https://wiki.geneontology.org/api.php?action=feedcontributions&user=Bmeldal&feedformat=atomGO Wiki - User contributions [en]2024-03-28T16:00:27ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2021-04-20&diff=80115Annotation Conf. Call 2021-04-202021-04-20T15:14:40Z<p>Bmeldal: </p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== GOC Meetings, Other Announcements ==<br />
<br />
=== May Consortium Meeting ===<br />
* Virtual Consortium Meeting -Tuesday May 4th - Friday May 7th (note shift forward by one day)<br />
* [https://www.eventbrite.com/e/gene-ontology-main-meeting-remote-tickets-150240357955 Registration]<br />
** [https://docs.google.com/document/d/1QVruWj797NOHJgs06859Hy3WvsL504H5XcTEwSiGqUQ/edit Agenda/Minutes] - review topics for breakout groups and/or workshops<br />
* Group presentations:<br />
** Organize around topics<br />
*** Community Curation and Automated Approaches<br />
*** GO Annotation of Host-Pathogen Interactions<br />
<br />
=== GO-CAM Office Hours ===<br />
* [https://docs.google.com/document/d/1_ZIasvb0hhmJ1teEQ-wegvPob5T74-JeV4UGcZn_evE Agenda]<br />
<br />
=== Noctua Outages ===<br />
* Weekend of April 23rd (this coming weekend)<br />
** Planned LBL outages<br />
<br />
== GAF 2.2 ==<br />
* Waiting for an official release<br />
* Some issues along the way have prevented a public release<br />
* Snapshot ran on Sunday, April 18th<br />
* One meeting workshop - [https://docs.google.com/spreadsheets/d/1JTvDVpggXgpsmCpHHdurqM6NxiTGK4LXkxdQr66jf48 capturing metadata] about annotation file flow, gene product-to-term relations, group contacts<br />
<br />
= Attendance =<br />
* On call: Birgit, Chris, David, Dustin, Edith, Giulia, Harold, Helen, Kimberly, Li, Malcolm, Mary K, Midori, Pascale, Penelope, Petra, Raymond, Rob, Robert, Ruth, Seth, Stan, Suzi<br />
<br />
[[Category:Annotation Working Group]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Requesting_a_New_Complex_ID_from_ComplexPortal&diff=79139Requesting a New Complex ID from ComplexPortal2020-11-17T10:01:23Z<p>Bmeldal: </p>
<hr />
<div>Users can request complex IDs from Complex Portal by sending a message via the yellow tile on the [https://www.ebi.ac.uk/complexportal/home Homepage] "Request Complex for curation" or emailing complexportal@ebi.ac.uk with as much detail as possible.<br />
<br />
==Complex submission template==<br />
<br />
* Please supply as much information as possible to allow us to make your term.<br />
* Find definition at: http://www.ebi.ac.uk/complexportal/documentation/data_content and http://wiki.geneontology.org/index.php/Guidelines_on_%27protein_complex%27_terms<br />
<br />
===Complex names===<br />
* Most commonly known name (recommended name):<br />
* Synonyms (could be any and many!):<br />
<br />
===Participants===<br />
* [http://www.uniprot.org UniProt] IDs for proteins (and their binding regions and stoichiometry - if available)<br />
* [https://www.ebi.ac.uk/chebi ChEBI] IDs for small molecules (and stoichiometry - if available)<br />
* [http://rnacentral.org RNAcentral] IDs for ncRNAs (and stoichiometry - if available)<br />
<br />
===Evidence===<br />
* PMID for papers showing that the complex exists<br />
* Optional: Cross-reference to a evidence database, e.g. from [https://www.ebi.ac.uk/intact IntAct], [https://www.ebi.ac.uk/pdbe PDBe] or [https://www.ebi.ac.uk/pdbe/emdb/searchForm.html/ EMDB]<br />
* '''Note:''' The interaction evidence should include all or almost all complex members, not lots of binaries and not from high throughput experiments.<br />
<br />
===Description===<br />
* A nice, concise description would help, similar to that required for GO term submissions.<br />
<br />
===GO annotations===<br />
Any terms that apply to the COMPLEX (as far as it's known):<br />
* CC for the complex (child of GO:0032991 protein-containing complex)<br />
* CC for cellular location (e.g. nucleus, plasma membrane…)<br />
* MF: at least the central function of the complex<br />
* BPs: the process(es) the complex is involved in<br />
* Please supply PMIDs<br />
<br />
<br />
== Review Status ==<br />
<br />
Last reviewed: Nov 17, 2020<br />
<br />
[[Category:GO Editors]][[Category:Ontology]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=760832019 Berkeley GOC Meeting Logistics2019-09-02T08:46:09Z<p>Bmeldal: </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): [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| SAB Meeting], UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley). More details soon.<br />
<br />
=SAB Meeting=<br />
* SAB 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 />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 8, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 9, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
If you're staying around until Friday, there's an optional expedition on Thursday evening (see above).<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| 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 />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Nash Hotel<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not booked yet<br />
| not yet<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not yet booked<br />
|<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| <br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| <br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Malcolm Fisher (Xenbase) will attend remotely.<br />
<br />
Birgit Meldal (EBI Complex Portal) - remotely if required (need to see schedule) / manageable (I'm +8 hours)<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=2019_Berkeley_GOC_Meeting_Logistics&diff=760822019 Berkeley GOC Meeting Logistics2019-09-02T08:45:52Z<p>Bmeldal: </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): [http://wiki.geneontology.org/index.php/2019_Berkeley_SAB_Meeting_Logistics| SAB Meeting], UC Berkeley campus (Stanley Hall). (SAB dinner will be Thursday, Oct 10)<br />
<br />
==Consortium dinner==<br />
* Wednesday, Oct 9, 6pm, in Berkeley<br />
* More details coming soon<br />
<br />
=User Meeting=<br />
* Monday, October 7 at the same location as the main meeting (717 Potter St., Berkeley). More details soon.<br />
<br />
=SAB Meeting=<br />
* SAB 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 />
==Things to do in the Berkeley area==<br />
The popular [http://www.hardlystrictlybluegrass.com/2019/ "Hardly Strictly Bluegrass" festival] (which leans more towards alternative rock than bluegrass) will take place in San Francisco, Fri-Sun October 4-6.<br />
<br />
On Wednesday, Oct 8, we will break early for an optional hike in Tilden Park.<br />
<br />
On Thursday, Oct 9, there will be an optional outing to the Exploratorium in San Francisco. The Exploratorium is open [https://www.exploratorium.edu/visit/calendar/after-dark Thursday evenings until 10pm for adults only (18+)]. To add to the fun, we'll take the [https://www.tidelinetickets.com/commute ferry to San Francisco from the Berkeley Marina] and then get dinner near there.<br />
<br />
= Departure = <br />
The GOC meeting will adjourn at 12:30pm on Thursday, October 10; lunch will not be provided (but there are places nearby to buy lunch).<br />
You should allow 1/2 hour to get to Oakland airport by car and 1 hour to get to SFO.<br />
<br />
If you're staying around until Friday, there's an optional expedition on Thursday evening (see above).<br />
<br />
=Attendees=<br />
Please add yourself to the table if you plan to attend! Don't forget to register and pay via [https://www.eventbrite.com/e/2019-goc-berkeley-tickets-68218159351%7C| Eventbrite].<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! GOC meeting (Oct 8-10)?<br />
! GOC dinner (Oct 9)?<br />
! User Meeting (Oct 7)?<br />
! Hotel<br />
! Paid via Eventbrite<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Nomi Harris<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Seth Carbon<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eric Douglass<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Peter D'Eustachio<br />
| NYULMC / Reactome<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
|<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
|<br />
|-<br />
|Judy Blake<br />
|JAX<br />
|Yes<br />
|Yes<br />
|Yes<br />
|Four Points<br />
|Yes<br />
|-<br />
| Ben Good<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| 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 />
| Yes<br />
|-<br />
| David Hill<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| No<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Harold Drabkin<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| No<br />
| Four Points<br />
| Yes<br />
|-<br />
| Karen Christie<br />
| MGI, GO - The Jackson Laboratory<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| Yes<br />
|-<br />
| Laurent-Philippe Albou<br />
| USC, LBNL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Yes<br />
| Yes<br />
| No<br />
| N/A<br />
|<br />
|-<br />
| Tanya Berardini<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Leonore Reiser<br />
| TAIR, Phoenix<br />
| Fo' sho<br />
| yes<br />
| yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Eva Huala<br />
| TAIR, Phoenix<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Suzi Aleksander<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
|<br />
|-<br />
| Mike Cherry<br />
| SGD, Stanford<br />
| Yes<br />
| Yes<br />
| No<br />
| Nash Hotel<br />
| yes<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Yes<br />
| Yes<br />
| Maybe<br />
| Four Points<br />
|<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not booked yet<br />
| not yet<br />
|-<br />
| Adam Wright<br />
| OICR<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Hilton Garden Inn<br />
| Yes<br />
|-<br />
| Justin Reese<br />
| LBL<br />
| Yes<br />
| Yes<br />
| Yes<br />
| N/A<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase, Northwestern<br />
| Yes<br />
| Yes<br />
| Yes<br />
| not yet booked<br />
|<br />
|-<br />
| Dustin Ebert<br />
| USC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Oakland airbnb<br />
| Yes<br />
|-<br />
| Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
| Yes<br />
| airbnb<br />
| not yet<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Yes<br />
| Yes<br />
| Yes<br />
| Four Points<br />
| <br />
|-<br />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| <br />
|-<br />
| Michelle Giglio<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
| Suvarna Nadendla<br />
| IGS<br />
| Yes<br />
| Yes<br />
| Yes<br />
| TBD<br />
| not yet<br />
|-<br />
|}<br />
<br />
'''NOT attending (please indicate if you will attend remotely):'''<br/><br />
<br />
Malcolm Fisher (Xenbase) will attend remotely.<br />
Birgit Meldal (EBI Complex Portal) - remotely if required (need to see schedule) / manageable (I'm +8 hours)<br />
<br />
Remote attendees can join us via Zoom (Zoom link will be sent out before the meeting)<br />
[[Category: GO Consortium Meetings]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2019-07-09&diff=75695Annotation Conf. Call 2019-07-092019-07-09T15:25:09Z<p>Bmeldal: /* Minutes */</p>
<hr />
<div>= Agenda =<br />
<br />
== github submission for InterPro2GO mappings ==<br />
* [https://github.com/geneontology/go-annotation/issues/2472 Tagging InterPro in issues]<br />
* Lorna has requested that we tag InterPro curators so they can be alerted to issues relevant to them (can find relevant gitHub handles on the group-contacts.yaml file: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv)<br />
* Please also add the InterPro mapping label (always good practice to add labels)<br />
<br />
== Protein oligomerization terms in GO ==<br />
* Follow up to 2019-06-11 annotation conference call to review recommendations and actions<br />
* [https://docs.google.com/document/d/1JxzNwl1fr5Fj-IJy_Fo1lLfAlAQB8IxPDwwYKxIXBZo Proposal and Recommendations]<br />
* Biological Process Annotations<br />
** [https://docs.google.com/spreadsheets/d/15tIvSts5PcWidtMpXTQQfjFY3LTYcfjOc62Y5_FeRpU Protein Complex Oligomerization]<br />
** [https://docs.google.com/spreadsheets/d/1tVkRG81cfLxbrnS279RlJ-u1k20ee_NwHRXlWKUeWuo Regulation of Protein Complex Oligomerization]<br />
* Molecular Function Annotations<br />
** [https://docs.google.com/spreadsheets/d/1xOvmAmg5agQxo11pqYa6sGvbuJhOIyRGkZRjrcZHF8s Protein Dimerization Activity (includes regulation of activity)]<br />
** For MF annotations using the IPI evidence code, we are proposing term merges, so curators hopefully will not have to do manual revision here (programmatic upgrades can be done locally?)<br />
*** For example, protein homodimerization activity, should be handled by merging into 'identical protein binding'<br />
**However, there are some evidence code issues/questions that we should review<br />
*** For IC, NAS, and TAS evidence codes, recommend upgrading to an experimentally supported annotation or removing<br />
** For IDA annotations, we'd like to convert as many of those as possible into IPI, even if the With field will contain the same ID as the annotated entity. This allows for consistent representation of binding annotations in GO.<br />
*** ~1200 IDA annotations to 'protein homodimerization activity'. These should be automatically converted (locally) to 'identical protein binding' using IPI and the annotated entity in the With field.<br />
*** ~350 IDA annotations to 'protein heterodimerization activity'. Are these all cases where the interactor could not be assigned an ID? Or are these cases where curators didn't feel the assay fit with IPI?<br />
** There are also IGI, IMP, and RCA annotations - can any of these be converted to IPI (if there isn't a corresponding IPI already)<br />
*** IGI (4) to 'protein heterodimerization activity' - are these supporting evidence in addition to IPI? Or something else?<br />
*** IMP (133) to one of the MF terms - are these supporting evidence in addition to IPI? Or something else?<br />
*** RCA (21) to one of the MF terms - most of these are older annotations from Gramene, a handful from AgBase<br />
* [https://gitter.im/geneontology/go-annotation Gitter question] from Petra<br />
<br />
== QC Reports ==<br />
<br />
=== Pipeline Reports ===<br />
<br />
*[http://snapshot.geneontology.org/reports/index.html snapshot reports]<br />
<br />
=== Matrix QC checks ===<br />
* How is this work going for people?<br />
* Questions, comments?<br />
<br />
== GO-CAMs and Annotation Extensions ==<br />
* After USC hackathon in June, we formed a small working group to fully articulate the GO-CAM model specifications<br />
* This will allow uniform QC across workbenches, projects (e.g. Reactome and MOD imports)<br />
* Will also allow us to move forward with harmonizing AE relations used in GO-CAM and conventional annotation<br />
<br />
= Minutes =<br />
*Present: Birgit, Bob, David, Dmitry, Edith, Giulia, Harold, Karen, Kimberly, Laurent-Philippe, Midori, Pascale, Petra, Sabrina, Suzi, Tanya, Tom<br />
<br />
[[Category:Annotation Working Group]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_complexes&diff=72779Protein complexes2019-01-29T09:31:04Z<p>Bmeldal: </p>
<hr />
<div><br />
<br />
=Definition of a Protein Complex=<br />
A cellular component should include more than one gene product; complexes of one gene product with a cofactor, e.g. heme and chlorophyll, should not be included. Homomultimeric proteins, e.g. the homodimeric alcohol dehydrogenase, may be included as cellular component terms, as should heteromultimeric proteins, e.g. hemoglobin with alpha and beta chains. All complexes in the component ontology should be given parentage under the general term GO:0032991 protein-containing complex. To distinguish cellular components from functions, use 'complex' in the term name of a component, and append enzyme names with the word 'activity'. For example, the molecular function term GO:0004738 pyruvate dehydrogenase activity describes the enzyme activity whereas the cellular component term GO:0005967 mitochondrial pyruvate dehydrogenase complex describes the multi-subunit structure in which the enzyme activity resides.<br />
<br />
=Receptor-ligand complexes=<br />
As a rule, GO terms to indicate association of a receptor with its ligand should not be created, as their complex may not always be stable, and there could be a potential explosion of terms. However, we should allow for exceptions. The Complex Portal database wouldn't curate receptor-ligand complexes if these consisted of a single chain of each, but it will curate complexes when the ligand is not monomeric and receptors oligomerize upon ligand binding. An example of this is GO:1990270 'platelet-derived growth factor receptor-ligand complex', where the ligands are always dimeric and the receptor dimerizes upon ligand binding. (Also, in the case of GO:1990270, the complex has been shown to exist in a variety of experiments, including crystals, pull downs, comigrations, competition assays and more.)<br />
<br />
<br />
=Notes from working group=<br />
*NOTE: This is a work in progress and includes continuing discussion with Complex Portal as well as the GOC.<br />
*Last updated: 9/6/2015, Paola. Minor updates: 29/1/19, Birgit.<br />
<br />
*Main working group 2019: Birgit, Kimberly, Pascale, Harold, Val, Edith, Leonore, Helen, Sandra, Peter.<br />
<br />
== Background and rationale ==<br />
<br />
Recently, GO and Complex Portal have started to work together to improve the 'protein complex' branch in GO, making it less flat and more informative, and to provide species-agnostic GO terms that Complex Portal can reference to for their species-specific curation projects, namely the [http://www.ebi.ac.uk/complexportal/ Complex Portal]. At the time of writing (Spring 2015) the focus of the Complex Portal lies on human, mouse, yeast and E.coli, but it can take direct curation requests as well (please ). Other MODs are encouraged to collaborate directly. <br />
<br />
Here, we collect current guidelines on protein complex terms, to aid GO curators in discerning whether a protein complex belongs in GO or not, and if yes, in including all necessary information when requesting a new protein complex.<br />
<br />
== Protein complexes in GO ==<br />
<br />
=== Rule 1: Is the complex stable? ===<br />
<br />
In GO, 'protein complex' is defined as "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical."<br />
<br />
When in doubt, how can a curator figure out if a complex is really stable?<br />
<br />
We can refer to the Complex Portal Rules [http://www.ebi.ac.uk/complexportal/documentation/]. These are reported below for reference, and in a definition comment to 'protein complex' to serve as annotation guidance:<br />
<br />
===== What can be described as a complex? =====<br />
<br />
'''A stable set of (two or more) interacting macromolecules such as proteins which can be co-purified by an acceptable method and have been shown to exist as an isolated, functional unit in vivo. Any interacting non-protein molecules (e.g. small molecules, nucleic acids) will also be included.'''<br />
<br />
===== What should not be captured: =====<br />
*Enzyme/substrate, receptor/ligand or any similar transient interactions unless these are a critical part of the complex assembly (e.g. PDGF receptors only become 'dimeric' when linked by the dimeric ligand forming a tetramer).<br />
*Proteins associated in a pulldown/coimmunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose affinity complex.<br />
*Any literature complex where the only evidence is based on genetic interaction data.<br />
*Partial complexes.<br />
<br />
Note:<br />
*If the complex is not stable, it's just protein binding. Interactions can then be captured by a protein-protein interaction DB such as IntAct. <br />
*Beware of partial complexes shown experimentally, especially when crystallised. Some subunits (e.g. transmembrane subunits) cannot be expressed as recombinant proteins and are 'left out' of detailed studies. More reading is often necessary to find out what the full complex is thought to be.<br />
<br />
===== Tricky cases we DO (or could) capture in the Complex Portal: =====<br />
<br />
*Substrates or ligands if the enzyme or receptor complex only forms in their presence (see PDGF receptors above, e.g. [http://www.ebi.ac.uk/complexportal/complex/CPX-2883 CPX-2883]). These terms would also qualify for GO.<br />
<br />
*Homologous proteins, with the same functionality, which would be inferred by sequence similarity to form a complex but for which no physical link has been demonstrated, e.g. proteins A and B have been shown to physically interact and form a functional complex, protein C is a homologue of protein B by sequence similarity and is know to have the same function as B but protein A-C interaction has not been demonstrated experimentally. E.g. SUMO - E1 ligase complexes where there is interaction evidence for binding with SUMO1 ([http://www.ebi.ac.uk/complexportal/complex/CPX-3042 CPX-3042]) but not with SUMO2 ([http://www.ebi.ac.uk/complexportal/complex/CPX-3044 CPX-3044]).<br />
<br />
*The Complex Portal could also hold transient complexes, e.g. signaling complexes. We have not created any of these to date but they are possible, and controlled vocabulary terms exist to distinguish the two classes. BUT - they would probably fall outside the scope of GO if GO limit themselves to stable complexes.<br />
<br />
*We can also curate complexes that lack full experimental evidence but are commonly regarded as existing, e.g. complexes submitted by ChEMBL for which we only have pharmacological evidence. These complexes are tagged with ECO:0005547 - inferred from background scientific knowledge by manual assertion. E.g GABA ([http://www.ebi.ac.uk/complexportal/complex/CPX-410 CPX-410]) receptors and many other transmembrane receptors.<br />
<br />
===== Expanded definition comment for GO:0032991 'protein-containing complex’: =====<br />
<br />
"A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole."<br />
<br />
=== Rule 2: Is the complex species-agnostic? ===<br />
<br />
*GO should host species-agnostic complexes, ideally conserved across taxa. Where this isn't known, we should still make the definition generic, and add 'For example, in human this complex contains...' as a definition gloss or definition comment.<br />
<br />
*Species-specific complexes don't belong in GO, but Complex Portal and/or PRO can take them. (We acknowledge that GO contains many historic terms that contravene this rule. For the time being, the agreement is that we will not review them globally, though we may fix them if and when we come across them.)<br />
<br />
*We may, however, need taxon restrictions on a case-by-case basis such as complexes that only exist in prokaryotes or eukaryotes. Curators are encouraged to provide these information, if applicable, when they request a new term (or come across an existing one).<br />
<br />
=== Rule 3: Does the complex have a molecular function? ===<br />
<br />
*If yes, add capable_of link(s) to molecular function terms. These links are used by the reasoner to place the complex into the correct branch under 'protein complex'.<br />
<br />
=== Rule 4: Is the complex known to be involved in one or more biological processes? ===<br />
<br />
*If yes, add capable_of_part_of links to biological process(es).<br />
<br />
*Note: we decided not to use BP as a qualifier for making grouping terms for complexes as these would become too unspecific, e.g. 'regulatory complex' could include most complexes!<br />
<br />
=== Rule 5: Does the complex contain conserved subunits? ===<br />
<br />
*Many complexes are defined by their subunit composition rather than their activity. Such complexes will still be accepted into the GO. The curator should endeavour to place the new complex as child of a functional parent or a parent term also defined by its composition, in some cases this may be difficult and those complex terms will be direct children of 'protein complex'.<br />
<br />
*Complex definitions should include their function or the process they are involved in as well as the defining subunits (using the style "In human, it is composed of..."). However, we need to be careful not to explode the subunit composition in the definition if they turn out to be rather different in the different branches of the tree of life. In such a situation, the curator and editor should consider broadening the term name and adding the various subunit-defined names as narrow synonyms. This should be handled on a case-by-case basis.<br />
<br />
*Complexes defined by their subunits but functionally identical to a more generic parent term should not be created as separate GO terms but added to the parent term as narrow synonyms. The specific complex belongs in the Complex Portal.<br />
<br />
[DOS to look into some automatic reasoning across subunits but we think it may become tricky. To be discussed among editors.]<br />
<br />
=== Rule 6: Where is the complex located? ===<br />
<br />
*Indicate cellular location as specifically as possible, unless parent already has one.<br />
<br />
*The CC location is meant for the complex as a whole. We discussed this in the context of transmembrane complexes where one or more members of the complex are located on one side of the membrane only or have no membrane attachment at all. As gene products have the part_of relationship with the complexes this is fine (and the only way of reflecting the CC for the complex as a whole).<br />
<br />
*If we have complexes defined by their location (see below under 'Futures Plans'), does the reasoner take the part_of relationship to place them automatically into the right complex-by-location branch? [DOS?]<br />
<br />
*Complexes simply defined by the cell type they are expressed in are not permitted.<br />
<br />
=== Rule 7: Adding appropriate is_a relationships ===<br />
<br />
*We are trying to avoid placing complexes as direct is_a children of 'protein-containing complex', by adding some granularity to this ontology branch.<br />
<br />
*An is_a parent of a complex can be a <br />
# complex defined by its activity, via the complex-by-activity TG template<br />
# complex defined by its location, such as 'plasma membrane complex'. [Update: DOS added some useful protein complex grouping terms based on location, such as 'membrane protein complex'.]<br />
# complex defined by its subunit composition. This may be related to protein families but it may be difficult to make it a rule/template (see above).<br />
*We decided NOT to define complexes by their process or MF binding as they would become too generic.<br />
<br />
*Note: Complexes can have multiple parents!<br />
<br />
*Note: if capable_of MF links are added, and/or if location information is provided as part_of CC, the automatic assert-inference script will take care of placing most newly created protein complex terms more granularly in the ontology.<br />
<br />
=== Rule 8: Adding appropriate part_of relationships ===<br />
<br />
*All complexes should have a part_of link to a cellular component term, even if it's very generic, such as 'cell'.<br />
*CC does not have to be added manually if it's the same as the parent term as it will be inferred.<br />
*If the CC is more specific than the parent, the part_of relationship must be added manually.<br />
*Complexes can be subcomplexes of larger entities and can therefore be part_of another protein complex. If the larger complex necessarily needs the smaller one as its component in order to be functional, a has_part link should also be added (larger complex has_part smaller complex).<br />
*Complexes cannot have several part_of relationships to different CCs, as part_of must ALWAYS be true. If a complex can be part of several larger complexes or be found in several locations, such as cytoplasm and nucleus where it may have different functions, separate terms may have to be considered. [This point is still open to discussion, see https://sourceforge.net/p/geneontology/ontology-requests/10745/, now with DOS. To be discussed on Editor's call.]<br />
<br />
== How to request protein complexes in GO based on the above ==<br />
<br />
*Use the GO-ontology GitHub tracker https://github.com/geneontology/go-ontology/issues<br />
<br />
*Name:<br />
*Definition:<br />
*relationships: is_a [complex parent], part_of [subcellular location], capable_of MF, capable_of_part_of BP<br />
*Synonym(s):<br />
<br />
*We no longer require dbxrefs to the Complex Portal as these will be directly imported.<br />
<br />
*Complex Portal is happy to curate requested complexes at the same time as adding to the GO structure. Curators are encouraged to curate complexes directly into the Complex Portal after being trained by us. SGD and UCL are doing this already. Contact us via the yellow "request complex" tile on the home page: http://www.ebi.ac.uk/complexportal/<br />
<br />
== Complex Definition field ==<br />
<br />
The way definitions of older protein complex terms are structured is not always consistent. Currently, we recommend the following:<br />
<br />
*Start the definition referring to the function (if applicable), such as 'A protein complex capable of X function...'.<br />
<br />
*Processes can also be mentioned in the def. <br />
<br />
*Subunits should only be listed in the definition if the complex is defined by its composition rather than function (see Rule 5 above). If the complex is defined by its function, subunit composition should go into a definition comment or be added as narrow synonyms.<br />
<br />
*Complexes should NOT be defined by their stoichiometry, though this may be mentioned in the def as a 'soft' comment (definition gloss), or in a definition comment. The rationale behind this recommendation is that, as knowledge advances and more examples are found, stoichiometry defs would have to be updated, causing a lot of work. It is perfectly fine though to mention something like 'usually consists of a catalytic and a regulatory subunit and possibly further accessory subunits...'. <br />
<br />
*We are aware that many older terms' definitions do not conform to these guidelines. At the moment, however, we do not plan on fixing all of them. We may make corrections on a case-by-case basis and/or when working on a given branch.<br />
<br />
== Future plans ==<br />
as discussed in a meeting with Birgit Meldal, Sandra Orchard, David Osumi-Sunderland and Paola Roncaglia on 28/4/2015<br />
<br />
We discussed how we can make 'quick gains' in making the ontology more granular beyond the fixes Birgit does on a case by case basis. This is to target historic terms that have only 'protein complex' as a parent because they have no annotation extensions. The aim is to have most complexes grouped either by their function, location or subunit composition.<br />
<br />
*Do a pass through term names and definitions to find major groups of complexes that can be grouped by function, e.g. 'catalytic complex' (the term exists but many historic terms have not automatically been classified as such as they have no capable_of extensions). Other keywords: kinase, activity, viral, receptor, respiratory chain... [BM, SO & DOS]<br />
<br />
*Add parent terms based on location, such as 'membrane complex' and children or 'mitochondrial complex'. Can the reasoner place complexes automatically into this branch based on their part_of relationship (see above Rule 6)? Should we have a TG template for this? [BM, DOS]<br />
<br />
*Combine activity and location, such as 'membrane receptor complex'.<br />
<br />
*We discussed grouping by protein families but this may be tricky. Decide on a case by case basis. A working example are the BCL protein family complexes which cannot be grouped by function as they may be pro- and/or antiapoptotic.<br />
<br />
== Previous work ==<br />
<br />
Emily started documentation here, in case it's helpful, but this wasn't worked on since 2011:<br />
http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects<br />
<br />
<br />
Birgit's comments [from email to Paola]: <br />
<br />
Inheritance of annotations:<br />
I agree with the wiki, you cannot inherit MF from a complex to a subunit and even a CC is problematic, see the transmembrane example above. This needs more thinking about. I don't know what you are doing right now...<br />
<br />
Orthologies:<br />
We infer within taxon groups, e.g. human to mouse to rat or any other mammal etc, depending on where the exp evidence comes from. We systematically infer human-mouse. We have a few pombe complexes inferred from yeast (Sc!) but we don't do it systematically.<br />
<br />
Paralogues:<br />
We make inferences between related complexes in the same species when the gene products are very similar, e.g. hemoglobin chains for adult and developmental complexes.<br />
<br />
'Large' complexes:<br />
We have tackled the 'mediator' and we can now link to RNACentral for RNAs so time permitting we'll tackle the 'biggies' soon!<br />
<br />
Pro:<br />
We have a list of Pro complexes that we consult for refs.<br />
<br />
== Useful links ==<br />
<br />
Complex Portal, http://www.ebi.ac.uk/complexportal/<br />
<br />
<br />
----<br />
[[Category:GO Editors]][[Category:Ontology]]<br />
[[Notes_on_specific_terms |Back to: Notes on specific terms]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_complexes&diff=72778Protein complexes2019-01-29T09:29:01Z<p>Bmeldal: </p>
<hr />
<div><br />
<br />
=Definition of a Protein Complex=<br />
A cellular component should include more than one gene product; complexes of one gene product with a cofactor, e.g. heme and chlorophyll, should not be included. Homomultimeric proteins, e.g. the homodimeric alcohol dehydrogenase, may be included as cellular component terms, as should heteromultimeric proteins, e.g. hemoglobin with alpha and beta chains. All complexes in the component ontology should be given parentage under the general term GO:0032991 protein-containing complex. To distinguish cellular components from functions, use 'complex' in the term name of a component, and append enzyme names with the word 'activity'. For example, the molecular function term GO:0004738 pyruvate dehydrogenase activity describes the enzyme activity whereas the cellular component term GO:0005967 mitochondrial pyruvate dehydrogenase complex describes the multi-subunit structure in which the enzyme activity resides.<br />
<br />
=Receptor-ligand complexes=<br />
As a rule, GO terms to indicate association of a receptor with its ligand should not be created, as their complex may not always be stable, and there could be a potential explosion of terms. However, we should allow for exceptions. The Complex Portal database wouldn't curate receptor-ligand complexes if these consisted of a single chain of each, but it will curate complexes when the ligand is not monomeric and receptors oligomerize upon ligand binding. An example of this is GO:1990270 'platelet-derived growth factor receptor-ligand complex', where the ligands are always dimeric and the receptor dimerizes upon ligand binding. (Also, in the case of GO:1990270, the complex has been shown to exist in a variety of experiments, including crystals, pull downs, comigrations, competition assays and more.)<br />
<br />
<br />
=Notes from working group=<br />
*NOTE: This is a work in progress and includes continuing discussion with Complex Portal as well as the GOC.<br />
*Last updated: 9/6/2015, Paola. Minor updates: 29/1/19, Birgit.<br />
<br />
*Main working group 2019: Birgit, Kimberly, Pascale, Harold, Val, Edith, Leonore, Helen, Sandra, Peter.<br />
<br />
== Background and rationale ==<br />
<br />
Recently, GO and Complex Portal have started to work together to improve the 'protein complex' branch in GO, making it less flat and more informative, and to provide species-agnostic GO terms that Complex Portal can reference to for their species-specific curation projects, namely the [http://www.ebi.ac.uk/complexportal/ Complex Portal]. At the time of writing (Spring 2015) the focus of the Complex Portal lies on human, mouse, yeast and E.coli, but it can take direct curation requests as well (please ). Other MODs are encouraged to collaborate directly. <br />
<br />
Here, we collect current guidelines on protein complex terms, to aid GO curators in discerning whether a protein complex belongs in GO or not, and if yes, in including all necessary information when requesting a new protein complex.<br />
<br />
== Protein complexes in GO ==<br />
<br />
=== Rule 1: Is the complex stable? ===<br />
<br />
In GO, 'protein complex' is defined as "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical."<br />
<br />
When in doubt, how can a curator figure out if a complex is really stable?<br />
<br />
We can refer to the Complex Portal Rules [http://www.ebi.ac.uk/complexportal/documentation/]. These are reported below for reference, and in a definition comment to 'protein complex' to serve as annotation guidance:<br />
<br />
===== What can be described as a complex? =====<br />
<br />
'''A stable set of (two or more) interacting macromolecules such as proteins which can be co-purified by an acceptable method and have been shown to exist as an isolated, functional unit in vivo. Any interacting non-protein molecules (e.g. small molecules, nucleic acids) will also be included.'''<br />
<br />
===== What should not be captured: =====<br />
*Enzyme/substrate, receptor/ligand or any similar transient interactions unless these are a critical part of the complex assembly (e.g. PDGF receptors only become 'dimeric' when linked by the dimeric ligand forming a tetramer).<br />
*Proteins associated in a pulldown/coimmunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose affinity complex.<br />
*Any literature complex where the only evidence is based on genetic interaction data.<br />
*Partial complexes.<br />
<br />
Note:<br />
*If the complex is not stable, it's just protein binding. Interactions can then be captured by a protein-protein interaction DB such as IntAct. <br />
*Beware of partial complexes shown experimentally, especially when crystallised. Some subunits (e.g. transmembrane subunits) cannot be expressed as recombinant proteins and are 'left out' of detailed studies. More reading is often necessary to find out what the full complex is thought to be.<br />
<br />
===== Tricky cases we DO (or could) capture in the Complex Portal: =====<br />
<br />
*Substrates or ligands if the enzyme or receptor complex only forms in their presence (see PDGF receptors above, e.g. [http://www.ebi.ac.uk/complexportal/complex/CPX-2883 CPX-2883]). These terms would also qualify for GO.<br />
<br />
*Homologous proteins, with the same functionality, which would be inferred by sequence similarity to form a complex but for which no physical link has been demonstrated, e.g. proteins A and B have been shown to physically interact and form a functional complex, protein C is a homologue of protein B by sequence similarity and is know to have the same function as B but protein A-C interaction has not been demonstrated experimentally. E.g. SUMO - E1 ligase complexes where there is interaction evidence for binding with SUMO1 ([http://www.ebi.ac.uk/complexportal/complex/CPX-3042 CPX-3042]) but not with SUMO2 ([http://www.ebi.ac.uk/complexportal/complex/CPX-3044 CPX-3044]).<br />
<br />
*The Complex Portal could also hold transient complexes, e.g. signaling complexes. We have not created any of these to date but they are possible, and controlled vocabulary terms exist to distinguish the two classes. BUT - they would probably fall outside the scope of GO if GO limit themselves to stable complexes.<br />
<br />
*We can also curate complexes that lack full experimental evidence but are commonly regarded as existing, e.g. complexes submitted by ChEMBL for which we only have pharmacological evidence. These complexes are tagged with ECO:0005547 - inferred from background scientific knowledge by manual assertion. E.g GABA ([http://www.ebi.ac.uk/complexportal/complex/CPX-2159 CPX-2159]) receptors and many other transmembrane receptors.<br />
<br />
===== Expanded definition comment for GO:0032991 'protein-containing complex’: =====<br />
<br />
"A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole."<br />
<br />
=== Rule 2: Is the complex species-agnostic? ===<br />
<br />
*GO should host species-agnostic complexes, ideally conserved across taxa. Where this isn't known, we should still make the definition generic, and add 'For example, in human this complex contains...' as a definition gloss or definition comment.<br />
<br />
*Species-specific complexes don't belong in GO, but Complex Portal and/or PRO can take them. (We acknowledge that GO contains many historic terms that contravene this rule. For the time being, the agreement is that we will not review them globally, though we may fix them if and when we come across them.)<br />
<br />
*We may, however, need taxon restrictions on a case-by-case basis such as complexes that only exist in prokaryotes or eukaryotes. Curators are encouraged to provide these information, if applicable, when they request a new term (or come across an existing one).<br />
<br />
=== Rule 3: Does the complex have a molecular function? ===<br />
<br />
*If yes, add capable_of link(s) to molecular function terms. These links are used by the reasoner to place the complex into the correct branch under 'protein complex'.<br />
<br />
=== Rule 4: Is the complex known to be involved in one or more biological processes? ===<br />
<br />
*If yes, add capable_of_part_of links to biological process(es).<br />
<br />
*Note: we decided not to use BP as a qualifier for making grouping terms for complexes as these would become too unspecific, e.g. 'regulatory complex' could include most complexes!<br />
<br />
=== Rule 5: Does the complex contain conserved subunits? ===<br />
<br />
*Many complexes are defined by their subunit composition rather than their activity. Such complexes will still be accepted into the GO. The curator should endeavour to place the new complex as child of a functional parent or a parent term also defined by its composition, in some cases this may be difficult and those complex terms will be direct children of 'protein complex'.<br />
<br />
*Complex definitions should include their function or the process they are involved in as well as the defining subunits (using the style "In human, it is composed of..."). However, we need to be careful not to explode the subunit composition in the definition if they turn out to be rather different in the different branches of the tree of life. In such a situation, the curator and editor should consider broadening the term name and adding the various subunit-defined names as narrow synonyms. This should be handled on a case-by-case basis.<br />
<br />
*Complexes defined by their subunits but functionally identical to a more generic parent term should not be created as separate GO terms but added to the parent term as narrow synonyms. The specific complex belongs in the Complex Portal.<br />
<br />
[DOS to look into some automatic reasoning across subunits but we think it may become tricky. To be discussed among editors.]<br />
<br />
=== Rule 6: Where is the complex located? ===<br />
<br />
*Indicate cellular location as specifically as possible, unless parent already has one.<br />
<br />
*The CC location is meant for the complex as a whole. We discussed this in the context of transmembrane complexes where one or more members of the complex are located on one side of the membrane only or have no membrane attachment at all. As gene products have the part_of relationship with the complexes this is fine (and the only way of reflecting the CC for the complex as a whole).<br />
<br />
*If we have complexes defined by their location (see below under 'Futures Plans'), does the reasoner take the part_of relationship to place them automatically into the right complex-by-location branch? [DOS?]<br />
<br />
*Complexes simply defined by the cell type they are expressed in are not permitted.<br />
<br />
=== Rule 7: Adding appropriate is_a relationships ===<br />
<br />
*We are trying to avoid placing complexes as direct is_a children of 'protein-containing complex', by adding some granularity to this ontology branch.<br />
<br />
*An is_a parent of a complex can be a <br />
# complex defined by its activity, via the complex-by-activity TG template<br />
# complex defined by its location, such as 'plasma membrane complex'. [Update: DOS added some useful protein complex grouping terms based on location, such as 'membrane protein complex'.]<br />
# complex defined by its subunit composition. This may be related to protein families but it may be difficult to make it a rule/template (see above).<br />
*We decided NOT to define complexes by their process or MF binding as they would become too generic.<br />
<br />
*Note: Complexes can have multiple parents!<br />
<br />
*Note: if capable_of MF links are added, and/or if location information is provided as part_of CC, the automatic assert-inference script will take care of placing most newly created protein complex terms more granularly in the ontology.<br />
<br />
=== Rule 8: Adding appropriate part_of relationships ===<br />
<br />
*All complexes should have a part_of link to a cellular component term, even if it's very generic, such as 'cell'.<br />
*CC does not have to be added manually if it's the same as the parent term as it will be inferred.<br />
*If the CC is more specific than the parent, the part_of relationship must be added manually.<br />
*Complexes can be subcomplexes of larger entities and can therefore be part_of another protein complex. If the larger complex necessarily needs the smaller one as its component in order to be functional, a has_part link should also be added (larger complex has_part smaller complex).<br />
*Complexes cannot have several part_of relationships to different CCs, as part_of must ALWAYS be true. If a complex can be part of several larger complexes or be found in several locations, such as cytoplasm and nucleus where it may have different functions, separate terms may have to be considered. [This point is still open to discussion, see https://sourceforge.net/p/geneontology/ontology-requests/10745/, now with DOS. To be discussed on Editor's call.]<br />
<br />
== How to request protein complexes in GO based on the above ==<br />
<br />
*Use the GO-ontology GitHub tracker https://github.com/geneontology/go-ontology/issues<br />
<br />
*Name:<br />
*Definition:<br />
*relationships: is_a [complex parent], part_of [subcellular location], capable_of MF, capable_of_part_of BP<br />
*Synonym(s):<br />
<br />
*We no longer require dbxrefs to the Complex Portal as these will be directly imported.<br />
<br />
*Complex Portal is happy to curate requested complexes at the same time as adding to the GO structure. Curators are encouraged to curate complexes directly into the Complex Portal after being trained by us. SGD and UCL are doing this already. Contact us via the yellow "request complex" tile on the home page: http://www.ebi.ac.uk/complexportal/<br />
<br />
== Complex Definition field ==<br />
<br />
The way definitions of older protein complex terms are structured is not always consistent. Currently, we recommend the following:<br />
<br />
*Start the definition referring to the function (if applicable), such as 'A protein complex capable of X function...'.<br />
<br />
*Processes can also be mentioned in the def. <br />
<br />
*Subunits should only be listed in the definition if the complex is defined by its composition rather than function (see Rule 5 above). If the complex is defined by its function, subunit composition should go into a definition comment or be added as narrow synonyms.<br />
<br />
*Complexes should NOT be defined by their stoichiometry, though this may be mentioned in the def as a 'soft' comment (definition gloss), or in a definition comment. The rationale behind this recommendation is that, as knowledge advances and more examples are found, stoichiometry defs would have to be updated, causing a lot of work. It is perfectly fine though to mention something like 'usually consists of a catalytic and a regulatory subunit and possibly further accessory subunits...'. <br />
<br />
*We are aware that many older terms' definitions do not conform to these guidelines. At the moment, however, we do not plan on fixing all of them. We may make corrections on a case-by-case basis and/or when working on a given branch.<br />
<br />
== Future plans ==<br />
as discussed in a meeting with Birgit Meldal, Sandra Orchard, David Osumi-Sunderland and Paola Roncaglia on 28/4/2015<br />
<br />
We discussed how we can make 'quick gains' in making the ontology more granular beyond the fixes Birgit does on a case by case basis. This is to target historic terms that have only 'protein complex' as a parent because they have no annotation extensions. The aim is to have most complexes grouped either by their function, location or subunit composition.<br />
<br />
*Do a pass through term names and definitions to find major groups of complexes that can be grouped by function, e.g. 'catalytic complex' (the term exists but many historic terms have not automatically been classified as such as they have no capable_of extensions). Other keywords: kinase, activity, viral, receptor, respiratory chain... [BM, SO & DOS]<br />
<br />
*Add parent terms based on location, such as 'membrane complex' and children or 'mitochondrial complex'. Can the reasoner place complexes automatically into this branch based on their part_of relationship (see above Rule 6)? Should we have a TG template for this? [BM, DOS]<br />
<br />
*Combine activity and location, such as 'membrane receptor complex'.<br />
<br />
*We discussed grouping by protein families but this may be tricky. Decide on a case by case basis. A working example are the BCL protein family complexes which cannot be grouped by function as they may be pro- and/or antiapoptotic.<br />
<br />
== Previous work ==<br />
<br />
Emily started documentation here, in case it's helpful, but this wasn't worked on since 2011:<br />
http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects<br />
<br />
<br />
Birgit's comments [from email to Paola]: <br />
<br />
Inheritance of annotations:<br />
I agree with the wiki, you cannot inherit MF from a complex to a subunit and even a CC is problematic, see the transmembrane example above. This needs more thinking about. I don't know what you are doing right now...<br />
<br />
Orthologies:<br />
We infer within taxon groups, e.g. human to mouse to rat or any other mammal etc, depending on where the exp evidence comes from. We systematically infer human-mouse. We have a few pombe complexes inferred from yeast (Sc!) but we don't do it systematically.<br />
<br />
Paralogues:<br />
We make inferences between related complexes in the same species when the gene products are very similar, e.g. hemoglobin chains for adult and developmental complexes.<br />
<br />
'Large' complexes:<br />
We have tackled the 'mediator' and we can now link to RNACentral for RNAs so time permitting we'll tackle the 'biggies' soon!<br />
<br />
Pro:<br />
We have a list of Pro complexes that we consult for refs.<br />
<br />
== Useful links ==<br />
<br />
Complex Portal, http://www.ebi.ac.uk/complexportal/<br />
<br />
<br />
----<br />
[[Category:GO Editors]][[Category:Ontology]]<br />
[[Notes_on_specific_terms |Back to: Notes on specific terms]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_complexes&diff=72777Protein complexes2019-01-29T09:24:08Z<p>Bmeldal: </p>
<hr />
<div><br />
<br />
=Definition of a Protein Complex=<br />
A cellular component should include more than one gene product; complexes of one gene product with a cofactor, e.g. heme and chlorophyll, should not be included. Homomultimeric proteins, e.g. the homodimeric alcohol dehydrogenase, may be included as cellular component terms, as should heteromultimeric proteins, e.g. hemoglobin with alpha and beta chains. All complexes in the component ontology should be given parentage under the general term GO:0032991 protein-containing complex. To distinguish cellular components from functions, use 'complex' in the term name of a component, and append enzyme names with the word 'activity'. For example, the molecular function term GO:0004738 pyruvate dehydrogenase activity describes the enzyme activity whereas the cellular component term GO:0005967 mitochondrial pyruvate dehydrogenase complex describes the multi-subunit structure in which the enzyme activity resides.<br />
<br />
=Receptor-ligand complexes=<br />
As a rule, GO terms to indicate association of a receptor with its ligand should not be created, as their complex may not always be stable, and there could be a potential explosion of terms. However, we should allow for exceptions. The Complex Portal database wouldn't curate receptor-ligand complexes if these consisted of a single chain of each, but it will curate complexes when the ligand is not monomeric and receptors oligomerize upon ligand binding. An example of this is GO:1990270 'platelet-derived growth factor receptor-ligand complex', where the ligands are always dimeric and the receptor dimerizes upon ligand binding. (Also, in the case of GO:1990270, the complex has been shown to exist in a variety of experiments, including crystals, pull downs, comigrations, competition assays and more.)<br />
<br />
<br />
=Notes from working group=<br />
*NOTE: This is a work in progress and includes continuing discussion with Complex Portal as well as the GOC.<br />
*Last updated: 9/6/2015, Paola. Minor updates: 29/1/19, Birgit.<br />
<br />
*Main working group 2019: Birgit, Kimberly, Pascale, Harold, Val, Edith, Leonore, Helen, Sandra, Peter.<br />
<br />
== Background and rationale ==<br />
<br />
Recently, GO and Complex Portal have started to work together to improve the 'protein complex' branch in GO, making it less flat and more informative, and to provide species-agnostic GO terms that Complex Portal can reference to for their species-specific curation projects, namely the [http://www.ebi.ac.uk/complexportal/ Complex Portal]. At the time of writing (Spring 2015) the focus of the Complex Portal lies on human, mouse, yeast and E.coli, but it can take direct curation requests as well (please ). Other MODs are encouraged to collaborate directly. <br />
<br />
Here, we collect current guidelines on protein complex terms, to aid GO curators in discerning whether a protein complex belongs in GO or not, and if yes, in including all necessary information when requesting a new protein complex.<br />
<br />
== Protein complexes in GO ==<br />
<br />
=== Rule 1: Is the complex stable? ===<br />
<br />
In GO, 'protein complex' is defined as "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical."<br />
<br />
When in doubt, how can a curator figure out if a complex is really stable?<br />
<br />
We can refer to the Complex Portal Rules [http://www.ebi.ac.uk/complexportal/documentation/]. These are reported below for reference, and in a definition comment to 'protein complex' to serve as annotation guidance:<br />
<br />
===== What can be described as a complex? =====<br />
<br />
'''A stable set of (two or more) interacting macromolecules such as proteins which can be co-purified by an acceptable method and have been shown to exist as an isolated, functional unit in vivo. Any interacting non-protein molecules (e.g. small molecules, nucleic acids) will also be included.'''<br />
<br />
===== What should not be captured: =====<br />
*Enzyme/substrate, receptor/ligand or any similar transient interactions unless these are a critical part of the complex assembly (e.g. PDGF receptors only become 'dimeric' when linked by the dimeric ligand forming a tetramer).<br />
*Proteins associated in a pulldown/coimmunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose affinity complex.<br />
*Any literature complex where the only evidence is based on genetic interaction data.<br />
*Partial complexes.<br />
<br />
Note:<br />
*If the complex is not stable, it's just protein binding. Interactions can then be captured by a protein-protein interaction DB such as IntAct. <br />
*Beware of partial complexes shown experimentally, especially when crystallised. Some subunits (e.g. transmembrane subunits) cannot be expressed as recombinant proteins and are 'left out' of detailed studies. More reading is often necessary to find out what the full complex is thought to be.<br />
<br />
===== Tricky cases we DO (or could) capture in the Complex Portal: =====<br />
<br />
*Substrates or ligands if the enzyme or receptor complex only forms in their presence (see PDGF receptors above, e.g. [http://www.ebi.ac.uk/complexportal/details/CPX-2883 CPX-2883]). These terms would also qualify for GO.<br />
<br />
*Homologous proteins, with the same functionality, which would be inferred by sequence similarity to form a complex but for which no physical link has been demonstrated, e.g. proteins A and B have been shown to physically interact and form a functional complex, protein C is a homologue of protein B by sequence similarity and is know to have the same function as B but protein A-C interaction has not been demonstrated experimentally. E.g. SUMO - E1 ligase complexes where there is interaction evidence for binding with SUMO1 ([http://www.ebi.ac.uk/complexportal/details/CPX-3042 CPX-3042]) but not with SUMO2 ([http://www.ebi.ac.uk/complexportal/details/CPX-3044 CPX-3044]).<br />
<br />
*The Complex Portal could also hold transient complexes, e.g. signaling complexes. We have not created any of these to date but they are possible, and controlled vocabulary terms exist to distinguish the two classes. BUT - they would probably fall outside the scope of GO if GO limit themselves to stable complexes.<br />
<br />
*We can also curate complexes that lack full experimental evidence but are commonly regarded as existing, e.g. complexes submitted by ChEMBL for which we only have pharmacological evidence. These complexes are tagged with ECO:0005547 - inferred from background scientific knowledge by manual assertion. E.g GABA ([http://www.ebi.ac.uk/complexportal/details/CPX-2159 CPX-2159]) receptors and many other transmembrane receptors.<br />
<br />
===== Expanded definition comment for GO:0032991 'protein-containing complex’: =====<br />
<br />
"A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole."<br />
<br />
=== Rule 2: Is the complex species-agnostic? ===<br />
<br />
*GO should host species-agnostic complexes, ideally conserved across taxa. Where this isn't known, we should still make the definition generic, and add 'For example, in human this complex contains...' as a definition gloss or definition comment.<br />
<br />
*Species-specific complexes don't belong in GO, but Complex Portal and/or PRO can take them. (We acknowledge that GO contains many historic terms that contravene this rule. For the time being, the agreement is that we will not review them globally, though we may fix them if and when we come across them.)<br />
<br />
*We may, however, need taxon restrictions on a case-by-case basis such as complexes that only exist in prokaryotes or eukaryotes. Curators are encouraged to provide these information, if applicable, when they request a new term (or come across an existing one).<br />
<br />
=== Rule 3: Does the complex have a molecular function? ===<br />
<br />
*If yes, add capable_of link(s) to molecular function terms. These links are used by the reasoner to place the complex into the correct branch under 'protein complex'.<br />
<br />
=== Rule 4: Is the complex known to be involved in one or more biological processes? ===<br />
<br />
*If yes, add capable_of_part_of links to biological process(es).<br />
<br />
*Note: we decided not to use BP as a qualifier for making grouping terms for complexes as these would become too unspecific, e.g. 'regulatory complex' could include most complexes!<br />
<br />
=== Rule 5: Does the complex contain conserved subunits? ===<br />
<br />
*Many complexes are defined by their subunit composition rather than their activity. Such complexes will still be accepted into the GO. The curator should endeavour to place the new complex as child of a functional parent or a parent term also defined by its composition, in some cases this may be difficult and those complex terms will be direct children of 'protein complex'.<br />
<br />
*Complex definitions should include their function or the process they are involved in as well as the defining subunits (using the style "In human, it is composed of..."). However, we need to be careful not to explode the subunit composition in the definition if they turn out to be rather different in the different branches of the tree of life. In such a situation, the curator and editor should consider broadening the term name and adding the various subunit-defined names as narrow synonyms. This should be handled on a case-by-case basis.<br />
<br />
*Complexes defined by their subunits but functionally identical to a more generic parent term should not be created as separate GO terms but added to the parent term as narrow synonyms. The specific complex belongs in the Complex Portal.<br />
<br />
[DOS to look into some automatic reasoning across subunits but we think it may become tricky. To be discussed among editors.]<br />
<br />
=== Rule 6: Where is the complex located? ===<br />
<br />
*Indicate cellular location as specifically as possible, unless parent already has one.<br />
<br />
*The CC location is meant for the complex as a whole. We discussed this in the context of transmembrane complexes where one or more members of the complex are located on one side of the membrane only or have no membrane attachment at all. As gene products have the part_of relationship with the complexes this is fine (and the only way of reflecting the CC for the complex as a whole).<br />
<br />
*If we have complexes defined by their location (see below under 'Futures Plans'), does the reasoner take the part_of relationship to place them automatically into the right complex-by-location branch? [DOS?]<br />
<br />
*Complexes simply defined by the cell type they are expressed in are not permitted.<br />
<br />
=== Rule 7: Adding appropriate is_a relationships ===<br />
<br />
*We are trying to avoid placing complexes as direct is_a children of 'protein-containing complex', by adding some granularity to this ontology branch.<br />
<br />
*An is_a parent of a complex can be a <br />
# complex defined by its activity, via the complex-by-activity TG template<br />
# complex defined by its location, such as 'plasma membrane complex'. [Update: DOS added some useful protein complex grouping terms based on location, such as 'membrane protein complex'.]<br />
# complex defined by its subunit composition. This may be related to protein families but it may be difficult to make it a rule/template (see above).<br />
*We decided NOT to define complexes by their process or MF binding as they would become too generic.<br />
<br />
*Note: Complexes can have multiple parents!<br />
<br />
*Note: if capable_of MF links are added, and/or if location information is provided as part_of CC, the automatic assert-inference script will take care of placing most newly created protein complex terms more granularly in the ontology.<br />
<br />
=== Rule 8: Adding appropriate part_of relationships ===<br />
<br />
*All complexes should have a part_of link to a cellular component term, even if it's very generic, such as 'cell'.<br />
*CC does not have to be added manually if it's the same as the parent term as it will be inferred.<br />
*If the CC is more specific than the parent, the part_of relationship must be added manually.<br />
*Complexes can be subcomplexes of larger entities and can therefore be part_of another protein complex. If the larger complex necessarily needs the smaller one as its component in order to be functional, a has_part link should also be added (larger complex has_part smaller complex).<br />
*Complexes cannot have several part_of relationships to different CCs, as part_of must ALWAYS be true. If a complex can be part of several larger complexes or be found in several locations, such as cytoplasm and nucleus where it may have different functions, separate terms may have to be considered. [This point is still open to discussion, see https://sourceforge.net/p/geneontology/ontology-requests/10745/, now with DOS. To be discussed on Editor's call.]<br />
<br />
== How to request protein complexes in GO based on the above ==<br />
<br />
*Use the GO-ontology GitHub tracker https://github.com/geneontology/go-ontology/issues<br />
<br />
*Name:<br />
*Definition:<br />
*relationships: is_a [complex parent], part_of [subcellular location], capable_of MF, capable_of_part_of BP<br />
*Synonym(s):<br />
<br />
*We no longer require dbxrefs to the Complex Portal as these will be directly imported.<br />
<br />
*Complex Portal is happy to curate requested complexes at the same time as adding to the GO structure. Curators are encouraged to curate complexes directly into the Complex Portal after being trained by us. SGD and UCL are doing this already. Contact us via the yellow "request complex" tile on the home page: http://www.ebi.ac.uk/complexportal/<br />
<br />
== Complex Definition field ==<br />
<br />
The way definitions of older protein complex terms are structured is not always consistent. Currently, we recommend the following:<br />
<br />
*Start the definition referring to the function (if applicable), such as 'A protein complex capable of X function...'.<br />
<br />
*Processes can also be mentioned in the def. <br />
<br />
*Subunits should only be listed in the definition if the complex is defined by its composition rather than function (see Rule 5 above). If the complex is defined by its function, subunit composition should go into a definition comment or be added as narrow synonyms.<br />
<br />
*Complexes should NOT be defined by their stoichiometry, though this may be mentioned in the def as a 'soft' comment (definition gloss), or in a definition comment. The rationale behind this recommendation is that, as knowledge advances and more examples are found, stoichiometry defs would have to be updated, causing a lot of work. It is perfectly fine though to mention something like 'usually consists of a catalytic and a regulatory subunit and possibly further accessory subunits...'. <br />
<br />
*We are aware that many older terms' definitions do not conform to these guidelines. At the moment, however, we do not plan on fixing all of them. We may make corrections on a case-by-case basis and/or when working on a given branch.<br />
<br />
== Future plans ==<br />
as discussed in a meeting with Birgit Meldal, Sandra Orchard, David Osumi-Sunderland and Paola Roncaglia on 28/4/2015<br />
<br />
We discussed how we can make 'quick gains' in making the ontology more granular beyond the fixes Birgit does on a case by case basis. This is to target historic terms that have only 'protein complex' as a parent because they have no annotation extensions. The aim is to have most complexes grouped either by their function, location or subunit composition.<br />
<br />
*Do a pass through term names and definitions to find major groups of complexes that can be grouped by function, e.g. 'catalytic complex' (the term exists but many historic terms have not automatically been classified as such as they have no capable_of extensions). Other keywords: kinase, activity, viral, receptor, respiratory chain... [BM, SO & DOS]<br />
<br />
*Add parent terms based on location, such as 'membrane complex' and children or 'mitochondrial complex'. Can the reasoner place complexes automatically into this branch based on their part_of relationship (see above Rule 6)? Should we have a TG template for this? [BM, DOS]<br />
<br />
*Combine activity and location, such as 'membrane receptor complex'.<br />
<br />
*We discussed grouping by protein families but this may be tricky. Decide on a case by case basis. A working example are the BCL protein family complexes which cannot be grouped by function as they may be pro- and/or antiapoptotic.<br />
<br />
== Previous work ==<br />
<br />
Emily started documentation here, in case it's helpful, but this wasn't worked on since 2011:<br />
http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects<br />
<br />
<br />
Birgit's comments [from email to Paola]: <br />
<br />
Inheritance of annotations:<br />
I agree with the wiki, you cannot inherit MF from a complex to a subunit and even a CC is problematic, see the transmembrane example above. This needs more thinking about. I don't know what you are doing right now...<br />
<br />
Orthologies:<br />
We infer within taxon groups, e.g. human to mouse to rat or any other mammal etc, depending on where the exp evidence comes from. We systematically infer human-mouse. We have a few pombe complexes inferred from yeast (Sc!) but we don't do it systematically.<br />
<br />
Paralogues:<br />
We make inferences between related complexes in the same species when the gene products are very similar, e.g. hemoglobin chains for adult and developmental complexes.<br />
<br />
'Large' complexes:<br />
We have tackled the 'mediator' and we can now link to RNACentral for RNAs so time permitting we'll tackle the 'biggies' soon!<br />
<br />
Pro:<br />
We have a list of Pro complexes that we consult for refs.<br />
<br />
== Useful links ==<br />
<br />
Complex Portal, http://www.ebi.ac.uk/complexportal/<br />
<br />
<br />
----<br />
[[Category:GO Editors]][[Category:Ontology]]<br />
[[Notes_on_specific_terms |Back to: Notes on specific terms]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_complexes&diff=72776Protein complexes2019-01-29T09:23:12Z<p>Bmeldal: </p>
<hr />
<div><br />
<br />
=Definition of a Protein Complex=<br />
A cellular component should include more than one gene product; complexes of one gene product with a cofactor, e.g. heme and chlorophyll, should not be included. Homomultimeric proteins, e.g. the homodimeric alcohol dehydrogenase, may be included as cellular component terms, as should heteromultimeric proteins, e.g. hemoglobin with alpha and beta chains. All complexes in the component ontology should be given parentage under the general term GO:0032991 protein-containing complex. To distinguish cellular components from functions, use 'complex' in the term name of a component, and append enzyme names with the word 'activity'. For example, the molecular function term GO:0004738 pyruvate dehydrogenase activity describes the enzyme activity whereas the cellular component term GO:0005967 mitochondrial pyruvate dehydrogenase complex describes the multi-subunit structure in which the enzyme activity resides.<br />
<br />
=Receptor-ligand complexes=<br />
As a rule, GO terms to indicate association of a receptor with its ligand should not be created, as their complex may not always be stable, and there could be a potential explosion of terms. However, we should allow for exceptions. The Complex Portal database wouldn't curate receptor-ligand complexes if these consisted of a single chain of each, but it will curate complexes when the ligand is not monomeric and receptors oligomerize upon ligand binding. An example of this is GO:1990270 'platelet-derived growth factor receptor-ligand complex', where the ligands are always dimeric and the receptor dimerizes upon ligand binding. (Also, in the case of GO:1990270, the complex has been shown to exist in a variety of experiments, including crystals, pull downs, comigrations, competition assays and more.)<br />
<br />
<br />
=Notes from working group=<br />
*NOTE: This is a work in progress and includes continuing discussion with Complex Portal as well as the GOC.<br />
*Last updated: 9/6/2015, Paola. Minor updates: 29/1/19, Birgit.<br />
<br />
*Main working group 2019: Birgit, Kimberly, Pascale, Harold, Val, Edith, Leonore, Helen, Sandra, Peter.<br />
<br />
== Background and rationale ==<br />
<br />
Recently, GO and Complex Portal have started to work together to improve the 'protein complex' branch in GO, making it less flat and more informative, and to provide species-agnostic GO terms that Complex Portal can reference to for their species-specific curation projects, namely the [http://www.ebi.ac.uk/complexportal/ Complex Portal]. At the time of writing (Spring 2015) the focus of the Complex Portal lies on human, mouse, yeast and E.coli, but it can take direct curation requests as well (please ). Other MODs are encouraged to collaborate directly. <br />
<br />
Here, we collect current guidelines on protein complex terms, to aid GO curators in discerning whether a protein complex belongs in GO or not, and if yes, in including all necessary information when requesting a new protein complex.<br />
<br />
== Protein complexes in GO ==<br />
<br />
=== Rule 1: Is the complex stable? ===<br />
<br />
In GO, 'protein complex' is defined as "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical."<br />
<br />
When in doubt, how can a curator figure out if a complex is really stable?<br />
<br />
We can refer to the Complex Portal Rules [http://www.ebi.ac.uk/complexportal/documentation/]. These are reported below for reference, and in a definition comment to 'protein complex' to serve as annotation guidance:<br />
<br />
===== What can be described as a complex? =====<br />
<br />
'''A stable set of (two or more) interacting macromolecules such as proteins which can be co-purified by an acceptable method and have been shown to exist as an isolated, functional unit in vivo. Any interacting non-protein molecules (e.g. small molecules, nucleic acids) will also be included.'''<br />
<br />
===== What should not be captured: =====<br />
*Enzyme/substrate, receptor/ligand or any similar transient interactions unless these are a critical part of the complex assembly (e.g. PDGF receptors only become 'dimeric' when linked by the dimeric ligand forming a tetramer).<br />
*Proteins associated in a pulldown/coimmunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose affinity complex.<br />
*Any literature complex where the only evidence is based on genetic interaction data.<br />
*Partial complexes.<br />
<br />
Note:<br />
*If the complex is not stable, it's just protein binding. Interactions can then be captured by a protein-protein interaction DB such as IntAct. <br />
*Beware of partial complexes shown experimentally, especially when crystallised. Some subunits (e.g. transmembrane subunits) cannot be expressed as recombinant proteins and are 'left out' of detailed studies. More reading is often necessary to find out what the full complex is thought to be.<br />
<br />
===== Tricky cases we DO (or could) capture in the Complex Portal: =====<br />
<br />
*Substrates or ligands if the enzyme or receptor complex only forms in their presence (see PDGF receptors above, e.g. [http://www.ebi.ac.uk/complexportal/details/CPX-2883 CPX-2883]). These terms would also qualify for GO.<br />
<br />
*Homologous proteins, with the same functionality, which would be inferred by sequence similarity to form a complex but for which no physical link has been demonstrated, e.g. proteins A and B have been shown to physically interact and form a functional complex, protein C is a homologue of protein B by sequence similarity and is know to have the same function as B but protein A-C interaction has not been demonstrated experimentally. E.g. SUMO - E1 ligase complexes where there is interaction evidence for binding with SUMO1 ([http://www.ebi.ac.uk/complexportal/details/CPX-3042 CPX-3042]) but not with SUMO2 ([http://www.ebi.ac.uk/complexportal/details/CPX-3044 CPX-3044]).<br />
<br />
*The Complex Portal could also hold transient complexes, e.g. signaling complexes. We have not created any of these to date but they are possible, and controlled vocabulary terms exist to distinguish the two classes. BUT - they would probably fall outside the scope of GO if GO limit themselves to stable complexes.<br />
<br />
*We can also curate complexes that lack full experimental evidence but are commonly regarded as existing, e.g. complexes submitted by ChEMBL for which we only have pharmacological evidence. These complexes are tagged with ECO:0005547 - inferred from background scientific knowledge by manual assertion. E.g GABA ([http://www.ebi.ac.uk/complexportal/details/CPX- EBI-9008426]) receptors and many other transmembrane receptors.<br />
<br />
===== Expanded definition comment for GO:0032991 'protein-containing complex’: =====<br />
<br />
"A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole."<br />
<br />
=== Rule 2: Is the complex species-agnostic? ===<br />
<br />
*GO should host species-agnostic complexes, ideally conserved across taxa. Where this isn't known, we should still make the definition generic, and add 'For example, in human this complex contains...' as a definition gloss or definition comment.<br />
<br />
*Species-specific complexes don't belong in GO, but Complex Portal and/or PRO can take them. (We acknowledge that GO contains many historic terms that contravene this rule. For the time being, the agreement is that we will not review them globally, though we may fix them if and when we come across them.)<br />
<br />
*We may, however, need taxon restrictions on a case-by-case basis such as complexes that only exist in prokaryotes or eukaryotes. Curators are encouraged to provide these information, if applicable, when they request a new term (or come across an existing one).<br />
<br />
=== Rule 3: Does the complex have a molecular function? ===<br />
<br />
*If yes, add capable_of link(s) to molecular function terms. These links are used by the reasoner to place the complex into the correct branch under 'protein complex'.<br />
<br />
=== Rule 4: Is the complex known to be involved in one or more biological processes? ===<br />
<br />
*If yes, add capable_of_part_of links to biological process(es).<br />
<br />
*Note: we decided not to use BP as a qualifier for making grouping terms for complexes as these would become too unspecific, e.g. 'regulatory complex' could include most complexes!<br />
<br />
=== Rule 5: Does the complex contain conserved subunits? ===<br />
<br />
*Many complexes are defined by their subunit composition rather than their activity. Such complexes will still be accepted into the GO. The curator should endeavour to place the new complex as child of a functional parent or a parent term also defined by its composition, in some cases this may be difficult and those complex terms will be direct children of 'protein complex'.<br />
<br />
*Complex definitions should include their function or the process they are involved in as well as the defining subunits (using the style "In human, it is composed of..."). However, we need to be careful not to explode the subunit composition in the definition if they turn out to be rather different in the different branches of the tree of life. In such a situation, the curator and editor should consider broadening the term name and adding the various subunit-defined names as narrow synonyms. This should be handled on a case-by-case basis.<br />
<br />
*Complexes defined by their subunits but functionally identical to a more generic parent term should not be created as separate GO terms but added to the parent term as narrow synonyms. The specific complex belongs in the Complex Portal.<br />
<br />
[DOS to look into some automatic reasoning across subunits but we think it may become tricky. To be discussed among editors.]<br />
<br />
=== Rule 6: Where is the complex located? ===<br />
<br />
*Indicate cellular location as specifically as possible, unless parent already has one.<br />
<br />
*The CC location is meant for the complex as a whole. We discussed this in the context of transmembrane complexes where one or more members of the complex are located on one side of the membrane only or have no membrane attachment at all. As gene products have the part_of relationship with the complexes this is fine (and the only way of reflecting the CC for the complex as a whole).<br />
<br />
*If we have complexes defined by their location (see below under 'Futures Plans'), does the reasoner take the part_of relationship to place them automatically into the right complex-by-location branch? [DOS?]<br />
<br />
*Complexes simply defined by the cell type they are expressed in are not permitted.<br />
<br />
=== Rule 7: Adding appropriate is_a relationships ===<br />
<br />
*We are trying to avoid placing complexes as direct is_a children of 'protein-containing complex', by adding some granularity to this ontology branch.<br />
<br />
*An is_a parent of a complex can be a <br />
# complex defined by its activity, via the complex-by-activity TG template<br />
# complex defined by its location, such as 'plasma membrane complex'. [Update: DOS added some useful protein complex grouping terms based on location, such as 'membrane protein complex'.]<br />
# complex defined by its subunit composition. This may be related to protein families but it may be difficult to make it a rule/template (see above).<br />
*We decided NOT to define complexes by their process or MF binding as they would become too generic.<br />
<br />
*Note: Complexes can have multiple parents!<br />
<br />
*Note: if capable_of MF links are added, and/or if location information is provided as part_of CC, the automatic assert-inference script will take care of placing most newly created protein complex terms more granularly in the ontology.<br />
<br />
=== Rule 8: Adding appropriate part_of relationships ===<br />
<br />
*All complexes should have a part_of link to a cellular component term, even if it's very generic, such as 'cell'.<br />
*CC does not have to be added manually if it's the same as the parent term as it will be inferred.<br />
*If the CC is more specific than the parent, the part_of relationship must be added manually.<br />
*Complexes can be subcomplexes of larger entities and can therefore be part_of another protein complex. If the larger complex necessarily needs the smaller one as its component in order to be functional, a has_part link should also be added (larger complex has_part smaller complex).<br />
*Complexes cannot have several part_of relationships to different CCs, as part_of must ALWAYS be true. If a complex can be part of several larger complexes or be found in several locations, such as cytoplasm and nucleus where it may have different functions, separate terms may have to be considered. [This point is still open to discussion, see https://sourceforge.net/p/geneontology/ontology-requests/10745/, now with DOS. To be discussed on Editor's call.]<br />
<br />
== How to request protein complexes in GO based on the above ==<br />
<br />
*Use the GO-ontology GitHub tracker https://github.com/geneontology/go-ontology/issues<br />
<br />
*Name:<br />
*Definition:<br />
*relationships: is_a [complex parent], part_of [subcellular location], capable_of MF, capable_of_part_of BP<br />
*Synonym(s):<br />
<br />
*We no longer require dbxrefs to the Complex Portal as these will be directly imported.<br />
<br />
*Complex Portal is happy to curate requested complexes at the same time as adding to the GO structure. Curators are encouraged to curate complexes directly into the Complex Portal after being trained by us. SGD and UCL are doing this already. Contact us via the yellow "request complex" tile on the home page: http://www.ebi.ac.uk/complexportal/<br />
<br />
== Complex Definition field ==<br />
<br />
The way definitions of older protein complex terms are structured is not always consistent. Currently, we recommend the following:<br />
<br />
*Start the definition referring to the function (if applicable), such as 'A protein complex capable of X function...'.<br />
<br />
*Processes can also be mentioned in the def. <br />
<br />
*Subunits should only be listed in the definition if the complex is defined by its composition rather than function (see Rule 5 above). If the complex is defined by its function, subunit composition should go into a definition comment or be added as narrow synonyms.<br />
<br />
*Complexes should NOT be defined by their stoichiometry, though this may be mentioned in the def as a 'soft' comment (definition gloss), or in a definition comment. The rationale behind this recommendation is that, as knowledge advances and more examples are found, stoichiometry defs would have to be updated, causing a lot of work. It is perfectly fine though to mention something like 'usually consists of a catalytic and a regulatory subunit and possibly further accessory subunits...'. <br />
<br />
*We are aware that many older terms' definitions do not conform to these guidelines. At the moment, however, we do not plan on fixing all of them. We may make corrections on a case-by-case basis and/or when working on a given branch.<br />
<br />
== Future plans ==<br />
as discussed in a meeting with Birgit Meldal, Sandra Orchard, David Osumi-Sunderland and Paola Roncaglia on 28/4/2015<br />
<br />
We discussed how we can make 'quick gains' in making the ontology more granular beyond the fixes Birgit does on a case by case basis. This is to target historic terms that have only 'protein complex' as a parent because they have no annotation extensions. The aim is to have most complexes grouped either by their function, location or subunit composition.<br />
<br />
*Do a pass through term names and definitions to find major groups of complexes that can be grouped by function, e.g. 'catalytic complex' (the term exists but many historic terms have not automatically been classified as such as they have no capable_of extensions). Other keywords: kinase, activity, viral, receptor, respiratory chain... [BM, SO & DOS]<br />
<br />
*Add parent terms based on location, such as 'membrane complex' and children or 'mitochondrial complex'. Can the reasoner place complexes automatically into this branch based on their part_of relationship (see above Rule 6)? Should we have a TG template for this? [BM, DOS]<br />
<br />
*Combine activity and location, such as 'membrane receptor complex'.<br />
<br />
*We discussed grouping by protein families but this may be tricky. Decide on a case by case basis. A working example are the BCL protein family complexes which cannot be grouped by function as they may be pro- and/or antiapoptotic.<br />
<br />
== Previous work ==<br />
<br />
Emily started documentation here, in case it's helpful, but this wasn't worked on since 2011:<br />
http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects<br />
<br />
<br />
Birgit's comments [from email to Paola]: <br />
<br />
Inheritance of annotations:<br />
I agree with the wiki, you cannot inherit MF from a complex to a subunit and even a CC is problematic, see the transmembrane example above. This needs more thinking about. I don't know what you are doing right now...<br />
<br />
Orthologies:<br />
We infer within taxon groups, e.g. human to mouse to rat or any other mammal etc, depending on where the exp evidence comes from. We systematically infer human-mouse. We have a few pombe complexes inferred from yeast (Sc!) but we don't do it systematically.<br />
<br />
Paralogues:<br />
We make inferences between related complexes in the same species when the gene products are very similar, e.g. hemoglobin chains for adult and developmental complexes.<br />
<br />
'Large' complexes:<br />
We have tackled the 'mediator' and we can now link to RNACentral for RNAs so time permitting we'll tackle the 'biggies' soon!<br />
<br />
Pro:<br />
We have a list of Pro complexes that we consult for refs.<br />
<br />
== Useful links ==<br />
<br />
Complex Portal, http://www.ebi.ac.uk/complexportal/<br />
<br />
<br />
----<br />
[[Category:GO Editors]][[Category:Ontology]]<br />
[[Notes_on_specific_terms |Back to: Notes on specific terms]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_complexes&diff=72775Protein complexes2019-01-29T09:14:19Z<p>Bmeldal: </p>
<hr />
<div><br />
<br />
=Definition of a Protein Complex=<br />
A cellular component should include more than one gene product; complexes of one gene product with a cofactor, e.g. heme and chlorophyll, should not be included. Homomultimeric proteins, e.g. the homodimeric alcohol dehydrogenase, may be included as cellular component terms, as should heteromultimeric proteins, e.g. hemoglobin with alpha and beta chains. All complexes in the component ontology should be given parentage under the general term GO:0032991 protein-containing complex. To distinguish cellular components from functions, use 'complex' in the term name of a component, and append enzyme names with the word 'activity'. For example, the molecular function term pyruvate dehydrogenase activity ; GO:0004738 describes the enzyme activity whereas the cellular component term pyruvate dehydrogenase complex ; GO:0045254 describes the multi-subunit structure in which the enzyme activity resides.<br />
<br />
=Receptor-ligand complexes=<br />
As a rule, GO terms to indicate association of a receptor with its ligand should not be created, as their complex may not always be stable, and there could be a potential explosion of terms. However, we should allow for exceptions. The Complex Portal database wouldn't curate receptor-ligand complexes if these consisted of a single chain of each, but it will curate complexes when the ligand is not monomeric and receptors oligomerize upon ligand binding. An example of this is GO:1990270 'platelet-derived growth factor receptor-ligand complex', where the ligands are always dimeric and the receptor dimerizes upon ligand binding. (Also, in the case of GO:1990270, the complex has been shown to exist in a variety of experiments, including crystals, pull downs, comigrations, competition assays and more.)<br />
<br />
<br />
=Notes from working group=<br />
*NOTE: This is a work in progress and includes continuing discussion with Complex Portal as well as the GOC.<br />
*Last updated: 9/6/2015, Paola. Minor updates: 29/1/19, Birgit.<br />
<br />
*Main working group 2019: Birgit, Kimberly, Pascale, Harold, Val, Edith, Leonore, Helen, Sandra, Peter.<br />
<br />
== Background and rationale ==<br />
<br />
Recently, GO and Complex Portal have started to work together to improve the 'protein complex' branch in GO, making it less flat and more informative, and to provide species-agnostic GO terms that Complex Portal can reference to for their species-specific curation projects, namely the [http://www.ebi.ac.uk/complexportal/ Complex Portal]. At the time of writing (Spring 2015) the focus of the Complex Portal lies on human, mouse, yeast and E.coli, but it can take direct curation requests as well (please ). Other MODs are encouraged to collaborate directly. <br />
<br />
Here, we collect current guidelines on protein complex terms, to aid GO curators in discerning whether a protein complex belongs in GO or not, and if yes, in including all necessary information when requesting a new protein complex.<br />
<br />
== Protein complexes in GO ==<br />
<br />
=== Rule 1: Is the complex stable? ===<br />
<br />
In GO, 'protein complex' is defined as "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical."<br />
<br />
When in doubt, how can a curator figure out if a complex is really stable?<br />
<br />
We can refer to the Complex Portal Rules [http://www.ebi.ac.uk/complexportal/documentation/]. These are reported below for reference, and in a definition comment to 'protein complex' to serve as annotation guidance:<br />
<br />
===== What can be described as a complex? =====<br />
<br />
'''A stable set of (two or more) interacting macromolecules such as proteins which can be co-purified by an acceptable method and have been shown to exist as an isolated, functional unit in vivo. Any interacting non-protein molecules (e.g. small molecules, nucleic acids) will also be included.'''<br />
<br />
===== What should not be captured: =====<br />
*Enzyme/substrate, receptor/ligand or any similar transient interactions unless these are a critical part of the complex assembly (e.g. PDGF receptors only become 'dimeric' when linked by the dimeric ligand forming a tetramer).<br />
*Proteins associated in a pulldown/coimmunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose affinity complex.<br />
*Any literature complex where the only evidence is based on genetic interaction data.<br />
*Partial complexes.<br />
<br />
Note:<br />
*If the complex is not stable, it's just protein binding. Interactions can then be captured by a protein-protein interaction DB such as IntAct. <br />
*Beware of partial complexes shown experimentally, especially when crystallised. Some subunits (e.g. transmembrane subunits) cannot be expressed as recombinant proteins and are 'left out' of detailed studies. More reading is often necessary to find out what the full complex is thought to be.<br />
<br />
===== Tricky cases we DO (or could) capture in the Complex Portal: =====<br />
<br />
*Substrates or ligands if the enzyme or receptor complex only forms in their presence (see PDGF receptors above, e.g. [http://www.ebi.ac.uk/complexportal/details/CPX-2883 CPX-2883]). These terms would also qualify for GO.<br />
<br />
*Homologous proteins, with the same functionality, which would be inferred by sequence similarity to form a complex but for which no physical link has been demonstrated, e.g. proteins A and B have been shown to physically interact and form a functional complex, protein C is a homologue of protein B by sequence similarity and is know to have the same function as B but protein A-C interaction has not been demonstrated experimentally. E.g. SUMO - E1 ligase complexes where there is interaction evidence for binding with SUMO1 ([http://www.ebi.ac.uk/complexportal/details/CPX-3042 CPX-3042]) but not with SUMO2 ([http://www.ebi.ac.uk/complexportal/details/CPX-3044 CPX-3044]).<br />
<br />
*The Complex Portal could also hold transient complexes, e.g. signaling complexes. We have not created any of these to date but they are possible, and controlled vocabulary terms exist to distinguish the two classes. BUT - they would probably fall outside the scope of GO if GO limit themselves to stable complexes.<br />
<br />
*We can also curate complexes that lack full experimental evidence but are commonly regarded as existing, e.g. complexes submitted by ChEMBL for which we only have pharmacological evidence. These complexes are tagged with ECO:0005547 - inferred from background scientific knowledge by manual assertion. E.g GABA ([http://www.ebi.ac.uk/complexportal/details/CPX- EBI-9008426]) receptors and many other transmembrane receptors.<br />
<br />
===== Expanded definition comment for GO:0032991 'protein-containing complex’: =====<br />
<br />
"A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole."<br />
<br />
=== Rule 2: Is the complex species-agnostic? ===<br />
<br />
*GO should host species-agnostic complexes, ideally conserved across taxa. Where this isn't known, we should still make the definition generic, and add 'For example, in human this complex contains...' as a definition gloss or definition comment.<br />
<br />
*Species-specific complexes don't belong in GO, but Complex Portal and/or PRO can take them. (We acknowledge that GO contains many historic terms that contravene this rule. For the time being, the agreement is that we will not review them globally, though we may fix them if and when we come across them.)<br />
<br />
*We may, however, need taxon restrictions on a case-by-case basis such as complexes that only exist in prokaryotes or eukaryotes. Curators are encouraged to provide these information, if applicable, when they request a new term (or come across an existing one).<br />
<br />
=== Rule 3: Does the complex have a molecular function? ===<br />
<br />
*If yes, add capable_of link(s) to molecular function terms. These links are used by the reasoner to place the complex into the correct branch under 'protein complex'.<br />
<br />
=== Rule 4: Is the complex known to be involved in one or more biological processes? ===<br />
<br />
*If yes, add capable_of_part_of links to biological process(es).<br />
<br />
*Note: we decided not to use BP as a qualifier for making grouping terms for complexes as these would become too unspecific, e.g. 'regulatory complex' could include most complexes!<br />
<br />
=== Rule 5: Does the complex contain conserved subunits? ===<br />
<br />
*Many complexes are defined by their subunit composition rather than their activity. Such complexes will still be accepted into the GO. The curator should endeavour to place the new complex as child of a functional parent or a parent term also defined by its composition, in some cases this may be difficult and those complex terms will be direct children of 'protein complex'.<br />
<br />
*Complex definitions should include their function or the process they are involved in as well as the defining subunits (using the style "In human, it is composed of..."). However, we need to be careful not to explode the subunit composition in the definition if they turn out to be rather different in the different branches of the tree of life. In such a situation, the curator and editor should consider broadening the term name and adding the various subunit-defined names as narrow synonyms. This should be handled on a case-by-case basis.<br />
<br />
*Complexes defined by their subunits but functionally identical to a more generic parent term should not be created as separate GO terms but added to the parent term as narrow synonyms. The specific complex belongs in the Complex Portal.<br />
<br />
[DOS to look into some automatic reasoning across subunits but we think it may become tricky. To be discussed among editors.]<br />
<br />
=== Rule 6: Where is the complex located? ===<br />
<br />
*Indicate cellular location as specifically as possible, unless parent already has one.<br />
<br />
*The CC location is meant for the complex as a whole. We discussed this in the context of transmembrane complexes where one or more members of the complex are located on one side of the membrane only or have no membrane attachment at all. As gene products have the part_of relationship with the complexes this is fine (and the only way of reflecting the CC for the complex as a whole).<br />
<br />
*If we have complexes defined by their location (see below under 'Futures Plans'), does the reasoner take the part_of relationship to place them automatically into the right complex-by-location branch? [DOS?]<br />
<br />
*Complexes simply defined by the cell type they are expressed in are not permitted.<br />
<br />
=== Rule 7: Adding appropriate is_a relationships ===<br />
<br />
*We are trying to avoid placing complexes as direct is_a children of 'protein-containing complex', by adding some granularity to this ontology branch.<br />
<br />
*An is_a parent of a complex can be a <br />
# complex defined by its activity, via the complex-by-activity TG template<br />
# complex defined by its location, such as 'plasma membrane complex'. [Update: DOS added some useful protein complex grouping terms based on location, such as 'membrane protein complex'.]<br />
# complex defined by its subunit composition. This may be related to protein families but it may be difficult to make it a rule/template (see above).<br />
*We decided NOT to define complexes by their process or MF binding as they would become too generic.<br />
<br />
*Note: Complexes can have multiple parents!<br />
<br />
*Note: if capable_of MF links are added, and/or if location information is provided as part_of CC, the automatic assert-inference script will take care of placing most newly created protein complex terms more granularly in the ontology.<br />
<br />
=== Rule 8: Adding appropriate part_of relationships ===<br />
<br />
*All complexes should have a part_of link to a cellular component term, even if it's very generic, such as 'cell'.<br />
*CC does not have to be added manually if it's the same as the parent term as it will be inferred.<br />
*If the CC is more specific than the parent, the part_of relationship must be added manually.<br />
*Complexes can be subcomplexes of larger entities and can therefore be part_of another protein complex. If the larger complex necessarily needs the smaller one as its component in order to be functional, a has_part link should also be added (larger complex has_part smaller complex).<br />
*Complexes cannot have several part_of relationships to different CCs, as part_of must ALWAYS be true. If a complex can be part of several larger complexes or be found in several locations, such as cytoplasm and nucleus where it may have different functions, separate terms may have to be considered. [This point is still open to discussion, see https://sourceforge.net/p/geneontology/ontology-requests/10745/, now with DOS. To be discussed on Editor's call.]<br />
<br />
== How to request protein complexes in GO based on the above ==<br />
<br />
*Use the GO-ontology GitHub tracker https://github.com/geneontology/go-ontology/issues<br />
<br />
*Name:<br />
*Definition:<br />
*relationships: is_a [complex parent], part_of [subcellular location], capable_of MF, capable_of_part_of BP<br />
*Synonym(s):<br />
<br />
*We no longer require dbxrefs to the Complex Portal as these will be directly imported.<br />
<br />
*Complex Portal is happy to curate requested complexes at the same time as adding to the GO structure. Curators are encouraged to curate complexes directly into the Complex Portal after being trained by us. SGD and UCL are doing this already. Contact us via the yellow "request complex" tile on the home page: http://www.ebi.ac.uk/complexportal/<br />
<br />
== Complex Definition field ==<br />
<br />
The way definitions of older protein complex terms are structured is not always consistent. Currently, we recommend the following:<br />
<br />
*Start the definition referring to the function (if applicable), such as 'A protein complex capable of X function...'.<br />
<br />
*Processes can also be mentioned in the def. <br />
<br />
*Subunits should only be listed in the definition if the complex is defined by its composition rather than function (see Rule 5 above). If the complex is defined by its function, subunit composition should go into a definition comment or be added as narrow synonyms.<br />
<br />
*Complexes should NOT be defined by their stoichiometry, though this may be mentioned in the def as a 'soft' comment (definition gloss), or in a definition comment. The rationale behind this recommendation is that, as knowledge advances and more examples are found, stoichiometry defs would have to be updated, causing a lot of work. It is perfectly fine though to mention something like 'usually consists of a catalytic and a regulatory subunit and possibly further accessory subunits...'. <br />
<br />
*We are aware that many older terms' definitions do not conform to these guidelines. At the moment, however, we do not plan on fixing all of them. We may make corrections on a case-by-case basis and/or when working on a given branch.<br />
<br />
== Future plans ==<br />
as discussed in a meeting with Birgit Meldal, Sandra Orchard, David Osumi-Sunderland and Paola Roncaglia on 28/4/2015<br />
<br />
We discussed how we can make 'quick gains' in making the ontology more granular beyond the fixes Birgit does on a case by case basis. This is to target historic terms that have only 'protein complex' as a parent because they have no annotation extensions. The aim is to have most complexes grouped either by their function, location or subunit composition.<br />
<br />
*Do a pass through term names and definitions to find major groups of complexes that can be grouped by function, e.g. 'catalytic complex' (the term exists but many historic terms have not automatically been classified as such as they have no capable_of extensions). Other keywords: kinase, activity, viral, receptor, respiratory chain... [BM, SO & DOS]<br />
<br />
*Add parent terms based on location, such as 'membrane complex' and children or 'mitochondrial complex'. Can the reasoner place complexes automatically into this branch based on their part_of relationship (see above Rule 6)? Should we have a TG template for this? [BM, DOS]<br />
<br />
*Combine activity and location, such as 'membrane receptor complex'.<br />
<br />
*We discussed grouping by protein families but this may be tricky. Decide on a case by case basis. A working example are the BCL protein family complexes which cannot be grouped by function as they may be pro- and/or antiapoptotic.<br />
<br />
== Previous work ==<br />
<br />
Emily started documentation here, in case it's helpful, but this wasn't worked on since 2011:<br />
http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects<br />
<br />
<br />
Birgit's comments [from email to Paola]: <br />
<br />
Inheritance of annotations:<br />
I agree with the wiki, you cannot inherit MF from a complex to a subunit and even a CC is problematic, see the transmembrane example above. This needs more thinking about. I don't know what you are doing right now...<br />
<br />
Orthologies:<br />
We infer within taxon groups, e.g. human to mouse to rat or any other mammal etc, depending on where the exp evidence comes from. We systematically infer human-mouse. We have a few pombe complexes inferred from yeast (Sc!) but we don't do it systematically.<br />
<br />
Paralogues:<br />
We make inferences between related complexes in the same species when the gene products are very similar, e.g. hemoglobin chains for adult and developmental complexes.<br />
<br />
'Large' complexes:<br />
We have tackled the 'mediator' and we can now link to RNACentral for RNAs so time permitting we'll tackle the 'biggies' soon!<br />
<br />
Pro:<br />
We have a list of Pro complexes that we consult for refs.<br />
<br />
== Useful links ==<br />
<br />
Complex Portal, http://www.ebi.ac.uk/complexportal/<br />
<br />
<br />
----<br />
[[Category:GO Editors]][[Category:Ontology]]<br />
[[Notes_on_specific_terms |Back to: Notes on specific terms]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_complexes&diff=72774Protein complexes2019-01-29T09:12:53Z<p>Bmeldal: </p>
<hr />
<div><br />
<br />
=Definition of a Protein Complex=<br />
A cellular component should include more than one gene product; complexes of one gene product with a cofactor, e.g. heme and chlorophyll, should not be included. Homomultimeric proteins, e.g. the homodimeric alcohol dehydrogenase, may be included as cellular component terms, as should heteromultimeric proteins, e.g. hemoglobin with alpha and beta chains. All complexes in the component ontology should be given parentage under the general term protein complex ; GO:0043234 . To distinguish cellular components from functions, use 'complex' in the term name of a component, and append enzyme names with the word 'activity'. For example, the molecular function term pyruvate dehydrogenase activity ; GO:0004738 describes the enzyme activity whereas the cellular component term pyruvate dehydrogenase complex ; GO:0045254 describes the multi-subunit structure in which the enzyme activity resides.<br />
<br />
=Receptor-ligand complexes=<br />
As a rule, GO terms to indicate association of a receptor with its ligand should not be created, as their complex may not always be stable, and there could be a potential explosion of terms. However, we should allow for exceptions. The Complex Portal database wouldn't curate receptor-ligand complexes if these consisted of a single chain of each, but it will curate complexes when the ligand is not monomeric and receptors oligomerize upon ligand binding. An example of this is GO:1990270 'platelet-derived growth factor receptor-ligand complex', where the ligands are always dimeric and the receptor dimerizes upon ligand binding. (Also, in the case of GO:1990270, the complex has been shown to exist in a variety of experiments, including crystals, pull downs, comigrations, competition assays and more.)<br />
<br />
<br />
=Notes from working group=<br />
*NOTE: This is a work in progress and includes continuing discussion with Complex Portal as well as the GOC.<br />
*Last updated: 9/6/2015, Paola. Minor updates: 29/1/19, Birgit.<br />
<br />
*Main working group 2019: Birgit, Kimberly, Pascale, Harold, Val, Edith, Leonore, Helen, Sandra, Peter.<br />
<br />
== Background and rationale ==<br />
<br />
Recently, GO and Complex Portal have started to work together to improve the 'protein complex' branch in GO, making it less flat and more informative, and to provide species-agnostic GO terms that Complex Portal can reference to for their species-specific curation projects, namely the [http://www.ebi.ac.uk/complexportal/ Complex Portal]. At the time of writing (Spring 2015) the focus of the Complex Portal lies on human, mouse, yeast and E.coli, but it can take direct curation requests as well (please ). Other MODs are encouraged to collaborate directly. <br />
<br />
Here, we collect current guidelines on protein complex terms, to aid GO curators in discerning whether a protein complex belongs in GO or not, and if yes, in including all necessary information when requesting a new protein complex.<br />
<br />
== Protein complexes in GO ==<br />
<br />
=== Rule 1: Is the complex stable? ===<br />
<br />
In GO, 'protein complex' is defined as "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical."<br />
<br />
When in doubt, how can a curator figure out if a complex is really stable?<br />
<br />
We can refer to the Complex Portal Rules [http://www.ebi.ac.uk/complexportal/documentation/]. These are reported below for reference, and in a definition comment to 'protein complex' to serve as annotation guidance:<br />
<br />
===== What can be described as a complex? =====<br />
<br />
'''A stable set of (two or more) interacting macromolecules such as proteins which can be co-purified by an acceptable method and have been shown to exist as an isolated, functional unit in vivo. Any interacting non-protein molecules (e.g. small molecules, nucleic acids) will also be included.'''<br />
<br />
===== What should not be captured: =====<br />
*Enzyme/substrate, receptor/ligand or any similar transient interactions unless these are a critical part of the complex assembly (e.g. PDGF receptors only become 'dimeric' when linked by the dimeric ligand forming a tetramer).<br />
*Proteins associated in a pulldown/coimmunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose affinity complex.<br />
*Any literature complex where the only evidence is based on genetic interaction data.<br />
*Partial complexes.<br />
<br />
Note:<br />
*If the complex is not stable, it's just protein binding. Interactions can then be captured by a protein-protein interaction DB such as IntAct. <br />
*Beware of partial complexes shown experimentally, especially when crystallised. Some subunits (e.g. transmembrane subunits) cannot be expressed as recombinant proteins and are 'left out' of detailed studies. More reading is often necessary to find out what the full complex is thought to be.<br />
<br />
===== Tricky cases we DO (or could) capture in the Complex Portal: =====<br />
<br />
*Substrates or ligands if the enzyme or receptor complex only forms in their presence (see PDGF receptors above, e.g. [http://www.ebi.ac.uk/complexportal/details/CPX-2883 CPX-2883]). These terms would also qualify for GO.<br />
<br />
*Homologous proteins, with the same functionality, which would be inferred by sequence similarity to form a complex but for which no physical link has been demonstrated, e.g. proteins A and B have been shown to physically interact and form a functional complex, protein C is a homologue of protein B by sequence similarity and is know to have the same function as B but protein A-C interaction has not been demonstrated experimentally. E.g. SUMO - E1 ligase complexes where there is interaction evidence for binding with SUMO1 ([http://www.ebi.ac.uk/complexportal/details/CPX-3042 CPX-3042]) but not with SUMO2 ([http://www.ebi.ac.uk/complexportal/details/CPX-3044 CPX-3044]).<br />
<br />
*The Complex Portal could also hold transient complexes, e.g. signaling complexes. We have not created any of these to date but they are possible, and controlled vocabulary terms exist to distinguish the two classes. BUT - they would probably fall outside the scope of GO if GO limit themselves to stable complexes.<br />
<br />
*We can also curate complexes that lack full experimental evidence but are commonly regarded as existing, e.g. complexes submitted by ChEMBL for which we only have pharmacological evidence. These complexes are tagged with ECO:0005547 - inferred from background scientific knowledge by manual assertion. E.g GABA ([http://www.ebi.ac.uk/complexportal/details/CPX- EBI-9008426]) receptors and many other transmembrane receptors.<br />
<br />
===== Expanded definition comment for GO:0032991 'protein-containing complex’: =====<br />
<br />
"A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole."<br />
<br />
=== Rule 2: Is the complex species-agnostic? ===<br />
<br />
*GO should host species-agnostic complexes, ideally conserved across taxa. Where this isn't known, we should still make the definition generic, and add 'For example, in human this complex contains...' as a definition gloss or definition comment.<br />
<br />
*Species-specific complexes don't belong in GO, but Complex Portal and/or PRO can take them. (We acknowledge that GO contains many historic terms that contravene this rule. For the time being, the agreement is that we will not review them globally, though we may fix them if and when we come across them.)<br />
<br />
*We may, however, need taxon restrictions on a case-by-case basis such as complexes that only exist in prokaryotes or eukaryotes. Curators are encouraged to provide these information, if applicable, when they request a new term (or come across an existing one).<br />
<br />
=== Rule 3: Does the complex have a molecular function? ===<br />
<br />
*If yes, add capable_of link(s) to molecular function terms. These links are used by the reasoner to place the complex into the correct branch under 'protein complex'.<br />
<br />
=== Rule 4: Is the complex known to be involved in one or more biological processes? ===<br />
<br />
*If yes, add capable_of_part_of links to biological process(es).<br />
<br />
*Note: we decided not to use BP as a qualifier for making grouping terms for complexes as these would become too unspecific, e.g. 'regulatory complex' could include most complexes!<br />
<br />
=== Rule 5: Does the complex contain conserved subunits? ===<br />
<br />
*Many complexes are defined by their subunit composition rather than their activity. Such complexes will still be accepted into the GO. The curator should endeavour to place the new complex as child of a functional parent or a parent term also defined by its composition, in some cases this may be difficult and those complex terms will be direct children of 'protein complex'.<br />
<br />
*Complex definitions should include their function or the process they are involved in as well as the defining subunits (using the style "In human, it is composed of..."). However, we need to be careful not to explode the subunit composition in the definition if they turn out to be rather different in the different branches of the tree of life. In such a situation, the curator and editor should consider broadening the term name and adding the various subunit-defined names as narrow synonyms. This should be handled on a case-by-case basis.<br />
<br />
*Complexes defined by their subunits but functionally identical to a more generic parent term should not be created as separate GO terms but added to the parent term as narrow synonyms. The specific complex belongs in the Complex Portal.<br />
<br />
[DOS to look into some automatic reasoning across subunits but we think it may become tricky. To be discussed among editors.]<br />
<br />
=== Rule 6: Where is the complex located? ===<br />
<br />
*Indicate cellular location as specifically as possible, unless parent already has one.<br />
<br />
*The CC location is meant for the complex as a whole. We discussed this in the context of transmembrane complexes where one or more members of the complex are located on one side of the membrane only or have no membrane attachment at all. As gene products have the part_of relationship with the complexes this is fine (and the only way of reflecting the CC for the complex as a whole).<br />
<br />
*If we have complexes defined by their location (see below under 'Futures Plans'), does the reasoner take the part_of relationship to place them automatically into the right complex-by-location branch? [DOS?]<br />
<br />
*Complexes simply defined by the cell type they are expressed in are not permitted.<br />
<br />
=== Rule 7: Adding appropriate is_a relationships ===<br />
<br />
*We are trying to avoid placing complexes as direct is_a children of 'protein-containing complex', by adding some granularity to this ontology branch.<br />
<br />
*An is_a parent of a complex can be a <br />
# complex defined by its activity, via the complex-by-activity TG template<br />
# complex defined by its location, such as 'plasma membrane complex'. [Update: DOS added some useful protein complex grouping terms based on location, such as 'membrane protein complex'.]<br />
# complex defined by its subunit composition. This may be related to protein families but it may be difficult to make it a rule/template (see above).<br />
*We decided NOT to define complexes by their process or MF binding as they would become too generic.<br />
<br />
*Note: Complexes can have multiple parents!<br />
<br />
*Note: if capable_of MF links are added, and/or if location information is provided as part_of CC, the automatic assert-inference script will take care of placing most newly created protein complex terms more granularly in the ontology.<br />
<br />
=== Rule 8: Adding appropriate part_of relationships ===<br />
<br />
*All complexes should have a part_of link to a cellular component term, even if it's very generic, such as 'cell'.<br />
*CC does not have to be added manually if it's the same as the parent term as it will be inferred.<br />
*If the CC is more specific than the parent, the part_of relationship must be added manually.<br />
*Complexes can be subcomplexes of larger entities and can therefore be part_of another protein complex. If the larger complex necessarily needs the smaller one as its component in order to be functional, a has_part link should also be added (larger complex has_part smaller complex).<br />
*Complexes cannot have several part_of relationships to different CCs, as part_of must ALWAYS be true. If a complex can be part of several larger complexes or be found in several locations, such as cytoplasm and nucleus where it may have different functions, separate terms may have to be considered. [This point is still open to discussion, see https://sourceforge.net/p/geneontology/ontology-requests/10745/, now with DOS. To be discussed on Editor's call.]<br />
<br />
== How to request protein complexes in GO based on the above ==<br />
<br />
*Use the GO-ontology GitHub tracker https://github.com/geneontology/go-ontology/issues<br />
<br />
*Name:<br />
*Definition:<br />
*relationships: is_a [complex parent], part_of [subcellular location], capable_of MF, capable_of_part_of BP<br />
*Synonym(s):<br />
<br />
*We no longer require dbxrefs to the Complex Portal as these will be directly imported.<br />
<br />
*Complex Portal is happy to curate requested complexes at the same time as adding to the GO structure. Curators are encouraged to curate complexes directly into the Complex Portal after being trained by us. SGD and UCL are doing this already. Contact us via the yellow "request complex" tile on the home page: http://www.ebi.ac.uk/complexportal/<br />
<br />
== Complex Definition field ==<br />
<br />
The way definitions of older protein complex terms are structured is not always consistent. Currently, we recommend the following:<br />
<br />
*Start the definition referring to the function (if applicable), such as 'A protein complex capable of X function...'.<br />
<br />
*Processes can also be mentioned in the def. <br />
<br />
*Subunits should only be listed in the definition if the complex is defined by its composition rather than function (see Rule 5 above). If the complex is defined by its function, subunit composition should go into a definition comment or be added as narrow synonyms.<br />
<br />
*Complexes should NOT be defined by their stoichiometry, though this may be mentioned in the def as a 'soft' comment (definition gloss), or in a definition comment. The rationale behind this recommendation is that, as knowledge advances and more examples are found, stoichiometry defs would have to be updated, causing a lot of work. It is perfectly fine though to mention something like 'usually consists of a catalytic and a regulatory subunit and possibly further accessory subunits...'. <br />
<br />
*We are aware that many older terms' definitions do not conform to these guidelines. At the moment, however, we do not plan on fixing all of them. We may make corrections on a case-by-case basis and/or when working on a given branch.<br />
<br />
== Future plans ==<br />
as discussed in a meeting with Birgit Meldal, Sandra Orchard, David Osumi-Sunderland and Paola Roncaglia on 28/4/2015<br />
<br />
We discussed how we can make 'quick gains' in making the ontology more granular beyond the fixes Birgit does on a case by case basis. This is to target historic terms that have only 'protein complex' as a parent because they have no annotation extensions. The aim is to have most complexes grouped either by their function, location or subunit composition.<br />
<br />
*Do a pass through term names and definitions to find major groups of complexes that can be grouped by function, e.g. 'catalytic complex' (the term exists but many historic terms have not automatically been classified as such as they have no capable_of extensions). Other keywords: kinase, activity, viral, receptor, respiratory chain... [BM, SO & DOS]<br />
<br />
*Add parent terms based on location, such as 'membrane complex' and children or 'mitochondrial complex'. Can the reasoner place complexes automatically into this branch based on their part_of relationship (see above Rule 6)? Should we have a TG template for this? [BM, DOS]<br />
<br />
*Combine activity and location, such as 'membrane receptor complex'.<br />
<br />
*We discussed grouping by protein families but this may be tricky. Decide on a case by case basis. A working example are the BCL protein family complexes which cannot be grouped by function as they may be pro- and/or antiapoptotic.<br />
<br />
== Previous work ==<br />
<br />
Emily started documentation here, in case it's helpful, but this wasn't worked on since 2011:<br />
http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects<br />
<br />
<br />
Birgit's comments [from email to Paola]: <br />
<br />
Inheritance of annotations:<br />
I agree with the wiki, you cannot inherit MF from a complex to a subunit and even a CC is problematic, see the transmembrane example above. This needs more thinking about. I don't know what you are doing right now...<br />
<br />
Orthologies:<br />
We infer within taxon groups, e.g. human to mouse to rat or any other mammal etc, depending on where the exp evidence comes from. We systematically infer human-mouse. We have a few pombe complexes inferred from yeast (Sc!) but we don't do it systematically.<br />
<br />
Paralogues:<br />
We make inferences between related complexes in the same species when the gene products are very similar, e.g. hemoglobin chains for adult and developmental complexes.<br />
<br />
'Large' complexes:<br />
We have tackled the 'mediator' and we can now link to RNACentral for RNAs so time permitting we'll tackle the 'biggies' soon!<br />
<br />
Pro:<br />
We have a list of Pro complexes that we consult for refs.<br />
<br />
== Useful links ==<br />
<br />
Complex Portal, http://www.ebi.ac.uk/complexportal/<br />
<br />
<br />
----<br />
[[Category:GO Editors]][[Category:Ontology]]<br />
[[Notes_on_specific_terms |Back to: Notes on specific terms]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_complexes&diff=72773Protein complexes2019-01-29T08:59:10Z<p>Bmeldal: </p>
<hr />
<div><br />
<br />
=Definition of a Protein Complex=<br />
A cellular component should include more than one gene product; complexes of one gene product with a cofactor, e.g. heme and chlorophyll, should not be included. Homomultimeric proteins, e.g. the homodimeric alcohol dehydrogenase, may be included as cellular component terms, as should heteromultimeric proteins, e.g. hemoglobin with alpha and beta chains. All complexes in the component ontology should be given parentage under the general term protein complex ; GO:0043234 . To distinguish cellular components from functions, use 'complex' in the term name of a component, and append enzyme names with the word 'activity'. For example, the molecular function term pyruvate dehydrogenase activity ; GO:0004738 describes the enzyme activity whereas the cellular component term pyruvate dehydrogenase complex ; GO:0045254 describes the multi-subunit structure in which the enzyme activity resides.<br />
<br />
=Receptor-ligand complexes=<br />
As a rule, GO terms to indicate association of a receptor with its ligand should not be created, as their complex may not always be stable, and there could be a potential explosion of terms. However, we should allow for exceptions. The IntAct database wouldn't curate receptor-ligand complexes if these consisted of a single chain of each, but it will curate complexes when the ligand is not monomeric and receptors oligomerize upon ligand binding. An example of this is GO:1990270 'platelet-derived growth factor receptor-ligand complex', where the ligands are always dimeric and the receptor dimerizes upon ligand binding. (Also, in the case of GO:1990270, the complex has been shown to exist in a variety of experiments, including crystals, pull downs, comigrations, competition assays and more.)<br />
<br />
<br />
=Notes from working group=<br />
*NOTE: This is a work in progress and includes continuing discussion with IntAct as well as the GOC.<br />
*Last updated: 9/6/2015, Paola.<br />
<br />
*Main working group: Birgit, David Osumi-Sutherland (DOS), Paola, Sandra.<br />
<br />
== Background and rationale ==<br />
<br />
Recently, GO and IntAct have started to work together to improve the 'protein complex' branch in GO, making it less flat and more informative, and to provide species-agnostic GO terms that IntAct can reference to for their species-specific curation projects, namely the [http://www.ebi.ac.uk/intact/complex/ Complex Portal]. At the time of writing (Spring 2015) the focus of the Complex Portal lies on human, mouse, yeast and E.coli, but it can take direct curation requests as well (intact-help@ebi.ac.uk). Other MODs are encouraged to collaborate directly. <br />
<br />
Here, we collect current guidelines on protein complex terms, to aid GO curators in discerning whether a protein complex belongs in GO or not, and if yes, in including all necessary information when requesting a new protein complex.<br />
<br />
== Protein complexes in GO ==<br />
<br />
=== Rule 1: Is the complex stable? ===<br />
<br />
In GO, 'protein complex' is defined as "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical."<br />
<br />
When in doubt, how can a curator figure out if a complex is really stable?<br />
<br />
We can refer to the IntAct Complex Portal Rules [http://www.ebi.ac.uk/intact/complex/documentation/]. These are reported below for reference, and in a definition comment to 'protein complex' to serve as annotation guidance:<br />
<br />
===== What can be described as a complex? =====<br />
<br />
'''A stable set of (two or more) interacting macromolecules such as proteins which can be co-purified by an acceptable method and have been shown to exist as an isolated, functional unit in vivo. Any interacting non-protein molecules (e.g. small molecules, nucleic acids) will also be included.'''<br />
<br />
===== What should not be captured: =====<br />
*Enzyme/substrate, receptor/ligand or any similar transient interactions unless these are a critical part of the complex assembly (e.g. PDGF receptors only become 'dimeric' when linked by the dimeric ligand forming a tetramer).<br />
*Proteins associated in a pulldown/coimmunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose affinity complex.<br />
*Any literature complex where the only evidence is based on genetic interaction data.<br />
*Partial complexes.<br />
<br />
Note:<br />
*If the complex is not stable, it's just protein binding. Interactions can then be captured by a protein-protein interaction DB such as IntAct. <br />
*Beware of partial complexes shown experimentally, especially when crystallised. Some subunits (e.g. transmembrane subunits) cannot be expressed as recombinant proteins and are 'left out' of detailed studies. More reading is often necessary to find out what the full complex is thought to be.<br />
<br />
===== Tricky cases we DO (or could) capture in the IntAct Complex Portal: =====<br />
<br />
*Substrates or ligands if the enzyme or receptor complex only forms in their presence (see PDGF receptors above, e.g. [http://www.ebi.ac.uk/intact/complex/details/EBI-9082861 EBI-9082861]). These terms would also qualify for GO.<br />
<br />
*Homologous proteins, with the same functionality, which would be inferred by sequence similarity to form a complex but for which no physical link has been demonstrated, e.g. proteins A and B have been shown to physically interact and form a functional complex, protein C is a homologue of protein B by sequence similarity and is know to have the same function as B but protein A-C interaction has not been demonstrated experimentally. E.g. SUMO - E1 ligase complexes where there is interaction evidence for binding with SUMO1 ([http://www.ebi.ac.uk/intact/complex/details/EBI-9345927 EBI-9345927]) but not with SUMO2 ([http://www.ebi.ac.uk/intact/complex/details/EBI-9349603 EBI-9349603]).<br />
<br />
*The Complex Portal could also hold transient complexes, e.g. signaling complexes. We have not created any of these to date but they are possible, and controlled vocabulary terms exist to distinguish the two classes. BUT - they would probably fall outside the scope of GO if GO limit themselves to stable complexes.<br />
<br />
*We can also curate complexes that lack full experimental evidence but are commonly regarded as existing, e.g. complexes submitted by ChEMBL for which we only have pharmacological evidence. These complexes are tagged with ECO:0000306 - inferred from background scientific knowledge by manual assertion. E.g GABA ([http://www.ebi.ac.uk/intact/complex/details/EBI-9008426 EBI-9008426]) receptors and many other transmembrane receptors.<br />
<br />
===== Expanded definition comment for GO:0032991 'protein-containing complex’: =====<br />
<br />
"A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole."<br />
<br />
=== Rule 2: Is the complex species-agnostic? ===<br />
<br />
*GO should host species-agnostic complexes, ideally conserved across taxa. Where this isn't known, we should still make the definition generic, and add 'For example, in human this complex contains...' as a definition gloss or definition comment.<br />
<br />
*Species-specific complexes don't belong in GO, but IntAct/Complex Portal and/or PRO can take them. (We acknowledge that GO contains many historic terms that contravene this rule. For the time being, the agreement is that we will not review them globally, though we may fix them if and when we come across them.)<br />
<br />
*We may, however, need taxon restrictions on a case-by-case basis such as complexes that only exist in prokaryots or eukaryotes. Curators are encouraged to provide these information, if applicable, when they request a new term (or come across an existing one).<br />
<br />
=== Rule 3: Does the complex have a molecular function? ===<br />
<br />
*If yes, add capable_of link(s) to molecular function terms. These links are used by the reasoner to place the complex into the correct branch under 'protein complex'.<br />
<br />
=== Rule 4: Is the complex known to be involved in one or more biological processes? ===<br />
<br />
*If yes, add capable_of_part_of links to biological process(es).<br />
<br />
*Note: we decided not to use BP as a qualifier for making grouping terms for complexes as these would become too unspecific, e.g. 'regulatory complex' could include most complexes!<br />
<br />
=== Rule 5: Does the complex contain conserved subunits? ===<br />
<br />
*Many complexes are defined by their subunit composition rather than their activity. Such complexes will still be accepted into the GO. The curator should endeavour to place the new complex as child of a functional parent or a parent term also defined by its composition, in some cases this may be difficult and those complex terms will be direct children of 'protein complex'.<br />
<br />
*Complex definitions should include their function or the process they are involved in as well as the defining subunits (using the style "In human, it is composed of..."). However, we need to be careful not to explode the subunit composition in the definition if they turn out to be rather different in the different branches of the tree of life. In such a situation, the curator and editor should consider broadening the term name and adding the various subunit-defined names as narrow synonyms. This should be handled on a case-by-case basis.<br />
<br />
*Complexes defined by their subunits but functionally identical to a more generic parent term should not be created as separate GO terms but added to the parent term as narrow synonyms. The specific complex belongs in the Complex Portal.<br />
<br />
[DOS to look into some automatic reasoning across subunits but we think it may become tricky. To be discussed among editors.]<br />
<br />
=== Rule 6: Where is the complex located? ===<br />
<br />
*Indicate cellular location as specifically as possible, unless parent already has one.<br />
<br />
*The CC location is meant for the complex as a whole. We discussed this in the context of transmembrane complexes where one or more members of the complex are located on one side of the membrane only or have no membrane attachment at all. As gene products have the part_of relationship with the complexes this is fine (and the only way of reflecting the CC for the complex as a whole).<br />
<br />
*If we have complexes defined by their location (see below under 'Futures Plans'), does the reasoner take the part_of relationship to place them automatically into the right complex-by-location branch? [DOS?]<br />
<br />
*Complexes simply defined by the cell type they are expressed in are not permitted.<br />
<br />
=== Rule 7: Adding appropriate is_a relationships ===<br />
<br />
*We are trying to avoid placing complexes as direct is_a children of 'protein-containing complex', by adding some granularity to this ontology branch.<br />
<br />
*An is_a parent of a complex can be a <br />
# complex defined by its activity, via the complex-by-activity TG template<br />
# complex defined by its location, such as 'plasma membrane complex'. [Update: DOS added some useful protein complex grouping terms based on location, such as 'membrane protein complex'.]<br />
# complex defined by its subunit composition. This may be related to protein families but it may be difficult to make it a rule/template (see above).<br />
*We decided NOT to define complexes by their process or MF binding as they would become too generic.<br />
<br />
*Note: Complexes can have multiple parents!<br />
<br />
*Note: if capable_of MF links are added, and/or if location information is provided as part_of CC, the automatic assert-inference script will take care of placing most newly created protein complex terms more granularly in the ontology.<br />
<br />
=== Rule 8: Adding appropriate part_of relationships ===<br />
<br />
*All complexes should have a part_of link to a cellular component term, even if it's very generic, such as 'cell'.<br />
*CC does not have to be added manually if it's the same as the parent term as it will be inferred.<br />
*If the CC is more specific than the parent, the part_of relationship must be added manually.<br />
*Complexes can be subcomplexes of larger entities and can therefore be part_of another protein complex. If the larger complex necessarily needs the smaller one as its component in order to be functional, a has_part link should also be added (larger complex has_part smaller complex).<br />
*Complexes cannot have several part_of relationships to different CCs, as part_of must ALWAYS be true. If a complex can be part of several larger complexes or be found in several locations, such as cytoplasm and nucleus where it may have different functions, separate terms may have to be considered. [This point is still open to discussion, see https://sourceforge.net/p/geneontology/ontology-requests/10745/, now with DOS. To be discussed on Editor's call.]<br />
<br />
== How to request protein complexes in GO based on the above ==<br />
<br />
*Use the GO-ontology GitHub tracker https://github.com/geneontology/go-ontology/issues<br />
<br />
*Name:<br />
*Definition:<br />
*relationships: is_a [complex parent], part_of [subcellular location], capable_of MF, capable_of_part_of BP<br />
*Synonym(s):<br />
<br />
*We no longer require dbxrefs to the Complex Portal as these will be directly imported.<br />
<br />
*Complex Portal is happy to curate requested complexes at the same time as adding to the GO structure. Curators are encouraged to curate complexes directly into the Complex Portal after being trained by us. SGD and UCL are doing this already. Contact us via the yellow "request complex" tile on the home page: http://www.ebi.ac.uk/complexportal/<br />
<br />
== Complex Definition field ==<br />
<br />
The way definitions of older protein complex terms are structured is not always consistent. Currently, we recommend the following:<br />
<br />
*Start the definition referring to the function (if applicable), such as 'A protein complex capable of X function...'.<br />
<br />
*Processes can also be mentioned in the def. <br />
<br />
*Subunits should only be listed in the definition if the complex is defined by its composition rather than function (see Rule 5 above). If the complex is defined by its function, subunit composition should go into a definition comment or be added as narrow synonyms.<br />
<br />
*Complexes should NOT be defined by their stoichiometry, though this may be mentioned in the def as a 'soft' comment (definition gloss), or in a definition comment. The rationale behind this recommendation is that, as knowledge advances and more examples are found, stoichiometry defs would have to be updated, causing a lot of work. It is perfectly fine though to mention something like 'usually consists of a catalytic and a regulatory subunit and possibly further accessory subunits...'. <br />
<br />
*We are aware that many older terms' definitions do not conform to these guidelines. At the moment, however, we do not plan on fixing all of them. We may make corrections on a case-by-case basis and/or when working on a given branch.<br />
<br />
== Future plans ==<br />
as discussed in a meeting with Birgit Meldal, Sandra Orchard, David Osumi-Sunderland and Paola Roncaglia on 28/4/2015<br />
<br />
We discussed how we can make 'quick gains' in making the ontology more granular beyond the fixes Birgit does on a case by case basis. This is to target historic terms that have only 'protein complex' as a parent because they have no annotation extensions. The aim is to have most complexes grouped either by their function, location or subunit composition.<br />
<br />
*Do a pass through term names and definitions to find major groups of complexes that can be grouped by function, e.g. 'catalytic complex' (the term exists but many historic terms have not automatically been classified as such as they have no capable_of extensions). Other keywords: kinase, activity, viral, receptor, respiratory chain... [BM, SO & DOS]<br />
<br />
*Add parent terms based on location, such as 'membrane complex' and children or 'mitochondrial complex'. Can the reasoner place complexes automatically into this branch based on their part_of relationship (see above Rule 6)? Should we have a TG template for this? [BM, DOS]<br />
<br />
*Combine activity and location, such as 'membrane receptor complex'.<br />
<br />
*We discussed grouping by protein families but this may be tricky. Decide on a case by case basis. A working example are the BCL protein family complexes which cannot be grouped by function as they may be pro- and/or antiapoptotic.<br />
<br />
== Previous work ==<br />
<br />
Emily started documentation here, in case it's helpful, but this wasn't worked on since 2011:<br />
http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects<br />
<br />
<br />
Birgit's comments [from email to Paola]: <br />
<br />
Inheritance of annotations:<br />
I agree with the wiki, you cannot inherit MF from a complex to a subunit and even a CC is problematic, see the transmembrane example above. This needs more thinking about. I don't know what you are doing right now...<br />
<br />
Orthologies:<br />
We infer within taxon groups, e.g. human to mouse to rat or any other mammal etc, depending on where the exp evidence comes from. We systematically infer human-mouse. We have a few pombe complexes inferred from yeast (Sc!) but we don't do it systematically.<br />
<br />
Paralogues:<br />
We make inferences between related complexes in the same species when the gene products are very similar, e.g. hemoglobin chains for adult and developmental complexes.<br />
<br />
'Large' complexes:<br />
We have tackled the 'mediator' and we can now link to RNACentral for RNAs so time permitting we'll tackle the 'biggies' soon!<br />
<br />
Pro:<br />
We have a list of Pro complexes that we consult for refs.<br />
<br />
== Useful links ==<br />
<br />
Complex Portal, http://www.ebi.ac.uk/complexportal/<br />
<br />
<br />
----<br />
[[Category:GO Editors]][[Category:Ontology]]<br />
[[Notes_on_specific_terms |Back to: Notes on specific terms]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=726292019 Cambridge GOC Meeting Logistics2019-01-14T08:43:28Z<p>Bmeldal: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
<br />
==Planned Schedule== <br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|}<br />
<br />
NOT attending (please indicate if you 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 (checkout 13th). <br />
* Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 1 min 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 />
=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>Bmeldalhttps://wiki.geneontology.org/index.php?title=2019_Cambridge_GOC_Meeting_Logistics&diff=726282019 Cambridge GOC Meeting Logistics2019-01-14T08:43:11Z<p>Bmeldal: /* Attendees */</p>
<hr />
<div>=GOC Meeting, Cambridge , April 11th - 12th, 2019=<br />
<br />
* Location: <br />
** [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
<br />
<br />
==Registration==<br />
* Please register at: XXXXXXXXX at [http://www.unicen.cam.ac.uk/ Cambridge University Centre], Hicks Room.<br />
* The meeting will be £XXX in total. Please bring cash (GBP). You will receive an invoice upon payment at registration.<br />
<br />
<br />
==Planned Schedule== <br />
<br />
<br />
==Meeting Venue and Directions==<br />
* Address Granta Place, Mill Lane, Cambridge, CB2 1RU<br />
** [https://map.cam.ac.uk/University+Centre#52.201128,0.116362,18 Map]<br />
<br />
=Arriving=<br />
<br />
==By Plane==<br />
<br />
(see taxi options from airport in section below)<br />
====Arriving from London Heathrow airport====<br />
<br />
The bus is the cheapest option from Heathrow Airport: there is an hourly bus to Cambridge which leaves from stops at both Heathrow Central Bus Station and Terminal 5. You can check the [http://www.nationalexpress.com/home.aspx National Express website] for timetables and prices. The journey takes around two hours and arrives at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
A faster way to travel would be via taking the London Underground Piccadilly line from the airport to London King's Cross. You can then travel by train from London King's Cross station to Cambridge (the train ticket is approximately £20).<br />
<br />
Another option to reach King's Cross is to take the [https://www.heathrowexpress.com/ Heathrow Express] to Paddington station and change to the London Underground Circle or Hammersmith & City lines. Note that this option is more expensive (around £25, plus £20 for the King's Cross-Cambridge trip) and not much faster than the underground one. If you arrive during the weekend and you book well in advance you may find cheaper tickets for the Heathrow Express service.<br />
<br />
However you reach King's Cross, the trip from there to Cambridge, depending on which train you pick, takes between 50 minutes to 1h and 20 minutes. Add at least 20 minutes to this if you plan to use this occasion to take a picture at Platform 9&#190;, as there will most certainly be a queue!<br />
<br />
You can check trains and times from King's Cross at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
====Arriving from London Stansted airport====<br />
This is the nearest airport to Cambridge, an around 30 minute trip.<br />
Depending on your time of arrival, you will find every half an hour or hourly a direct train to Cambridge, which takes approximately 30 minutes to reach the town. The cost of a one-way ticket is £10. You can check trains and times on [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx]. You can also download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device. Just remember to activate the ticket before going on the train. <br />
<br />
An alternative to the train for arriving in Cambridge from Stansted is via using the National Express coach service. You can check [http://www.nationalexpress.com/home.aspx their website] for times and prices. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Luton airport====<br />
You can go to the [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and prices of buses from Luton to Cambridge. The ride takes approximately 2 hours. The airport bus stops at [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====Arriving from London Gatwick airport====<br />
The best way to get from London Gatwick airport to Cambridge is to take the train. There is a frequent service from Gatwick to St. Pancras station, which is adjacent to King's Cross station, where you can catch a train to Cambridge. Check train timetables from Luton at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx].<br />
<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
==Taxis==<br />
<br />
If you prefer to reach Cambridge from any airport via a taxi transfer, a company that we can suggest is [http://www.kenwaycars.co.uk/ Kenway]. You can make a booking enquiry through their website or by sending an email to info@kenwaycars.org, specifying airport, flight number, and a destination address.<br />
<br />
If you need a taxi company once in Cambridge, you can use companies like [https://www.panthertaxis.co.uk/ Panther taxi] (01223 715715) or [http://www.camcab.co.uk/ Camcab] (01223 704704). There is Uber in Cambridge, but since the taxis are quite cheap, a Uber ride can often cost the same or more (in rush hours) than a regular taxi ride.<br />
<br />
==From London City Center==<br />
<br />
In case you are going to spend some time in London before coming to Cambridge, you have a few options for coming here.<br />
<br />
====By Train====<br />
<br />
Cambridge is directly connected to London King's Cross and London Liverpool Street. <br />
You can check trains and times at [http://www.nationalrail.co.uk/default.aspx http://www.nationalrail.co.uk/default.aspx] and download the [https://www.thetrainline.com/ trainline app] on your phone if you want to get e-tickets directly on your device.<br />
<br />
'''''N.B. If you arrive at Cambridge via train, you will need your train ticket to exit the station.'''''<br />
<br />
====By Bus====<br />
<br />
Check [http://www.nationalexpress.com/home.aspx National Express website] to see timetables and info. The bus services stop on [https://www.google.co.uk/maps/place/Parkside,+Cambridge+CB1+1JE/@52.2033603,0.127031,17z/data=!3m1!4b1!4m5!3m4!1s0x47d87090f452bfc3:0x7edb60c4a5b37510!8m2!3d52.203357!4d0.1292197 Parkside, Parker's Piece].<br />
<br />
====By Car====<br />
<br />
If you arrive by car a suggestion would be to use the Park and Ride services (details at [http://cambridgeparkandride.info/ http://cambridgeparkandride.info/]), as parking in Cambridge is a nightmare.<br />
<br />
=Attendees=<br />
Please add your name to the table if you intend to attend the meeting and whether you will be booking accommodation (or have booked) at the Double Tree hotel using the discount code, so we can get an estimate.<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! I am going to stay at the Double Tree Hotel (Yes/No)<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| No<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Yes<br />
| Yes<br />
|-<br />
| Judy Blake<br />
| Jackson Lab<br />
| Yes<br />
| Yes<br />
-<br />
| Birgit Meldal<br />
| EBI (ComplexPortal / IntAct)<br />
| Yes<br />
| No<br />
|}<br />
<br />
NOT attending (please indicate if you 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 (checkout 13th). <br />
* Address: DoubleTree by Hilton Cambridge City Centre, Granta Place, Mill Lane, Cambridge, CB2 1RT, UK (about 1 min 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 />
=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>Bmeldalhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2019-01-08&diff=72603Annotation Conf. Call 2019-01-082019-01-09T09:28:38Z<p>Bmeldal: /* Minutes */</p>
<hr />
<div>= Meeting URL =<br />
*https://stanford.zoom.us/j/976175422<br />
<br />
= Agenda =<br />
== 2019 Plans ==<br />
=== Annotation Group Priorities ===<br />
==== Annotation Review ====<br />
*[http://snapshot.geneontology.org/reports/index.html Reports from pipeline]<br />
**Manual annotations<br />
**Mapping files, e.g. InterPro2GO<br />
***Still some 'gocheck_do_not_annotate' mappings in InterPro2GO<br />
*Molecular Function refactor<br />
*Transcription<br />
*Annotation to regulation terms - what does GO mean by 'regulation'?<br />
*Other methods to identify annotations to review<br />
**Matrix<br />
<br />
==== Metrics ====<br />
*Tracking, reporting number of publications as a measure of information content<br />
*Tracking changes to annotations over time<br />
<br />
==== Topic-Specific Projects ====<br />
*Tie-up an loose ends for existing signaling projects<br />
**GPCR, JAK/STAT, Wnt (ideally a GO-CAM model for each pathway - as a template)<br />
*Continue with additional signaling pathways<br />
*Transcription<br />
*Protein-containing complexes<br />
**Revive the working group<br />
**[https://docs.google.com/document/d/1vRbTsaPJQEToMPQW4CRogGUS82Zo-xzGQhI60nR4N8s/edit?usp=sharing Summary of open protein complexes issues]<br />
<br />
==== GO-CAM/Noctua ====<br />
*Continued discussion of modeling questions<br />
*Generation and use of templates<br />
*Import of Reactome pathways<br />
*Import of whole genomes<br />
<br />
==== Documentation ====<br />
*Relations and their use in annotation and ontology development<br />
**gp2term relations<br />
**GO-CAM relations<br />
**new relations in ontology development, e.g. describing participants in metabolic processes<br />
<br />
==== PAINT ====<br />
*Continue curation of families with at least one human gene<br />
*Review families with new or revised experimental annotation<br />
<br />
==== Pipeline ====<br />
*Any questions or issues that groups are having?<br />
*Finalize specs for new gpad/gpi file formats and transition to using these two files for internal consortium data exchange<br />
*Literature tracking system - gather requirements<br />
**Track curation status of papers<br />
**Add comments to papers<br />
<br />
=== Meetings ===<br />
==== Conference Calls ====<br />
*Tuesdays at 8am PDT<br />
**1st Tuesday: Alliance Biological Function<br />
**2nd Tuesday: GO Consortium<br />
**3rd Tuesday: GO-CAM Working Group<br />
**4th Tuesday: GO-CAM Working Group<br />
**5th Tuesday: Alliance Biological Function<br />
*One Zoom URL for all - https://stanford.zoom.us/j/976175422<br />
<br />
==== Consortium Meetings ====<br />
*GOC meeting - Cambridge, UK April 11th - 12th (right after ISB meeting)<br />
*GOC meeting - Berkeley, CA October 7th - 10th ???<br />
**SAB<br />
**GO user's meeting<br />
<br />
==== Working Meetings ====<br />
*Whole genome import - CA last week of January<br />
<br />
= Minutes =<br />
*On call: Barbara, Birgit (late), Chris M., David, Dustin, Giulia, Harold, Helen, Kevin M, Kimberly, Laurent-Philippe, Li, Liz, Midori, Patrick, Petra, Rob, Ruth, Sabrina, Seth, Shur-Jen, Stacia, Stan, Suzi, Tanya<br />
<br />
== 2019 Plans ==<br />
=== Annotation Group Priorities ===<br />
==== Annotation Review ====<br />
*We discussed the various topics and methods for and of annotation review<br />
**InterPro2GO mappings - need to follow-up with InterPro on the gocheck_do_not_annotate subset<br />
**Transcription<br />
***Some work still to be done here<br />
***Issues surrounding SO terms used; plan is to collaborate with SO on refining the ontology wrt definitions and placement of promoter and related terms<br />
**Process and regulation of process<br />
***This will likely be a big project, but we want to get the ball rolling.<br />
***Jim B.'s work may help here, as well as the matrix tool<br />
***QC/QA working group will follow-up with this<br />
====Metrics====<br />
*Lists of papers used for annotation can be retrieved from GAFs, QuickGO<br />
*Tracking annotation changes over time will need to be part of our metrics going forward<br />
*ISB - there will be a workshop on evaluating curation database resources; metrics is part of this discussion<br />
==== Topic-Specific Projects ====<br />
*Signaling<br />
**AI: Add documentation on annotating specific signaling pathways to the existing, more general documentation<br />
***Include in this documentation, GO-CAM models and templates that delineate what activities are considered part of the pathway vs regulatory or causally upstream<br />
**Additional pathways to consider reviewing in 2019<br />
***Notch, insulin<br />
****FlyBase has found that one difficulty in delineating pathway members is how to consider transcription factors and branched pathways<br />
*Protein-containing complexes<br />
**Protein complexes WG will re-form in 2019 and try to address the remaining outstanding issues<br />
**Would also be helpful to review criteria for what constitutes membership in a protein-containing complex<br />
==== Pipeline ====<br />
*Literature tracking system will likely be developed in collaboration with the Alliance<br />
<br />
[[Category:Annotation Working Group]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2018-03-27&diff=68289Annotation Conf. Call 2018-03-272018-03-27T06:46:53Z<p>Bmeldal: </p>
<hr />
<div>= Agenda = <br />
== GOC Meeting, NYU, New York, NY, May 12-14th ==<br />
*Reminder to register, and reserve your hotel room before April 6th if staying at the Shelburne NYC<br />
*[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Logistics Logistics]<br />
*[http://wiki.geneontology.org/index.php/2018_NYU_GOC_Meeting_Agenda Agenda]<br />
<br />
== 20th Anniversary GO Meeting, Montreal, CA ==<br />
*Dates set for Oct 17-20<br />
<br />
== Updates on Projects ==<br />
*[https://github.com/geneontology/go-annotation/issues/1592 MAPK cascade- Signaling Project]<br />
*[https://github.com/geneontology/go-ontology/projects/9 Extracellular matrix revisions]<br />
<br />
== Evidence Codes ==<br />
=== RCA ===<br />
*[https://github.com/geneontology/go-annotation/issues/1801 Review RCA evidence code] - Please can the groups listed below review their RCA annotations and decide if they'd still like to keep them and if RCA is still the appropriate evidence code?<br />
**Thank you to everyone who has reviewed their existing RCA annotations.<br />
**Many RCA annotations were removed, but some groups are keeping annotations from papers that use methodology consistent with the definition of RCA.<br />
**Since these annotations come from papers, the originally proposed one-year restriction does not make sense and will not be an annotation rule.<br />
***Please send Kimberly PMIDs for papers that were kept for use as examples in our evidence code documentation.<br />
**That said, periodic annotation review is always a good idea.<br />
**Remaining groups will be contacted individually.<br />
<br />
== Annotating High Throughput Experiments ==<br />
*[https://github.com/geneontology/go-annotation/issues/1796 Proposal for curating extracellular matrix proteins from proteomics experiments]<br />
*[https://github.com/geneontology/go-annotation/issues/1885 Review reference guidelines for GAF, GPAD]<br />
<br />
== Annotation Survey ==<br />
*We are putting together a survey on annotation practices across the GOC<br />
*Should be ready very soon<br />
*Would like results before the GOC meeting in NY<br />
<br />
== GO-CAM/Noctua ==<br />
*Next call tomorrow, Wednesday, March 28th at 11:00am EDT (see Google calendar)<br />
<br />
== Protein Complexes Working Group ==<br />
*Next call on Monday, April 23rd at 1:10pm EDT (see Google calendar)<br />
<br />
= Minutes = <br />
*On call:<br />
<br />
<br />
[[Category:Annotation Working Group]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Logistics&diff=675342018 NYU GOC Meeting Logistics2018-02-16T08:27:31Z<p>Bmeldal: /* 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 />
=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 />
| 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 />
|Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Seth Carbon<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 />
|}<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 />
|}<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>Bmeldalhttps://wiki.geneontology.org/index.php?title=2018_NYU_GOC_Meeting_Logistics&diff=675332018 NYU GOC Meeting Logistics2018-02-16T08:27:17Z<p>Bmeldal: /* 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 />
=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 />
| 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 />
|Pascale Gaudet<br />
| SIB/GOC<br />
| Yes<br />
| Yes<br />
|-<br />
|Seth Carbon<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 />
|}<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 />
| no<br />
| maybe<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>Bmeldalhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=650562017 Cambridge GOC Meeting Logistics2017-09-06T07:40:22Z<p>Bmeldal: /* 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 />
| Moni Munoz-Torres<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 />
<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>Bmeldalhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=650192017 Cambridge GOC Meeting Logistics2017-09-05T07:38:15Z<p>Bmeldal: /* 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 />
| Yes, w/Liz, (1) signaling<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 />
|Astrid Laegreid<br />
|NTNU<br />
|Yes<br />
|Yes<br />
|No<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>Bmeldalhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=644892017 Cambridge GOC Meeting Logistics2017-07-17T09:59:41Z<p>Bmeldal: /* 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 />
* International Flights and travel to Cambridge (to be added)<br />
<br />
===Meeting Dinner===<br />
* Dinner will be on Monday or 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 />
|<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-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 />
| 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 />
| Sabrina Toro<br />
| ZFIN<br />
| Yes<br />
| Yes<br />
|<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Yes<br />
| Yes<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 />
|}<br />
<br />
NOT attending:<br />
<br />
Peter D'Eustachio<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 />
** To book phone +44 (0)1223 351631. 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>Bmeldalhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=635902017 Cambridge GOC Meeting Logistics2017-04-21T09:52:16Z<p>Bmeldal: /* 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 November 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday November 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 />
* International Flights and travel to Cambridge (to be added)<br />
<br />
===Meeting Dinner===<br />
* Dinner will be on Monday or 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 />
<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Seth Carbon<br />
| BBOP<br />
| Yes<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Sandra Orchard<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
|}<br />
<br />
NOT attending:<br />
<br />
==Accommodations==<br />
<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=2017_Cambridge_GOC_Meeting_Logistics&diff=635892017 Cambridge GOC Meeting Logistics2017-04-21T09:51:57Z<p>Bmeldal: /* 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 November 3rd''': <br />
:* Meeting will run from 9am to 5pm.<br />
<br />
*'''Wednesday November 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 />
* International Flights and travel to Cambridge (to be added)<br />
<br />
===Meeting Dinner===<br />
* Dinner will be on Monday or 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 />
<br />
|-<br />
| Valerie Wood<br />
| PomBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Paola Roncaglia<br />
| EMBL-EBI<br />
| Yes<br />
| Yes<br />
|-<br />
| Petra Fey<br />
| dictyBase<br />
| Yes<br />
| Yes<br />
|-<br />
| Seth Carbon<br />
| BBOP<br />
| Yes<br />
| Yes<br />
|-<br />
| Helen Attrill<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase (Cambridge)<br />
| Yes<br />
| Yes<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Rachael Huntley<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Nancy Campbell<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Barbara Kramarz<br />
| UCL<br />
| Yes<br />
| Yes<br />
|-<br />
| Sandra Orchard<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
|-<br />
| Birgit Meldal<br />
| EBI-IntAct<br />
| Yes<br />
| Yes<br />
<br />
<br />
|}<br />
<br />
NOT attending:<br />
<br />
==Accommodations==<br />
<br />
<br />
== Local activities ==<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Annotation_Conf._Call_2016-04-26&diff=60554Annotation Conf. Call 2016-04-262016-04-26T16:07:50Z<p>Bmeldal: </p>
<hr />
<div>=Conference call Format=<br />
Standard Bluejeans link from meeting home page: https://bluejeans.com/993661940<br />
<br />
=Agenda=<br />
==IDA or IEP for an isoform annotation==<br />
Recently Karen was annotating a paper where an isoform-agnostic antibody was used to detect the presence of a protein in a cell. Subsequent experiments showed that an RNA coding for a specific isoform had the same localization, supporting that the protein isoform was localized to that component. The question came up as to whether we should use IDA or IEP for evidence to support this. Since the experiment did not address the protein isoform itself, is it an IDA? <br />
<br />
Also worth noting that if we decide that this is IEP, we will need to change the rules on the validation script that checks GAFs since IEP is currently only allowed for Process annotations.<br />
<br />
==Switching over automated pipelines for high-throughput studies and bulk annotations==<br />
<br />
We will work with Marcos to get an ECO code to use for GO<br />
annotations that derive from high-throughput experiments. Once we have<br />
this, annotators should apply it moving forward, and also retroactively to<br />
existing HT annotations. We are hoping to design ways to help groups identify<br />
existing annotations from high-throughput studies.<br />
<br />
How difficult would it be for submitters of GAF files to put “InterPro<br />
Consortium” in the “assigned by” field, for IEA annotations derived from<br />
that source? Likewise, for other IEA methods, we should try to identify<br />
an appropriate assigner, so we give them appropriate credit for the<br />
annotations.<br />
<br />
==Annotation Extension Announcements==<br />
* The regulates relation and its children are now allowed in annotation extensions<br />
* The 'dependent_on', 'requires_substance' and 'localization_dependent_on' relations are now obsolete. If these are being used, it is causing a GAF to fail the Jenkins check. Please be sure that your group modifies or removes these extensions in a timely manner.<br />
<br />
==Annotation Consistency Exercise==<br />
<br />
Perhaps the perfect time to remind people of this:<br />
https://github.com/geneontology/go-ontology/issues/11709<br />
<br />
From PomBase<br />
<br />
PMID: 11493649<br />
Fission yeast mfr1 activates APC and coordinates meiotic nuclear division with sporulation.<br />
<br />
Related Github tickets (These are quite long so I'll attempt to summarize):<br />
<br />
https://github.com/geneontology/go-ontology/issues/11977<br />
The question here, was whether we needed a term for the APC complexed with its various inhibitors (researchers usually refer to these complexes as APC-(inhibitor/activator superscript) ). This gets quite complicated, because there are different activators and activators for different substrates at different cell cycle transitions, and for mitotic and meiotic cell cycles. <br />
I believe that the consensus from the GO meeting is that we don't need these terms, and we use "x complex binding" to represent these specific inhibitor/activator-complex interactions (the logic being that only the functional complex is represented in GO)? <br />
<br />
The second issue, was that we were following a precedent, and requesting these specific "APC-activator activity" terms.<br />
https://github.com/geneontology/go-ontology/issues/11757<br />
The solution here was simple. The terms will all be merged back to the "function" term (i.e ubiquitin ligase activity, ubiquitin ligase inhibitor activity, and ubiquitin ligase activator activity). So, although these terms still exist they will be merged very soon.<br />
<br />
{|<br />
| Gene || Qualifier || Term || ID || Number of annotations || Evidence code || with || Extensions || Comments<br />
|-<br />
| MOLECULAR FUNCTION || || || || || || || || <br />
|-<br />
| mfr1 || || protein complex binding || GO:0032403 || 1/4 || IPI || cut20 || has_input anaphase-promoting complex GO:0005680 || <br />
|-<br />
| mfr1 || || anaphase-promoting complex binding || GO:0010997 || 1/4 || IPI || cut20 || || <br />
|-<br />
| cdc2 || || cyclin-dependent protein kinase activity || GO:0097472 || 1/4 || IDA || || happens_during meiosis II cell cycle || <br />
|-<br />
| BIOLOGICAL PROCESS || || || || || || || || <br />
|-<br />
| mfr1 || || sporulation resulting in formation of a cellular spore || GO:0030435 || 1/4 || IMP || || || couldn’t decide between these P two terms [2nd requires background knowledge])<br />
|-<br />
| mfr1 || || negative regulation of ascospore formation || GO:0075297 || 1/4 || IMP || || || couldn’t decide between these P two terms [2nd requires background knowledge])<br />
|-<br />
| mfr1 || || positive regulation of ascospore formation || GO:0075296 || 3/4 || IMP || || || <br />
|-<br />
| mfr1 || || positive regulation of protein catabolic process || GO:1903364 || 1/4 || IMP || || has_input cdc13,happens_during meiosis II cell cycle phase || <br />
|-<br />
| mfr1 || || positive regulation of cyclin catabolic process || GO:2000600 || 1/4 || IMP || || has_input cdc13, happens_during GO:0007138 (meiotic anaphase II) &#124; causally_upstream_of GO:1904030 (negative regulation of cyclin-dependent protein kinase activity) || <br />
|-<br />
| mfr1 || || anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process || || 1/4 || IMP || || has_input cdc13 || <br />
|-<br />
| mfr1 || || negative regulation of cyclin-dependent protein kinase activity || GO:1904030 || 1/4 || IMP || || regualtes_o_has_agent cdc2, regulates_o_happens_during meiosis anaphase II, happens_during meiosis II anaphase II || <br />
|-<br />
| mfr1 || || NTR positive regulation of meiotic exit || || 1/4 || IMP || || || <br />
|-<br />
| cdc13 || || NTR negative regulation of meiotic exit || || 1/4 || IMP || || || <br />
|-<br />
| cdc13 || || negative regulation of ascospore formation || GO:0075297 || 4/4 || IDA/IMP || || happens_during meiosis II cell cycle || <br />
|-<br />
| CELLULAR COMPONENT || || || || || || || || <br />
|-<br />
| cut20 || || nucleus || GO:0005634 || 1/4 || IDA || || || even though they say this, I am not convinced. I would look for other evidence.<br />
|-<br />
| mfr1 || || nucleus || GO:0005634 || 1/4 || IDA || || || even though they say this, I am not convinced. I would look for other evidence.<br />
|-<br />
| mfr1 || colocalizes_with || anaphase-promoting complex || || 1/4 || || || exists_during GO:0007138 (meiotic anaphase II) || (I am being quite uncharitable here as they never show more than an IP and some IF)<br />
|-<br />
| mfr1 || || APC-Fzr1/Mfr1 complex || GO:1990857 || 2/4 || IPI || cut20 || happens_during 7135 meiosis II || <br />
|}<br />
<br />
=Minutes=<br />
==In attendance==<br />
*Berkeley: Chris, Moni, Suzi<br />
*EBI: Aleks, Melanie, Paola<br />
*FlyBase: Helen<br />
*IntAct: Birgit<br />
*MGI: David H., Karen<br />
*PomBase: Antonia, Midori, Val<br />
*RGD: Stan<br />
*SGD: Edith<br />
*TAIR: Tanya<br />
*USC: Paul T.<br />
*WB: Kimberly<br />
*Zfin: Sabrina<br />
IntAct: Birgit (4.10 pm BST)<br />
<br />
==IDA vs IEP==<br />
*Paper looking at isoform-specific mRNA localized to a specific region of the cell <br />
*Annotation using IEP for the protein's CC annotation<br />
*IEP is usually only used for BP, so this annotation is getting flagged as an error<br />
*Can change EC to IDA to avoid flagging, but is this correct?<br />
*Should the identifier in Col. 17 be the protein isoform or an RNA isoform?<br />
*Is there another evidence code that could be used?<br />
*The spirit of the experiment is more in line with IDA<br />
*Will leave evidence code as IDA, no change needed to IEP evidence rules<br />
<br />
==High-throughput Experiments and Evidence Codes==<br />
*Will work with Marcus to generate evidence codes for high-throughput experiments<br />
*Then users can distinguish between evidence from an HTP experiment vs evidence generated in an hypothesis-driven manner<br />
*We will need to define what we consider high-throughput experiments<br />
*Will then retrofit existing annotations<br />
<br />
==IEA Pipelines==<br />
*Currently, in the Assigned_by field of the GAF, IEAs are attributed to the group who ran the algorithm/program<br />
*Propose a change to more accurately attribute the annotations<br />
*For example, if MGI runs InterProScan, InterPro would get credit for the Assigned_by field, but MGI would still be the source of the annotation<br />
*For groups doing this, would it be possible to change the Assigned_by field to reflect, and give credit to, the group that actually makes the manual mappings?<br />
<br />
==Annotation Extensions==<br />
*Regulates and child relations are now allowed in annotation extensions<br />
*Obsolete relations: dependent_on, localization_dependent_on, and requires_substance<br />
*Jenkins will flag annotations using these relations and the GAF will fail the QC check<br />
<br />
==Annotation Consistency Exercise==<br />
*'''ACTION ITEM:''' Check meiosis annotations to be consistent with definition: https://github.com/geneontology/go-ontology/issues/11709<br />
*Val - background slides<br />
**Anaphase Promoting Complex (APC) regulates cell cycle transitions<br />
**The APC has a lot of variations, although there is a core complex of 12 subunits, conserved across species<br />
**For example, there are different activators (Fizzy) and inhibitors<br />
**Authors designate different APC complexes as APC-cdc20, for example<br />
**Should we be creating different protein complex terms for each of these variations on the complex?<br />
**There would be a lot of new complex terms, then, and where would you stop?<br />
**For annotation, we want to be representing the active form of the complex<br />
**Could instead just annotate different activators and inhibitors with 'APC complex binding'?<br />
*Antonia - paper<br />
**Fission yeast background<br />
**Mfr1 has sequence similarity to an APC activator<br />
**Mfr1 expressed specifically during meiosis<br />
**Mfr1 null mutations results in delayed sporulation and cdc13 cyclin is stabilized<br />
**Mfr1 co-localizes with and interacts with APC during anaphase II<br />
*Annotations<br />
**Four different groups submitted annotations<br />
***Molecular Functions<br />
****Different annotations for APC complex binding (specific term vs AE), but they are semantically equivalent<br />
***Biological Process<br />
****Generally the same annotations, but curators chose terms with different granularity<br />
****Various flavors of ascospore formation, catabolic process, meiotic exit, regulation of kinase activity<br />
****Antonia and Val discussed whether it was more accurate to annotate to ascospore formation or meiotic exit, but regulation of ascospore formation seemed appropriate in this case.<br />
***Cellular Component<br />
****For Mfr1 - nucleus, APC complex, or individual APC complexes, e.g. APC-Fzr1/Mfr1 complex<br />
*Original question - do we need these specific complex terms in GO?<br />
**The activator is required for the complex to have its activity<br />
**Does the complex function differently when complexed with its different activators or inhibitors? If not, then perhaps the specific complex terms are not needed.<br />
**The complexes have the same activity, but different targets; does that make them different?<br />
**Yes it probably does because the substrate specificity allows the APC complexes to function as different machines<br />
**Can look at recent papers and consult with experts and follow up<br />
**Can we come up with a way to assess different inferences based upon the alternative representations?<br />
**Could load models into Protege, run OWL reasoner, do DL queries, and see if the outcomes make sense<br />
**'''ACTION ITEM''': Work out SOP for testing different model representations<br />
<br />
<br />
<br />
<br />
[[Category: Annotation Working Group]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_complexes&diff=59418Protein complexes2015-12-09T09:30:20Z<p>Bmeldal: </p>
<hr />
<div>*NOTE: This is a work in progress and includes continuing discussion with IntAct as well as the GOC.<br />
*Last updated: 9/6/2015, Paola.<br />
<br />
*Main working group: Birgit, David Osumi-Sutherland (DOS), Paola, Sandra.<br />
<br />
<br />
<br />
== Background and rationale ==<br />
<br />
Recently, GO and IntAct have started to work together to improve the 'protein complex' branch in GO, making it less flat and more informative, and to provide species-agnostic GO terms that IntAct can reference to for their species-specific curation projects, namely the [http://www.ebi.ac.uk/intact/complex/ Complex Portal]. At the time of writing (Spring 2015) the focus of the Complex Portal lies on human, mouse, yeast and E.coli, but it can take direct curation requests as well (intact-help@ebi.ac.uk). Other MODs are encouraged to collaborate directly. <br />
<br />
Here, we collect current guidelines on protein complex terms, to aid GO curators in discerning whether a protein complex belongs in GO or not, and if yes, in including all necessary information when requesting a new protein complex.<br />
<br />
== Protein complexes in GO ==<br />
<br />
=== Rule 1: Is the complex stable? ===<br />
<br />
In GO, 'protein complex' is defined as "A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical."<br />
<br />
When in doubt, how can a curator figure out if a complex is really stable?<br />
<br />
We can refer to the IntAct Complex Portal Rules [http://www.ebi.ac.uk/intact/complex/documentation/]. These are reported below for reference, and in a definition comment to 'protein complex' to serve as annotation guidance:<br />
<br />
===== What can be described as a complex? =====<br />
<br />
'''A stable set of (two or more) interacting macromolecules such as proteins which can be co-purified by an acceptable method and have been shown to exist as an isolated, functional unit in vivo. Any interacting non-protein molecules (e.g. small molecules, nucleic acids) will also be included.'''<br />
<br />
===== What should not be captured: =====<br />
*Enzyme/substrate, receptor/ligand or any similar transient interactions unless these are a critical part of the complex assembly (e.g. PDGF receptors only become 'dimeric' when linked by the dimeric ligand forming a tetramer).<br />
*Proteins associated in a pulldown/coimmunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose affinity complex.<br />
*Any literature complex where the only evidence is based on genetic interaction data.<br />
*Partial complexes.<br />
<br />
Note:<br />
*If the complex is not stable, it's just protein binding. Interactions can then be captured by a protein-protein interaction DB such as IntAct. <br />
*Beware of partial complexes shown experimentally, especially when crystallised. Some subunits (e.g. transmembrane subunits) cannot be expressed as recombinant proteins and are 'left out' of detailed studies. More reading is often necessary to find out what the full complex is thought to be.<br />
<br />
===== Tricky cases we DO (or could) capture in the IntAct Complex Portal: =====<br />
<br />
*Substrates or ligands if the enzyme or receptor complex only forms in their presence (see PDGF receptors above, e.g. [http://www.ebi.ac.uk/intact/complex/details/EBI-9082861 EBI-9082861]). These terms would also qualify for GO.<br />
<br />
*Homologous proteins, with the same functionality, which would be inferred by sequence similarity to form a complex but for which no physical link has been demonstrated, e.g. proteins A and B have been shown to physically interact and form a functional complex, protein C is a homologue of protein B by sequence similarity and is know to have the same function as B but protein A-C interaction has not been demonstrated experimentally. E.g. SUMO - E1 ligase complexes where there is interaction evidence for binding with SUMO1 ([http://www.ebi.ac.uk/intact/complex/details/EBI-9345927 EBI-9345927]) but not with SUMO2 ([http://www.ebi.ac.uk/intact/complex/details/EBI-9349603 EBI-9349603]).<br />
<br />
*The Complex Portal could also hold transient complexes, e.g. signaling complexes. We have not created any of these to date but they are possible, and controlled vocabulary terms exist to distinguish the two classes. BUT - they would probably fall outside the scope of GO if GO limit themselves to stable complexes.<br />
<br />
*We can also curate complexes that lack full experimental evidence but are commonly regarded as existing, e.g. complexes submitted by ChEMBL for which we only have pharmacological evidence. These complexes are tagged with ECO:0000306 - inferred from background scientific knowledge by manual assertion. E.g GABA ([http://www.ebi.ac.uk/intact/complex/details/EBI-9008426 EBI-9008426]) receptors and many other transmembrane receptors.<br />
<br />
===== Expanded definition comment for GO:0043234 ‘protein complex’: =====<br />
<br />
"A protein complex in this context is meant as a stable set of interacting proteins which can be co-purified by an acceptable method, and where the complex has been shown to exist as an isolated, functional unit in vivo. Acceptable experimental methods include stringent protein purification followed by detection of protein interaction. The following methods should be considered non-acceptable: simple immunoprecipitation, pull-down experiments from cell extracts without further purification, colocalization and 2-hybrid screening. Interactions that should not be captured as protein complexes include: 1) enzyme/substrate, receptor/ligand or any similar transient interactions, unless these are a critical part of the complex assembly or are required e.g. for the receptor to be functional; 2) proteins associated in a pull-down/co-immunoprecipitation assay with no functional link or any evidence that this is a defined biological entity rather than a loose-affinity complex; 3) any complex where the only evidence is based on genetic interaction data; 4) partial complexes, where some subunits (e.g. transmembrane ones) cannot be expressed as recombinant proteins and are excluded from experiments (in this case, independent evidence is necessary to find out the composition of the full complex, if known). Interactions that may be captured as protein complexes include: 1) enzyme/substrate or receptor/ligand if the complex can only assemble and become functional in the presence of both classes of subunits; 2) complexes where one of the members has not been shown to be physically linked to the other(s), but is a homologue of, and has the same functionality as, a protein that has been experimentally demonstrated to form a complex with the other member(s); 3) complexes whose existence is accepted based on localization and pharmacological studies, but for which experimental evidence is not yet available for the complex as a whole."<br />
<br />
=== Rule 2: Is the complex species-agnostic? ===<br />
<br />
*GO should host species-agnostic complexes, ideally conserved across taxa. Where this isn't known, we should still make the definition generic, and add 'For example, in human this complex contains...' as a definition gloss or definition comment.<br />
<br />
*Species-specific complexes don't belong in GO, but IntAct/Complex Portal and/or PRO can take them. (We acknowledge that GO contains many historic terms that contravene this rule. For the time being, the agreement is that we will not review them globally, though we may fix them if and when we come across them.)<br />
<br />
*We may, however, need taxon restrictions on a case-by-case basis such as complexes that only exist in prokaryots or eukaryotes. Curators are encouraged to provide these information, if applicable, when they request a new term (or come across an existing one).<br />
<br />
=== Rule 3: Does the complex have a molecular function? ===<br />
<br />
*If yes, add capable_of link(s) to molecular function terms. These links are used by the reasoner to place the complex into the correct branch under 'protein complex'.<br />
<br />
=== Rule 4: Is the complex known to be involved in one or more biological processes? ===<br />
<br />
*If yes, add capable_of_part_of links to biological process(es).<br />
<br />
*Note: we decided not to use BP as a qualifier for making grouping terms for complexes as these would become too unspecific, e.g. 'regulatory complex' could include most complexes!<br />
<br />
=== Rule 5: Does the complex contain conserved subunits? ===<br />
<br />
*Many complexes are defined by their subunit composition rather than their activity. Such complexes will still be accepted into the GO. The curator should endeavour to place the new complex as child of a functional parent or a parent term also defined by its composition, in some cases this may be difficult and those complex terms will be direct children of 'protein complex'.<br />
<br />
*Complex definitions should include their function or the process they are involved in as well as the defining subunits (using the style "In human, it is composed of..."). However, we need to be careful not to explode the subunit composition in the definition if they turn out to be rather different in the different branches of the tree of life. In such a situation, the curator and editor should consider broadening the term name and adding the various subunit-defined names as narrow synonyms. This should be handled on a case-by-case basis.<br />
<br />
*Complexes defined by their subunits but functionally identical to a more generic parent term should not be created as separate GO terms but added to the parent term as narrow synonyms. The specific complex belongs in the Complex Portal.<br />
<br />
[DOS to look into some automatic reasoning across subunits but we think it may become tricky. To be discussed among editors.]<br />
<br />
=== Rule 6: Where is the complex located? ===<br />
<br />
*Indicate cellular location as specifically as possible, unless parent already has one.<br />
<br />
*The CC location is meant for the complex as a whole. We discussed this in the context of transmembrane complexes where one or more members of the complex are located on one side of the membrane only or have no membrane attachment at all. As gene products have the part_of relationship with the complexes this is fine (and the only way of reflecting the CC for the complex as a whole).<br />
<br />
*If we have complexes defined by their location (see below under 'Futures Plans'), does the reasoner take the part_of relationship to place them automatically into the right complex-by-location branch? [DOS?]<br />
<br />
*Complexes simply defined by the cell type they are expressed in are not permitted.<br />
<br />
=== Rule 7: Adding appropriate is_a relationships ===<br />
<br />
*We are trying to avoid placing complexes as direct is_a children of 'protein complex', by adding some granularity to this ontology branch.<br />
<br />
*An is_a parent of a complex can be a <br />
# complex defined by its activity, via the complex-by-activity TG template<br />
# complex defined by its location, such as 'plasma membrane complex'. [Update: DOS added some useful protein complex grouping terms based on location, such as 'membrane protein complex'.]<br />
# complex defined by its subunit composition. This may be related to protein families but it may be difficult to make it a rule/template (see above).<br />
*We decided NOT to define complexes by their process or MF binding as they would become too generic.<br />
<br />
*Note: Complexes can have multiple parents!<br />
<br />
*Note: if capable_of MF links are added, and/or if location information is provided as part_of CC, the automatic assert-inference script will take care of placing most newly created protein complex terms more granularly in the ontology.<br />
<br />
=== Rule 8: Adding appropriate part_of relationships ===<br />
<br />
*All complexes should have a part_of link to a cellular component term, even if it's very generic, such as 'cell'.<br />
*CC does not have to be added manually if it's the same as the parent term as it will be inferred.<br />
*If the CC is more specific than the parent, the part_of relationship must be added manually.<br />
*Complexes can be subcomplexes of larger entities and can therefore be part_of another protein complex. If the larger complex necessarily needs the smaller one as its component in order to be functional, a has_part link should also be added (larger complex has_part smaller complex).<br />
*Complexes cannot have several part_of relationships to different CCs, as part_of must ALWAYS be true. If a complex can be part of several larger complexes or be found in several locations, such as cytoplasm and nucleus where it may have different functions, separate terms may have to be considered. [This point is still open to discussion, see https://sourceforge.net/p/geneontology/ontology-requests/10745/, now with DOS. To be discussed on Editor's call.]<br />
<br />
== How to request protein complexes in GO based on the above (TG template, TG freeform) ==<br />
<br />
*If the complex is generic and its function exists as a GO term, use the TG complex-by-activity template (and add relevant synonyms as discussed above). <br />
<br />
*If the function does not yet exist in GO but is clearly defined, create the new MF term first (via SF or TG FF (freeform) depending on the curator's experience), then create the new complex term via the TG complex-by-activity template.<br />
<br />
*If the complex-by-activity template is not applicable, create the complex term either via SF or TG FF depending on the curator's experience.<br />
<br />
*If a complex is known to be involved in a broader biological process (but not to have a specific molecular function), request the new term using TG FF (by filling in the capable_of_part_of field), or using SF depending on curator's experience. TG FF allows both capable_of and capable_of_part_of links in case a function is known and a process too, but the function is not part of that process.<br />
<br />
*IntAct is happy to curate requested complexes into the Complex Portal at the same time as adding to the GO structure. Curators are encouraged to curate complexes directly into the Complex Portal after being trained by IntAct. SGD and UCL are doing this already. Contact intact-help@ebi.ac.uk for either use case.<br />
<br />
== Complex Definition field ==<br />
<br />
The way definitions of older protein complex terms are structured is not always consistent. Currently, we recommend the following:<br />
<br />
*Start the definition referring to the function (if applicable), such as 'A protein complex capable of X function...'.<br />
<br />
*Processes can also be mentioned in the def. <br />
<br />
*Subunits should only be listed in the definition if the complex is defined by its composition rather than function (see Rule 5 above). If the complex is defined by its function, subunit composition should go into a definition comment or be added as narrow synonyms.<br />
<br />
*Complexes should NOT be defined by their stoichiometry, though this may be mentioned in the def as a 'soft' comment (definition gloss), or in a definition comment. The rationale behind this recommendation is that, as knowledge advances and more examples are found, stoichiometry defs would have to be updated, causing a lot of work. It is perfectly fine though to mention something like 'usually consists of a catalytic and a regulatory subunit and possibly further accessory subunits...'. <br />
<br />
*We are aware that many older terms' definitions do not conform to these guidelines. At the moment, however, we do not plan on fixing all of them. We may make corrections on a case-by-case basis and/or when working on a given branch.<br />
<br />
== Future plans ==<br />
as discussed in a meeting with Birgit Meldal, Sandra Orchard, David Osumi-Sunderland and Paola Roncaglia on 28/4/2015<br />
<br />
We discussed how we can make 'quick gains' in making the ontology more granular beyond the fixes Birgit does on a case by case basis. This is to target historic terms that have only 'protein complex' as a parent because they have no annotation extensions. The aim is to have most complexes grouped either by their function, location or subunit composition.<br />
<br />
*Do a pass through term names and definitions to find major groups of complexes that can be grouped by function, e.g. 'catalytic complex' (the term exists but many historic terms have not automatically been classified as such as they have no capable_of extensions). Other keywords: kinase, activity, viral, receptor, respiratory chain... [BM, SO & DOS]<br />
<br />
*Add parent terms based on location, such as 'membrane complex' and children or 'mitochondrial complex'. Can the reasoner place complexes automatically into this branch based on their part_of relationship (see above Rule 6)? Should we have a TG template for this? [BM, DOS]<br />
<br />
*Combine activity and location, such as 'membrane receptor complex'.<br />
<br />
*We discussed grouping by protein families but this may be tricky. Decide on a case by case basis. A working example are the BCL protein family complexes which cannot be grouped by function as they may be pro- and/or antiapoptotic.<br />
<br />
== Previous work ==<br />
<br />
Emily started documentation here, in case it's helpful, but this wasn't worked on since 2011:<br />
http://wiki.geneontology.org/index.php/Protein_Complex_ids_as_GO_annotation_objects<br />
<br />
<br />
Birgit's comments [from email to Paola]: <br />
<br />
Inheritance of annotations:<br />
I agree with the wiki, you cannot inherit MF from a complex to a subunit and even a CC is problematic, see the transmembrane example above. This needs more thinking about. I don't know what you are doing right now...<br />
<br />
Orthologies:<br />
We infer within taxon groups, e.g. human to mouse to rat or any other mammal etc, depending on where the exp evidence comes from. We systematically infer human-mouse. We have a few pombe complexes inferred from yeast (Sc!) but we don't do it systematically.<br />
<br />
Paralogues:<br />
We make inferences between related complexes in the same species when the gene products are very similar, e.g. hemoglobin chains for adult and developmental complexes.<br />
<br />
'Large' complexes:<br />
We have tackled the 'mediator' and we can now link to RNACentral for RNAs so time permitting we'll tackle the 'biggies' soon!<br />
<br />
Pro:<br />
We have a list of Pro complexes that we consult for refs.<br />
<br />
== Useful links ==<br />
<br />
IntAct Complex Portal, http://www.ebi.ac.uk/intact/complex/<br />
<br />
<br />
[[Category:Ontology]]</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_June19,_2015&diff=58053Protein Complex Conference Call June19, 20152015-08-20T08:00:24Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
==Agenda==<br />
===Background===<br />
<br />
IntAct Portal is curating complexes and associating these complexes with GO terms. This meeting is to come up with guidelines on annotating complexes to GO terms.<br />
* There are two levels of annotation:<br />
** Annotation that are shown on the Complex Portal Website<br />
** Annotations that are exported from IntAct to GO or directly annotated in P2GO<br />
Here, we are discussing which annotations should be exported from IntAct and which Complex identifiers should be available as annotation objects in P2GO.<br />
<br />
Slides: https://drive.google.com/folderview?id=0B0BzQEtrvNZlfjJmbk5wRG5PYlZPU1N3R0tmZ2M2aUxTTTNIWHVJYnNiTUlTdWpoN0hieWc&usp=sharing<br />
<br />
<br />
===Questions for consideration===<br />
* Does it make sense to annotate an IntAct complex to a GO complex? Is this meaningful? is this a mapping or an annotation? Should we instead annotate it to the location in the cell? e.g. ATPase complex (IntAct ID) is part_of mitochondrion (GO:5635). This will be similar to gene_product A is part of mitochondrion.<br />
The other issue with associating an IntAct complex with a GO complex is the evidence code. If you use IPI you need to say the subunits in the With column, but this requires that you know which subunit interacts with which. <br />
<br />
* The other issue is the current default relation between the entity in Column 2 and the GO term for CC is part_of, which is not true in this case. So annotating complexes to complexes should be revisited.<br />
<br />
* MF/BP of complex (case 4 in the slides, Full MF/BP evidence available)<br />
How does IMP work here? If authors are deleting one subunit and inferring the MF/BP of the complex, can that be used for the entire complex? Would you put the allele information in With column ?<br />
* Case 6, BP inferred from MF (where MF has evidence)4- BP can be inferred from MF. Since there is Exp. evidence for MF annotation, use the same PMID for the BP annotation.<br />
<br />
==Discussion==<br />
Present: Rama, Birgit, Sandra, JudyB, Harold, Kimberly, Chris, Ruth, Pascale<br />
<br />
* Birgit showed their IntAct interface where they associate IntAct complexes with GO terms. <br />
* Rama: Considering that you guys and protein2GO are neighbors, why aren't you using protein2go to curate? protein2go can handle complex IDs now and it is easier to maintain the annotations in one place. In the GOC we are encouraging curators to curate into one tool to help with consistency/data checks etc.<br />
** Sandra: There is a significant time lag in getting the IntAct complex IDs in protein2GO and we wanted to make the GO annotations while we were curating the complex and not wait for the complex ID to be available/integrated into protein2GO. <br />
** Judy: If this step can be sped up would you consider moving to protein2GO?<br />
** Sandra: Yes. <br />
AI: Sandra/Judy will talk to Tony.<br />
<br />
* Case 3: Handling complexes that are inferred based on Chemogenomics etc (as opposed to verified)? We should have a rule to not export those annotations and IDs. The ECO code can be used to flag such complexes in IntAct as 'do not export'. <br />
AI: discuss at GOC meeting.<br />
<br />
* Case 1: Should we associate IntAct complexes to GO complexes? Is this merely a mapping?<br />
** Harold: In PRO (which is an ontology) the logical definition takes care of the relationship between a GO and PRO complex. So this association wouldn't be necessary. PRO also annotates to MF and BP.<br />
** Rama: IntAct is not an Ontology though (it is just a hierarchy). So we can't treat it the same way.<br />
** Ruth: What if we want to capture that the complex is found in a certain cell type using col-16? <br />
** Pascale: The complex terms in GO are generic, while the IntAct ones are specific. So it might be okay to make this association.<br />
** Birgit: We will have this mapping on the Complex Portal website but can flag it as 'do not export' if we decide to go that way. Although that doesn't help Ruth's case.<br />
AI: GOC meeting<br />
<br />
* Case 1: Using IPI to associate IntAct complex with GO complex. Although we said we could use IPI for this annotation, it is not very satisfactory because we can't put anything in the With column. Switch it to IDA?<br />
AI: GOC meeting. If we decide to go with IDA we need to re-annotate in IntAct. Also depends on decision for point above.<br />
<br />
* Cases 2/5/7: If there is Exp evidence for a protein complex in Mouse, and if IntAct inferred the complex in Human using ISO, should we make GO MF/BP annotations for the inferred complexes?<br />
** Rama: I would say no. <br />
** Birgit: So should be tagged as 'do not export' in IntAct.<br />
AI: discuss at GOC meeting<br />
<br />
* Case 4: Can we use IMP to annotate MF or BP to complexes? <br />
** Sandra: Maybe not, as whole chain is usually knocked out/omitted.<br />
** Rama: If we capture this, we should put the missing chain in the With/From column.<br />
AI: discuss at GOC meeting<br />
<br />
* Case 6: For the IC annotation, Reference should be the PMID and not the GO_REF and the IntAct ID of the complex should be put in the With/From column. Should we allow IntAct IDs or the GO complex ID in the With/From column? The GO complex ID helps with book keeping though. Not sure!<br />
AI: discuss at GOC meeting<br />
<br />
* Case 2 (7 for MF/BP): If we export complexes inferred by orthology/homology, put complex AC into With/From column.<br />
<br />
* Annotating to X binding? e.g. heme binding in hemaglobin complex. <br />
** Rama: Hemaglobin's function is not heme binding. So don't make that heme binding. <br />
AI: Birgit to correct annotations in IntAct.<br />
<br />
* How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
** Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. But we need to decide on a similarity cut-off.<br />
AI: discuss at next call.<br />
<br />
* Does it make sense to have process annotations with IPI? <br />
AI: discuss at next call.<br />
<br />
* Add to agenda for the GOC meeting (done- http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Meeting_Agenda)</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_June19,_2015&diff=58052Protein Complex Conference Call June19, 20152015-08-20T07:54:38Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
==Agenda==<br />
===Background===<br />
<br />
IntAct Portal is curating complexes and associating these complexes with GO terms. This meeting is to come up with guidelines on annotating complexes to GO terms.<br />
* There are two levels of annotation:<br />
** Annotation that are shown on the Complex Portal Website<br />
** Annotations that are exported from IntAct to GO or directly annotated in P2GO<br />
Here, we are discussing which annotations should be exported from IntAct and which Complex identifiers should be available as annotation objects in P2GO.<br />
<br />
Slides: https://drive.google.com/folderview?id=0B0BzQEtrvNZlfjJmbk5wRG5PYlZPU1N3R0tmZ2M2aUxTTTNIWHVJYnNiTUlTdWpoN0hieWc&usp=sharing<br />
<br />
<br />
===Questions for consideration===<br />
* Does it make sense to annotate an IntAct complex to a GO complex? Is this meaningful? is this a mapping or an annotation? Should we instead annotate it to the location in the cell? e.g. ATPase complex (IntAct ID) is part_of mitochondrion (GO:5635). This will be similar to gene_product A is part of mitochondrion.<br />
The other issue with associating an IntAct complex with a GO complex is the evidence code. If you use IPI you need to say the subunits in the With column, but this requires that you know which subunit interacts with which. <br />
<br />
* The other issue is the current default relation between the entity in Column 2 and the GO term for CC is part_of, which is not true in this case. So annotating complexes to complexes should be revisited.<br />
<br />
* MF/BP of complex (case 4 in the slides, Full MF/BP evidence available)<br />
How does IMP work here? If authors are deleting one subunit and inferring the MF/BP of the complex, can that be used for the entire complex? Would you put the allele information in With column ?<br />
* Case 6, BP inferred from MF (where MF has evidence)4- BP can be inferred from MF. Since there is Exp. evidence for MF annotation, use the same PMID for the BP annotation.<br />
<br />
==Discussion==<br />
Present: Rama, Birgit, Sandra, JudyB, Harold, Kimberly, Chris, Ruth, Pascale<br />
<br />
* Birgit showed their IntAct interface where they associate IntAct complexes with GO terms. <br />
* Rama: Considering that you guys and protein2GO are neighbors, why aren't you using protein2go to curate? protein2go can handle complex IDs now and it is easier to maintain the annotations in one place. In the GOC we are encouraging curators to curate into one tool to help with consistency/data checks etc.<br />
** Sandra: There is a significant time lag in getting the IntAct complex IDs in protein2GO and we wanted to make the GO annotations while we were curating the complex and not wait for the complex ID to be available/integrated into protein2GO. <br />
** Judy: If this step can be sped up would you consider moving to protein2GO?<br />
** Sandra: Yes. <br />
AI: Sandra/Judy will talk to Tony.<br />
<br />
* Case 3: Handling complexes that are inferred based on Chemogenomics etc (as opposed to verified)? We should have a rule to not export those annotations and IDs. The ECO code can be used to flag such complexes in IntAct as 'do not export'. <br />
AI: discuss at GOC meeting.<br />
<br />
* Case 1: Should we associate IntAct complexes to GO complexes? Is this merely a mapping?<br />
** Harold: In PRO (which is an ontology) the logical definition takes care of the relationship between a GO and PRO complex. So this association wouldn't be necessary. PRO also annotates to MF and BP.<br />
** Rama: IntAct is not an Ontology though (it is just a hierarchy). So we can't treat it the same way.<br />
** Ruth: What if we want to capture that the complex is found in a certain cell type using col-16? <br />
** Pascale: The complex terms in GO are generic, while the IntAct ones are specific. So it might be okay to make this association.<br />
** Birgit: We will have this mapping on the Complex Portal website but can flag it as 'do not export' if we decide to go that way. Although that doesn't help Ruth's case.<br />
AI: GOC meeting<br />
<br />
* Case 1: Using IPI to associate IntAct complex with GO complex. Although we said we could use IPI for this annotation, it is not very satisfactory because we can't put anything in the With column. Switch it to IDA?<br />
AI: GOC meeting. If we decide to go with IDA we need to re-annotate in IntAct. Also depends on decision for point above.<br />
<br />
* Cases 2/5/7: If there is Exp evidence for a protein complex in Mouse, and if IntAct inferred the complex in Human using ISO, should we make GO MF/BP annotations for the inferred complexes?<br />
** Rama: I would say no. <br />
** Birgit: So should be tagged as 'do not export' in IntAct.<br />
AI: discuss at GOC meeting<br />
<br />
* Case 4: Can we use IMP to annotate MF or BP to complexes? <br />
** Sandra: Maybe not, as whole chain is usually knocked out/omitted.<br />
** Rama: If we capture this, we should put the missing chain in the With/From column.<br />
AI: discuss at GOC meeting<br />
<br />
* Case 6: For the IC annotation, Reference should be the PMID and not the GO_REF and the IntAct ID of the complex should be put in the With/From column. Should we allow IntAct IDs or the GO complex ID in the With/From column? The GO complex ID helps with book keeping though. Not sure!<br />
AI: discuss at GOC meeting<br />
<br />
* Case 3: If we export complexes inferred by orthology/homology, put complex AC into With/From column.<br />
<br />
* Annotating to X binding? e.g. heme binding in hemaglobin complex. <br />
** Rama: Hemaglobin's function is not heme binding. So don't make that heme binding. <br />
AI: Birgit to correct annotations in IntAct.<br />
<br />
* How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
** Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. But we need to decide on a similarity cut-off.<br />
AI: discuss at next call.<br />
<br />
* Does it make sense to have process annotations with IPI? <br />
AI: discuss at next call.<br />
<br />
* Add to agenda for the GOC meeting (done- http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Meeting_Agenda)</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57688Protein Complex Conference Call July15, 20152015-07-20T09:27:22Z<p>Bmeldal: /* IPI for BP */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP (Complex Portal) to GO (Birgit):<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?<br />
<br />
==Discussion==<br />
<br />
===Curating in protein2GO===<br />
* IntAct will continue to curate in their portal because it takes some time for these complex_IDs to make it to protein2GO. <br />
* May be in a year's time the pipeline can be optimized.<br />
<br />
===Binding small molecules===<br />
* Peter asked if IntAct can capture the specifics of covalently vs non-covalently bound small molecules. <br />
** Sandra mentioned that they can.<br />
<br />
* Maltose transport complex- should the definition be modified in GO? <br />
** No. The definition is based on the function and not composition. The logical definition does include the detail about transporting maltose. <br />
** If in doubt, the curator can follow the link to the Complex Portal and see if the small molecule has been defined as an integral part of the complex.<br />
<br />
===Multispecies===<br />
<br />
======Mixed experimental evidence:======<br />
* If there is a crystal structure of a complex where a human protein is complexed with a mouse and a rat protein (3 proteins altogether), how do we capture this?<br />
** NOW: IntAct curates these and uses the crystal as evidence only if the similarity is (nearly) 100%.<br />
** NOW: If similarity is not (nearly) 100% the complex in the CP has ECO:0000306 (inference from background scientific knowledge used in manual assertion). These complexes could be flagged as 'do-not-export'.<br />
** Should the corresponding complex be captured in IntAct with ECO:0000088 (biological system reconstituted)? Or ISO? (because two subunits are going to be inferred based on similarity to mouse and rat)<br />
*** Birgit: ECO:0000088 implies that all of the components are known in one system but here our evidence is mixed-species...?<br />
** What should the evidence be in GO for CC, MF and BP? Since there is no direct experimental evidence for the complex in any one species, this may not be annotatable by GO?<br />
<br />
* Example 1: 2x mouse, 1x rat<br />
** As mouse and rat orthologs were 100% identical so we used the structure as evidence for both species and then inferred to human from the mouse entry.<br />
** EM structure: http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-2013/<br />
** CP entry http://www.ebi.ac.uk/intact/complex/details/EBI-10817173 (mouse)<br />
<br />
======Inference via similarity:======<br />
* CP routinely infers complexes between related species (eg human/mouse) or paralogs within a species:<br />
** We do want to annotate (using GO) to complexes that are inferred by similarity but we should be able to trace the function back to some experimental evidence. That is not the case in the reconstitution example (above). <br />
** These complex ID can be exported to GO and tagged with ISS/ISO.<br />
** This is conceptually the same as using inferred gene products as annotation objects (Val).<br />
** We won't set a fixed similarity cut-off value. It's more important to know that the orthologs have been shown to have some function, too.<br />
<br />
* Example 2: 60% similarity<br />
** The shelterin complex has one protein (ADC) that has only 60% similarity between human and mouse (curation in progress so no CP link available)<br />
** UniProt align: http://www.uniprot.org/align/A201507162HHGWPKF0R<br />
** Because the genes are identified as orthologs we curated the human complex and infer to mouse by ISO.<br />
<br />
===IPI for BP===<br />
* Rama: It doesn't make sense to make a Process annotation with IPI. Just because proteinA interacts with proteinB doesn't mean it is involved in the same process. <br />
* Val : We do it, not very often, but sometimes it is the best evidence we have. See for example: <br />
** http://curation.pombase.org/pombe/curs/1ae670cde3faca1e/ro/ (PMID:26122634)<br />
** Seems reasonable to me......(we have only 80 examples) I think they could all also be ISO to SGD. I prefer IPI with a paper if the author intent of detecting the conserved interaction was to demonstrate the likelihood an additional proteins involvement in a conserved process.</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57687Protein Complex Conference Call July15, 20152015-07-20T09:26:22Z<p>Bmeldal: /* IPI for BP */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP (Complex Portal) to GO (Birgit):<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?<br />
<br />
==Discussion==<br />
<br />
===Curating in protein2GO===<br />
* IntAct will continue to curate in their portal because it takes some time for these complex_IDs to make it to protein2GO. <br />
* May be in a year's time the pipeline can be optimized.<br />
<br />
===Binding small molecules===<br />
* Peter asked if IntAct can capture the specifics of covalently vs non-covalently bound small molecules. <br />
** Sandra mentioned that they can.<br />
<br />
* Maltose transport complex- should the definition be modified in GO? <br />
** No. The definition is based on the function and not composition. The logical definition does include the detail about transporting maltose. <br />
** If in doubt, the curator can follow the link to the Complex Portal and see if the small molecule has been defined as an integral part of the complex.<br />
<br />
===Multispecies===<br />
<br />
======Mixed experimental evidence:======<br />
* If there is a crystal structure of a complex where a human protein is complexed with a mouse and a rat protein (3 proteins altogether), how do we capture this?<br />
** NOW: IntAct curates these and uses the crystal as evidence only if the similarity is (nearly) 100%.<br />
** NOW: If similarity is not (nearly) 100% the complex in the CP has ECO:0000306 (inference from background scientific knowledge used in manual assertion). These complexes could be flagged as 'do-not-export'.<br />
** Should the corresponding complex be captured in IntAct with ECO:0000088 (biological system reconstituted)? Or ISO? (because two subunits are going to be inferred based on similarity to mouse and rat)<br />
*** Birgit: ECO:0000088 implies that all of the components are known in one system but here our evidence is mixed-species...?<br />
** What should the evidence be in GO for CC, MF and BP? Since there is no direct experimental evidence for the complex in any one species, this may not be annotatable by GO?<br />
<br />
* Example 1: 2x mouse, 1x rat<br />
** As mouse and rat orthologs were 100% identical so we used the structure as evidence for both species and then inferred to human from the mouse entry.<br />
** EM structure: http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-2013/<br />
** CP entry http://www.ebi.ac.uk/intact/complex/details/EBI-10817173 (mouse)<br />
<br />
======Inference via similarity:======<br />
* CP routinely infers complexes between related species (eg human/mouse) or paralogs within a species:<br />
** We do want to annotate (using GO) to complexes that are inferred by similarity but we should be able to trace the function back to some experimental evidence. That is not the case in the reconstitution example (above). <br />
** These complex ID can be exported to GO and tagged with ISS/ISO.<br />
** This is conceptually the same as using inferred gene products as annotation objects (Val).<br />
** We won't set a fixed similarity cut-off value. It's more important to know that the orthologs have been shown to have some function, too.<br />
<br />
* Example 2: 60% similarity<br />
** The shelterin complex has one protein (ADC) that has only 60% similarity between human and mouse (curation in progress so no CP link available)<br />
** UniProt align: http://www.uniprot.org/align/A201507162HHGWPKF0R<br />
** Because the genes are identified as orthologs we curated the human complex and infer to mouse by ISO.<br />
<br />
===IPI for BP===<br />
* Rama: It doesn't make sense to make a Process annotation with IPI. Just because proteinA interacts with proteinB doesn't mean it is involved in the same process. <br />
* Val : We do it, not very often, but sometimes it is the best evidence we have. See for example: <br />
** http://curation.pombase.org/pombe/curs/1ae670cde3faca1e/ro/ (PMID:26122634)<br />
** Seems reasonable to me......(we have only 80 examples<br />
** I think they could all also be ISO to SGD. I prefer IPI with a paper if the author intent of detecting the conserved interaction was to demonstrate the likelihood an additional proteins involvement in a conserved process.</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57686Protein Complex Conference Call July15, 20152015-07-20T09:24:50Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP (Complex Portal) to GO (Birgit):<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?<br />
<br />
==Discussion==<br />
<br />
===Curating in protein2GO===<br />
* IntAct will continue to curate in their portal because it takes some time for these complex_IDs to make it to protein2GO. <br />
* May be in a year's time the pipeline can be optimized.<br />
<br />
===Binding small molecules===<br />
* Peter asked if IntAct can capture the specifics of covalently vs non-covalently bound small molecules. <br />
** Sandra mentioned that they can.<br />
<br />
* Maltose transport complex- should the definition be modified in GO? <br />
** No. The definition is based on the function and not composition. The logical definition does include the detail about transporting maltose. <br />
** If in doubt, the curator can follow the link to the Complex Portal and see if the small molecule has been defined as an integral part of the complex.<br />
<br />
===Multispecies===<br />
<br />
======Mixed experimental evidence:======<br />
* If there is a crystal structure of a complex where a human protein is complexed with a mouse and a rat protein (3 proteins altogether), how do we capture this?<br />
** NOW: IntAct curates these and uses the crystal as evidence only if the similarity is (nearly) 100%.<br />
** NOW: If similarity is not (nearly) 100% the complex in the CP has ECO:0000306 (inference from background scientific knowledge used in manual assertion). These complexes could be flagged as 'do-not-export'.<br />
** Should the corresponding complex be captured in IntAct with ECO:0000088 (biological system reconstituted)? Or ISO? (because two subunits are going to be inferred based on similarity to mouse and rat)<br />
*** Birgit: ECO:0000088 implies that all of the components are known in one system but here our evidence is mixed-species...?<br />
** What should the evidence be in GO for CC, MF and BP? Since there is no direct experimental evidence for the complex in any one species, this may not be annotatable by GO?<br />
<br />
* Example 1: 2x mouse, 1x rat<br />
** As mouse and rat orthologs were 100% identical so we used the structure as evidence for both species and then inferred to human from the mouse entry.<br />
** EM structure: http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-2013/<br />
** CP entry http://www.ebi.ac.uk/intact/complex/details/EBI-10817173 (mouse)<br />
<br />
======Inference via similarity:======<br />
* CP routinely infers complexes between related species (eg human/mouse) or paralogs within a species:<br />
** We do want to annotate (using GO) to complexes that are inferred by similarity but we should be able to trace the function back to some experimental evidence. That is not the case in the reconstitution example (above). <br />
** These complex ID can be exported to GO and tagged with ISS/ISO.<br />
** This is conceptually the same as using inferred gene products as annotation objects (Val).<br />
** We won't set a fixed similarity cut-off value. It's more important to know that the orthologs have been shown to have some function, too.<br />
<br />
* Example 2: 60% similarity<br />
** The shelterin complex has one protein (ADC) that has only 60% similarity between human and mouse (curation in progress so no CP link available)<br />
** UniProt align: http://www.uniprot.org/align/A201507162HHGWPKF0R<br />
** Because the genes are identified as orthologs we curated the human complex and infer to mouse by ISO.<br />
<br />
===IPI for BP===<br />
* Rama: It doesn't make sense to make a Process annotation with IPI. Just because proteinA interacts with proteinB doesn't mean it is involved in the same process. <br />
* Val : We do it, not very often, but sometimes it is the best evidence we have. See for example: <br />
http://curation.pombase.org/pombe/curs/1ae670cde3faca1e/ro/ (PMID:26122634)<br />
Seems reasonable to me......(we have only 80 examples<br />
I think they could all also be ISO to SGD. I prefer IPI with a paper if the author intent of detecting the conserved interaction was to demonstrate the likelihood an additional proteins involvement in a conserved process.</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57671Protein Complex Conference Call July15, 20152015-07-16T15:45:09Z<p>Bmeldal: /* Multispecies */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP (Complex Portal) to GO (Birgit):<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?<br />
<br />
==Discussion==<br />
<br />
===Curating in protein2GO===<br />
* IntAct will continue to curate in their portal because it takes some time for these complex_IDs to make it to protein2GO. <br />
* May be in a year's time the pipeline can be optimized.<br />
<br />
===Binding small molecules===<br />
* Peter asked if IntAct can capture the specifics of covalently vs non-covalently bound small molecules. <br />
** Sandra mentioned that they can.<br />
<br />
* Maltose transport complex- should the definition be modified in GO? <br />
** No. The definition is based on the function and not composition. The logical definition does include the detail about transporting maltose. <br />
** If in doubt, the curator can follow the link to the Complex Portal and see if the small molecule has been defined as an integral part of the complex.<br />
<br />
===Multispecies===<br />
<br />
======Mixed experimental evidence:======<br />
* If there is a crystal structure of a complex where a human protein is complexed with a mouse and a rat protein (3 proteins altogether), how do we capture this?<br />
** NOW: IntAct curates these and uses the crystal as evidence only if the similarity is (nearly) 100%.<br />
** NOW: If similarity is not (nearly) 100% the complex in the CP has ECO:0000306 (inference from background scientific knowledge used in manual assertion). These complexes could be flagged as 'do-not-export'.<br />
** Should the corresponding complex be captured in IntAct with ECO:0000088 (biological system reconstituted)? Or ISO? (because two subunits are going to be inferred based on similarity to mouse and rat)<br />
*** Birgit: ECO:0000088 implies that all of the components are known in one system but here our evidence is mixed-species...?<br />
** What should the evidence be in GO for CC, MF and BP? Since there is no direct experimental evidence for the complex in any one species, this may not be annotatable by GO?<br />
<br />
* Example 1: 2x mouse, 1x rat<br />
** As mouse and rat orthologs were 100% identical so we used the structure as evidence for both species and then inferred to human from the mouse entry.<br />
** EM structure: http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-2013/<br />
** CP entry http://www.ebi.ac.uk/intact/complex/details/EBI-10817173 (mouse)<br />
<br />
======Inference via similarity:======<br />
* CP routinely infers complexes between related species (eg human/mouse) or paralogs within a species:<br />
** We do want to annotate (using GO) to complexes that are inferred by similarity but we should be able to trace the function back to some experimental evidence. That is not the case in the reconstitution example (above). <br />
** These complex ID can be exported to GO and tagged with ISS/ISO.<br />
** This is conceptually the same as using inferred gene products as annotation objects (Val).<br />
** We won't set a fixed similarity cut-off value. It's more important to know that the orthologs have been shown to have some function, too.<br />
<br />
* Example 2: 60% similarity<br />
** The shelterin complex has one protein (ADC) that has only 60% similarity between human and mouse (curation in progress so no CP link available)<br />
** UniProt align: http://www.uniprot.org/align/A201507162HHGWPKF0R<br />
** Because the genes are identified as orthologs we curated the human complex and infer to mouse by ISO.<br />
<br />
===IPI for BP===<br />
* Rama: It doesn't make sense to make a Process annotation with IPI. Just because proteinA interacts with proteinB doesn't mean it is involved in the same process. <br />
* Val: It should be okay to make Process annotations with IPI. She will send some examples.</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57669Protein Complex Conference Call July15, 20152015-07-16T15:32:46Z<p>Bmeldal: /* Mixed experimental evidence: */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP (Complex Portal) to GO (Birgit):<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?<br />
<br />
==Discussion==<br />
<br />
===Curating in protein2GO===<br />
* IntAct will continue to curate in their portal because it takes some time for these complex_IDs to make it to protein2GO. <br />
* May be in a year's time the pipeline can be optimized.<br />
<br />
===Binding small molecules===<br />
* Peter asked if IntAct can capture the specifics of covalently vs non-covalently bound small molecules. <br />
** Sandra mentioned that they can.<br />
<br />
* Maltose transport complex- should the definition be modified in GO? <br />
** No. The definition is based on the function and not composition. The logical definition does include the detail about transporting maltose. <br />
** If in doubt, the curator can follow the link to the Complex Portal and see if the small molecule has been defined as an integral part of the complex.<br />
<br />
===Multispecies===<br />
<br />
======Mixed experimental evidence:======<br />
* If there is a crystal structure of a complex where a human protein is complexed with a mouse and a rat protein (3 proteins altogether), how do we capture this?<br />
** NOW: IntAct curates these and uses the crystal as evidence only if the similarity is (nearly) 100%.<br />
** NOW: If similarity is not (nearly) 100% the complex in the CP has ECO:0000306 (inference from background scientific knowledge used in manual assertion). These complexes could be flagged as 'do-not-export'.<br />
** Should the corresponding complex be captured in IntAct with ECO:0000088 (biological system reconstituted)? Or ISO? (because two subunits are going to be inferred based on similarity to mouse and rat)<br />
*** Birgit: ECO:0000088 implies that all of the components are known in one system but here our evidence is mixed-species...?<br />
** What should the evidence be in GO for CC, MF and BP? Since there is no direct experimental evidence for the complex in any one species, this may not be annotatable by GO?<br />
<br />
* Example 1: 2x mouse, 1x rat<br />
** As mouse and rat orthologs were 100% identical so we used the structure as evidence for both species and then inferred to human from the mouse entry.<br />
** EM structure: http://www.ebi.ac.uk/pdbe/entry/emdb/EMD-2013/<br />
** CP entry http://www.ebi.ac.uk/intact/complex/details/EBI-10817173 (mouse)<br />
<br />
* Example 2: 60% similarity<br />
** The shelterin complex has one protein that only had 60% similarity between human and mouse<br />
** UniProt align: http://www.uniprot.org/align/A201507162HHGWPKF0R<br />
** Because the genes are identified as orthologs we curated the human complex and infer to mouse by ISO.<br />
<br />
======Inference via similarity:======<br />
* CP routinely infers complexes between related species (eg human/mouse) or paralogs within a species:<br />
** We do want to annotate (using GO) to complexes that are inferred by similarity but we should be able to trace the function back to some experimental evidence. That is not the case in the reconstitution example (above). <br />
** These complex ID can be exported to GO and tagged with ISS/ISO.<br />
** This is conceptually the same as using inferred gene products as annotation objects (Val).<br />
** We won't set a fixed similarity cut-off value. It's more important to know that the orthologs have been shown to have some function, too.<br />
<br />
===IPI for BP===<br />
* Rama: It doesn't make sense to make a Process annotation with IPI. Just because proteinA interacts with proteinB doesn't mean it is involved in the same process. <br />
* Val: It should be okay to make Process annotations with IPI. She will send some examples.</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57665Protein Complex Conference Call July15, 20152015-07-16T11:56:20Z<p>Bmeldal: /* IPI for BP */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP (Complex Portal) to GO (Birgit):<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?<br />
<br />
==Discussion==<br />
<br />
===Curating in protein2GO===<br />
* IntAct will continue to curate in their portal because it takes some time for these complex_IDs to make it to protein2GO. <br />
* May be in a year's time the pipeline can be optimized.<br />
<br />
===Binding small molecules===<br />
* Peter asked if IntAct can capture the specifics of covalently vs non-covalently bound small molecules. <br />
** Sandra mentioned that they can.<br />
<br />
* Maltose transport complex- should the definition be modified in GO? <br />
** No. The definition is based on the function and not composition. The logical definition does include the detail about transporting maltose. <br />
** If in doubt, the curator can follow the link to the Complex Portal and see if the small molecule has been defined as an integral part of the complex.<br />
<br />
===Multispecies===<br />
<br />
======Mixed experimental evidence:======<br />
* If there is a crystal structure of a complex where a human protein is complexed with a mouse and a rat protein (3 proteins altogether), how do we capture this?<br />
** NOW: IntAct curates these and uses the crystal as evidence only if the similarity is (nearly) 100%.<br />
** NOW: If similarity is not (nearly) 100% the complex in the CP has ECO:0000306 (inference from background scientific knowledge used in manual assertion). These complexes could be flagged as 'do-not-export'.<br />
** Should the corresponding complex be captured in IntAct with ECO:0000088 (biological system reconstituted)? Or ISO? (because two subunits are going to be inferred based on similarity to mouse and rat)<br />
*** Birgit: ECO:0000088 implies that all of the components are known in one system but here our evidence is mixed-species...?<br />
** What should the evidence be in GO for CC, MF and BP? Since there is no direct experimental evidence for the complex in any one species, this may not be annotatable by GO?<br />
<br />
======Inference via similarity:======<br />
* CP routinely infers complexes between related species (eg human/mouse) or paralogs within a species:<br />
** We do want to annotate (using GO) to complexes that are inferred by similarity but we should be able to trace the function back to some experimental evidence. That is not the case in the reconstitution example (above). <br />
** These complex ID can be exported to GO and tagged with ISS/ISO.<br />
** This is conceptually the same as using inferred gene products as annotation objects (Val).<br />
** We won't set a fixed similarity cut-off value. It's more important to know that the orthologs have been shown to have some function, too.<br />
<br />
===IPI for BP===<br />
* Rama: It doesn't make sense to make a Process annotation with IPI. Just because proteinA interacts with proteinB doesn't mean it is involved in the same process. <br />
* Val: It should be okay to make Process annotations with IPI. She will send some examples.</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57664Protein Complex Conference Call July15, 20152015-07-16T11:55:55Z<p>Bmeldal: /* Mixed experimental Evidence: */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP (Complex Portal) to GO (Birgit):<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?<br />
<br />
==Discussion==<br />
<br />
===Curating in protein2GO===<br />
* IntAct will continue to curate in their portal because it takes some time for these complex_IDs to make it to protein2GO. <br />
* May be in a year's time the pipeline can be optimized.<br />
<br />
===Binding small molecules===<br />
* Peter asked if IntAct can capture the specifics of covalently vs non-covalently bound small molecules. <br />
** Sandra mentioned that they can.<br />
<br />
* Maltose transport complex- should the definition be modified in GO? <br />
** No. The definition is based on the function and not composition. The logical definition does include the detail about transporting maltose. <br />
** If in doubt, the curator can follow the link to the Complex Portal and see if the small molecule has been defined as an integral part of the complex.<br />
<br />
===Multispecies===<br />
<br />
======Mixed experimental evidence:======<br />
* If there is a crystal structure of a complex where a human protein is complexed with a mouse and a rat protein (3 proteins altogether), how do we capture this?<br />
** NOW: IntAct curates these and uses the crystal as evidence only if the similarity is (nearly) 100%.<br />
** NOW: If similarity is not (nearly) 100% the complex in the CP has ECO:0000306 (inference from background scientific knowledge used in manual assertion). These complexes could be flagged as 'do-not-export'.<br />
** Should the corresponding complex be captured in IntAct with ECO:0000088 (biological system reconstituted)? Or ISO? (because two subunits are going to be inferred based on similarity to mouse and rat)<br />
*** Birgit: ECO:0000088 implies that all of the components are known in one system but here our evidence is mixed-species...?<br />
** What should the evidence be in GO for CC, MF and BP? Since there is no direct experimental evidence for the complex in any one species, this may not be annotatable by GO?<br />
<br />
======Inference via similarity:======<br />
* CP routinely infers complexes between related species (eg human/mouse) or paralogs within a species:<br />
** We do want to annotate (using GO) to complexes that are inferred by similarity but we should be able to trace the function back to some experimental evidence. That is not the case in the reconstitution example (above). <br />
** These complex ID can be exported to GO and tagged with ISS/ISO.<br />
** This is conceptually the same as using inferred gene products as annotation objects (Val).<br />
** We won't set a fixed similarity cut-off value. It's more important to know that the orthologs have been shown to have some function, too.<br />
<br />
===IPI for BP===<br />
Rama: It doesn't make sense to make a Process annotation with IPI. Just because proteinA interacts with proteinB doesn't mean it is involved in the same process. <br />
* Val: It should be okay to make Process annotations with IPI. She will send some examples.</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57663Protein Complex Conference Call July15, 20152015-07-16T11:55:26Z<p>Bmeldal: /* Multispecies */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP (Complex Portal) to GO (Birgit):<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?<br />
<br />
==Discussion==<br />
<br />
===Curating in protein2GO===<br />
* IntAct will continue to curate in their portal because it takes some time for these complex_IDs to make it to protein2GO. <br />
* May be in a year's time the pipeline can be optimized.<br />
<br />
===Binding small molecules===<br />
* Peter asked if IntAct can capture the specifics of covalently vs non-covalently bound small molecules. <br />
** Sandra mentioned that they can.<br />
<br />
* Maltose transport complex- should the definition be modified in GO? <br />
** No. The definition is based on the function and not composition. The logical definition does include the detail about transporting maltose. <br />
** If in doubt, the curator can follow the link to the Complex Portal and see if the small molecule has been defined as an integral part of the complex.<br />
<br />
===Multispecies===<br />
<br />
======Mixed experimental Evidence:======<br />
* If there is a crystal structure of a complex where a human protein is complexed with a mouse and a rat protein (3 proteins altogether), how do we capture this?<br />
** NOW: IntAct curates these and uses the crystal as evidence only if the similarity is (nearly) 100%.<br />
** NOW: If similarity is not (nearly) 100% the complex in the CP has ECO:0000306 (inference from background scientific knowledge used in manual assertion). These complexes could be flagged as 'do-not-export'.<br />
** Should the corresponding complex be captured in IntAct with ECO:0000088 (biological system reconstituted)? Or ISO? (because two subunits are going to be inferred based on similarity to mouse and rat)<br />
*** Birgit: ECO:0000088 implies that all of the components are known in one system but here our evidence is mixed-species...?<br />
** What should the evidence be in GO for CC, MF and BP? Since there is no direct experimental evidence for the complex in any one species, this may not be annotatable by GO?<br />
<br />
======Inference via similarity:======<br />
* CP routinely infers complexes between related species (eg human/mouse) or paralogs within a species:<br />
** We do want to annotate (using GO) to complexes that are inferred by similarity but we should be able to trace the function back to some experimental evidence. That is not the case in the reconstitution example (above). <br />
** These complex ID can be exported to GO and tagged with ISS/ISO.<br />
** This is conceptually the same as using inferred gene products as annotation objects (Val).<br />
** We won't set a fixed similarity cut-off value. It's more important to know that the orthologs have been shown to have some function, too.<br />
<br />
===IPI for BP===<br />
Rama: It doesn't make sense to make a Process annotation with IPI. Just because proteinA interacts with proteinB doesn't mean it is involved in the same process. <br />
* Val: It should be okay to make Process annotations with IPI. She will send some examples.</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57662Protein Complex Conference Call July15, 20152015-07-16T11:51:38Z<p>Bmeldal: /* Discussion */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP (Complex Portal) to GO (Birgit):<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?<br />
<br />
==Discussion==<br />
<br />
===Curating in protein2GO===<br />
* IntAct will continue to curate in their portal because it takes some time for these complex_IDs to make it to protein2GO. <br />
* May be in a year's time the pipeline can be optimized.<br />
<br />
===Binding small molecules===<br />
* Peter asked if IntAct can capture the specifics of covalently vs non-covalently bound small molecules. <br />
** Sandra mentioned that they can.<br />
<br />
* Maltose transport complex- should the definition be modified in GO? <br />
** No. The definition is based on the function and not composition. The logical definition does include the detail about transporting maltose. <br />
** If in doubt, the curator can follow the link to the Complex Portal and see if the small molecule has been defined as an integral part of the complex.<br />
<br />
===Multispecies===<br />
<br />
=====Mixed experimental Evidence:=====<br />
* If there is a crystal structure of a complex where a human protein is complexed with a mouse and a rat protein (3 proteins altogether), how do we capture this?<br />
** NOW: IntAct curates these and uses the crystal as evidence only if the similarity is (nearly) 100%.<br />
** NOW: If similarity is not (nearly) 100% the complex in the CP has ECO:0000306 (inference from background scientific knowledge used in manual assertion). These complexes could be flagged as 'do-not-export'.<br />
** Should the corresponding complex be captured in IntAct with ECO:0000088 (biological system reconstituted)? Or ISO? (because two subunits are going to be inferred based on similarity to mouse and rat)<br />
*** Birgit: ECO:0000088 implies that all of the components are known in one system but here our evidence is mixed-species...?<br />
** What should the evidence be in GO for CC, MF and BP? Since there is no direct experimental evidence for the complex in any one species, this may not be annotatable by GO?<br />
<br />
=====Inference via similarity:=====<br />
* CP routinely infers complexes between related species (eg human/mouse) or paralogs within a species:<br />
** We do want to annotate (using GO) to complexes that are inferred by similarity but we should be able to trace the function back to some experimental evidence. That is not the case in the reconstitution example (above). <br />
** These complex ID can be exported to GO and tagged with ISS/ISO.<br />
** This is conceptually the same as using inferred gene products as annotation objects (Val).<br />
** We won't set a fixed similarity cut-off value. It's more important to know that the orthologs have been shown to have some function, too.<br />
<br />
* ===IPI for BP===<br />
Rama: It doesn't make sense to make a Process annotation with IPI. Just because proteinA interacts with proteinB doesn't mean it is involved in the same process. <br />
* Val: It should be okay to make Process annotations with IPI. She will send some examples.</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57612Protein Complex Conference Call July15, 20152015-07-13T12:40:57Z<p>Bmeldal: /* Matters arising from last meeting */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP to GO (Birgit):<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57611Protein Complex Conference Call July15, 20152015-07-13T12:39:55Z<p>Bmeldal: /* Matters arising from last meeting */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP to GO:<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57610Protein Complex Conference Call July15, 20152015-07-13T12:38:52Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP to GO:<br />
<br />
* Annotating in CP vs GO - philosophical contemplations by Birgit...<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO for orthologous proteins (between species) and ISS when the proteins are paraloguous, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57608Protein Complex Conference Call July15, 20152015-07-13T10:52:19Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP to GO:<br />
<br />
* Annotating in CP vs GO - philosophical contemplations by Birgit...<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
** Should the GO entry have a xref to the molecule in ChEBI?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO between species and ISS when the proteins are homologues from the same species, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57607Protein Complex Conference Call July15, 20152015-07-13T10:50:41Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP to GO:<br />
<br />
* Annotating in CP vs GO - philosophical contemplations by Birgit...<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nancy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO between species and ISS when the proteins are homologues from the same species, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57606Protein Complex Conference Call July15, 20152015-07-13T10:50:16Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP to GO:<br />
<br />
* Annotating in CP vs GO - philosophical contemplations by Birgit...<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
* Defs in GO: Nncy pointed out that the def for the maltose transporter does not mention the maltose. Do we need to change the defs for those complexes where the no-protein entity is part of the complex but not mentioned so that CP and GO are aligned?<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO between species and ISS when the proteins are homologues from the same species, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57605Protein Complex Conference Call July15, 20152015-07-13T10:43:04Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP to GO:<br />
<br />
* Annotating in CP vs GO - philosophical contemplations by Birgit...<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO between species and ISS when the proteins are homologues from the same species, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57604Protein Complex Conference Call July15, 20152015-07-13T10:41:28Z<p>Bmeldal: /* Bumped from last meeting */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP to GO:<br />
<br />
* Annotating in CP vs GO - philosophical contemplations by Birgit...<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
* We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
* Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
====Mixed species evidence====<br />
<br />
* Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
* Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
====Inferring annotations between species====<br />
<br />
* In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
* We use ISO between species and ISS when the proteins are homologues from the same species, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
* Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57603Protein Complex Conference Call July15, 20152015-07-13T10:39:36Z<p>Bmeldal: /* Matter arising from last meeting */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matters arising from last meeting==<br />
<br />
* Export of annotations from CP to GO:<br />
<br />
* Annotating in CP vs GO - philosophical contemplations by Birgit...<br />
** The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
** So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
* Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
* Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
- We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
- Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
====Mixed species evidence====<br />
<br />
- Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
- Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
====Inferring annotations between species====<br />
<br />
- In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
- We use ISO between species and ISS when the proteins are homologues from the same species, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
- Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57602Protein Complex Conference Call July15, 20152015-07-13T10:35:17Z<p>Bmeldal: /* Matter arising from last meeting */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matter arising from last meeting==<br />
<br />
- Export of annotations from CP to GO:<br />
<br />
- Birgit: The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
- So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
- Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
- Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
- We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
- Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
====Mixed species evidence====<br />
<br />
- Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
- Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
====Inferring annotations between species====<br />
<br />
- In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
- We use ISO between species and ISS when the proteins are homologues from the same species, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
- Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57601Protein Complex Conference Call July15, 20152015-07-13T10:28:55Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matter arising from last meeting==<br />
<br />
# Export of annotations from CP to GO:<br />
<br />
- Birgit: The last call made me think about the fundamentally different philosophies of the annotations between the CP and GO: In the CP we can annotate to a complex with full experimental evidence or a complex that is assumed to exist. In both cases we create a unique, stable identifier for the complex that can be reused by other DBs. The question is, should we export GO annotation we make in the CP into GO if the evidence is inferred? I got the feeling the answer should be 'no' for complexes with no evidence even in related species, however, it might be 'yes' for those inferred by ISS/ISO as the codes can be transferred into the GOA. This can easily be filtered using ECO annotation on the complexes. (NB: We have overall ECO annotation for the complex and separate ECO annotations for each GO annotation line)<br />
- So, when it comes to mixed species evidence (see below) this distinction may become rather relevant!<br />
<br />
# Integration of curation via P2GO: Sandra/Tony to sort out account if we go this route.<br />
<br />
# Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
====Annotating to non-protein molecule binding====<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
- We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
- Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyone's life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
====Mixed species evidence====<br />
<br />
- Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
- Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. In another case the similarity if only ~50% but the proteins are thought to be homologuous. But we need to decide on a similarity cut-off.<br />
<br />
====Inferring annotations between species====<br />
<br />
- In the CP we infer between closely related spp, eg. mouse and human, if the orthology is 1:1 and the sequences 'fairly identical' but we haven't put a cut-off in yet.<br />
- We use ISO between species and ISS when the proteins are homologues from the same species, usually within the same protein family.<br />
<br />
<br />
====Process annotations====<br />
<br />
- Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_July15,_2015&diff=57599Protein Complex Conference Call July15, 20152015-07-13T09:28:55Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
<br />
==Agenda==<br />
<br />
Minutes from last call- http://wiki.geneontology.org/index.php/Protein_Complex_Conference_Call_June19,_2015<br />
<br />
==Matter arising from last meeting==<br />
<br />
# Integration of curation via P2GO: any communication between Sandra, Judy and Tony?<br />
# Correcting binding to small molecules that are part of the complex: Birgit still to fix annotations in the CP.<br />
<br />
==Bumped from last meeting==<br />
<br />
# annotating to non-protein molecule binding<br />
<br />
Example:<br />
Maltose transport complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-6477643<br />
where I did annotate with the maltose binding term although maltose is an integral part of the complex.<br />
On the other hand, the ATP binding annotation is valid in any case, as ATP is not part of the complex.<br />
<br />
Telomerase catalytic core complex<br />
http://www.ebi.ac.uk/intact/complex/details/EBI-10045577<br />
where I didn't annotate with an RNA binding term as the RNA is part of the complex. But as it binds the telomeric DNA I have THAT MF binding term!<br />
<br />
- We thought this was decided last time but it wasn't clear to some people who were not on the call. Does it need better documenting?<br />
<br />
- Ruth (copied form email thread): The truth is that there are very few examples where a protein is binding something because it is the function of a protein to bind something (other than enzymes binding their substrate). Many interactions are occurring because these are necessary interactions in order for a protein to carry out its ‘function’ or for its function to be regulated. I do appreciate that the binding terms are listed under the MF ontology and possibly it would make everyones life easier if we actually had 4 ontologies: CC, BP, MF and Interactions! Then the interactions could, when appropriate, have part_of relationships to specific functions and processes (note I haven’t actually thought this through, it is just that I seem to often have discussions which start with the concept that binding isn’t a function).<br />
<br />
# Mixed species evidence<br />
<br />
- Ruth/Birgit: How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
- Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. But we need to decide on a similarity cut-off.<br />
<br />
# Ruth: Does it make sense to have process annotations with IPI?</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_June19,_2015&diff=57417Protein Complex Conference Call June19, 20152015-06-23T09:17:45Z<p>Bmeldal: /* Discussion */</p>
<hr />
<div>[[Category:Protein Complex]]<br />
==Agenda==<br />
===Background===<br />
<br />
IntAct Portal is curating complexes and associating these complexes with GO terms. This meeting is to come up with guidelines on annotating complexes to GO terms.<br />
* There are two levels of annotation:<br />
** Annotation that are shown on the Complex Portal Website<br />
** Annotations that are exported from IntAct to GO or directly annotated in P2GO<br />
Here, we are discussing which annotations should be exported from IntAct and which Complex identifiers should be available as annotation objects in P2GO.<br />
<br />
Slides: https://drive.google.com/folderview?id=0B0BzQEtrvNZlfjJmbk5wRG5PYlZPU1N3R0tmZ2M2aUxTTTNIWHVJYnNiTUlTdWpoN0hieWc&usp=sharing<br />
<br />
<br />
===Questions for consideration===<br />
* Does it make sense to annotate an IntAct complex to a GO complex? Is this meaningful? is this a mapping or an annotation? Should we instead annotate it to the location in the cell? e.g. ATPase complex (IntAct ID) is part_of mitochondrion (GO:5635). This will be similar to gene_product A is part of mitochondrion.<br />
The other issue with associating an IntAct complex with a GO complex is the evidence code. If you use IPI you need to say the subunits in the With column, but this requires that you know which subunit interacts with which. <br />
<br />
* The other issue is the current default relation between the entity in Column 2 and the GO term for CC is part_of, which is not true in this case. So annotating complexes to complexes should be revisited.<br />
<br />
* MF/BP of complex (case 4 in the slides, Full MF/BP evidence available)<br />
How does IMP work here? If authors are deleting one subunit and inferring the MF/BP of the complex, can that be used for the entire complex? Would you put the allele information in With column ?<br />
* Case 6, BP inferred from MF (where MF has evidence)4- BP can be inferred from MF. Since there is Exp. evidence for MF annotation, use the same PMID for the BP annotation.<br />
<br />
==Discussion==<br />
Present: Rama, Birgit, Sandra, JudyB, Harold, Kimberly, Chris, Ruth, Pascale<br />
<br />
* Birgit showed their IntAct interface where they associate IntAct complexes with GO terms. <br />
* Rama: Considering that you guys and protein2GO are neighbors, why aren't you using protein2go to curate? protein2go can handle complex IDs now and it is easier to maintain the annotations in one place. In the GOC we are encouraging curators to curate into one tool to help with consistency/data checks etc.<br />
** Sandra: There is a significant time lag in getting the IntAct complex IDs in protein2GO and we wanted to make the GO annotations while we were curating the complex and not wait for the complex ID to be available/integrated into protein2GO. <br />
** Judy: If this step can be sped up would you consider moving to protein2GO?<br />
** Sandra: Yes. <br />
AI: Sandra/Judy will talk to Tony.<br />
<br />
* Case 3: Handling complexes that are inferred based on Chemogenomics etc (as opposed to verified)? We should have a rule to not export those annotations and IDs. The ECO code can be used to flag such complexes in IntAct as 'do not export'. <br />
AI: discuss at GOC meeting.<br />
<br />
* Case 1: Should we associate IntAct complexes to GO complexes? Is this merely a mapping?<br />
** Harold: In PRO (which is an ontology) the logical definition takes care of the relationship between a GO and PRO complex. So this association wouldn't be necessary. PRO also annotates to MF and BP.<br />
** Rama: IntAct is not an Ontology though (it is just a hierarchy). So we can't treat it the same way.<br />
** Ruth: What if we want to capture that the complex is found in a certain cell type using col-16? <br />
** Pascale: The complex terms in GO are generic, while the IntAct ones are specific. So it might be okay to make this association.<br />
** Birgit: We will have this mapping on the Complex Portal website but can flag it as 'do not export' if we decide to go that way. Although that doesn't help Ruth's case.<br />
AI: GOC meeting<br />
<br />
* Case 1: Using IPI to associate IntAct complex with GO complex. Although we said we could use IPI for this annotation, it is not very satisfactory because we can't put anything in the With column. Switch it to IDA?<br />
AI: GOC meeting. If we decide to go with IDA we need to re-annotate in IntAct. Also depends on decision for point above.<br />
<br />
* Cases 2/5/7: If there is Exp evidence for a protein complex in Mouse, and if IntAct inferred the complex in Human using ISO, should we make GO MF/BP annotations for the inferred complexes?<br />
** Rama: I would say no. <br />
** Birgit: So should be tagged as 'do not export' in IntAct.<br />
AI: discuss at GOC meeting<br />
<br />
* Case 4: Can we use IMP to annotate MF or BP to complexes? <br />
** Sandra: Maybe not, as whole chain is usually knocked out/omitted.<br />
** Rama: If we capture this, we should put the missing chain in the With/From column.<br />
AI: discuss at GOC meeting<br />
<br />
* Case 6: For the IC annotation, Reference should be the PMID and not the GO_REF and the IntAct ID of the complex should be put in the With/From column. Should we allow IntAct IDs or the GO complex ID in the With/From column? The GO complex ID helps with book keeping though. Not sure!<br />
AI: discuss at GOC meeting<br />
<br />
* Case 7: If we export complexes inferred by orthology/homology, put complex AC into With/From column.<br />
<br />
* Annotating to X binding? e.g. heme binding in hemaglobin complex. <br />
** Rama: Hemaglobin's function is not heme binding. So don't make that heme binding. <br />
AI: Birgit to correct annotations in IntAct.<br />
<br />
* How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
** Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. But we need to decide on a similarity cut-off.<br />
AI: discuss at next call.<br />
<br />
* Does it make sense to have process annotations with IPI? <br />
AI: discuss at next call.<br />
<br />
* Add to agenda for the GOC meeting (done- http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Meeting_Agenda)</div>Bmeldalhttps://wiki.geneontology.org/index.php?title=Protein_Complex_Conference_Call_June19,_2015&diff=57416Protein Complex Conference Call June19, 20152015-06-23T09:15:36Z<p>Bmeldal: </p>
<hr />
<div>[[Category:Protein Complex]]<br />
==Agenda==<br />
===Background===<br />
<br />
IntAct Portal is curating complexes and associating these complexes with GO terms. This meeting is to come up with guidelines on annotating complexes to GO terms.<br />
* There are two levels of annotation:<br />
** Annotation that are shown on the Complex Portal Website<br />
** Annotations that are exported from IntAct to GO or directly annotated in P2GO<br />
Here, we are discussing which annotations should be exported from IntAct and which Complex identifiers should be available as annotation objects in P2GO.<br />
<br />
Slides: https://drive.google.com/folderview?id=0B0BzQEtrvNZlfjJmbk5wRG5PYlZPU1N3R0tmZ2M2aUxTTTNIWHVJYnNiTUlTdWpoN0hieWc&usp=sharing<br />
<br />
<br />
===Questions for consideration===<br />
* Does it make sense to annotate an IntAct complex to a GO complex? Is this meaningful? is this a mapping or an annotation? Should we instead annotate it to the location in the cell? e.g. ATPase complex (IntAct ID) is part_of mitochondrion (GO:5635). This will be similar to gene_product A is part of mitochondrion.<br />
The other issue with associating an IntAct complex with a GO complex is the evidence code. If you use IPI you need to say the subunits in the With column, but this requires that you know which subunit interacts with which. <br />
<br />
* The other issue is the current default relation between the entity in Column 2 and the GO term for CC is part_of, which is not true in this case. So annotating complexes to complexes should be revisited.<br />
<br />
* MF/BP of complex (case 4 in the slides, Full MF/BP evidence available)<br />
How does IMP work here? If authors are deleting one subunit and inferring the MF/BP of the complex, can that be used for the entire complex? Would you put the allele information in With column ?<br />
* Case 6, BP inferred from MF (where MF has evidence)4- BP can be inferred from MF. Since there is Exp. evidence for MF annotation, use the same PMID for the BP annotation.<br />
<br />
==Discussion==<br />
Present: Rama, Birgit, Sandra, JudyB, Harold, Kimberly, Chris, Ruth, Pascale<br />
<br />
* Birgit showed their IntAct interface where they associate IntAct complexes with GO terms. <br />
* Rama: Considering that you guys and protein2GO are neighbors, why aren't you using protein2go to curate? protein2go can handle complex IDs now and it is easier to maintain the annotations in one place. In the GOC we are encouraging curators to curate into one tool to help with consistency/data checks etc.<br />
** Sandra: There is a significant time lag in getting the IntAct complex IDs in protein2GO and we wanted to make the GO annotations while we were curating the complex and not wait for the complex ID to be available/integrated into protein2GO. <br />
** Judy: If this step can be sped up would you consider moving to protein2GO?<br />
** Sandra: Yes. <br />
AI: Sandra/Judy will talk to Tony.<br />
<br />
* Case 3: Handling complexes that are inferred based on Chemogenomics etc (as opposed to verified)? We should have a rule to not export those annotations and IDs. The ECO code can be used to flag such complexes in IntAct as 'do not export'. <br />
AI: discuss at GOC meeting.<br />
<br />
* Case 1: Should we associate IntAct complexes to GO complexes? Is this merely a mapping?<br />
** Harold: In PRO (which is an ontology) the logical definition takes care of the relationship between a GO and PRO complex. So this association wouldn't be necessary. PRO also annotates to MF and BP.<br />
** Rama: IntAct is not an Ontology though (it is just a hierarchy). So we can't treat it the same way.<br />
** Ruth: What if we want to capture that the complex is found in a certain cell type using col-16? <br />
** Pascale: The complex terms in GO are generic, while the IntAct ones are specific. So it might be okay to make this association.<br />
** Birgit: We will have this mapping on the Complex Portal website but can flag it as 'do not export' if we decide to go that way. Although that doesn't help Ruth's case.<br />
AI: GOC meeting<br />
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* Case 1: Using IPI to associate IntAct complex with GO complex. Although we said we could use IPI for this annotation, it is not very satisfactory because we can't put anything in the With column. Switch it to IDA?<br />
AI: GOC meeting. If we decide to go with IDA as need to re-annotate in IntAct. Also depends on decision for point above.<br />
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* Cases 2/5/7: If there is Exp evidence for a protein complex in Mouse, and if IntAct inferred the complex in Human using ISO, should we make GO MF/BP annotations for the inferred complexes?<br />
** Rama: I would say no. <br />
** Birgit: So should be tagged as 'do not export' in IntAct.<br />
AI: discuss at GOC meeting<br />
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* Case 4: Can we use IMP to annotate MF or BP to complexes? <br />
** Sandra: Maybe not, as whole chain is usually knocked out/omitted.<br />
** Rama: If we capture this, we should put the missing chain in the With/From column.<br />
AI: discuss at GOC meeting<br />
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* Case 6: For the IC annotation, Reference should be the PMID and not the GO_REF and the IntAct ID of the complex should be put in the With/From column. Should we allow IntAct IDs or the GO complex ID in the With/From column? The GO complex ID helps with book keeping though. Not sure!<br />
AI: discuss at GOC meeting<br />
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* Case 7: If we export complexes inferred by orthology/homology, put complex AC into With/From column.<br />
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* Annotating to X binding? e.g. heme binding in hemaglobin complex. <br />
** Rama: Hemaglobin's function is not heme binding. So don't make that heme binding. <br />
AI: Birgit to correct annotations in IntAct.<br />
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* How do you handle human proteins expressed in mouse, mixed species? Something to think about!<br />
** Birgit: We have a case I have been working on with Nancy. In that case the 2 sequences were identical, so we used the mixed-species evidence for both complexes. But we need to decide on a similarity cut-off.<br />
AI: discuss at next call.<br />
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* Does it make sense to have process annotations with IPI? <br />
AI: discuss at next call.<br />
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* Add to agenda for the GOC meeting (done- http://wiki.geneontology.org/index.php/2015_Washington_DC_GOC_Meeting_Agenda)</div>Bmeldal