https://wiki.geneontology.org/index.php?title=Special:NewPages&feed=atom&hideliu=&hidepatrolled=&hidebots=&hideredirs=1&limit=50&namespace=0GO Wiki - New pages [en]2024-03-29T07:04:24ZFrom GO WikiMediaWiki 1.40.0https://wiki.geneontology.org/Projects_update_meeting_2024-03-27Projects update meeting 2024-03-272024-03-26T15:54:58Z<p>Pascale: /* Pipeline */</p>
<hr />
<div>= Attendees =<br />
* Members: Kimberly, Pascale, Seth, Suzi, Jim, Huaiyu, Paul, Chris, Cynthia<br />
* Present:<br />
* Regrets:<br />
<br />
= Discussion topics =<br />
<br />
==GO meeting==<br />
* Registration form by March 15th<br />
* Agenda by May 1st<br />
* Which days do we need on either side?<br />
* Draft agenda: https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.2jptrbvdxk9r<br />
* GO Users meeting: https://docs.google.com/document/d/1sIamECzTS5IMOy4GeldzWXdawnmOLvT9s5vClMAs3Bo/edit<br />
<br />
==Update on projects==<br />
===[https://github.com/geneontology/project-management/issues/88 Pipeline]===<br />
* New system with snapshot being promoted to a release being put in place<br />
* Pascale checked diff: long lag, many differences<br />
* QUESTION: Should we release TreeGrafter annotations? considering quite a few errors, I think because IBD are not picked up and therefore not filtered by the P2GO pipeline<br />
* Request is for GOA to filter the 143 Panther species; Alex was reluctant to do that, but it seems we're adding a lot of undesired annotations <br />
* AI Pascale create gorule <br />
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[[Category: GO Managers Meetings]]</div>Pascalehttps://wiki.geneontology.org/Ontology_meeting_2024-04-08Ontology meeting 2024-04-082024-03-26T10:24:16Z<p>Pascale: </p>
<hr />
<div>* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul<br />
* '''Present: '''<br />
<br />
<br />
=Discussion points= <br />
<br />
==Ontobot actions==<br />
===Triggering multiple actions???=== <br />
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.") (questing indirectly coming from https://github.com/geneontology/go-ontology/issues/27194) <br />
* Should Ontobot also do that? <br />
* Can we/should we add a check that all 'do not annotate' terms have a comment? <br />
<br />
===Proposals for new ontobot actions===<br />
====Removing a term from a subset====<br />
====Obsoletion====<br />
* Edits needed to obsolete a term: <br />
** term label (=append obsolete)<br />
** term definition (=append OBSOLETE.)<br />
** insert obsoletion comment (note that this clashes when there is another existing comment; is this restriction useful?)<br />
** insert 'replace by' or 'consider'<br />
** remove obsolete cross-references (can be done as an automated post-processing step? ie create a check that removes any obsolete/deprecated cross reference from obsolete terms)<br />
<br />
====Obsoletion & 'consider' terms in the logical definition====<br />
* This would be useful to bulk obsolete pre-composed terms<br />
<br />
====Bulk update specific keywords====<br />
* Workflow 1: replacement of a ChEBI term in the logical definitions of x terms (or asserted superclasses) <br />
(see PR here: https://github.com/geneontology/go-ontology/commit/fb12048ab6385e6890621d2971e9aed6862692ec; this is just 3-4 ChEBI terms, and some terms are not fully updated yet)<br />
(For example for the ChEBI 7.3 work: we want to replace 'tyrosine' by 'L-tyrosine' in all the terms that use L-tyrosine in the LD): <br />
** step 1: replace all instances of chebi:tyrosine to chebi:L-tyrosine (this would be manual or at least a separate PR to ensure that this replacement doesn't go on unintended terms) <br />
** automatic steps<br />
*** replace chebi:tyrosine to chebi:L-tyrosine in ***term label*** (note that we also need to insert the old term label as a broad synonym or we will get a Travis error; maybe this can be relaxed)<br />
*** replace chebi:tyrosine to chebi:L-tyrosine in ***term definition***<br />
*** replace chebi:tyrosine to chebi:L-tyrosine in ***term synonyms***<br />
<br />
<br />
==New subsets yaml==<br />
* 2 points are not checked off here: https://github.com/geneontology/go-ontology/pull/27414#event-12256156352<br />
** add checks to github actions (@balhoff @kltm we are using latest-ish version of odk? in which case linkml is included)<br />
** make an OBO PURL that resolves to this<br />
do they need to be done? <br />
* should we make sure we use the 'main label' for each field, and not aliases (ie 'type' versus 'role'). In other words, how are users interacting with this file? Are we sure that they will be able to use field with various/varied labels ? (it's not more work for us to be consistent)<br />
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[[Category:Meetings]]</div>Pascalehttps://wiki.geneontology.org/Annotation_Conf._Call_2024-03-26Annotation Conf. Call 2024-03-262024-03-26T00:30:48Z<p>Suzialeksander: /* AI summary */</p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== Meetings and Announcements ==<br />
<br />
=== Noctua ===<br />
* Next regularly scheduled Noctua outage:<br />
** Thursday, March 28th, 4-6pm PDT<br />
*** [https://github.com/geneontology/noctua/issues/869 Outage tasks]<br />
<br />
=== No GO Calls Week ===<br />
* Next week (week of April 1st) is a no GO calls week<br />
<br />
=== Next In-Person Consortium Meeting ===<br />
* Week of May 20th - actual meeting dates: Tuesday, May 21 - Thursday, May 23<br />
* Users Meeting, Monday, May 20th<br />
* Hosted by Jim Balhoff in Chapel Hill, NC<br />
* Start thinking about [https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.faqtkfatd45w agenda items, special topics, breakout groups]<br />
* [https://www.ticketleap.events/tickets/geneontology/spring2024goc Registration] - Deadline: April 12th<br />
<br />
== GO Release Pipeline ==<br />
* March release.....<br />
** A snapshot release is out; Seth is going to do a little checking<br />
** Up-to-date ontology files are now being produced independently, though<br />
** Pascale will provide more information on how to access these for your curation tools/pipelines<br />
** https://wiki.geneontology.org/Rolling_build_of_the_Gene_Ontology<br />
* #release-pipeline Slack channel for updates<br />
<br />
== AmiGO ==<br />
<br />
== Annotation ==<br />
<br />
=== Work on Annotation Reviews ===<br />
* We will use the remainder of the call to work together on annotation reviews.<br />
<br />
== GO-CAM and Noctua ==<br />
<br />
== Ontology ==<br />
<br />
= AI summary=<br />
Wudpecker (https://app.wudpecker.io/shared/cb3b5920-a970-4fd7-ac9e-38a77aa47f19)<br />
<br />
Key Decisions<br />
<br />
Agreement to consider recording calls for future use and review the notes it takes.<br />
Approval of an upcoming outage on Thursday from 4 to 6 PM PDT, with a link provided for regular outage tasks.<br />
Decision to hold the next in-person consortium meeting in May in Chapel Hill, North Carolina, with both in-person and virtual options available.<br />
<br />
Recording Calls<br />
<br />
Kimberly Van Auken suggests considering recording calls for future use.<br />
Suzi Aleksander agrees to try it and review the notes it takes.<br />
Malcolm Fisher comments on the usefulness of automated transcripts but acknowledges their limitations with technical language.<br />
<br />
Upcoming Outage and Meetings<br />
<br />
An outage is announced for Thursday from 4 to 6 PM PDT.<br />
The next in-person consortium meeting will be held in May, hosted by Jim Balhoff in Chapel Hill, North Carolina.<br />
There will be both in-person and virtual options for attending the meeting.<br />
<br />
Go Release Pipeline Update<br />
<br />
Seth Carbon provides an update on the go release pipeline, mentioning that a snapshot may have cleared and they are feeling good about starting the release process soon.<br />
Pascale Gaudet confirms the existence of a snapshot and mentions ongoing work to ensure its quality.<br />
Kimberly Van Auken expresses satisfaction with the progress and asks about independently producing up-to-date ontology files.<br />
<br />
Ontology Building Process<br />
<br />
Pascale Gaudet explains that Protein2GO is now loading the ontology daily and provides a link to the Wiki page with more information.<br />
Seth Carbon elaborates on the automated extended QC process for the ontology and how it is used to produce the rolling release of the ontology multiple times a day.<br />
Kimberly Van Auken seeks clarification on the frequency and expectations of the rolling release.<br />
<br />
Annotation Reviews<br />
<br />
Issues with annotation reviews not being updated in a timely manner were discussed.<br />
The source used for annotation reviews is AmiGO, but there can be delays between releases.<br />
Importance of immediate access to curation databases to avoid wasting time and energy was highlighted.<br />
<br />
<br />
<br />
<br />
== Attendees ==<br />
*On call: Debby, Dmitry, Dustin, Edith, Kimberly, Leonore, Li, Malcolm, Mary, Pascal, Pascale, Patrick, Raymond, Rossana, Seth, Sridhar, Steven, Suzi, Val<br />
<br />
[[Category:Annotation Working Group]]</div>Vanaukenkhttps://wiki.geneontology.org/Ontology_meeting_2024-03-25Ontology meeting 2024-03-252024-03-25T08:38:04Z<p>Pascale: </p>
<hr />
<div>* '''Group members:''' Pascale, Raymond, Edith, Val, Jim, Tanya, Kimberly, Peter, Chris, Paul<br />
* '''Present: ''' Raymond, Kimberly, Li, Peter, Pascale, Steven, Edith, Val, Tanya <br />
* '''Regrets: ''' Jim, Chris, Paul<br />
<br />
<br />
=Discussion points= <br />
* Pascale made a new ticket for obsolete ECs: https://github.com/geneontology/go-ontology/issues/27410<br />
* Pascale to check with Elisabeth Coudert of RHEA to answer Steven's question here: https://github.com/geneontology/go-ontology/issues/27278#issuecomment-2009066470<br />
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[[Category:Meetings]]</div>Pascalehttps://wiki.geneontology.org/Daily_version_of_the_Gene_OntologyDaily version of the Gene Ontology2024-03-19T18:26:12Z<p>Pascale: </p>
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<div>=Purpose of the rolling build of GO=<br />
As of March 18, 2024, GO will attempt to produce the latest version of the ontology 3 times a day. '''This version is not checked or versioned or archived, therefore not citable. If there are problems with the ontology build, the frequency may be less.'''<br />
<br />
* The latest build of the ontology can be found here: https://ontology-build.geneontology.org/<br />
* Note that if there is a failure of the ontology build, the ontology production will be automatically halted until the issue is resolved. Please look in the file header to see when the file was generated.<br />
<br />
==Who should use this file==<br />
This file should only be used for obtaining up-to-date build of the ontology in for use in annotation tools.<br />
<br />
==Official GO release==<br />
For documentation of official release of GO, please refer to the [[Release_Pipeline]] page.<br />
The official release should be used for any analyses using GO, as these are archived and these analyses can be reproduced.<br />
<br />
[[Category:Ontology]][[Category:GO Editors]]</div>Pascalehttps://wiki.geneontology.org/Annotation_Conf._Call_2024-03-19Annotation Conf. Call 2024-03-192024-03-18T21:17:22Z<p>Vanaukenk: /* GO Release Pipeline */</p>
<hr />
<div>= Agenda and Minutes =<br />
<br />
== Meetings and Announcements ==<br />
<br />
=== Noctua ===<br />
* Next regularly scheduled Noctua outage:<br />
** Thursday, March 28th, 4-6pm PDT<br />
*** [https://github.com/geneontology/noctua/issues/869 Outage tasks]<br />
<br />
=== Next In-Person Consortium Meeting ===<br />
* Week of May 20th - actual meeting dates: Tuesday, May 21 - Thursday, May 23<br />
* Users Meeting, Monday, May 20th<br />
* Hosted by Jim Balhoff in Chapel Hill, NC<br />
* Start thinking about [https://docs.google.com/document/d/1FwGxa4jx8rJFjWBcbn4Q7ZzOHCY6-oF0azOrtK3quyk/edit#heading=h.faqtkfatd45w agenda items, special topics, breakout groups]<br />
* [https://www.ticketleap.events/tickets/geneontology/spring2024goc Registration] - Deadline: April 12th<br />
<br />
== GO Release Pipeline ==<br />
* March release.....<br />
** Still trying to get a snapshot release out - waiting on some new hardware<br />
** Uo-to-date ontology files are now being produced independently, though<br />
** Pascale will provide more information on how to access these for your curation tools/pipelines<br />
* #release-pipeline Slack channel for updates<br />
<br />
== AmiGO ==<br />
* Not showing taxon constraints anymore, since it was only showing 'only in taxon' and not 'never in taxon'. We will restore once the indexing issue is resolved. <br />
<br />
== Annotation ==<br />
<br />
=== gocheck_do_not_annotate ===<br />
* Remove filtering of ‘do_not_annotate’ terms in QuickGO<br />
* Are we all good with this one?<br />
<br />
=== 'Unfolding annotation extensions in Protein2GO ===<br />
* Annotations of "Gene X 'involved in' BP ‘part_of’ BP y" will be unfolded to also create the annotation "Gene X 'involved in' BP y". <br />
* This is correct because of the transitivity of the 'part of' relation.<br />
* Alex needs to do some work to implement this, but we want to confirm that curators are on board with this. <br />
* This unfolding will create 13k new annotations.<br />
<br />
== GO-CAM and Noctua ==<br />
<br />
== Ontology ==<br />
<br />
<br />
== Attendees ==<br />
*On call: Antonia, Chris, Debby, Dmitry, Dustin, Edith, Giulia, Helen, Karen, Kimberly, Leonore, Li, Malcolm, Mary, Pascal, Pascale, Raymond, Rob, Rossana, Seth, Sridhar, Steve, Suzi, Val<br />
<br />
[[Category:Annotation Working Group]]</div>Vanaukenkhttps://wiki.geneontology.org/Procedure_to_check_subset_coverageProcedure to check subset coverage2024-03-15T09:41:19Z<p>Pascale: </p>
<hr />
<div># Checking maximum GO annotation coverage<br />
#* Go to [https://www.ebi.ac.uk/QuickGO/ QuickGO], click on [https://www.ebi.ac.uk/QuickGO/annotations View Annotations]<br />
#* On the drop down menus at the top of the page, add filters as appropriate: <br />
#** Taxon(s) or taxonomic range (it is possible to select for example NBCITaxon:2 for all bacteria)<br />
#** Gene Products: it is usually desirable to select only Reviewed entry and Reference proteomes (either "Gene centric, canonical", or "Gene centric, other isoforms")<br />
## On the results page listing annotations, click on the Statistics tab<br />
#** The Summary tab shows the total number of annotations and of gene products annotated.<br />
#** The Aspect tab shows the number of gene products annotated by GO aspect. This is the maximum coverage possible by aspect.<br />
# Checking GO annotation coverage for the subset<br />
#* Go to [https://www.ebi.ac.uk/QuickGO/ QuickGO], click on [https://www.ebi.ac.uk/QuickGO/slimming Explore Biology]<br />
#* Under Select Terms, slick on the Tab "Input your own"<br />
#* Enter the list of terms in your draft subset by GO ID. '''This should be done on an aspect-by-aspect basis to avoid effects of inter-ontology links.''' <br />
#* In the Additional Options, it is possible to select a species or a taxonomic range, if appropriate. Note the the results will be calculated faster for smaller sets of genes. <br />
## Repeat the same steps as in 1.2 to get the number of genes annotated with the subset. Compare the results to see if the coverage of the subset is acceptable; otherwise edit the list of GO terms and redo the analysis.<br />
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<br />
== Review Status ==<br />
<br />
Last reviewed: March 15, 2024<br />
<br />
Reviewed by Pascale Gaudet<br />
<br />
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[[Ontology_Development#Editing_the_Ontology |Back to: Editing the Ontology]]<br />
<br />
[[Category:GO Editors]][[Category:Ontology]][[Category:Editor_Guide_2018]]</div>Pascale