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Logs
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  • 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...")
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