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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).

Logs
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  • 12:15, 29 September 2022 David talk contribs created page Causally upstream of negative effect (Created page with "== Overview == *The 'causally upstream of, negative effect' 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 understood **the activities of the gene products in the upstream process occur before events in the downstream process **the execution of the upstream event decreases the execution of the downstream event == Example...")
  • 11:53, 29 September 2022 David talk contribs created page Indirectly causally upstream of (Created page with "== Overview == *The 'indirectly causally upstream of' relation is used to relate GO Biological Processes (BP) and/or GO Molecular Functions (MF) when: **The mechanism that relates the upstream event (MF or BP) to the downstream event (MF or BP) is understood **The upstream event has an effect on the execution of the downstream event **There is a third event that happens between the upstream event and the downstream event **The upstream event is causally upstream of the t...")
  • 11:05, 29 September 2022 David talk contribs created page Removes input for (Created page with "== Overview == *The 'removes input for' relation is used to relate GO Molecular Functions (MF) when: **The upstream MF occurs before the downstream MF **The upstream MF has a negative effect on the downstream MF **The execution of the upstream MF is restricted to a specific condition **The execution of the upstream MF results in an input of the downstream MF becoming unavailable for the downstream MF == Examples of Usage == * == Quality Control Checks == * Shex '''(S...")
  • 10:31, 29 September 2022 David talk contribs created page Constitutively upstream of (Created page with "== Overview == *The 'constitutively upstream of' relation is used to relate GO Biological Processes (BP) and/or GO Molecular Functions (MF) when: **The mechanism that relates the upstream event (MF or BP) to the downstream event (MF or BP) is understood **The activities in the upstream event occur before events in the downstream event **The upstream event has an effect on the downstream event **The execution of the upstream event is approximately constant == Examples of...")
  • 05:37, 29 September 2022 Pascale talk contribs created page Noctua documentation from Help in Noctua Editor (Created page with "==Noctua: the Gene Ontology's GO Annotation Tool Suite== Noctua documentation from Help in Noctua Editor [http://noctua.geneontology.org/ Noctua] is a web-based annotation tool developed by the GO Consortium. Noctua can be used to create standard GO annotations as well as [http://geneontology.org/docs/gocam-overview/ GO-CAMs (Gene Ontology Causal Activity Models)] in a collaborative manner, i. e. multiple users can work on the same model at the same time. ===Getti...")
  • 10:03, 27 September 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-09-27 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * Entirely virtual * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] ** See agenda for pswd * Presentation of [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items and breakout group topics] === Noctua === *Next regularly scheduled Noctua outag...")
  • 08:24, 27 September 2022 Pascale talk contribs created page Ontology meeting 2022-10-03 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Announcements= =Editors discussion items= ==Relations== Pascale [https://github.com/oborel/obo-relations/issues/631 RO Ticket for directly positively regulates and activates & directly negatively regulates and inhibits] ==Topics postponed from previous calls== ===Stem cell taxonomic range=== https://github.com/geneontolog...")
  • 08:18, 27 September 2022 Pascale talk contribs created page Projects update meeting 2022-09-28 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =GOC meeting= * The week after next (Oct 11-13) * The following week will be a no GO calls week (week of Sept 17th) =Priorities until the end of the year= Pascale - I have updated the ‘main tasks’ document: https://docs.google.com/document/d/17ikwodMNC_xwEGZhBre_tilw4Fd8NI1IWZ8KxefSPBU/edit (I realize that Sept is almost over, but this is a mix...")
  • 13:02, 23 September 2022 Mi talk contribs created page 5th Oct 2022 PAINT Conference call (Created page with "==Present== ==Agenda== ===Conversion PAINT to PANTHER17.0=== ===New features for PAINT software=== ===Continue discussing PAINT human paper=== Here is the link to the manuscript: https://docs.google.com/document/d/1-8wVCPg7GEZQ9l3ox85hBO48YBoknRXOG_B9AJ6YZ0Q/edit?usp=sharing Category:PAINT")
  • 15:36, 19 September 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-09-20 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] - '''PLEASE REGISTER by SEPT. 1st''' ** See agenda for pswd * Please think about [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items] and breakout group to...")
  • 10:39, 13 September 2022 Vanaukenk talk contribs created page Projects update meeting 2022-09-21 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris (few mins late), Cynthia * Present: * Regrets: =GOC meeting= * currently 58 registered (18 in person/40 remote) * Agenda: https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M/edit# =Priorities= Today we discuss the next GO priorities based on this document: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# ==SGD and WB...")
  • 09:11, 6 September 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-09-06 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] - '''PLEASE REGISTER by SEPT. 1st''' ** See agenda for pswd * Please think about [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items] and breakout group to...")
  • 06:16, 6 September 2022 Pascale talk contribs created page Projects update meeting 2022-09-07 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =GOC meeting= * currently 58 registered (18 in person/40 remote) * Agenda: https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M/edit# =Priorities= Today we discuss the next GO priorities based on this document: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# Category: GO Managers Meet...")
  • 18:18, 2 September 2022 Mi talk contribs created page 7th Sept 2022 PAINT Conference call (Created page with "==Present== ==Agenda== ===Continue discussing PAINT human paper=== Here is the link to the manuscript: https://docs.google.com/document/d/1-8wVCPg7GEZQ9l3ox85hBO48YBoknRXOG_B9AJ6YZ0Q/edit?usp=sharing Category:PAINT")
  • 02:07, 1 September 2022 Pascale talk contribs created page Ontology meeting 2022-09-26 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Announcements= =Editors discussion items= ==Stem cell taxonomic range== https://github.com/geneontology/go-ontology/issues/23764 =='Nested' regulation== https://github.com/geneontology/go-ontology/issues/12976 I think we are obsoleting these terms? "regulation of X by regulation of Y" We still have 'regulation of x by regulati...")
  • 04:10, 31 August 2022 Pascale talk contribs created page Projects update meeting 2022-08-31 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Priorities= Today we discuss the next GO priorities based on this document: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# Category: GO Managers Meetings")
  • 12:19, 29 August 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-08-30 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] - '''PLEASE REGISTER by SEPT. 1st''' ** See agenda for pswd * Please think about [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items] and breakout group to...")
  • 01:55, 23 August 2022 Pascale talk contribs created page Ontology meeting 2022-09-19 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Announcements= =Editors discussion items= ==Stem cell taxonomic range== https://github.com/geneontology/go-ontology/issues/23764 ==Follow up on previous discussion topics== ==Regulation of a process in another organism== * AI (Pascale) should create a new triad of relations for linking the modulation of a process in another...")
  • 13:10, 19 August 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-08-23 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * [https://geneontology.ticketleap.com/fall-2022/ Registration form] - PLEASE REGISTER by SEPT. 1st ** See agenda for pswd * Please think about [https://docs.google.com/document/d/1YdM-RRosNJh1i4w4MLCF5lGfRrFIv7EqyNhEQD_QL0M agenda items] and breakout group topics...")
  • 05:21, 19 August 2022 Pascale talk contribs created page Projects update meeting 2022-08-24 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Priorities= Today we discuss the next GO priorities based on this document: https://docs.google.com/document/d/1TrxTZMRMAS0BCektM79nqvcZq8R3PXEMVWd_CbW-RfI/edit# Category: GO Managers Meetings")
  • 03:17, 16 August 2022 Pascale talk contribs created page Ontology meeting 2022-08-22 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= Aligning GO and EC (or RHEA, or any other ontology): https://github.com/geneontology/go-ontology/issues/23829#issuecomment-1216214500 The [https://wiki.geneontology.org/Guidelines_for_new_Molecular_Functions GO guidelines] state that we do not create terms for substrates, for example GO:0102113 hyp...")
  • 17:04, 15 August 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-08-16 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * Will send out registration form soon * Please think about agenda items and breakout group topics === Noctua === *Next regularly scheduled Noctua outage: **Thursday, September 8th == GO Release Pipeline == * August release still pending? == AmiGO == == Ontology...")
  • 11:58, 15 August 2022 Pascale talk contribs created page Projects update meeting 2022-08-17 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: =Announcements= ==GOC meeting== Oct 11-13 at CalTech; a mix of in-person and remote =Discussion items= == How to get Xenbase prioritized== ** Alliance moving forward with direct upstream ingest ==Timeline for SGD and WB import into Noctua== ** Proposal: prioritize this work for mid-October after the GOC meeting with the aim of completing by the end o...")
  • 16:16, 12 August 2022 Vanaukenk talk contribs created page Ontology meeting 2022-08-15 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= ==Question about parentage of life stage terms in go-lego== *Organismal life stage terms look to be typed as 'occurents' in go-lego but can/should they be typed more granularly as a 'biological phase' (GO:0044848)? Category:Meetings Category:Ontology")
  • 13:47, 2 August 2022 Mi talk contribs created page 3rd Aug 2022 PAINT Conference call (Created page with " ==Present== ==Agenda== ===Continue discussing PAINT human paper=== Here is the link to the manuscript: https://docs.google.com/document/d/1-8wVCPg7GEZQ9l3ox85hBO48YBoknRXOG_B9AJ6YZ0Q/edit?usp=sharing Category:PAINT")
  • 15:39, 26 July 2022 Sjcarbon talk contribs created page Projects update meeting 2022-07-27 (Created page with "* How to get Xenbase prioritized * Alliance moving forward with direct upstream ingest")
  • 12:42, 25 July 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-07-26 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA, Tuesday, October 11th - Thursday, October 13th * Will send out registration form asap === Noctua === *Regularly scheduled Noctua outage: **Thursday, July 28th === Annotation Call Schedule === *No meeting August 2nd *No meeting August 9th === Google Drive Migration === *Please check the old GO drive for files...")
  • 10:47, 25 July 2022 Pascale talk contribs created page Ontology meeting 2022-07-25 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' David, Peter, Chris, Jim Category:Meetings Category:Ontology")
  • 13:55, 18 July 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-07-19 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * In person with remote accommodation * At Caltech, Pasadena, CA Tuesday, October 11th - Thursday, October 13th === Noctua === *Regularly scheduled Noctua outage: **Thursday, July 28th == GO Release Pipeline == * July release is out * Some issues with snapshot releases ** Could not rebuild NEO (Noctua Entity Ontology) last Thursday == AmiGO == == Ontology == === Membrane...")
  • 12:51, 5 July 2022 Mi talk contribs created page 6th July 2022 PAINT Conference Call (Created page with " ==Present== ==Agenda== ===Discuss PAINT human paper=== Here is the link to the manuscript: https://docs.google.com/document/d/1-8wVCPg7GEZQ9l3ox85hBO48YBoknRXOG_B9AJ6YZ0Q/edit?usp=sharing Category:PAINT")
  • 02:02, 5 July 2022 Pascale talk contribs created page Ontology meeting 2022-07-18 (Created page with "* '''Group members:''' Pascale, Karen, Harold, Raymond, Peter, Jim, Tanya, Kimberly, David, Chris, Paul * '''Present:''' * '''Regrets: ''' =Editors discussion tickets= ==Uberon taxon constraints are too stringent== See https://github.com/geneontology/go-ontology/issues/23445 Do we need to remove the relation 'GO:0110165 cellular anatomical entity' is_a 'CARO_0000000 anatomical entity'? ==ChEBI documentation edited== New section on External Ontologies https://...")
  • 08:58, 30 June 2022 Pascale talk contribs created page External ontologies (Created page with "GO uses external ontologies for the logical definitions of some terms. =ChEBI= Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. ChEBI is used to describe compounds in GO, as well as in RHEA. Compounds used in GO are the forms present at pH 7, the physiological pH under most conditions in most organisms annotated with GO. The pH is not 7.3 in all organelles, organs and orga...")
  • 11:49, 29 June 2022 Pascale talk contribs created page Projects update meeting 2022-07-06 (Created page with "= Attendees = * Members: David, Huaiyu, Kimberly, Pascale, Seth, Suzi, Paul, Chris, Cynthia * Present: * Regrets: ==GOC meeting== == Ongoing work updates == ===Google drive move=== https://github.com/orgs/geneontology/projects/90 * Suzy to report on status ===[https://github.com/orgs/geneontology/projects/80 Model copy]=== * Status === Adding SO terms as valid range for 'occurs in' annotation extension === * Curators would like to be able to specify chromosomal...")
  • 08:43, 29 June 2022 Pascale talk contribs created page Deprecated relations (Created page with "==Deprecated Relations== These relations are not supported in the ontology, in GO-CAM or in Protein2GO anymore: *occurs_at - use occurs_in instead * dependent_on *has_agent - not in RO: in AE graph the parent for this term is 'has_participant' * has_direct_input * in_absence_of * in_presence_of * independent_of * localization_dependent_o...")
  • 08:06, 29 June 2022 Vanaukenk talk contribs created page Annotation Conf. Call 2022-07-05 (Created page with "= Agenda and Minutes = == Meetings and Announcements == === Fall 2022 Consortium Meeting === * Likely at Caltech, October 11th - 13th * Please still fill out the meeting survey from Pascale === 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 topolog...")
  • 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")
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