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Logs
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  • 09:46, 28 June 2022 Vanaukenk talk contribs created page Projects update meeting 2022-06-29 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: == Ongoing work updates == ===Release/snapshop update=== New release started ==SOP for project management== https://docs.google.com/document/d/1yWU8xy-lK34p6bSp2EDlTvonbbEr6mCzN2mdLhjNXv0/edit# === Adding SO terms as valid range for 'occurs in' annotation extension === * Curators would like to be able to specify chromosomal regions where MFs occur * Right now, SO...")
  • 10:57, 22 June 2022 Cjm talk contribs created page Projects update meeting 2022-07-20 (Created page with " Paper planning: Chris and Nomi")
  • 07:42, 20 June 2022 Pascale talk contribs created page Ontology meeting 2022-06-27 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= ==Protein processing & specificity (Raymond, Helen)== https://github.com/geneontology/go-ontology/issues/23378 see also notes from last call: Ontology_meeting_2022-06-6 ==Glycosylation ontology== Email from Alex Diehl Hi Chris, Darren, and Pascale, Over the past year or so I worked with T...")
  • 09:16, 16 June 2022 Pascale talk contribs created page File:Activity unit.jpg
  • 09:16, 16 June 2022 Pascale talk contribs uploaded File:Activity unit.jpg
  • 08:44, 16 June 2022 Pascale talk contribs created page Category:Reports - Sequence Ontology (Created page with "Reports - sequence ontology")
  • 08:44, 16 June 2022 Pascale talk contribs deleted page Category:Software Progress (content was: "A collection of software pages that can show visible signs of progress (as opposed to design documents, schema, rationals, etc.).", and the only contributor was "Sjcarbon" (talk))
  • 08:41, 16 June 2022 Pascale talk contribs deleted page Category:Reports - Sequence Ontology (content was: "About the Sequence Ontology (SO).")
  • 08:38, 16 June 2022 Pascale talk contribs deleted page Category:GO News (content was: "Contains links to GO News information.", and the only contributor was "Gail" (talk))
  • 08:38, 16 June 2022 Pascale talk contribs deleted page Category:GAF (content was: "Category:File Format GAF is an acronym for ''Gene Association File'', a file format "where each line represents a single link between a gene product (protein, gene, transcript, etc.) and a GO term". See the [http://www.geneontology.org/GO.format.annotation.shtml formal specification] for more.")
  • 08:35, 16 June 2022 Pascale talk contribs deleted page GO-CAM (content was: "Category:GO-CAM == Causal Activity Models == * GO-CAM Documentation == Noctua == * http://noctua.geneontology.org * Noctua")
  • 08:35, 16 June 2022 Pascale talk contribs deleted page GO-CAM Documentation (content was: "Category:GO-CAM")
  • 08:34, 16 June 2022 Pascale talk contribs created page Category:GO-CAM Documentation (Created page with "GO-CAM Documentation category")
  • 05:07, 10 June 2022 Pascale talk contribs created page Ontology meeting 2022-06-20 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= * Protein processing & specificity (Raymond): https://github.com/geneontology/go-ontology/issues/23378 ===For a future call=== * Antiporters & specificity (Pascale): https://github.com/geneontology/go-ontology/issues/23374 * Antiporters reorganization: https://docs.google.com/presentation/d/11-...")
  • 06:32, 8 June 2022 Pascale talk contribs created page Projects update meeting 2022-06-22 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: =Today's meeting is to establish the next medium (~6 months) and short term (1-2 months) priorities= ==Potential priorities short list== https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit#heading=h.nntgv5th4cph Category: GO Managers Meetings")
  • 16:25, 6 June 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-06-21 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === *Possible in-person meeting; location and dates still TBD === Noctua === *Regularly scheduled Noctua outage: **Thursday, June 23rd == GO Release Pipeline == * June release == AmiGO == == Ontology == === Membrane CC Terms === *Proposal to obsolete and reorganize CC ontology for membrane annotations ** Capturing membrane protein topology will no longer be under the purview o...")
  • 14:20, 31 May 2022 Pascale talk contribs created page Projects update meeting 2022-06-08 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: =Today's meeting is to establish the next medium (~6 months) and short term (1-2 months) priorities= ==Potential priorities short list== https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit#heading=h.nntgv5th4cph Category: GO Managers Meetings")
  • 11:42, 31 May 2022 Pascale talk contribs created page Projects update meeting 2022-06-01 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: =Today's meeting is to establish the next medium term and short term priorities= ==Potential priorities short list== https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit#heading=h.nntgv5th4cph ==Task Matrix== [https://docs.google.com/document/d/1r3aWGjyz2nXNpyzETPO-ah276HQDc1ClNs57Cm6Nwv0/edit Main tasks - Jan-July 2022] == Current...")
  • 09:57, 31 May 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-06-07 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === *Possible in-person meeting; location and dates still TBD === Noctua === *Regularly scheduled Noctua outage: **Thursday, May 26th == GO Release Pipeline == * May release went out Friday, 2022-05-20 == AmiGO == == Ontology == === Non-catalytic Molecular Functions === [https://wiki.geneontology.org/Non-catalytic_Molecular_Functions List and Definitions] === Membrane CC Terms...")
  • 02:03, 25 May 2022 Pascale talk contribs created page Ontology meeting 2022-06-6 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= * Antiporters (Pascale) https://github.com/geneontology/go-ontology/issues/23374 *User requests: **[https://github.com/geneontology/go-ontology/issues/23268 proteinogenic amino acid biosynthesis] and [https://github.com/geneontology/go-ontology/issues/23269 non-proteinogenic amino acid biosynthe...")
  • 02:23, 24 May 2022 Pascale talk contribs created page Projects update meeting 2022-05-25 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: David =Reminder= We will have our 'priorities' discussion next week, hopefully everyone can be present. =Discussion= New groups (and groups in general): it would be nice to have guidelines as to what is a group, when to create a new group Decision from last week: We will add a parent field to groups and ensure every group other than GOC has a parent...")
  • 10:40, 23 May 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-05-24 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === *Possible in-person meeting; still being discussed === Noctua === *Regularly scheduled Noctua outage: **Thursday, May 12th * Automatic ontology updates implemented on Thursday, April 14th * April 28th Noctua systems outage - we did not do the ontology updates due to an issue with upstream ontologies that would have resulted in an EMAPA term being automatically replaced by an U...")
  • 02:45, 23 May 2022 Pascale talk contribs created page Ontology meeting 2022-05-23 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= * [https://github.com/geneontology/go-ontology/issues/22106 peptide alpha-N-acetyltransferase activity children cause true path violation] Harold * [https://github.com/geneontology/go-ontology/issues/21524 UDP-beta-L-arabinofuranose transport & transporter ] Pascale: subclasses calculated by Prot...")
  • 05:28, 19 May 2022 Pascale talk contribs created page Non-catalytic Molecular Functions (Created page with "==General considerations== Each gene product should be annotated to at least 1 GO term per GO aspect For MF, we aim for an annotation to a term other than binding or protein binding In the course of MF refactoring we have created several terms to represent non-catalytic functions ==Main non-catalytic Molecular Functions== ===molecular carrier activity (GO:0140104)=== Definition: Directly binding to a specific ion or molecule and delivering it either to an acceptor molec...")
  • 01:06, 18 May 2022 Pascale talk contribs created page Projects update meeting 2022-05-18 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Project updates= ==Projects near completion== Can we assign time to complete the tasks? * [https://github.com/orgs/geneontology/projects/65 Noctua 2021] (3 tickets left) ** Kimberly will ask Tremayne for a time estimate on Friday's Noctua workbenches call * [https://github.com/orgs/geneontology/projects/84 Visual Pathway editor v1.0]: Need to comple...")
  • 09:52, 12 May 2022 Pascale talk contribs created page Principles for catalytic activity terms (Created page with " ==NAD/NADP cofactors== * Reactions represented with NAD(P) in GO indicates that it is not know whether an enzyme uses NAD or NADP (note that this is different from the IUBMB practice). ** If the cofactor (NAD or NADP) is unknown for a class of reactions, then we only create a single GO term with [NAD(P)]. *** If there are RHEA IDs for both NAD and NADP-dependent reactions, we add these as NARROW xref to the general [NAD(P)]. * If the specific cofactor is known, we c...")
  • 08:58, 12 May 2022 Pascale talk contribs created page Projects update meeting 2022-05-12 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: ==Discuss priorities for upcoming period (1 month?)== Proposals by each manager: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# Category: GO Managers Meetings")
  • 08:52, 12 May 2022 Pascale talk contribs deleted page GO Projects stand up Calls (content was: "#REDIRECT Project_stand_up_meetings Category:GO Managers Meetings == GO Projects stand up Calls == ''(changed from GO Managers meeting Feb 2021)'' === When === Calls are at 11:00AM Eastern time, '''every Wednesday'''. === How to Join === * Recurring meeting URL: check GO's Google calendar * To join via phone: enter Meeting ID after dialing the Zoom phone number....", and the only contributor was "Pascale" (talk))
  • 02:33, 12 May 2022 Pascale talk contribs created page Ontology meeting 2022-05-16 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =NAD/NADP issue= https://github.com/geneontology/go-ontology/issues/23235 GO:0004448 isocitrate dehydrogenase activity is the parent for NAD and NADP versions; in this case it seems the enzymes are specific for either cofactors. I think our guidelines are that GO:0004448 isocitrate dehydrogenase activity should be obsoleted?...")
  • 10:30, 10 May 2022 Pascale talk contribs created page Noctua Landing Page (Created page with "= Noctua Landing Page = The Noctua landing page is the portal by which curators can browse or search and filter models. It is also the starting point for curation and where individual GPAD and OWL files for a model can be downloaded. By default, the Noctua landing page displays models by date, descending order, i.e. the most recently edited models are shown at the top of the list. Note that curators must be logged into Noctua to create new models or edit existing...")
  • 09:01, 3 May 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-05-02 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === *Possible in-person meeting; still being discussed === Noctua === *Regularly scheduled Noctua outage: **Thursday, May 12th == GO Release Pipeline == * April release? * From Slack #release-pipeline: ontology build failure * Other issues? == AmiGO == == Ontology == == Annotation == * Please remember to keep checking the [http://current.geneontology.org/reports/index.html rep...")
  • 03:13, 29 April 2022 Pascale talk contribs created page Projects update meeting 2022-05-04 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Fall GOC meeting== Decide on date, location =Spring GOC meeting= [https://docs.google.com/document/d/1Dv5UsRLfpH0ngjpxui5L2AK0GcK9VO2lrkZok6Qs-Co/edit# Action points] =Project updates= (Update Task Matrix and Wiki project table) =Future topic/project= Seth * What stats do we want to track, what do we need? Thinking grants, official reports, etc....")
  • 06:26, 26 April 2022 Pascale talk contribs created page Ontology meeting 2022-05-02 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' ==Annotation review requests instructions== (did not discuss) Detailed procedure here: Annotation_Review_Request * Added links to the procedure in the instructions for obsoletion and for merge ==Debrief GOC meeting== ==Debrief single-step process jambor...")
  • 01:58, 20 April 2022 Pascale talk contribs created page GO Central (GOC) QC Procedure (Created page with "GO Central rules are documented here: https://github.com/geneontology/go-site/blob/master/metadata/rules/README.md ===GO rules=== * (Documentation in progress): https://github.com/geneontology/go-site/tree/master/metadata/rules * The QC checks consist of either "filters" or "reports". Filters exclude annotations from the files that the GO consortium generates; reports allow the annotations to be exported, but contributing groups get notified to correct annotations. *...")
  • 01:37, 20 April 2022 Pascale talk contribs created page Ontology meeting 2022-04-25 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Discussion = ==GOC meeting April 26-28th== * Agenda: [https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/edit# Draft agenda] * Ontology presentation: ==Annotation review requests instructions== ==Feedback single-step process jamboree& next steps== Category:Meetings Category:Ontology")
  • 14:55, 18 April 2022 Mi talk contribs created page 20 Apr 2022 PAINT Conference Call (Created page with " ==Present== '''This meeting was rescheduled from April 6, 2022''' ==Agenda== ===Milestone achieved: completion of PAINT curation of all families with human genes=== ===Prepare for GO meeting=== ===Update PAINT to PANTHER17.0=== Category:PAINT")
  • 13:32, 18 April 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-04-19 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Spring 2022 Consortium Meeting === *Virtual *Tuesday April 26th to Thursday April 28th, from 7AM-11AM Pacific (4PM-8PM Europe) *Participants need to register with EventBrite **Invitation went out from Suzi A on Friday, April 1st **Also a link from the [https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/ Agenda, Logistics, Minutes] *Please email Pascale if you have topics for the ag...")
  • 20:20, 15 April 2022 Sjcarbon talk contribs created page Projects update meeting 2022-04-20 (Created page with "= Attendees = * Members: * Present: * Regrets: =Future topic/project= * What stats do we want to track, what do we need? Thinking grants, official reports, etc. ** End-of-year summary stats for users, downloads? ** Coming from consideration of log retention (policy) for some systems Category: GO Managers Meetings")
  • 08:57, 4 April 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-04-05 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Spring 2022 Consortium Meeting === *Virtual *Tuesday April 26th to Thursday April 28th, from 7AM-11AM Pacific (4PM-8PM Europe) *[https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/ Agenda, Logistics, Minutes] *Please email Pascale if you have topics for the agenda ** On the agenda: Continue goslim_generic discussion: review MF and CC slims, also, a session using the matrix to check...")
  • 02:32, 1 April 2022 Pascale talk contribs created page Projects update meeting 2022-04-06 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: David, Pascale, Seth, Suzi, Huaiyu, * Regrets: Chris, Cynthia, Kimberly [https://docs.google.com/document/d/1r3aWGjyz2nXNpyzETPO-ah276HQDc1ClNs57Cm6Nwv0/edit Main tasks - Jan-July 2022] =Announcements= * Preparing GOC meeting: start planning the agenda: https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/edit * Fall meeting in Baltimore?...")
  • 01:50, 1 April 2022 Pascale talk contribs created page Ontology meeting 2022-04-04 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' ==Announcements== * GOC meeting April 26-28th, Virtual * [https://docs.google.com/document/d/1q1_OfUz-EZvw28WJhDnbuNUGFAZz-21-uynNybdJcqg/edit# Draft agenda] ==Reminder== Please move your files to the New GO Shared Drive ==Jamboree: [https://github.com/geneontology/go-ontology/projects/26 Single Step BPs]== Category:Me...")
  • 12:40, 31 March 2022 Mi talk contribs created page 6 Apr 2022 PAINT Conference Call (Created page with "==Present== ==Agenda== ===Milestone achieved: completion of PAINT curation of all families with human genes=== ===Prepare for GO meeting=== Category:PAINT")
  • 03:40, 29 March 2022 Pascale talk contribs created page Projects update meeting 2022-03-30 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: [https://docs.google.com/document/d/1r3aWGjyz2nXNpyzETPO-ah276HQDc1ClNs57Cm6Nwv0/edit Main tasks - Jan-July 2022] =Announcements= * Preparing GOC meeting: start planning the agenda: https://drive.google.com/drive/folders/1Y5DfKpQu4tGxDmJaH-nHDDNkFy5x-w6B == Follow up from last meeting== * [http://wiki.geneontology.org/index.php/Projects_update_meeting_2...")
  • 10:15, 28 March 2022 Pascale talk contribs created page Ontology meeting 2022-03-28 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' Peter, Kimberly ==Discussion points== ===Moving the Google drive to a 'Shared' drive=== See details here: https://github.com/geneontology/go-site/issues/1813 Please move the files you own: ===Missing inferences from external ontologies=== see [https://github.com/geneontology/go-ontology/issues/22941 Missing part-of relation...")
  • 11:43, 9 March 2022 Ruth.lovering talk contribs uploaded a new version of File:MiRNADecisiontree2020.png
  • 08:42, 3 March 2022 Pascale talk contribs deleted page GO Project stand up meeting Template (content was: "* Present: * Regrets: * Managers: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Judy, Paul, Chris = Agenda = == Announcements ==...", and the only contributor was "Pascale" (talk))
  • 04:28, 22 February 2022 Pascale talk contribs moved page Ontology meeting 2022-02-21 to Ontology meeting 2022-02-28
  • 06:10, 9 February 2022 Pascale talk contribs moved page Enables to GeneProduct to GOTerm Relation:enables
  • 11:45, 14 December 2021 Pascale talk contribs moved page New Member Onboarding to New member onboarding
  • 11:08, 26 October 2021 Cjm talk contribs deleted page Background and Instructions (content was: "Category:Immunology == Return to Immunology Home Page == == Overview == In order to encourage s...", and the only contributor was "Ruth.lovering" (talk))
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