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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).
- 00:59, 24 April 2024 Pascale talk contribs created page Ontology meeting 2024-04-29 (Created page with "* '''Group members:''' Pascale, Raymond, Val, Jim, Tanya, Li, Kimberly, Peter, Chris, Paul * '''Present: ''' Pascale, Raymond, Val, Jim, Tanya, Li, Kimberly, Peter, Chris, Paul * '''Regrets:''' Kimberly ==Update on Guidelines for definition defxrefs== '''Review Proposal''': https://github.com/geneontology/go-ontology/issues/27568#issuecomment-2067504245 ==Complicated EC mapping ticket - GO:0103111 D-glucosamine PTS permease activity== https://github.com/geneontology/g...")
- 17:57, 19 April 2024 Pascale talk contribs deleted page AmiGO 2 Manual: Linking (content was: "See newer documentation on https://geneontology.org/docs/faq/ AmiGO 2 now offers a stable set of URLs for linking. This page contains the supported methods for linking into AmiGO 2. Users may also be interested in some of the more RESTy aspects of AmiGO 2 or the possibility of incorporating the widgets and int...", and the only contributor was "Sjcarbon" (talk))
- 11:27, 19 April 2024 Pascale talk contribs created page Projects update meeting 2024-04-24 (Created page with "= Attendees = * Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia * Present: * Regrets: ==GO meeting== * Registration 'closed' * Monday: users meeting: https://docs.google.com/document/d/1sIamECzTS5IMOy4GeldzWXdawnmOLvT9s5vClMAs3Bo/edit * Friday: managers meeting * Draft agenda: https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.2jptrbvdxk9r ==GO calls: reduced frequency== * Managers: twice monthly (un...")
- 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...")