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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).
- 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
- 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...")
- 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")
- 11:54, 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...")
- 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")
- 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...")
- 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...")
- 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....")
- 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")
- 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.")
- 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...")
- 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
- 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")
- 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
- 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")
- 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...")
- 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")
- 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...")
- 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...")
- 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...")
- 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...")