <br />
| Yes<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Yes<br />
| <br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| WormBase<br />
| Yes<br />
| <br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Doug Howe<br />
| Zfin<br />
| <br />
| <br />
| Maybe<br />
|-<br />
| Pascale Gaudet<br />
| GOC/nextprot<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Tanya Berardini/TAIR rep<br />
| TAIR<br />
| Yes<br />
| No<br />
| Cannot attend<br />
|-<br />
| Chris Mungall<br />
| LBNL<br />
| To the extent I can<br />
| Yes<br />
| Yes<br />
|-<br />
| Shur-Jen Wang<br />
| RGD<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Elizabeth Bolton<br />
| RGD<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Petra Fey<br />
|dictyBase<br />
| Yes<br />
| Yes<br />
| Yes<br />
|}<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]] <br />
[[Category: Working Groups]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Signalling_Workshop&diff=642022017 Cambridge GOC Signalling Workshop2017-06-28T16:14:43Z<p>TanyaB: /* Attendees */</p>
<hr />
<div>==Planned Schedule== <br />
<br />
* '''Sunday October 1st''': <br />
:* Meeting will run from 9am to 5:00pm.<br />
<br />
==Agenda==<br />
<br />
[[Signalling Workshop Agenda ]]<br />
<br />
==Minutes and useful links==<br />
<br />
[https://docs.google.com/document/d/1wCzCkPL9ft20ZP5XnTn8IQAcxoFEduaBmzVWKN0hbU0/edit?usp=sharing google minutes] Signaling workshop hopefully this link will enable everyone to edit the doc<br />
<br />
[http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2017-06-27 27June17 annotation call minutes]<br />
<br />
[http://www.geneontology.org/page/go-annotation-conventions#ligand annotation conventions ligand]<br />
<br />
[http://wiki.geneontology.org/index.php/Signaling Ontology signaling project started 2009]<br />
<br />
==Items agreed==<br />
Hopefully no further discussion required:<br />
# All signaling ontology terms should have a defined start and end - work on the ontology is required<br />
# GO-CAM models will be created to present clear views of what is part of a pathway, what regulates the pathway, and what is causally upstream of the pathway<br />
# The Cambridge meeting will focus on a selection of specific pathways<br />
# Annotation conference calls will spend some time (approx 20 min each call) looking at these<br />
<br />
==Pre-meeting github tickets==<br />
<br />
[https://github.com/geneontology/go-annotation/projects/4 signaling project at GitHub]<br />
<br />
==Attendees==<br />
Please add your name to the table and indicate if you intend to participate in the pre-meeting discussions<br />
<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Participate in pre-meeting discussions<br />
! Request funding for Saturday night hotel accomodation near meeting<br />
! Interested in attending Sunday 1st October<br />
<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| <br />
| No<br />
| Yes<br />
|-<br />
| Suzanna Lewis<br />
| BBOP (LBNL)<br />
| <br />
| <br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| No<br />
| Yes<br />
|-<br />
| Sandra Orchard<br />
| EBI-IntAct<br />
| <br />
| No<br />
| Yes<br />
|-<br />
| David Hill<br />
| GOC/Jackson Laboratory<br />
| Yes<br />
| <br />
| Yes<br />
|-<br />
| Judy Blake<br />
| GOC/MGI (Jackson)<br />
| <br />
| <br />
| Yes<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| <br />
| <br />
| Yes<br />
|-<br />
| Kimberly Van Auken<br />
| Wormbase<br />
| Yes<br />
| <br />
| Yes<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| <br />
| <br />
| Yes<br />
|-<br />
| Doug Howe<br />
| Zfin<br />
| <br />
| <br />
| Maybe<br />
|-<br />
| Pascale Gaudet<br />
| NeXtProt<br />
| <br />
| <br />
| Yes<br />
|-<br />
| Tanya Berardini/TAIR rep<br />
| TAIR<br />
| Yes<br />
| Maybe<br />
| Yes but may not make it<br />
|}<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]] <br />
[[Category: Working Groups]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2017-05-12&diff=63809Ontology meeting 2017-05-122017-05-11T19:23:40Z<p>TanyaB: /* Annotation Documentation */</p>
<hr />
<div>*Bluejeans: https://bluejeans.com/164681006<br />
<br />
= Agenda =<br />
<br />
Kimberly will chair the call.<br />
<br />
== GOC Meeting, Corvallis, Oregon ==<br />
*GOC Meeting Agenda - Ontology-Related Issues<br />
**http://wiki.geneontology.org/index.php/2017_Corvallis_GOC_Meeting_Agenda<br />
**Add discussion points as needed <br />
<br />
==Annotation Documentation==<br />
https://github.com/geneontology/go-ontology/issues/13384<br />
<br />
==Ontology Editing (Protege/GitHub) Documentation==<br />
What's up with this? Final version somewhere?<br />
<br />
==Inference e-mails are Back ==<br />
https://github.com/geneontology/go-ontology/issues/13396<br />
<br />
David has checked the file and has noted the strange ones in the ticket.<br />
*The response ones are pretty easy. They don't have necessary and sufficient logical defs.<br />
*The dentin transport one is a weird result of the reasoning.<br />
*The protein ones are technically correct but misleading. I am pretty sure it is due to the equivalence between PRO and ChEBI. I suspect Pascale might have these in her sights for clean up.<br />
<br />
== Ontology Developer Training == <br />
Follow up on idea of doing an advanced Ontology Developer Training workshop this summer <br />
* Who will participate ?<br />
** People who are currently active in editing the ontology. <br />
* Where will it be? <br />
**The Bay area.<br />
* When will it be?<br />
**Second week of August is best, but we won't have Seth.<br />
* Potential Topics<br />
**Equivalence axioms - editors would like more guidelines on how to construct these.<br />
**OWL GCIs- Where do they live and how do they work?<br />
**Advanced Querying?<br />
**Pipelines and how they run. Starting jobs with ROBOT.<br />
**Build failures<br />
***Document the various fail messages and how to correct the issues.<br />
**Problematic GitHub tickets/mini Projects<br />
<br />
== Github Ticket Discussion==<br />
https://github.com/geneontology/go-ontology/projects/1<br />
<br />
= Minutes =<br />
*On call: <br />
<br />
<br />
[[Category: Ontology]]<br />
[[Category: Meetings]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Gohelp&diff=63300Gohelp2017-03-01T21:20:38Z<p>TanyaB: </p>
<hr />
<div>'''Starting March 1, 2017'''<br />
<br />
GO JIRA system has been retired. All GO help queries are now routed to the [https://github.com/geneontology/helpdesk/issues Github GO Helpdesk tracker ]<br />
<br />
<br />
Recommended actions for tracker.<br />
<br />
- Triage queries. Assign queries to the person with appropriate expertise.<br />
<br />
- Check the [http://geneontology.org/faq-page FAQ]. Answers might already be there.<br />
<br />
- If needed, improve FAQ documentation on website, or assign task to others (contact Seth or Moni if you need help with the website).<br />
<br />
<br />
=Help with queries=<br />
<br />
*There is a [[gohelp people list]] of the best people to assign the different queries to.<br />
<br />
* For problems with GO term enrichment, also forward the email to go-software@lists.stanford.edu to reach programmers who are not on go-help.<br />
<br />
*The archive from the old mailman system is still available for searching: [https://mailman.stanford.edu/pipermail/go-helpdesk/].<br />
<br />
*The EBI gohelp JIRA set up is also still available for searching: [https://www.ebi.ac.uk/panda/jira/browse/GOHELP]<br />
<br />
[[Category:Advocacy and Outreach]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Gohelp&diff=63299Gohelp2017-03-01T21:18:58Z<p>TanyaB: </p>
<hr />
<div>'''Starting March 1, 2017'''<br />
<br />
GO JIRA system has been retired. All GO help queries are now routed to the [https://github.com/geneontology/helpdesk/issues Github GO Helpdesk tracker ]<br />
<br />
<br />
'''Summary of duties of a GO helper'''<br />
<br />
- Triage queries. Assign queries to others or to yourself. Resolve queries assigned to you if any.<br />
<br />
- Check the [http://geneontology.org/faq-page FAQ]. Answers might already be there.<br />
<br />
- If needed, improve FAQ documentation on website, or assign task to others (contact Seth or Moni if you need help with the website).<br />
<br />
- Post on the website: interesting papers that use GO, significant updates to annotation files and to ontology structure/content, etc.<br />
<br />
=Help with queries=<br />
<br />
*There is a [[gohelp people list]] of the best people to assign the different queries to.<br />
<br />
* For problems with GO term enrichment, also forward the email to go-software@lists.stanford.edu to reach programmers who are not on go-help.<br />
<br />
*The archive from the old mailman system is still available for searching: [https://mailman.stanford.edu/pipermail/go-helpdesk/].<br />
<br />
*The EBI gohelp JIRA set up is also still available for searching: [https://www.ebi.ac.uk/panda/jira/browse/GOHELP]<br />
<br />
[[Category:Advocacy and Outreach]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2016&diff=63232TAIR December 20162017-02-22T22:56:21Z<p>TanyaB: </p>
<hr />
<div> <br />
== TAIR, The Arabidopsis Information Resource, December 2016 ==<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini (0.35 FTE), Donghui Li (0.3 FTE), Leonore Reiser (0.5 FTE)<br />
<br />
The total number of FTE working on GOC tasks is 1.15.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 22786 ||23902 ||+ 1116 ||14584 || 15707 ||+ 1123 || 56339 ||56832|| + 493 ||<br />
|-<br />
| IEA || 5689 || 5441 || - 248 ||9236 || 8603 || - 633 || 1354 || 966 || - 388 ||<br />
|-<br />
| ND ||8106 || 7921 || - 185 || 4861|| 4753 || - 108 || 4065|| 4053 || - 12 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9730 || 9646 || - 84 || 8020 || 8417 || + 397 ||23782 || 23810 || + 28 ||<br />
|-<br />
| IEA || 4593 || 4785 || - 192 || 6574 || 66112 || - 38 || 1224 || 899 || - 325 ||<br />
|-<br />
| ND ||8106 || 7921 || - 185 || 4861|| 4753 || - 108 || 4065|| 4053 || - 12||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. INTERPRO2GO-based IEA annotations from UniProtKB<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
Donghui, Leonore, and Tanya review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2016 GO 2016 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Berardini TZ, Li D, Muller R, Strait EM, Li Q, Mezheritsky Y, Vetushko A, Huala E.<br />
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. Database (Oxford). 2016 Mar 17;2016. pii: baw018. doi: 10.1093/database/baw018.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Donghui Li, TAIR: A Sustainable Community Resource for Arabidopsis Research, International Conference on Arabidopsis Research (ICAR 2016), GyeongJu, Korea<br />
<br />
Tanya Berardini, Using biological ontologies to accelerate progress in plant biology research, ASPB Plant Biology Annual Meeting, 2016, Minneapolis, MN<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participates in the rota for GitHub (formerly Sourceforge) requests (4 total people in rota, one week at a time, biweekly conference call)<br />
*participates in the rota for the gatekeeper for the TermGenie requests (4 total people in rota, one week at a time)<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
* '''PAINT annotation'''<br />
<br />
Donghui Li does PAINT-based annotation. <br />
*attends PAINT annotation conference calls<br />
*curated 40 families.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui Li participate in manning the GO helpdesk. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2015&diff=63231TAIR December 20152017-02-22T22:55:14Z<p>TanyaB: </p>
<hr />
<div><br />
== TAIR, The Arabidopsis Information Resource, December 2015 ==<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini (0.35 FTE), Donghui Li (0.3 FTE), Leonore Reiser (0.5 FTE)<br />
<br />
The total number of FTE working on GOC tasks is 1.15.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
In October 2015, we dropped about 37K RCA annotations from a single 2012 paper that we deemed out of date and that many community members had criticized as unreliable. This adversely affects many of the numbers shown below and the increase in experimentally based annotations is masked to some degree. Going forward, it may be more useful to show and compare the number of experimentally based annotations (IDA, IGI, IPI, IMP, IEP) as a better measure of literature based curation.<br />
<br />
Dates are 12/15 = 12/31/2015 and 12/14 = 12/09/14.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/15)<br />
! BP (12/14)<br />
! change<br />
! MF (12/15)<br />
! MF (12/14)<br />
! change<br />
! CC (12/15)<br />
! CC (12/14)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 22786 || 58326 ||- 35540 ||14584 ||14098 ||+ 486 || 56339 || 55941 || + 398 ||<br />
|-<br />
| IEA || 5689 || 17211 || - 11522 ||9236 || 33757 || -24521 || 1354 || 7158 || -5804 ||<br />
|-<br />
| ND ||8106 || 9176 || - 1070 || 4861|| 5193 || - 332 || 4065|| 4452 || - 387 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/15)<br />
! BP (12/14)<br />
! change<br />
! MF (12/15)<br />
! MF (12/14)<br />
! change<br />
! CC (12/15)<br />
! CC (12/14)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9730 ||13406 || -4036 || 8020 || 7870 || + 150 ||23782 || 23756 || + 26 ||<br />
|-<br />
| IEA || 4593 || 9840 || - 5247 || 6574 ||12434 || - 5860 || 1224 || 4379 || - 3152 ||<br />
|-<br />
| ND ||8106 || 9176 || - 1070 || 4861|| 5193 || - 332 || 4065|| 4452 || - 387 ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. We have transitioned to incorporating UniProtKB's INTERPRO2GO-based IEA annotations on a monthly basis. This replaces our in-house pipeline for<br />
generating a similar dataset.<br />
<br />
c. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. INTERPRO2GO-based IEA annotations from UniProtKB<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
d. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
e. Review of user-submitted annotations (see TOAST section below)<br />
Donghui, Leonore, and Tanya review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2015 GO 2015 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Berardini TZ, Reiser L, Li D, Mezheritsky Y, Muller R, Strait E, Huala E. The Arabidopsis information resource: Making and mining the "gold standard" annotated reference plant genome. Genesis. 2015 Aug;53(8):474-85. doi: 10.1002/dvg.22877.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
None<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini and Donghui Li have created 90 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', 'created_by: dhl', 'created_by: donghui', date range: 1/1/2015 to 12/31/2015).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*continues to participate in creating cross-products for terms within and among the three GO namespaces <br />
*continues to participate in creation, testing, and deployment of new TermGenie templates for use by the broader community<br />
*participates in the rota for GitHub (formerly Sourceforge) requests (4 total people in rota, one week at a time, biweekly conference call)<br />
*participates in the rota for the gatekeeper for the TermGenie requests (4 total people in rota, one week at a time)<br />
*attends weekly GO editors conference call<br />
*periodically attends biweekly GO annotation conference calls<br />
<br />
Donghui Li:<br />
*attends GO annotation conference calls<br />
*request and create GO terms related to Arabiodopsis and plants<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
* '''PAINT annotation'''<br />
Donghui Li does PAINT-based annotation. <br />
*attends regular PAINT annotation conference calls<br />
*curated 43 families.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui Li participate in manning the GO helpdesk. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=Protege_setup_for_GO_Eds&diff=63110Protege setup for GO Eds2017-02-10T21:39:39Z<p>TanyaB: /* Installing plugins: */</p>
<hr />
<div>= Protege setup for GO =<br />
<br />
== Which Protege version: ==<br />
<br />
Protege 4.3 is stable and relatively free of bugs. However, it does not support OBO to OWL conversion and so requires that GO be converted to OWL for editing and then converted back again for committing to the repository.<br />
<br />
Protege 5 beta21 and higher correctly load and save OBO files. However, preliminary testing suggests that beta21 is not sufficiently stable for anything but relatively brief editing sessions. It also doesn't support the OBO graph view plugin (see below).<br />
<br />
Protege 5.0.0 is currently recommended by Chris (06.20.16)<br />
"And by Protege 5, I mean the stable release version, not the beta. Get this from [http://protege.stanford.edu protege.stanford.edu]<br />
Don't use 4, or a 5-beta"<br />
<br />
== Setting memory ==<br />
<br />
Protege needs at least 4G of RAM to cope with the GO. This is set by specifying the following -Xmx argument for the java. E.g. for 6G, specify -Xmx6000M. How to set this varies with the OS and Protege version. If launching from ./run.command, edit run.command to jre/bin/java -Xmx6000M. If running from Protege_n.app on a mac, you need to find and edit the -Xmx entry in an XML file called info.plist under Protege_n.app/.<br />
<br />
Update for P5: apparently no need to increase memory settings. The info.plist file now has an Xss option which specifies the stack size. It was increased from the default to support reasoning with some particular biomedical ontologies (see https://github.com/protegeproject/protege/issues/457).<br />
<br />
== Protege layout: ==<br />
<br />
Protege has a highly configurable layout and a plugin architecture. You can control which components are visible from the window menu. Selecting something from the view menu allows you to create a new subwindow in a tab with the component of your choice - just move the target icon to the location you want and click.<br />
<br />
[[Image:Protege_setup_images-media-image03.png]]<br />
<br />
As many plugins come with the standard download, the default layout may be intimidating, but can easily be simplified: The following tabs are sufficient for GO work:<br />
<br />
[[Image:Protege_setup_images-media-image08.png]]<br />
<br />
You'll have to create the OBO graph tab yourself. (see below, as part of the Installing Plugins section)<br />
<br />
== Installing plugins: ==<br />
<br />
The following plugins should be installed from the Protégé menus: File&gt;Check for plugins&gt; <br />
<br />
<ul><br />
<li><blockquote><p>Search Annotations –search for terms and displays the list of matching results</p></blockquote></li></ul> (according to Chris, no longer necessary with P5)<br />
<br />
The following plugins should be dropped into the plugins folder of your Protege installation (this varies with OS and Protege version. Example for Protege 4.3 on a mac: cp &lt;some_plugin&gt;.jar Protege-4.3.app/Contents/Resources/Java/plugins/. <br />
<br />
This directory structure for P5 is<br />
'''Protege-5.0.0.app/Contents/Java/plugins/'''. <br />
To see the directory structure so that <br />
you can drag and drop files, you'll need to control-click/right click on the app icon, then select 'Show Package Contents' and drill down to <br />
the directory you want. Note there are two plugins folders. Make sure you use the correct one.<br />
<br />
<ol style="list-style-type: decimal;"><br />
<li><blockquote><p>[https://github.com/liveontologies/elk-reasoner/releases ''ELK OWL reasoner''] Make sure you choose a version appropriate to your Protege version.</p></blockquote> (In P5, the latest ELK can be found using File>Check for Plugins)</li><br />
<li><blockquote><p>[https://github.com/hdietze/protege-obo-plugins/raw/master/org.protege.oboeditor.jar ''OBO Annotation '']– add and edit terms more easily</p></blockquote> (In P5, the OBO Annotation plugin can be found using File>Check for Plugins) Have this view show up by going to the Entities tab, selecting Window>Views>OBO Views>OBO Annotation. Drag the black circle that appears to the area where you want it and click. The panel will appear.</li><br />
<li><blockquote><p>[http://code.google.com/p/obographview/ ''OBO Graph View Component''] – For all you hairball fans - this plugin displays an OBO-style connected graph of classification (is_a) and other relationship types. (Be careful what you wish for).</p></blockquote><br />
To make this a tab:<br />
<br />
*Window > Create New Tab<br />
[[File:OBO_Graph_plugin.png]]<br />
*Window > Views > Ontology Views > OBO Graph View Component<br />
*Take the black circle, put into the Tab you just created and click within it.<br />
</li><br />
<li><blockquote><p>[https://github.com/balhoff/obo-actions/downloads ''Obsoletion plugin''] - Once installed, you should see an &quot;obsolete&quot; option in your Edit menu..</p></blockquote></li></ol><br />
<br />
[[File:Obsoletion_option.png]]<br />
<br />
== Setting ID range ==<br />
<br />
Protege>Preferences>New Entities Tab<br />
<br />
Click on Preferences under the main menu to get this window.<br />
<br />
[[Image:Protege_setup_images-media-image09.png]]<br />
<br />
WARNING: The ID generator in Protege doesn't overwrite existing IRIs, but it can't cope with the OBO alt_id system - where losing IDs following a merge are stored in annotation properties This system is problematic for OWL translations as it leads to the loss or IRIs. Without IRIs, this ID generator doesn't know about the IDs and will stomp on them if they fall in the specified ID range. Until this is fixed,<br />
<br />
We plan to move to a system in which obsolete classes with these IRIs are created for all alt_ids on OBO to OWL translation.<br />
<br />
== Setting username and auto-adding creation date ==<br />
<br />
Protege>Preferences>New Entities Metadata tab<br />
[[File:New_entity_metadata.png]]<br />
<br />
<br />
Broken in 5.0 See: https://github.com/protegeproject/protege/issues/283#issuecomment-177656593<br />
Seems to work in 5.1<br />
<br />
== Setting Rendering ==<br />
<br />
(The default settings may be fine, but details are included for reference)<br />
<br />
Protege allows users to set the annotation property to be used for rendering OWL entities (classes, object properties, annotation properties, individuals) in graphs, trees and text etc. This should be set to rdfs:label, as follows:<br />
<br />
[[Image:Protege_setup_images-media-image07.png]]<br />
<br />
[[Image:Protege_setup_images-media-image02.png]]<br />
<br />
'''Background on rendering.''' All entities in OWL are identified by an IRI. This includes annotation properties such as label. In the absence of an annotation to annotation property specified as suitable for rendering, the short form of this IRI (the bit following a '#' or a '/') is used.<br />
<br />
[[Category:GO Editors]]<br />
[[Category:Protege]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2016&diff=63109TAIR December 20162017-02-10T19:48:24Z<p>TanyaB: /* 2. Annotation progress */</p>
<hr />
<div>'''<span style="color:#FF0000">IN PROGRESS</span>''' <br />
<br />
== TAIR, The Arabidopsis Information Resource, December 2016 ==<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini (0.35 FTE), Donghui Li (0.3 FTE), Leonore Reiser (0.5 FTE)<br />
<br />
The total number of FTE working on GOC tasks is 1.15.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates of query are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 22786 ||23902 ||+ 1116 ||14584 || 15707 ||+ 1123 || 56339 ||56832|| + 493 ||<br />
|-<br />
| IEA || 5689 || 5441 || - 248 ||9236 || 8603 || - 633 || 1354 || 966 || - 388 ||<br />
|-<br />
| ND ||8106 || 7921 || - 185 || 4861|| 4753 || - 108 || 4065|| 4053 || - 12 ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9730 || 9646 || - 84 || 8020 || 8417 || + 397 ||23782 || 23810 || + 28 ||<br />
|-<br />
| IEA || 4593 || 4785 || - 192 || 6574 || 66112 || - 38 || 1224 || 899 || - 325 ||<br />
|-<br />
| ND ||8106 || 7921 || - 185 || 4861|| 4753 || - 108 || 4065|| 4053 || - 12||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. INTERPRO2GO-based IEA annotations from UniProtKB<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
Donghui, Leonore, and Tanya review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2016 GO 2016 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Berardini TZ, Li D, Muller R, Strait EM, Li Q, Mezheritsky Y, Vetushko A, Huala E.<br />
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. Database (Oxford). 2016 Mar 17;2016. pii: baw018. doi: 10.1093/database/baw018.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Donghui Li, TAIR: A Sustainable Community Resource for Arabidopsis Research, International Conference on Arabidopsis Research (ICAR 2016), GyeongJu, Korea<br />
<br />
Tanya Berardini, Using biological ontologies to accelerate progress in plant biology research, ASPB Plant Biology Annual Meeting, 2016, Minneapolis, MN<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participates in the rota for GitHub (formerly Sourceforge) requests (4 total people in rota, one week at a time, biweekly conference call)<br />
*participates in the rota for the gatekeeper for the TermGenie requests (4 total people in rota, one week at a time)<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
* '''PAINT annotation'''<br />
<br />
'''<span style="color:#FF0000">TO BE UPDATED</span>''' <br />
<br />
Donghui Li does PAINT-based annotation. <br />
*attends PAINT annotation conference calls<br />
*curated '''<span style="color:#FF0000">XX</span>''' families.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui Li participate in manning the GO helpdesk. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2016&diff=63108TAIR December 20162017-02-10T19:44:59Z<p>TanyaB: </p>
<hr />
<div>'''<span style="color:#FF0000">IN PROGRESS</span>''' <br />
<br />
== TAIR, The Arabidopsis Information Resource, December 2016 ==<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini (0.35 FTE), Donghui Li (0.3 FTE), Leonore Reiser (0.5 FTE)<br />
<br />
The total number of FTE working on GOC tasks is 1.15.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 22786 || ||- ||14584 || ||+ || 56339 || || + ||<br />
|-<br />
| IEA || 5689 || || - ||9236 || || - || 1354 || || - ||<br />
|-<br />
| ND ||8106 || || - || 4861|| || - || 4065|| || - ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9730 || || - || 8020 || || + ||23782 || || + ||<br />
|-<br />
| IEA || 4593 || || - || 6574 || || - || 1224 || || - ||<br />
|-<br />
| ND ||8106 || || - || 4861|| || - || 4065|| || - ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. INTERPRO2GO-based IEA annotations from UniProtKB<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
Donghui, Leonore, and Tanya review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2016 GO 2016 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Berardini TZ, Li D, Muller R, Strait EM, Li Q, Mezheritsky Y, Vetushko A, Huala E.<br />
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. Database (Oxford). 2016 Mar 17;2016. pii: baw018. doi: 10.1093/database/baw018.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Donghui Li, TAIR: A Sustainable Community Resource for Arabidopsis Research, International Conference on Arabidopsis Research (ICAR 2016), GyeongJu, Korea<br />
<br />
Tanya Berardini, Using biological ontologies to accelerate progress in plant biology research, ASPB Plant Biology Annual Meeting, 2016, Minneapolis, MN<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participates in the rota for GitHub (formerly Sourceforge) requests (4 total people in rota, one week at a time, biweekly conference call)<br />
*participates in the rota for the gatekeeper for the TermGenie requests (4 total people in rota, one week at a time)<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
* '''PAINT annotation'''<br />
<br />
'''<span style="color:#FF0000">TO BE UPDATED</span>''' <br />
<br />
Donghui Li does PAINT-based annotation. <br />
*attends PAINT annotation conference calls<br />
*curated '''<span style="color:#FF0000">XX</span>''' families.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui Li participate in manning the GO helpdesk. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2016&diff=63107TAIR December 20162017-02-10T19:44:10Z<p>TanyaB: /* 5. Other Highlights */</p>
<hr />
<div>'''<span style="color:#FF0000">IN PROGRESS</span>''' <br />
<br />
== TAIR, The Arabidopsis Information Resource, December 2016 ==<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini (0.35 FTE), Donghui Li (0.3 FTE), Leonore Reiser (0.5 FTE)<br />
<br />
The total number of FTE working on GOC tasks is 1.15.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 22786 || ||- ||14584 || ||+ || 56339 || || + ||<br />
|-<br />
| IEA || 5689 || || - ||9236 || || - || 1354 || || - ||<br />
|-<br />
| ND ||8106 || || - || 4861|| || - || 4065|| || - ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9730 || || - || 8020 || || + ||23782 || || + ||<br />
|-<br />
| IEA || 4593 || || - || 6574 || || - || 1224 || || - ||<br />
|-<br />
| ND ||8106 || || - || 4861|| || - || 4065|| || - ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. INTERPRO2GO-based IEA annotations from UniProtKB<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
Donghui, Leonore, and Tanya review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2016 GO 2016 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Berardini TZ, Li D, Muller R, Strait EM, Li Q, Mezheritsky Y, Vetushko A, Huala E.<br />
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. Database (Oxford). 2016 Mar 17;2016. pii: baw018. doi: 10.1093/database/baw018.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Donghui Li, TAIR: A Sustainable Community Resource for Arabidopsis Research, International Conference on Arabidopsis Research (ICAR 2016), GyeongJu, Korea<br />
<br />
Tanya Berardini, Using biological ontologies to accelerate progress in plant biology research, ASPB Plant Biology Annual Meeting, 2016, Minneapolis, MN<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participates in the rota for GitHub (formerly Sourceforge) requests (4 total people in rota, one week at a time, biweekly conference call)<br />
*participates in the rota for the gatekeeper for the TermGenie requests (4 total people in rota, one week at a time)<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
* '''PAINT annotation'''<br />
updated needed<br />
<br />
Donghui Li does PAINT-based annotation. <br />
*attends PAINT annotation conference calls<br />
*curated XX families.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui Li participate in manning the GO helpdesk. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaBhttps://wiki.geneontology.org/index.php?title=TAIR_December_2016&diff=63106TAIR December 20162017-02-10T19:43:47Z<p>TanyaB: /* 4. Presentations and publications */</p>
<hr />
<div>'''<span style="color:#FF0000">IN PROGRESS</span>''' <br />
<br />
== TAIR, The Arabidopsis Information Resource, December 2016 ==<br />
<br />
=== 1. Staff working on GOC tasks ===<br />
<br />
Tanya Berardini (0.35 FTE), Donghui Li (0.3 FTE), Leonore Reiser (0.5 FTE)<br />
<br />
The total number of FTE working on GOC tasks is 1.15.<br />
<br />
=== 2. Annotation progress ===<br />
<br />
Dates are 12/15 = 12/31/2015 and 12/16 = 12/31/2016.<br />
<br />
'''Table 1: Number of Annotations to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Annotations<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 22786 || ||- ||14584 || ||+ || 56339 || || + ||<br />
|-<br />
| IEA || 5689 || || - ||9236 || || - || 1354 || || - ||<br />
|-<br />
| ND ||8106 || || - || 4861|| || - || 4065|| || - ||<br />
<br />
|}<br />
<br />
<br />
'''Table 2: Number of Genes Annotated to Various GO Aspects'''<br />
<br />
{| border="1"<br />
|-<br />
! Genes<br />
! BP (12/15)<br />
! BP (12/16)<br />
! change<br />
! MF (12/15)<br />
! MF (12/16)<br />
! change<br />
! CC (12/15)<br />
! CC (12/16)<br />
! change<br />
|-<br />
| non-IEA/non-ND|| 9730 || || - || 8020 || || + ||23782 || || + ||<br />
|-<br />
| IEA || 4593 || || - || 6574 || || - || 1224 || || - ||<br />
|-<br />
| ND ||8106 || || - || 4861|| || - || 4065|| || - ||<br />
<br />
|}<br />
<br />
=== 3. Methods and strategies for annotation ===<br />
<br />
a. Literature curation: We continue to put most of our annotation effort (95%) into annotation of gene products from the literature.<br />
<br />
b. Integration of non-TAIR Arabidopsis annotations: The following types of external annotations are included in our Arabidopsis gene association file:<br />
<br />
1. Literature-based annotations made by TAIR curators<br />
2. Community annotations made via TAIR's TOAST annotation tool (see below)<br />
3. GOA annotations for Arabidopsis with experimental evidence codes<br />
4. PAINT-based Arabidopsis annotations from RefGenome group<br />
5. Function-Process link-based annotations from GOC <br />
6. INTERPRO2GO-based IEA annotations from UniProtKB<br />
7. TIGR's annotations from Arabidopsis functional annotation project<br />
<br />
c. Priorities for annotation: <br />
<br />
1. literature describing the characterization of previously undescribed ('novel') genes, <br />
2. genes that do not have any GO annotations at all (none of the three aspects),<br />
3. recent literature from high impact factor journals<br />
4. user requested annotation requests<br />
<br />
d. Review of user-submitted annotations (see TOAST section below)<br />
Donghui, Leonore, and Tanya review the annotations submitted via TOAST, <br />
making sure that terms were mapped correctly and that the proper <br />
evidence_with information is entered, if necessary. Sometimes, <br />
follow-up with the submitter via email is necessary.<br />
<br />
=== 4. Presentations and publications ===<br />
[http://wiki.geneontology.org/index.php/Publications,_Talks,_Posters_2016 GO 2016 Publications, Talks, Posters]<br />
<br />
'''Publications - GO-related but not primarily about GO'''<br />
<br />
Reiser L, Berardini TZ, Li D, Muller R, Strait EM, Li Q, Mezheritsky Y, Vetushko A, Huala E.<br />
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. Database (Oxford). 2016 Mar 17;2016. pii: baw018. doi: 10.1093/database/baw018.<br />
<br />
'''Talks - GO-related but not primarily about GO'''<br />
<br />
Donghui Li, TAIR: A Sustainable Community Resource for Arabidopsis Research, International Conference on Arabidopsis Research (ICAR 2016), GyeongJu, Korea<br />
<br />
Tanya Berardini, Using biological ontologies to accelerate progress in plant biology research, ASPB Plant Biology Annual Meeting, 2016, Minneapolis, MN<br />
<br />
=== 5. Other Highlights ===<br />
<br />
'''A. Ontology Development Contributions'''<br />
* '''GO terms contributed by TAIR'''<br />
<br />
Tanya Berardini have created 102 new GO terms using TermGenie and Obo-Edit (search GO flat file by 'created_by: tanyaberardini', 'created_by: tb', date range: 1/1/16 - 12/31/16).<br />
<br />
* '''Other ontology development work'''<br />
<br />
Tanya Berardini:<br />
*participates in the rota for GitHub (formerly Sourceforge) requests (4 total people in rota, one week at a time, biweekly conference call)<br />
*participates in the rota for the gatekeeper for the TermGenie requests (4 total people in rota, one week at a time)<br />
*attends weekly GO editors conference call<br />
*attends biweekly GO annotation conference calls<br />
<br />
<br />
'''B. Annotation outreach and user advocacy efforts'''<br />
<br />
* '''PAINT annotation'''<br />
updated needed<br />
<br />
Donghui Li does PAINT-based annotation. <br />
*attends PAINT annotation conference calls<br />
*curated XX families.<br />
<br />
* '''TOAST (TAIR Online Annotation Submission Tool)'''<br />
<br />
TAIR continues to collect controlled vocabulary annotations via its online tool. <br />
[http://www.arabidopsis.org/doc/submit/functional_annotation/123 TOAST ]<br />
<br />
TAIR can accept annotations based on any journal article, regardless of the journal it was published in, provided that the article has a DOI or a PMID. Submitters must be registered at TAIR.<br />
<br />
* '''GO help'''<br />
<br />
Tanya Berardini and Donghui Li participate in manning the GO helpdesk. This involves answering the questions that come in through the gohelp email address or forwarding them to the appropriate parties for response. There are several GOC curators that rotate this task, one week at a time. <br />
<br />
'''C. Other highlights'''<br />
<br />
<br />
[[Category:Reports]]<br />
[[Category:TAIR]]</div>TanyaB