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Combined display of all available logs of GO Wiki. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).
- 12:10, 11 April 2024 Pascale talk contribs moved page Ontology meeting 2024-04-15 to Ontology meeting 2024-04-22
- 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...")
- 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...")
- 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...")
- 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...")
- 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.")
- 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))
- 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...")
- 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...")
- 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")
- 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...")
- 15:03, 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...")
- 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...")
- 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...")
- 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...")
- 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")
- 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")
- 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...")
- 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")
- 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...")
- 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...")
- 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 ::...")
- 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...")
- 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...")
- 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...")
- 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?...")
- 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
- 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...")
- 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")
- 10:22, 13 February 2023 Pascale talk contribs created page Ontology meeting 2023-02-13 (Created page with "* '''Group members:''' Pascale, Harold, Raymond, Val, Edith, Peter, Jim, Tanya, Karen, Kimberly, David, Chris, Paul * '''Present:''' Pascale, Harold, Raymond, Val, Edith, Jim, Tanya, Karen, Kimberly, David, Chris, Peter, Paul * '''Regrets: ''' =Announcements= * Harold's last week ! ==GOC consortium== * April 27th-29th, Padua, Italy * If you plan to attend, please register ASAP. geneontology.ticketleap.com/goc2023 password: goc2023 ==Annotation reviews at MGI==...")
- 12:31, 10 February 2023 Pascale talk contribs deleted page Category:Publications (content was: "All GO-related publications from GOC members", and the only contributor was "Cjm" (talk))
- 12:31, 10 February 2023 Pascale talk contribs deleted page Publications, tutorials, talks, posters (content was: "Publications, Talks, Posters 2018 Publications, Talks, Posters 2017 Publications, Talks, Posters 2016 Publications, Talks, Posters 2015 Publications, Talks, Posters 2014 Publications, Talks, Posters 2013 Publications, Talks, Posters 2010-2012 Publications, Talks, Posters 2007-2009 Publications, Talks, Posters 2003-2006 Category:Publications")
- 12:31, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2018 (content was: "Huntley RP, Kramarz B, Sawford T, Umrao Z, Kalea AZ, Acquaah V, Martin MJ, Mayr M, Lovering RC. (2018 Advance publication) [http://rnajournal.cshlp.org/content/early/2018/06/05/rna.065565.118.abstract Expanding the horizons of microRNA bioinformatics]. RNA. Jun 5. doi: 10.1261/rna.065565.118. Lovering RC, Roncaglia P, Howe DG, Laulederkind SJF, Khodiyar VK, Berardini TZ, Tweedie S, Foulger RE, Osumi-Sutherland D, Campbell NH, Huntley RP, Talmud PJ, Blake JA, Breckenridge R, Ri...")
- 12:30, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2017 (content was: "Roncaglia P, van Dam TJP, Christie KR, Nacheva L, Toedt G, Huynen MA, Huntley RP, Gibson TJ, Lomax J. The Gene Ontology of eukaryotic cilia and flagella. Cilia. 2017 6:10. https://doi.org/10.1186/s13630-017-0054-8 Category:Archived")
- 12:28, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2016 (content was: "Category:Archived ==List of papers published by GOC in 2016== Please list all article publications below in chronological order; the most recent publication should appear first. ====Acknowledge funding by GOC NHGRI grant==== * Hill DP, D'Eustachio P, Berardini TZ, Mungall CJ, Renedo N, Blake JA. Modeling biochemical pathways in the gene ontology. Database (Oxford). 2016 Sep 1. PMID 27589964. * Huntley RP, Sitnikov D, Orlic-Milacic M, Balakrishnan R, D'Eustachio P, Gille...")
- 12:26, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2015 (content was: "Category:Publications ==List of papers published by GOC in 2015== Please list all article publications below in chronological order; the most recent publication should appear first. ====Acknowledge funding by GOC NHGRI grant==== * Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Eme...")
- 12:23, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2014 (content was: "Category:Archived ==List of Papers published by GOC in 2014 (Chronologically, most recent first)== * Ascensao JA, Dolan ME, Hill, DP and Blake JA. 2014. Methodology for the inference of gene function from phenotype data. <i>BMC Bioinformatics</i>. 15:405 doi:10.1186/s12859-014-0405-z. * The Gene Ontology Consortium. 2014. Gene Ontology Consortium: Going Forward. ''Nucl. Acids Res.'' Database Issue doi: 10.1093/nar/gku1179. * Dietze H, Berardini TZ, Foulger RE, Hill DP,...")
- 12:18, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2013 (content was: "Category:Archived == Journal Publications == Blake JA . 2013 Ten Quick Tips for Using the Gene Ontology. PLoS Comput Biol 9(11): e1003343. doi:10.1371/journal.pcbi.1003343. Aranguren ME, Fernández-Breis JT, Mungall C, Antezana E, González AR, & Wilkinson MD. 2013. OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows. Journal of biomedical semantics, 4(1), 2. [http://www.ncbi.nlm.nih.gov/pubmed/23286517 PMID:23286517] Assel...")
- 12:16, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2010-2012 (content was: "Note there is now a GO group on Mendeley: http://www.mendeley.com/groups/1250271/gene-ontology-consortium/papers/ Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members during 2010 reporting year. === Publications (alphabetical) === * Dutkowski J, Kramer M, Surma MA, Balakrishnan R, Cherry JM, Krogan NJ, Ideker T. A gene ontology inferred from molecular networks. Nat Biotechnol. 2012 Dec 16. doi: 10....")
- 12:13, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2010- (content was: "#REDIRECT Publications, Talks, Posters 2010-2011", and the only contributor was "Jl242" (talk))
- 12:13, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2010-2011 (content was: "#REDIRECT Publications, Talks, Posters 2010-2012", and the only contributor was "Cjm" (talk))
- 11:56, 10 February 2023 Pascale talk contribs deleted page GO publications 2009 (content was: "Category:Publications Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members during 2009 reporting year. === 2009 Publications === #Alterovitz, G., Xiang, M., Hill, D., Lomax, J., Liu, J., Mungall, C., Harris, M., Dolan, M.E., Blake, J.A., Ramoni, M.F. Engineering Biomedical Ontologies: The Gene Ontology [Accepted, In Press, Nature Biotechnology] #Barrell D., Dimmer E., Huntley R.P., Binns D., O'...")
- 11:43, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2007-2009 (content was: "'''GO publications, Tutorials and Workshops, Presentations, and Posters'''<br> '''For the GO grant HG –02273'''<br> '''2007 – 2009''' <br> Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members. ==2009== GO_2009_Publications,_Tutorials_&_Workshops,_Presentations,_Posters,_and_Resources ==2008== ===2008 Publications === Altman, R., Bergman, C., Blake, J.A., Blaschke, C., Cohen, A., Gann...")
- 11:39, 10 February 2023 Pascale talk contribs deleted page Publications, Talks, Posters 2003-2006 (content was: "=Moved to [https://docs.google.com/document/d/1w8nR5llrexyqCKk3NTlj3v3s7gKBA-DPtAT3LiIe5jo/edit#heading=h.ol811igyzk6h Google drive]= '''GO publications, Tutorials and Workshops, Presentations, and Posters'''<br> '''For the GO grant HG –02273'''<br> '''2003 – 2006''' <br> Here we list publications, tutorials, talks and posters focused primarily on the GO and use of the GO, and presented by GOC members. ==2006== ===2006 Publications === Rubin, D.L., Lewis, S.E., M...")
- 10:59, 10 February 2023 Pascale talk contribs deleted page Category:Pages with broken file links (content was: "", and the only contributor was "Pascale" (talk))
- 10:57, 10 February 2023 Pascale talk contribs created page Category:Pages with broken file links (Created blank page)
- 10:57, 10 February 2023 Pascale talk contribs deleted page Category:Metrics (content was: "Pages describing metrics for ontology development", and the only contributor was "Midori" (talk))
- 10:56, 10 February 2023 Pascale talk contribs deleted page Taxon Trigger File Metrics (content was: "For more details see Taxon_Main_Page. This is a list of the stages that we need to complete in the implementation of the taxon trigger file for the project to be considered complete. Where blockages have been hit, these are noted. ===In order:=== * Figure out the theory - '''Done''' * Agree the theory with the GO Consortium - '''Done''' * Agree the theory of Union_of terms with Consortium - '''Not Done''' * Set up the files in scratch and make filtering perl scripts - '...")
- 10:53, 10 February 2023 Pascale talk contribs deleted page Category:Timelines (content was: "Timelines associated with various projects in GO.", and the only contributor was "Gail" (talk))
- 10:51, 10 February 2023 Pascale talk contribs deleted page Cross Product Timeline (content was: "Category:Archived * See also Cross Product Guide == Blessing of mature XP files == Mature xps currently live in scratch dir: cvs/go/scratch/xps biological_process_xp_cellular_component.obo biological_process_xp_cell.obo cvs/go/scratch/regulates_xp_live We will officially bless these and move them out of scratch into go/ontology/editors/xps/ This will happen after the RO meeting ('''May 2008''') Note these will still be external to the main GO file....")
- 10:47, 10 February 2023 Pascale talk contribs deleted page OBO-Edit Release Timeline (content was: "Category:Archived The OBO-Edit calendar tracks releases and working group meeting dates. It's on google and open to the public domain. *[http://www.google.com/calendar/embed?src=cDN1bXNkOG45bDMyYW5kbGR1M2xqcjNuazhAZ3JvdXAuY2FsZW5kYXIuZ29vZ2xlLmNvbQ View the OBO-Edit calendar] = Projected Dates = Refer calendar - If the projected dates are not in the future the calendar has not been able to refresh - access web google calendar externally. [http://wiki.geneontology.org/i...")
- 10:47, 10 February 2023 Pascale talk contribs deleted page Category:To be reviewed (content was: "Pages that David, Kimberly and Pascale have identified as needing review.", and the only contributor was "Pascale" (talk))
- 10:41, 10 February 2023 Pascale talk contribs deleted page Tracker wishlist (content was: "Category:Archived ==Requirements for a GO wiki/tracker system== ===Our high priorities:=== *General **Calendar / time lines / to do lists to show what curators have planned **Create personal pages which show what someone is working on *Tracker **Add user configurable categories to an entry, e.g. how easy it is to complete, whether it would need people to look at annotations, which interest groups it may affect **Be able to configure the order of comments, perhaps with a hy...")
- 10:39, 10 February 2023 Pascale talk contribs deleted page Category:Pages with broken file links (content was: "", and the only contributor was "Pascale" (talk))
- 10:38, 10 February 2023 Pascale talk contribs created page Category:Pages with broken file links (Created blank page)
- 10:10, 10 February 2023 Pascale talk contribs created page Category:Ontology Relations (Created page with "This page lists the relations in the gene ontology.")
- 10:09, 10 February 2023 Pascale talk contribs deleted page Category:Logos (content was: "Miscellaneous logos. Category exists to make it easy to find logos that have already been uploaded to this site. However, most logos that have been uploaded were uploaded before this category was created.", and the only contributor was "Clements" (talk))
- 10:03, 10 February 2023 Pascale talk contribs deleted page Browse help page (content was: "<h2>Browsing the Ontology</h2> <p> In AmiGO, the ontology is presented as a tree of terms. An example of part of a tree is displayed below: </p> <br> Image:Organelle.jpg <br> <p> The level of a term is represented by its indentation within the tree, with general terms being less indented than more specific terms. In the above image, you can see that "extracellular organelle" is a child (less specific) term of "organelle", and a sibling term of "intracellular organelle". Eac...")
- 10:00, 10 February 2023 Pascale talk contribs deleted page Regular Expressions accepted by UniProt for use in the 'with' field (content was: "Category:Archived =This information is now in https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml= { prefix => 'UniProt(?:KB)?', id => '[A-Z][0-9][A-Z0-9]{3}[0-9]((-([0-9]+)|:PRO_[0-9]{10}))?' }, { prefix => 'CGD', id => '(CAL|CAF)[0-9]{7}' }, { prefix => 'SGD', id => 'S[0-9]{9}' }, { prefix => 'dictyBase', id => 'DDB_G[0-9]{7}' }, { prefix => 'FB', id => 'FBgn[0-9]{7}' }, { prefix => 'GeneDB_Spombe|PomBase', id =>...")
- 09:58, 10 February 2023 Pascale talk contribs deleted page Category:ZFIN (content was: "#REDIRECT Category:Reports:ZFIN", and the only contributor was "Pascale" (talk))
- 09:57, 10 February 2023 Pascale talk contribs deleted page Category:WormBase (content was: "#REDIRECT Category:Reports:WormBase", and the only contributor was "Pascale" (talk))
- 09:57, 10 February 2023 Pascale talk contribs deleted page Category:Reports:WormBase (content was: "#REDIRECT Category:Reports - WormBase", and the only contributor was "Pascale" (talk))
- 09:56, 10 February 2023 Pascale talk contribs deleted page Category:Sequence Ontology (content was: "#REDIRECT Category:Reports - Sequence Ontology", and the only contributor was "Pascale" (talk))
- 09:56, 10 February 2023 Pascale talk contribs deleted page Category:Reports:ZFIN (content was: "#REDIRECT Category:Reports - ZFIN", and the only contributor was "Pascale" (talk))
- 09:55, 10 February 2023 Pascale talk contribs deleted page Category:SGD (content was: "#REDIRECT Category:Reports - SGD", and the only contributor was "Pascale" (talk))
- 09:55, 10 February 2023 Pascale talk contribs deleted page Category:TAIR (content was: "#REDIRECT Category:Reports - TAIR", and the only contributor was "Pascale" (talk))
- 09:43, 10 February 2023 Pascale talk contribs deleted page ID Mapping Requirements (content was: "== Requirements == Users frequently want to query GO annotations using a variety of ID-spaces. This includes queries of the single-gene variety, as well as bulk queries and tools such as map2slim and term enrichment. Examples: * Find GO annotations for UniProt ID P000001 * View (as HTML) all annotations for a small batch of Ensembl Protein IDs * Download all annotations (tab-del) for a large batch of genbank GI numbers * Perform term enrichment for a collection of genes iden...")
- 09:42, 10 February 2023 Pascale talk contribs deleted page Gp2rna file (content was: "==What is a gp2RNA file== A gp2rna file is a tab-delimited file that provides mapping between the MOD database object IDs and ncRNA gene/sequence IDs. Contribution of this file is a new requirement (starting mm/2012). ==Need for gp2RNA file== * This file will be used to download sequences of ncRNAs from NCBI, search in AmiGO and for book keeping/tracking annotation, removing redundant annotations etc. * This file is required from all GO groups who annotate to ncRNAs. * If y...")
- 09:42, 10 February 2023 Pascale talk contribs deleted page Gp2protein file (content was: "==What is a gp2protein file?== A gp2protein file is a tab-delimited file that provides a mapping between database object IDs and protein sequence IDs. Files contributed from annotation groups are available [http://www.geneontology.org/gp2protein here] ==Need for gp2protein file== * Used for downloading sequences from UniProt/NCBI. These sequences are used for AmiGO BLAST and for phylogenetic inferencing (PAINT) * The sequence IDs (UniProt or NCBI) can be used in AmiGO to s...")
- 09:41, 10 February 2023 Pascale talk contribs deleted page Gp2protein (content was: "For the RefG project it is critical we can build complete protein sequence sets for homology and phylogenetic analysis. In theory there should be a deterministic mapping from the gene in col2 of the GAF to the gp2protein mappings to a collection of FASTA files. In practice this is difficult due to some outstanding issues. The gp2protein files are located in cvs in the [http://www.geneontology.org/gp2protein/ go/gp2protein] directory. See the [http://www.geneontology.org/gp...")
- 09:41, 10 February 2023 Pascale talk contribs deleted page Gp unlocalized file (content was: "If your database supplies gene identifiers that have been manually curated from the literature, but where no sequence or genomic location is known (such genes have been variously described as 'unlocalised genes', 'single heritable traits' or 'phenotypic orphans'), then you should additionally supply a complete gp_unlocalized_file. This file should contain all the non-genome localized identifiers available in your database, including those not annotated to GO. Category:A...")
- 09:35, 10 February 2023 Pascale talk contribs deleted page Implementation (content was: " Category:Archived - Ontology == 13rd November, 2007 == I have solved problems about almost all child terms of "response to drug" term. The changes are already in the lived file.<br> I have asked to ChEBI people (Kirill) if it would be possible to have these substance in ChEBI molecular structure ontology.We are waiting for that! List of substances: METHOTREXATE<br> CHEBI:44185 unclassified<br> CLOMIPRAMINE<br> tricyclic antidepressant<br> KEGG ID C06918<br> CAS...")
- 09:34, 10 February 2023 Pascale talk contribs deleted page DEPRECATED: Response to drug (content was: " Category:Archived - Ontology Erika Feltrin presented her plan (below) for the response to drug terms at a skype conference call in late October. Original SourceForge item: [https://sourceforge.net/tracker/?func=detail&atid=440764&aid=1494526&group_id=36855| SF 1494526] Description of the project<br> Implementation")
- 09:34, 10 February 2023 Pascale talk contribs deleted page Description of the project (content was: " Category:Archived - Ontology == CASE OF "RESPONSE TO ORGANIC SUBSTANCE" GO: 0010033 == In the ChEBI ontology there is "organic molecular compound" CHEBI:25700, defined as a molecular entity that contain carbon and its synonyms are: organic compounds and organic entity. In the GO the definition of "response to organic substance" GO:0010033 term is: a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene exp...")
- 09:23, 10 February 2023 Pascale talk contribs created page Category:Archived - Ontology (Created blank page)
- 09:21, 10 February 2023 Pascale talk contribs deleted page Ontology QC Metrics (content was: "Category:Ontology ===The reasoner and regulation terms (2008)=== ====Checks==== *Identified inconsistencies between the ‘regulates’ hierarchy and the rest of biological process *Identified missing links *Identified more specific and complete is_a parentage for ‘regulation’ terms. ====Stats from first round==== *Terms: **279 reviewed. **40 added. **5 term merges took place. **207 names changed. **272 general dbxrefs were added. *Definitions: **40 added. **45 improved...")
- 09:21, 10 February 2023 Pascale talk contribs deleted page Ontology Quality Control (content was: "This page documents the quality control measures used to flag (or, ideally, avoid) various types of errors and inconsistencies in GO. ==OBO-Edit verification system== (NOTE: need links to O-E documentation, but the "Ontology Verification" section is missing from the online version at http://www.oboedit.org/docs/index.html) *built-in checks - these are run manually or during editing **text checks on comments, definitions, names and synonyms **name redundancy check **dbxref che...")
- 09:19, 10 February 2023 Pascale talk contribs deleted page Relationship type requirements (content was: "Category:Cross Products Category:Relations This page summarises the requirements for relations used in future versions of the GO, for example in Category:Cross Products Some of these relations already exist in [http://www.obofoundry.org/ro/RO]. Others are pending, in [http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo.html ro_proposed] (see description...", and the only contributor was "Cjm" (talk))
- 11:47, 9 February 2023 Pascale talk contribs created page Ontology editors' manual (Created page with " = Documentation= Useful reference: [https://oboacademy.github.io/obook/ On becoming an OBO Semantic Engineer], by James Overton, Becky Jackson, Nicole Vasilevsky, Nicolas Matentzoglu, and Shawn Tan. This book provides best practices as recommended by OBO Foundry. Note that some parts of this book may be more general than the documentation presented in this wiki. ==Protégé 5.5 setup== ==Installing and Using git== ==Ontology Edit...")
- 10:39, 9 February 2023 Pascale talk contribs moved page GeneProduct to GOTerm Relation:enables to Enables over redirect
- 10:39, 9 February 2023 Pascale talk contribs deleted redirect Enables by overwriting (Deleted to make way for move from "GeneProduct to GOTerm Relation:enables")
- 10:36, 9 February 2023 Pascale talk contribs deleted page Category:GO-CAM Documentation (content was: "GO-CAM Documentation category", and the only contributor was "Pascale" (talk))
- 10:35, 9 February 2023 Pascale talk contribs deleted page GOA FAQ (content was: "==What is GOA?== The GOA project aims to provide high-quality Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB) and International Protein Index (IPI), and is a central dataset for other major multi-species databases; such as Ensembl and NCBI. GOA has been a member of the GO Consortium <http://www.geneontology.org/> since 2001, and is responsible for the integration and release of GO annotations to the human, chicken and cow proteomes. In 2006...")
- 10:35, 9 February 2023 Pascale talk contribs deleted page Category:Defunct (content was: "", and the only contributor was "Pascale" (talk))
- 10:33, 9 February 2023 Pascale talk contribs created page Category:Defunct (Created blank page)
- 10:32, 9 February 2023 Pascale talk contribs deleted page Category:Cell Cycle (content was: "All things Cell Cycle.", and the only contributor was "Gail" (talk))
- 10:27, 9 February 2023 Pascale talk contribs moved page Part 3 to Regulation Worksheet - Part 3
- 10:26, 9 February 2023 Pascale talk contribs moved page Part 2 to Regulation Worksheet - Part 2
- 10:26, 9 February 2023 Pascale talk contribs moved page Part 1 to Regulation Worksheet - Part 1
- 10:25, 9 February 2023 Pascale talk contribs moved page Regulates Documentation to Regulates Documentation (2007)
- 10:20, 9 February 2023 Pascale talk contribs created page Category:Meeting Minutes - Regulation (Created blank page)
- 10:18, 9 February 2023 Pascale talk contribs deleted page Regulation of molecular function (content was: "See [ftp://ftp.geneontology.org/pub/go/scratch/regulates_xp_live/go_reglive_withPosNeg_withPF.obo go_reglive_withPosNeg_withPF.obo] we had to remove the P-F links when making this live; they will be reinstated eventually Category:Deprecated")
- 10:16, 9 February 2023 Pascale talk contribs deleted page Regulates icons in OBO-Edit (content was: "Category:Deprecated ==Arrow Icons== Arrow icons, at 30px Image:Regs-all-arrows.gif Arrow icons at the size they would appear in AmiGO Image:Regulates-arrows.gif Arrow icons as they appear in OBO-Edit (Note that this was made using the gifs as OBO-Edit would not accept the svgs) Image:blackarrow.png ==Triangle Icons== Triangle icons, at 30px Image:Regs-all-triangles.gif Triangle icons at the size they would appear in AmiGO Image:Regulates-triang...")
- 10:15, 9 February 2023 Pascale talk contribs deleted page Transitive over part of documentation (content was: "Category:Deprecated File to refer to: http://gocwiki.geneontology.org/index.php/Image:Mp-asserted.doc mp-asserted.doc Email thread: Chris, Tanya and I have started to go through these here is one that seems funny: GO:0000706 "meiotic DNA double-strand break processing" PART_OF GO:0006311 "meiotic gene conversion" GO:0000706 "meiotic DNA double-strand break processing" PART_OF GO:0007131 "meiotic recombination" The issue here GO:0000706 is both a part of GO:000631...")
- 10:07, 9 February 2023 Pascale talk contribs created page Is small molecule inhibitor of (Created page with "=WIP= == Overview and Scope of Use== == Annotation Usage Guidelines== *'''What to capture''' * '''What not to capture''' == Examples == ==Ontology Usage Guidelines== This relation is not used in the ontology. == Cross Reference to the Relation Ontology (RO) == [http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0012006 is small molecule inhibitor of] == Review Status == Last reviewed: February 9, 2023 Reviewed by: Pascale Gaudet [http:...")
- 10:06, 9 February 2023 Pascale talk contribs created page Is small molecule activator of (Created page with "== Overview and Scope of Use== == Annotation Usage Guidelines== *'''What to capture''' * '''What not to capture''' == Examples == ==Ontology Usage Guidelines== This relation is not used in the ontology. == Cross Reference to the Relation Ontology (RO) == [http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/obo/RO_0012005 is small molecule activator of] == Review Status == Last reviewed: February 9, 2023 Reviewed by: Pascale Gaudet [http://wiki...")
- 09:55, 9 February 2023 Pascale talk contribs created page Causally upstream of or within (Created page with "== Overview and Scope of Use == * This relation shoud not be used for annotation, either in standard annotation extensions or in GO-CAMs. *The 'causally upstream of of or within' relation is used to relate GO Biological Processes (BP) and/or GO Molecular Functions (MF) when: **the mechanism that relates the upstream process (BP or MF) to the downstream process (BP or MF) is not known **it is not known whether the activities of the gene products in the upstream process oc...")
- 09:39, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:part of to Part of over redirect
- 09:39, 9 February 2023 Pascale talk contribs deleted redirect Part of by overwriting (Deleted to make way for move from "Annotation Extension Relation:part of")
- 09:37, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:occurs in to Occurs in over redirect
- 09:37, 9 February 2023 Pascale talk contribs deleted redirect Occurs in by overwriting (Deleted to make way for move from "Annotation Extension Relation:occurs in")
- 09:33, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:has output to Has output over redirect
- 09:33, 9 February 2023 Pascale talk contribs deleted redirect Has output by overwriting (Deleted to make way for move from "Annotation Extension Relation:has output")
- 09:29, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:has input to Has input over redirect
- 09:29, 9 February 2023 Pascale talk contribs deleted redirect Has input by overwriting (Deleted to make way for move from "Annotation Extension Relation:has input")
- 09:24, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:has participant to Has participant
- 09:20, 9 February 2023 Pascale talk contribs deleted page Has function in location (content was: "Category:Deprecated '''THIS RELATION WAS NOT IMPLEMENTED''' <pre style="color:#808080"> See [http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo.html#OBO_REL:has_function_in has_function_in] in ro_proposed </pre>")
- 09:19, 9 February 2023 Pascale talk contribs deleted page Has function during (content was: "Category:Deprecated THIS RELATION WAS NOT IMPLEMENTED <pre style="color:#808080"> See [http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo.html#OBO_REL:has_function_during has_function_during] in ro_proposed </pre>")
- 09:19, 9 February 2023 Pascale talk contribs deleted page Has function (content was: "Category:Deprecated '''THIS RELATION WAS NOT IMPLEMENTED''' <pre style="color:#808080"> See [http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo.html#OBO_REL:has_function has_function] in ro_proposed </pre>")
- 09:17, 9 February 2023 Pascale talk contribs deleted page Has participant (content was: "#REDIRECT Annotation Extension Relation:has participant", and the only contributor was "Huntley" (talk))
- 09:13, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:results in formation of to Results in formation of
- 09:10, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:exists during to Exists during
- 09:10, 9 February 2023 Pascale talk contribs deleted page Exists during (content was: "#REDIRECT Annotation Extension Relation:exists during", and the only contributor was "Huntley" (talk))
- 09:08, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:acts on population of to Acts on population of
- 09:03, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:happens during to Happens during
- 09:03, 9 February 2023 Pascale talk contribs deleted page Happens during (content was: "#REDIRECT Annotation Extension Relation:happens during", and the only contributor was "Huntley" (talk))
- 09:01, 9 February 2023 Pascale talk contribs moved page Annotation Extension Relation:causally upstream of to Causally upstream of
- 08:53, 9 February 2023 Pascale talk contribs moved page Causally upstream of negative effect to Causally upstream of, negative effect
- 07:16, 9 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:in presence of (content was: "#REDIRECT Annotation '''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== Identifies a chemical, gene product or complex in the presence of which an ontology term is observed to apply to the annotated gene product. ==Child terms== * None. ==Scope of use== ===Domain=== BFO:0000001 ! entity (Biological Process, Molecular Function or Cellular Component) ===Range=== ENTITY_UNION:0000005 ! chemical, gene product, or complex === DEPRECATIO...")
- 07:07, 9 February 2023 Pascale talk contribs created page Located in (Created page with " == Overview == The 'located' relation is used to relate a gene or gene product to a GO Cellular Component, specifically a 'cellular anatomical anatomy' or 'virion component', in which a gene product has been detected. Note that 'is active in' is not used for relating gene products to a 'protein-containing complex'; those associations use 'part of'. == Examples of Usage == == Relations Ontology == [http://www.ontobee.org/ontology/RO?iri=http://purl.obolibrary.org/ob...")
- 06:13, 9 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:occurs at (content was: "#REDIRECT Annotation_Extension_Relation:occurs_in '''THIS RELATION IS DEPRECATED''' Curators should use [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:occurs_in occurs in] to capture locations in which Molecular Functions occurs <pre style="color:#808080"> ==Definition== Identifies the Cellular Component or sequence feature at which the Molecular Function or Biological Process is executed. ==Child terms== * None. ==Scope of use== ===Domain=...")
- 06:13, 9 February 2023 Pascale talk contribs undeleted page Annotation Extension Relation:occurs at (22 revisions)
- 06:12, 9 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:occurs at (content was: "#REDIRECT Annotation_Extension_Relation:occurs_in '''THIS RELATION IS DEPRECATED''' Curators should use [http://wiki.geneontology.org/index.php/Annotation_Extension_Relation:occurs_in occurs in] to capture locations in which Molecular Functions occurs <pre style="color:#808080"> ==Definition== Identifies the Cellular Component or sequence feature at which the Molecular Function or Biological Process is executed. ==Child terms== * None. ==Scope of use== ===Domain=...")
- 06:11, 9 February 2023 Pascale talk contribs deleted page Deprecated relations (content was: "The following relations are not supported in the ontology, in GO-CAM or in Protein2GO anymore: *occurs_at: use occurs_in instead * dependent_on * has_agent * has_direct_input * in_absence_of * in_presence_of * independent_of * localization_dependent_on * modified_by * not_during * not_ex...", and the only contributor was "Pascale" (talk))
- 06:11, 9 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:has agent (content was: "#REDIRECT: Deprecated_relations =Note that this relation has been deprecated= ==Definition== The relationship that links an entity with a Molecular Function or Biological Process in which the entity participates in the Function or Process by serving as the continuant that is responsible for the execution of the Function or Process. ==Comment== ==Synonyms== has_active_participant ==Child terms== * None ==Scope of use== ===Domain=== BFO:0000007 ! process (Biologi...")
- 10:05, 8 February 2023 Pascale talk contribs created page File:Removes input-2.png
- 10:05, 8 February 2023 Pascale talk contribs uploaded File:Removes input-2.png
- 09:42, 8 February 2023 Pascale talk contribs created page File:Removes input.png
- 09:42, 8 February 2023 Pascale talk contribs uploaded File:Removes input.png
- 06:00, 8 February 2023 Pascale talk contribs created page File:Provides input.png
- 06:00, 8 February 2023 Pascale talk contribs uploaded File:Provides input.png
- 05:49, 8 February 2023 Pascale talk contribs moved page Directly provides input for to Provides input for
- 13:06, 7 February 2023 Pascale talk contribs created page File:Indirect neg.png
- 13:06, 7 February 2023 Pascale talk contribs uploaded File:Indirect neg.png
- 13:02, 7 February 2023 Pascale talk contribs created page File:Indirect pos.png
- 13:02, 7 February 2023 Pascale talk contribs uploaded File:Indirect pos.png
- 12:49, 7 February 2023 Pascale talk contribs deleted page Annotation Cross Products (Retired) (content was: "#REDIRECT:Annotation <span style ="color:red">'''Please note, this page no longer contains the primary documenation for the annotation extension field. Information here is being moved to the main Annotation Extension wiki page, and supporting pages.'''</span> <strike>'''NB: Annotation cross-products are now referred to as annotation extensions''' Each GO annotation pairs a si...", and the only contributor was "Cjm" (talk))
- 12:49, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:requires target sequence feature (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== Identifies a specific sequence feature required in the interacting gene product to enable the cellular component location or occurence of the function or process ==Child terms== * None. ==Scope of use== ===Domain=== BFO:0000001 ! entity (Biological Process, Molecular Function or Cellular Component) ===Range=== SO:0000110 ! sequence feature ==Annotation Extension Usage Examples== ---- -...")
- 12:48, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:requires substance (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== The annotated gene product participates in a Biological Process or executes a Molecular Function only in presence of a substance ==Child terms== None ==Scope of use== ===Domain=== BFO:0000007 ! process (Biological Process or Molecular Function) ===Range=== CHEBI:24431 ! chemical entity === DEPRECATION WARNING === The GO editors have agreed that this relation should be deprecated. The re...")
- 12:48, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:requires sequence feature (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== A sequence feature, such as a protein domain or motif, of the annotated gene product required for its participation in the Molecular Function or Biological Process. ==Comment== Strictly speaking, these fall outside the scope of GO, even with extended annotations. ==Synonym== requires_feature (BROAD) ==Child terms== * None. ==Scope of use== === DEPRECATION WARNING === The GO editors have ag...")
- 12:48, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:requires modification (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== The annotated gene product must be modified as described by the annotation extension to participate in molecular function or biological process. ==Comment== Note this relation is not intended for use in GO annotation. Discussion about using PR ID in column 17 instead; if we agree on that, this relation will be made obsolete. ==Child terms== * None. ==Scope of use== ===Domain=== BFO:0000007 !...")
- 12:48, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:requires localization (content was: "'''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== The annotated gene product participates in the Biological Process only if the Biological Process is located at the Cellular Component. ==Synonym== dependent_on_localization (EXACT) ==Child terms== * None. ==Scope of use== ===Domain=== GO:0008150 ! biological_process ===Range=== GO:0005575 ! cellular component ==Annotation Extension Usage Examples== ---- </pre> Back to [http://wiki.gen...")
- 12:47, 7 February 2023 Pascale talk contribs deleted page Annotation Extension Relation:localization dependent on (content was: " '''THIS RELATION IS DEPRECATED''' <pre style="color:#808080"> ==Definition== Identifies a requirement under which the gene product is located at the specified cellular component. ==Child terms== * None ==Scope of use== === DEPRECATION WARNING === The GO editors have agreed that this relation should be deprecated. The relation does not extend the meaning of the GO term, as annotation relations are meant to, but instead specifies conditions under which the annotation i...")
- 12:25, 7 February 2023 Pascale talk contribs deleted page Regulation (content was: "=Regulation= Note that some of this content is deprecated Biological regulation is defined as any process that modulates the frequency, rate or extent of any biological process, quality or function. =The regulates relation= In addition to terms, the ontology uses the regulates relationship means that the term is a process that modulates its parent process. For example, regulation of transcription regulates transcription. The regulation of a process is not a part of the...")
- 10:10, 7 February 2023 Pascale talk contribs created page File:Gef.png
- 10:10, 7 February 2023 Pascale talk contribs uploaded File:Gef.png
- 10:06, 7 February 2023 Pascale talk contribs created page File:Mapk inhibitor.png