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Combined display of all available logs of GO Wiki. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).
- 12:10, 11 April 2024 Pascale talk contribs moved page Ontology meeting 2024-04-15 to Ontology meeting 2024-04-22
- 17:54, 9 April 2024 Suzialeksander talk contribs created page File:Downloadstable.png (table for downloads)
- 17:54, 9 April 2024 Suzialeksander talk contribs uploaded File:Downloadstable.png (table for downloads)
- 14:49, 9 April 2024 Pascale talk contribs created page Projects update meeting 2024-04-09 (Created page with "= Attendees = * Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia * Present: * Regrets: ==GO meeting== * Registration by April 12th * Agenda by May 1st * Which days do we need on either side? * Draft agenda: https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.2jptrbvdxk9r * GO Users meeting: https://docs.google.com/document/d/1sIamECzTS5IMOy4GeldzWXdawnmOLvT9s5vClMAs3Bo/edit Category: GO Managers...")
- 16:08, 8 April 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-04-09 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, March 28th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/869 Outage tasks] === No GO Calls Week === * Next week (week of April 1st) is a no GO calls week === Next In-Person Consortium Meeting === * Week of May 20th - actual meeting dates: Tuesday, May 21 - Thursday, May 23 * Users Meeting, Monday, May 20th * Hosted by Jim Balho...")
- 10:17, 8 April 2024 Pascale talk contribs created page Ontology meeting 2024-04-15 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present: ''' * '''Regrets:''' Jim Category:Meetings")
- 11:57, 4 April 2024 Mi talk contribs created page 10 April 2024 PAINT Conference Call (Created page with "==Present== ==Agenda== ==="Do not annotate" terms=== Anushya gathered all the IBDs and the families that will be impacted if these annotations are removed. ===New PAINT release=== This version contains a GUI update so that curators can detect horizontal transfer nodes easily. The fill color of horizontal transfer nodes is now white. Clades where horizontal transfer occurs can also be detected easily using Tree->Color tree->color based on horizontal transfer. ===GO...")
- 15:13, 26 March 2024 Suzialeksander talk contribs created page Talk:Annotation Conf. Call 2024-03-26 (Created page with "GO Annotation Call Today at 09:00 wpk Notes Generated by Wudpecker Like what you see? Try Wudpecker. For free. Try Wudpecker 00:00 /53:49 Kimberly Van Auken 00:17 Susie, did you just set up the recording? Suzi Aleksander 00:23 I did not set it up. I thought I think Stasha set it up on all of SGDs. I don't didn't she didn't say she applied it to this. Okay. Kimberly Van Auken 00:32 Bye. I'm just wondering. Suzi Aleksander 00:34 Yeah. It's like an AI thing that takes not...")
- 11:54, 26 March 2024 Pascale talk contribs created page Projects update meeting 2024-03-27 (Created page with "= Attendees = * Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia * Present: * Regrets: = Discussion topics = ==GO meeting== * Registration form by March 15th * Agenda by May 1st * Which days do we need on either side? * Draft agenda: https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.2jptrbvdxk9r * GO Users meeting: https://docs.google.com/document/d/1sIamECzTS5IMOy4GeldzWXdawnmOLvT9s5vClMAs3Bo/edit...")
- 06:24, 26 March 2024 Pascale talk contribs created page Ontology meeting 2024-04-08 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present: ''' =Discussion points= * Ontobot action to add a term to the 'do not annotate' subset does not create the comment we used to have (something like, "This term should not be used for direct annotation. It should be possible to make a more specific annotation to one of the children of this term.") ** Should Ontobot also do that? ** Can we/should we add a check t...")
- 20:30, 25 March 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-03-26 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, March 28th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/869 Outage tasks] === Next In-Person Consortium Meeting === * Week of May 20th - actual meeting dates: Tuesday, May 21 - Thursday, May 23 * Users Meeting, Monday, May 20th * Hosted by Jim Balhoff in Chapel Hill, NC * Start thinking about [https://docs.google.com/document/d...")
- 04:38, 25 March 2024 Pascale talk contribs created page Ontology meeting 2024-03-25 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present: ''' =Discussion points= Category:Meetings")
- 15:33, 20 March 2024 Pascale talk contribs moved page Daily version of the Gene Ontology to Rolling build of the Gene Ontology
- 14:26, 19 March 2024 Pascale talk contribs created page Daily version of the Gene Ontology (Created page with " Category:OntologyCategory:GO Editors")
- 17:17, 18 March 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-03-19 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, March 28th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/869 Outage tasks] === Next In-Person Consortium Meeting === * Week of May 20th - actual meeting dates: Tuesday, May 21 - Thursday, May 23 * Users Meeting, Monday, May 20th * Hosted by Jim Balhoff in Chapel Hill, NC * Start thinking about [https://docs.google.com/document/d...")
- 06:07, 18 March 2024 Pascale talk contribs created page File:Travis error inferences diff.png
- 06:07, 18 March 2024 Pascale talk contribs uploaded File:Travis error inferences diff.png
- 05:41, 15 March 2024 Pascale talk contribs created page Procedure to check subset coverage (Created page with "# Checking GO annotation coverage #* Go to [https://www.ebi.ac.uk/QuickGO/ QuickGO], click on [https://www.ebi.ac.uk/QuickGO/annotations View Annotations] #* On the drop down menus at the top of the page, add filters as appropriate: #** Taxon(s) or taxonomic range (it is possible to select for example NBCITaxon:2 for all bacteria) #** Gene Products: it is usually desirable to select only Reviewed entry and Reference proteomes (either "Gene centric, canonical", or "Gene...")
- 06:58, 12 March 2024 Pascale talk contribs created page Projects update meeting 2024-03-13 (Created page with "= Attendees = * Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia * Present: = Discussion topics = ==GO meeting== * Registration form by March 15th * Agenda by May 1st ==Update on projects== ===[https://github.com/orgs/geneontology/projects/61 SGD Noctua migration]=== ===[https://github.com/geneontology/project-management/issues/77 MGI remainders]=== * GAF/GPAD and Isoforms * '''Questions:''' * Which ‘upstream annotations’ are converted...")
- 05:50, 12 March 2024 Pascale talk contribs created page Ontology meeting 2024-03-18 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present: ''' =Discussion points= ==Refactoring nitrogen cycle processes== Chris' proposal to refactor nitrogen cycle processes (important for proks and plants, but also general lessons learned): https://github.com/geneontology/go-ontology/issues/27217 ==How to add terms in batch to a do-not-annotate subset directly from the github web interface== See documentation he...")
- 18:44, 11 March 2024 Vanaukenk talk contribs moved page Annotation Conf. Call 2024-03-11 to Annotation Conf. Call 2024-03-12 (wrong date)
- 18:31, 11 March 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-03-11 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, March 14th, 4-6pm PST *** [https://github.com/geneontology/noctua/issues/866 Outage tasks] === Next In-Person Consortium Meeting === * Week of May 20th - actual meeting dates: Tuesday, May 21 - Thursday, May 23 * Hosted by Jim Balhoff in Chapel Hill, NC * Start thinking about [https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0...")
- 02:02, 11 March 2024 Pascale talk contribs created page Ontology meeting 2024-03-11 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present: ''' =Discussion points= ==Refactoring nitrogen cycle processes== Chris' proposal to refactor nitrogen cycle processes (important for proks and plants, but also general lessons learned): https://github.com/geneontology/go-ontology/issues/27217 ==How to add terms in batch to a do-not-annotate subset directly from the github web interface== ==Using an ensemble...")
- 21:02, 6 March 2024 Mi talk contribs created page 13 March 2024 PAINT Conference Call (Created page with "==Present== ==Agenda== ===Taxon Constraint Curation === We are correcting the taxon constraint violations in the current PAINT data using this [https://docs.google.com/spreadsheets/d/1fm2AVtvnhJoa7BUaDpg9Fc-w9cHmyzZrFZsylAUuUhw/edit?usp=sharing Google sheet file]. The PAINT tool implemented a taxon constraint check a few years ago, so it is highly unlikely that TCVs are introduced during the curation. There two likely sources for the TCVs. First, these are really old...")
- 15:49, 4 March 2024 Jamesbalhoff talk contribs created page 2024 Chapel Hill GOC Meeting Logistics (Created page with "=GOC Meeting, RENCI, Chapel Hill, North Carolina, May 21-23, 2024= * Location: [https://renci.org RENCI (Renaissance Computing Institute) at University of North Carolina, Chapel Hill, USA] ==Registration== Register for in-person attendance as follows: * First register at TicketLeap. '''Registration deadline is April 12, 2024'''. :* https://www.ticketleap.events/tickets/geneontology/spring2024goc * Pay registration fee (TBA) Remote attendees are asked to add their...")
- 09:38, 28 February 2024 Pascale talk contribs created page Projects update meeting 2024-02-28 (Created page with "= Attendees = * Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia * Present: = Discussion topics = ==Update on projects== ===[https://github.com/orgs/geneontology/projects/61 SGD Noctua migration]=== ===[https://github.com/geneontology/project-management/issues/77 MGI remainders] * GAF/GPAD and Isoforms * '''Questions:''' * Which ‘upstream annotations’ are converted from PR to MGI identifiers? * Possible approaches: *# Do nothing, i.e....")
- 16:20, 26 February 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-02-27 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, March 14th, 4-6pm PST *** [https://github.com/geneontology/noctua/issues/866 Outage tasks] === Next In-Person Consortium Meeting === * Week of May 20th * Hosted by Jim Balhoff in Chapel Hill, NC * Start thinking about [https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.faqtkfatd45w agenda items, speci...")
- 11:00, 23 February 2024 Pascale talk contribs created page Ontology meeting 2024-02-26 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present: ''' =Discussion points= ==CheEBI 7.3 list== https://github.com/geneontology/go-ontology/issues/27059 Category:Meetings")
- 09:25, 20 February 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-02-20 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, February 22nd, 4-6pm PST *** [https://github.com/geneontology/noctua/issues/865 Outage tasks] === Next In-Person Consortium Meeting === * Week of May 20th * Hosted by Jim Balhoff in Chapel Hill, NC * Start thinking about [https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.faqtkfatd45w agenda items, sp...")
- 14:29, 13 February 2024 Mi talk contribs created page 14 Feb 2024 PAINT Conference Call (Created page with "==Present== ==Agenda== ===New certificates=== Installation instructions. ===PAINT paper=== * Latest draft: https://docs.google.com/document/d/1cjIPb4LP8ifmq7k3ryECw5w9YsB8PdB_/edit * Supplemental materials: https://docs.google.com/document/d/1KN4ROPx6ddxsXOaUg5puc4LzgCtuUUYb/edit#heading=h.gjdgxs * Enrichment test site. Category:PAINT")
- 11:35, 13 February 2024 Pascale talk contribs deleted page Indirectly localizes (content was: "Category:Deprecated =This relation is deprecated in GO.= ==Definition== Identifies the gene product or substance whose location is established or maintained a process in which the annotated gene product is involved, but where the annotated gene product is known not to act directly. ==Child terms== * None. ==Annotation Extension Usage Examples==")
- 10:43, 13 February 2024 Pascale talk contribs deleted page Has participant (content was: "This relation is not used in GO extensions. Consider Has_input or Has_output ==Definition== Identifies an entity affected by the gene product's participation in a molecular function or biological process ==Cross-reference to Relations Ontology (RO) term== [http://purl.obolibrary.org/obo/RO_0000057 RO:0000057 has participant] ---- Date last Reviewed: 2021-12-15 Back to [http://wiki.geneontology.org/index.php/Annotation_usage_examples_for_each_annotation_extensi...")
- 09:18, 13 February 2024 Pascale talk contribs created page Talk:Stabilizes (Created page with "==== Heading text ==== This relation has been deprecated.")
- 11:50, 12 February 2024 Vanaukenk talk contribs created page Projects update meeting 2024-02-14 (Created page with "= Attendees = * Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia * Present: = Discussion topics = ==Active projects== ==[https://github.com/orgs/geneontology/projects/61 SGD Noctua migration]== import timeline; file and data location review <br /> (from convo w/dustin about order of operations moving forward) ===[https://github.com/orgs/geneontology/projects/148 Noctua Form UI improvement]=== Paul, Kimberly, Tremayne * Minimal changes to pre...")
- 11:20, 12 February 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-02-13 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, February 8th, 4-6pm PST *** [https://github.com/geneontology/noctua/issues/857 Outage tasks] == GO Release Pipeline == * January release on the 17th * #release-pipeline Slack channel for updates == Annotation == === Updating 'has input' and 'has output' extension relations to 'has primary input' and 'has primary output' === * RO has relations...")
- 10:04, 6 February 2024 Pascale talk contribs created page Ontology meeting 2024-02-12 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present: =Discussion points= ==Automatic mappings== From Chris in this ticket: https://github.com/geneontology/go-ontology/issues/26941 skos:exactMatch is transitive so we can assert inferences from this. GO:x exactMatch RHEA:y exactMatch MetaCyc:z ==> GO:x exactMatch MetaCyc:z * Can we have a script that handles this? * RHEA Exact matches? ==Blocking issues==...")
- 06:00, 6 February 2024 Pascale talk contribs created page Currency chemicals (Created page with " {| class="wikitable" |+ Caption text |- ! ChEBI ID !! Chemical |- | [https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:15377 CHEBI:15377] || H2O |- | Example || Example |- | Example || Example |- | Example || Example |- | Example || Example |- | Example || Example |- | Example || Example |- | Example || Example |- | Example || Example |- | Example || Example |- | Example || Example |- | Example || Example |- | Example || Example |- | Example || Example |- | Example...")
- 17:34, 29 January 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-01-30 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, February 8th, 4-6pm PST *** [https://github.com/geneontology/noctua/issues/857 Outage tasks] == GO Release Pipeline == * January release on the 17th * #release-pipeline Slack channel for updates == Annotation == === Updating 'has input' and 'has output' extension relations to 'has primary input' and 'has primary output' === * RO has relations...")
- 12:57, 24 January 2024 Pascale talk contribs created page Ontology meeting 2024-01-29 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present: =Discussion points= ==Blocking issues on ongoing tickets== ==Proposal to switch to 'has primary input'== * Relations have been changed in the ontology months ago * Proposal (Kimberly): ** update existing annotations in Noctua and Protein2GO ** Get the list of currency chemicals (Reactome?) - added to Pathways2GO agend for 2024-01-25 ** Curator call: discuss u...")
- 11:31, 23 January 2024 Pascale talk contribs uploaded a new version of File:Precomposed term replacement.png
- 11:31, 23 January 2024 Pascale talk contribs deleted page File:Precomposed term replacement.png (Deleted old revision 20240123152520!Precomposed_term_replacement.png)
- 11:25, 23 January 2024 Pascale talk contribs uploaded a new version of File:Precomposed term replacement.png
- 11:21, 23 January 2024 Pascale talk contribs created page File:Precomposed term replacement.png
- 11:21, 23 January 2024 Pascale talk contribs uploaded File:Precomposed term replacement.png
- 14:55, 22 January 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-01-23 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, February 8th, 4-6pm PST *** [https://github.com/geneontology/noctua/issues/857 Outage tasks] == GO Release Pipeline == * January snapshot release on the 12th * #release-pipeline Slack channel for updates == Annotation == === Automatic replacements for 'x signaling involved in y' BPs === * Replace annotations with 'x signaling' and an annotatio...")
- 04:13, 22 January 2024 Pascale talk contribs created page Ontology meeting 2024-01-22 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present:''' * '''Regrets:''' =Announcements= =Discussion points= ==Objectives & Priorities for 2024== ===New term requests=== Remain high priority ===BP refactor=== Pascale & Paul ===Review design patterns (continued from last week)=== Repo: https://github.com/geneontology/go-ontology/tree/master/docs/patterns * [https://github.com/geneontology/go-ontology/labels/desi...")
- 04:46, 18 January 2024 Pascale talk contribs deleted page Microbial ontology development and annotation (content was: "Category:Ontology ===Staff=== Lead by: Suzi Others: Jane, Pascale, Michelle, Jim Hu ? ===Contacts=== '''Bruno Sobral''', Virginia Bioinformatics Institute [http://patric.vbi.vt.edu/ Pathogen Portal, PathoSystems Resource Integration Center (PATRIC)] '''Philippe le Mercier''' SIB, [http://www.expasy.ch/viralzone/ ViralZone] '''Jonathan Eisen''' UCD [http://bobcat.genomecenter.ucdavis.edu/mediawiki/index.php/Main_Page his project's wiki] '''Simon Kasif''' Boston Univer...")
- 02:14, 17 January 2024 Pascale talk contribs created page Projects update meeting 2024-01-17 (Created page with "= Attendees = * Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia * Present: =Announcements= Category: GO Managers Meetings")
- 20:08, 15 January 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-01-16 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, February 8th, 4-6pm PST *** [https://github.com/geneontology/noctua/issues/857 Outage tasks] * LBL Electrical System Maintenance Outage ** Done, but please let us know if you have any issues, particularly with login == GO Release Pipeline == * No December release * #release-pipeline Slack channel for updates == Annotation == == GO-CAM and Noc...")
- 04:22, 11 January 2024 Pascale talk contribs created page Protein2GO specific processes (Created page with "* Annotation blacklist: https://www.ebi.ac.uk/internal-tools/protein2go/talisman.html?database=production&alias=goapro Category: Annotation")
- 15:59, 10 January 2024 Pascale talk contribs created page Projects update meeting 2024-01-24 (Created page with "= Attendees = * Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia * Present: https://github.com/geneontology/noctua/issues/856 ==Objectives Jan/Feb 2024== Assuming we still aim for 2-month sprints; maybe this work requires more than 2 months ===Pipeline stabilization=== Agree on objectives: * for eg 1 snapshot a week * minimally we need to produce the ontology and export annotations generated in Noctua. * Maybe for stability, data export and...")
- 05:45, 9 January 2024 Pascale talk contribs created page File:New entities.png
- 05:45, 9 January 2024 Pascale talk contribs uploaded File:New entities.png
- 19:00, 8 January 2024 Mi talk contribs created page 10 Jan 2024 PAINT Conference Call (Created page with "==Present== ==Agenda== ===PAINT paper=== We are going to focus our discussion on the new draft of human functionome paper. Here is the link to the draft. https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit?usp=sharing There are some new data. Huaiyu circulated some of them. We can discuss about them. Category:PAINT")
- 10:06, 8 January 2024 Pascale talk contribs created page Ontology meeting 2024-01-08 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present:''' * '''Regrets:''' =Discussion points= Category:Meetings")
- 10:05, 8 January 2024 Pascale talk contribs created page Ontology editors' conference call minutes 2024 (Created page with "* Jan 1 - No GO calls - holidays * Jan 8 * Jan 15 ---- No call - US holiday - MLK * Jan 22 * Jan 29 Category:Meetings Category:Ontology")
- 21:47, 7 January 2024 Vanaukenk talk contribs created page Annotation Conf. Call 2024-01-09 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, January 11th, 4-6pm PST *** [https://github.com/geneontology/noctua/issues/855 Outage tasks] * LBL Electrical System Maintenance Outage ** Friday, January 12th, 4pm PST - Saturday, January 13th, 7pm PST == GO Release Pipeline == * No December release * #release-pipeline Slack channel for updates == Annotation == == GO-CAM and Noctua == * Noct...")
- 21:39, 7 January 2024 Vanaukenk talk contribs created page Annotation Call 2024 Agenda and Minutes (Created page with "* Annotation Conf. Call 2024--01-09")
- 10:05, 19 December 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-12-19 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Annotation Calls === * Tuesday, January 2nd - no GO calls week * Tuesday, January 9th - Noctua training session === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, January 11th, 4-6pm PST *** [https://github.com/geneontology/noctua/issues/855 Outage tasks] === Github 2FA === * GitHub users are now required to enable two-factor authentication as an additional security measure. Your activity...")
- 04:40, 18 December 2023 Pascale talk contribs created page Projects update meeting 2024-01-10 (Created page with "= Attendees = * Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia * Present: =Announcements= Calls are now scheduled for the 2nd and 4th Wednesday of the month. =Projects status= * [https://github.com/orgs/geneontology/projects/108/views/1 https://github.com/geneontology/project-management/issues/85] * Pipeline stablilization objectives: ** for eg 1 snapshot a week ** minimally we need to produce the ontology and export annotations generated i...")
- 18:41, 11 December 2023 Mi talk contribs created page 13 December 2023 PAINT Conference Call (Created page with "==Present== ==Agenda== Please suggest topics to discuss. Category:PAINT")
- 16:15, 11 December 2023 Pascale talk contribs created page Projects update meeting 2023-12-13 (Created page with "= Attendees = * Members: David, Jim, Kimberly, Pascale, Seth, Suzi, Huaiyu, Paul, Chris, Cynthia * Present: =Projects status= https://github.com/orgs/geneontology/projects/108/views/1 Category: GO Managers Meetings")
- 16:50, 5 December 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-12-12 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, December 14th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/849 Outage tasks] == GO Release Pipeline == * November release - done * #release-pipeline Slack channel for updates == Annotation == === Annotation Relations === * colocalizes_with - we have discussed retiring this gp2term relation * [https://github.com/geneontology/g...")
- 09:32, 1 December 2023 Pascale talk contribs created page Ontology meeting 2023-12-11 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Discussion points= ==Def and synonym cross-references== EC and RHEA are sometimes used in def xref, and EC if often used in synonym xref. This is really tedious to update when the EC or RHEA IDs change. Can we change this to, for example: GOC:EC and GOC:RHEA, and only maintain the actual cross references in xrefs? Example [Te...")
- 16:13, 27 November 2023 Ga362 talk contribs uploaded a new version of File:MiRNA Decision Tree 2023.pptx
- 16:12, 27 November 2023 Ga362 talk contribs uploaded a new version of File:MiRNA Decision Tree.pdf
- 16:10, 27 November 2023 Ga362 talk contribs uploaded a new version of File:MiRNA Decision Tree.jpg
- 16:09, 27 November 2023 Ga362 talk contribs uploaded a new version of File:LncRNA Decision Tree.pdf
- 16:06, 27 November 2023 Ga362 talk contribs uploaded a new version of File:LncRNA Decision Tree.jpg
- 10:25, 27 November 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-11-28 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, November 30th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/851 Outage tasks] ** Next outage December 14th == GO Release Pipeline == * November release - done * #release-pipeline Slack channel for updates == Annotation == === Annotation Review === * Review annotations to [https://github.com/geneontology/go-annotation/issues/4...")
- 08:30, 27 November 2023 Pascale talk contribs created page Projects update meeting 2023-11-29 (Created page with "= Attendees = * Members: David, Jim, Kimberly, Pascale, Seth, Suzi, Huaiyu, Paul, Chris, Cynthia * Present: * Regrets: =Main points and AI from Fall 2023 GOC meeting= https://docs.google.com/document/d/15ePOkbY4whF5kQIabieFD5JfxfHdclUqoHcyykmqzK0/edit Category: GO Managers Meetings")
- 11:27, 24 November 2023 Pascale talk contribs created page Ontology meeting 2023-11-27 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Discussion points= * MetaCyc now requires a subscription; what is the GO policy WRT links? * Pascale - I dont have access to the site anymore, so I cannot verify the reactions. * One suggestion would be to limit to using RHEA mappings : https://ftp.expasy.org/databases/rhea/tsv/rhea2metacyc.tsv and any mapping not there would be r...")
- 05:23, 17 November 2023 Pascale talk contribs created page Ontology meeting 2023-11-20 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Steven, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Ontology tickets= ==Questions/follow up on ongoing tickets== [https://github.com/geneontology/go-ontology/issues/23268 proteinogenic amino acid biosynthesis] * '''AI''' Edith to create a spreadsheet with the 20 proteinogenic amino acids biosynthesis terms, and we'll see which we need both an L and a D form. Category:Meetin...")
- 12:59, 16 November 2023 Ga362 talk contribs uploaded a new version of File:MiRNA Decision Tree 2023.pptx
- 12:57, 16 November 2023 Ga362 talk contribs uploaded a new version of File:MiRNA Decision Tree.pdf
- 12:52, 16 November 2023 Ga362 talk contribs uploaded a new version of File:MiRNA Decision Tree.jpg
- 14:54, 15 November 2023 Ga362 talk contribs uploaded a new version of File:LncRNA Decision Tree.pdf
- 14:50, 15 November 2023 Ga362 talk contribs uploaded a new version of File:LncRNA Decision Tree.jpg
- 14:48, 15 November 2023 Ga362 talk contribs uploaded a new version of File:LncRNA Decision Tree.jpg
- 08:04, 2 November 2023 Pascale talk contribs created page Ontology meeting 2023-11-13 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Steven, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' Peter, Chris, Val, Pascale, Edith, Raymond, Jim, Kimberly * '''Regrets:''' David ==Computed taxon constraints== Jim * Computed TCs (from Uberon and other ontologies) are now in go-plus * There are now redundant asserted TCs and computed TCs: should we remove redundant asserted TCs? * (need to check that GO rules still uses go-plus in the GAFre...")
- 10:19, 30 October 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-10-31 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, November 9th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/848 Outage tasks] ** Second Thursday of November is the Thanksgiving holiday in the US - no outage == GO Release Pipeline == * October release - done * #release-pipeline Slack channel for updates == Annotation == === Signaling Cassettes Project === *Signaling Cassette...")
- 02:59, 30 October 2023 Pascale talk contribs created page Ontology meeting 2023-10-30 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Steven, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present:''' * '''Regrets:''' ==[https://github.com/geneontology/go-ontology/issues/25933 Cell to cell signaling terms]== Request was to * Replace "epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification GO:0060802, with epiblast cell-extraembryonic ectoderm cell signaling (Single EXP to PMID:14511481) * Replace "...")
- 12:04, 25 October 2023 Pascale talk contribs deleted page Annotation Cross Products (Retired) (content was: "#REDIRECT:Annotation <span style ="color:red">'''Please note, this page no longer contains the primary documenation for the annotation extension field. Information here is being moved to the main Annotation Extension wiki page, and supporting pages.'''</span> <strike>'''NB: Annotation cross-products are now referred to as annotation extensions''' Each GO annotation pairs a si...", and the only contributor was "Cjm" (talk))
- 12:03, 25 October 2023 Pascale talk contribs undeleted page Annotation Cross Products (Retired) (155 revisions)
- 05:19, 24 October 2023 Pascale talk contribs created page Projects update meeting 2023-11-15 (Created page with "= Attendees = * Members: David, Jim, Kimberly, Pascale, Seth, Suzi, Huaiyu, Paul, Chris, Cynthia * Present: * Regrets: =Debrief SAB meeting= Nov 7, 2023 * [https://docs.google.com/document/d/1vWp76TEN3bsqs9VlzzkQJeR6kSL2As-jN1ZILKK8aC0/edit Draft agenda] (based on 2020-10 agenda) * Presentation from [https://docs.google.com/presentation/d/1EBKv0Y_Ybqiddd3Hma9Iupn_kF-wgEeeh3ONBHoe1p4/edit#slide=id.g6098edfb95_0_0 Oct 2020] =Main points and AI from Fall 2023 GOC meet...")
- 05:18, 24 October 2023 Pascale talk contribs created page Projects update meeting 2023-11-01 (Created page with "= Attendees = * Members: David, Jim, Kimberly, Pascale, Seth, Suzi, Huaiyu, Paul, Chris, Cynthia * Present: * Regrets: =Prepare for SAB meeting= Nov 7, 2023 * [https://docs.google.com/document/d/1vWp76TEN3bsqs9VlzzkQJeR6kSL2As-jN1ZILKK8aC0/edit Draft agenda] (based on 2020-10 agenda) * Presentation from [https://docs.google.com/presentation/d/1EBKv0Y_Ybqiddd3Hma9Iupn_kF-wgEeeh3ONBHoe1p4/edit#slide=id.g6098edfb95_0_0 Oct 2020] =Main points and AI from Fall 2023 GOC...")
- 12:59, 23 October 2023 Pascale talk contribs created page Ontology meeting 2023-10-23 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Steven, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present:''' * '''Regrets:''' ==[https://github.com/geneontology/go-ontology/issues/25933 Cell to cell signaling terms]== Request was to * Replace "epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification GO:0060802, with epiblast cell-extraembryonic ectoderm cell signaling (Single EXP to PMID:14511481) * Replace "...")
- 13:23, 17 October 2023 Pascale talk contribs created page Projects update meeting 2023-10-25 (Created page with "= Attendees = * Members: David, Jim, Kimberly, Pascale, Seth, Suzi, Huaiyu, Paul, Chris, Cynthia * Present: * Regrets: =Prepare for SAB meeting= Nov 7, 2023 Category: GO Managers Meetings")
- 01:49, 16 October 2023 Pascale talk contribs created page File:Catalytic activity.png
- 01:49, 16 October 2023 Pascale talk contribs uploaded File:Catalytic activity.png
- 01:48, 16 October 2023 Pascale talk contribs created page File:Go reaction participants.png
- 01:48, 16 October 2023 Pascale talk contribs uploaded File:Go reaction participants.png
- 01:37, 16 October 2023 Pascale talk contribs created page Interpretation of Travis checks errors (Created page with " == Review Status == Last reviewed: In progress Reviewed by [http://wiki.geneontology.org/index.php/Ontology_Editing_Guide Back to: Ontology Editing Guide] Category:GO EditorsCategory:OntologyCategory:Editor_Guide_2018")
- 05:20, 12 October 2023 Pascale talk contribs created page Ontology meeting 2023-10-16 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Val, Steven, Jim, Tanya, Kimberly, Peter, Chris, Paul * '''Present:''' * '''Regrets:''' =Discussion points= ==Switching from has in/output to has primary in/output== * '''TBC''' OK to merge, in the sense that the inferences are no worse than current and no equivalent terms are being created * Need decision on relation to use for [https://github.com/geneontology/go-ontology/issues/26217 receptor activity] ==[https://gith...")
- 16:41, 11 October 2023 User account ERASEME001 talk contribs was created by Sjcarbon talk contribs and password was sent by email (This is a GO meeting test)
- 09:18, 10 October 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-10-10 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, October 12th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/843 Outage tasks] === Fall GOC Meeting === * Virtual meeting * [https://docs.google.com/document/d/18ipImQU4_NnJ2iiw88Gwa4BTargC4cPBteyHF2RFR_M/edit Draft agenda] * October 17th - 19th (Tuesday - Thursday) * October 18th is also a [https://www.biocuration.org/ virtual IS...")
- 03:25, 9 October 2023 Pascale talk contribs created page Projects update meeting 2023-10-11 (Created page with "= Attendees = * Members: David, Jim, Kimberly, Pascale, Seth, Suzi, Huaiyu, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= * GOC meeting: October 17-19, 2023 ** Review and finalize agenda: [https://docs.google.com/document/d/18ipImQU4_NnJ2iiw88Gwa4BTargC4cPBteyHF2RFR_M/edit Draft agenda] ** ISB is having a 1.5h session on the 18th =Administrative points= * Is this call moving to every other week or the second and fourth weeks of the month? In the past...")
- 03:03, 26 September 2023 Pascale talk contribs created page Ontology meeting 2023-10-02 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Discussion points= ==Usage of 'has input' versus 'has primary input'== * [https://github.com/geneontology/go-ontology/issues/26169 Ticket to test changing all 'has input' to 'has primary input'] * Table of ‘pros and cons’ for the two options, see: https://docs.google.com/spreadsheets/d/1tYXUa8RhnihwOVCokpgvARobZ9CmCHCvWrVWdjXRSC4/e...")
- 03:01, 26 September 2023 Pascale talk contribs created page Ontology meeting 2023-10-09 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Discussion points= ==Usage of 'has input' versus 'has primary input'== * [https://github.com/geneontology/go-ontology/issues/26169 Ticket to test changing all 'has input' to 'has primary input'] * Table of ‘pros and cons’ for the two options, see: https://docs.google.com/spreadsheets/d/1tYXUa8RhnihwOVCokpgvARobZ9CmCHCvWrVWdjXRSC4/e...")
- 17:10, 25 September 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-09-26 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, September 28th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/843 Outage tasks] * Extended outage coming in early October ** This is now cancelled === Fall GOC Meeting === * Virtual meeting * [https://docs.google.com/document/d/18ipImQU4_NnJ2iiw88Gwa4BTargC4cPBteyHF2RFR_M/edit Draft agenda] * October 17th - 19th (Tuesday - Thurs...")
- 02:42, 21 September 2023 Pascale talk contribs created page Projects update meeting 2023-09-27 (Created page with "= Attendees = * Members: David, Jim, Kimberly, Pascale, Seth, Suzi, Huaiyu, Paul, Chris, Cynthia * Present: =Announcements= * GOC meeting: October 17-19, 2023 ** [https://docs.google.com/document/d/18ipImQU4_NnJ2iiw88Gwa4BTargC4cPBteyHF2RFR_M/edit Draft agenda] ** ISB is having a 1.5h session on the 18th * SAB meeting: November 7th, 2023 * Next week is the no GO calls week = Feedback request = == Proposal: need more information in GPI == Starting proposal to add t...")
- 08:35, 20 September 2023 Pascale talk contribs created page Ontology meeting 2023-09-25 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Discussion points= ==Usage of 'has input' versus 'has primary input'== We wanted to decide whether to switch in the ontology all ‘has input’ for ‘has primary input’ (as appropriate). I have made a table of ‘pros and cons’ for the two options, see: https://docs.google.com/spreadsheets/d/1tYXUa8RhnihwOVCokpgvARobZ9CmCHCvWrV...")
- 14:20, 18 September 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-09-19 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, September 28th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/843 Outage tasks] * Extended outage coming in early October ** Will re-visit as we get closer to work out exact dates and times === Fall GOC Meeting === * Virtual meeting * October 17th - 19th (Tuesday - Thursday) * October 18th is also a virtual ISB meeting - have a...")
- 07:58, 18 September 2023 Pascale talk contribs deleted page Ontology meeting 2023-09-11 (content was: "* '''Group members:''' Pascale, Raymond, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Precompute inferred taxon constraints and add to ontology release= See https://github.com/geneontology/go-ontology/issues/19759 =[https://github.com/geneontology/go-ontology/issues/21211 Odd parent - child relationships for binding MF terms]=...", and the only contributor was "Pascale" (talk))
- 07:56, 18 September 2023 Pascale talk contribs created page Ontology meeting 2023-09-18 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Precompute inferred taxon constraints and add to ontology release= See https://github.com/geneontology/go-ontology/issues/19759 =[https://github.com/geneontology/go-ontology/issues/21211 Odd parent - child relationships for binding MF terms]= Edith =Has_part guidelines= =Protein complex guidelines= * Protein_complexes * Versi...")
- 03:38, 13 September 2023 Pascale talk contribs deleted page Category:Protein Complex (content was: "All things protein complex.", and the only contributor was "Gail" (talk))
- 03:32, 13 September 2023 Pascale talk contribs created page Category:Archived file formats (Created page with "This category groups pages discussion retired file formats. Current documentation is on GitHub and on the main GO website.")
- 03:28, 13 September 2023 Pascale talk contribs created page Category:Archived annotation (Created page with "This category groups pages for meetings, workshops and general notes of discussions of specific annotation topics.")
- 12:51, 12 September 2023 Mi talk contribs created page 20 September 2023 PAINT Conference Call (Created page with "==Present== ==Agenda== ===PANTHER17 tree review=== Here is the [https://docs.google.com/spreadsheets/d/1fYPOdrtXvhoaCJN0ZA-SeZP4zogH%20CEuD79xWAjV5p4/edit spreadsheet] with missing human IBAs between v.15 and v.17. Missing annotations can be due to multiple reasons. A common one is the replaced GO terms are not used for the obsoleted term. ===Shortening the cycle between new experimental annotations and PAINT=== Currently, once new experimental annotations are rele...")
- 03:40, 12 September 2023 Pascale talk contribs deleted page Creating new GO terms (content was: " Category:OntologyCategory:GO Editors", and the only contributor was "Pascale" (talk))
- 10:55, 11 September 2023 Jamesbalhoff talk contribs created page Molecular Function reaction participants (Created page with "Molecular functions with Rhea xrefs are automatically linked to ChEBI terms identifying the chemicals participating in the reaction. The ChEBI participants are extracted from data provided by Rhea. The generated file is imported into go-edit.obo and merged into the go-plus.owl release. It can be viewed on GitHub here: * https://github.com/geneontology/go-ontology/blob/master/src/ontology/imports/go-catalytic-activities-participants.owl * https://github.com/geneontology...")
- 07:05, 7 September 2023 Pascale talk contribs created page Projects update meeting 2023-09-13 (Created page with "= Attendees = * Members: David, Jim, Kimberly, Pascale, Seth, Suzi, Huaiyu, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= * GOC meeting: October 17-19, 2023 * SAB meeting: November 7th, 2023 * Going to 1 meeting every 2 weeks>> no meeting next week =Active projects= https://github.com/orgs/geneontology/projects/108/views/1 How close are we to closing these projects? * [https://github.com/geneontology/project-management/issues/14 GO API refactor] ** Nee...")
- 09:45, 5 September 2023 Vanaukenk talk contribs created page Noctua to Standard Annotation Conversion Table (Created page with "= Noctua to Standard Annotation Conversion Table (work in progress) = <span style="color:red">In Google doc for now: https://docs.google.com/spreadsheets/d/1vkBVTyUg1tjipUtYGan5Ob0vE14H_j6O-PuTH9619eg/edit#gid=0</span> {| class="wikitable" !colspan="9"| Molecular Function |- !rowspan="2"| Link !rowspan="2"| Curation Statement !rowspan="2"| Allowed values (range) !colspan="2"| GO-CAM !colspan="4"| GPAD Output |- !rowspan="1"| GO-CAM relation !rowspan="1"| GO-CA...")
- 10:04, 31 August 2023 Pascale talk contribs created page Ontology meeting 2023-09-11 (Created page with "* '''Group members:''' Pascale, Raymond, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Tickets to discuss= Following up on * [https://github.com/geneontology/go-ontology/issues/25933 Cell cell-signaling terms] Request was to ** Replace "epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification GO:0060802, with *** Single EXP to PMID:14511481 ** Replace "cerebellar Purkinje...")
- 14:27, 28 August 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-08-29 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, September 14th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/843 Outage tasks] * Extended outage coming in early October ** Will re-visit as we get closer to work out exact dates and times === Fall GOC Meeting === * Virtual meeting * October 17th - 19th (Tuesday - Thursday) * Do you know of external groups that might like to pr...")
- 07:30, 24 August 2023 Pascale talk contribs created page Projects update meeting 2023-08-30 (Created page with "= Attendees = * Members: Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia, David, Jim * Present: * Regrets: =Announcements= * GOC meeting: October 17-19, 2023 * SAB meeting: November 7th, 2023 =Upcoming projects= TBD =Project-specific questions= * Use of "GO_Central" for MGI remainders =Projects updates= https://github.com/orgs/geneontology/projects/108")
- 18:35, 22 August 2023 User account Test002 talk contribs was created by Sjcarbon talk contribs
- 18:31, 22 August 2023 User account Test001 talk contribs was created by Sjcarbon talk contribs
- 17:57, 21 August 2023 User account Civihosting talk contribs was created automatically
- 04:15, 21 August 2023 Pascale talk contribs created page Ontology meeting 2023-08-28 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Tickets to discuss= * [https://github.com/geneontology/go-ontology/issues/25933 Cell cell-signaling terms] ** To replace "epiblast cell-extraembryonic ectoderm cell signaling involved in anterior/posterior axis specification GO:0060802, please add: epiblast cell-extraembryonic ectoderm cell signaling *** Single EXP to PMID:14511481...")
- 15:22, 16 August 2023 Sjcarbon talk contribs created page Projects update meeting 2023-08-23 (Created page with "= Attendees = * Present: * Regrets: =Announcements= TBD =Upcoming projects= TBD =Project-specific questions= * Use of "GO_Central" for MGI remainders =Projects updates= https://github.com/orgs/geneontology/projects/108")
- 20:55, 15 August 2023 Sjcarbon talk contribs created page Projects update meeting 2023-08-16 (Created page with "= Attendees = * Present: * Regrets: =Announcements= ... =Upcoming projects= * Clarify actions for Noctua roadmap (Chris and PaulT present) ** [https://docs.google.com/document/d/1I808pPEG06uoNXCM86eGa_t4Ei-JGxRGkRSf1ZSuAA4 Meeting agenda and minutes] =Projects updates= https://github.com/orgs/geneontology/projects/108")
- 15:18, 8 August 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-08-15 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, August 24th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/841 Outage tasks] === Fall GOC Meeting === * Virtual meeting * October 17th - 19th (Tuesday - Thursday) * Do you know of external groups that might like to present their GO-related work? * Think about useful break out sessions == GO Release Pipeline == * July release out...")
- 15:33, 31 July 2023 Sjcarbon talk contribs created page Projects update meeting 2023-08-02 (Created page with "= Attendees = * Present: * Regrets: =Announcements= ... =Upcoming projects= * Need owner/etc for https://github.com/geneontology/project-management/issues/73 * Clarify actions for Noctua roadmap =Projects updates= https://github.com/orgs/geneontology/projects/108")
- 14:33, 31 July 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-08-01 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, August 10th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/841 Outage tasks] === Fall GOC Meeting === * Virtual meeting * October 17th - 19th (Tuesday - Thursday) * Do you know of external groups that might like to present their GO-related work? * Think about useful break out sessions == GO Release Pipeline == * July release in...")
- 12:32, 31 July 2023 Mi talk contribs created page 13 September 2023 PAINT Conference Call (Created page with "==Present== ==Agenda== ===Shortening the cycle between new experimental annotations and PAINT=== Currently, once new experimental annotations are released by GO, it takes up to one month to be visible in PAINT tool. The question is whether the cycle can be shortened. Below are a few ideas. *Snapshot is loaded weekly. *Noctua annotations could be loaded directly. *Literature curation is done directly in PAINT. Category:PAINT")
- 15:03, 24 July 2023 Pascale talk contribs created page Projects update meeting 2023-07-26 (Created page with "= Attendees = * Members: Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia, David, Jim * Present: * Regrets: =Announcements= * GOC meeting Oct 17-19th * Any suggestions for outside groups we should invite to give a talk ? =New GO grant= Please remember to cite the new grant in paper!! grant number HG012212 =TreeGrafter = * Will be integrated into InterPro pipeline * is everyone OK using a PMID as the reference? Other IEAs use a GO_REF =clean out old us...")
- 11:07, 20 July 2023 Pascale talk contribs created page Ontology meeting 2023-07-31 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' Val =Announcements= Pascale away: * July 31 * Aug 7 (no GO calls week) * Aug 14th ==GO:0000904 'cell morphogenesis involved in differentiation now obsoleted== * https://github.com/geneontology/go-ontology/issues/24299 * Can we now proceed with implementation of the automated inferences of part_of relations? ==Revert to using 'h...")
- 10:18, 19 July 2023 Ruth.lovering talk contribs created page File:MiRNA Decision Tree.pdf
- 10:18, 19 July 2023 Ruth.lovering talk contribs uploaded File:MiRNA Decision Tree.pdf
- 10:14, 19 July 2023 Ruth.lovering talk contribs uploaded a new version of File:MiRNA Decision Tree 2023.pptx
- 10:10, 19 July 2023 Ruth.lovering talk contribs created page File:MiRNA Decision Tree.jpg
- 10:10, 19 July 2023 Ruth.lovering talk contribs uploaded File:MiRNA Decision Tree.jpg
- 10:06, 19 July 2023 Ruth.lovering talk contribs created page File:LncRNA Decision Tree.jpg
- 10:06, 19 July 2023 Ruth.lovering talk contribs uploaded File:LncRNA Decision Tree.jpg
- 09:02, 19 July 2023 Pascale talk contribs created page Projects update meeting 2023-07-19 (Created page with "= Attendees = * Members: Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia, David, Jim * Present: * Regrets: Kimberly =Announcements= * GOC meeting Oct 17-19th * Any suggestions for outside groups we should invite to give a talk ? =New GO grant= Please remember to cite the new grant in paper!! grant number HG012212 = Displaying GO-plus in OLS= AI: Jim will contact the OLS developers to switch to GO-plus after the next release =Review priorities from GOC...")
- 08:10, 19 July 2023 Ruth.lovering talk contribs created page File:LncRNA Decision Tree.pdf
- 08:10, 19 July 2023 Ruth.lovering talk contribs uploaded File:LncRNA Decision Tree.pdf
- 06:28, 19 July 2023 Pascale talk contribs created page LncRNA GO annotation manual (Created page with " Category:Annotation Guidelines")
- 09:08, 18 July 2023 Pascale talk contribs created page Ontology meeting 2023-07-24 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Announcements= Pascale away: * July 31 * Aug 7 (no GO calls week) * Aug 14th =Discussion points= ==Update on ontology maintenance project== https://github.com/orgs/geneontology/projects/135 ==Further improving the efficiency of term obsoletion == These small tweeks: # When we create the annotation files, 4 files are not crea...")
- 16:09, 17 July 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-07-18 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, July 20th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/834 Outage tasks] === Fall GOC Meeting === * Virtual meeting * October 17th - 19th (Tuesday - Thursday) * Do you know of external groups that might like to present their GO-related work? == GO Release Pipeline == * June release out June 11th * No July release at this point...")
- 03:19, 15 July 2023 Valwood talk contribs created page Ontology meeting 2023-07-17 (Created page with " Suggested item. Further improving the efficiency of term obsoletion. These small tweeks: 1. When we create the annotation files, 4 files are not created and we need to look at them all to see if they have any contents. Is it possible to not create the file if there are no annotations? 2. We still need to create a lot of tickets for the obsoletion, and then do the e-mail. Can we think of any other ways to streamline further?")
- 11:38, 12 July 2023 Hla28 talk contribs uploaded a new version of File:MiRNA Annotation Decision Tree 2023.png
- 11:35, 12 July 2023 Hla28 talk contribs reverted File:MiRNA Annotation Decision Tree 2023.png to an old version (Reverted to version as of 09:12, 12 July 2023 (EDT))
- 11:32, 12 July 2023 Hla28 talk contribs uploaded a new version of File:MiRNA Annotation Decision Tree 2023.png
- 09:12, 12 July 2023 Ga362 talk contribs uploaded a new version of File:MiRNA Annotation Decision Tree 2023.png
- 09:07, 12 July 2023 Ga362 talk contribs reverted File:MiRNA Annotation Decision Tree 2023.png to an old version (Reverted to version as of 06:06, 12 July 2023 (EDT))
- 06:11, 12 July 2023 Ruth.lovering talk contribs uploaded a new version of File:MiRNA Annotation Decision Tree 2023.png
- 06:06, 12 July 2023 Ruth.lovering talk contribs created page File:MiRNA Annotation Decision Tree 2023.png
- 06:06, 12 July 2023 Ruth.lovering talk contribs uploaded File:MiRNA Annotation Decision Tree 2023.png
- 05:59, 12 July 2023 Ruth.lovering talk contribs reverted File:MiRNADecisiontree2020.png to an old version (Reverted to version as of 10:43, 9 March 2022 (EST))
- 05:57, 12 July 2023 Ruth.lovering talk contribs created page File:MiRNA Decision Tree 2023.pptx
- 05:57, 12 July 2023 Ruth.lovering talk contribs uploaded File:MiRNA Decision Tree 2023.pptx
- 05:55, 12 July 2023 Ruth.lovering talk contribs uploaded a new version of File:MiRNADecisiontree2020.png
- 10:54, 10 July 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-07-11 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, July 20th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/834 Outage tasks] === Fall GOC Meeting === * Virtual meeting * October 17th - 19th (Tuesday - Thursday) == GO Release Pipeline == * June release out June 11th * No July release at this point * #release-pipeline Slack channel for updates == Annotation == === Protein2GO Up...")
- 07:41, 7 July 2023 Pascale talk contribs created page Projects update meeting 2023-07-12 (Created page with "= Attendees = * Members: Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia, David, Jim * Present: * Regrets: =Announcements= =Announcements= No GO calls week next week =New GO grant= Please remember to cite the new grant in paper!! grant number HG012212 = Displaying GO-plus in OLS= AI: Jim will contact the OLS developers to switch to GO-plus =Continue GPAD/GPI specs= =Projects reviews= https://github.com/orgs/geneontology/projects/108/views/3 =Rev...")
- 02:54, 5 July 2023 Pascale talk contribs created page Ontology meeting 2023-07-03 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Announcements= =Discussion points= ==Regulation of neurotransmitter levels== * Causes taxon constraints problems, see https://github.com/geneontology/go-ontology/issues/25594 ==RNA capping and processing== Tickets : * [https://github.com/geneontology/go-ontology/issues/21409 NTR:dpCoA-cap decapping] (Shyamala) * [https://github.c...")
- 09:03, 28 June 2023 Pascale talk contribs created page Projects update meeting 2023-06-28 (Created page with "= Attendees = * Members: Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia, David, Jim * Present: Kimberly, Pascale, Seth, Jim, David * Regrets: Kimberly, Chris, Seth, Huaiyu =Announcements= No GO calls week next week =Continue GPAD/GPI specs= =Projects reviews= https://github.com/orgs/geneontology/projects/108/views/3 =Review priorities from GOC meeting= [https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# GO priorities...")
- 11:24, 19 June 2023 Pascale talk contribs created page Projects update meeting 2023-06-21 (Created page with "= Attendees = * Members: Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia, David, Jim * Present: * Regrets: =Announcements= =Discussion points= ==Annotation extensions projects== is there an update since last week? ==Many new user requests== Do we have an SOP for onboarding and training? =Projects reviews= https://github.com/orgs/geneontology/projects/108/views/3 =Review priorities from GOC meeting= [https://docs.google.com/document/d/1TrxTZMRMAS0BCe...")
- 16:46, 16 June 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-06-20 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, June 22nd, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/834 Outage tasks] ** Summer schedule: next outage will be July 20th === Fall GOC Meeting === * Virtual meeting * October 17th - 19th (Tuesday - Thursday) == GO Release Pipeline == * June release out June 11th * #release-pipeline Slack channel for updates == Annotation ==...")
- 08:10, 16 June 2023 Pascale talk contribs created page Ontology meeting 2023-06-26 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Announcements= =Discussion points= ==LD for transcription== https://github.com/geneontology/go-ontology/issues/25419#issuecomment-1593239731 ==Blocking tickets== ===RNA capping and processing=== Tickets : * [https://github.com/geneontology/go-ontology/issues/21409 NTR:dpCoA-cap decapping] (Shyamala) * [https://github.com/geneonto...")
- 10:40, 13 June 2023 Pascale talk contribs deleted page Small molecule to Molecular Function relations (content was: "== Relations for Small molecule to Molecular Function == {| class="wikitable" !Ontology Pair !Relation !Usage |- |rowspan="4"| Small molecule to Molecular function |has small molecular activator | Links a small molecule (ChEBI) to a Molecular Function or Biological Process the small molecule activates. |- |Has small molecular inhibitor...", and the only contributor was "Pascale" (talk))
- 05:31, 13 June 2023 Pascale talk contribs created page Small molecule to Molecular Function relations (Created page with "== Relations for Small molecule to Molecular Function == {| class="wikitable" !Ontology Terms to Link !Allowed Relation !Usage |- | Has small molecular activator | | | |- | Has small molecular inhibitor | | | |- | input of | | | |- | output of | | | |- |} == Review Status == Last reviewed: Reviewed by: Category: Relations")
- 17:54, 12 June 2023 Mi talk contribs created page 14 June 2023 PAINT Conference Call (Created page with "==Present== Marc, Dustin, Anushya, Paul T, Huaiyu, Pascale ==Agenda== ===PANTHER 18 build=== The node forward tracking from v.15 to v.18 is not better than that from v.15 to 17. After more careful review of trees, the conclusion from the last call that trees map better from 15 to 18 is not true either. It seems that the differences in tree topology were caused by the sequence alignment. <Dustin, please add some stats here> Here is the proposed plan based on these dat...")
- 09:55, 9 June 2023 Pascale talk contribs deleted page Annotation Extension Relation:during (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== Identifies a process during which a molecular function or biological process occurs or a cellular component is present. ==Child terms== * exists_during * happens_during ==Scope of use== ===Domain=== BFO:0000001 ! entity (Biological Process, Molecular Function or Cellular Component) ===Range=== BF...")
- 09:49, 9 June 2023 Pascale talk contribs moved page Annotation Extension Relation:inhibited by to Has small molecular inhibitor
- 09:49, 9 June 2023 Pascale talk contribs moved page Annotation Extension Relation:activated by to Has small molecular activator
- 11:59, 5 June 2023 Pascale talk contribs created page Ontology meeting 2023-06-12 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Announcements= =Discussion points= ==[https://github.com/orgs/geneontology/projects/135 Ontology maintenance project]== ==Priorities== ==Blocking tickets== =BP refactor: separate 'developmental process' and 'cellular developmental process'= See draft plan here: https://docs.google.com/document/d/1FafBfb44nAk-7PwUDj42XQLgwJYx...")
- 09:22, 2 June 2023 Pascale talk contribs created page Projects update meeting 2023-06-14 (Created page with "= Attendees = * Members: Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia, David, Jim * Present: * Regrets: =Announcements= =Discussion points= =Projects reviews= https://github.com/orgs/geneontology/projects/108/views/3 =Review priorities from GOC meeting= [https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# GO priorities ] Category: GO Managers Meetings")
- 20:42, 30 May 2023 Sjcarbon talk contribs created page Projects update meeting 2023-05-31 (Created page with " * Note: HTTPS-ification of the GO site.")
- 08:38, 30 May 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-05-30 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, June 9th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/832 Outage tasks] === Fall GOC Meeting === * Virtual meeting * October 17th - 19th (Tuesday - Thursday) == GO Release Pipeline == * June release will start this week * #release-pipeline Slack channel for updates == Annotation == === Contributor-based annotation reports ==...")
- 09:06, 24 May 2023 Vanaukenk talk contribs created page GO-CAM Overview and Curation Strategy (Created page with "= GO-CAM Principles = == Standard GO Annotations and GO-CAM Models == === Standard GO Annotations === [http://geneontology.org/docs/go-annotations/ GO annotations] have been a key component of GO since its inception. Standard annotations are defined as an association between a gene and a biological concept from one of the [http://geneontology.org/docs/ontology-documentation/ three GO aspects]: Molecular Function (MF), Biological Process (BP), and Cellular Component (CC...")
- 14:46, 23 May 2023 Pascale talk contribs created page Projects update meeting 2023-05-24 (Created page with "= Attendees = * Members: Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia, David, Jim * Present: * Regrets: =Announcements= =Discussion points= * [https://www.biostars.org/p/9563221/ Biostars question] "I need to define a ground truth/correct answer set of GO terms for proteins" ** Was the reply sent? Do we need t go over it again? =Review priorities from GOC meeting= [https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/ed...")
- 11:15, 22 May 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-05-23 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, May 25th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/831 Outage tasks] === Fall GOC Meeting === * Virtual meeting * October 17th - 19th (Tuesday - Thursday) == GO Release Pipeline == * May release coming * #release-pipeline Slack channel for updates == Spring GOC Meeting - Follow up == * Padua, Italy - April, 27-29 * [https:...")
- 09:49, 22 May 2023 Pascale talk contribs created page Ontology meeting 2023-05-22 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Announcements= No call for the next 2 weeks : * Memorial Day- May 29th * No GO calls week June 5th Category:Meetings Category:Ontology")
- 08:21, 16 May 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-05-16 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, May 11th, 4-6pm PDT *** [https://github.com/geneontology/noctua/issues/830 Outage tasks] === Fall GOC Meeting === * Virtual meeting * October 17th - 19th (Tuesday - Thursday) == GO Release Pipeline == * May release pending * Stuck on an issue related to obsolete ontology classes (ChEBI?) == Spring GOC Meeting - Follow up == * Padua, Italy - A...")
- 02:19, 16 May 2023 Pascale talk contribs created page Projects update meeting 2023-05-17 (Created page with "= Attendees = * Members: Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia, David, Jim * Present: * Regrets: =Announcements= =Discussion points= * [https://www.biostars.org/p/9563221/ Biostars question] "I need to define a ground truth/correct answer set of GO terms for proteins" =Review priorities from GOC meeting= [https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# GO priorities ] =Projects reviews= https://github.c...")
- 17:21, 11 May 2023 Mi talk contribs created page 17 May 2023 PAINT Conference Call (Created page with "==Present== Marc, Dustin, Anushya, Paul T, Huaiyu, Pascale ==Agenda== ===Propping mouse and rat IMP annotations from the PAINT load (by Pascale)=== We need justification. ===PAN-GO paper=== Status update. What remains to be do? Category:PAINT")
- 02:40, 10 May 2023 Pascale talk contribs created page Ontology meeting 2023-05-15 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, Peter, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Action points from last call= Chris to send the dictionary for the script that generates annotation reports =New QC check= * Obsolete IDs in slims will now cause a Travis error; ontology editors need to remove subsets when obsoleting terms =Annotation review scripts= Now also include mappings =Ontology priorities= * BP refactoring...")
- 02:07, 10 May 2023 Pascale talk contribs moved page Projects update meeting 2023-05-11 to Projects update meeting 2023-05-10
- 03:30, 8 May 2023 Pascale talk contribs created page Ontology meeting 2023-05-08 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Next GOC consortium meeting= * October 17th-19th, 2023, Virtual =GOC meeting recap= =Editors discussion items from previous calls= ==Asserted classes versus logical definitions== Example: mRNA phosphatase activity is_a pyrophosphatase, not a phosphatase :: not sure this is the easiest example Cjm (talk) 2...")
- 03:33, 1 May 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-05-09 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outage: ** Thursday, May 11th *** [https://github.com/geneontology/noctua/issues/830 Outage tasks] === Spring GOC Meeting - Follow up === * Padua, Italy - April, 27-29 * [https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ Agenda and Minutes] ==== Annotation Discussions ==== ===== Annotation Review ===== ===== Metrics and Attribution for...")
- 05:20, 28 April 2023 Pascale talk contribs created page File:GOC-group picture-2023-04-28.jpg
- 05:20, 28 April 2023 Pascale talk contribs uploaded File:GOC-group picture-2023-04-28.jpg
- 12:47, 20 April 2023 Pascale talk contribs created page Projects update meeting 2023-05-11 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= ==GOC consortium== ==Fall GOC meeting== Virtual: Tuesday Oct 17th to Thursday Oct 19th =Discussion points= ==Reactome mappings== * why are they in the ontology? since they are not maintained the ontology ==MOD identifiers for references== * Are they on or out? MGI identifiers are partially in GO; did we make the decision to remove th...")
- 10:38, 17 April 2023 Pascale talk contribs created page Ontology meeting 2023-04-17 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets:''' ==GOC consortium== * April 27th-29th, Padua, Italy Ontology group draft presentation: https://docs.google.com/presentation/d/1MJC9gw0wuqrLwA8WjJF6rnsXxFrUsTxUl-D5V169qos/edit#slide=id.p =Editors discussion items= ==Asserted classes versus logical definitions== Example: mRNA phosphatase activity is_a pyrophosphatase, not a phosphatase ::...")
- 07:53, 15 April 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-04-18 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, May 11th ** No outage on Thursday, April 25th - GOC meeting in Padua ** [https://github.com/geneontology/noctua/issues/830 Outage tasks] === Spring GOC Meeting - Almost here! === * Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Schedule: Thursday, Friday with group outing late Friday afternoon, and group dinner Frida...")
- 09:34, 14 April 2023 Vanaukenk talk contribs created page Projects update meeting 2023-04-19 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= ==GOC consortium== * April 27th-29th, Padua, Italy ==Fall GOC meeting== Virtual: Tuesday Oct 17th to Thursday Oct 19th =Discussion points= Any blocking issues on projects? * SGD load into Noctua * [https://github.com/geneontology/noctua/issues/827 Queries to assess use of MF-to-BP relations in Noctua models] ==GOC meeting agenda== *...")
- 10:06, 12 April 2023 Pascale talk contribs created page Projects update meeting 2023-04-12 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= ==GOC consortium== * April 27th-29th, Padua, Italy ==Fall GOC meeting== Virtual: Tuesday Oct 17th to Thursday Oct 19th =Discussion points= Any blocking issues on projects? ==GOC meeting agenda== * Draft agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit# =Projects reviews= https://github.c...")
- 08:23, 11 April 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-04-11 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, April 13th ** [https://github.com/geneontology/noctua/issues/824 Outage tasks] === Spring GOC Meeting - Almost here! === * Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Schedule: Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM * [https://docs.google.com/document/d...")
- 01:36, 6 April 2023 Pascale talk contribs created page Ontology meeting 2023-04-10 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Announcements= ==GOC consortium== * April 27th-29th, Padua, Italy =Following up on previous Editors discussion items= == Pharynx terms in GO == * Pharynx terms used for C. elegans annotations get flagged if the GO term uses the UBERON pharynx (or child) term in the logical definition * We might be stalled here by UBERON work: https://gi...")
- 13:26, 5 April 2023 Mi talk contribs created page 12 April 2023 PAINT Conference Call (Created page with "==Present== ==Agenda== ===PANTHER17 release and family review=== ===PAINT paper=== Here is the link to the draft. https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit?usp=sharing Category:PAINT")
- 03:43, 23 March 2023 Pascale talk contribs created page Updating EC mappings (Created page with "= Guidelines for updating transferred or obsolete ECs = In Protégé, search for the old and the new EC numbers in the ontology. * Case 1: The old CE is assigned to a single GO term and the new EC is not used in the ontology * Case 2: The old CE is assigned to a single GO term and the new EC is already used in the ontology * Case 3: The old EC is assigned to more than 1 GO term ==Case 1 The new EC is not used in the ontology and the old CE is assigned to a single GO...")
- 04:27, 20 March 2023 Pascale talk contribs created page Projects update meeting 2023-03-22 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= ==GOC consortium== * April 27th-29th, Padua, Italy * Draft agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit# ==Alliance all hands meeting== Next week: Tuesday 28-Thursday 30 March * GO calls cancelled ==Setting dates for Fall GOC meeting== [https://doodle.com/meeting/participate/id/bY72QVAe...")
- 16:34, 17 March 2023 Vanaukenk talk contribs created page Ontology meeting 2023-03-20 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets:''' ==GOC consortium== * April 27th-29th, Padua, Italy * Any suggestions for working group sessions? =New Protege version= * New Instruction page Protege5_6_setup_for_GO_Eds in progress * Jim testing ontology build: [https://github.com/geneontology/go-ontology/issues/25019#issuecomment-1444987133] * Noting issue with ID range...")
- 09:41, 17 March 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-03-21 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, March 23rd ** [https://github.com/geneontology/noctua/issues/824 Outage tasks] === No GO Calls Week - March 27 - 31 === * Alliance meeting at Caltech this week === Spring GOC Meeting Plans === * Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Schedule: Thursday, Friday with group outing late Friday afternoon, and gro...")
- 08:46, 16 March 2023 Vanaukenk talk contribs deleted page Causally upstream of (We no longer want to use causal relations without directionality.)
- 06:37, 14 March 2023 Pascale talk contribs created page Projects update meeting 2023-03-15 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= ==GOC consortium== * April 27th-29th, Padua, Italy * Draft agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit# =Discussion points= ==uniprot-all file== Following up on last week's discussion: uniprot-all file : filtered for MODs (14M annotations, according to Alex). Should we rename the file?...")
- 10:55, 13 March 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-03-14 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, March 16th - we postponed for a week ** [https://github.com/geneontology/noctua/issues/821 Outage tasks] *** MF-MF relations will be updated === Spring GOC Meeting Plans === * Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Schedule: Thursday, Friday with group outing late Friday afternoon, and group dinner Friday nig...")
- 04:38, 9 March 2023 Pascale talk contribs moved page Guidelines for equivalence axioms to Guidelines for logical definitions
- 11:27, 8 March 2023 Pascale talk contribs created page File:View inferences-1.png
- 11:27, 8 March 2023 Pascale talk contribs uploaded File:View inferences-1.png
- 11:24, 8 March 2023 Pascale talk contribs created page File:View inferences.png
- 11:24, 8 March 2023 Pascale talk contribs uploaded File:View inferences.png
- 11:24, 8 March 2023 Pascale talk contribs created page File:Reasoner.png
- 11:24, 8 March 2023 Pascale talk contribs uploaded File:Reasoner.png
- 08:41, 8 March 2023 Pascale talk contribs created page Project organization (Created page with "*GO Leadership | GO Managers *Consortium Meetings *Working Groups **Ontology Development **Annotation **Phylogenetic Annotation **Quality Control *Working Groups (archived or no longer maintained on the wiki) **User Advocacy **Data Capture Working Group **Software and Utilities **OBO-Edit working group Category:GOC Overview")
- 08:38, 8 March 2023 Pascale talk contribs created page File:GO Group Photo Oct 2022.jpg
- 08:38, 8 March 2023 Pascale talk contribs uploaded File:GO Group Photo Oct 2022.jpg
- 10:31, 2 March 2023 Pascale talk contribs moved page Part of (GP2Term) to Part of relation
- 10:30, 2 March 2023 Pascale talk contribs moved page Part of to Part of - deprecated
- 20:56, 1 March 2023 Suzialeksander talk contribs created page 2023 Padua GOC Managers Meeting Logistics (Created page with "=GOC Managers Meeting, Padua, April 30, 2023= * Location: [https://www.hotelgalileopadova.it/en/home-page.aspx Best Western Plus Hotel Galileo- Padua, Italy] * Agenda: coming soon! ==Registration== By invitation. '''Registration deadline was February 17th, 2023'''. Payment options (for in-person attendees) will be posted shortly. ==Local activities== See also https://www.unipd.it/en/getting-around-padua ==Hotel Reservation== The host hotel is the [https://www.ho...")
- 17:58, 1 March 2023 Debert talk contribs created page File:PTHR24418 DROME 17.png
- 17:58, 1 March 2023 Debert talk contribs uploaded File:PTHR24418 DROME 17.png
- 17:54, 1 March 2023 Debert talk contribs created page File:PTHR24418 DROME 15.png
- 17:54, 1 March 2023 Debert talk contribs uploaded File:PTHR24418 DROME 15.png
- 15:42, 28 February 2023 Mi talk contribs created page 1 March 2023 PAINT Conference Call (Created page with "==Present== ==Agenda== ===PANTHER17 release update=== *PANTHER17 was released. See minutes in the November PAINT call. *A bug was identified in December that missed some forward track of IBDs. As a result, the number of lost IBAs will decrease once the bug is fixed. **Only affects IBDs that were not forward-tracked via PTN and instead tracked to a descendant node. More specifically, these IBDs that wer...")
- 12:22, 27 February 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-02-28 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, March 9th ** [https://github.com/geneontology/noctua/issues/821 Outage tasks] === Spring GOC Meeting Plans === * Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Schedule: Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM * Please respond to Suzi's email if you registe...")
- 08:54, 22 February 2023 Pascale talk contribs moved page Guidelines for 'database cross references' and 'definition database cross references' to Guidelines for database cross references
- 08:38, 22 February 2023 Pascale talk contribs deleted page Editor Guide to Regulates (content was: "==How to make new terms== <br> When making a new set of regulates terms here are the things you need to know. <br> You make new terms like this:<br> <br> [i] isotropic growth The process being regulated. ---[r] regulation of isotropic growth standard regulation term. ------[pr] positive regulation of isotropic growth standard regulation term. ---------[i] photoreceptor response to blue light The process doing the...")
- 08:35, 22 February 2023 Pascale talk contribs deleted page Regulates Documentation (2007) (content was: "Category:Regulation ==GO Website Documentation== Image:Regulates_documentation.doc")
- 08:35, 22 February 2023 Pascale talk contribs deleted page File:Regulates documentation.doc (Deprecated)
- 08:34, 22 February 2023 Pascale talk contribs deleted page File:Curator regulates documentation.doc (Deprecated)
- 08:30, 22 February 2023 Pascale talk contribs created page Category:Workshops - Ontology Editors (Created page with "Category:Workshops - Ontology Editors")
- 08:18, 22 February 2023 Pascale talk contribs created page Category:Workshops - 2010 GO Annotation Camp (Created page with "Category:Workshops - 2010 GO Annotation Camp")
- 08:10, 22 February 2023 Pascale talk contribs deleted page Binding discussion emails (content was: "Category:Deprecated =GO RULE: [https://github.com/geneontology/go-site/tree/master/metadata/rules#gorule0000007 IPI should not be used with GO:0003824 catalytic activity or descendents]= == Links == 2010_GO_camp_binding_documentation_issues 2010_GO_camp_binding_documentation_issues#Agenda_for_discussion_26-05-2010 == Using column 16 in conjunction with an catalytic activity annotation == Would it be possible to include a further discussion on column 16 in th...")
- 07:42, 22 February 2023 Pascale talk contribs deleted page Enzyme Alignment (content was: "Category:Ontology ==Summary== Align the reaction / catalytic activity terms in GO with those in external databases such as MetaCyc, EC, KEGG, etc.. ==Personnel== Amelia, Chris, David, Jane, Tanya ==Plan of Action== The plan is to create GO terms that correspond to the reactions that enzymes catalyse; rather than follow EC's system, which is gene product-based, and allows an enzyme to catalyse a number of different reactions, follow a system like that of MetaCyc, KEGG r...")
- 06:49, 22 February 2023 Pascale talk contribs deleted page Regulators (content was: "The goal is to clean up existing enzyme/catalytic activity regulator, activator and inhibitor terms in MF: we should only keep those that represent a direct molecular activity that regulates the activity of another gene product. Examples that we would allow include classical competitive inhibition, and probably noncompetitive and uncompetitive inhibition as well (must confirm)....", and the only contributor was "Midori" (talk))
- 06:49, 22 February 2023 Pascale talk contribs deleted page Enzyme binding discussion (content was: "Category:Binding == '''enzyme binding ; GO:0019899 Interacting selectively and non-covalently with any enzyme.''' == <span style=color:GREEN> '''Q1: Can this term be used to annotate binding to ANY subunit of an enzyme complex, or is it restricted to binding to the CATALYTIC SUBUNIT ONLY ?</span>''' Related SF item: https://sourceforge.net/tracker/?func=detail&aid=2983894&group_id=36855&atid=440764 This will also affect the ontology structure, because we have: protei...")
- 20:52, 21 February 2023 User account ErasableTest001 talk contribs was created by Sjcarbon talk contribs and password was sent by email
- 08:13, 21 February 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-02-21 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, February 23rd ** [https://github.com/geneontology/noctua/issues/819 Outage tasks] === Spring GOC Meeting Plans === * Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Schedule: Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM * Registration deadline was Friday, Februar...")
- 14:17, 16 February 2023 Jamesbalhoff talk contribs created page File:Protege-warning-2.jpg
- 14:17, 16 February 2023 Jamesbalhoff talk contribs uploaded File:Protege-warning-2.jpg
- 14:14, 16 February 2023 Jamesbalhoff talk contribs created page File:Protege-warning.jpg
- 14:14, 16 February 2023 Jamesbalhoff talk contribs uploaded File:Protege-warning.jpg
- 12:57, 16 February 2023 Pascale talk contribs moved page Enzymes and EC mappings to RHEA and EC mappings
- 11:43, 16 February 2023 Pascale talk contribs created page Projects update meeting 2023-03-01 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= ==GOC consortium== * April 27th-29th, Padua, Italy * Draft agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit# =Discussion points= * [https://github.com/geneontology/project-management/issues/42 Discuss and create roadmap for integrating remaining resource upstream files] David =Projects reviews...")
- 11:41, 16 February 2023 Pascale talk contribs created page Ontology meeting 2023-03-13 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * '''Present:''' * '''Regrets:''' =Announcements= ==GOC consortium== * April 27th-29th, Padua, Italy * Draft agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit# =Discussion points= * [https://github.com/geneontology/project-management/issues/42 Discuss and create roadmap for integrating remaining resource upstream files] D...")
- 11:35, 16 February 2023 Pascale talk contribs created page Projects update meeting 2023-02-22 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= ==GOC meeting== will be held immediately after Biocuration, in Padua, Italy (Thursday April 27th to Saturday April 29th) * Best Western Galileo * Apparently hotels are filling quickly for the biocuration meeting * Draft agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit# * Plan to stay Saturday...")
- 11:07, 16 February 2023 Pascale talk contribs created page Ontology meeting 2023-02-27 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets:''' =Announcements= ==GOC consortium== * April 27th-29th, Padua, Italy * If you plan to attend, please register ASAP. geneontology.ticketleap.com/goc2023 password: goc2023 =Editors discussion items= ==Script to download annotations== * Move the script in the go-annotation repo - status ==New Protege version== * Plan: Jim to ma...")
- 11:03, 16 February 2023 Pascale talk contribs created page Protege5 6 setup for GO Eds (Created page with " Copy and edit [Protege5_5_setup_for_GO_Eds] = Review Status = Last reviewed: [http://wiki.geneontology.org/index.php/Ontology_Developmente Back to: Ontology_Development] Category:GO EditorsCategory:Editor_Guide_2018 Category:Protege")
- 09:42, 16 February 2023 Vanaukenk talk contribs deleted page Indirectly causally upstream of (content was: "===Annotation usage=== This relation should not be used for annotation, either in standard annotation extensions or in GO-CAMs. ''Curators should always strive to use one of the more specific child relations that capture the directionality of the effect, either positive or negative.'' === Ontology usage === This relation should not be used in the ontology. == Relations Ontology == [https://ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0012011 indirectly causal...")
- 09:23, 14 February 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-02-14 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, February 23rd ** [https://github.com/geneontology/noctua/issues/819 Outage tasks] === Spring GOC Meeting Plans === * Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Schedule: Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM * Please register by this Friday, February...")
- 10:22, 13 February 2023 Pascale talk contribs created page Ontology meeting 2023-02-13 (Created page with "* '''Group members:''' Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul * '''Present:''' Pascale, Harold, Raymond, Val, Edith, Jim, Tanya, Karen, Kimberly, David, Chris, Peter, Paul * '''Regrets: ''' =Announcements= * Harold's last week ! ==GOC consortium== * April 27th-29th, Padua, Italy * If you plan to attend, please register ASAP. geneontology.ticketleap.com/goc2023 password: goc2023 ==Annotation reviews at MGI==...")
- 12:31, 10 February 2023 Pascale talk contribs deleted page Category:Publications (content was: "All GO-related publications from GOC members", and the only contributor was "Cjm" (talk))
- 12:31, 10 February 2023 Pascale talk contribs deleted page Publications, tutorials, talks, posters (content was: "Publications, Talks, Posters 2018 Publications, Talks, Posters 2017 Publications, Talks, Posters 2016 Publications, Talks, Posters 2015 Publications, Talks, Posters 2014 Publications, Talks, Posters 2013 Publications, Talks, Posters 2010-2012 Publications, Talks, Posters 2007-2009 Publications, Talks, Posters 2003-2006 Category:Publications")
- 12:31, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2018 (content was: "Huntley RP, Kramarz B, Sawford T, Umrao Z, Kalea AZ, Acquaah V, Martin MJ, Mayr M, Lovering RC. (2018 Advance publication) [http://rnajournal.cshlp.org/content/early/2018/06/05/rna.065565.118.abstract Expanding the horizons of microRNA bioinformatics]. RNA. Jun 5. doi: 10.1261/rna.065565.118. Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Ri...")
- 12:30, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2017 (content was: "Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. The Gene Ontology of eukaryotic cilia and flagella. Cilia. 2017 6:10. https://doi.org/10.1186/s13630-017-0054-8 Category:Archived")
- 12:28, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2016 (content was: "Category:Archived ==List of papers published by GOC in 2016== Please list all article publications below in chronological order; the most recent publication should appear first. ====Acknowledge funding by GOC NHGRI grant==== * Hill DP, D'Eustachio P, Berardini TZ, Mungall CJ, Renedo N, Blake JA. Modeling biochemical pathways in the gene ontology. Database (Oxford). 2016 Sep 1. PMID 27589964. * Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gille...")
- 12:26, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2015 (content was: "Category:Publications ==List of papers published by GOC in 2015== Please list all article publications below in chronological order; the most recent publication should appear first. ====Acknowledge funding by GOC NHGRI grant==== * Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Eme...")
- 12:23, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2014 (content was: "Category:Archived ==List of Papers published by GOC in 2014 (Chronologically, most recent first)== * Ascensao JA, Dolan ME, Hill, DP and Blake JA. 2014. Methodology for the inference of gene function from phenotype data. <i>BMC Bioinformatics</i>. 15:405 doi:10.1186/s12859-014-0405-z. * The Gene Ontology Consortium. 2014. Gene Ontology Consortium: Going Forward. ''Nucl. Acids Res.'' Database Issue doi: 10.1093/nar/gku1179. * Dietze H, Berardini TZ, Foulger RE, Hill DP,...")
- 12:18, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2013 (content was: "Category:Archived == Journal Publications == Blake JA . 2013 Ten Quick Tips for Using the Gene Ontology. PLoS Comput Biol 9(11): e1003343. doi:10.1371/journal.pcbi.1003343. Aranguren ME, Fernández-Breis JT, Mungall C, Antezana E, González AR, & Wilkinson MD. 2013. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. Journal of biomedical semantics, 4(1), 2. [http://www.ncbi.nlm.nih.gov/pubmed/23286517 PMID:23286517] Assel...")
- 12:16, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2010-2012 (content was: "Note there is now a GO group on Mendeley: http://www.mendeley.com/groups/1250271/gene-ontology-consortium/papers/ Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members during 2010 reporting year. === Publications (alphabetical) === * Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nat Biotechnol. 2012 Dec 16. doi: 10....")
- 12:13, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2010- (content was: "#REDIRECT Publications, Talks, Posters 2010-2011", and the only contributor was "Jl242" (talk))
- 12:13, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2010-2011 (content was: "#REDIRECT Publications, Talks, Posters 2010-2012", and the only contributor was "Cjm" (talk))
- 11:56, 10 February 2023 Pascale talk contribs deleted page GO publications 2009 (content was: "Category:Publications Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members during 2009 reporting year. === 2009 Publications === #Alterovitz, G., Xiang, M., Hill, D., Lomax, J., Liu, J., Mungall, C., Harris, M., Dolan, M.E., Blake, J.A., Ramoni, M.F. Engineering Biomedical Ontologies: The Gene Ontology [Accepted, In Press, Nature Biotechnology] #Barrell D., Dimmer E., Huntley R.P., Binns D., O'...")
- 11:43, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2007-2009 (content was: "'''GO publications, Tutorials and Workshops, Presentations, and Posters'''<br> '''For the GO grant HG –02273'''<br> '''2007 – 2009''' <br> Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members. ==2009== GO_2009_Publications,_Tutorials_&_Workshops,_Presentations,_Posters,_and_Resources ==2008== ===2008 Publications === Altman, R., Bergman, C., Blake, J.A., Blaschke, C., Cohen, A., Gann...")
- 11:39, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2003-2006 (content was: "=Moved to [https://docs.google.com/document/d/1w8nR5llrexyqCKk3NTlj3v3s7gKBA-DPtAT3LiIe5jo/edit#heading=h.ol811igyzk6h Google drive]= '''GO publications, Tutorials and Workshops, Presentations, and Posters'''<br> '''For the GO grant HG –02273'''<br> '''2003 – 2006''' <br> Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members. ==2006== ===2006 Publications === Rubin, D.L., Lewis, S.E., M...")
- 10:59, 10 February 2023 Pascale talk contribs deleted page Category:Pages with broken file links (content was: "", and the only contributor was "Pascale" (talk))
- 10:57, 10 February 2023 Pascale talk contribs created page Category:Pages with broken file links (Created blank page)
- 10:57, 10 February 2023 Pascale talk contribs deleted page Category:Metrics (content was: "Pages describing metrics for ontology development", and the only contributor was "Midori" (talk))
- 10:56, 10 February 2023 Pascale talk contribs deleted page Taxon Trigger File Metrics (content was: "For more details see Taxon_Main_Page. This is a list of the stages that we need to complete in the implementation of the taxon trigger file for the project to be considered complete. Where blockages have been hit, these are noted. ===In order:=== * Figure out the theory - '''Done''' * Agree the theory with the GO Consortium - '''Done''' * Agree the theory of Union_of terms with Consortium - '''Not Done''' * Set up the files in scratch and make filtering perl scripts - '...")
- 10:53, 10 February 2023 Pascale talk contribs deleted page Category:Timelines (content was: "Timelines associated with various projects in GO.", and the only contributor was "Gail" (talk))
- 10:51, 10 February 2023 Pascale talk contribs deleted page Cross Product Timeline (content was: "Category:Archived * See also Cross Product Guide == Blessing of mature XP files == Mature xps currently live in scratch dir: cvs/go/scratch/xps biological_process_xp_cellular_component.obo biological_process_xp_cell.obo cvs/go/scratch/regulates_xp_live We will officially bless these and move them out of scratch into go/ontology/editors/xps/ This will happen after the RO meeting ('''May 2008''') Note these will still be external to the main GO file....")
- 10:47, 10 February 2023 Pascale talk contribs deleted page OBO-Edit Release Timeline (content was: "Category:Archived The OBO-Edit calendar tracks releases and working group meeting dates. It's on google and open to the public domain. *[http://www.google.com/calendar/embed?src=cDN1bXNkOG45bDMyYW5kbGR1M2xqcjNuazhAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ View the OBO-Edit calendar] = Projected Dates = Refer calendar - If the projected dates are not in the future the calendar has not been able to refresh - access web google calendar externally. [http://wiki.geneontology.org/i...")
- 10:47, 10 February 2023 Pascale talk contribs deleted page Category:To be reviewed (content was: "Pages that David, Kimberly and Pascale have identified as needing review.", and the only contributor was "Pascale" (talk))
- 10:41, 10 February 2023 Pascale talk contribs deleted page Tracker wishlist (content was: "Category:Archived ==Requirements for a GO wiki/tracker system== ===Our high priorities:=== *General **Calendar / time lines / to do lists to show what curators have planned **Create personal pages which show what someone is working on *Tracker **Add user configurable categories to an entry, e.g. how easy it is to complete, whether it would need people to look at annotations, which interest groups it may affect **Be able to configure the order of comments, perhaps with a hy...")
- 10:39, 10 February 2023 Pascale talk contribs deleted page Category:Pages with broken file links (content was: "", and the only contributor was "Pascale" (talk))
- 10:38, 10 February 2023 Pascale talk contribs created page Category:Pages with broken file links (Created blank page)
- 10:10, 10 February 2023 Pascale talk contribs created page Category:Ontology Relations (Created page with "This page lists the relations in the gene ontology.")
- 10:09, 10 February 2023 Pascale talk contribs deleted page Category:Logos (content was: "Miscellaneous logos. Category exists to make it easy to find logos that have already been uploaded to this site. However, most logos that have been uploaded were uploaded before this category was created.", and the only contributor was "Clements" (talk))
- 10:03, 10 February 2023 Pascale talk contribs deleted page Browse help page (content was: "<h2>Browsing the Ontology</h2> <p> In AmiGO, the ontology is presented as a tree of terms. An example of part of a tree is displayed below: </p> <br> Image:Organelle.jpg <br> <p> The level of a term is represented by its indentation within the tree, with general terms being less indented than more specific terms. In the above image, you can see that "extracellular organelle" is a child (less specific) term of "organelle", and a sibling term of "intracellular organelle". Eac...")
- 10:00, 10 February 2023 Pascale talk contribs deleted page Regular Expressions accepted by UniProt for use in the 'with' field (content was: "Category:Archived =This information is now in https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml= { prefix => 'UniProt(?:KB)?', id => '[A-Z][0-9][A-Z0-9]{3}[0-9]((-([0-9]+)|:PRO_[0-9]{10}))?' }, { prefix => 'CGD', id => '(CAL|CAF)[0-9]{7}' }, { prefix => 'SGD', id => 'S[0-9]{9}' }, { prefix => 'dictyBase', id => 'DDB_G[0-9]{7}' }, { prefix => 'FB', id => 'FBgn[0-9]{7}' }, { prefix => 'GeneDB_Spombe|PomBase', id =>...")
- 09:58, 10 February 2023 Pascale talk contribs deleted page Category:ZFIN (content was: "#REDIRECT Category:Reports:ZFIN", and the only contributor was "Pascale" (talk))
- 09:57, 10 February 2023 Pascale talk contribs deleted page Category:WormBase (content was: "#REDIRECT Category:Reports:WormBase", and the only contributor was "Pascale" (talk))
- 09:57, 10 February 2023 Pascale talk contribs deleted page Category:Reports:WormBase (content was: "#REDIRECT Category:Reports - WormBase", and the only contributor was "Pascale" (talk))
- 09:56, 10 February 2023 Pascale talk contribs deleted page Category:Sequence Ontology (content was: "#REDIRECT Category:Reports - Sequence Ontology", and the only contributor was "Pascale" (talk))
- 09:56, 10 February 2023 Pascale talk contribs deleted page Category:Reports:ZFIN (content was: "#REDIRECT Category:Reports - ZFIN", and the only contributor was "Pascale" (talk))
- 09:55, 10 February 2023 Pascale talk contribs deleted page Category:SGD (content was: "#REDIRECT Category:Reports - SGD", and the only contributor was "Pascale" (talk))
- 09:55, 10 February 2023 Pascale talk contribs deleted page Category:TAIR (content was: "#REDIRECT Category:Reports - TAIR", and the only contributor was "Pascale" (talk))
- 09:43, 10 February 2023 Pascale talk contribs deleted page ID Mapping Requirements (content was: "== Requirements == Users frequently want to query GO annotations using a variety of ID-spaces. This includes queries of the single-gene variety, as well as bulk queries and tools such as map2slim and term enrichment. Examples: * Find GO annotations for UniProt ID P000001 * View (as HTML) all annotations for a small batch of Ensembl Protein IDs * Download all annotations (tab-del) for a large batch of genbank GI numbers * Perform term enrichment for a collection of genes iden...")
- 09:42, 10 February 2023 Pascale talk contribs deleted page Gp2rna file (content was: "==What is a gp2RNA file== A gp2rna file is a tab-delimited file that provides mapping between the MOD database object IDs and ncRNA gene/sequence IDs. Contribution of this file is a new requirement (starting mm/2012). ==Need for gp2RNA file== * This file will be used to download sequences of ncRNAs from NCBI, search in AmiGO and for book keeping/tracking annotation, removing redundant annotations etc. * This file is required from all GO groups who annotate to ncRNAs. * If y...")
- 09:42, 10 February 2023 Pascale talk contribs deleted page Gp2protein file (content was: "==What is a gp2protein file?== A gp2protein file is a tab-delimited file that provides a mapping between database object IDs and protein sequence IDs. Files contributed from annotation groups are available [http://www.geneontology.org/gp2protein here] ==Need for gp2protein file== * Used for downloading sequences from UniProt/NCBI. These sequences are used for AmiGO BLAST and for phylogenetic inferencing (PAINT) * The sequence IDs (UniProt or NCBI) can be used in AmiGO to s...")
- 09:41, 10 February 2023 Pascale talk contribs deleted page Gp2protein (content was: "For the RefG project it is critical we can build complete protein sequence sets for homology and phylogenetic analysis. In theory there should be a deterministic mapping from the gene in col2 of the GAF to the gp2protein mappings to a collection of FASTA files. In practice this is difficult due to some outstanding issues. The gp2protein files are located in cvs in the [http://www.geneontology.org/gp2protein/ go/gp2protein] directory. See the [http://www.geneontology.org/gp...")
- 09:41, 10 February 2023 Pascale talk contribs deleted page Gp unlocalized file (content was: "If your database supplies gene identifiers that have been manually curated from the literature, but where no sequence or genomic location is known (such genes have been variously described as 'unlocalised genes', 'single heritable traits' or 'phenotypic orphans'), then you should additionally supply a complete gp_unlocalized_file. This file should contain all the non-genome localized identifiers available in your database, including those not annotated to GO. Category:A...")
- 09:35, 10 February 2023 Pascale talk contribs deleted page Implementation (content was: " Category:Archived - Ontology == 13rd November, 2007 == I have solved problems about almost all child terms of "response to drug" term. The changes are already in the lived file.<br> I have asked to ChEBI people (Kirill) if it would be possible to have these substance in ChEBI molecular structure ontology.We are waiting for that! List of substances: METHOTREXATE<br> CHEBI:44185 unclassified<br> CLOMIPRAMINE<br> tricyclic antidepressant<br> KEGG ID C06918<br> CAS...")
- 09:34, 10 February 2023 Pascale talk contribs deleted page DEPRECATED: Response to drug (content was: " Category:Archived - Ontology Erika Feltrin presented her plan (below) for the response to drug terms at a skype conference call in late October. Original SourceForge item: [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1494526&group_id=36855| SF 1494526] Description of the project<br> Implementation")
- 09:34, 10 February 2023 Pascale talk contribs deleted page Description of the project (content was: " Category:Archived - Ontology == CASE OF "RESPONSE TO ORGANIC SUBSTANCE" GO: 0010033 == In the ChEBI ontology there is "organic molecular compound" CHEBI:25700, defined as a molecular entity that contain carbon and its synonyms are: organic compounds and organic entity. In the GO the definition of "response to organic substance" GO:0010033 term is: a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene exp...")
- 09:23, 10 February 2023 Pascale talk contribs created page Category:Archived - Ontology (Created blank page)
- 09:21, 10 February 2023 Pascale talk contribs deleted page Ontology QC Metrics (content was: "Category:Ontology ===The reasoner and regulation terms (2008)=== ====Checks==== *Identified inconsistencies between the ‘regulates’ hierarchy and the rest of biological process *Identified missing links *Identified more specific and complete is_a parentage for ‘regulation’ terms. ====Stats from first round==== *Terms: **279 reviewed. **40 added. **5 term merges took place. **207 names changed. **272 general dbxrefs were added. *Definitions: **40 added. **45 improved...")
- 09:21, 10 February 2023 Pascale talk contribs deleted page Ontology Quality Control (content was: "This page documents the quality control measures used to flag (or, ideally, avoid) various types of errors and inconsistencies in GO. ==OBO-Edit verification system== (NOTE: need links to O-E documentation, but the "Ontology Verification" section is missing from the online version at http://www.oboedit.org/docs/index.html) *built-in checks - these are run manually or during editing **text checks on comments, definitions, names and synonyms **name redundancy check **dbxref che...")
- 09:19, 10 February 2023 Pascale talk contribs deleted page Relationship type requirements (content was: "Category:Cross Products Category:Relations This page summarises the requirements for relations used in future versions of the GO, for example in Category:Cross Products Some of these relations already exist in [http://www.obofoundry.org/ro/RO]. Others are pending, in [http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo.html ro_proposed] (see description...", and the only contributor was "Cjm" (talk))
- 11:47, 9 February 2023 Pascale talk contribs created page Ontology editors' manual (Created page with " = Documentation= Useful reference: [https://oboacademy.github.io/obook/ On becoming an OBO Semantic Engineer], by James Overton, Becky Jackson, Nicole Vasilevsky, Nicolas Matentzoglu, and Shawn Tan. This book provides best practices as recommended by OBO Foundry. Note that some parts of this book may be more general than the documentation presented in this wiki. ==Protégé 5.5 setup== ==Installing and Using git== ==Ontology Edit...")
- 11:42, 9 February 2023 Vanaukenk talk contribs created page Annotation guidelines (Created page with "= Annotation Documentation = Annotation Guidelines ==General Annotation Documentation== {| class="wikitable" !Topic ! Status ! Last reviewed |- |[http://geneontology.org/docs/go-annotations/ General introduction to GO annotation - GO website] | Current | 2021-01-27 |- |Elements of an annotation | Current | 2019-04-11 |- |Guide to GO Evidence Codes | Current | 2018-02-23 |- |Tips to Produce High Quality Annotations | Current | 2019-04-11 |- | Annota...")
- 10:39, 9 February 2023 Pascale talk contribs moved page GeneProduct to GOTerm Relation:enables to Enables over redirect
- 10:39, 9 February 2023 Pascale talk contribs deleted redirect Enables by overwriting (Deleted to make way for move from "GeneProduct to GOTerm Relation:enables")
- 10:36, 9 February 2023 Pascale talk contribs deleted page Category:GO-CAM Documentation (content was: "GO-CAM Documentation category", and the only contributor was "Pascale" (talk))
- 10:35, 9 February 2023 Pascale talk contribs deleted page GOA FAQ (content was: "==What is GOA?== The GOA project aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI), and is a central dataset for other major multi-species databases; such as Ensembl and NCBI. GOA has been a member of the GO Consortium <http://www.geneontology.org/> since 2001, and is responsible for the integration and release of GO annotations to the human, chicken and cow proteomes. In 2006...")
- 10:35, 9 February 2023 Pascale talk contribs deleted page Category:Defunct (content was: "", and the only contributor was "Pascale" (talk))
- 10:33, 9 February 2023 Pascale talk contribs created page Category:Defunct (Created blank page)
- 10:32, 9 February 2023 Pascale talk contribs deleted page Category:Cell Cycle (content was: "All things Cell Cycle.", and the only contributor was "Gail" (talk))
- 10:27, 9 February 2023 Pascale talk contribs moved page Part 3 to Regulation Worksheet - Part 3
- 10:26, 9 February 2023 Pascale talk contribs moved page Part 2 to Regulation Worksheet - Part 2
- 10:26, 9 February 2023 Pascale talk contribs moved page Part 1 to Regulation Worksheet - Part 1
- 10:25, 9 February 2023 Pascale talk contribs moved page Regulates Documentation to Regulates Documentation (2007)
- 10:20, 9 February 2023 Pascale talk contribs created page Category:Meeting Minutes - Regulation (Created blank page)
- 10:18, 9 February 2023 Pascale talk contribs deleted page Regulation of molecular function (content was: "See [ftp://ftp.geneontology.org/pub/go/scratch/regulates_xp_live/go_reglive_withPosNeg_withPF.obo go_reglive_withPosNeg_withPF.obo] we had to remove the P-F links when making this live; they will be reinstated eventually Category:Deprecated")
- 10:16, 9 February 2023 Pascale talk contribs deleted page Regulates icons in OBO-Edit (content was: "Category:Deprecated ==Arrow Icons== Arrow icons, at 30px Image:Regs-all-arrows.gif Arrow icons at the size they would appear in AmiGO Image:Regulates-arrows.gif Arrow icons as they appear in OBO-Edit (Note that this was made using the gifs as OBO-Edit would not accept the svgs) Image:blackarrow.png ==Triangle Icons== Triangle icons, at 30px Image:Regs-all-triangles.gif Triangle icons at the size they would appear in AmiGO Image:Regulates-triang...")
- 10:15, 9 February 2023 Pascale talk contribs deleted page Transitive over part of documentation (content was: "Category:Deprecated File to refer to: http://gocwiki.geneontology.org/index.php/Image:Mp-asserted.doc mp-asserted.doc Email thread: Chris, Tanya and I have started to go through these here is one that seems funny: GO:0000706 "meiotic DNA double-strand break processing" PART_OF GO:0006311 "meiotic gene conversion" GO:0000706 "meiotic DNA double-strand break processing" PART_OF GO:0007131 "meiotic recombination" The issue here GO:0000706 is both a part of GO:000631...")
- 10:07, 9 February 2023 Pascale talk contribs created page Is small molecule inhibitor of (Created page with "=WIP= == Overview and Scope of Use== == Annotation Usage Guidelines== *'''What to capture''' * '''What not to capture''' == Examples == ==Ontology Usage Guidelines== This relation is not used in the ontology. == Cross Reference to the Relation Ontology (RO) == [http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0012006 is small molecule inhibitor of] == Review Status == Last reviewed: February 9, 2023 Reviewed by: Pascale Gaudet [http:...")
- 10:06, 9 February 2023 Pascale talk contribs created page Is small molecule activator of (Created page with "== Overview and Scope of Use== == Annotation Usage Guidelines== *'''What to capture''' * '''What not to capture''' == Examples == ==Ontology Usage Guidelines== This relation is not used in the ontology. == Cross Reference to the Relation Ontology (RO) == [http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0012005 is small molecule activator of] == Review Status == Last reviewed: February 9, 2023 Reviewed by: Pascale Gaudet [http://wiki...")
- 09:55, 9 February 2023 Pascale talk contribs created page Causally upstream of or within (Created page with "== Overview and Scope of Use == * This relation shoud not be used for annotation, either in standard annotation extensions or in GO-CAMs. *The 'causally upstream of of or within' relation is used to relate GO Biological Processes (BP) and/or GO Molecular Functions (MF) when: **the mechanism that relates the upstream process (BP or MF) to the downstream process (BP or MF) is not known **it is not known whether the activities of the gene products in the upstream process oc...")
- 09:39, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:part of to Part of over redirect
- 09:39, 9 February 2023 Pascale talk contribs deleted redirect Part of by overwriting (Deleted to make way for move from "Annotation Extension Relation:part of")
- 09:37, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:occurs in to Occurs in over redirect
- 09:37, 9 February 2023 Pascale talk contribs deleted redirect Occurs in by overwriting (Deleted to make way for move from "Annotation Extension Relation:occurs in")
- 09:33, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:has output to Has output over redirect
- 09:33, 9 February 2023 Pascale talk contribs deleted redirect Has output by overwriting (Deleted to make way for move from "Annotation Extension Relation:has output")
- 09:29, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:has input to Has input over redirect
- 09:29, 9 February 2023 Pascale talk contribs deleted redirect Has input by overwriting (Deleted to make way for move from "Annotation Extension Relation:has input")
- 09:24, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:has participant to Has participant
- 09:20, 9 February 2023 Pascale talk contribs deleted page Has function in location (content was: "Category:Deprecated '''THIS RELATION WAS NOT IMPLEMENTED''' <pre style="color:#808080"> See [http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo.html#OBO_REL:has_function_in has_function_in] in ro_proposed </pre>")
- 09:19, 9 February 2023 Pascale talk contribs deleted page Has function during (content was: "Category:Deprecated THIS RELATION WAS NOT IMPLEMENTED <pre style="color:#808080"> See [http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo.html#OBO_REL:has_function_during has_function_during] in ro_proposed </pre>")
- 09:19, 9 February 2023 Pascale talk contribs deleted page Has function (content was: "Category:Deprecated '''THIS RELATION WAS NOT IMPLEMENTED''' <pre style="color:#808080"> See [http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo.html#OBO_REL:has_function has_function] in ro_proposed </pre>")
- 09:17, 9 February 2023 Pascale talk contribs deleted page Has participant (content was: "#REDIRECT Annotation Extension Relation:has participant", and the only contributor was "Huntley" (talk))
- 09:13, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:results in formation of to Results in formation of
- 09:10, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:exists during to Exists during
- 09:10, 9 February 2023 Pascale talk contribs deleted page Exists during (content was: "#REDIRECT Annotation Extension Relation:exists during", and the only contributor was "Huntley" (talk))
- 09:08, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:acts on population of to Acts on population of
- 09:03, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:happens during to Happens during
- 09:03, 9 February 2023 Pascale talk contribs deleted page Happens during (content was: "#REDIRECT Annotation Extension Relation:happens during", and the only contributor was "Huntley" (talk))
- 09:01, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:causally upstream of to Causally upstream of
- 08:53, 9 February 2023 Pascale talk contribs moved page Causally upstream of negative effect to Causally upstream of, negative effect
- 07:16, 9 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:in presence of (content was: "#REDIRECT Annotation '''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product. ==Child terms== * None. ==Scope of use== ===Domain=== BFO:0000001 ! entity (Biological Process, Molecular Function or Cellular Component) ===Range=== ENTITY_UNION:0000005 ! chemical, gene product, or complex === DEPRECATIO...")
- 07:07, 9 February 2023 Pascale talk contribs created page Located in (Created page with " == Overview == The 'located' relation is used to relate a gene or gene product to a GO Cellular Component, specifically a 'cellular anatomical anatomy' or 'virion component', in which a gene product has been detected. Note that 'is active in' is not used for relating gene products to a 'protein-containing complex'; those associations use 'part of'. == Examples of Usage == == Relations Ontology == [http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/ob...")
- 06:13, 9 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:occurs at (content was: "#REDIRECT Annotation_Extension_Relation:occurs_in '''THIS RELATION IS DEPRECATED''' Curators should use [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:occurs_in occurs in] to capture locations in which Molecular Functions occurs <pre style="color:#808080"> ==Definition== Identifies the Cellular Component or sequence feature at which the Molecular Function or Biological Process is executed. ==Child terms== * None. ==Scope of use== ===Domain=...")
- 06:13, 9 February 2023 Pascale talk contribs undeleted page Annotation Extension Relation:occurs at (22 revisions)
- 06:12, 9 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:occurs at (content was: "#REDIRECT Annotation_Extension_Relation:occurs_in '''THIS RELATION IS DEPRECATED''' Curators should use [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:occurs_in occurs in] to capture locations in which Molecular Functions occurs <pre style="color:#808080"> ==Definition== Identifies the Cellular Component or sequence feature at which the Molecular Function or Biological Process is executed. ==Child terms== * None. ==Scope of use== ===Domain=...")
- 06:11, 9 February 2023 Pascale talk contribs deleted page Deprecated relations (content was: "The following relations are not supported in the ontology, in GO-CAM or in Protein2GO anymore: *occurs_at: use occurs_in instead * dependent_on * has_agent * has_direct_input * in_absence_of * in_presence_of * independent_of * localization_dependent_on * modified_by * not_during * not_ex...", and the only contributor was "Pascale" (talk))
- 06:11, 9 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:has agent (content was: "#REDIRECT: Deprecated_relations =Note that this relation has been deprecated= ==Definition== The relationship that links an entity with a Molecular Function or Biological Process in which the entity participates in the Function or Process by serving as the continuant that is responsible for the execution of the Function or Process. ==Comment== ==Synonyms== has_active_participant ==Child terms== * None ==Scope of use== ===Domain=== BFO:0000007 ! process (Biologi...")
- 10:05, 8 February 2023 Pascale talk contribs created page File:Removes input-2.png
- 10:05, 8 February 2023 Pascale talk contribs uploaded File:Removes input-2.png
- 09:42, 8 February 2023 Pascale talk contribs created page File:Removes input.png
- 09:42, 8 February 2023 Pascale talk contribs uploaded File:Removes input.png
- 09:24, 8 February 2023 Vanaukenk talk contribs created page File:Casually upstream of positive effect GO-CAM example.png
- 09:24, 8 February 2023 Vanaukenk talk contribs uploaded File:Casually upstream of positive effect GO-CAM example.png
- 06:00, 8 February 2023 Pascale talk contribs created page File:Provides input.png
- 06:00, 8 February 2023 Pascale talk contribs uploaded File:Provides input.png
- 05:49, 8 February 2023 Pascale talk contribs moved page Directly provides input for to Provides input for
- 20:59, 7 February 2023 Sjcarbon talk contribs created page Projects update meeting 2023-02-15 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= TBD =Topics= * What ontologies could be dropped if we wanted to go with the "ontology removal" strategy? (Added as AI from software all) <br /> https://github.com/geneontology/amigo/issues/559#issuecomment-1421718871 =Projects reviews= TBD Category: GO Managers Meetings")
- 13:06, 7 February 2023 Pascale talk contribs created page File:Indirect neg.png
- 13:06, 7 February 2023 Pascale talk contribs uploaded File:Indirect neg.png
- 13:02, 7 February 2023 Pascale talk contribs created page File:Indirect pos.png
- 13:02, 7 February 2023 Pascale talk contribs uploaded File:Indirect pos.png
- 12:49, 7 February 2023 Pascale talk contribs deleted page Annotation Cross Products (Retired) (content was: "#REDIRECT:Annotation <span style ="color:red">'''Please note, this page no longer contains the primary documenation for the annotation extension field. Information here is being moved to the main Annotation Extension wiki page, and supporting pages.'''</span> <strike>'''NB: Annotation cross-products are now referred to as annotation extensions''' Each GO annotation pairs a si...", and the only contributor was "Cjm" (talk))
- 12:49, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:requires target sequence feature (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== Identifies a specific sequence feature required in the interacting gene product to enable the cellular component location or occurence of the function or process ==Child terms== * None. ==Scope of use== ===Domain=== BFO:0000001 ! entity (Biological Process, Molecular Function or Cellular Component) ===Range=== SO:0000110 ! sequence feature ==Annotation Extension Usage Examples== ---- -...")
- 12:48, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:requires substance (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== The annotated gene product participates in a Biological Process or executes a Molecular Function only in presence of a substance ==Child terms== None ==Scope of use== ===Domain=== BFO:0000007 ! process (Biological Process or Molecular Function) ===Range=== CHEBI:24431 ! chemical entity === DEPRECATION WARNING === The GO editors have agreed that this relation should be deprecated. The re...")
- 12:48, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:requires sequence feature (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== A sequence feature, such as a protein domain or motif, of the annotated gene product required for its participation in the Molecular Function or Biological Process. ==Comment== Strictly speaking, these fall outside the scope of GO, even with extended annotations. ==Synonym== requires_feature (BROAD) ==Child terms== * None. ==Scope of use== === DEPRECATION WARNING === The GO editors have ag...")
- 12:48, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:requires modification (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== The annotated gene product must be modified as described by the annotation extension to participate in molecular function or biological process. ==Comment== Note this relation is not intended for use in GO annotation. Discussion about using PR ID in column 17 instead; if we agree on that, this relation will be made obsolete. ==Child terms== * None. ==Scope of use== ===Domain=== BFO:0000007 !...")
- 12:48, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:requires localization (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== The annotated gene product participates in the Biological Process only if the Biological Process is located at the Cellular Component. ==Synonym== dependent_on_localization (EXACT) ==Child terms== * None. ==Scope of use== ===Domain=== GO:0008150 ! biological_process ===Range=== GO:0005575 ! cellular component ==Annotation Extension Usage Examples== ---- </pre> Back to [http://wiki.gen...")
- 12:47, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:localization dependent on (content was: " '''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== Identifies a requirement under which the gene product is located at the specified cellular component. ==Child terms== * None ==Scope of use== === DEPRECATION WARNING === The GO editors have agreed that this relation should be deprecated. The relation does not extend the meaning of the GO term, as annotation relations are meant to, but instead specifies conditions under which the annotation i...")
- 12:25, 7 February 2023 Pascale talk contribs deleted page Regulation (content was: "=Regulation= Note that some of this content is deprecated Biological regulation is defined as any process that modulates the frequency, rate or extent of any biological process, quality or function. =The regulates relation= In addition to terms, the ontology uses the regulates relationship means that the term is a process that modulates its parent process. For example, regulation of transcription regulates transcription. The regulation of a process is not a part of the...")
- 10:10, 7 February 2023 Pascale talk contribs created page File:Gef.png
- 10:10, 7 February 2023 Pascale talk contribs uploaded File:Gef.png
- 10:06, 7 February 2023 Pascale talk contribs created page File:Mapk inhibitor.png
- 10:06, 7 February 2023 Pascale talk contribs uploaded File:Mapk inhibitor.png
- 03:24, 7 February 2023 Pascale talk contribs uploaded a new version of File:Egf.png
- 03:20, 7 February 2023 Pascale talk contribs created page File:Mapk.png
- 03:20, 7 February 2023 Pascale talk contribs uploaded File:Mapk.png
- 03:20, 7 February 2023 Pascale talk contribs created page File:Egf.png
- 03:20, 7 February 2023 Pascale talk contribs uploaded File:Egf.png
- 03:13, 7 February 2023 Pascale talk contribs moved page File:Consititutively upstream.png to File:Constitutively upstream.png
- 03:13, 7 February 2023 Pascale talk contribs created page File:Consititutively upstream.png
- 03:13, 7 February 2023 Pascale talk contribs uploaded File:Consititutively upstream.png
- 12:32, 6 February 2023 Pascale talk contribs created page MF Relations outline (Created page with " * causally upstream of or within * * causally upstream of * * * indirectly causally upstream of * * * immediately causally upstream of * * * regulates * * * causally upstream of, negative effect * * * * removes input for * * * * negatively regulates * * * * * [Directly_negatively_regulates] * * * * * indirectly negatively regulates * * * causally upstream of, positive effect * * * * constitutively upstream of: * * * * * positively regulates * * * * * [Directly_posi...")
- 11:40, 1 February 2023 Vanaukenk talk contribs created page Indirectly positively regulates (Created page with "== Overview and Scope of Use== * The 'indirectly positively regulates' relation is used to relate GO Molecular Functions (MF) when: ** The upstream activity occurs before the downstream activity, but there are intervening activities between them (indirect) ** The mechanism that relates the upstream activity to the downstream activity is understood ** The upstream activity promotes execution of the downstream activity (positive) ** Execution of the upstream activity is co...")
- 10:45, 31 January 2023 Pascale talk contribs created page Projects update meeting 2023-02-01 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= ==GOC meeting== will be held immediately after Biocuration, in Padua, Italy (Thursday April 27th to Saturday April 29th) * '''Note that the location has not yet been finalized - but likely Best Western Galileo''' * Apparently hotels are filling quickly for the biocuration meeting * Draft agenda: https://docs.google.com/document/d/1eTKwfGT4...")
- 17:23, 30 January 2023 Mi talk contribs created page 1 Feb 2023 PAINT Conference Call (Created page with "==Present== ==Agenda== We are going to focus our discussion on the new draft of human functionome paper. Here is the link to the draft. https://docs.google.com/document/d/1UHaO-ti3WN7r4zcbZnyRyMYUEhJh-d5NqljTktzLQyg/edit?usp=sharing Category:PAINT")
- 11:59, 30 January 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-01-31 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, February 9th ** [https://github.com/geneontology/noctua/issues/816 Outage tasks] === No GO Calls Week === * First full week of February (5th - 10th) === Spring GOC Meeting Plans === * Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Thursday, Friday with group outing late Friday afternoon, and group dinner Friday nigh...")
- 20:06, 27 January 2023 Suzialeksander talk contribs created page 2023 Padua GOC Meeting Logistics (Created page with "=GOC Meeting, Padua, April 27-29, 2023= * Location: [https://www.nh-hotels.com/hotel/nh-padova | Hotel NH Padua, Italy] * Agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit?usp=sharing ==Registration== Register at TicketLeap. '''Registration deadline is February 17th, 2023'''. Payment options (for in-person attendees) will be posted shortly. ==Consortium dinner== Included in the final registration cost.")
- 11:06, 27 January 2023 Pascale talk contribs created page Ontology meeting 2023-01-30 (Created page with "=Editors discussion items= ==Announcements== ===Annotation reviews at MGI=== * Li (@LiNiMGI) will be replacing Harold for annotation tickets review. * The group-contacts.csv file has been updated: https://github.com/geneontology/go-site/blob/master/metadata/group-contacts.csv ===GOC consortium=== * April 27th-29th, Padua, Italy * If you plan to attend, please register ASAP. geneontology.ticketleap.com/goc2023 password: goc2023 ===Update missing MetaCyc2GO mappings...")
- 10:36, 26 January 2023 Vanaukenk talk contribs created page Indirectly negatively regulates (Created page with "== Overview and Scope of Use== * The 'indirectly negatively regulates' relation is used to relate GO Molecular Functions (MF) when: ** The upstream activity occurs before the downstream activity, but there are intervening activities between them (indirect) ** The mechanism that relates the upstream activity to the downstream activity is understood ** The upstream activity reduces execution of the downstream activity (negative) ** Execution of the upstream activity is con...")
- 04:04, 23 January 2023 Pascale talk contribs created page Projects update meeting 2023-01-25 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= * Reminder: GOC meeting will be held immediately after Biocuration, in Padua, Italy (Thursday April 27th to Saturday April 29th) * '''Note that the location has not yet been finalized - dont book the hotel yet''' * Draft agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit# * Plan to stay Saturday P...")
- 12:21, 20 January 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-01-24 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, January 26th ** [https://github.com/geneontology/noctua/issues/815 Outage tasks] === Spring GOC Meeting Plans === * Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM == GO Release Pipeline == * January release out * Err...")
- 21:43, 18 January 2023 User account RaymondLee talk contribs was created by Sjcarbon talk contribs
- 15:36, 18 January 2023 User account Raymond talk contribs was created by Sjcarbon talk contribs and password was sent by email
- 20:03, 16 January 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-01-17 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, January 26th ** [https://github.com/geneontology/noctua/issues/815 Outage tasks] === Spring GOC Meeting Plans === * Padua, Italy - April, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM == GO Release Pipeline == * January release out == A...")
- 13:25, 11 January 2023 Pascale talk contribs created page Projects update meeting 2023-01-18 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= * Reminder: GOC meeting will be held immediately after Biocuration, in Padua, Italy (Thursday April 27th to Saturday April 29th) * Draft agenda: https://docs.google.com/document/d/1eTKwfGT4o4w85HM2OYOekgmIJ5Hpm9LYBNWvg0udsRQ/edit# * Plan to stay Saturday PM / Sunday AM for a managers planning meeting =Projects reviews= https://github.co...")
- 03:09, 10 January 2023 Pascale talk contribs created page Ontology meeting 2023-01-23 (Created page with "=Editors discussion items= ==New file for some MF terms== * src/ontology/imports/go-catalytic-activities-participants.owl Need to edit the file when obsoleting MFs that are part of this file - see for example: https://github.com/geneontology/go-ontology/pull/24613/commits/a8f04973219e91f7742bf2df8c84655305f65701 ==Consider moving taxon constraints back into ontology== Jim, See https://github.com/geneontology/go-ontology/issues/24490 ==Is hormone secretion intended on...")
- 11:42, 9 January 2023 Pascale talk contribs created page Projects update meeting 2023-01-11 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= * GOC meeting: Just after Biocuration, in Padua, Italy (Thursday April 27th to Saturday April 29th) =Projects reviews= https://github.com/orgs/geneontology/projects/108/views/3 * [https://github.com/geneontology/project-management/issues/12 Move GO Google drive to a shared drive] (Suzi) * [https://github.com/geneontology/project-manage...")
- 12:27, 6 January 2023 Vanaukenk talk contribs created page Annotation Conf. Call 2023-01-10 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === * Next regularly scheduled Noctua outages: ** Thursday, January 12th ** [https://github.com/geneontology/noctua/issues/807 Outage tasks] === Spring GOC Meeting Plans === * Padua, Italy - lApril, 27-29 (ISB is from Sunday to Wednesday 23rd-26th) * Tentative schedule: Thursday, Friday with group outing late Friday afternoon, and group dinner Friday night, Saturday AM == GO Release Pipeline == * Jan...")
- 12:22, 6 January 2023 Vanaukenk talk contribs created page Annotation Call 2023 Agenda and Minutes (Created page with "* Annotation Conf. Call 2023-01-10")
- 05:43, 6 January 2023 Pascale talk contribs created page Ontology meeting 2023-01-09 (Created page with "* '''Group members:''' Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Announcements= Next week is MLK's Day, there is no ontology call. =New file= * src/ontology/imports/go-catalytic-activities-participants.owl Need to edit the file when obsoleting MFs that are part of this file - see for example: https://github.com/geneontology/go-ontology/pull/24613/commits/a8f04973219e91f7742bf2...")
- 03:57, 6 January 2023 Pascale talk contribs created page Ontology editors' conference call minutes 2023 (Created page with "* Jan 2 - No GO calls - holidays * * Jan 9 * Jan 16 ---- No call - US holiday - MLK * Jan 23 * Jan 30 * Feb 6 ---- No GO calls week * Feb 13 * Feb 20 --- No call - US holiday Presidents' Day * Feb 27 * Mar 6 ---- No GO calls week * Mar 13 * Mar 20 *...")
- 06:46, 6 December 2022 Pascale talk contribs created page Projects update meeting 2022-12-07 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= * This is the last call of the year * Next call will be Jan 11th (GO calendar is updated)")
- 18:31, 5 December 2022 Mi talk contribs created page 7th Dec 2022 PAINT Conference call (Created page with "==Present== ==Agenda== ===PAINT human paper discussion=== Topics to discuss *Rearrange the sections? *Move some sections to supplemental materials https://docs.google.com/document/d/1-8wVCPg7GEZQ9l3ox85hBO48YBoknRXOG_B9AJ6YZ0Q/edit?usp=sharing Category:PAINT")
- 09:54, 5 December 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-12-06 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === *Next regularly scheduled Noctua outage: **Thursday, December 15th **[https://github.com/geneontology/noctua/issues/803 Outage tasks] === 2022 - 2023 Annotation Calls === * Last call: Tuesday, December 6th, 2022 * No calls: December 13th and 20th * Tentative: no GO calls first week of January * Tentative: first annotation call: January 10th === Spring GOC Meeting Plans === * Padua, Italy - late Ap...")
- 04:46, 29 November 2022 Pascale talk contribs created page Projects update meeting 2022-11-30 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= * Next week is the last call of the year * Week of Dec 12th is the no GO calls week * Propose to cancel calls from December 12th to January 6th * Technically the week of Jan 9th is a no GO calls week, but we propose to skip this since we have 4 weeks with no calls (Dec 12- Jan 6th): is everyone OK with this? =Projects reviews= https://...")
- 11:26, 28 November 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-11-29 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === *Next regularly scheduled Noctua outage: **Thursday, December 1st and December 15th **[https://github.com/geneontology/noctua/issues/803 Outage tasks] === Spring GOC Meeting Plans === * [https://docs.google.com/forms/d/e/1FAIpQLSfIyUWDaI1Ch1C1-I5sPDPFtvAIFAdFOWY7Veb6GwI2jhqa9g/viewform?usp=sf_link Survey] - please reply ** Padua, Italy - late April, before the ISB meeting ***Another Italy option -...")
- 06:29, 24 November 2022 Pascale talk contribs created page Ontology meeting 2022-11-28 (Created page with "* '''Group members:''' Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Tickets by ontology editors= =Following up on prevous items= ==Design patterns== ===NAD, NADH, NADPH processes logical definitions inconsistencies=== Jim https://github.com/geneontology/go-ontology/issues/24279 ===regulation of pH=== Jim https://github.com/geneontology/go-ontology/pull/24256/files ===cell morph...")
- 02:22, 22 November 2022 Pascale talk contribs created page Ontology meeting 2022-12-05 (Created page with "* '''Group members:''' Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion items= ==Differentiation:== * Pascale & David have proposed new definitions for 'cell differentiation' and main children (cell development, cell fate specification, cell fate determination, etc), see https://github.com/geneontology/go-ontology/issues/24390 * We'd like to discuss these and get feedb...")
- 14:17, 21 November 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-11-22 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === *Next regularly scheduled Noctua outage: **Thursday, December 1st and December 15th **[https://github.com/geneontology/noctua/issues/803 Outage tasks] === Spring GOC Meeting Plans === * [https://docs.google.com/forms/d/e/1FAIpQLSfIyUWDaI1Ch1C1-I5sPDPFtvAIFAdFOWY7Veb6GwI2jhqa9g/viewform?usp=sf_link Survey] - please reply ** Padua, Italy - late April, before the ISB meeting ***Another Italy option -...")
- 11:29, 21 November 2022 Pascale talk contribs created page Ontology meeting 2022-11-21 (Created page with "* '''Group members:''' Pascale, Harold, Raymond, Val, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion items= =Design patterns doc= https://docs.google.com/document/d/1cmcMbXmEY3Ko1emGZX3Gd6ttDi9_iQB2fLAprLD3aGI/edit# =Tickets by ontology editors= Category:Meetings Category:Ontology")
- 11:45, 14 November 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-11-15 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Next week - no GO calls week === === Noctua === *Next regularly scheduled Noctua outage: **Thursday, December 1st (?) **[https://github.com/geneontology/noctua/issues/803 Outage tasks] === Fall GOC Meeting Follow-Up === * Survey - has everyone replied? == GO Release Pipeline == * November release will start this week ** Encourage people to check #release-pipeline channel on Slack for up-to-date info == Usi...")
- 08:57, 14 November 2022 Pascale talk contribs created page Ontology meeting 2022-11-14 (Created page with "* '''Group members:''' Pascale, Harold, Raymond, Val, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion items= =Tickets by ontology editors= ==Neutral amino acid transporter== https://github.com/geneontology/go-ontology/issues/24323 'Neutral amino acid' is not in CHEBI - neither is 'acidic or basic' - so these need to be asserted manually, or we could get rid of the distinction. The distinction can be use...")
- 05:32, 14 November 2022 Pascale talk contribs created page Projects update meeting 2022-11-16 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Documents= '''Proposed priorities for the next 6 months''' * [https://docs.google.com/document/d/17ikwodMNC_xwEGZhBre_tilw4Fd8NI1IWZ8KxefSPBU/edit Main tasks Oct 22-March 23] * [https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit#heading=h.97mb5dzeroql GO priorities] ==Projects update== https://github.com/orgs/geneont...")
- 15:47, 3 November 2022 Mi talk contribs created page File:PAINT MSA key residue.png (Screenshot of PAINT MSA key residue view. This is used for the PAINT user guide.)
- 15:47, 3 November 2022 Mi talk contribs uploaded File:PAINT MSA key residue.png (Screenshot of PAINT MSA key residue view. This is used for the PAINT user guide.)
- 15:46, 3 November 2022 Mi talk contribs created page File:PAINT MSA domain.png (Screenshot of PAINT MSA domain view.)
- 15:46, 3 November 2022 Mi talk contribs uploaded File:PAINT MSA domain.png (Screenshot of PAINT MSA domain view.)
- 14:33, 1 November 2022 Mi talk contribs created page 2nd Nov 2022 PAINT Conference call (Created page with "==Present== ==Agenda== ===PANTHER17.0 release update=== ===New PAINT software release on Oct.31st, 2022=== ===Continue discussing PAINT human paper=== Here is the link to the manuscript: https://docs.google.com/document/d/1-8wVCPg7GEZQ9l3ox85hBO48YBoknRXOG_B9AJ6YZ0Q/edit?usp=sharing Category:PAINT")
- 04:08, 31 October 2022 Pascale talk contribs created page Projects update meeting 2022-11-02 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Documents= '''Proposed priorities for the next 6 months''' * [https://docs.google.com/document/d/17ikwodMNC_xwEGZhBre_tilw4Fd8NI1IWZ8KxefSPBU/edit Main tasks Oct 22-March 23] * [https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit#heading=h.97mb5dzeroql GO priorities] Category: GO Managers Meetings")
- 04:42, 25 October 2022 Pascale talk contribs created page Ontology meeting 2022-10-31 (Created page with "* '''Group members:''' Pascale, Harold, Raymond, Val, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion items= ==Follow up on MF to MF Relations== * Jim AI: RO release ==Are the ShEx rules the "source of truth" for the ontology as well as annotation? == * AI: Kimberly to create a ticket to get all relations used in the ontology * We may want to distinguish LD from asserted axioms? ==GO practice for obsol...")
- 12:30, 24 October 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-11-01 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === *Next regularly scheduled Noctua outage: **Thursday, October 27th **[https://github.com/geneontology/noctua/issues/795 Outage tasks] == GO Release Pipeline == * October release done ** Encourage people to check #release-pipeline channel on Slack for up-to-date info == Using PRO in GO Annotation == *Presentation from Darren Natale on using PRO to create modified forms of proteins for GO annotation...")
- 15:57, 21 October 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-10-25 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Noctua === *Next regularly scheduled Noctua outage: **Thursday, October 27th **[https://github.com/geneontology/noctua/issues/795 Outage tasks] == GO Release Pipeline == * October release done ** Encourage people to check #release-pipeline channel on Slack for up-to-date info == AmiGO == == Ontology == *BP refactor? === Annotation error reports and annotation review === * Please remember to keep checking t...")
- 03:31, 21 October 2022 Pascale talk contribs created page Projects update meeting 2022-10-26 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Resources= * David 60% * Kimberly 30% * Tremayne 50% (including Alliance) * Sierra 33% * Jim 30% * Seth 100% * Pascale 100% * Dustin 50% * Huaiyu 10% * Anushya 40% Category: GO Managers Meetings")
- 10:38, 20 October 2022 Pascale talk contribs created page Ontology meeting 2022-10-24 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Announcements= =Editors discussion items= ==Follow up on MF to MF Relations== Pascale [https://github.com/oborel/obo-relations/issues/631 RO Ticket for directly positively regulates and activates & directly negatively regulates and inhibits] ==Are the ShEx to be the "source of truth" for the ontology? == Need to define the...")
- 13:44, 4 October 2022 Pascale talk contribs created page Projects update meeting 2022-10-05 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =GOC meeting= * The week after next (Oct 11-13) * The following week will be a no GO calls week (week of Sept 17th) =Priorities until the end of the year= Main tasks’ document: https://docs.google.com/document/d/17ikwodMNC_xwEGZhBre_tilw4Fd8NI1IWZ8KxefSPBU/edit where we list on which project we are each working on. This is based on the proposed pri...")
- 12:15, 29 September 2022 David talk contribs created page Causally upstream of negative effect (Created page with "== Overview == *The 'causally upstream of, negative effect' relation is used to relate GO Biological Processes (BP) and/or GO Molecular Functions (MF) when: **the mechanism that relates the upstream process (BP or MF) to the downstream process (BP or MF) is understood **the activities of the gene products in the upstream process occur before events in the downstream process **the execution of the upstream event decreases the execution of the downstream event == Example...")
- 11:53, 29 September 2022 David talk contribs created page Indirectly causally upstream of (Created page with "== Overview == *The 'indirectly causally upstream of' relation is used to relate GO Biological Processes (BP) and/or GO Molecular Functions (MF) when: **The mechanism that relates the upstream event (MF or BP) to the downstream event (MF or BP) is understood **The upstream event has an effect on the execution of the downstream event **There is a third event that happens between the upstream event and the downstream event **The upstream event is causally upstream of the t...")
- 11:05, 29 September 2022 David talk contribs created page Removes input for (Created page with "== Overview == *The 'removes input for' relation is used to relate GO Molecular Functions (MF) when: **The upstream MF occurs before the downstream MF **The upstream MF has a negative effect on the downstream MF **The execution of the upstream MF is restricted to a specific condition **The execution of the upstream MF results in an input of the downstream MF becoming unavailable for the downstream MF == Examples of Usage == * == Quality Control Checks == * Shex '''(S...")
- 10:31, 29 September 2022 David talk contribs created page Constitutively upstream of (Created page with "== Overview == *The 'constitutively upstream of' relation is used to relate GO Biological Processes (BP) and/or GO Molecular Functions (MF) when: **The mechanism that relates the upstream event (MF or BP) to the downstream event (MF or BP) is understood **The activities in the upstream event occur before events in the downstream event **The upstream event has an effect on the downstream event **The execution of the upstream event is approximately constant == Examples of...")
- 05:37, 29 September 2022 Pascale talk contribs created page Noctua documentation from Help in Noctua Editor (Created page with "==Noctua: the Gene Ontology's GO Annotation Tool Suite== Noctua documentation from Help in Noctua Editor [http://noctua.geneontology.org/ Noctua] is a web-based annotation tool developed by the GO Consortium. Noctua can be used to create standard GO annotations as well as [http://geneontology.org/docs/gocam-overview/ GO-CAMs (Gene Ontology Causal Activity Models)] in a collaborative manner, i. e. multiple users can work on the same model at the same time. ===Getti...")
- 10:03, 27 September 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-09-27 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * Entirely virtual * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] ** See agenda for pswd * Presentation of [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items and breakout group topics] === Noctua === *Next regularly scheduled Noctua outag...")
- 08:24, 27 September 2022 Pascale talk contribs created page Ontology meeting 2022-10-03 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Announcements= =Editors discussion items= ==Relations== Pascale [https://github.com/oborel/obo-relations/issues/631 RO Ticket for directly positively regulates and activates & directly negatively regulates and inhibits] ==Topics postponed from previous calls== ===Stem cell taxonomic range=== https://github.com/geneontolog...")
- 08:18, 27 September 2022 Pascale talk contribs created page Projects update meeting 2022-09-28 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =GOC meeting= * The week after next (Oct 11-13) * The following week will be a no GO calls week (week of Sept 17th) =Priorities until the end of the year= Pascale - I have updated the ‘main tasks’ document: https://docs.google.com/document/d/17ikwodMNC_xwEGZhBre_tilw4Fd8NI1IWZ8KxefSPBU/edit (I realize that Sept is almost over, but this is a mix...")
- 13:02, 23 September 2022 Mi talk contribs created page 5th Oct 2022 PAINT Conference call (Created page with "==Present== ==Agenda== ===Conversion PAINT to PANTHER17.0=== ===New features for PAINT software=== ===Continue discussing PAINT human paper=== Here is the link to the manuscript: https://docs.google.com/document/d/1-8wVCPg7GEZQ9l3ox85hBO48YBoknRXOG_B9AJ6YZ0Q/edit?usp=sharing Category:PAINT")
- 15:36, 19 September 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-09-20 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] - '''PLEASE REGISTER by SEPT. 1st''' ** See agenda for pswd * Please think about [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items] and breakout group to...")
- 10:39, 13 September 2022 Vanaukenk talk contribs created page Projects update meeting 2022-09-21 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris (few mins late), Cynthia * Present: * Regrets: =GOC meeting= * currently 58 registered (18 in person/40 remote) * Agenda: https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M/edit# =Priorities= Today we discuss the next GO priorities based on this document: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# ==SGD and WB...")
- 09:11, 6 September 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-09-06 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] - '''PLEASE REGISTER by SEPT. 1st''' ** See agenda for pswd * Please think about [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items] and breakout group to...")
- 06:16, 6 September 2022 Pascale talk contribs created page Projects update meeting 2022-09-07 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =GOC meeting= * currently 58 registered (18 in person/40 remote) * Agenda: https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M/edit# =Priorities= Today we discuss the next GO priorities based on this document: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# Category: GO Managers Meet...")
- 18:18, 2 September 2022 Mi talk contribs created page 7th Sept 2022 PAINT Conference call (Created page with "==Present== ==Agenda== ===Continue discussing PAINT human paper=== Here is the link to the manuscript: https://docs.google.com/document/d/1-8wVCPg7GEZQ9l3ox85hBO48YBoknRXOG_B9AJ6YZ0Q/edit?usp=sharing Category:PAINT")
- 02:07, 1 September 2022 Pascale talk contribs created page Ontology meeting 2022-09-26 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Announcements= =Editors discussion items= ==Stem cell taxonomic range== https://github.com/geneontology/go-ontology/issues/23764 =='Nested' regulation== https://github.com/geneontology/go-ontology/issues/12976 I think we are obsoleting these terms? "regulation of X by regulation of Y" We still have 'regulation of x by regulati...")
- 04:10, 31 August 2022 Pascale talk contribs created page Projects update meeting 2022-08-31 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Priorities= Today we discuss the next GO priorities based on this document: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# Category: GO Managers Meetings")
- 12:19, 29 August 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-08-30 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] - '''PLEASE REGISTER by SEPT. 1st''' ** See agenda for pswd * Please think about [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items] and breakout group to...")
- 01:55, 23 August 2022 Pascale talk contribs created page Ontology meeting 2022-09-19 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Announcements= =Editors discussion items= ==Stem cell taxonomic range== https://github.com/geneontology/go-ontology/issues/23764 ==Follow up on previous discussion topics== ==Regulation of a process in another organism== * AI (Pascale) should create a new triad of relations for linking the modulation of a process in another...")
- 13:10, 19 August 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-08-23 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] - PLEASE REGISTER by SEPT. 1st ** See agenda for pswd * Please think about [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items] and breakout group topics...")
- 05:21, 19 August 2022 Pascale talk contribs created page Projects update meeting 2022-08-24 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Priorities= Today we discuss the next GO priorities based on this document: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# Category: GO Managers Meetings")
- 03:17, 16 August 2022 Pascale talk contribs created page Ontology meeting 2022-08-22 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= Aligning GO and EC (or RHEA, or any other ontology): https://github.com/geneontology/go-ontology/issues/23829#issuecomment-1216214500 The [https://wiki.geneontology.org/Guidelines_for_new_Molecular_Functions GO guidelines] state that we do not create terms for substrates, for example GO:0102113 hyp...")
- 17:04, 15 August 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-08-16 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * Will send out registration form soon * Please think about agenda items and breakout group topics === Noctua === *Next regularly scheduled Noctua outage: **Thursday, September 8th == GO Release Pipeline == * August release still pending? == AmiGO == == Ontology...")
- 11:58, 15 August 2022 Pascale talk contribs created page Projects update meeting 2022-08-17 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= ==GOC meeting== Oct 11-13 at CalTech; a mix of in-person and remote =Discussion items= == How to get Xenbase prioritized== ** Alliance moving forward with direct upstream ingest ==Timeline for SGD and WB import into Noctua== ** Proposal: prioritize this work for mid-October after the GOC meeting with the aim of completing by the end o...")
- 16:16, 12 August 2022 Vanaukenk talk contribs created page Ontology meeting 2022-08-15 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= ==Question about parentage of life stage terms in go-lego== *Organismal life stage terms look to be typed as 'occurents' in go-lego but can/should they be typed more granularly as a 'biological phase' (GO:0044848)? Category:Meetings Category:Ontology")
- 13:47, 2 August 2022 Mi talk contribs created page 3rd Aug 2022 PAINT Conference call (Created page with " ==Present== ==Agenda== ===Continue discussing PAINT human paper=== Here is the link to the manuscript: https://docs.google.com/document/d/1-8wVCPg7GEZQ9l3ox85hBO48YBoknRXOG_B9AJ6YZ0Q/edit?usp=sharing Category:PAINT")
- 15:39, 26 July 2022 Sjcarbon talk contribs created page Projects update meeting 2022-07-27 (Created page with "* How to get Xenbase prioritized * Alliance moving forward with direct upstream ingest")
- 12:42, 25 July 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-07-26 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * Will send out registration form asap === Noctua === *Regularly scheduled Noctua outage: **Thursday, July 28th === Annotation Call Schedule === *No meeting August 2nd *No meeting August 9th === Google Drive Migration === *Please check the old GO drive for files...")
- 10:47, 25 July 2022 Pascale talk contribs created page Ontology meeting 2022-07-25 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' David, Peter, Chris, Jim Category:Meetings Category:Ontology")
- 13:55, 18 July 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-07-19 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA Tuesday, October 11th - Thursday, October 13th === Noctua === *Regularly scheduled Noctua outage: **Thursday, July 28th == GO Release Pipeline == * July release is out * Some issues with snapshot releases ** Could not rebuild NEO (Noctua Entity Ontology) last Thursday == AmiGO == == Ontology == === Membrane...")
- 12:51, 5 July 2022 Mi talk contribs created page 6th July 2022 PAINT Conference Call (Created page with " ==Present== ==Agenda== ===Discuss PAINT human paper=== Here is the link to the manuscript: https://docs.google.com/document/d/1-8wVCPg7GEZQ9l3ox85hBO48YBoknRXOG_B9AJ6YZ0Q/edit?usp=sharing Category:PAINT")
- 02:02, 5 July 2022 Pascale talk contribs created page Ontology meeting 2022-07-18 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= ==Uberon taxon constraints are too stringent== See https://github.com/geneontology/go-ontology/issues/23445 Do we need to remove the relation 'GO:0110165 cellular anatomical entity' is_a 'CARO_0000000 anatomical entity'? ==ChEBI documentation edited== New section on External Ontologies https://...")
- 08:58, 30 June 2022 Pascale talk contribs created page External ontologies (Created page with "GO uses external ontologies for the logical definitions of some terms. =ChEBI= Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. ChEBI is used to describe compounds in GO, as well as in RHEA. Compounds used in GO are the forms present at pH 7, the physiological pH under most conditions in most organisms annotated with GO. The pH is not 7.3 in all organelles, organs and orga...")
- 11:49, 29 June 2022 Pascale talk contribs created page Projects update meeting 2022-07-06 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: ==GOC meeting== == Ongoing work updates == ===Google drive move=== https://github.com/orgs/geneontology/projects/90 * Suzy to report on status ===[https://github.com/orgs/geneontology/projects/80 Model copy]=== * Status === Adding SO terms as valid range for 'occurs in' annotation extension === * Curators would like to be able to specify chromosomal...")
- 08:43, 29 June 2022 Pascale talk contribs created page Deprecated relations (Created page with "==Deprecated Relations== These relations are not supported in the ontology, in GO-CAM or in Protein2GO anymore: *occurs_at - use occurs_in instead * dependent_on *has_agent - not in RO: in AE graph the parent for this term is 'has_participant' * has_direct_input * in_absence_of * in_presence_of * independent_of * localization_dependent_o...")
- 08:06, 29 June 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-07-05 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * Likely at Caltech, October 11th - 13th * Please still fill out the meeting survey from Pascale === Noctua === *Regularly scheduled Noctua outage: **Thursday, June 23rd == GO Release Pipeline == * June release == AmiGO == == Ontology == === Membrane CC Terms === *Proposal to obsolete and reorganize CC ontology for membrane annotations ** Capturing membrane protein topolog...")
- 09:46, 28 June 2022 Vanaukenk talk contribs created page Projects update meeting 2022-06-29 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: == Ongoing work updates == ===Release/snapshop update=== New release started ==SOP for project management== https://docs.google.com/document/d/1yWU8xy-lK34p6bSp2EDlTvonbbEr6mCzN2mdLhjNXv0/edit# === Adding SO terms as valid range for 'occurs in' annotation extension === * Curators would like to be able to specify chromosomal regions where MFs occur * Right now, SO...")
- 10:57, 22 June 2022 Cjm talk contribs created page Projects update meeting 2022-07-20 (Created page with " Paper planning: Chris and Nomi")
- 07:42, 20 June 2022 Pascale talk contribs created page Ontology meeting 2022-06-27 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= ==Protein processing & specificity (Raymond, Helen)== https://github.com/geneontology/go-ontology/issues/23378 see also notes from last call: Ontology_meeting_2022-06-6 ==Glycosylation ontology== Email from Alex Diehl Hi Chris, Darren, and Pascale, Over the past year or so I worked with T...")
- 09:16, 16 June 2022 Pascale talk contribs created page File:Activity unit.jpg
- 09:16, 16 June 2022 Pascale talk contribs uploaded File:Activity unit.jpg
- 08:44, 16 June 2022 Pascale talk contribs created page Category:Reports - Sequence Ontology (Created page with "Reports - sequence ontology")
- 08:44, 16 June 2022 Pascale talk contribs deleted page Category:Software Progress (content was: "A collection of software pages that can show visible signs of progress (as opposed to design documents, schema, rationals, etc.).", and the only contributor was "Sjcarbon" (talk))
- 08:41, 16 June 2022 Pascale talk contribs deleted page Category:Reports - Sequence Ontology (content was: "About the Sequence Ontology (SO).")
- 08:38, 16 June 2022 Pascale talk contribs deleted page Category:GO News (content was: "Contains links to GO News information.", and the only contributor was "Gail" (talk))
- 08:38, 16 June 2022 Pascale talk contribs deleted page Category:GAF (content was: "Category:File Format GAF is an acronym for ''Gene Association File'', a file format "where each line represents a single link between a gene product (protein, gene, transcript, etc.) and a GO term". See the [http://www.geneontology.org/GO.format.annotation.shtml formal specification] for more.")
- 08:35, 16 June 2022 Pascale talk contribs deleted page GO-CAM (content was: "Category:GO-CAM == Causal Activity Models == * GO-CAM Documentation == Noctua == * http://noctua.geneontology.org * Noctua")
- 08:35, 16 June 2022 Pascale talk contribs deleted page GO-CAM Documentation (content was: "Category:GO-CAM")
- 08:34, 16 June 2022 Pascale talk contribs created page Category:GO-CAM Documentation (Created page with "GO-CAM Documentation category")
- 05:07, 10 June 2022 Pascale talk contribs created page Ontology meeting 2022-06-20 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= * Protein processing & specificity (Raymond): https://github.com/geneontology/go-ontology/issues/23378 ===For a future call=== * Antiporters & specificity (Pascale): https://github.com/geneontology/go-ontology/issues/23374 * Antiporters reorganization: https://docs.google.com/presentation/d/11-...")
- 06:32, 8 June 2022 Pascale talk contribs created page Projects update meeting 2022-06-22 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: =Today's meeting is to establish the next medium (~6 months) and short term (1-2 months) priorities= ==Potential priorities short list== https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit#heading=h.nntgv5th4cph Category: GO Managers Meetings")
- 16:25, 6 June 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-06-21 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === *Possible in-person meeting; location and dates still TBD === Noctua === *Regularly scheduled Noctua outage: **Thursday, June 23rd == GO Release Pipeline == * June release == AmiGO == == Ontology == === Membrane CC Terms === *Proposal to obsolete and reorganize CC ontology for membrane annotations ** Capturing membrane protein topology will no longer be under the purview o...")
- 14:20, 31 May 2022 Pascale talk contribs created page Projects update meeting 2022-06-08 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: =Today's meeting is to establish the next medium (~6 months) and short term (1-2 months) priorities= ==Potential priorities short list== https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit#heading=h.nntgv5th4cph Category: GO Managers Meetings")
- 11:42, 31 May 2022 Pascale talk contribs created page Projects update meeting 2022-06-01 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: =Today's meeting is to establish the next medium term and short term priorities= ==Potential priorities short list== https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit#heading=h.nntgv5th4cph ==Task Matrix== [https://docs.google.com/document/d/1r3aWGjyz2nXNpyzETPO-ah276HQDc1ClNs57Cm6Nwv0/edit Main tasks - Jan-July 2022] == Current...")
- 09:57, 31 May 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-06-07 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === *Possible in-person meeting; location and dates still TBD === Noctua === *Regularly scheduled Noctua outage: **Thursday, May 26th == GO Release Pipeline == * May release went out Friday, 2022-05-20 == AmiGO == == Ontology == === Non-catalytic Molecular Functions === [https://wiki.geneontology.org/Non-catalytic_Molecular_Functions List and Definitions] === Membrane CC Terms...")
- 02:03, 25 May 2022 Pascale talk contribs created page Ontology meeting 2022-06-6 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= * Antiporters (Pascale) https://github.com/geneontology/go-ontology/issues/23374 *User requests: **[https://github.com/geneontology/go-ontology/issues/23268 proteinogenic amino acid biosynthesis] and [https://github.com/geneontology/go-ontology/issues/23269 non-proteinogenic amino acid biosynthe...")
- 02:23, 24 May 2022 Pascale talk contribs created page Projects update meeting 2022-05-25 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: David =Reminder= We will have our 'priorities' discussion next week, hopefully everyone can be present. =Discussion= New groups (and groups in general): it would be nice to have guidelines as to what is a group, when to create a new group Decision from last week: We will add a parent field to groups and ensure every group other than GOC has a parent...")
- 10:40, 23 May 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-05-24 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === *Possible in-person meeting; still being discussed === Noctua === *Regularly scheduled Noctua outage: **Thursday, May 12th * Automatic ontology updates implemented on Thursday, April 14th * April 28th Noctua systems outage - we did not do the ontology updates due to an issue with upstream ontologies that would have resulted in an EMAPA term being automatically replaced by an U...")
- 02:45, 23 May 2022 Pascale talk contribs created page Ontology meeting 2022-05-23 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= * [https://github.com/geneontology/go-ontology/issues/22106 peptide alpha-N-acetyltransferase activity children cause true path violation] Harold * [https://github.com/geneontology/go-ontology/issues/21524 UDP-beta-L-arabinofuranose transport & transporter ] Pascale: subclasses calculated by Prot...")
- 05:28, 19 May 2022 Pascale talk contribs created page Non-catalytic Molecular Functions (Created page with "==General considerations== Each gene product should be annotated to at least 1 GO term per GO aspect For MF, we aim for an annotation to a term other than binding or protein binding In the course of MF refactoring we have created several terms to represent non-catalytic functions ==Main non-catalytic Molecular Functions== ===molecular carrier activity (GO:0140104)=== Definition: Directly binding to a specific ion or molecule and delivering it either to an acceptor molec...")
- 01:06, 18 May 2022 Pascale talk contribs created page Projects update meeting 2022-05-18 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Project updates= ==Projects near completion== Can we assign time to complete the tasks? * [https://github.com/orgs/geneontology/projects/65 Noctua 2021] (3 tickets left) ** Kimberly will ask Tremayne for a time estimate on Friday's Noctua workbenches call * [https://github.com/orgs/geneontology/projects/84 Visual Pathway editor v1.0]: Need to comple...")
- 09:52, 12 May 2022 Pascale talk contribs created page Principles for catalytic activity terms (Created page with " ==NAD/NADP cofactors== * Reactions represented with NAD(P) in GO indicates that it is not know whether an enzyme uses NAD or NADP (note that this is different from the IUBMB practice). ** If the cofactor (NAD or NADP) is unknown for a class of reactions, then we only create a single GO term with [NAD(P)]. *** If there are RHEA IDs for both NAD and NADP-dependent reactions, we add these as NARROW xref to the general [NAD(P)]. * If the specific cofactor is known, we c...")
- 08:58, 12 May 2022 Pascale talk contribs created page Projects update meeting 2022-05-12 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: ==Discuss priorities for upcoming period (1 month?)== Proposals by each manager: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# Category: GO Managers Meetings")
- 08:52, 12 May 2022 Pascale talk contribs deleted page GO Projects stand up Calls (content was: "#REDIRECT Project_stand_up_meetings Category:GO Managers Meetings == GO Projects stand up Calls == ''(changed from GO Managers meeting Feb 2021)'' === When === Calls are at 11:00AM Eastern time, '''every Wednesday'''. === How to Join === * Recurring meeting URL: check GO's Google calendar * To join via phone: enter Meeting ID after dialing the Zoom phone number....", and the only contributor was "Pascale" (talk))
- 02:33, 12 May 2022 Pascale talk contribs created page Ontology meeting 2022-05-16 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =NAD/NADP issue= https://github.com/geneontology/go-ontology/issues/23235 GO:0004448 isocitrate dehydrogenase activity is the parent for NAD and NADP versions; in this case it seems the enzymes are specific for either cofactors. I think our guidelines are that GO:0004448 isocitrate dehydrogenase activity should be obsoleted?...")
- 10:30, 10 May 2022 Pascale talk contribs created page Noctua Landing Page (Created page with "= Noctua Landing Page = The Noctua landing page is the portal by which curators can browse or search and filter models. It is also the starting point for curation and where individual GPAD and OWL files for a model can be downloaded. By default, the Noctua landing page displays models by date, descending order, i.e. the most recently edited models are shown at the top of the list. Note that curators must be logged into Noctua to create new models or edit existing...")
- 09:01, 3 May 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-05-02 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === *Possible in-person meeting; still being discussed === Noctua === *Regularly scheduled Noctua outage: **Thursday, May 12th == GO Release Pipeline == * April release? * From Slack #release-pipeline: ontology build failure * Other issues? == AmiGO == == Ontology == == Annotation == * Please remember to keep checking the [http://current.geneontology.org/reports/index.html rep...")
- 03:13, 29 April 2022 Pascale talk contribs created page Projects update meeting 2022-05-04 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Fall GOC meeting== Decide on date, location =Spring GOC meeting= [https://docs.google.com/document/d/1Dv5UsRLfpH0ngjpxui5L2AK0GcK9VO2lrkZok6Qs-Co/edit# Action points] =Project updates= (Update Task Matrix and Wiki project table) =Future topic/project= Seth * What stats do we want to track, what do we need? Thinking grants, official reports, etc....")
- 06:26, 26 April 2022 Pascale talk contribs created page Ontology meeting 2022-05-02 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' ==Annotation review requests instructions== (did not discuss) Detailed procedure here: Annotation_Review_Request * Added links to the procedure in the instructions for obsoletion and for merge ==Debrief GOC meeting== ==Debrief single-step process jambor...")
- 01:58, 20 April 2022 Pascale talk contribs created page GO Central (GOC) QC Procedure (Created page with "GO Central rules are documented here: https://github.com/geneontology/go-site/blob/master/metadata/rules/README.md ===GO rules=== * (Documentation in progress): https://github.com/geneontology/go-site/tree/master/metadata/rules * The QC checks consist of either "filters" or "reports". Filters exclude annotations from the files that the GO consortium generates; reports allow the annotations to be exported, but contributing groups get notified to correct annotations. *...")
- 01:37, 20 April 2022 Pascale talk contribs created page Ontology meeting 2022-04-25 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Discussion = ==GOC meeting April 26-28th== * Agenda: [https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/edit# Draft agenda] * Ontology presentation: ==Annotation review requests instructions== ==Feedback single-step process jamboree& next steps== Category:Meetings Category:Ontology")
- 14:55, 18 April 2022 Mi talk contribs created page 20 Apr 2022 PAINT Conference Call (Created page with " ==Present== '''This meeting was rescheduled from April 6, 2022''' ==Agenda== ===Milestone achieved: completion of PAINT curation of all families with human genes=== ===Prepare for GO meeting=== ===Update PAINT to PANTHER17.0=== Category:PAINT")
- 13:32, 18 April 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-04-19 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Spring 2022 Consortium Meeting === *Virtual *Tuesday April 26th to Thursday April 28th, from 7AM-11AM Pacific (4PM-8PM Europe) *Participants need to register with EventBrite **Invitation went out from Suzi A on Friday, April 1st **Also a link from the [https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/ Agenda, Logistics, Minutes] *Please email Pascale if you have topics for the ag...")
- 20:20, 15 April 2022 Sjcarbon talk contribs created page Projects update meeting 2022-04-20 (Created page with "= Attendees = * Members: * Present: * Regrets: =Future topic/project= * What stats do we want to track, what do we need? Thinking grants, official reports, etc. ** End-of-year summary stats for users, downloads? ** Coming from consideration of log retention (policy) for some systems Category: GO Managers Meetings")
- 08:57, 4 April 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-04-05 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Spring 2022 Consortium Meeting === *Virtual *Tuesday April 26th to Thursday April 28th, from 7AM-11AM Pacific (4PM-8PM Europe) *[https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/ Agenda, Logistics, Minutes] *Please email Pascale if you have topics for the agenda ** On the agenda: Continue goslim_generic discussion: review MF and CC slims, also, a session using the matrix to check...")
- 02:32, 1 April 2022 Pascale talk contribs created page Projects update meeting 2022-04-06 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: David, Pascale, Seth, Suzi, Huaiyu, * Regrets: Chris, Cynthia, Kimberly [https://docs.google.com/document/d/1r3aWGjyz2nXNpyzETPO-ah276HQDc1ClNs57Cm6Nwv0/edit Main tasks - Jan-July 2022] =Announcements= * Preparing GOC meeting: start planning the agenda: https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/edit * Fall meeting in Baltimore?...")
- 01:50, 1 April 2022 Pascale talk contribs created page Ontology meeting 2022-04-04 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' ==Announcements== * GOC meeting April 26-28th, Virtual * [https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/edit# Draft agenda] ==Reminder== Please move your files to the New GO Shared Drive ==Jamboree: [https://github.com/geneontology/go-ontology/projects/26 Single Step BPs]== Category:Me...")
- 12:40, 31 March 2022 Mi talk contribs created page 6 Apr 2022 PAINT Conference Call (Created page with "==Present== ==Agenda== ===Milestone achieved: completion of PAINT curation of all families with human genes=== ===Prepare for GO meeting=== Category:PAINT")
- 03:40, 29 March 2022 Pascale talk contribs created page Projects update meeting 2022-03-30 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: [https://docs.google.com/document/d/1r3aWGjyz2nXNpyzETPO-ah276HQDc1ClNs57Cm6Nwv0/edit Main tasks - Jan-July 2022] =Announcements= * Preparing GOC meeting: start planning the agenda: https://drive.google.com/drive/folders/1Y5DfKpQu4tGxDmJaH-nHDDNkFy5x-w6B == Follow up from last meeting== * [http://wiki.geneontology.org/index.php/Projects_update_meeting_2...")
- 10:15, 28 March 2022 Pascale talk contribs created page Ontology meeting 2022-03-28 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' Peter, Kimberly ==Discussion points== ===Moving the Google drive to a 'Shared' drive=== See details here: https://github.com/geneontology/go-site/issues/1813 Please move the files you own: ===Missing inferences from external ontologies=== see [https://github.com/geneontology/go-ontology/issues/22941 Missing part-of relation...")
- 11:43, 9 March 2022 Ruth.lovering talk contribs uploaded a new version of File:MiRNADecisiontree2020.png
- 08:42, 3 March 2022 Pascale talk contribs deleted page GO Project stand up meeting Template (content was: "* Present: * Regrets: * Managers: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Judy, Paul, Chris = Agenda = == Announcements ==...", and the only contributor was "Pascale" (talk))
- 04:28, 22 February 2022 Pascale talk contribs moved page Ontology meeting 2022-02-21 to Ontology meeting 2022-02-28