https://wiki.geneontology.org/api.php?action=feedcontributions&user=David+os&feedformat=atomGO Wiki - User contributions [en]2024-03-28T17:58:17ZUser contributionsMediaWiki 1.40.0https://wiki.geneontology.org/index.php?title=Ontology_meeting_2017-09-22&diff=65198Ontology meeting 2017-09-222017-09-22T14:55:49Z<p>David os: /* Agenda */</p>
<hr />
<div>= Conference Line =<br />
<br />
*Zoom: https://stanford.zoom.us/j/828418143<br />
<br />
= Agenda =<br />
<br />
== Eric will give a tour of the new QC checks ==<br />
<br />
== David OS: MF refactoring, receptors & GOCAM rules - presentation ==<br />
<br />
==GH project link==<br />
<br />
https://github.com/geneontology/go-ontology/projects/1<br />
<br />
==Orverview of the GOC meeting Agenda==<br />
<br />
http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Meeting_Agenda<br />
<br />
http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Signalling_Workshop<br />
<br />
==Discussion==<br />
*On call:<br />
<br />
<br />
<br />
[[Category: Ontology]]<br />
[[Category: Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=GO-CAM_ectopic_meeting_July_19th_2017&diff=64553GO-CAM ectopic meeting July 19th 20172017-07-19T16:34:06Z<p>David os: /* contributes_to inference: */</p>
<hr />
<div>= Zoom URL =<br />
https://stanford.zoom.us/j/679970729<br />
<br />
= Agenda =<br />
<br />
Discussion of inference on Wnt signaling LEGO model<br />
<br />
http://noctua.berkeleybop.org/editor/graph/gomodel:5966411600000538<br />
<br />
===Missing/New inferences: ===<br />
<br />
==== contributes_to inference: ====<br />
Added to RO:<br />
part of'(?x, ?y) ^ enables(?y, ?z) ^ molecular_function(?z) -> 'contributes to'(?x, ?z) <br />
e.g. GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z<br />
<br />
Paul suggests:<br />
<br />
'contributes to'(?x, ?y) ^ part_of(?y, ?z) -> 'involved in'(?x, ?z)<br />
<br />
This inference is considered safe because in GO-CAM models a whole complex will only be annotated if the complex is required to perform the molecular function in the context of the process.<br />
One could imagine cases with unsafe inference, for example a complex with a negative regulators subunit that regulates an activity that is part of a process. But Paul suggests that annotations rules should get around this: In this case there should be no annotation to the complex.<br />
<br />
This may be one we have to revisit if odd annotations start showing up.<br />
<br />
====Annotation to compound molecular function => annotation to its parts====<br />
<br />
enables(?x, ?y) ^ 'has part'(?y, ?z) ^ molecular_function(?y) -> enables(?x, ?z) <br />
<br />
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'<br />
<br />
====Inferences from molecular function regulators====<br />
<br />
https://github.com/geneontology/go-ontology/issues/13492)<br />
<br />
e.g.: <br />
<br />
X <— enabled by— protein binding —directly_positively_regulates --> protein kinase activity —enabled_by--> Y<br />
<br />
=> <br />
<br />
X enables ‘protein binding activity' has_input Y *<br />
X enables 'protein kinase activator activity’ has_input Y *<br />
<br />
<br />
\* Comes from a new rule:<br />
molecular_function(?x) ^ molecular_function(?y) ^ 'directly regulates'(?x, ?y) ^ enables(?z, ?y) -> 'has input'(?x, ?z) <br />
<br />
e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z<br />
<br />
=== Wrong inferences that need to be trimmed: ===<br />
<br />
regulates o part_of->regulates<br />
<br />
https://github.com/geneontology/go-ontology/issues/13926#issuecomment-316054054<br />
<br />
<br />
=== Strategies for trimming down superfluous inference ===<br />
<br />
<br />
# enables and other GP/Complex -> MF/BP relations never go in extensions. Inference of the ‘contributes to’ qualifier would make up for this.<br />
# some very high level classes should be blacklisted from extensions (molecular_function, regulation of molecular function. We could perhaps existing no annotation subset flags for these.)<br />
# If we have ‘X regulation’ then the GPAD has only GP involved_in 'regulation of X', not GP involved_in_regulation_of X. <br />
This is hard to implement: simpler alternative would be to just drop this GP-GO term relation and rely on named regulation classes alone<br />
<br />
= Minutes =<br />
*On call: David H, David OS, Kimberly, Paul T.<br />
<br />
== Protein Complex Annotations ==<br />
*New rule will allow for individual members of the complex to inherit the MF annotation with a contributes_to qualifier<br />
*For BP annotations, if the MF is performed by a protein complex, and the MF is part_of the BP, then each member of the complex is involved_in the BP<br />
<br />
<br />
[[Category:Annotation Working Group]]</div>David oshttps://wiki.geneontology.org/index.php?title=GO-CAM_ectopic_meeting_July_19th_2017&diff=64550GO-CAM ectopic meeting July 19th 20172017-07-19T16:06:17Z<p>David os: /* Strategies for trimming down superfluous inference */</p>
<hr />
<div>= Zoom URL =<br />
https://stanford.zoom.us/j/679970729<br />
<br />
= Agenda =<br />
<br />
Discussion of inference on Wnt signaling LEGO model<br />
<br />
http://noctua.berkeleybop.org/editor/graph/gomodel:5966411600000538<br />
<br />
===Missing/New inferences: ===<br />
<br />
==== contributes_to inference: ====<br />
Added to RO:<br />
part of'(?x, ?y) ^ enables(?y, ?z) ^ molecular_function(?z) -> 'contributes to'(?x, ?z) <br />
e.g. GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z<br />
<br />
====Annotation to compound molecular function => annotation to its parts====<br />
<br />
enables(?x, ?y) ^ 'has part'(?y, ?z) ^ molecular_function(?y) -> enables(?x, ?z) <br />
<br />
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'<br />
<br />
====Inferences from molecular function regulators====<br />
<br />
https://github.com/geneontology/go-ontology/issues/13492)<br />
<br />
e.g.: <br />
<br />
X <— enabled by— protein binding —directly_positively_regulates --> protein kinase activity —enabled_by--> Y<br />
<br />
=> <br />
<br />
X enables ‘protein binding activity' has_input Y *<br />
X enables 'protein kinase activator activity’ has_input Y *<br />
<br />
<br />
\* Comes from a new rule:<br />
molecular_function(?x) ^ molecular_function(?y) ^ 'directly regulates'(?x, ?y) ^ enables(?z, ?y) -> 'has input'(?x, ?z) <br />
<br />
e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z<br />
<br />
=== Wrong inferences that need to be trimmed: ===<br />
<br />
regulates o part_of->regulates<br />
<br />
https://github.com/geneontology/go-ontology/issues/13926#issuecomment-316054054<br />
<br />
<br />
=== Strategies for trimming down superfluous inference ===<br />
<br />
<br />
# enables and other GP/Complex -> MF/BP relations never go in extensions. Inference of the ‘contributes to’ qualifier would make up for this.<br />
# some very high level classes should be blacklisted from extensions (molecular_function, regulation of molecular function. We could perhaps existing no annotation subset flags for these.)<br />
# If we have ‘X regulation’ then the GPAD has only GP involved_in 'regulation of X', not GP involved_in_regulation_of X. <br />
This is hard to implement: simpler alternative would be to just drop this GP-GO term relation and rely on named regulation classes alone</div>David oshttps://wiki.geneontology.org/index.php?title=GO-CAM_ectopic_meeting_July_19th_2017&diff=64549GO-CAM ectopic meeting July 19th 20172017-07-19T16:03:18Z<p>David os: /* Missing/New inferences: */</p>
<hr />
<div>= Zoom URL =<br />
https://stanford.zoom.us/j/679970729<br />
<br />
= Agenda =<br />
<br />
Discussion of inference on Wnt signaling LEGO model<br />
<br />
http://noctua.berkeleybop.org/editor/graph/gomodel:5966411600000538<br />
<br />
===Missing/New inferences: ===<br />
<br />
==== contributes_to inference: ====<br />
Added to RO:<br />
part of'(?x, ?y) ^ enables(?y, ?z) ^ molecular_function(?z) -> 'contributes to'(?x, ?z) <br />
e.g. GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z<br />
<br />
====Annotation to compound molecular function => annotation to its parts====<br />
<br />
enables(?x, ?y) ^ 'has part'(?y, ?z) ^ molecular_function(?y) -> enables(?x, ?z) <br />
<br />
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'<br />
<br />
====Inferences from molecular function regulators====<br />
<br />
https://github.com/geneontology/go-ontology/issues/13492)<br />
<br />
e.g.: <br />
<br />
X <— enabled by— protein binding —directly_positively_regulates --> protein kinase activity —enabled_by--> Y<br />
<br />
=> <br />
<br />
X enables ‘protein binding activity' has_input Y *<br />
X enables 'protein kinase activator activity’ has_input Y *<br />
<br />
<br />
\* Comes from a new rule:<br />
molecular_function(?x) ^ molecular_function(?y) ^ 'directly regulates'(?x, ?y) ^ enables(?z, ?y) -> 'has input'(?x, ?z) <br />
<br />
e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z<br />
<br />
=== Wrong inferences that need to be trimmed: ===<br />
<br />
regulates o part_of->regulates<br />
<br />
https://github.com/geneontology/go-ontology/issues/13926#issuecomment-316054054<br />
<br />
<br />
=== Strategies for trimming down superfluous inference ===</div>David oshttps://wiki.geneontology.org/index.php?title=GO-CAM_ectopic_meeting_July_19th_2017&diff=64548GO-CAM ectopic meeting July 19th 20172017-07-19T16:01:08Z<p>David os: Created page with "= Zoom URL = https://stanford.zoom.us/j/679970729 = Agenda = Discussion of inference on Wnt signaling LEGO model http://noctua.berkeleybop.org/editor/graph/gomodel:5966411..."</p>
<hr />
<div>= Zoom URL =<br />
https://stanford.zoom.us/j/679970729<br />
<br />
= Agenda =<br />
<br />
Discussion of inference on Wnt signaling LEGO model<br />
<br />
http://noctua.berkeleybop.org/editor/graph/gomodel:5966411600000538<br />
<br />
===Missing/New inferences: ===<br />
<br />
1. contributes_to inference:<br />
Added to RO:<br />
part of'(?x, ?y) ^ enables(?y, ?z) ^ molecular_function(?z) -> 'contributes to'(?x, ?z) <br />
e.g. GP(X) part_of complex(Y) enables MF(Z) -> X contributes_to Z<br />
<br />
2. Annotation to compound molecular function => annotation to its parts<br />
<br />
enables(?x, ?y) ^ 'has part'(?y, ?z) ^ molecular_function(?y) -> enables(?x, ?z) <br />
<br />
e.g. if GP X enables ATPase coupled transporter activity' and 'ATPase coupled transporter activity' has_part 'ATPase activity' then GP(X) enables 'ATPase activity'<br />
<br />
3. Inferences from Implementing the design pattern for molecular function regulators (https://github.com/geneontology/go-ontology/issues/13492)<br />
<br />
e.g.: <br />
<br />
X <— enabled by— protein binding —directly_positively_regulates --> protein kinase activity —enabled_by--> Y<br />
<br />
=> <br />
<br />
X enables ‘protein binding activity' has_input Y *<br />
X enables 'protein kinase activator activity’ has_input Y *<br />
<br />
<br />
* Comes from a new rule:<br />
molecular_function(?x) ^ molecular_function(?y) ^ 'directly regulates'(?x, ?y) ^ enables(?z, ?y) -> 'has input'(?x, ?z) <br />
<br />
e.g. if 'protein kinase activity'(X) directly_regulates 'protein binding activity (Y)and this is enabled by GP(Z) then X has_input Z<br />
<br />
<br />
=== Wrong inferences that need to be trimmed: ===<br />
<br />
regulates o part_of->regulates<br />
<br />
https://github.com/geneontology/go-ontology/issues/13926#issuecomment-316054054<br />
<br />
<br />
=== Strategies for trimming down superfluous inference ===</div>David oshttps://wiki.geneontology.org/index.php?title=Annotation&diff=64538Annotation2017-07-19T15:48:57Z<p>David os: /* Combined GO-CAM/GPAD calls */</p>
<hr />
<div>[[Category: Annotation]] [[Category:Working Groups]]<br />
==Group Leaders==<br />
David Hill (MGI) and Kimberly Van Auken (WB)<br />
<br />
==GO Annotation Meetings==<br />
[http://gocwiki.geneontology.org/index.php/2010_GO_camp_Meeting_Logistics 2010 GO Annotation Camp in Geneva, Switzerland, June 16-18 2010 ]<br />
<br />
[[Guidelines from Annotation Camp]]<br />
<br />
[http://wiki.geneontology.org/index.php/2012_Annotation_Meeting_Stanford Annotation Meeting Stanford, CA, Feb 2012]<br />
<br />
==Migration of annotating groups to Protein2GO==<br />
<br />
[[Procedure for migration of protein annotations to Protein2GO]]<br />
<br />
[[Extension of Protein2GO to non-UniProtKB Identifiers]]<br />
<br />
<br />
<br />
==Activities==<br />
<br />
*[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2010 Roadmap 2010]<br />
*[http://wiki.geneontology.org/index.php/Annotation_Advocacy_Roadmap_2011 Roadmap 2011]<br />
*[[Media:AnnotationRoadMap.pdf | RoadMap]] (PDF file - provides project goals with time line)<br />
*Educate GOC curators about best annotation practice; <br />
*Enforce annotation rules/policies within GOC<br />
*Maintain the annotation/evidence code documentation<br />
**[[Mock-ups of new GOC Annotation pages]]<br />
*Train/assist new groups with annotations: see [[How_External_Communities_can_contribute_annotations_to_the_GO_Consortium]]<br />
*Educate and keep all the annotating groups up-to-date with changes in GAF format<br />
<br />
*Annotation Extensions<br />
**[[Annotation Extension Relation Subsets]]<br />
**[[Column 16: Cell Type]]<br />
**[[Column 16: Targets]]<br />
**[[Issues with Annotation Extension relations]]<br />
**[[Annotation Extension Relation Documentation Jamboree]]<br />
**[[Guidance for updating deprecated Annotation Extension Relations]]<br />
<br />
*Keep all curators up-to-date with ontology development and how it affects annotations<br />
<br />
*[[Chain of Evidence]]- Proposal to represent chain/summation of evidence in an annotation.<br />
*[[Evidence Code Ontology (ECO)]] - Proposal to represent evidence in an ontology<br />
*[[Proposal for cron tabs]] - Proposal for setting up cron tabs for generating PAINT and MF-BP inferences<br />
*[[Examples for phylogeny based evidence codes]]<br />
*[[Ideas for GOC community curation tool]]<br />
*[[Protein Complex ids as GO annotation objects]]<br />
** [[Annotation guidelines for annotating complexes as annotation objects]]<br />
** [[Protein Complex Conference Call June19, 2015]]<br />
** [[Protein Complex Conference Call July15, 2015]]<br />
*[[LEGO-style annotation ideas]]<br />
* [[Proposed Developments to the GAF annotation format]]<br />
*[[InterPro2GO Session October 4th 2011]]<br />
*[[MF-BP inferences]]<br />
*[[Protein Binding clean up]]<br />
*[[Annotation Guidance Pages]]<br />
*[[Evidence Code proposals]]<br />
*[[With/From field restrictions for evidence codes]]<br />
*[[Core Consortium annotation activities]]<br />
*[[:Category:GPAD|GPAD]]<br />
<br />
*[[Common Annotation Framework Specification]]<br />
*[[gp2protein file]]<br />
*[[gp2rna file]]<br />
*[[gp_unlocalized file]]<br />
*[[mechanisms for reducing annotation redundancy]]<br />
*[[Annotations to Cell Fraction-type terms]]<br />
*[[TermEnrichment: Gold Standard Data Sets]]<br />
*[["Response to" terms]]<br />
*[[GAF 2.1 specs]]<br />
<br />
==How To?==<br />
====How to load the ontology file into Obo-Edit tool directly from the web without downloading the file from cvs etc?====<br />
OBO-Edit can load files from the disk OR from a URL.<br><br />
Choose the "File -> Load..." menu option<br><br />
Choose the OBO File Adapter<br><br />
Type http://www.geneontology.org/ontology/gene_ontology.obo into the filename box<br><br />
(From:http://www.geneontology.org/newsletter/archive/200705.shtml#tip)<br />
<br />
To see the has_part relationships, use this URL for the extended GO version:<br><br />
<br />
http://www.geneontology.org/ontology/obo_format_1_2/gene_ontology_ext.obo<br />
<br />
====How to run Mike Cherry's filtering script locally before checking the GAF into SVN?====<br />
*You need access to SVN to run the script locally. If you don't have access please write to go-admin@genome.stanford.edu<br />
*Familiarize yourself with SVN commands (http://geneontology.org/page/svn-help)<br />
*You need to check out the following files from SVN. The script will fail or will give you inaccurate reports if you don't have the current version of any of the files.<br />
<br />
<pre><br />
<br />
> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/ontology go/ontology<br />
username@ext.geneontology.org's password:<br />
[this will co the entire directory]<br />
<br />
> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/gene-associations/submission go/gene-associations/submission<br />
username@ext.geneontology.org's password:<br />
[this will co the entire directory]<br />
<br />
>svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/software/utilities go/software/utilities<br />
username@ext.geneontology.org's password:<br />
<br />
> svn --non-interactive --trust-server-cert --ignore-externals co svn+ssh://username@ext.geneontology.org/share/go/svn/trunk/doc/ go/doc<br />
username@ext.geneontology.org's password:<br />
<br />
</pre><br />
<br />
Now you have the necessary files to run the script in your space.<br />
<br />
* cd to the gene-associations/submission directory<br />
<pre> <br />
>cd go/gene-associations/submission<br />
<br />
>../../software/utilities/filter-gene-association.pl -e -i gene_association.sgd.gz<br />
<br />
You should see the filtering script report once the script runs through the file.<br />
</pre><br />
<br />
==Annotation Conference calls==<br />
<br />
*[[Annotation Call 2017 Minutes]]<br />
<br />
*[[LEGO Discussion Rota]]<br />
<br />
* Calls are held on the 2nd and 4th Tuesday of each month. at 4pm GMT, 8am PDT. <br />
* Please contact David and Kimberly if there are items you would like to add to the agenda.<br />
* Recurring meeting URL: https://stanford.zoom.us/j/976175422<br />
<br />
to join via phone: enter Meeting ID 976175422 after dialing in<br />
*from US: +1 408 638 0968 (US Toll) or +1 646 558 8656 (US Toll)<br />
*from UK: +44 (0) 20 3695 0088 or +44 (0) 80 0031 5717<br />
*from Switzerland: +41 (0) 31 528 0988 or +41 800 002 622<br />
<br />
* Past Annotation Call Minutes: [[Annotation Call 2010 Minutes | 2010]] | [[Annotation Call 2011 Minutes |2011]] | [[Annotation Call 2012 Minutes | 2012]] | [[Annotation Call 2013 Minutes | 2013]] | [[Annotation Call 2014 Minutes | 2014]] | [[Annotation Call 2015 Minutes | 2015]] | [[Annotation Call 2016 Minutes | 2016]]<br />
*Curation Consistency Rota: [[Curation Consistency Rota | 2015]] | [[Curation Consistency Rota 2016 | 2016]]<br />
<br />
==Combined GO-CAM/GPAD calls==<br />
Meetings are the 2nd and 4th Wednesday of each month 11:00AM Eastern, 4:00PM Greenwich, 8:00AM Pacific<br />
<br />
<br />
*[[LEGO Annotation Calls 2015 Minutes | 2015]]<br />
*2016<br />
[[LEGO January 4, 2016]]<br />
<br />
[[LEGO January 18, 2016]]<br />
<br />
[[LEGO February 1, 2016]]<br />
<br />
[[LEGO February 15, 2016]]<br />
<br />
[[LEGO March 7, 2016]]<br />
<br />
[[LEGO March 21, 2016]]<br />
<br />
[[LEGO March 28, 2016]]<br />
<br />
[[LEGO April 4, 2016]]<br />
<br />
[[LEGO April 25, 2016]]<br />
<br />
[[LEGO May 2, 2016]]<br />
<br />
[[LEGO May 9, 2016]]<br />
<br />
[[LEGO May 16, 2016]]<br />
<br />
[[LEGO May 23, 2016]]<br />
<br />
[[LEGO June 6, 2016]]<br />
<br />
[[LEGO June 13, 2016]]<br />
<br />
[[LEGO June 20, 2016]]<br />
<br />
[[LEGO June 27, 2016]]<br />
<br />
[[LEGO July 11, 2016]]<br />
<br />
[[LEGO July 18, 2016]]<br />
<br />
[[LEGO July 25, 2016]]<br />
<br />
[[LEGO August 8, 2016]]<br />
<br />
[[LEGO August 15, 2016]]<br />
<br />
[[LEGO August 22, 2016]]<br />
<br />
[[LEGO August 29, 2016]]<br />
<br />
[[LEGO September 12, 2016]]<br />
<br />
[[LEGO September 19, 2016]]<br />
<br />
[[LEGO September 26, 2016]]<br />
<br />
[[LEGO October 5, 2016]]<br />
<br />
[[LEGO October 10, 2016]]<br />
<br />
[[LEGO October 17, 2016]]<br />
<br />
[[LEGO October 24, 2016]]<br />
<br />
[[LEGO October 31, 2016]]<br />
<br />
[[GO-CAM May 10th, 2016]]<br />
<br />
[[GO-CAM May 24th, 2017]]<br />
<br />
[[GO-CAM June 14th, 2017]]<br />
<br />
[[GO-CAM June 28th, 2017]]<br />
<br />
[[GO-CAM July 12th, 2017]]<br />
<br />
[[GO-CAM ectopic meeting July 19th 2017]]<br />
<br />
==Old GPAD Calls==<br />
<br />
<br />
[[LEGO GAF/GPAD September 28, 2016]]<br />
<br />
[[LEGO GAF/GPAD October 5, 2016]]<br />
<br />
<br />
[[Category:LEGO]]<br />
<br />
==Monthly Reports==<br />
*[[September2011_Annotation_Advocacy_Report|September 2011]]<br />
*[[August2011_Annotation_Advocacy_Report|August 2011]]<br />
*[[July2011_Annotation_Advocacy_Report|July 2011]]<br />
*[[June2011_Annotation_Advocacy_Report|June 2011]]<br />
*[[May2011_Annotation_Advocacy_Report|May 2011]]<br />
*[[April2011_Annotation_Advocacy_Report|April 2011]]<br />
*[[March2011_Annotation_Advocacy_Report|March 2011]]<br />
*[[February2011_Annotation_Advocacy_Report|February 2011]]<br />
*[[January2011_Annotation_Advocacy_Report|January 2011]]<br />
*[[December2010_Annotation_Advocacy_Report|December 2010]]<br />
*[[November2010_Annotation_Advocacy_Report|November 2010]]<br />
*[[October2010_Annotation_Advocacy_Report|October 2010]]<br />
*[[September2010_Annotation_Advocacy_Report|September 2010]]<br />
*[[August2010_Annotation_Advocacy_Report|August 2010]]<br />
*[[July2010_Annotation_Advocacy_Report|July 2010]]<br />
*[[Jun2010_Annotation_Advocacy_Report|June 2010]]<br />
<br />
==Meeting calendar==<br />
[[Annotation_topics for next meeting]]<br />
<br />
[[Annotation_31Jan10]]<br />
<br />
[[Annotation_21Dec10]]<br />
<br />
[[Annotation_19Oct10]]<br />
<br />
[[Annotation_21Sept10]]<br />
<br />
[[Annotation_17Aug10]]<br />
<br />
[[Annotation_04Aug10]]<br />
<br />
[[Annotation_19July10]]<br />
<br />
[[Annotation_22June10]]<br />
<br />
[[Annotation_08June10]]<br />
<br />
[[Annotation_01June10]]<br />
<br />
[[Annotation_17May10]]<br />
<br />
[[Annotation_29Apr10]]<br />
<br />
[[Annotation_15Apr10]]<br />
<br />
[[Annotation_08Apr10]]<br />
<br />
[[Annotation_22Mar10]]<br />
<br />
[[Annotation_15Mar10]]<br />
<br />
[[Annotation_10Apr10]]<br />
<br />
==Metrics of success==<br />
* [[Proposal for Author Feedback for annotations]]<br />
<br />
* [[Annotations removed as a result of Annotation QCs]]<br />
<br />
* [http://go.berkeleybop.org/news4go/node/80| Moved to GAF2.0 format on the 1st June 2010]<br />
<br />
==Process==<br />
<br />
[http://gocwiki.geneontology.org/index.php/Annotation_Issues_and_Management Annotation Issues]<br />
<br />
==Issues for the Annotation Group==<br />
# Division of annotation and GO content development effort and feedback between participating databases (UniProtKB and MODs)<br />
<br />
[[Annotations to Catalytic activity with IPI]]<br />
<br />
[[Annotation Quality Control Checks]]<br />
<br />
[[Action items from March 2010 GOC meeting]]</div>David oshttps://wiki.geneontology.org/index.php?title=2017_Berkeley_GO_Editors_Workshop_II&diff=640512017 Berkeley GO Editors Workshop II2017-06-09T17:03:49Z<p>David os: </p>
<hr />
<div>= Agenda (Draft) =<br />
<br />
== Topics ==<br />
<br />
=== Fundamentals ===<br />
* Understanding OWL reasoning. A practical sessions with problem solving exercises, covering:<br />
* Equivalent Class, SubClass; Relations: Characteristics, hierarchy, chains, domain and range; GCIs; advanced querying; explanations.<br />
* Understanding the current GO relation set. (A practical session with problem solving exercises + aim to develop better doc)<br />
* The art of designing robust equivalence axioms & design patterns ( editors would like more guidelines on how to construct these.)<br />
<br />
=== Infrastructure ===<br />
* Design pattern infrastructure<br />
* Pipelines and how they run. Starting jobs with ROBOT.<br />
* Build failures<br />
* Document the various fail messages and how to correct the issues.<br />
<br />
=== Content ===<br />
* Problematic GitHub tickets/mini Projects<br />
<br />
= Logistics =<br />
<br />
== Accommodations ==<br />
<br />
* http://www.fourpointssanfranciscobaybridge.com/<br />
<br />
Getting there:<br />
<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/MacArthur+BART+Station,+40th+Street,+Oakland,+CA/@37.8346259,-122.2866117,15z/am=t/data=!3m1!5s0x80857e0870dbdd83:0x571df460c4d9d3cb!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857de2a98ae50d:0xc5fce433b2157d9f!2m2!1d-122.267047!2d37.8290643!3e3 shuttle from MacArthur BART]<br />
<br />
Taxis also available from either MacArthur or Ashby<br />
<br />
== Meeting Location ==<br />
<br />
[http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/ Berkeley Lab, Aquatic Park Offices]<br />
<br />
Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley<br />
Physical address: 717 Potter Street, Berkeley, CA 94710<br />
<br />
=== Travel between hotel and meeting ===<br />
<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8448697,-122.3011831,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e2 Walk, 1.3 miles]<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8450306,-122.3024045,15z/am=t/data=!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e3 Free Hollis Shuttle ]<br />
* Taxi/Lyft/Uber<br />
<br />
Aim to be at the lab for 9am<br />
<br />
== Participants ==<br />
<br />
{| {{Prettytable}}<br />
|-<br />
! Name<br />
! Organization<br />
! Comments<br />
|-<br />
| David Hill<br />
| Jackson Laboratory<br />
| <br />
|<br />
|-<br />
|Harold Drabkin<br />
| Jackson Laboratory<br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| Caltech<br />
| <br />
|-<br />
| Pascale Gaudet<br />
| SIB Swiss Institute of Bioinformatics<br />
| <br />
|-<br />
| David Osumi-Sutherland<br />
| EBI<br />
| <br />
|-<br />
| Karen Christie<br />
| Jackson Laboratory<br />
| <br />
|-<br />
|}<br />
<br />
[[Category:Meetings]]<br />
[[Category:Protege]]</div>David oshttps://wiki.geneontology.org/index.php?title=2017_Berkeley_GO_Editors_Workshop_II&diff=640492017 Berkeley GO Editors Workshop II2017-06-09T11:40:16Z<p>David os: /* Topics */</p>
<hr />
<div>= Agenda =<br />
<br />
== Topics ==<br />
<br />
=== Fundamentals ===<br />
* Understanding OWL reasoning. A practical sessions with problem solving exercises, covering:<br />
* Equivalent Class, SubClass; Relations: Characteristics, hierarchy, chains, domain and range; GCIs; advanced querying; explanations.<br />
* Understanding the current GO relation set. (A practical session with problem solving exercises + aim to develop better doc)<br />
* The art of designing robust equivalence axioms & design patterns ( editors would like more guidelines on how to construct these.)<br />
<br />
=== Infrastructure ===<br />
* Design pattern infrastructure<br />
* Pipelines and how they run. Starting jobs with ROBOT.<br />
* Build failures<br />
* Document the various fail messages and how to correct the issues.<br />
<br />
=== Content ===<br />
* Problematic GitHub tickets/mini Projects<br />
<br />
= Logistics =<br />
<br />
== Accommodations ==<br />
<br />
* http://www.fourpointssanfranciscobaybridge.com/<br />
<br />
Getting there:<br />
<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/MacArthur+BART+Station,+40th+Street,+Oakland,+CA/@37.8346259,-122.2866117,15z/am=t/data=!3m1!5s0x80857e0870dbdd83:0x571df460c4d9d3cb!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857de2a98ae50d:0xc5fce433b2157d9f!2m2!1d-122.267047!2d37.8290643!3e3 shuttle from MacArthur BART]<br />
<br />
Taxis also available from either MacArthur or Ashby<br />
<br />
== Meeting Location ==<br />
<br />
[http://biosciopsatberkeley.lbl.gov/location/aquatic-park-office/ Berkeley Lab, Aquatic Park Offices]<br />
<br />
Lawrence Berkeley National Laboratory (LBNL), Aquatic Park office of Biosciences Operations at Berkeley<br />
Physical address: 717 Potter Street, Berkeley, CA 94710<br />
<br />
=== Travel between hotel and meeting ===<br />
<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8448697,-122.3011831,15z/data=!3m1!4b1!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e2 Walk, 1.3 miles]<br />
* [https://www.google.com/maps/dir/Four+Points+by+Sheraton+San+Francisco+Bay+Bridge,+Powell+Street,+Emeryville,+CA/717+Potter+St,+Berkeley,+CA+94710/@37.8450306,-122.3024045,15z/am=t/data=!4m14!4m13!1m5!1m1!1s0x80857e44a03ff3e3:0xc502416c1c31eb3a!2m2!1d-122.2939195!2d37.8381923!1m5!1m1!1s0x80857ef68fea8821:0xeaa3c4e92d0ec6a9!2m2!1d-122.294537!2d37.85145!3e3 Free Hollis Shuttle ]<br />
* Taxi/Lyft/Uber<br />
<br />
Aim to be at the lab for 9am<br />
<br />
== Participants ==<br />
<br />
{| {{Prettytable}}<br />
|-<br />
! Name<br />
! Organization<br />
! Comments<br />
|-<br />
| David Hill<br />
| Jackson Laboratory<br />
| <br />
|<br />
|-<br />
| Kimberly Van Auken<br />
| Caltech<br />
| <br />
|-<br />
| Pascale Gaudet<br />
| SIB Swiss Institute of Bioinformatics<br />
| <br />
|-<br />
| David Osumi-Sutherland<br />
| EBI<br />
| <br />
|-<br />
| Karen Christie<br />
| Jackson Laboratory<br />
| <br />
|-<br />
|}<br />
<br />
[[Category:Meetings]]<br />
[[Category:Protege]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2017-05-26&diff=63963Ontology meeting 2017-05-262017-05-29T16:01:30Z<p>David os: /* Adding 'transport' as a relation in RO */</p>
<hr />
<div>= Conference Line =<br />
*Bluejeans: https://bluejeans.com/164681006<br />
<br />
= Agenda =<br />
<br />
== github Ontology Projects ==<br />
*See: [https://github.com/geneontology/go-ontology/projects/1 Ontology call May 26, 2017]<br />
<br />
== Discussion points (Pascale): ==<br />
# NTR RO: 'transports' https://github.com/oborel/obo-relations/issues/161<br />
# Keeping old stanzas as synonyms for merged terms: Could this rule be relaxed? Sometimes the other name is not appropriate. <br />
# Otherwise- is it possible to move secondary IDs ? For example "GO:0019060 intracellular transport of viral protein in host cell " (https://github.com/geneontology/go-ontology/issues/13478) has synonyms <br />
#* viral capsid transport in host cell nucleus,<br />
#* intracellular viral protein transport,<br />
#* intracellular viral capsid transport and<br />
#* viral capsid transport in host cell cytoplasm<br />
Presumably the merge was done to the wrong term, these seem like synonyms for 'GO:0075733 intracellular transport of virus'<br />
<br />
== GO Ontology Editors Documentation ==<br />
* Moni has deployed the GO editors docs on RTD, available at http://go-ontology.readthedocs.io/en/latest/ <br />
** It's not yet complete; e.g. we should add a page about how you edit the docs themselves. Now we have everything in place, it's easy!<br />
** All of the pages are an individual md page in our repo. See: https://github.com/geneontology/go-ontology/tree/master/docs E.g. https://github.com/geneontology/go-ontology/blob/master/docs/Installgit.md<br />
** These can be edited like any other file on github. You can do this from your local copies of the files, but you may find it more convenient to edit via the github web interface, just click the pencil icon. After the changes go into master, it gets deployed on RTD!<br />
** Adding new pages is also easy, do this the usual way, and make sure the TOC in index.rst is updated.<br />
** David OS - do you think it makes sense to fold in the auto-generated pattern docs here?<br />
<br />
== GOC Meeting ==<br />
*Review agenda items<br />
<br />
= Minutes =<br />
*On call: Chris, David OS, Eric, Harold, Jim, Karen, Kimberly, Moni, Pascale, Suzi, Tanya<br />
<br />
== Adding 'transport' as a relation in RO ==<br />
*The existing relation, 'transports or maintains localization of', may be more than is needed for some terms<br />
*A simpler 'transport' relation could be added as a child of 'transports of maintains localization of'<br />
**This would not, presumably, break things<br />
**We do still need the 'maintains' concept in a parent relation, though<br />
<br />
*There is also import and export and these are not used quite consistently throughout the ontology<br />
**The high level terms for import and export do not specify from where to where, so are not very useful.<br />
** Their usage should be reviewed.<br />
** Specific import and export terms can be defined entirely wrt start and end points - no need for specific relations.<br />
<br />
*How best do we distinguish maintenance vs transport. <br />
** The definitions for each branch are now reasonably clear. But guidance for evidence may be tricky.<br />
*This is an area of GO that may be overly complicated<br />
**Localization is mixed with location<br />
**It will be a pretty big job to untangle all of this.<br />
<br />
<br />
*AI: Make new 'transports' and 'occurs across' relations. The latter will replace 'results in transport across'<br />
https://github.com/oborel/obo-relations/issues/166<br />
<br />
== Old term names as synonyms ==<br />
*Right now, there is a check that requires the merged term name to be kept as a synonym<br />
*But, sometimes, the new term name might not be appropriate<br />
*Or, if two terms were incorrectly merged, then you might want to remove some synonyms<br />
*Some term names are actually confusing, and if the term is merged, then it might be nice to have the option to remove the term name altogether <br />
*Is it worth keeping the check in just in case people forget to add them?<br />
*Yes, since there's another way around removing synonyms<br />
== Viral processes ==<br />
*Pascale has worked on this branch of the ontology to make sure that viral proteins are not annotated to cellular processes<br />
*Kimberly and Pascale will check on some existing annotations<br />
== Design patterns for compound functions ==<br />
*Using has_part relations for receptor terms fails to classify receptors with receptor and effector functions and would break GO-CAM inferences<br />
*Solution is to use has_component relations and its children<br />
*Using ATPase as an example, the annotated entity would be inferred to be an ATPase, but that relation would not exist in the ontology<br />
*Using transcription factor example, has_necessary_component DNA binding<br />
**Side discussion about representing protein complexes in Noctua - what will best practices be?<br />
**Side discussion about Noctua template for transcription <br />
**In order to get the proper reasoning, brought back a superclass of 'transcriptional regulator' activity<br />
== Editors Documentation ==<br />
*Now on [http://go-ontology.readthedocs.io/en/latest/ Read the Docs]<br />
*Please double-check and send any feedback to Moni<br />
*Still some comments on the Google doc that are unresolved<br />
*At this point, edits should be made on the md files on github and then generate a pull request<br />
<br />
<br />
[[Category: Ontology]]<br />
[[Category: Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=637342017 Corvallis GOC Meeting Agenda2017-05-05T16:44:19Z<p>David os: /* Attendees */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
https://github.com/geneontology/go-ontology/issues/13472<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this?<br />
*Parts of GO infrastructure being re-used by AGR (Chris)<br />
** db-xrefs.yaml<br />
<br />
==Update on Ontology Editing==<br />
<br />
* David + Chris 20min<br />
* Design Pattern Updates: David OS + Chris 20 mins<br />
* Ontology Documentation: Moni 10 mins<br />
* [https://github.com/geneontology/go-ontology/issues/13384 Curator notes and propagation]<br />
* Proposal: text mining github tickets for ontology terms (Chris, Kimberly)<br />
<br />
==MF refactoring (Paul, DavidOS) ==<br />
<br />
30 mins<br />
<br />
* Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
<br />
Emphasis on practical implications for LEGO curation (templates).<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
IS THERE A TICKET FOR THIS ON THE ECO TRACKER?<br />
<br />
I think it might be this one:<br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/117<br />
<br />
There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.: <br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854<br />
<br />
== Noctua and SIGNOR2 ==<br />
<br />
* https://github.com/geneontology/noctua/issues/413<br />
<br />
Chris/PaulT<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
<br />
https://github.com/geneontology/noctua/issues/418<br />
<br />
David + others? 30 min<br />
<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
*GP-CC Should we allow direct GO part_of CC assertion (rather than via GO <-- enabled_by MF occurs_in --> CC). This is more accurate in some cases e.g. for membrane components.<br />
<br />
== Use of Qualifiers in Legacy Annotations ==<br />
<br />
(this should probably come before the go-cam->gaf pipeline above)<br />
<br />
* RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
** [https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit# Additional document]<br />
* [https://gist.github.com/cmungall/4ed28123c3db832a7d99cbdd8e8a5920 Straw man BP refactor] Chris<br />
<br />
==Annotation of Viral Processes==<br />
*[https://github.com/geneontology/go-ontology/issues/13214 13214]<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
**Transcription, translation of viral genome<br />
<br />
* DOS proposal for multi-organism annotation (reviving old proposal) - poss allowing non-cannonical function to be separable<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Helen, Pascale & Sylvain<br />
<br />
See notes /list of papers:<br />
<br />
=== Transcription-Factor decision tree===<br />
Ruth (20mins?)<br />
<br />
https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
=== GO Rules System ===<br />
Eric<br />
<br />
===Consistent use of the type field in GAFs/GPAD===<br />
<br />
Chris <br />
<br />
* E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
* Via ontobio python library (Chris)<br />
** Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
<br />
== PAINT update==<br />
Pascale and Huaiyu<br />
<br />
* Analysis of the PAINT annotation.<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|-<br />
| David OS<br />
| EBI<br />
| Y<br />
| Y<br />
| N<br />
| AM<br />
| N<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=637332017 Corvallis GOC Meeting Agenda2017-05-05T16:42:57Z<p>David os: /* Annotation of Viral Processes */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
https://github.com/geneontology/go-ontology/issues/13472<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this?<br />
*Parts of GO infrastructure being re-used by AGR (Chris)<br />
** db-xrefs.yaml<br />
<br />
==Update on Ontology Editing==<br />
<br />
* David + Chris 20min<br />
* Design Pattern Updates: David OS + Chris 20 mins<br />
* Ontology Documentation: Moni 10 mins<br />
* [https://github.com/geneontology/go-ontology/issues/13384 Curator notes and propagation]<br />
* Proposal: text mining github tickets for ontology terms (Chris, Kimberly)<br />
<br />
==MF refactoring (Paul, DavidOS) ==<br />
<br />
30 mins<br />
<br />
* Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
<br />
Emphasis on practical implications for LEGO curation (templates).<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
IS THERE A TICKET FOR THIS ON THE ECO TRACKER?<br />
<br />
I think it might be this one:<br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/117<br />
<br />
There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.: <br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854<br />
<br />
== Noctua and SIGNOR2 ==<br />
<br />
* https://github.com/geneontology/noctua/issues/413<br />
<br />
Chris/PaulT<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
<br />
https://github.com/geneontology/noctua/issues/418<br />
<br />
David + others? 30 min<br />
<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
*GP-CC Should we allow direct GO part_of CC assertion (rather than via GO <-- enabled_by MF occurs_in --> CC). This is more accurate in some cases e.g. for membrane components.<br />
<br />
== Use of Qualifiers in Legacy Annotations ==<br />
<br />
(this should probably come before the go-cam->gaf pipeline above)<br />
<br />
* RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
** [https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit# Additional document]<br />
* [https://gist.github.com/cmungall/4ed28123c3db832a7d99cbdd8e8a5920 Straw man BP refactor] Chris<br />
<br />
==Annotation of Viral Processes==<br />
*[https://github.com/geneontology/go-ontology/issues/13214 13214]<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
**Transcription, translation of viral genome<br />
<br />
* DOS proposal for multi-organism annotation (reviving old proposal) - poss allowing non-cannonical function to be separable<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Helen, Pascale & Sylvain<br />
<br />
See notes /list of papers:<br />
<br />
=== Transcription-Factor decision tree===<br />
Ruth (20mins?)<br />
<br />
https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
=== GO Rules System ===<br />
Eric<br />
<br />
===Consistent use of the type field in GAFs/GPAD===<br />
<br />
Chris <br />
<br />
* E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
* Via ontobio python library (Chris)<br />
** Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
<br />
== PAINT update==<br />
Pascale and Huaiyu<br />
<br />
* Analysis of the PAINT annotation.<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=637322017 Corvallis GOC Meeting Agenda2017-05-05T16:34:19Z<p>David os: /* GAFs and GPADs from Noctua models */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
https://github.com/geneontology/go-ontology/issues/13472<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this?<br />
*Parts of GO infrastructure being re-used by AGR (Chris)<br />
** db-xrefs.yaml<br />
<br />
==Update on Ontology Editing==<br />
<br />
* David + Chris 20min<br />
* Design Pattern Updates: David OS + Chris 20 mins<br />
* Ontology Documentation: Moni 10 mins<br />
* [https://github.com/geneontology/go-ontology/issues/13384 Curator notes and propagation]<br />
* Proposal: text mining github tickets for ontology terms (Chris, Kimberly)<br />
<br />
==MF refactoring (Paul, DavidOS) ==<br />
<br />
30 mins<br />
<br />
* Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
<br />
Emphasis on practical implications for LEGO curation (templates).<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
IS THERE A TICKET FOR THIS ON THE ECO TRACKER?<br />
<br />
I think it might be this one:<br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/117<br />
<br />
There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.: <br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854<br />
<br />
== Noctua and SIGNOR2 ==<br />
<br />
* https://github.com/geneontology/noctua/issues/413<br />
<br />
Chris/PaulT<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
<br />
https://github.com/geneontology/noctua/issues/418<br />
<br />
David + others? 30 min<br />
<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
*GP-CC Should we allow direct GO part_of CC assertion (rather than via GO <-- enabled_by MF occurs_in --> CC). This is more accurate in some cases e.g. for membrane components.<br />
<br />
== Use of Qualifiers in Legacy Annotations ==<br />
<br />
(this should probably come before the go-cam->gaf pipeline above)<br />
<br />
* RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
** [https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit# Additional document]<br />
* [https://gist.github.com/cmungall/4ed28123c3db832a7d99cbdd8e8a5920 Straw man BP refactor] Chris<br />
<br />
==Annotation of Viral Processes==<br />
*[https://github.com/geneontology/go-ontology/issues/13214 13214]<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
**Transcription, translation of viral genome<br />
<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Helen, Pascale & Sylvain<br />
<br />
See notes /list of papers:<br />
<br />
=== Transcription-Factor decision tree===<br />
Ruth (20mins?)<br />
<br />
https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
=== GO Rules System ===<br />
Eric<br />
<br />
===Consistent use of the type field in GAFs/GPAD===<br />
<br />
Chris <br />
<br />
* E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
* Via ontobio python library (Chris)<br />
** Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
<br />
== PAINT update==<br />
Pascale and Huaiyu<br />
<br />
* Analysis of the PAINT annotation.<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=637302017 Corvallis GOC Meeting Agenda2017-05-05T16:16:09Z<p>David os: /* ECO */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
https://github.com/geneontology/go-ontology/issues/13472<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this?<br />
*Parts of GO infrastructure being re-used by AGR (Chris)<br />
** db-xrefs.yaml<br />
<br />
==Update on Ontology Editing==<br />
<br />
* David + Chris 20min<br />
* Design Pattern Updates: David OS + Chris 20 mins<br />
* Ontology Documentation: Moni 10 mins<br />
* [https://github.com/geneontology/go-ontology/issues/13384 Curator notes and propagation]<br />
* Proposal: text mining github tickets for ontology terms (Chris, Kimberly)<br />
<br />
==MF refactoring (Paul, DavidOS) ==<br />
<br />
30 mins<br />
<br />
* Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
<br />
Emphasis on practical implications for LEGO curation (templates).<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
IS THERE A TICKET FOR THIS ON THE ECO TRACKER?<br />
<br />
I think it might be this one:<br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/117<br />
<br />
There are lots of things under the ECO code that maps to IDA that are perturbations, not assays e.g.: <br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854<br />
<br />
== Noctua and SIGNOR2 ==<br />
<br />
* https://github.com/geneontology/noctua/issues/413<br />
<br />
Chris/PaulT<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
<br />
David + others? 30 min<br />
<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
<br />
== Use of Qualifiers in Legacy Annotations ==<br />
<br />
(this should probably come before the go-cam->gaf pipeline above)<br />
<br />
* RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
** [https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit# Additional document]<br />
* [https://gist.github.com/cmungall/4ed28123c3db832a7d99cbdd8e8a5920 Straw man BP refactor] Chris<br />
<br />
==Annotation of Viral Processes==<br />
*[https://github.com/geneontology/go-ontology/issues/13214 13214]<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
**Transcription, translation of viral genome<br />
<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Helen, Pascale & Sylvain<br />
<br />
See notes /list of papers:<br />
<br />
=== Transcription-Factor decision tree===<br />
Ruth (20mins?)<br />
<br />
https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
=== GO Rules System ===<br />
Eric<br />
<br />
===Consistent use of the type field in GAFs/GPAD===<br />
<br />
Chris <br />
<br />
* E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
* Via ontobio python library (Chris)<br />
** Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
<br />
== PAINT update==<br />
Pascale and Huaiyu<br />
<br />
* Analysis of the PAINT annotation.<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=637292017 Corvallis GOC Meeting Agenda2017-05-05T16:14:10Z<p>David os: /* ECO */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
https://github.com/geneontology/go-ontology/issues/13472<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this?<br />
*Parts of GO infrastructure being re-used by AGR (Chris)<br />
** db-xrefs.yaml<br />
<br />
==Update on Ontology Editing==<br />
<br />
* David + Chris 20min<br />
* Design Pattern Updates: David OS + Chris 20 mins<br />
* Ontology Documentation: Moni 10 mins<br />
* [https://github.com/geneontology/go-ontology/issues/13384 Curator notes and propagation]<br />
* Proposal: text mining github tickets for ontology terms (Chris, Kimberly)<br />
<br />
==MF refactoring (Paul, DavidOS) ==<br />
<br />
30 mins<br />
<br />
* Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
<br />
Emphasis on practical implications for LEGO curation (templates).<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
IS THERE A TICKET FOR THIS ON THE ECO TRACKER?<br />
<br />
I think it might be this one:<br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/117<br />
<br />
There are lots of things under IDA <br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/123#issuecomment-281041854<br />
<br />
== Noctua and SIGNOR2 ==<br />
<br />
* https://github.com/geneontology/noctua/issues/413<br />
<br />
Chris/PaulT<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
<br />
David + others? 30 min<br />
<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
<br />
== Use of Qualifiers in Legacy Annotations ==<br />
<br />
(this should probably come before the go-cam->gaf pipeline above)<br />
<br />
* RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
** [https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit# Additional document]<br />
* [https://gist.github.com/cmungall/4ed28123c3db832a7d99cbdd8e8a5920 Straw man BP refactor] Chris<br />
<br />
==Annotation of Viral Processes==<br />
*[https://github.com/geneontology/go-ontology/issues/13214 13214]<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
**Transcription, translation of viral genome<br />
<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Helen, Pascale & Sylvain<br />
<br />
See notes /list of papers:<br />
<br />
=== Transcription-Factor decision tree===<br />
Ruth (20mins?)<br />
<br />
https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
=== GO Rules System ===<br />
Eric<br />
<br />
===Consistent use of the type field in GAFs/GPAD===<br />
<br />
Chris <br />
<br />
* E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
* Via ontobio python library (Chris)<br />
** Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
<br />
== PAINT update==<br />
Pascale and Huaiyu<br />
<br />
* Analysis of the PAINT annotation.<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=637282017 Corvallis GOC Meeting Agenda2017-05-05T16:12:25Z<p>David os: /* MF refactoring (Paul, DavidOS) */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
*This year's goals<br />
<br />
==Pipeline Migration== <br />
Seth & Chris 20 mins<br />
<br />
== New APIs==<br />
<br />
Seth & Chris 20 mins<br />
<br />
== TermGenie replacement ==<br />
<br />
https://github.com/geneontology/go-ontology/issues/13472<br />
Chris 20 mins<br />
<br />
== Graph Store update ==<br />
Eric 10 mins<br />
<br />
==GO and AGR==<br />
*What does GO need to do for AGR?<br />
*Is there anything that GO curators should do any differently for this?<br />
*Parts of GO infrastructure being re-used by AGR (Chris)<br />
** db-xrefs.yaml<br />
<br />
==Update on Ontology Editing==<br />
<br />
* David + Chris 20min<br />
* Design Pattern Updates: David OS + Chris 20 mins<br />
* Ontology Documentation: Moni 10 mins<br />
* [https://github.com/geneontology/go-ontology/issues/13384 Curator notes and propagation]<br />
* Proposal: text mining github tickets for ontology terms (Chris, Kimberly)<br />
<br />
==MF refactoring (Paul, DavidOS) ==<br />
<br />
30 mins<br />
<br />
* Issues: https://github.com/geneontology/molecular_function_refactoring/issues<br />
<br />
Emphasis on practical implications for LEGO curation (templates).<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
IS THERE A TICKET FOR THIS ON THE ECO TRACKER?<br />
<br />
I think it might be this one:<br />
<br />
https://github.com/evidenceontology/evidenceontology/issues/117<br />
<br />
== Noctua and SIGNOR2 ==<br />
<br />
* https://github.com/geneontology/noctua/issues/413<br />
<br />
Chris/PaulT<br />
<br />
== GAFs and GPADs from Noctua models ==<br />
<br />
David + others? 30 min<br />
<br />
*Where do we stand?<br />
*Challenges with complex models (evidence)<br />
*All of PRO IDS should be available in Noctua (ids for human, pombe, etc); can these be loaded from PRO directly?<br />
<br />
== Use of Qualifiers in Legacy Annotations ==<br />
<br />
(this should probably come before the go-cam->gaf pipeline above)<br />
<br />
* RO subset for use with GAF/GPAD in qualifier column (Chris/Kimberly/DavidOS)<br />
<br />
== The fate of simple processes==<br />
* What do we consider a single-step process and what is their future?<br />
* [https://github.com/geneontology/go-ontology/issues/12859 GH ticket about single step processes]<br />
* [https://github.com/geneontology/go-ontology/issues/13012 Is this a single step process?]<br />
<br />
==The distinction between cellular processes and processes, do we need it?==<br />
* [https://github.com/geneontology/go-ontology/issues/12849 GH ticket about cellular processes]<br />
** [https://docs.google.com/document/d/1QpfUY_LgeIryMj6EEAE05FXLE_894GalkerBU8dMuVU/edit# Additional document]<br />
* [https://gist.github.com/cmungall/4ed28123c3db832a7d99cbdd8e8a5920 Straw man BP refactor] Chris<br />
<br />
==Annotation of Viral Processes==<br />
*[https://github.com/geneontology/go-ontology/issues/13214 13214]<br />
*Taxon restriction?<br />
*Annotation of host proteins involved in, or co-opted for, viral reproduction<br />
**Transcription, translation of viral genome<br />
<br />
<br />
== Annotation QC issues ==<br />
=== HTP papers ===<br />
Helen, Pascale & Sylvain<br />
<br />
See notes /list of papers:<br />
<br />
=== Transcription-Factor decision tree===<br />
Ruth (20mins?)<br />
<br />
https://github.com/geneontology/go-annotation/issues/1463<br />
<br />
=== Modified protein binding ===<br />
Pascale & Sylvain<br />
<br />
https://github.com/geneontology/go-ontology/issues/12787<br />
<br />
=== GO Rules System ===<br />
Eric<br />
<br />
===Consistent use of the type field in GAFs/GPAD===<br />
<br />
Chris <br />
<br />
* E.g. https://github.com/geneontology/go-annotation/issues/1554<br />
<br />
== Enrichment Analysis ==<br />
Val & Seth<br />
* by default have the enrichment tool run directly on the GO annotation dataset <br />
* by default enable loading a background<br />
* currently missing a substantial number of annotations (e.g. fission yeast)<br />
* Via ontobio python library (Chris)<br />
** Example jupyter notebook: https://github.com/biolink/ontobio/blob/master/notebooks/Phenotype_Enrichment.ipynb<br />
<br />
== PAINT update==<br />
Pascale and Huaiyu<br />
<br />
* Analysis of the PAINT annotation.<br />
<br />
== Contacts for Curation Groups ==<br />
Pascale & David<br />
<br />
Some annotation groups are now gone (no longer annotating), therefore, can't dispute annotations and have no mechanism to update or change them, if needed. <br />
We need to have a mechanism for tracking the status better github go-annotation tracker for annotation disputes can we have some GOC superuser status in Protein2GO that allows GO curators to update annotations<br />
Some groups like JCVI, PAMGO no longer annotate - can GOC take control of these experimental annotations?<br />
<br />
= Attendees =<br />
<br />
Please add your name to the table if you intend to attend the meeting, the dinner, the Noctua workshop, and the Reactome workshop so we can get a headcount estimate. Thank you!<br />
{| {{Prettytable}} class='sortable'<br />
|-<br />
! Name<br />
! Organization<br />
! Are you planning to attend the GOC meeting<br />
! Are you planning to attend the GOC dinner<br />
! Are you bringing a poster? how many?<br />
! Are you planning to attend the Noctua workshop the day after the meeting, Sunday, June 4th?<br />
! Are you planning to attend the Reactome workshop on Monday, June 5th?<br />
|-<br />
| Giulia Antonazzo<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Helen Attrill<br />
| FlyBase<br />
| Y<br />
| Y<br />
|<br />
| N<br />
| N<br />
|-<br />
| Judy Blake<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| N<br />
| N<br />
|-<br />
| Seth Carbon<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Mike Cherry<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Paul Thomas<br />
| USC<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Laurel Cooper<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stacia Engel<br />
| SGD<br />
| Y<br />
| N<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Priyanka Garg<br />
| <br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Parul Gupta<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Tom Hayman<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Emily Heald<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Hill<br />
| MGI<br />
| Y<br />
| Y<br />
| Y-1<br />
| Y<br />
| N<br />
|-<br />
| Doug Howe<br />
| ZFIN<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Ceri Van Slyke<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Sridhar Ramachandran<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| David Fashena<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Leyla Ruzica<br />
| ZFIN<br />
| N<br />
| N<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Pankaj Jaiswal<br />
| Reactome/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Stan Laulederkind<br />
| RGD<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Suzi Lewis<br />
| Berkeley/LBL<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Ruth Lovering<br />
| UCL<br />
| Y<br />
| Y<br />
| Y-3<br />
| Y<br />
| Y<br />
|-<br />
| Austin Meier<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Moni Munoz-Torres<br />
| Berkeley/LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| N<br />
|-<br />
| Sushma Naithani<br />
| Jaiswal Group/Oregon State<br />
| Y<br />
| <br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Darren Natale<br />
| PRO<br />
| Y<br />
| <br />
|<br />
| N<br />
| N<br />
|-<br />
| Sabrina Toro<br />
| Zfin<br />
| Y<br />
| maybe<br />
| N<br />
| Y<br />
| Y<br />
|-<br />
| Kimberly Van Auken<br />
| WB<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Edith Wong<br />
| SGD<br />
| Y<br />
| Y<br />
| N<br />
| Y<br />
| N<br />
|-<br />
| Huaiyu Mi<br />
| USC<br />
| Y<br />
| <br />
|<br />
| Y<br />
| N<br />
|-<br />
| Chris Mungall<br />
| LBL<br />
| Y<br />
| Y<br />
|<br />
| Y<br />
| Y<br />
|-<br />
| Peter D'Eustachio<br />
| Reactome<br />
| Y<br />
| Y<br />
| N?<br />
| Y<br />
| Y<br />
|-<br />
| Maria Martin<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| N<br />
| N<br />
|-<br />
| Tony Sawford<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| N<br />
| N<br />
| N<br />
|-<br />
| Alice Shypitsyna<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| ?<br />
|-<br />
| George Georghiou<br />
| EMBL-EBI<br />
| Y<br />
| Y<br />
| Y(1)<br />
| Y<br />
| Y<br />
|-<br />
| Pascale Gaudet<br />
| GOC/SIB Swiss Institute of Bioinformtaics<br />
| Y<br />
| Y<br />
| ?<br />
| Y<br />
| Y<br />
|-<br />
|}<br />
<br />
*NOT ATTENDING:<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=632122017 Corvallis GOC Meeting Agenda2017-02-20T10:52:13Z<p>David os: /* MF refactoring */</p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
<br />
==Introduction to Ontology Editing (David, Chris)==<br />
*How are new terms added?<br />
<br />
==MF refactoring (Paul, David) ==<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2017_Corvallis_GOC_Meeting_Agenda&diff=632112017 Corvallis GOC Meeting Agenda2017-02-20T10:51:39Z<p>David os: </p>
<hr />
<div>=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics ==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
<br />
==Overview/Plan for Upcoming Year==<br />
*GO PIs presentation<br />
<br />
==Introduction to Ontology Editing (David, Chris)==<br />
*How are new terms added?<br />
<br />
==MF refactoring==<br />
<br />
== ECO ==<br />
<br />
Mapping to classic GO evidence codes. The official mapping of IMP to ECO is not sufficiently broad. Should cover non-genetic perturbations (e.g. pharmacological).<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Protege_setup_for_GO_Eds&diff=62789Protege setup for GO Eds2016-12-20T16:16:14Z<p>David os: /* Setting username and auto-adding creation date */</p>
<hr />
<div>= Protege setup for GO =<br />
<br />
== Which Protege version: ==<br />
<br />
Protege 4.3 is stable and relatively free of bugs. However, it does not support OBO to OWL conversion and so requires that GO be converted to OWL for editing and then converted back again for committing to the repository.<br />
<br />
Protege 5 beta21 and higher correctly load and save OBO files. However, preliminary testing suggests that beta21 is not sufficiently stable for anything but relatively brief editing sessions. It also doesn't support the OBO graph view plugin (see below).<br />
<br />
Protege 5.0.0 is currently recommended by Chris (06.20.16)<br />
"And by Protege 5, I mean the stable release version, not the beta. Get this from [http://protege.stanford.edu protege.stanford.edu]<br />
Don't use 4, or a 5-beta"<br />
<br />
== Setting memory ==<br />
<br />
Protege needs at least 4G of RAM to cope with the GO. This is set by specifying the following -Xmx argument for the java. E.g. for 6G, specify -Xmx6000M. How to set this varies with the OS and Protege version. If launching from ./run.command, edit run.command to jre/bin/java -Xmx6000M. If running from Protege_n.app on a mac, you need to find and edit the -Xmx entry in an XML file called info.plist under Protege_n.app/.<br />
<br />
Update for P5: apparently no need to increase memory settings. The info.plist file now has an Xss option which specifies the stack size. It was increased from the default to support reasoning with some particular biomedical ontologies (see https://github.com/protegeproject/protege/issues/457).<br />
<br />
== Protege layout: ==<br />
<br />
Protege has a highly configurable layout and a plugin architecture. You can control which components are visible from the window menu. Selecting something from the view menu allows you to create a new subwindow in a tab with the component of your choice - just move the target icon to the location you want and click.<br />
<br />
[[Image:Protege_setup_images-media-image03.png]]<br />
<br />
As many plugins come with the standard download, the default layout may be intimidating, but can easily be simplified: The following tabs are sufficient for GO work:<br />
<br />
[[Image:Protege_setup_images-media-image08.png]]<br />
<br />
You'll have to create the OBO graph tab yourself. (see below, as part of the Installing Plugins section)<br />
<br />
== Installing plugins: ==<br />
<br />
The following plugins should be installed from the Protégé menus: File&gt;Check for plugins&gt; <br />
<br />
<ul><br />
<li><blockquote><p>Search Annotations –search for terms and displays the list of matching results</p></blockquote></li></ul> (according to Chris, no longer necessary with P5)<br />
<br />
The following plugins should be dropped into the plugins folder of your Protege installation (this varies with OS and Protege version. Example for Protege 4.3 on a mac: cp &lt;some_plugin&gt;.jar Protege-4.3.app/Contents/Resources/Java/plugins/. <br />
<br />
This directory structure for P5 is<br />
'''Protege-5.0.0.app/Contents/Java/plugins/'''. <br />
To see the directory structure so that <br />
you can drag and drop files, you'll need to control-click/right click on the app icon, then select 'Show Package Contents' and drill down to <br />
the directory you want. Note there are two plugins folders. Make sure you use the correct one.<br />
<br />
<ol style="list-style-type: decimal;"><br />
<li><blockquote><p>[https://github.com/liveontologies/elk-reasoner/releases ''ELK OWL reasoner''] Make sure you choose a version appropriate to your Protege version.</p></blockquote> (In P5, the latest ELK can be found using File>Check for Plugins)</li><br />
<li><blockquote><p>[https://github.com/hdietze/protege-obo-plugins/raw/master/org.protege.oboeditor.jar ''OBO Annotation '']– add and edit terms more easily</p></blockquote> Have this view show up by going to the Entities tab, selecting Window>Views>OBO Views>OBO Annotation. Drag the black circle that appears to the area where you want it and click. The panel will appear.</li><br />
<li><blockquote><p>[http://code.google.com/p/obographview/ ''OBO Graph View Component''] – For all you hairball fans - this plugin displays an OBO-style connected graph of classification (is_a) and other relationship types. (Be careful what you wish for).</p></blockquote><br />
To make this a tab:<br />
<br />
*Window > Create New Tab<br />
[[File:OBO_Graph_plugin.png]]<br />
*Window > Views > Ontology Views > OBO Graph View Component<br />
*Take the black circle, put into the Tab you just created and click within it.<br />
</li><br />
<li><blockquote><p>[https://github.com/balhoff/obo-actions/downloads ''Obsoletion plugin''] - Once installed, you should see an &quot;obsolete&quot; option in your Edit menu..</p></blockquote></li></ol><br />
<br />
[[File:Obsoletion_option.png]]<br />
<br />
== Setting ID range ==<br />
<br />
Protege>Preferences>New Entities Tab<br />
<br />
Click on Preferences under the main menu to get this window.<br />
<br />
[[Image:Protege_setup_images-media-image09.png]]<br />
<br />
WARNING: The ID generator in Protege doesn't overwrite existing IRIs, but it can't cope with the OBO alt_id system - where losing IDs following a merge are stored in annotation properties This system is problematic for OWL translations as it leads to the loss or IRIs. Without IRIs, this ID generator doesn't know about the IDs and will stomp on them if they fall in the specified ID range. Until this is fixed,<br />
<br />
We plan to move to a system in which obsolete classes with these IRIs are created for all alt_ids on OBO to OWL translation.<br />
<br />
== Setting username and auto-adding creation date ==<br />
<br />
Protege>Preferences>New Entities Metadata tab<br />
[[File:New_entity_metadata.png]]<br />
<br />
<br />
Broken in 5.0 See: https://github.com/protegeproject/protege/issues/283#issuecomment-177656593<br />
Seems to work in 5.1<br />
<br />
== Setting Rendering ==<br />
<br />
(The default settings may be fine, but details are included for reference)<br />
<br />
Protege allows users to set the annotation property to be used for rendering OWL entities (classes, object properties, annotation properties, individuals) in graphs, trees and text etc. This should be set to rdfs:label, as follows:<br />
<br />
[[Image:Protege_setup_images-media-image07.png]]<br />
<br />
[[Image:Protege_setup_images-media-image02.png]]<br />
<br />
'''Background on rendering.''' All entities in OWL are identified by an IRI. This includes annotation properties such as label. In the absence of an annotation to annotation property specified as suitable for rendering, the short form of this IRI (the bit following a '#' or a '/') is used.<br />
<br />
[[Category:GO Editors]]<br />
[[Category:Protege]]</div>David oshttps://wiki.geneontology.org/index.php?title=Protege_setup_for_GO_Eds&diff=62788Protege setup for GO Eds2016-12-20T16:15:20Z<p>David os: Undo revision 62787 by David os (talk)</p>
<hr />
<div>= Protege setup for GO =<br />
<br />
== Which Protege version: ==<br />
<br />
Protege 4.3 is stable and relatively free of bugs. However, it does not support OBO to OWL conversion and so requires that GO be converted to OWL for editing and then converted back again for committing to the repository.<br />
<br />
Protege 5 beta21 and higher correctly load and save OBO files. However, preliminary testing suggests that beta21 is not sufficiently stable for anything but relatively brief editing sessions. It also doesn't support the OBO graph view plugin (see below).<br />
<br />
Protege 5.0.0 is currently recommended by Chris (06.20.16)<br />
"And by Protege 5, I mean the stable release version, not the beta. Get this from [http://protege.stanford.edu protege.stanford.edu]<br />
Don't use 4, or a 5-beta"<br />
<br />
== Setting memory ==<br />
<br />
Protege needs at least 4G of RAM to cope with the GO. This is set by specifying the following -Xmx argument for the java. E.g. for 6G, specify -Xmx6000M. How to set this varies with the OS and Protege version. If launching from ./run.command, edit run.command to jre/bin/java -Xmx6000M. If running from Protege_n.app on a mac, you need to find and edit the -Xmx entry in an XML file called info.plist under Protege_n.app/.<br />
<br />
Update for P5: apparently no need to increase memory settings. The info.plist file now has an Xss option which specifies the stack size. It was increased from the default to support reasoning with some particular biomedical ontologies (see https://github.com/protegeproject/protege/issues/457).<br />
<br />
== Protege layout: ==<br />
<br />
Protege has a highly configurable layout and a plugin architecture. You can control which components are visible from the window menu. Selecting something from the view menu allows you to create a new subwindow in a tab with the component of your choice - just move the target icon to the location you want and click.<br />
<br />
[[Image:Protege_setup_images-media-image03.png]]<br />
<br />
As many plugins come with the standard download, the default layout may be intimidating, but can easily be simplified: The following tabs are sufficient for GO work:<br />
<br />
[[Image:Protege_setup_images-media-image08.png]]<br />
<br />
You'll have to create the OBO graph tab yourself. (see below, as part of the Installing Plugins section)<br />
<br />
== Installing plugins: ==<br />
<br />
The following plugins should be installed from the Protégé menus: File&gt;Check for plugins&gt; <br />
<br />
<ul><br />
<li><blockquote><p>Search Annotations –search for terms and displays the list of matching results</p></blockquote></li></ul> (according to Chris, no longer necessary with P5)<br />
<br />
The following plugins should be dropped into the plugins folder of your Protege installation (this varies with OS and Protege version. Example for Protege 4.3 on a mac: cp &lt;some_plugin&gt;.jar Protege-4.3.app/Contents/Resources/Java/plugins/. <br />
<br />
This directory structure for P5 is<br />
'''Protege-5.0.0.app/Contents/Java/plugins/'''. <br />
To see the directory structure so that <br />
you can drag and drop files, you'll need to control-click/right click on the app icon, then select 'Show Package Contents' and drill down to <br />
the directory you want. Note there are two plugins folders. Make sure you use the correct one.<br />
<br />
<ol style="list-style-type: decimal;"><br />
<li><blockquote><p>[https://github.com/liveontologies/elk-reasoner/releases ''ELK OWL reasoner''] Make sure you choose a version appropriate to your Protege version.</p></blockquote> (In P5, the latest ELK can be found using File>Check for Plugins)</li><br />
<li><blockquote><p>[https://github.com/hdietze/protege-obo-plugins/raw/master/org.protege.oboeditor.jar ''OBO Annotation '']– add and edit terms more easily</p></blockquote> Have this view show up by going to the Entities tab, selecting Window>Views>OBO Views>OBO Annotation. Drag the black circle that appears to the area where you want it and click. The panel will appear.</li><br />
<li><blockquote><p>[http://code.google.com/p/obographview/ ''OBO Graph View Component''] – For all you hairball fans - this plugin displays an OBO-style connected graph of classification (is_a) and other relationship types. (Be careful what you wish for).</p></blockquote><br />
To make this a tab:<br />
<br />
*Window > Create New Tab<br />
[[File:OBO_Graph_plugin.png]]<br />
*Window > Views > Ontology Views > OBO Graph View Component<br />
*Take the black circle, put into the Tab you just created and click within it.<br />
</li><br />
<li><blockquote><p>[https://github.com/balhoff/obo-actions/downloads ''Obsoletion plugin''] - Once installed, you should see an &quot;obsolete&quot; option in your Edit menu..</p></blockquote></li></ol><br />
<br />
[[File:Obsoletion_option.png]]<br />
<br />
== Setting ID range ==<br />
<br />
Protege>Preferences>New Entities Tab<br />
<br />
Click on Preferences under the main menu to get this window.<br />
<br />
[[Image:Protege_setup_images-media-image09.png]]<br />
<br />
WARNING: The ID generator in Protege doesn't overwrite existing IRIs, but it can't cope with the OBO alt_id system - where losing IDs following a merge are stored in annotation properties This system is problematic for OWL translations as it leads to the loss or IRIs. Without IRIs, this ID generator doesn't know about the IDs and will stomp on them if they fall in the specified ID range. Until this is fixed,<br />
<br />
We plan to move to a system in which obsolete classes with these IRIs are created for all alt_ids on OBO to OWL translation.<br />
<br />
== Setting username and auto-adding creation date ==<br />
<br />
Protege>Preferences>New Entities Metadata tab<br />
[[File:Createdy_by_date.png]]<br />
See:<br />
https://github.com/protegeproject/protege/issues/283#issuecomment-177656593<br />
<br />
== Setting Rendering ==<br />
<br />
(The default settings may be fine, but details are included for reference)<br />
<br />
Protege allows users to set the annotation property to be used for rendering OWL entities (classes, object properties, annotation properties, individuals) in graphs, trees and text etc. This should be set to rdfs:label, as follows:<br />
<br />
[[Image:Protege_setup_images-media-image07.png]]<br />
<br />
[[Image:Protege_setup_images-media-image02.png]]<br />
<br />
'''Background on rendering.''' All entities in OWL are identified by an IRI. This includes annotation properties such as label. In the absence of an annotation to annotation property specified as suitable for rendering, the short form of this IRI (the bit following a '#' or a '/') is used.<br />
<br />
[[Category:GO Editors]]<br />
[[Category:Protege]]</div>David oshttps://wiki.geneontology.org/index.php?title=Protege_setup_for_GO_Eds&diff=62787Protege setup for GO Eds2016-12-20T16:14:39Z<p>David os: /* Setting ID range */</p>
<hr />
<div>= Protege setup for GO =<br />
<br />
== Which Protege version: ==<br />
<br />
Protege 4.3 is stable and relatively free of bugs. However, it does not support OBO to OWL conversion and so requires that GO be converted to OWL for editing and then converted back again for committing to the repository.<br />
<br />
Protege 5 beta21 and higher correctly load and save OBO files. However, preliminary testing suggests that beta21 is not sufficiently stable for anything but relatively brief editing sessions. It also doesn't support the OBO graph view plugin (see below).<br />
<br />
Protege 5.0.0 is currently recommended by Chris (06.20.16)<br />
"And by Protege 5, I mean the stable release version, not the beta. Get this from [http://protege.stanford.edu protege.stanford.edu]<br />
Don't use 4, or a 5-beta"<br />
<br />
== Setting memory ==<br />
<br />
Protege needs at least 4G of RAM to cope with the GO. This is set by specifying the following -Xmx argument for the java. E.g. for 6G, specify -Xmx6000M. How to set this varies with the OS and Protege version. If launching from ./run.command, edit run.command to jre/bin/java -Xmx6000M. If running from Protege_n.app on a mac, you need to find and edit the -Xmx entry in an XML file called info.plist under Protege_n.app/.<br />
<br />
Update for P5: apparently no need to increase memory settings. The info.plist file now has an Xss option which specifies the stack size. It was increased from the default to support reasoning with some particular biomedical ontologies (see https://github.com/protegeproject/protege/issues/457).<br />
<br />
== Protege layout: ==<br />
<br />
Protege has a highly configurable layout and a plugin architecture. You can control which components are visible from the window menu. Selecting something from the view menu allows you to create a new subwindow in a tab with the component of your choice - just move the target icon to the location you want and click.<br />
<br />
[[Image:Protege_setup_images-media-image03.png]]<br />
<br />
As many plugins come with the standard download, the default layout may be intimidating, but can easily be simplified: The following tabs are sufficient for GO work:<br />
<br />
[[Image:Protege_setup_images-media-image08.png]]<br />
<br />
You'll have to create the OBO graph tab yourself. (see below, as part of the Installing Plugins section)<br />
<br />
== Installing plugins: ==<br />
<br />
The following plugins should be installed from the Protégé menus: File&gt;Check for plugins&gt; <br />
<br />
<ul><br />
<li><blockquote><p>Search Annotations –search for terms and displays the list of matching results</p></blockquote></li></ul> (according to Chris, no longer necessary with P5)<br />
<br />
The following plugins should be dropped into the plugins folder of your Protege installation (this varies with OS and Protege version. Example for Protege 4.3 on a mac: cp &lt;some_plugin&gt;.jar Protege-4.3.app/Contents/Resources/Java/plugins/. <br />
<br />
This directory structure for P5 is<br />
'''Protege-5.0.0.app/Contents/Java/plugins/'''. <br />
To see the directory structure so that <br />
you can drag and drop files, you'll need to control-click/right click on the app icon, then select 'Show Package Contents' and drill down to <br />
the directory you want. Note there are two plugins folders. Make sure you use the correct one.<br />
<br />
<ol style="list-style-type: decimal;"><br />
<li><blockquote><p>[https://github.com/liveontologies/elk-reasoner/releases ''ELK OWL reasoner''] Make sure you choose a version appropriate to your Protege version.</p></blockquote> (In P5, the latest ELK can be found using File>Check for Plugins)</li><br />
<li><blockquote><p>[https://github.com/hdietze/protege-obo-plugins/raw/master/org.protege.oboeditor.jar ''OBO Annotation '']– add and edit terms more easily</p></blockquote> Have this view show up by going to the Entities tab, selecting Window>Views>OBO Views>OBO Annotation. Drag the black circle that appears to the area where you want it and click. The panel will appear.</li><br />
<li><blockquote><p>[http://code.google.com/p/obographview/ ''OBO Graph View Component''] – For all you hairball fans - this plugin displays an OBO-style connected graph of classification (is_a) and other relationship types. (Be careful what you wish for).</p></blockquote><br />
To make this a tab:<br />
<br />
*Window > Create New Tab<br />
[[File:OBO_Graph_plugin.png]]<br />
*Window > Views > Ontology Views > OBO Graph View Component<br />
*Take the black circle, put into the Tab you just created and click within it.<br />
</li><br />
<li><blockquote><p>[https://github.com/balhoff/obo-actions/downloads ''Obsoletion plugin''] - Once installed, you should see an &quot;obsolete&quot; option in your Edit menu..</p></blockquote></li></ol><br />
<br />
[[File:Obsoletion_option.png]]<br />
<br />
== Setting ID range ==<br />
<br />
Protege>Preferences>New Entities Tab<br />
<br />
Click on Preferences under the main menu to get this window.<br />
<br />
[[Image:New_entity_metadata.png]]<br />
<br />
WARNING: The ID generator in Protege doesn't overwrite existing IRIs, but it can't cope with the OBO alt_id system - where losing IDs following a merge are stored in annotation properties This system is problematic for OWL translations as it leads to the loss or IRIs. Without IRIs, this ID generator doesn't know about the IDs and will stomp on them if they fall in the specified ID range. Until this is fixed,<br />
<br />
We plan to move to a system in which obsolete classes with these IRIs are created for all alt_ids on OBO to OWL translation.<br />
<br />
== Setting username and auto-adding creation date ==<br />
<br />
Protege>Preferences>New Entities Metadata tab<br />
[[File:Createdy_by_date.png]]<br />
See:<br />
https://github.com/protegeproject/protege/issues/283#issuecomment-177656593<br />
<br />
== Setting Rendering ==<br />
<br />
(The default settings may be fine, but details are included for reference)<br />
<br />
Protege allows users to set the annotation property to be used for rendering OWL entities (classes, object properties, annotation properties, individuals) in graphs, trees and text etc. This should be set to rdfs:label, as follows:<br />
<br />
[[Image:Protege_setup_images-media-image07.png]]<br />
<br />
[[Image:Protege_setup_images-media-image02.png]]<br />
<br />
'''Background on rendering.''' All entities in OWL are identified by an IRI. This includes annotation properties such as label. In the absence of an annotation to annotation property specified as suitable for rendering, the short form of this IRI (the bit following a '#' or a '/') is used.<br />
<br />
[[Category:GO Editors]]<br />
[[Category:Protege]]</div>David oshttps://wiki.geneontology.org/index.php?title=File:New_entity_metadata.png&diff=62786File:New entity metadata.png2016-12-20T16:13:34Z<p>David os: </p>
<hr />
<div></div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-11-17&diff=62510Ontology meeting 2016-11-172016-11-16T10:31:43Z<p>David os: </p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
Tickets for discussion at this meeting:<br />
<br />
#[https://github.com/geneontology/go-ontology/issues/12786 Discussion of 'positive regulation' and 'maintenance']<br />
#[https://github.com/geneontology/go-ontology/issues/12766 toxin receptor binding]<br />
#[https://github.com/geneontology/go-ontology/issues/12779 remove cellular from the component root]<br />
#[https://github.com/geneontology/go-ontology/issues/12721 MP: (recently removed ) parentage in amino acid metabolism]<br />
#[https://github.com/geneontology/go-ontology/issues/12735 chebi_import no longer has bio-chebi GCIs]<br />
#[https://github.com/geneontology/go-ontology/issues/12775 Making so_import broken due to issue with SO URIs]<br />
#[https://github.com/geneontology/go-ontology/issues/12795 Persona shutdown]<br />
# LA AI schedule formal ontology development training for some curators<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-11-10&diff=62505Ontology meeting 2016-11-102016-11-12T11:21:27Z<p>David os: /* Modified Proteins Proposal */</p>
<hr />
<div>Attendees:<br />
<br />
Minutes: David OS?<br />
<br />
Regrets: <br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
===GitHub projects page (we'll try to follow this, as a test - see columns "Ontology meeting TBD" and "Ready to be worked on"): https://github.com/geneontology/go-ontology/projects/1===<br />
Agenda below is there as backup.<br />
<br />
===Debrief from GOC meeting: ontology group update and breakout session on ontology priorities===<br />
<br />
For reference, minutes are here: https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#<br />
<br />
<br />
From ontology priorities discussion:<br />
<br />
David H: <br />
1. Some suggestions for how to automate finding area of ontology to work on based on annotations (see minutes)<br />
2. SIB - Viralzone complained about their edits taking too long. DOS: There seemed to be agreement that we should prioritise this as a project. Need to work on splitting out discrete tasks from monster ticket.<br />
<br />
AI: DOS to set up conf call on ViralZone terms with SIB eds + Jim Hu<br />
<br />
==== General discussion of how to prioritize tickets: ====<br />
<br />
Judy: Shouldn’t we be prioritizing closing tickets. Assigning some proportion of FTE to general ticket work. Do we have a page of priorities?<br />
<br />
David H: We should redo the wiki page. <br />
<br />
Judy: We should make a table with projects + who is on + priority. <br />
<br />
Paola: We have labels: high_priority, lower_priority, mini_project, jamboree/editors_discussion<br />
<br />
DOS: Can we clean up labels?<br />
<br />
Paola: complexity of labels indicates complexity of project. We have labels for project, we have labels for submitting group, we have labels for subject matter, priority….<br />
<br />
Judy: We need to work through priorities as a priority. Is there a plan we could implement in the next week or two to reorganize so we know what’s going on. <br />
<br />
Paola: We only have 12 high priority tickets. We can review those ASAP. <-- all agreed with this.<br />
<br />
===Discussion of 'positive regulation' and 'maintenance' from last annotation call===<br />
<br />
See http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2016-10-25#Discussion_of_Outstanding_github_Tickets_2<br />
<br />
Tanya: Please make discussion of this a high priority for the next meeting.<br />
<br />
===Modified Proteins Proposal===<br />
The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives. <br />
<br />
<br />
# Continue to add these terms by hand. Unsustainable?<br />
# Figure out a way to add these terms automatically. Use PRO?, Chebi?, PsiMod?, will this lead to annotation inconsistency. Probably.<br />
# Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.<br />
# Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.<br />
<br />
We discussed three possible semantic interpretations of modified protein binding terms:<br />
<br />
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h<br />
<br />
#. Binds a protein that happens to have a modification, but not necessarily the modification site <- We previously agreed in an Eds meeting that this was too broad.<br />
#. Binds to the modified part of a protein <- Sylvan wants this. Seems to be most broadly supported. <br />
#. Binding to some specific protein partner is dependent on the modification state of the partner even if binding is not to the modified bit. <- More controversial Pascale likes this, some other seem to support. DOS objection: this seems like annotating a property of the bound protein. Also specific to one binding interaction (whereas 2 is likely to be a general function) <br />
<br />
Number 2 in this list - binds to the modified part of a protein - had the most support. Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain<br />
<br />
For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is). This still leaves the question of how detailed we should get in specifying the target (see histone binding).<br />
<br />
Link to Judy's presentation on Post-Translational Modifications: http://wiki.geneontology.org/index.php/File:PROandModified_forms.pptx<br />
<br />
Notes on discussion can be found on this ticket: https://github.com/geneontology/go-ontology/issues/12787#issuecomment-259692111<br />
<br />
===Follow-up: contacts for UniProt annotations===<br />
Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#Update:_contacts_for_UniProt_annotations<br />
<br />
AI from last call was "Sylvain will discuss with Chris and David H at the GOC meeting". Any news on this please?<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-11-10&diff=62502Ontology meeting 2016-11-102016-11-10T18:17:09Z<p>David os: /* Discussion of 'positive regulation' and 'maintenance' from last annotation call */</p>
<hr />
<div>Attendees:<br />
<br />
Minutes: David OS?<br />
<br />
Regrets: <br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
===GitHub projects page (we'll try to follow this, as a test - see columns "Ontology meeting TBD" and "Ready to be worked on"): https://github.com/geneontology/go-ontology/projects/1===<br />
Agenda below is there as backup.<br />
<br />
===Debrief from GOC meeting: ontology group update and breakout session on ontology priorities===<br />
<br />
For reference, minutes are here: https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#<br />
<br />
<br />
From ontology priorities discussion:<br />
<br />
David H: <br />
1. Some suggestions for how to automate finding area of ontology to work on based on annotations (see minutes)<br />
2. SIB - Viralzone complained about their edits taking too long. DOS: There seemed to be agreement that we should prioritise this as a project. Need to work on splitting out discrete tasks from monster ticket.<br />
<br />
AI: DOS to set up conf call on ViralZone terms with SIB eds + Jim Hu<br />
<br />
==== General discussion of how to prioritize tickets: ====<br />
<br />
Judy: Shouldn’t we be prioritizing closing tickets. Assigning some proportion of FTE to general ticket work. Do we have a page of priorities?<br />
<br />
David H: We should redo the wiki page. <br />
<br />
Judy: We should make a table with projects + who is on + priority. <br />
<br />
Paola: We have labels: high_priority, lower_priority, mini_project, jamboree/editors_discussion<br />
<br />
DOS: Can we clean up labels?<br />
<br />
Paola: complexity of labels indicates complexity of project. We have labels for project, we have labels for submitting group, we have labels for subject matter, priority….<br />
<br />
Judy: We need to work through priorities as a priority. Is there a plan we could implement in the next week or two to reorganize so we know what’s going on. <br />
<br />
Paola: We only have 12 high priority tickets. We can review those ASAP. <-- all agreed with this.<br />
<br />
===Discussion of 'positive regulation' and 'maintenance' from last annotation call===<br />
<br />
See http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2016-10-25#Discussion_of_Outstanding_github_Tickets_2<br />
<br />
Tanya: Please make discussion of this a high priority for the next meeting.<br />
<br />
===Modified Proteins Proposal===<br />
The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives. <br />
<br />
<br />
# Continue to add these terms by hand. Unsustainable?<br />
# Figure out a way to add these terms automatically. Use PRO?, Chebi?, PsiMod?, will this lead to annotation inconsistency. Probably.<br />
# Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.<br />
# Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.<br />
<br />
We discussed three possible semantic interpretations of modified protein binding terms:<br />
<br />
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h<br />
<br />
1. Binds a protein that happens to have a modification, but not necessarily the modification site <- Editor's don't want this. No-one else does either.<br />
2. Binds to the modified part of a protein <- Sylvan wants this. Seems to be most broadly supported. <br />
3. Binding to some specific protein partner is dependent on the modification state of the partner even if binding is not to the modified bit. <- More controversial Pascale likes this, some other seem to support. DOS objection: this seems like annotating a property of the bound protein. Also specific to one binding interaction (whereas 2 is likely to be a general function) <br />
<br />
Number 2 in this list - binds to the modified part of a protein - had the most support. Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain<br />
<br />
For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is). This still leaves the question of how detailed we should get in specifying the target (see histone binding).<br />
<br />
===Follow-up: contacts for UniProt annotations===<br />
Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#Update:_contacts_for_UniProt_annotations<br />
<br />
AI from last call was "Sylvain will discuss with Chris and David H at the GOC meeting". Any news on this please?<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-11-10&diff=62501Ontology meeting 2016-11-102016-11-10T18:16:10Z<p>David os: /* Debrief from GOC meeting: ontology group update and breakout session on ontology priorities */</p>
<hr />
<div>Attendees:<br />
<br />
Minutes: David OS?<br />
<br />
Regrets: <br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
===GitHub projects page (we'll try to follow this, as a test - see columns "Ontology meeting TBD" and "Ready to be worked on"): https://github.com/geneontology/go-ontology/projects/1===<br />
Agenda below is there as backup.<br />
<br />
===Debrief from GOC meeting: ontology group update and breakout session on ontology priorities===<br />
<br />
For reference, minutes are here: https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#<br />
<br />
<br />
From ontology priorities discussion:<br />
<br />
David H: <br />
1. Some suggestions for how to automate finding area of ontology to work on based on annotations (see minutes)<br />
2. SIB - Viralzone complained about their edits taking too long. DOS: There seemed to be agreement that we should prioritise this as a project. Need to work on splitting out discrete tasks from monster ticket.<br />
<br />
AI: DOS to set up conf call on ViralZone terms with SIB eds + Jim Hu<br />
<br />
==== General discussion of how to prioritize tickets: ====<br />
<br />
Judy: Shouldn’t we be prioritizing closing tickets. Assigning some proportion of FTE to general ticket work. Do we have a page of priorities?<br />
<br />
David H: We should redo the wiki page. <br />
<br />
Judy: We should make a table with projects + who is on + priority. <br />
<br />
Paola: We have labels: high_priority, lower_priority, mini_project, jamboree/editors_discussion<br />
<br />
DOS: Can we clean up labels?<br />
<br />
Paola: complexity of labels indicates complexity of project. We have labels for project, we have labels for submitting group, we have labels for subject matter, priority….<br />
<br />
Judy: We need to work through priorities as a priority. Is there a plan we could implement in the next week or two to reorganize so we know what’s going on. <br />
<br />
Paola: We only have 12 high priority tickets. We can review those ASAP. <-- all agreed with this.<br />
<br />
===Discussion of 'positive regulation' and 'maintenance' from last annotation call===<br />
<br />
See http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2016-10-25#Discussion_of_Outstanding_github_Tickets_2<br />
<br />
===Modified Proteins Proposal===<br />
The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives. <br />
<br />
<br />
# Continue to add these terms by hand. Unsustainable?<br />
# Figure out a way to add these terms automatically. Use PRO?, Chebi?, PsiMod?, will this lead to annotation inconsistency. Probably.<br />
# Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.<br />
# Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.<br />
<br />
We discussed three possible semantic interpretations of modified protein binding terms:<br />
<br />
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h<br />
<br />
1. Binds a protein that happens to have a modification, but not necessarily the modification site <- Editor's don't want this. No-one else does either.<br />
2. Binds to the modified part of a protein <- Sylvan wants this. Seems to be most broadly supported. <br />
3. Binding to some specific protein partner is dependent on the modification state of the partner even if binding is not to the modified bit. <- More controversial Pascale likes this, some other seem to support. DOS objection: this seems like annotating a property of the bound protein. Also specific to one binding interaction (whereas 2 is likely to be a general function) <br />
<br />
Number 2 in this list - binds to the modified part of a protein - had the most support. Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain<br />
<br />
For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is). This still leaves the question of how detailed we should get in specifying the target (see histone binding).<br />
<br />
===Follow-up: contacts for UniProt annotations===<br />
Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#Update:_contacts_for_UniProt_annotations<br />
<br />
AI from last call was "Sylvain will discuss with Chris and David H at the GOC meeting". Any news on this please?<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-11-10&diff=62500Ontology meeting 2016-11-102016-11-10T17:40:16Z<p>David os: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes: David OS?<br />
<br />
Regrets: <br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
===GitHub projects page (we'll try to follow this, as a test - see columns "Ontology meeting TBD" and "Ready to be worked on"): https://github.com/geneontology/go-ontology/projects/1===<br />
Agenda below is there as backup.<br />
<br />
===Debrief from GOC meeting: ontology group update and breakout session on ontology priorities===<br />
<br />
For reference, minutes are here: https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#<br />
<br />
===Discussion of 'positive regulation' and 'maintenance' from last annotation call===<br />
<br />
See http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2016-10-25#Discussion_of_Outstanding_github_Tickets_2<br />
<br />
===Modified Proteins Proposal===<br />
The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives. <br />
<br />
<br />
# Continue to add these terms by hand. Unsustainable?<br />
# Figure out a way to add these terms automatically. Use PRO?, Chebi?, PsiMod?, will this lead to annotation inconsistency. Probably.<br />
# Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.<br />
# Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.<br />
<br />
We discussed three possible semantic interpretations of modified protein binding terms:<br />
<br />
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h<br />
<br />
1. Binds a protein that happens to have a modification, but not necessarily the modification site <- Editor's don't want this. No-one else does either.<br />
2. Binds to the modified part of a protein <- Sylvan wants this. Seems to be most broadly supported. <br />
3. Binding to some specific protein partner is dependent on the modification state of the partner even if binding is not to the modified bit. <- More controversial Pascale likes this, some other seem to support. DOS objection: this seems like annotating a property of the bound protein. Also specific to one binding interaction (whereas 2 is likely to be a general function) <br />
<br />
Number 2 in this list - binds to the modified part of a protein - had the most support. Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain<br />
<br />
For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is). This still leaves the question of how detailed we should get in specifying the target (see histone binding).<br />
<br />
===Follow-up: contacts for UniProt annotations===<br />
Background: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#Update:_contacts_for_UniProt_annotations<br />
<br />
AI from last call was "Sylvain will discuss with Chris and David H at the GOC meeting". Any news on this please?<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-11-10&diff=62491Ontology meeting 2016-11-102016-11-08T14:12:07Z<p>David os: /* Modified Proteins Proposal */</p>
<hr />
<div>Attendees:<br />
<br />
Minutes: <br />
<br />
Regrets: <br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
===Debrief from GOC meeting: ontology group update and breakout session on ontology priorities===<br />
<br />
For reference, minutes are here: https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#<br />
<br />
===Discussion of 'positive regulation' and 'maintenance' from last annotation call===<br />
<br />
See http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2016-10-25#Discussion_of_Outstanding_github_Tickets_2<br />
<br />
===Modified Proteins Proposal===<br />
The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives. <br />
<br />
<br />
# Continue to add these terms by hand. Unsustainable?<br />
# Figure out a way to add these terms automatically. Use PRO?, Chebi?, PsiMod?, will this lead to annotation inconsistency. Probably.<br />
# Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.<br />
# Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.<br />
<br />
We discussed three possible semantic interpretations of modified protein binding terms:<br />
<br />
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h<br />
<br />
Number 2 in this list - binds to the modified part of a protein - had the most support. Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain<br />
<br />
For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is). This still leaves the question of how detailed we should get in specifying the target (see histone binding).<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-11-10&diff=62490Ontology meeting 2016-11-102016-11-08T14:10:32Z<p>David os: /* Modified Proteins Proposal */</p>
<hr />
<div>Attendees:<br />
<br />
Minutes: <br />
<br />
Regrets: <br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
===Debrief from GOC meeting: ontology group update and breakout session on ontology priorities===<br />
<br />
For reference, minutes are here: https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#<br />
<br />
===Discussion of 'positive regulation' and 'maintenance' from last annotation call===<br />
<br />
See http://wiki.geneontology.org/index.php/Annotation_Conf._Call_2016-10-25#Discussion_of_Outstanding_github_Tickets_2<br />
<br />
===Modified Proteins Proposal===<br />
The proposal was not well received by annotators at the GO meeting. The annotators thought that these terms were too important biologically for them not to be in the ontology. We need to come up with alternatives. <br />
<br />
<br />
# Continue to add these terms by hand. Unsustainable?<br />
# Figure out a way to add these terms automatically. Use PRO?, Chebi?, PsiMod?, will this lead to annotation inconsistency. Probably.<br />
# Only add a few very high-level terms. What is the specificity cut off and what happens when annotators make a case that the very specific term that they want is important.<br />
# Have do-not-annotate' terms that are generated automatically as in #1 below and categorize gene products by the entity that is captured in binding annotations.<br />
<br />
We discussed three possible semantic interpretations of modified protein binding terms:<br />
<br />
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit#heading=h.vzsyf1ss0k8h<br />
<br />
Number 2 in this list - binds to the modified part of a protein - had the most support. Example: SH2 domain confers binding to phospho-tryosine in the context of a specific peptide motif: https://en.wikipedia.org/wiki/SH2_domain<br />
<br />
For terms like this, we could add a comment that it should only be used where there is high confidence that binding is to the modification + protein (simple dependency on phosphorylation of target is not sufficient but one that localizes the domain by deletion/mutagenesis analysis of the protein is).<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Agenda&diff=624782016 Los Angeles GOC Meeting Agenda2016-11-06T00:39:07Z<p>David os: /* Day 2 */</p>
<hr />
<div>==[https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit?usp=sharing Minutes]==<br />
<br />
=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics (Paul)==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit?usp=sharing<br />
<br />
https://drive.google.com/drive/folders/0B8kRPmmvPJU3dFhhcWhTSmlUcDA<br />
<br />
link to folder on Google drive: bit.ly/geneont-drive<br />
<br />
==Overview/Plan for Upcoming Five Years==<br />
*GO PIs presentation (Paul T)<br />
<br />
== Coffee break 10am-ish ==<br />
<br />
== Informatics and Infrastructure 5 year plan (Chris, LBNL) ==<br />
=== Update on various changes ===<br />
<br />
* replacement of svn<br />
* metadata-driven infrastructure - https://github.com/geneontology/go-site/tree/master/metadata<br />
* retiring MySQL - https://github.com/geneontology/go-site/issues/229<br />
* graphstore - https://github.com/geneontology/go-graphstore<br />
* new dataflow<br />
* retiring amigo1, yes?<br />
* amigo2 update<br />
* noctua update<br />
* migration of IT to LBNL from Stanford, Stanford's support for IT is greatly reduced.<br />
* ...<br />
<br />
=== Proposal ===<br />
<br />
* Switch to global monthly releases, but still provide daily snapshots<br />
<br />
== Lunch 11:45 - 1:00pm (on our own, must vacate room for seminar happening then) ==<br />
<br />
==Updates==<br />
===AmiGO and web site action items (Seth)===<br />
*AI: Mechanism to remove redundant TAS/ISS/IEA etc annotations that are covered by experimental annotations<br />
**See https://github.com/geneontology/amigo/issues/294<br />
*AI: GOC to extract this data and display annual stats on web page<br />
**See http://amigo.geneontology.org/amigo/base_statistics<br />
**AI: Include stats for % genome annotated<br />
*** https://github.com/geneontology/amigo/issues/348<br />
**AI: Include GOC extract ontology stats<br />
*** https://github.com/geneontology/go-site/issues/179<br />
**IEA annotations should be broken out by reference (this is the method used), and converted to a provider, e.g. GO_REF:0000019 is Ensembl Compara.<br />
*** TODO: Define in tracker (Done) https://github.com/geneontology/amigo/issues/399<br />
*term matrix (Val)<br />
<br />
===Update on UniProt GCRP sets (Maria)===<br />
===Update on gpi specifications and uses (Kimberly, Chris, 10-15 min)===<br />
* items?<br />
===Ontology Group Update (DavidH)===<br />
* Special Projects<br />
** Cilia<br />
** Autophagy<br />
** Apoptosis<br />
** Plant Enzymes<br />
** Synapse (DOS/PDT)<br />
* GO help report<br />
===Alliance of Genome Resources Update (Judy, Paul S)===<br />
<br />
== Coffee break 3pm ==<br />
<br />
==Breakout sessions to finalize development of various proposals ==<br />
The following are concurrent<br />
* Flowchart guidelines for transcription factor annotations [10 min Rachael/Ruth/Barbara] [http://wiki.geneontology.org/index.php/File:Expression_Transcription_Decision_Tree_2016.pptx presentation]. To improve consistency UCL team have created an annotation flowchart which is being circulated to GOC members.<br />
* PI +UniProt discussion<br />
* Community annotation web presence (Val, Ruth)<br />
<br />
=Day 2=<br />
<br />
==Start time 9am==<br />
<br />
==Hear report of conclusions and actions from remaining breakout groups==<br />
# Suggestions to prioritize Ontology refactoring 3:00 PM to 3:45 <br />
# Combining ontology design patterns and LEGO templates<br />
# Seth break out session that was lovely<br />
# Flowchart guidelines for transcription factor annotations<br />
<br />
==Annotation Issues - Conventional Annotations==<br />
<br />
===Modified Protein Binding===<br />
<br />
*Modified protein binding: GO terms & annotations are very inconsistent. (DavidH to present Paola's proposal)<br />
**Recent github issues: <br />
glycoprotein binding: https://github.com/geneontology/go-ontology/issues/12580#issuecomment-240782020<br />
ubiquitinated protein binding https://github.com/geneontology/go-ontology/issues/12582#issuecomment-240452320<br />
<br />
===Protein Family Terms in the Ontology===<br />
<br />
* Protein families in terms (DavidH)<br />
** Currently the inclusion of protein family information in term names is leading to inconsistent annotation.<br />
*** For now, the ontology editors have not been adding terms that specifically refer to protein families with the exception of signaling pathways. Should we make this a rule? If so, how will we capture the detail desired by annotators and how will we make this backward compatible?<br />
<br />
https://github.com/geneontology/go-ontology/issues/12440<br />
<br />
===Multiple Evidences to Support an Inference===<br />
<br />
* How are people capturing data where both direct assay AND protein motif/domains/sequence needs to be used by the curator to provide the annotation? [15 min Ruth, started by Rebecca] [http://wiki.geneontology.org/index.php/File:RFOULGER_IC_membrane_Sept_2016.pptx presentation] A system needs to be in place to enable the more specific annotations to be created for orthologous proteins (which cannot be done across all species with the IC evidence code) <br />
** eg transmembrane domain used as evidence to create the annotation 'integral to membrane' with IEA evidence; immunofluorescence localises protein to 'plasma membrane' (annotated with IDA evidence), ideal annotation to be created 'integral to plasma membrane'<br />
** 3 obvious options (any others?)<br />
*** new evidence code IDD 'inferred by direct assay AND protein domain(sequence/motif?)' (would probably also want IMD, IGD, IED)<br />
****Note that ECO has a combinatorial evidence code that could possibly be used as the parent for new GO combinatorial codes:<br />
*****combinatorial evidence used in manual assertion - ECO:0000244<br />
*** no new evidence code requires as this is implied by the 'inferred' aspect of the evidence code as well as 'author intent'<br />
*** Create a GOC pipeline that creates the CC annotations based on the IDA annotation (eg plasma membrane) and the IEA information (eg integral to membrane) to create the more specific annotation (eg integral to plasma membrane). <br />
<br />
<br />
===Consistent Classification of Signaling Pathway Terms===<br />
<br />
* Conventions for signalling pathway terms<br />
** Currently you can request signalling pathway terms along multiple axes of classification including:<br />
*** signalling module (MAPK cascade, GTPase etc)<br />
*** process regulated<br />
*** target TF's<br />
*** ligand /pheromone activating pathway<br />
*** Process regulated<br />
*** condition activating pathway (in response to hydrogen peroxide and other oxidants for oxidative stress pathway)<br />
This results in almost infinite number of ways to describe some pathways<br />
<br />
https://github.com/geneontology/go-ontology/issues/12701<br />
<br />
===Generating conventional annotations from Noctua models===<br />
* GAF/GPAD inference from LEGO models (Jim and David OS, Chris, Kimberly, David Hill, ...)<br />
** Introduction to inferring annotations from LEGO: Extended Gene Product to GO term relations; Reasoning across causal chains.<br />
***Jim Balhoff: Inference using Blazegraph & RDFox<br />
***DOS: Templates, design patterns and inference.<br />
*MGI's experience roundtripping with Noctua Models (DavidH)<br />
*Are we going to allow Noctua to generate conventional annotations to the root nodes of the ontology? <br />
**This would be useful for contextual annotations that are to otherwise root nodes. <br />
**However some groups block these kinds of annotations because in the past, these annotations were used to keep track of genes about which we had no information. <br />
**Note that the evidence code for a root node annotation in Noctua would/could be different in that the curator might assert that a gene product has some molecular function due to the observation that, when mutated, there is a phenotypic outcome, e.g. apoptosis execution fails.<br />
**This is a different statement from no biological data (ND) in which there is no information at all to assert a role in any biological process.<br />
*Are some conventional annotation rules inappropriate for Noctua annotation?<br />
**For a molecular function occurring in a cellular location, isn't IEP a more appropriate evidence code? IDA would mean that the function was assayed in situ. https://github.com/geneontology/go-annotation/issues/1395<br />
**Since binding is a part of many molecular functions, should we allow evidence codes other than IPI for binding (eg TAS)?<br />
<br />
===Annotations from High Throughput Experiments===<br />
<br />
*Annotations from high-throughput experiments (Pascale, Ruth, David Hill, Kimberly)<br />
*AI: discuss proposal for defining HTP data <br />
**How do we decide when to make annotations from high-throughput experiments?<br />
**If we decide that annotations from high-throughput experiments should be removed, what are the procedures (all annotations, some annotations)?<br />
**Do we want new evidence codes to indicate that the annotation was inferred from a high-throughput experiment?<br />
<br />
===Qualifiers that describe relationship of gene product (activity) to a biological process===<br />
<br />
DOS; Pascale.<br />
<br />
As a result of work on LEGO in conversion to GPAD/GAF, we now have a wider set of relations linking gene products to biological processes (GAF qualifiers/GPAD column 2). These are derived from the broader set of causal relations developed for LEGO. We need to discuss how these should be applied to conventional annotations. This builds on a proposal to agreed in DC but not yet implemented to distinguish annotations where it is clear that a gene product activity is part of a process from cases where it is not clear if the activity is part of the process or causally upstream of it.<br />
<br />
==Annotation Issues - LEGO Annotations==<br />
<br />
=== Regulation relations - proposal to improve definitions (DOS) ===<br />
<br />
Regulation and causal relations are central to LEGO annotation and to inference based on LEGO models, but definitions and guidelines still need work to ensure consistency and clarity. <br />
<br />
===Aligning Conventional and LEGO Annotations===<br />
<br />
*A proposal to make Conventional Annotation align better with LEGO modelling (F-P linking) (Val)<br />
<br />
https://github.com/geneontology/go-ontology/issues/12739#issuecomment-254623691<br />
<br />
===Evidence codes in Noctua===<br />
*How are we going to handle ECO codes in Noctua. Currently there are only a limited number of codes that fall under 'used in manual assertion'. If we use codes that are not specific to the manual assertion part of the ontology, then they map to EXP. Are we going to request the entire set of codes that we think we might want to use or are we going to have an automated way to map to the correct code?<br />
<br />
Example: http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001874<br />
<br />
<br />
<br />
<br />
<br />
==Conference Calls and Communication==<br />
Estimated time: 30 minutes<br />
*Discuss different options for reducing the number of conference calls, while still facilitating effective communication between the different GO groups, e.g. annotators, ontology editors, software team<br />
**Consolidate all annotation calls (Monday LEGO, Tuesday Annotation, Tuesday PAINT) into one Tuesday annotation call, frequency TBD<br />
**Consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one weekly GO call <br />
*Discussion on the design of new SOPs for mechanisms of communication<br />
**What is the best mechanism to alert annotation groups of changes to the ontology that will affect annotations? We have started a table of contacts, but is this how annotation groups would like to proceed?<br />
**Review of github repositories, what to record where, who is processing/clearing tickets, etc.<br />
*Discussion on what it means to be a member of the Gene Ontology Consortium, not just the NHGRI grant.<br />
**Agreed to standards, which ones?<br />
* Decide where and when to hold next GOC meeting (also whether to include SAB next time)<br />
<br />
== Wrap up, action items ==<br />
# Final Summary of Initiatives we will be working on to prepare for next meeting<br />
#* Kimberly and Pascale<br />
<br />
== Time permitting, or post-meeting breakout ==<br />
<br />
=== Annotation Metrics ===<br />
Estimated time: 1 hour<br />
*What are the optimal metrics to assess progress in GO annotation?<br />
**Number of annotations<br />
**Number of references<br />
***Recall ZFIN's 'paper complexity' measure as a way of normalizing for different paper content (Doug mentioned in Geneva)<br />
**Revised annotations, e.g. updating to a new term<br />
**Removing annotations, e.g. improving knowledge about how a gene product affects a downstream process<br />
**Adding appropriate contextual information to existing annotations<br />
**Percentage of genome annotated vs percentage of genome with annotatable information?<br />
*How does LEGO modeling change our assessment of a curator's contributions?<br />
**Attribution of annotations to enable credit for: <br />
***Noctua annotations (This was discussed during LEGO call (http://wiki.geneontology.org/index.php/LEGO_September_19,_2016)<br />
*Multiple funding bodies (Ruth)<br />
*Distinguishing annotations that are created automatically, e.g. inference pipelines (Tony)<br />
*Recognizing individual curators contributions via Orcid IDs. <br />
**Determine at what level attribution occurs<br />
**Inclusion of funding source<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Agenda&diff=624772016 Los Angeles GOC Meeting Agenda2016-11-06T00:38:15Z<p>David os: /* Day 2 */</p>
<hr />
<div>==[https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit?usp=sharing Minutes]==<br />
<br />
=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics (Paul)==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit?usp=sharing<br />
<br />
https://drive.google.com/drive/folders/0B8kRPmmvPJU3dFhhcWhTSmlUcDA<br />
<br />
link to folder on Google drive: bit.ly/geneont-drive<br />
<br />
==Overview/Plan for Upcoming Five Years==<br />
*GO PIs presentation (Paul T)<br />
<br />
== Coffee break 10am-ish ==<br />
<br />
== Informatics and Infrastructure 5 year plan (Chris, LBNL) ==<br />
=== Update on various changes ===<br />
<br />
* replacement of svn<br />
* metadata-driven infrastructure - https://github.com/geneontology/go-site/tree/master/metadata<br />
* retiring MySQL - https://github.com/geneontology/go-site/issues/229<br />
* graphstore - https://github.com/geneontology/go-graphstore<br />
* new dataflow<br />
* retiring amigo1, yes?<br />
* amigo2 update<br />
* noctua update<br />
* migration of IT to LBNL from Stanford, Stanford's support for IT is greatly reduced.<br />
* ...<br />
<br />
=== Proposal ===<br />
<br />
* Switch to global monthly releases, but still provide daily snapshots<br />
<br />
== Lunch 11:45 - 1:00pm (on our own, must vacate room for seminar happening then) ==<br />
<br />
==Updates==<br />
===AmiGO and web site action items (Seth)===<br />
*AI: Mechanism to remove redundant TAS/ISS/IEA etc annotations that are covered by experimental annotations<br />
**See https://github.com/geneontology/amigo/issues/294<br />
*AI: GOC to extract this data and display annual stats on web page<br />
**See http://amigo.geneontology.org/amigo/base_statistics<br />
**AI: Include stats for % genome annotated<br />
*** https://github.com/geneontology/amigo/issues/348<br />
**AI: Include GOC extract ontology stats<br />
*** https://github.com/geneontology/go-site/issues/179<br />
**IEA annotations should be broken out by reference (this is the method used), and converted to a provider, e.g. GO_REF:0000019 is Ensembl Compara.<br />
*** TODO: Define in tracker (Done) https://github.com/geneontology/amigo/issues/399<br />
*term matrix (Val)<br />
<br />
===Update on UniProt GCRP sets (Maria)===<br />
===Update on gpi specifications and uses (Kimberly, Chris, 10-15 min)===<br />
* items?<br />
===Ontology Group Update (DavidH)===<br />
* Special Projects<br />
** Cilia<br />
** Autophagy<br />
** Apoptosis<br />
** Plant Enzymes<br />
** Synapse (DOS/PDT)<br />
* GO help report<br />
===Alliance of Genome Resources Update (Judy, Paul S)===<br />
<br />
== Coffee break 3pm ==<br />
<br />
==Breakout sessions to finalize development of various proposals ==<br />
The following are concurrent<br />
* Flowchart guidelines for transcription factor annotations [10 min Rachael/Ruth/Barbara] [http://wiki.geneontology.org/index.php/File:Expression_Transcription_Decision_Tree_2016.pptx presentation]. To improve consistency UCL team have created an annotation flowchart which is being circulated to GOC members.<br />
* PI +UniProt discussion<br />
* Community annotation web presence (Val, Ruth)<br />
<br />
=Day 2=<br />
<br />
==Start time 9am==<br />
<br />
==Hear report of conclusions and actions from remaining breakout groups==<br />
# Suggestions to prioritize Ontology refactoring 3:00 PM to 3:45 <br />
# Combining ontology design patterns and LEGO templates<br />
# Seth break out session that was lovely<br />
# Flowchart guidelines for transcription factor annotations<br />
<br />
==Annotation Issues - Conventional Annotations==<br />
<br />
===Modified Protein Binding===<br />
<br />
*Modified protein binding: GO terms & annotations are very inconsistent. (DavidH to present Paola's proposal)<br />
**Recent github issues: <br />
glycoprotein binding: https://github.com/geneontology/go-ontology/issues/12580#issuecomment-240782020<br />
ubiquitinated protein binding https://github.com/geneontology/go-ontology/issues/12582#issuecomment-240452320<br />
<br />
===Protein Family Terms in the Ontology===<br />
<br />
* Protein families in terms (DavidH)<br />
** Currently the inclusion of protein family information in term names is leading to inconsistent annotation.<br />
*** For now, the ontology editors have not been adding terms that specifically refer to protein families with the exception of signaling pathways. Should we make this a rule? If so, how will we capture the detail desired by annotators and how will we make this backward compatible?<br />
<br />
https://github.com/geneontology/go-ontology/issues/12440<br />
<br />
===Multiple Evidences to Support an Inference===<br />
<br />
* How are people capturing data where both direct assay AND protein motif/domains/sequence needs to be used by the curator to provide the annotation? [15 min Ruth, started by Rebecca] [http://wiki.geneontology.org/index.php/File:RFOULGER_IC_membrane_Sept_2016.pptx presentation] A system needs to be in place to enable the more specific annotations to be created for orthologous proteins (which cannot be done across all species with the IC evidence code) <br />
** eg transmembrane domain used as evidence to create the annotation 'integral to membrane' with IEA evidence; immunofluorescence localises protein to 'plasma membrane' (annotated with IDA evidence), ideal annotation to be created 'integral to plasma membrane'<br />
** 3 obvious options (any others?)<br />
*** new evidence code IDD 'inferred by direct assay AND protein domain(sequence/motif?)' (would probably also want IMD, IGD, IED)<br />
****Note that ECO has a combinatorial evidence code that could possibly be used as the parent for new GO combinatorial codes:<br />
*****combinatorial evidence used in manual assertion - ECO:0000244<br />
*** no new evidence code requires as this is implied by the 'inferred' aspect of the evidence code as well as 'author intent'<br />
*** Create a GOC pipeline that creates the CC annotations based on the IDA annotation (eg plasma membrane) and the IEA information (eg integral to membrane) to create the more specific annotation (eg integral to plasma membrane). <br />
<br />
<br />
===Consistent Classification of Signaling Pathway Terms===<br />
<br />
* Conventions for signalling pathway terms<br />
** Currently you can request signalling pathway terms along multiple axes of classification including:<br />
*** signalling module (MAPK cascade, GTPase etc)<br />
*** process regulated<br />
*** target TF's<br />
*** ligand /pheromone activating pathway<br />
*** Process regulated<br />
*** condition activating pathway (in response to hydrogen peroxide and other oxidants for oxidative stress pathway)<br />
This results in almost infinite number of ways to describe some pathways<br />
<br />
https://github.com/geneontology/go-ontology/issues/12701<br />
<br />
===Generating conventional annotations from Noctua models===<br />
* GAF/GPAD inference from LEGO models (Jim and David OS, Chris, Kimberly, David Hill, ...)<br />
** Introduction to inferring annotations from LEGO: Extended Gene Product to GO term relations; Reasoning across causal chains.<br />
***Jim Balhoff: Inference using Blazegraph & RDFox<br />
***DOS: Templates, design patterns and inference.<br />
*MGI's experience roundtripping with Noctua Models (DavidH)<br />
*Are we going to allow Noctua to generate conventional annotations to the root nodes of the ontology? <br />
**This would be useful for contextual annotations that are to otherwise root nodes. <br />
**However some groups block these kinds of annotations because in the past, these annotations were used to keep track of genes about which we had no information. <br />
**Note that the evidence code for a root node annotation in Noctua would/could be different in that the curator might assert that a gene product has some molecular function due to the observation that, when mutated, there is a phenotypic outcome, e.g. apoptosis execution fails.<br />
**This is a different statement from no biological data (ND) in which there is no information at all to assert a role in any biological process.<br />
*Are some conventional annotation rules inappropriate for Noctua annotation?<br />
**For a molecular function occurring in a cellular location, isn't IEP a more appropriate evidence code? IDA would mean that the function was assayed in situ. https://github.com/geneontology/go-annotation/issues/1395<br />
**Since binding is a part of many molecular functions, should we allow evidence codes other than IPI for binding (eg TAS)?<br />
<br />
===Annotations from High Throughput Experiments===<br />
<br />
*Annotations from high-throughput experiments (Pascale, Ruth, David Hill, Kimberly)<br />
*AI: discuss proposal for defining HTP data <br />
**How do we decide when to make annotations from high-throughput experiments?<br />
**If we decide that annotations from high-throughput experiments should be removed, what are the procedures (all annotations, some annotations)?<br />
**Do we want new evidence codes to indicate that the annotation was inferred from a high-throughput experiment?<br />
<br />
===Qualifiers that describe relationship of gene product (activity) to a biological process===<br />
<br />
DOS; Pascale.<br />
<br />
As a result of work on LEGO in conversion to GPAD/GAF, we now have a wider set of relations linking gene products to biological processes (GAF qualifiers/GPAD column 2). These are derived from the broader set of causal relations developed for LEGO. We need to discuss how these should be applied to conventional annotations. This builds on a proposal to agreed in DC but not yet implemented to distinguish annotations where it is clear that a gene product activity is part of a process from cases where it is not clear if the activity is part of the process or causally upstream of it.<br />
<br />
==Annotation Issues - LEGO Annotations==<br />
<br />
== Regulation relations - proposal to improve definitions (DOS) ==<br />
<br />
Regulation and causal relations are central to LEGO annotation and to inference based on LEGO models, but definitions and guidelines still need work to ensure consistency and clarity. <br />
<br />
===Aligning Conventional and LEGO Annotations===<br />
<br />
*A proposal to make Conventional Annotation align better with LEGO modelling (F-P linking) (Val)<br />
<br />
https://github.com/geneontology/go-ontology/issues/12739#issuecomment-254623691<br />
<br />
===Evidence codes in Noctua===<br />
*How are we going to handle ECO codes in Noctua. Currently there are only a limited number of codes that fall under 'used in manual assertion'. If we use codes that are not specific to the manual assertion part of the ontology, then they map to EXP. Are we going to request the entire set of codes that we think we might want to use or are we going to have an automated way to map to the correct code?<br />
<br />
Example: http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001874<br />
<br />
<br />
<br />
<br />
<br />
==Conference Calls and Communication==<br />
Estimated time: 30 minutes<br />
*Discuss different options for reducing the number of conference calls, while still facilitating effective communication between the different GO groups, e.g. annotators, ontology editors, software team<br />
**Consolidate all annotation calls (Monday LEGO, Tuesday Annotation, Tuesday PAINT) into one Tuesday annotation call, frequency TBD<br />
**Consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one weekly GO call <br />
*Discussion on the design of new SOPs for mechanisms of communication<br />
**What is the best mechanism to alert annotation groups of changes to the ontology that will affect annotations? We have started a table of contacts, but is this how annotation groups would like to proceed?<br />
**Review of github repositories, what to record where, who is processing/clearing tickets, etc.<br />
*Discussion on what it means to be a member of the Gene Ontology Consortium, not just the NHGRI grant.<br />
**Agreed to standards, which ones?<br />
* Decide where and when to hold next GOC meeting (also whether to include SAB next time)<br />
<br />
== Wrap up, action items ==<br />
# Final Summary of Initiatives we will be working on to prepare for next meeting<br />
#* Kimberly and Pascale<br />
<br />
== Time permitting, or post-meeting breakout ==<br />
<br />
=== Annotation Metrics ===<br />
Estimated time: 1 hour<br />
*What are the optimal metrics to assess progress in GO annotation?<br />
**Number of annotations<br />
**Number of references<br />
***Recall ZFIN's 'paper complexity' measure as a way of normalizing for different paper content (Doug mentioned in Geneva)<br />
**Revised annotations, e.g. updating to a new term<br />
**Removing annotations, e.g. improving knowledge about how a gene product affects a downstream process<br />
**Adding appropriate contextual information to existing annotations<br />
**Percentage of genome annotated vs percentage of genome with annotatable information?<br />
*How does LEGO modeling change our assessment of a curator's contributions?<br />
**Attribution of annotations to enable credit for: <br />
***Noctua annotations (This was discussed during LEGO call (http://wiki.geneontology.org/index.php/LEGO_September_19,_2016)<br />
*Multiple funding bodies (Ruth)<br />
*Distinguishing annotations that are created automatically, e.g. inference pipelines (Tony)<br />
*Recognizing individual curators contributions via Orcid IDs. <br />
**Determine at what level attribution occurs<br />
**Inclusion of funding source<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Agenda&diff=624682016 Los Angeles GOC Meeting Agenda2016-11-05T15:01:18Z<p>David os: /* Qualifiers that describe relationship of gene product (activity) to a biological process */</p>
<hr />
<div>==[https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit?usp=sharing Minutes]==<br />
<br />
=Day 1=<br />
<br />
== 9am Welcome, schedule and logistics (Paul)==<br />
* Remote attendees call in via Bluejeans: https://bluejeans.com/993661940<br />
* Schedule<br />
* Introductions<br />
<br />
https://docs.google.com/document/d/1MAnnOfs-e2LY9MnqdCZscalbxbNUDSJ9pbMZ-f2WS9U/edit?usp=sharing<br />
<br />
https://drive.google.com/drive/folders/0B8kRPmmvPJU3dFhhcWhTSmlUcDA<br />
<br />
link to folder on Google drive: bit.ly/geneont-drive<br />
<br />
==Overview/Plan for Upcoming Five Years==<br />
*GO PIs presentation (Paul T)<br />
<br />
== Coffee break 10am-ish ==<br />
<br />
== Informatics and Infrastructure 5 year plan (Chris, LBNL) ==<br />
=== Update on various changes ===<br />
<br />
* replacement of svn<br />
* metadata-driven infrastructure - https://github.com/geneontology/go-site/tree/master/metadata<br />
* retiring MySQL - https://github.com/geneontology/go-site/issues/229<br />
* graphstore - https://github.com/geneontology/go-graphstore<br />
* new dataflow<br />
* retiring amigo1, yes?<br />
* amigo2 update<br />
* noctua update<br />
* migration of IT to LBNL from Stanford, Stanford's support for IT is greatly reduced.<br />
* ...<br />
<br />
=== Proposal ===<br />
<br />
* Switch to global monthly releases, but still provide daily snapshots<br />
<br />
== Lunch 11:45 - 1:00pm (on our own, must vacate room for seminar happening then) ==<br />
<br />
==Updates==<br />
===AmiGO and web site action items (Seth)===<br />
*AI: Mechanism to remove redundant TAS/ISS/IEA etc annotations that are covered by experimental annotations<br />
**See https://github.com/geneontology/amigo/issues/294<br />
*AI: GOC to extract this data and display annual stats on web page<br />
**See http://amigo.geneontology.org/amigo/base_statistics<br />
**AI: Include stats for % genome annotated<br />
*** https://github.com/geneontology/amigo/issues/348<br />
**AI: Include GOC extract ontology stats<br />
*** https://github.com/geneontology/go-site/issues/179<br />
**IEA annotations should be broken out by reference (this is the method used), and converted to a provider, e.g. GO_REF:0000019 is Ensembl Compara.<br />
*** TODO: Define in tracker (Done) https://github.com/geneontology/amigo/issues/399<br />
*term matrix (Val)<br />
<br />
===Update on UniProt GCRP sets (Maria)===<br />
===Update on gpi specifications and uses (Kimberly, Chris, 10-15 min)===<br />
* items?<br />
===Ontology Group Update (DavidH)===<br />
* Special Projects<br />
** Cilia<br />
** Autophagy<br />
** Apoptosis<br />
** Plant Enzymes<br />
** Synapse (DOS/PDT)<br />
* GO help report<br />
===Alliance of Genome Resources Update (Judy, Paul S)===<br />
<br />
== Coffee break 3pm ==<br />
<br />
==Breakout sessions to finalize development of various proposals ==<br />
The following are concurrent<br />
* Flowchart guidelines for transcription factor annotations [10 min Rachael/Ruth/Barbara] [http://wiki.geneontology.org/index.php/File:Expression_Transcription_Decision_Tree_2016.pptx presentation]. To improve consistency UCL team have created an annotation flowchart which is being circulated to GOC members.<br />
* PI +UniProt discussion<br />
* Community annotation web presence (Val, Ruth)<br />
<br />
=Day 2-3=<br />
<br />
==Annotation Issues - Conventional Annotations==<br />
<br />
===Modified Protein Binding===<br />
<br />
*Modified protein binding: GO terms & annotations are very inconsistent. (DavidH to present Paola's proposal)<br />
**Recent github issues: <br />
glycoprotein binding: https://github.com/geneontology/go-ontology/issues/12580#issuecomment-240782020<br />
ubiquitinated protein binding https://github.com/geneontology/go-ontology/issues/12582#issuecomment-240452320<br />
<br />
===Protein Family Terms in the Ontology===<br />
<br />
* Protein families in terms (DavidH)<br />
** Currently the inclusion of protein family information in term names is leading to inconsistent annotation.<br />
*** For now, the ontology editors have not been adding terms that specifically refer to protein families with the exception of signaling pathways. Should we make this a rule? If so, how will we capture the detail desired by annotators and how will we make this backward compatible?<br />
<br />
https://github.com/geneontology/go-ontology/issues/12440<br />
<br />
===Multiple Evidences to Support an Inference===<br />
<br />
* How are people capturing data where both direct assay AND protein motif/domains/sequence needs to be used by the curator to provide the annotation? [15 min Ruth, started by Rebecca] [http://wiki.geneontology.org/index.php/File:RFOULGER_IC_membrane_Sept_2016.pptx presentation] A system needs to be in place to enable the more specific annotations to be created for orthologous proteins (which cannot be done across all species with the IC evidence code) <br />
** eg transmembrane domain used as evidence to create the annotation 'integral to membrane' with IEA evidence; immunofluorescence localises protein to 'plasma membrane' (annotated with IDA evidence), ideal annotation to be created 'integral to plasma membrane'<br />
** 3 obvious options (any others?)<br />
*** new evidence code IDD 'inferred by direct assay AND protein domain(sequence/motif?)' (would probably also want IMD, IGD, IED)<br />
****Note that ECO has a combinatorial evidence code that could possibly be used as the parent for new GO combinatorial codes:<br />
*****combinatorial evidence used in manual assertion - ECO:0000244<br />
*** no new evidence code requires as this is implied by the 'inferred' aspect of the evidence code as well as 'author intent'<br />
*** Create a GOC pipeline that creates the CC annotations based on the IDA annotation (eg plasma membrane) and the IEA information (eg integral to membrane) to create the more specific annotation (eg integral to plasma membrane). <br />
<br />
<br />
===Consistent Classification of Signaling Pathway Terms===<br />
<br />
* Conventions for signalling pathway terms<br />
** Currently you can request signalling pathway terms along multiple axes of classification including:<br />
*** signalling module (MAPK cascade, GTPase etc)<br />
*** process regulated<br />
*** target TF's<br />
*** ligand /pheromone activating pathway<br />
*** Process regulated<br />
*** condition activating pathway (in response to hydrogen peroxide and other oxidants for oxidative stress pathway)<br />
This results in almost infinite number of ways to describe some pathways<br />
<br />
https://github.com/geneontology/go-ontology/issues/12701<br />
<br />
===Annotations from High Throughput Experiments===<br />
<br />
*Annotations from high-throughput experiments (Pascale, Ruth, David Hill, Kimberly)<br />
*AI: discuss proposal for defining HTP data (Pascale, 20 min)<br />
**How do we decide when to make annotations from high-throughput experiments?<br />
**If we decide that annotations from high-throughput experiments should be removed, what are the procedures (all annotations, some annotations)?<br />
**Do we want new evidence codes to indicate that the annotation was inferred from a high-throughput experiment?<br />
<br />
===Qualifiers that describe relationship of gene product (activity) to a biological process===<br />
<br />
DOS; Pascale.<br />
<br />
As a result of work on LEGO in conversion to GPAD/GAF, we now have a wider set of relations linking gene products to biological processes (GAF qualifiers/GPAD column 2). These are derived from the broader set of causal relations developed for LEGO. We need to discuss how these should be applied to conventional annotations. This builds on a proposal to agreed in DC but not yet implemented to distinguish annotations where it is clear that a gene product activity is part of a process from cases where it is not clear if the activity is part of the process or causally upstream of it.<br />
<br />
==Annotation Issues - LEGO Annotations==<br />
===Aligning Conventional and LEGO Annotations===<br />
<br />
*A proposal to make Conventional Annotation align better with LEGO modelling (F-P linking) (Val)<br />
<br />
https://github.com/geneontology/go-ontology/issues/12739#issuecomment-254623691<br />
<br />
===Evidence codes in Noctua===<br />
*How are we going to handle ECO codes in Noctua. Currently there are only a limited number of codes that fall under 'used in manual assertion'. If we use codes that are not specific to the manual assertion part of the ontology, then they map to EXP. Are we going to request the entire set of codes that we think we might want to use or are we going to have an automated way to map to the correct code?<br />
<br />
Example: http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001874<br />
<br />
===Generating conventional annotations from Noctua models===<br />
* GAF/GPAD inference from LEGO models (Jim and David OS, Chris, Kimberly, David Hill, ...)<br />
** Introduction to inferring annotations from LEGO: Extended Gene Product to GO term relations; Reasoning across causal chains.<br />
***Jim Balhoff: Inference using Blazegraph & RDFox<br />
***DOS: Templates, design patterns and inference.<br />
*MGI's experience roundtripping with Noctua Models (DavidH)<br />
*Are we going to allow Noctua to generate conventional annotations to the root nodes of the ontology? <br />
**This would be useful for contextual annotations that are to otherwise root nodes. <br />
**However some groups block these kinds of annotations because in the past, these annotations were used to keep track of genes about which we had no information. <br />
**Note that the evidence code for a root node annotation in Noctua would/could be different in that the curator might assert that a gene product has some molecular function due to the observation that, when mutated, there is a phenotypic outcome, e.g. apoptosis execution fails.<br />
**This is a different statement from no biological data (ND) in which there is no information at all to assert a role in any biological process.<br />
*Are some conventional annotation rules inappropriate for Noctua annotation?<br />
**For a molecular function occurring in a cellular location, isn't IEP a more appropriate evidence code? IDA would mean that the function was assayed in situ. https://github.com/geneontology/go-annotation/issues/1395<br />
**Since binding is a part of many molecular functions, should we allow evidence codes other than IPI for binding (eg TAS)?<br />
<br />
== Regulation relations ==<br />
<br />
Regulation and causal relations are central to LEGO annotation and to inference based on LEGO models, but definitions and guidelines still need work to ensure consistency and clarity. <br />
DOS: I would like to present progress on the development of the relevant relations along with a proposal for how to improve them. This would probably work best as a collaborative presentation with LEGO annotators where we can show application to LEGO models.<br />
<br />
<br />
<br />
==Conference Calls and Communication==<br />
Estimated time: 30 minutes<br />
*Discuss different options for reducing the number of conference calls, while still facilitating effective communication between the different GO groups, e.g. annotators, ontology editors, software team<br />
**Consolidate all annotation calls (Monday LEGO, Tuesday Annotation, Tuesday PAINT) into one Tuesday annotation call, frequency TBD<br />
**Consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one weekly GO call <br />
*Discussion on the design of new SOPs for mechanisms of communication<br />
**What is the best mechanism to alert annotation groups of changes to the ontology that will affect annotations? We have started a table of contacts, but is this how annotation groups would like to proceed?<br />
**Review of github repositories, what to record where, who is processing/clearing tickets, etc.<br />
*Discussion on what it means to be a member of the Gene Ontology Consortium, not just the NHGRI grant.<br />
**Agreed to standards, which ones?<br />
* Decide where and when to hold next GOC meeting (also whether to include SAB next time)<br />
<br />
== Wrap up, action items ==<br />
<br />
== Time permitting, or post-meeting breakout ==<br />
<br />
=== Annotation Metrics ===<br />
Estimated time: 1 hour<br />
*What are the optimal metrics to assess progress in GO annotation?<br />
**Number of annotations<br />
**Number of references<br />
***Recall ZFIN's 'paper complexity' measure as a way of normalizing for different paper content (Doug mentioned in Geneva)<br />
**Revised annotations, e.g. updating to a new term<br />
**Removing annotations, e.g. improving knowledge about how a gene product affects a downstream process<br />
**Adding appropriate contextual information to existing annotations<br />
**Percentage of genome annotated vs percentage of genome with annotatable information?<br />
*How does LEGO modeling change our assessment of a curator's contributions?<br />
**Attribution of annotations to enable credit for: <br />
***Noctua annotations (This was discussed during LEGO call (http://wiki.geneontology.org/index.php/LEGO_September_19,_2016)<br />
*Multiple funding bodies (Ruth)<br />
*Distinguishing annotations that are created automatically, e.g. inference pipelines (Tony)<br />
*Recognizing individual curators contributions via Orcid IDs. <br />
**Determine at what level attribution occurs<br />
**Inclusion of funding source<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Agenda&diff=623922016 Los Angeles GOC Meeting Agenda2016-11-02T19:36:36Z<p>David os: /* Ontology Group Update (DavidH) */</p>
<hr />
<div>=Agenda=<br />
<br />
==Overview/Plan for Upcoming Five Years==<br />
*GO PIs presentation<br />
<br />
==Review action items from GOC meeting in Geneva, April 2016==<br />
===Geneva===<br />
*AI: GOC to decide what is HTP data<br />
**Related issue for this meeting: [http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#Annotations_from_High_Throughput_Experiments Annotations from High Throughput Experiments]<br />
*AI: Mechanism to remove redundant annotations in GO display<br />
**See https://github.com/geneontology/amigo/issues/294<br />
*AI: GOC to extract this data and display annual stats on web page<br />
**See http://amigo.geneontology.org/amigo/base_statistics<br />
*AI: GOC extract ontology stats<br />
*AI: Protein complexes - several AIs wrt this issue<br />
*AI: Submit suggestions for go-site to github<br />
*AI: Val give presentation on call for term matrix<br />
*AI: Create stats for % genome annotated<br />
*AI: Use tracker to submit feedback<br />
*AI: Judith and Tony discuss this (annotation summary views)<br />
*AI: High level discussions needed to discuss development of browsers<br />
*AI: Seth, Chris and Tony to discuss proposed extension to GPAD to capture source data for certain annotations<br />
*AI: Working group to be set up to work on community annotation web presence<br />
**Slide presentation on behalf of Moni<br />
<br />
== Informatics and Infrastructure 5 year plan ==<br />
<br />
Can we have this on this first day? I will give up update on various changes [[User:Cjm|Cjm]] ([[User talk:Cjm|talk]]) 15:11, 5 October 2016 (UTC)<br />
<br />
* replacement of svn<br />
* metadata-driven infrastructure - https://github.com/geneontology/go-site/tree/master/metadata<br />
* retiring MySQL - https://github.com/geneontology/go-site/issues/229<br />
* graphstore - https://github.com/geneontology/go-graphstore<br />
* new dataflow<br />
* retiring amigo1, yes?<br />
* migration of IT to LBNL from Stanford, Stanford's support for IT is greatly reduced.<br />
* ...<br />
<br />
=== Proposal ===<br />
<br />
* Switch to global monthly releases (cjm)<br />
** Still provide daily snapshots<br />
<br />
==Conference Calls and Communication==<br />
Estimated time: 30 minutes<br />
*We'd like to discuss different options for reducing the number of conference calls, while still facilitating effective communication between the different GO groups, e.g. annotators, ontology editors, software team<br />
#Consolidate all annotation calls (Monday LEGO, Tuesday Annotation, Tuesday PAINT) into one Tuesday annotation call, frequency TBD<br />
#Consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one weekly GO call <br />
*Can we design new SOPs for mechanisms of communication<br />
**What is the best mechanism to alert annotation groups of changes to the ontology that will affect annotations? We have started a table of contacts, but is this how annotation groups would like to proceed?<br />
**Review of github repositories, what to record where, who is processing/clearing tickets, etc.<br />
<br />
== Annotation Metrics ==<br />
*Estimated time: 1 hour<br />
*What are the best metrics to assess progress in GO annotation?<br />
**Number of annotations<br />
**Number of references<br />
***Recall Zfin's 'paper complexity' measure as a way of normalizing for different paper content (Doug mentioned in Geneva)<br />
**Revised annotations, e.g. updating to a new term<br />
**Removing annotations, e.g. improving knowledge about how a gene product affects a downstream process<br />
**Adding appropriate contextual information to existing annotations<br />
**Percentage of genome annotated vs percentage of genome with annotatable information?<br />
*How does LEGO modeling change our assessment of curator contributions?<br />
**Attribution of annotations to enable credit for: <br />
***Noctua annotations (This was discussed during LEGO call (http://wiki.geneontology.org/index.php/LEGO_September_19,_2016)<br />
*Multiple funding bodies (Ruth)<br />
*Distinguishing annotations that are created automatically, e.g. inference pipelines (Tony)<br />
*Individual curators attribution via Orcid IDs, it is important to establish if this wanted, and if it is wanted at what level of information? At an annotation by annotation level or just as a summation of contribution.<br />
<br />
== Genetic entities in GO annotation ==<br />
*Can someone claim these two topics, if they are still interested in discussing them? <br />
** DOS: What genetic entities do we need to refer to as the primary object of GO annotation and in extended forms of conventional or LEGO annotation?<br />
**What conventions should we enforce regarding which identifiers to use to refer to these genetic features and how?<br />
* Update on UniProt GCRP sets (Maria)<br />
* Update on gpi specifications and uses (Kimberly, Chris) - 10-15 minutes<br />
<br />
==Ontology Group Update (DavidH)==<br />
* GH tracker progress<br />
* Special Projects<br />
** Cilia<br />
** Autophagy<br />
** Apoptosis<br />
** Plant Enzymes<br />
** Synapse (DOS/PDT)<br />
* GO help report<br />
<br />
==Annotation Issues - Conventional Annotations==<br />
===Aligning Conventional and LEGO Annotations===<br />
<br />
*A proposal to make Conventional Annotation align better with LEGO modelling (F-P linking) (Val)<br />
<br />
https://github.com/geneontology/go-ontology/issues/12739#issuecomment-254623691<br />
<br />
===Modified Protein Binding===<br />
<br />
*Modified protein binding: GO terms & annotations are very inconsistent. (DavidH to present Paola's proposal)<br />
**Recent github issues: <br />
glycoprotein binding: https://github.com/geneontology/go-ontology/issues/12580#issuecomment-240782020<br />
ubiquitinated protein binding https://github.com/geneontology/go-ontology/issues/12582#issuecomment-240452320<br />
<br />
===Protein Family Terms in the Ontology===<br />
<br />
* Protein families in terms (DavidH)<br />
** Currently the inclusion of protein family information in term names is leading to inconsistent annotation.<br />
*** For now, the ontology editors have not been adding terms that specifically refer to protein families with the exception of signaling pathways. Should we make this a rule? If so, how will we capture the detail desired by annotators and how will we make this backward compatible?<br />
<br />
https://github.com/geneontology/go-ontology/issues/12440<br />
<br />
===Multiple Evidences to Support an Inference===<br />
<br />
* How are people capturing data where both direct assay AND protein motif/domains/sequence needs to be used by the curator to provide the annotation? [15 min Ruth, started by Rebecca] [http://wiki.geneontology.org/index.php/File:RFOULGER_IC_membrane_Sept_2016.pptx presentation] A system needs to be in place to enable the more specific annotations to be created for orthologous proteins (which cannot be done across all species with the IC evidence code) <br />
** eg transmembrane domain used as evidence to create the annotation 'integral to membrane' with IEA evidence; immunofluorescence localises protein to 'plasma membrane' (annotated with IDA evidence), ideal annotation to be created 'integral to plasma membrane'<br />
** 3 obvious options (any others?)<br />
*** new evidence code IDD 'inferred by direct assay AND protein domain(sequence/motif?)' (would probably also want IMD, IGD, IED)<br />
****Note that ECO has a combinatorial evidence code that could possibly be used as the parent for new GO combinatorial codes:<br />
*****combinatorial evidence used in manual assertion - ECO:0000244<br />
*** no new evidence code requires as this is implied by the 'inferred' aspect of the evidence code as well as 'author intent'<br />
*** Create a GOC pipeline that creates the CC annotations based on the IDA annotation (eg plasma membrane) and the IEA information (eg integral to membrane) to create the more specific annotation (eg integral to plasma membrane). <br />
<br />
===Transcription Factor Annotation Decision Tree===<br />
<br />
* Flowchart guidelines for transcription factor annotations [10 min Rachael/Ruth/Barbara] [http://wiki.geneontology.org/index.php/File:Expression_Transcription_Decision_Tree_2016.pptx presentation]. To improve consistency UCL team have created an annotation flowchart which is being circulated to GOC members.<br />
<br />
===Consistent Classification of Signaling Pathway Terms===<br />
<br />
* Conventions for signalling pathway terms<br />
** Currently you can request signalling pathway terms along multiple axes of classification including:<br />
*** signalling module (MAPK cascade, GTPase etc)<br />
*** process regulated<br />
*** target TF's<br />
*** ligand /pheromone activating pathway<br />
*** Process regulated<br />
*** condition activating pathway (in response to hydrogen peroxide and other oxidants for oxidative stress pathway)<br />
This results in almost infinite number of ways to describe some pathways<br />
<br />
https://github.com/geneontology/go-ontology/issues/12701<br />
<br />
===Annotations from High Throughput Experiments===<br />
<br />
*Annotations from high-throughput experiments (Ruth, David Hill, Kimberly)<br />
**How do we decide when to make annotations from high-throughput experiments?<br />
**If we decide that annotations from high-throughput experiments should be removed, what are the procedures (all annotations, some annotations)?<br />
**Do we want new evidence codes to indicate that the annotation was inferred from a high-throughput experiment?<br />
<br />
==Annotation Issues - LEGO Annotations==<br />
*How are we going to handle ECO codes in Noctua. Currently there are only a limited number of codes that fall under 'used in manual assertion'. If we use codes that are not specific to the manual assertion part of the ontology, then they map to EXP. Are we going to request the entire set of codes that we think we might want to use or are we going to have an automated way to map to the correct code?<br />
<br />
Example: http://noctua.berkeleybop.org/editor/graph/gomodel:5745387b00001874<br />
<br />
*Generating conventional annotations from Noctua models<br />
**Are we going to allow Noctua to generate conventional annotations to the root nodes of the ontology? <br />
***This would be useful for contextual annotations that are to otherwise root nodes. <br />
***However some groups block these kinds of annotations because in the past, these annotations were used to keep track of genes about which we had no information. <br />
***Note that the evidence code for a root node annotation in Noctua would/could be different in that the curator might assert that a gene product has some molecular function due to the observation that, when mutated, there is a phenotypic outcome, e.g. apoptosis execution fails.<br />
***This is a different statement from no biological data (ND) in which there is no information at all to assert a role in any biological process.<br />
*Are some conventional annotation rules inappropriate for Noctua annotation?<br />
**For a molecular function occurring in a cellular location, isn't IEP a more appropriate evidence code? IDA would mean that the function was assayed in situ. https://github.com/geneontology/go-annotation/issues/1395<br />
**Since binding is a part of many molecular functions, should we allow evidence codes other than IPI for binding (eg TAS)?<br />
*MGI's experience roundtripping with Noctua Models (DavidH)<br />
<br />
== Regulation relations ==<br />
<br />
Regulation and causal relations are central to LEGO annotation and to inference based on LEGO models, but definitions and guidelines still need work to ensure consistency and clarity. <br />
DOS: I would like to present progress on the development of the relevant relations along with a proposal for how to improve them. This would probably work best as a collaborative presentation with LEGO annotators where we can show application to LEGO models.<br />
<br />
==GAF/GPAD inference from LEGO models ==<br />
<br />
Introduction to inferring annotations from LEGO: Extended Gene Product to GO term relations; Reasoning across causal chains.<br />
<br />
Jim Balhoff: Inference using Blazegraph & RDFox<br />
<br />
DOS: Templates, design patterns and inference.<br />
<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-10-20&diff=62206Ontology meeting 2016-10-202016-10-20T14:34:48Z<p>David os: /* equivalence axioms (GCIs) required for reasoning with ChEBI missing from editors file ? */</p>
<hr />
<div>Attendees:<br />
<br />
Minutes: David H or David OS?<br />
<br />
Regrets:<br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
===Protein complex discussion at GOC LA meeting===<br />
<br />
At the managers call on Oct 19th, the agenda for the upcoming GOC LA meeting was discussed. This point in particular: (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#Protein_Complexes) "Action item [from the 2015-09 Washington, D.C. meeting]: Form a working group to come up with a process for this migration of responsibilities from GO for protein complex definition. Curators, Darren (PRO), Sandra (IntAct), Paola (GO), David OS, Chris, Peter (Reactome) should be included."<br />
<br />
The question was raised of who could/should present a proposal at the GOC LA meeting to use to reach a resolution (rather than simply having another long discussion). Suzi asked: could David OS work with Peter to come up with a proposal to present? (Chris won't have the chance.)<br />
<br />
Here are the minutes from Geneva:<br />
<br />
https://docs.google.com/document/d/12CDf4s8YsylPMNHM3UuPis9NyVQ9WFpBpNYTFYAH7kc/edit#heading=h.wwwbdoeygi1h<br />
<pre><br />
DOS: Outcome of this agreement = PILOT PROJECT TO INFER ANNOTATIONS IS CANCELLED. Work on inferred classifications needs to shift back to the ontology. We still have no means for specifying species independent complexes by composition, apart, perhaps, from complexes made up oligomerised members of the same protein family (e.g. see smads). In cases where we have documentation of conservation, we can at least enumerate examples.<br />
</pre><br />
<br />
<br />
DOS: We need a consistent PI decision on this before any proposals can be made.<br />
<br />
===Merging GO calls===<br />
<br />
This will be discussed at the GOC LA meeting (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#Conference_Calls_and_Communication). The EBI office raised some concerns about merging the ontology call with others. David OS, could you please relay these comments in LA? <br />
<br />
===Adding items to the agenda for the GOC LA meeting===<br />
<br />
This is being finalised, so if any of us would like to add anything, please do so ASAP (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda).<br />
<br />
DOS: I've provisionally added a section on [http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#GAF.2FGPAD_inference_from_LEGO_models GAF/GPAD inference from LEGO models]<br />
<br />
* Introduction to inferring annotations from LEGO: Extended Gene Product to GO term relations; Reasoning across causal chains.<br />
* Jim Balhoff: Inference using Blazegraph<br />
* DOS: Templates, design patterns and inference.<br />
<br />
=== equivalence axioms (GCIs) required for reasoning with ChEBI missing from editors file ?===<br />
<br />
From last week's discussion:<br />
<br />
https://github.com/geneontology/go-ontology/issues/12721<br />
<br />
gene_ontology_write.obo imports cheb_import.owl. This lacks the equivalence axioms (GCIs). But we have a file called bio_chebi.owl which has them. bio_chebi.owl was last updated 19 months ago: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/extensions/bio-chebi.owl?view=log<br />
<br />
During the move to using ChEBI, a few issues wrt distinctions were introduced for the purpose of reasoning in OWL for GO. We mapped equivalent axioms; some terms were conflated. In BioCHEBI, the equivalences are made, but we don’t know the downstream pipeline. <br />
<br />
These equivalent axioms are not imported when you load gene_ontology_write.obo - they were at some point - but it needs an import statement to BioChEBI. It is in chebi_import.owl, but nothing shows that they’re being used.<br />
<br />
We need to fix BioChEBI input, or come up with an alternate strategy.<br />
<br />
Tanya: these are being used in TermGenie. So some process is updating that file at least for TermGenie.<br />
Heiko once said: “ontology uses BioCHEBI”, but it is not using it now. <br />
<br />
Relevant discussion has moved to this ticket: https://github.com/geneontology/go-ontology/issues/12735<br />
<br />
*ACTION*: We need Chris to please clarify.<br />
<br />
===Follow-up: SOP for merging terms in OBO-Edit===<br />
<br />
For background, see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#SOP_when_merging_terms. <br />
<br />
Paola tested and drafted an SOP, and added documentation here: http://wiki.geneontology.org/index.php/Editor_Guide#SOP_for_merging_terms_in_OBO-Edit<br />
<br />
===Jenkins github new tickets reports===<br />
<br />
From Melanie: Birgit mentioned that "For the last few weeks my daily Jenkins updates have no new notifications and very occasionally updates." I usually check the tracker directly and delete those, can someone have a look?<br />
<br />
[Paola] I confirm I haven't seen those reports at all lately - and there HAVE been new GH ontology tickets, as well as updates.<br />
<br />
===Follow-up: GitHub projects===<br />
<br />
See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-06#GitHub_Projects<br />
<br />
Plan is to look at https://github.com/geneontology/go-ontology/projects/1 and see how this works for us.<br />
<br />
Beginning with: https://github.com/geneontology/go-ontology/issues/12723<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-10-20&diff=62205Ontology meeting 2016-10-202016-10-20T14:00:48Z<p>David os: /* Adding items to the agenda for the GOC LA meeting */</p>
<hr />
<div>Attendees:<br />
<br />
Minutes: David H or David OS?<br />
<br />
Regrets:<br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
===Protein complex discussion at GOC LA meeting===<br />
<br />
At the managers call on Oct 19th, the agenda for the upcoming GOC LA meeting was discussed. This point in particular: (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#Protein_Complexes) "Action item [from the 2015-09 Washington, D.C. meeting]: Form a working group to come up with a process for this migration of responsibilities from GO for protein complex definition. Curators, Darren (PRO), Sandra (IntAct), Paola (GO), David OS, Chris, Peter (Reactome) should be included."<br />
<br />
The question was raised of who could/should present a proposal at the GOC LA meeting to use to reach a resolution (rather than simply having another long discussion). Suzi asked: could David OS work with Peter to come up with a proposal to present? (Chris won't have the chance.)<br />
<br />
Here are the minutes from Geneva:<br />
<br />
https://docs.google.com/document/d/12CDf4s8YsylPMNHM3UuPis9NyVQ9WFpBpNYTFYAH7kc/edit#heading=h.wwwbdoeygi1h<br />
<pre><br />
DOS: Outcome of this agreement = PILOT PROJECT TO INFER ANNOTATIONS IS CANCELLED. Work on inferred classifications needs to shift back to the ontology. We still have no means for specifying species independent complexes by composition, apart, perhaps, from complexes made up oligomerised members of the same protein family (e.g. see smads). In cases where we have documentation of conservation, we can at least enumerate examples.<br />
</pre><br />
<br />
<br />
DOS: We need a consistent PI decision on this before any proposals can be made.<br />
<br />
===Merging GO calls===<br />
<br />
This will be discussed at the GOC LA meeting (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#Conference_Calls_and_Communication). The EBI office raised some concerns about merging the ontology call with others. David OS, could you please relay these comments in LA? <br />
<br />
===Adding items to the agenda for the GOC LA meeting===<br />
<br />
This is being finalised, so if any of us would like to add anything, please do so ASAP (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda).<br />
<br />
DOS: I've provisionally added a section on [http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#GAF.2FGPAD_inference_from_LEGO_models GAF/GPAD inference from LEGO models]<br />
<br />
* Introduction to inferring annotations from LEGO: Extended Gene Product to GO term relations; Reasoning across causal chains.<br />
* Jim Balhoff: Inference using Blazegraph<br />
* DOS: Templates, design patterns and inference.<br />
<br />
=== equivalence axioms (GCIs) required for reasoning with ChEBI missing from editors file ?===<br />
<br />
From last week's discussion:<br />
<br />
https://github.com/geneontology/go-ontology/issues/12721<br />
<br />
gene_ontology_write.obo imports cheb_import.owl. This lacks the equivalence axioms (GCIs). But we have a file called bio_chebi.owl which has them. bio_chebi.owl was last updated 19 months ago: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/extensions/bio-chebi.owl?view=log<br />
<br />
During the move to using ChEBI, a few issues wrt distinctions were introduced for the purpose of reasoning in OWL for GO. We mapped equivalent axioms; some terms were conflated. In BioCHEBI, the equivalences are made, but we don’t know the downstream pipeline. <br />
<br />
These equivalent axioms are not imported when you load gene_ontology_write.obo - they were at some point - but it needs an import statement to BioChEBI. It is in chebi_import.owl, but nothing shows that they’re being used.<br />
<br />
We need to fix BioChEBI input, or come up with an alternate strategy.<br />
<br />
Tanya: these are being used in TermGenie. So some process is updating that file at least for TermGenie.<br />
Heiko once said: “ontology uses BioCHEBI”, but it is not using it now. <br />
<br />
*ACTION*: We need Chris to please clarify.<br />
<br />
===Follow-up: SOP for merging terms in OBO-Edit===<br />
<br />
For background, see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#SOP_when_merging_terms. <br />
<br />
Paola tested and drafted an SOP, and added documentation here: http://wiki.geneontology.org/index.php/Editor_Guide#SOP_for_merging_terms_in_OBO-Edit<br />
<br />
===Jenkins github new tickets reports===<br />
<br />
From Melanie: Birgit mentioned that "For the last few weeks my daily Jenkins updates have no new notifications and very occasionally updates." I usually check the tracker directly and delete those, can someone have a look?<br />
<br />
[Paola] I confirm I haven't seen those reports at all lately - and there HAVE been new GH ontology tickets, as well as updates.<br />
<br />
===Follow-up: GitHub projects===<br />
<br />
See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-06#GitHub_Projects<br />
<br />
Plan is to look at https://github.com/geneontology/go-ontology/projects/1 and see how this works for us.<br />
<br />
Beginning with: https://github.com/geneontology/go-ontology/issues/12723<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Agenda&diff=622042016 Los Angeles GOC Meeting Agenda2016-10-20T13:57:29Z<p>David os: </p>
<hr />
<div>=Agenda=<br />
<br />
==Overview/Plan for Upcoming Five Years==<br />
*GO PIs presentation<br />
<br />
== Follow-up on outstanding action items from previous GOC meeting in Geneva and Washington, DC==<br />
<br />
== Informatics and Infrastructure 5 year plan ==<br />
<br />
Can we have this on this first day? I will give up update on various changes [[User:Cjm|Cjm]] ([[User talk:Cjm|talk]]) 15:11, 5 October 2016 (UTC)<br />
<br />
* replacement of svn<br />
* metadata-driven infrastructure - https://github.com/geneontology/go-site/tree/master/metadata<br />
* retiring MySQL - https://github.com/geneontology/go-site/issues/229<br />
* graphstore - https://github.com/geneontology/go-graphstore<br />
* new dataflow<br />
* retiring amigo1, yes?<br />
* migration of IT to LBNL from Stanford, Stanford's support for IT is greatly reduced.<br />
* ...<br />
<br />
== Annotation Metrics ==<br />
*Estimated time: 1 hour<br />
*What are the best metrics to assess progress in GO annotation?<br />
**Improved information content - how would that be measured?<br />
**Number of annotations<br />
**Number of references<br />
**Percentage of genome annotated vs percentage of genome with annotatable information?<br />
*How does LEGO modeling change our assessment of curator contributions?<br />
*Attribution of annotations to enable credit for: <br />
**Noctua annotations (This was discussed during LEGO call (http://wiki.geneontology.org/index.php/LEGO_September_19,_2016)<br />
**Multiple funding bodies (Ruth)<br />
**Distinguishing annotations that are created automatically, e.g. inference pipelines (Tony)<br />
**Individual curators attribution via Orcid IDs, it is important to establish if this wanted, and if it is wanted at what level of information? At an annotation by annotation level or just as a summation of contribution.<br />
<br />
== Protein Complexes ==<br />
*Estimated time: 1-2 hours<br />
*Minutes on this from last meeting: https://docs.google.com/document/d/12CDf4s8YsylPMNHM3UuPis9NyVQ9WFpBpNYTFYAH7kc/edit#heading=h.wwwbdoeygi1h<br />
*Overview of complex creation within Noctua https://vimeo.com/channels/noctua/148800722<br />
*What protein complexes should be in the Cellular Component branch of the ontology?<br />
**These were the action items from the 2015-09 Washington, D.C. meeting:<br />
***Action item: new evidence code for capturing complexes, child of IPI (ECO:0000353)<br />
***Action item: new evidence code for reconstituted biological system consisting of components of more than one species<br />
***Action item: Form a working group to come up with a process for this migration of responsibilities from GO for protein complex definition. Curators, Darren (PRO), Sandra (IntAct), Paola (GO), David OS, Chris, Peter (Reactome) should be included.<br />
<br />
== Regulation relations ==<br />
<br />
Regulation and causal relations are central to LEGO annotation and to inference based on LEGO models, but definitions and guidelines still need work to ensure consistency and clarity. <br />
DOS: I would like to present progress on the development of the relevant relations along with a proposal for how to improve them. This would probably work best as a collaborative presentation with LEGO annotators where we can show application to LEGO models.<br />
<br />
==GAF/GPAD inference from LEGO models ==<br />
<br />
Introduction to inferring annotations from LEGO: Extended Gene Product to GO term relations; Reasoning across causal chains.<br />
<br />
Jim Balhoff: Inference using Blazegraph<br />
<br />
DOS: Templates, design patterns and inference.<br />
<br />
<br />
== Genetic entities in GO annotation ==<br />
*Can someone claim these two topics, if they are still interested in discussing them? <br />
** DOS: What genetic entities do we need to refer to as the primary object of GO annotation and in extended forms of conventional or LEGO annotation?<br />
**What conventions should we enforce regarding which identifiers to use to refer to these genetic features and how?<br />
* Update on UniProt GCRP sets (Maria)<br />
* Update on gpi specifications and uses (Kimberly, Chris) - 10-15 minutes<br />
<br />
==Conference Calls and Communication==<br />
Estimated time: 15 minutes<br />
*Proposal to consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one GO call held weekly on Tuesdays at 8am PST<br />
**These areas of annotation, and ontology development, are, or have been, converging for some time now and we think it would be a better use of everyone's time to have one weekly call where we discuss any annotation- or ontology-related issues<br />
*Can we design new SOPs for mechanisms of communication<br />
**What is the best mechanism to alert annotation groups of changes to the ontology that will affect annotations? We have started a table of contacts, but is this how annotation groups would like to proceed?<br />
**Review of github channels, what to record where, who is processing/clearing tickets, etc.<br />
<br />
==Annotation Issues - Conventional Annotations==<br />
<br />
*A proposal to make Conventional Annotation align better with LEGO modelling (F-P linking) (Val)<br />
<br />
https://github.com/geneontology/go-ontology/issues/12739#issuecomment-254623691<br />
<br />
<br />
*Modified protein binding: GO terms & annotations are very inconsistent. <br />
**Recent github issues: <br />
glycoprotein binding: https://github.com/geneontology/go-ontology/issues/12580#issuecomment-240782020<br />
ubiquitinated protein binding https://github.com/geneontology/go-ontology/issues/12582#issuecomment-240452320<br />
<br />
* How are people capturing data where both direct assay AND protein motif/domains/sequence needs to be used by the curator to provide the annotation? [15 min Ruth, started by Rebecca] A system needs to be in place to enable the more specific annotations to be created for orthologous proteins (which cannot be done across all species with the IC evidence code) <br />
** eg transmembrane domain used as evidence to create the annotation 'integral to membrane' with IEA evidence; immunofluorescence localises protein to 'plasma membrane' (annotated with IDA evidence), ideal annotation to be created 'integral to plasma membrane'<br />
** 3 obvious options (any others?)<br />
*** new evidence code IDD 'inferred by direct assay AND protein domain(sequence/motif?)' (would probably also want IMD, IGD, IED)<br />
*** no new evidence code requires as this is implied by the 'inferred' aspect of the evidence code as well as 'author intent'<br />
*** Create a GOC pipeline that creates the CC annotations based on the IDA annotation (eg plasma membrane) and the IEA information (eg integral to membrane) to create the more specific annotation (eg integral to plasma membrane). <br />
<br />
* Flowchart guidelines for transcription factor annotations [10 min Rachael/Ruth/Barbara]. To improve consistency UCL team have created an annotation flowchart which is being circulated to GOC members.<br />
<br />
* Protein families in terms<br />
** Currently the inclusion of protein family information in term names is leading to inconsistent annotation.<br />
*** For now, the ontology editors have not been adding terms that specifically refer to protein families with the exception of signaling pathways. Should we make this a rule? If so, how will we capture the detail desired by annotators and how will we make this backward compatible?<br />
<br />
https://github.com/geneontology/go-ontology/issues/12440<br />
<br />
* Conventions for signalling pathway terms<br />
** Currently you can request signalling pathway terms along multiple axes of classification including:<br />
*** signalling module (MAPK cascade, GTPase etc)<br />
*** process regulated<br />
*** target TF's<br />
*** ligand /pheromone activating pathway<br />
*** Process regulated<br />
*** condition activating pathway (in response to hydrogen peroxide and other oxidants for oxidative stress pathway)<br />
This results in almost infinite number of ways to describe some pathways<br />
<br />
https://github.com/geneontology/go-ontology/issues/12701<br />
<br />
<br />
*Annotations from high-throughput experiments<br />
**How do we decide when to make annotations from high-throughput experiments?<br />
**If we decide that annotations from high-throughput experiments should be removed, what are the procedures (all annotations, some annotations)?<br />
<br />
==Annotation Issues - LEGO Annotations (Sunday AM?)==<br />
*How are we going to handle ECO codes in Noctua. Currently there are only a limited number of codes that fall under 'used in manual assertion'. If we use codes that are not specific to the manual assertion part of the ontology, then they map to EXP. Are we going to request the entire set of codes that we think we might want to use or are we going to have an automated way to map to the correct code?<br />
*Generating conventional annotations from Noctua models<br />
**Since Noctua models are a much more detailed and complete picture of the biology as a whole, we need to be able to process that Noctua information to generate gafs and gpad files from it. We should discuss progress about strategies to digest this information into the conventional annotation paradigms.<br />
**Are we going to allow Noctua to generate conventional annotations to the root nodes of the ontology? <br />
***This would be useful for contextual annotations that are to otherwise root nodes. <br />
***However some groups block these kinds of annotations because in the past, these annotations were used to keep track of genes about which we had no information. <br />
***Note that the evidence code for a root node annotation in Noctua would/could be different in that the curator might assert that a gene product has some molecular function due to the observation that, when mutated, there is a phenotypic outcome, e.g. apoptosis execution fails. <br />
*Are some conventional annotation rules inappropriate for Noctua annotation?<br />
**For a molecular function occurring in a cellular location, isn't IEP a more appropriate evidence code? IDA would mean that the function was assayed in situ.<br />
**Since binding is a part of many molecular functions, should we allow evidence codes other than IPI for binding (eg TAS)?<br />
**This is a different statement from no biological data (ND) in which there is no information at all to assert a role in any biological process.<br />
*MGI's experience roundtripping with Noctua Models (DPH)<br />
==Brainstorm about visualization of GO data==<br />
<br />
== Production ==<br />
<br />
New data flow (Chris)<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Agenda&diff=622032016 Los Angeles GOC Meeting Agenda2016-10-20T13:42:03Z<p>David os: /* Genetic entities in GO annotation */</p>
<hr />
<div>=Agenda=<br />
<br />
==Overview/Plan for Upcoming Five Years==<br />
*GO PIs presentation<br />
<br />
== Follow-up on outstanding action items from previous GOC meeting in Geneva and Washington, DC==<br />
<br />
== Informatics and Infrastructure 5 year plan ==<br />
<br />
Can we have this on this first day? I will give up update on various changes [[User:Cjm|Cjm]] ([[User talk:Cjm|talk]]) 15:11, 5 October 2016 (UTC)<br />
<br />
* replacement of svn<br />
* metadata-driven infrastructure - https://github.com/geneontology/go-site/tree/master/metadata<br />
* retiring MySQL - https://github.com/geneontology/go-site/issues/229<br />
* graphstore - https://github.com/geneontology/go-graphstore<br />
* new dataflow<br />
* retiring amigo1, yes?<br />
* migration of IT to LBNL from Stanford, Stanford's support for IT is greatly reduced.<br />
* ...<br />
<br />
== Annotation Metrics ==<br />
*Estimated time: 1 hour<br />
*What are the best metrics to assess progress in GO annotation?<br />
**Improved information content - how would that be measured?<br />
**Number of annotations<br />
**Number of references<br />
**Percentage of genome annotated vs percentage of genome with annotatable information?<br />
*How does LEGO modeling change our assessment of curator contributions?<br />
*Attribution of annotations to enable credit for: <br />
**Noctua annotations (This was discussed during LEGO call (http://wiki.geneontology.org/index.php/LEGO_September_19,_2016)<br />
**Multiple funding bodies (Ruth)<br />
**Distinguishing annotations that are created automatically, e.g. inference pipelines (Tony)<br />
**Individual curators attribution via Orcid IDs, it is important to establish if this wanted, and if it is wanted at what level of information? At an annotation by annotation level or just as a summation of contribution.<br />
<br />
== Protein Complexes ==<br />
*Estimated time: 1-2 hours<br />
*Minutes on this from last meeting: https://docs.google.com/document/d/12CDf4s8YsylPMNHM3UuPis9NyVQ9WFpBpNYTFYAH7kc/edit#heading=h.wwwbdoeygi1h<br />
*Overview of complex creation within Noctua https://vimeo.com/channels/noctua/148800722<br />
*What protein complexes should be in the Cellular Component branch of the ontology?<br />
**These were the action items from the 2015-09 Washington, D.C. meeting:<br />
***Action item: new evidence code for capturing complexes, child of IPI (ECO:0000353)<br />
***Action item: new evidence code for reconstituted biological system consisting of components of more than one species<br />
***Action item: Form a working group to come up with a process for this migration of responsibilities from GO for protein complex definition. Curators, Darren (PRO), Sandra (IntAct), Paola (GO), David OS, Chris, Peter (Reactome) should be included.<br />
<br />
== Regulation relations ==<br />
<br />
Regulation and causal relations are central to LEGO annotation and to inference based on LEGO models, but definitions and guidelines still need work to ensure consistency and clarity. <br />
DOS: I would like to present progress on the development of the relevant relations along with a proposal for how to improve them. This would probably work best as a collaborative presentation with LEGO annotators where we can show application to LEGO models.<br />
<br />
== Genetic entities in GO annotation ==<br />
*Can someone claim these two topics, if they are still interested in discussing them?<br />
** DOS: What genetic entities do we need to refer to as the primary object of GO annotation and in extended forms of conventional or LEGO annotation?<br />
**What conventions should we enforce regarding which identifiers to use to refer to these genetic features and how?<br />
* Update on UniProt GCRP sets (Maria)<br />
* Update on gpi specifications and uses (Kimberly, Chris) - 10-15 minutes<br />
<br />
==Conference Calls and Communication==<br />
Estimated time: 15 minutes<br />
*Proposal to consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one GO call held weekly on Tuesdays at 8am PST<br />
**These areas of annotation, and ontology development, are, or have been, converging for some time now and we think it would be a better use of everyone's time to have one weekly call where we discuss any annotation- or ontology-related issues<br />
*Can we design new SOPs for mechanisms of communication<br />
**What is the best mechanism to alert annotation groups of changes to the ontology that will affect annotations? We have started a table of contacts, but is this how annotation groups would like to proceed?<br />
**Review of github channels, what to record where, who is processing/clearing tickets, etc.<br />
<br />
==Annotation Issues - Conventional Annotations==<br />
<br />
*A proposal to make Conventional Annotation align better with LEGO modelling (F-P linking) (Val)<br />
<br />
https://github.com/geneontology/go-ontology/issues/12739#issuecomment-254623691<br />
<br />
<br />
*Modified protein binding: GO terms & annotations are very inconsistent. <br />
**Recent github issues: <br />
glycoprotein binding: https://github.com/geneontology/go-ontology/issues/12580#issuecomment-240782020<br />
ubiquitinated protein binding https://github.com/geneontology/go-ontology/issues/12582#issuecomment-240452320<br />
<br />
* How are people capturing data where both direct assay AND protein motif/domains/sequence needs to be used by the curator to provide the annotation? [15 min Ruth, started by Rebecca] A system needs to be in place to enable the more specific annotations to be created for orthologous proteins (which cannot be done across all species with the IC evidence code) <br />
** eg transmembrane domain used as evidence to create the annotation 'integral to membrane' with IEA evidence; immunofluorescence localises protein to 'plasma membrane' (annotated with IDA evidence), ideal annotation to be created 'integral to plasma membrane'<br />
** 3 obvious options (any others?)<br />
*** new evidence code IDD 'inferred by direct assay AND protein domain(sequence/motif?)' (would probably also want IMD, IGD, IED)<br />
*** no new evidence code requires as this is implied by the 'inferred' aspect of the evidence code as well as 'author intent'<br />
*** Create a GOC pipeline that creates the CC annotations based on the IDA annotation (eg plasma membrane) and the IEA information (eg integral to membrane) to create the more specific annotation (eg integral to plasma membrane). <br />
<br />
* Flowchart guidelines for transcription factor annotations [10 min Rachael/Ruth/Barbara]. To improve consistency UCL team have created an annotation flowchart which is being circulated to GOC members.<br />
<br />
* Protein families in terms<br />
** Currently the inclusion of protein family information in term names is leading to inconsistent annotation.<br />
*** For now, the ontology editors have not been adding terms that specifically refer to protein families with the exception of signaling pathways. Should we make this a rule? If so, how will we capture the detail desired by annotators and how will we make this backward compatible?<br />
<br />
https://github.com/geneontology/go-ontology/issues/12440<br />
<br />
* Conventions for signalling pathway terms<br />
** Currently you can request signalling pathway terms along multiple axes of classification including:<br />
*** signalling module (MAPK cascade, GTPase etc)<br />
*** process regulated<br />
*** target TF's<br />
*** ligand /pheromone activating pathway<br />
*** Process regulated<br />
*** condition activating pathway (in response to hydrogen peroxide and other oxidants for oxidative stress pathway)<br />
This results in almost infinite number of ways to describe some pathways<br />
<br />
https://github.com/geneontology/go-ontology/issues/12701<br />
<br />
<br />
*Annotations from high-throughput experiments<br />
**How do we decide when to make annotations from high-throughput experiments?<br />
**If we decide that annotations from high-throughput experiments should be removed, what are the procedures (all annotations, some annotations)?<br />
<br />
==Annotation Issues - LEGO Annotations (Sunday AM?)==<br />
*How are we going to handle ECO codes in Noctua. Currently there are only a limited number of codes that fall under 'used in manual assertion'. If we use codes that are not specific to the manual assertion part of the ontology, then they map to EXP. Are we going to request the entire set of codes that we think we might want to use or are we going to have an automated way to map to the correct code?<br />
*Generating conventional annotations from Noctua models<br />
**Since Noctua models are a much more detailed and complete picture of the biology as a whole, we need to be able to process that Noctua information to generate gafs and gpad files from it. We should discuss progress about strategies to digest this information into the conventional annotation paradigms.<br />
**Are we going to allow Noctua to generate conventional annotations to the root nodes of the ontology? <br />
***This would be useful for contextual annotations that are to otherwise root nodes. <br />
***However some groups block these kinds of annotations because in the past, these annotations were used to keep track of genes about which we had no information. <br />
***Note that the evidence code for a root node annotation in Noctua would/could be different in that the curator might assert that a gene product has some molecular function due to the observation that, when mutated, there is a phenotypic outcome, e.g. apoptosis execution fails. <br />
*Are some conventional annotation rules inappropriate for Noctua annotation?<br />
**For a molecular function occurring in a cellular location, isn't IEP a more appropriate evidence code? IDA would mean that the function was assayed in situ.<br />
**Since binding is a part of many molecular functions, should we allow evidence codes other than IPI for binding (eg TAS)?<br />
**This is a different statement from no biological data (ND) in which there is no information at all to assert a role in any biological process.<br />
*MGI's experience roundtripping with Noctua Models (DPH)<br />
==Brainstorm about visualization of GO data==<br />
<br />
== Production ==<br />
<br />
New data flow (Chris)<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-10-20&diff=62202Ontology meeting 2016-10-202016-10-20T13:39:28Z<p>David os: /* Protein complex discussion at GOC LA meeting */</p>
<hr />
<div>Attendees:<br />
<br />
Minutes: David H or David OS?<br />
<br />
Regrets:<br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
===Protein complex discussion at GOC LA meeting===<br />
<br />
At the managers call on Oct 19th, the agenda for the upcoming GOC LA meeting was discussed. This point in particular: (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#Protein_Complexes) "Action item [from the 2015-09 Washington, D.C. meeting]: Form a working group to come up with a process for this migration of responsibilities from GO for protein complex definition. Curators, Darren (PRO), Sandra (IntAct), Paola (GO), David OS, Chris, Peter (Reactome) should be included."<br />
<br />
The question was raised of who could/should present a proposal at the GOC LA meeting to use to reach a resolution (rather than simply having another long discussion). Suzi asked: could David OS work with Peter to come up with a proposal to present? (Chris won't have the chance.)<br />
<br />
Here are the minutes from Geneva:<br />
<br />
https://docs.google.com/document/d/12CDf4s8YsylPMNHM3UuPis9NyVQ9WFpBpNYTFYAH7kc/edit#heading=h.wwwbdoeygi1h<br />
<pre><br />
DOS: Outcome of this agreement = PILOT PROJECT TO INFER ANNOTATIONS IS CANCELLED. Work on inferred classifications needs to shift back to the ontology. We still have no means for specifying species independent complexes by composition, apart, perhaps, from complexes made up oligomerised members of the same protein family (e.g. see smads). In cases where we have documentation of conservation, we can at least enumerate examples.<br />
</pre><br />
<br />
<br />
DOS: We need a consistent PI decision on this before any proposals can be made.<br />
<br />
===Merging GO calls===<br />
<br />
This will be discussed at the GOC LA meeting (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda#Conference_Calls_and_Communication). The EBI office raised some concerns about merging the ontology call with others. David OS, could you please relay these comments in LA? <br />
<br />
===Adding items to the agenda for the GOC LA meeting===<br />
<br />
This is being finalised, so if any of us would like to add anything, please do so ASAP (http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda).<br />
<br />
=== equivalence axioms (GCIs) required for reasoning with ChEBI missing from editors file ?===<br />
<br />
From last week's discussion:<br />
<br />
https://github.com/geneontology/go-ontology/issues/12721<br />
<br />
gene_ontology_write.obo imports cheb_import.owl. This lacks the equivalence axioms (GCIs). But we have a file called bio_chebi.owl which has them. bio_chebi.owl was last updated 19 months ago: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/extensions/bio-chebi.owl?view=log<br />
<br />
During the move to using ChEBI, a few issues wrt distinctions were introduced for the purpose of reasoning in OWL for GO. We mapped equivalent axioms; some terms were conflated. In BioCHEBI, the equivalences are made, but we don’t know the downstream pipeline. <br />
<br />
These equivalent axioms are not imported when you load gene_ontology_write.obo - they were at some point - but it needs an import statement to BioChEBI. It is in chebi_import.owl, but nothing shows that they’re being used.<br />
<br />
We need to fix BioChEBI input, or come up with an alternate strategy.<br />
<br />
Tanya: these are being used in TermGenie. So some process is updating that file at least for TermGenie.<br />
Heiko once said: “ontology uses BioCHEBI”, but it is not using it now. <br />
<br />
*ACTION*: We need Chris to please clarify.<br />
<br />
===Follow-up: SOP for merging terms in OBO-Edit===<br />
<br />
For background, see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-13#SOP_when_merging_terms. <br />
<br />
Paola tested and drafted an SOP, and added documentation here: http://wiki.geneontology.org/index.php/Editor_Guide#SOP_for_merging_terms_in_OBO-Edit<br />
<br />
===Jenkins github new tickets reports===<br />
<br />
From Melanie: Birgit mentioned that "For the last few weeks my daily Jenkins updates have no new notifications and very occasionally updates." I usually check the tracker directly and delete those, can someone have a look?<br />
<br />
[Paola] I confirm I haven't seen those reports at all lately - and there HAVE been new GH ontology tickets, as well as updates.<br />
<br />
===Follow-up: GitHub projects===<br />
<br />
See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-06#GitHub_Projects<br />
<br />
Plan is to look at https://github.com/geneontology/go-ontology/projects/1 and see how this works for us.<br />
<br />
Beginning with: https://github.com/geneontology/go-ontology/issues/12723<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-10-13&diff=62092Ontology meeting 2016-10-132016-10-13T15:09:31Z<p>David os: </p>
<hr />
<div>Attendees:<br />
<br />
Minutes: Moni??<br />
<br />
Regrets: Chris<br />
<br />
GoToMeeting invite: https://global.gotomeeting.com/join/859015101<br />
<br />
<br />
===SOP when merging terms===<br />
<br />
David H confirmed that the problem doesn’t stem from merging in OBO-Edit (“did a test merge in obo-edit and the resulting obo stanza looks fine. I suspect that the build problems arise in the pipeline downstream. No ghost terms after the merge and save.”), and suggests the following:<br />
<br />
“I think that whenever we merge, we need to check the inferences file [go_inferences.obo] for references to the merged terms. If they exist, they should be deleted. Then when the terms are merged, the cross-products need to be checked and edited as appropriate. Presumably then when the write file [gene_ontology_write.obo] is committed, the ghost inferences will not exist in the inference file and the ghost terms won't be created.”<br />
<br />
Let’s confirm. Comments here please: https://github.com/geneontology/go-ontology/issues/12729<br />
<br />
=== equivalence axioms (GCIs) required for reasoning with ChEBI missing from editors file ?===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12721<br />
<br />
gene_ontology_write.obo imports cheb_import.owl. This lacks the equivalence axioms (GCIs). But we have a file called bio_chebi.owl which has them. bio_chebi.owl was last updated 19 months ago: http://viewvc.geneontology.org/viewvc/GO-SVN/trunk/ontology/extensions/bio-chebi.owl?view=log<br />
<br />
===Update: contacts for UniProt annotations===<br />
<br />
As already mentioned, we should email the GOA helpdesk at goa@ebi.ac.uk for annotations assigned specifically by EBI UniProt (GOA) curators.<br />
Where annotations by SIB UniProt curators are or may be involved, please email help@uniprot.org. They distribute updates to all UniProt curators (GOA + SIB). I added this info to the Google spreadsheet (https://docs.google.com/spreadsheets/d/1nAquF0oXHU6d638Q97ZeQ7K7DOhuru84-rOMEL4A114/edit#gid=0), but we opted not to include email contacts on the corresponding GitHub page (https://github.com/geneontology/go-ontology/blob/master/curator_group_contacts.tsv).<br />
<br />
Also, [one for David OS?] Chris reminds us to coordinate with Seth on any metadata related to people, see https://github.com/geneontology/go-site/issues/231.<br />
<br />
===Update: membership go-ontology mailing-list===<br />
<br />
Do we want to restrict membership of the list or should it be a public one? (The current list of subscribers can be accessed upon logging in https://mailman.stanford.edu/mailman/listinfo/go-ontology)<br />
<br />
===Pending TG requests===<br />
<br />
Just a note so we don't forget to deal with these:<br />
<br />
regulation of memory terms (requested by Helen Attrill, FlyBase)<br />
<br />
heteroreceptor complex assembly/disassembly (requested by Paul Denny, UCL)<br />
<br />
===Follow-up: GitHub projects===<br />
<br />
See background here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-10-06#GitHub_Projects<br />
<br />
Paola added one card each to the 3 columns in https://github.com/geneontology/go-ontology/projects/1. Feel free to add as an experiment, and/or we could go over those. Then we can see how this works for us.<br />
<br />
Melanie: https://github.com/geneontology/go-ontology/issues/12723 "hypusine pathway", discussed with David Hill and thought worthwhile to bring to editors call.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-09-29&diff=61921Ontology meeting 2016-09-292016-09-29T17:37:53Z<p>David os: /* RHEA update request */</p>
<hr />
<div>Attendees: Paola, Tanya, Harold, Melanie, DavidOS, DavidH, PaulT, Chris<br />
<br />
Regrets: <br />
<br />
Minutes: Tanya<br />
<br />
===Follow-up: Reinstate daily report of terms and stats===<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
The ticket says that this is fixed, but no one has seen the report. Chris, any news on this one please?<br />
<br />
Some progress. See ticket for details.<br />
<br />
===Follow-up: Modified proteins===<br />
<br />
See background discussion here: http://wiki.geneontology.org/index.php/Ontology_meeting_2016-09-15#Modified_proteins<br />
<br />
At the time of writing, comments are still missing from some ontology group members. Please review the document here and comment, even if it's just to say that you agree with everything.<br />
<br />
https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit<br />
<br />
Then Paola will wrap up (or we could do it as a group) and we’ll present, whether it’s at an annotation call, by email to the wider group, in person at the GOC meeting, or all of the above.<br />
<br />
Chris needs to comment and then Paola can wrap up.<br />
<br />
===EC2GO annotation problems===<br />
<br />
Current EC2GO annotations are done using the xrefs from the GO ontology file. Main problem occurs if EC number contains one or more dashes, if a gene product is associated with an EC number (from UniProt files, Trembl record for instance), then it becomes associated<br />
to ALL of the GO terms that have that match the non-dash numbers.<br />
<br />
http://geneontology.org/external2go/ec2go<br />
<br />
What generates these annotations? Need to track down the script. Possibly one written by Chris, Heiko, someone else? This problem should be corrected at the source.<br />
<br />
Archeology: Found email thread titled '[go-ontology] Ec2GO mappings' March 9, 2015 - Harold raised issue, Chris <br />
generated some reports. <br />
go-ec-dash-no-generic-ec-parent.txt -- cases such as the one above where we have a dash xref but no corresponding <br />
generic xref<br />
go-ec-dash-inconsistent-with-generic.txt -- cases where the dash xref and generic xref exist but the GO term for the <br />
dash does not sit under the GO term for the generic<br />
<br />
Also, http://wiki.geneontology.org/index.php/Ontology_meeting_2016-02-25#ec2GO_Clean_up<br />
<br />
Action items from there:<br />
<br />
AI #1: Chris will remove ALL EC xrefs in the GO file that have a dash in the number, look like this<br />
xref: EC:2.-.-.-<br />
xref: EC:2.1.-.-<br />
xref: EC:2.2.3.-<br />
<br />
AI #2: Review 250 cases where there are GO terms with more than one FULL EC number (eyeball they are in different<br />
categories). Harold will look at these, Chris will send. (HJD and DPH have 1100 enzymes to add for Peifen.)<br />
<br />
AI #3: Do NOT add EC terms without dashes to new terms.<br />
<br />
===RHEA update request===<br />
<br />
Where are we?<br />
<br />
Chris went back over his plan presented at the Bar Harbour meeting in 2013. This attempted to hack representation of stochiometry <br />
and bidirectional relations into full logical definitions staying within OWL-EL. On reviewing these seem overly complex and may be <br />
unsafe (they may cause incorrect inference when the inputs/output of one reaction are all present in another).<br />
<br />
We decided to simply add subclassing axioms rather than equivalent class expressions. There are two ways to do this: <br />
1. Keep bidirectionality: using a pattern that translates the rxn X + Y -> A + B into <br />
SubClassOf has_participant_collection some ((has_component some X) and (has_component some Y))<br />
SubClassOf has_participant_collection some ((has_component some A) and (has_component some B))<br />
2. Encode directionality reflecting how these reactions are conventionally drawn and their predominant direcion under physiological conditions.<br />
i.g. Translate the rxn X + Y -> A + B into <br />
SubClassOf has_input some X<br />
SubClassOf has_input some Y<br />
SubClassOf has_output some A<br />
SubClassOf has_output some B<br />
<br />
After discussion, we decided to go with the latter, although review later if we run into inference problems (e.g. from use in LEGO to mean opposite direction). <br />
This approach maintains OBO compatibility and as easy to work with. We should probably add a standard comment to all terms explaining the design decision.<br />
Note: the first approach may also have its problems: reciprocal reactions would have the same axiomatisation.<br />
<br />
Neither approach => us autoclassification, but we may be able to find cases (e.g. transporters) where we could come up with full logical definitions that work.<br />
Where does classification come from?<br />
We agreed that we should extract classification from EC wherever possible. We can do this for Rhea reactions wherever they have a mapping to an EC <br />
- or an EC used as a classification.<br />
<br />
Open question: should we also create an experimental translation using cardinality constraints<br />
e.g. X + Y -> A + B becomes:<br />
<br />
EquivalentTo: (has_participant_collection some ((has_component exactly 1 X) and (has_component exactly 1 Y)) <br />
and has_participant_collection some ((has_component exactly 1 A) and (has_component exactly 1 B))<br />
<br />
One for the reasoner competition? Scaling might be OK if we treat MF axiomatisation as a separate module.<br />
<br />
===Consolidation of group calls into one (on USC agenda)===<br />
<br />
Intent to merge all the calls into one? LEGO, Annotation, PAINT, and Ontology Development calls into one GO call.<br />
<br />
Yes, that was the intent.<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=2016_Los_Angeles_GOC_Meeting_Agenda&diff=618792016 Los Angeles GOC Meeting Agenda2016-09-27T16:42:52Z<p>David os: /* Agenda */</p>
<hr />
<div>=Agenda=<br />
<br />
== Regulation relations ==<br />
<br />
Regulation and causal relations are central to LEGO annotation and to inference based on LEGO models, but definitions and guidelines still need work to ensure consistency and clarity. <br />
DOS: I would like to present progress on the development of the relevant relations along with a proposal for how to improve them. This would probably work best as a collaborative presentation with LEGO annotators (David H & Val?) where we can show application to LEGO models.<br />
<br />
== Genetic entities in GO annotation ==<br />
* What genetic entities do we need to refer to as the primary object of GO annotation and in extended forms of conventional or LEGO annotation?<br />
* What conventions should we enforce regarding which identifiers to use to refer to these genetic features and how?<br />
<br />
==Conference Calls==<br />
*Proposal to consolidate LEGO, Annotation, PAINT, and Ontology Development calls into one GO call held weekly on Tuesdays at 8am PST<br />
*These areas of annotation, and ontology development, are, or have been, converging for some time now and we think it would be a better use of everyone's time to have one weekly call where we discuss any annotation- or ontology-related issues<br />
<br />
==Annotation Issues - Conventional Annotations==<br />
*Modified protein binding: GO terms & annotations are very inconsistent. <br />
**Recent github issues: <br />
glycoprotein binding: https://github.com/geneontology/go-ontology/issues/12580#issuecomment-240782020<br />
ubiquitinated protein binding https://github.com/geneontology/go-ontology/issues/12582#issuecomment-240452320<br />
<br />
==Annotation Issues - LEGO Annotations (Sunday AM?)==<br />
*How are we going to handle ECO codes in Noctua. Currently there are only a limited number of codes that fall under 'used in manual assertion'. If we use codes that are not specific to the manual assertion part of the ontology, then they map to EXP. Are we going to request the entire set of codes that we think we might want to use or are we going to have an automated way to map to the correct code?<br />
*Are we going to allow Noctua to make annotations to the root nodes of the ontology? This would be useful for contextual annotations that are to otherwise root nodes. However some groups block these kinds of annotations because in the past, these annotations were used to keep track of genes about which we had no information.<br />
*MGI's experience roundtripping with Noctua Models (DPH)<br />
<br />
== Production ==<br />
<br />
New data flow (Chris)<br />
<br />
<br />
[[Category: GO Consortium Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-09-15&diff=61697Ontology meeting 2016-09-152016-09-15T13:51:58Z<p>David os: </p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
Minutes: <br />
<br />
<br />
===How to report potential/necessary changes to annotations resulting from edits ===<br />
<br />
There's been some renewed discussion of the need to be able to report annotation issues in one place. <br />
<br />
Some ideas:<br />
<br />
Can we get around the reluctance of some to use the go-annotation ticket tracker by use of GitHub CCs?<br />
Paola has done this quite effectively using the go-ontology tracker: <br />
This still requires knowing who to CC for each source though - we'd need documentation of that. Should we ask each group for a volunteer?<br />
<br />
Alternatively, can we get at least one person from each group to sign up to a tracker with slightly less volume than the current one?<br />
<br />
Side issue: It would help if we made sure everyone potentially has a GitHub account we know about. Not everyone is on here: https://github.com/orgs/geneontology/people?utf8=%E2%9C%93&query=<br />
Shall we put out a renewed call for people to sign up and share their logins?<br />
<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.<br />
Preliminary plan:<br />
1. Merge all the terms for modified protein binding (e.g. gylcosylated protein binding) into 'protein binding'<br />
2. Add comment to 'protein binding': Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein). In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)<br />
<br />
Please contribute to and comment on the draft proposal here: https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
'''Proposal:'''<br />
<br />
* macromolecular complex: update definition to say it contains at least one protein; <br />
* make ‘protein-containing complex’ a synonym of this term <br />
* protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, if you are looking for a more general term please consider using the parent ‘macromolecular complex’”<br />
* Classification of complex by function: switch genus to 'macromolecular complex' (for example of why this is necessary, see: https://github.com/geneontology/go-ontology/issues/12620#issuecomment-247048464)<br />
<br />
'''These edits have now been completed (DOS branch), but have not yet been committed. Are editors happy to commit ASAP?'''<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
<br />
Take to GO annotation call or GO meeting?<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
Discussion is ongoing and recorded in the GH ticket above.<br />
<br />
=== Implement a system for keeping partonomies in sync (Uberon & CC -> BP) ===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12658<br />
<br />
We have many cases where we manually maintain partonomies between Uberon and BP (most notably under the development branch, and between CC and BP (most notably in the organization branch). Ideally we'd have some way to keep these part hierarchies in sync automatically. Not having such a system causes problems and adds unnecessary work for editors.<br />
<br />
We can solve the problem by using GCIs to infer partonomy<br />
* These GCIs can be incorporated into Design patterns, TermGenie etc. <br />
* GCIs are visible in Protege 5 under terms used in them<br />
* We have a system for generating inferred partonomies. This will allow an edit file pipeline analogous to the one we use to generate automated classifications at each commit and add them to an imported file so that they are visible in OE or Protege.<br />
<br />
I propose we test this out on the organization branch.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-09-15&diff=61696Ontology meeting 2016-09-152016-09-15T11:03:38Z<p>David os: /* Protein complexes */</p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
Minutes: <br />
<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.<br />
Preliminary plan:<br />
1. Merge all the terms for modified protein binding (e.g. gylcosylated protein binding) into 'protein binding'<br />
2. Add comment to 'protein binding': Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein). In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)<br />
<br />
Please contribute to and comment on the draft proposal here: https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
'''Proposal:'''<br />
<br />
* macromolecular complex: update definition to say it contains at least one protein; <br />
* make ‘protein-containing complex’ a synonym of this term <br />
* protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, if you are looking for a more general term please consider using the parent ‘macromolecular complex’”<br />
* Classification of complex by function: switch genus to 'macromolecular complex' (for example of why this is necessary, see: https://github.com/geneontology/go-ontology/issues/12620#issuecomment-247048464)<br />
<br />
'''These edits have now been completed (DOS branch), but have not yet been committed. Are editors happy to commit ASAP?'''<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
<br />
Take to GO annotation call or GO meeting?<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
Discussion is ongoing and recorded in the GH ticket above.<br />
<br />
=== Implement a system for keeping partonomies in sync (Uberon & CC -> BP) ===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12658<br />
<br />
We have many cases where we manually maintain partonomies between Uberon and BP (most notably under the development branch, and between CC and BP (most notably in the organization branch). Ideally we'd have some way to keep these part hierarchies in sync automatically. Not having such a system causes problems and adds unnecessary work for editors.<br />
<br />
We can solve the problem by using GCIs to infer partonomy<br />
* These GCIs can be incorporated into Design patterns, TermGenie etc. <br />
* GCIs are visible in Protege 5 under terms used in them<br />
* We have a system for generating inferred partonomies. This will allow an edit file pipeline analogous to the one we use to generate automated classifications at each commit and add them to an imported file so that they are visible in OE or Protege.<br />
<br />
I propose we test this out on the organization branch.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-09-15&diff=61695Ontology meeting 2016-09-152016-09-15T11:03:01Z<p>David os: /* Protein complexes */</p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
Minutes: <br />
<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.<br />
Preliminary plan:<br />
1. Merge all the terms for modified protein binding (e.g. gylcosylated protein binding) into 'protein binding'<br />
2. Add comment to 'protein binding': Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein). In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)<br />
<br />
Please contribute to and comment on the draft proposal here: https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Proposal:<br />
<br />
macromolecular complex: update definition to say it contains at least one protein; <br />
make ‘protein-containing complex’ a synonym of this term <br />
<br />
protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, <br />
if you are looking for a more general term please consider using the parent ‘macromolecular complex’”<br />
<br />
Classification of complex by function: switch genus to 'macromolecular complex' (for example of why this is necessary, see: https://github.com/geneontology/go-ontology/issues/12620#issuecomment-247048464)<br />
<br />
'''These edits have now been completed (DOS branch), but have not yet been committed. Are editors happy to commit ASAP?'''<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
<br />
Take to GO annotation call or GO meeting?<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
Discussion is ongoing and recorded in the GH ticket above.<br />
<br />
=== Implement a system for keeping partonomies in sync (Uberon & CC -> BP) ===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12658<br />
<br />
We have many cases where we manually maintain partonomies between Uberon and BP (most notably under the development branch, and between CC and BP (most notably in the organization branch). Ideally we'd have some way to keep these part hierarchies in sync automatically. Not having such a system causes problems and adds unnecessary work for editors.<br />
<br />
We can solve the problem by using GCIs to infer partonomy<br />
* These GCIs can be incorporated into Design patterns, TermGenie etc. <br />
* GCIs are visible in Protege 5 under terms used in them<br />
* We have a system for generating inferred partonomies. This will allow an edit file pipeline analogous to the one we use to generate automated classifications at each commit and add them to an imported file so that they are visible in OE or Protege.<br />
<br />
I propose we test this out on the organization branch.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-09-15&diff=61694Ontology meeting 2016-09-152016-09-15T10:58:35Z<p>David os: /* Protein complexes */</p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
Minutes: <br />
<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.<br />
Preliminary plan:<br />
1. Merge all the terms for modified protein binding (e.g. gylcosylated protein binding) into 'protein binding'<br />
2. Add comment to 'protein binding': Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein). In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)<br />
<br />
Please contribute to and comment on the draft proposal here: https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Proposal:<br />
<br />
macromolecular complex: update definition to say it contains at least one protein; <br />
make ‘protein-containing complex’ a synonym of this term <br />
<br />
protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, <br />
if you are looking for a more general term please consider using the parent ‘macromolecular complex’”<br />
<br />
Classification of complex by function: switch genus to 'macromolecular complex':<br />
<br />
'''These edits have now been completed (DOS branch), but have not yet been committed. Are editors happy to commit ASAP?'''<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
<br />
Take to GO annotation call or GO meeting?<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
Discussion is ongoing and recorded in the GH ticket above.<br />
<br />
=== Implement a system for keeping partonomies in sync (Uberon & CC -> BP) ===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12658<br />
<br />
We have many cases where we manually maintain partonomies between Uberon and BP (most notably under the development branch, and between CC and BP (most notably in the organization branch). Ideally we'd have some way to keep these part hierarchies in sync automatically. Not having such a system causes problems and adds unnecessary work for editors.<br />
<br />
We can solve the problem by using GCIs to infer partonomy<br />
* These GCIs can be incorporated into Design patterns, TermGenie etc. <br />
* GCIs are visible in Protege 5 under terms used in them<br />
* We have a system for generating inferred partonomies. This will allow an edit file pipeline analogous to the one we use to generate automated classifications at each commit and add them to an imported file so that they are visible in OE or Protege.<br />
<br />
I propose we test this out on the organization branch.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-09-15&diff=61693Ontology meeting 2016-09-152016-09-15T10:58:11Z<p>David os: /* Protein complexes */</p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
Minutes: <br />
<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.<br />
Preliminary plan:<br />
1. Merge all the terms for modified protein binding (e.g. gylcosylated protein binding) into 'protein binding'<br />
2. Add comment to 'protein binding': Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein). In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)<br />
<br />
Please contribute to and comment on the draft proposal here: https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Proposal:<br />
<br />
macromolecular complex: update definition to say it contains at least one protein; <br />
make ‘protein-containing complex’ a synonym of this term <br />
<br />
protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, <br />
if you are looking for a more general term please consider using the parent ‘macromolecular complex’”<br />
<br />
Classification of complex by function: switch genus to 'macromolecular complex':<br />
<br />
'''These edits have now been completed (DOS branch), but have not yet been committed. Are editors' happy to commit ASAP?'''<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
<br />
Take to GO annotation call or GO meeting?<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
Discussion is ongoing and recorded in the GH ticket above.<br />
<br />
=== Implement a system for keeping partonomies in sync (Uberon & CC -> BP) ===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12658<br />
<br />
We have many cases where we manually maintain partonomies between Uberon and BP (most notably under the development branch, and between CC and BP (most notably in the organization branch). Ideally we'd have some way to keep these part hierarchies in sync automatically. Not having such a system causes problems and adds unnecessary work for editors.<br />
<br />
We can solve the problem by using GCIs to infer partonomy<br />
* These GCIs can be incorporated into Design patterns, TermGenie etc. <br />
* GCIs are visible in Protege 5 under terms used in them<br />
* We have a system for generating inferred partonomies. This will allow an edit file pipeline analogous to the one we use to generate automated classifications at each commit and add them to an imported file so that they are visible in OE or Protege.<br />
<br />
I propose we test this out on the organization branch.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-09-15&diff=61692Ontology meeting 2016-09-152016-09-15T10:56:05Z<p>David os: </p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
Minutes: <br />
<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.<br />
Preliminary plan:<br />
1. Merge all the terms for modified protein binding (e.g. gylcosylated protein binding) into 'protein binding'<br />
2. Add comment to 'protein binding': Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein). In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)<br />
<br />
Please contribute to and comment on the draft proposal here: https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Proposal:<br />
<br />
macromolecular complex: update definition to say it contains at least one protein; <br />
make ‘protein-containing complex’ a synonym of this term <br />
<br />
protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, <br />
if you are looking for a more general term please consider using the parent ‘macromolecular complex’”<br />
<br />
Classification of complex by function: switch genus to 'macromolecular complex':<br />
<br />
These edits have now been done (DOS branch), but have not yet been committed. Are editors' happy to commit ASAP?<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
<br />
Take to GO annotation call or GO meeting?<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
Discussion is ongoing and recorded in the GH ticket above.<br />
<br />
=== Implement a system for keeping partonomies in sync (Uberon & CC -> BP) ===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12658<br />
<br />
We have many cases where we manually maintain partonomies between Uberon and BP (most notably under the development branch, and between CC and BP (most notably in the organization branch). Ideally we'd have some way to keep these part hierarchies in sync automatically. Not having such a system causes problems and adds unnecessary work for editors.<br />
<br />
We can solve the problem by using GCIs to infer partonomy<br />
* These GCIs can be incorporated into Design patterns, TermGenie etc. <br />
* GCIs are visible in Protege 5 under terms used in them<br />
* We have a system for generating inferred partonomies. This will allow an edit file pipeline analogous to the one we use to generate automated classifications at each commit and add them to an imported file so that they are visible in OE or Protege.<br />
<br />
I propose we test this out on the organization branch.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-09-15&diff=61691Ontology meeting 2016-09-152016-09-15T10:42:44Z<p>David os: /* Protein complexes */</p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
Minutes: <br />
<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.<br />
Preliminary plan:<br />
1. Merge all the terms for modified protein binding (e.g. gylcosylated protein binding) into 'protein binding'<br />
2. Add comment to 'protein binding': Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein). In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)<br />
<br />
Please contribute to and comment on the draft proposal here: https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Proposal:<br />
<br />
macromolecular complex: update definition to say it contains at least one protein; <br />
make ‘protein-containing complex’ a synonym of this term <br />
<br />
protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, <br />
if you are looking for a more general term please consider using the parent ‘macromolecular complex’”<br />
<br />
Classification of complex by function: switch genus to 'macromolecular complex':<br />
<br />
These edits have now been done (DOS branch), but have not yet been committed. Are editors' happy to commit ASAP?<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
<br />
Take to GO annotation call or GO meeting?<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
Discussion is ongoing and recorded in the GH ticket above.<br />
<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-09-15&diff=61690Ontology meeting 2016-09-152016-09-15T10:42:09Z<p>David os: /* Protein complexes */</p>
<hr />
<div>Attendees: <br />
<br />
Regrets: <br />
<br />
Minutes: <br />
<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.<br />
Preliminary plan:<br />
1. Merge all the terms for modified protein binding (e.g. gylcosylated protein binding) into 'protein binding'<br />
2. Add comment to 'protein binding': Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein). In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)<br />
<br />
Please contribute to and comment on the draft proposal here: https://docs.google.com/document/d/17U1TD3n_QI9coCycJcOUBDa2nRf3ggPR-tKjDMa_ff8/edit<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Proposal:<br />
macromolecular complex: update definition to say it contains at least one protein; <br />
make ‘protein-containing complex’ a synonym of this term <br />
and suggest to Val to consider tweaking the search tool at PomBase? <br />
<br />
protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, <br />
if you are looking for a more general term please consider using the parent ‘macromolecular complex’”<br />
<br />
Classification of complex by function: switch genus to 'macromolecular complex':<br />
<br />
These edits have now been done (DOS branch), but have not yet been committed. Are editors' happy to commit ASAP?<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
<br />
Take to GO annotation call or GO meeting?<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
Discussion is ongoing and recorded in the GH ticket above.<br />
<br />
<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-08-25&diff=61612Ontology meeting 2016-08-252016-08-26T15:59:01Z<p>David os: /* Protein complexes */</p>
<hr />
<div>Attendees: Paola, David H, David OS, Harold, Judy, Tanya, Chris, Jim, Melanie<br />
<br />
Regrets:<br />
<br />
Minutes: Paola<br />
<br />
<br />
===xref error===<br />
<br />
These keep coming in at commit:<br />
<br />
:: ERROR: valid-id-space: bad xref: :develops_from Line: xref: :develops_from<br />
<br />
:: ERROR: valid-id-space: bad xref: :part_of Line: xref: :part_of<br />
<br />
Chris: solution: svn update the whole ontology directory and they should be gone forever (or possibly appear just once again).<br />
<br />
===TG freeform===<br />
<br />
Following up on last week's discussion (see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#TG_freeform), these were the action items:<br />
<br />
"FreeForm is currently broken so needs to be closed down. But could still be useful if fixed, e.g. for protein complexes (better for Birgit to add). AI: Chris to post ticket detailing problems and to look into whether there is some easy way to fix."<br />
<br />
Chris - could you update us please? In the meantime, shall I (Paola) send another reminder to go-consortium NOT to use the tool?<br />
<br />
We opened a ticket on the TG tracker for Chris to see how easy it is to turn TGFF off (https://github.com/geneontology/termgenie/issues/94).<br />
<br />
AI: Paola to email go-consortium reminding not to use TGFF, and stating that we may close it down soon (refer to the ticket above). DONE<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.<br />
Preliminary plan:<br />
1. Merge all the terms for modified protein binding (e.g. gylcosylated protein binding) into 'protein binding'<br />
2. Add comment to 'protein binding': Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein). In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Val says <br />
"many people use the "protein complex" term, and would expect that to retrieve complexes <br />
like the ribosome and the spliceosome and telomerase (I suspect) Is it possible to define a <br />
protein complex as a complex which has only proteins, or protein and RNA components?<br />
<br />
so <br />
protein complex<br />
--ribonucleoprotein complex<br />
<br />
Would that be crazy? then everything can go under protein complex, unless we know that it has an RNA component, <br />
then it moves down...<br />
<br />
This way people will retrieve all protein complexes with the protein complex term.<br />
Similarly protein-DNA complex (telosome), which is currently not retrieved by a "protein complex" <br />
search. I doubt there are any biologists who would not describe the telosome as a 'protein complex'<br />
https://en.wikipedia.org/wiki/Shelterin<br />
<br />
but you would not currently retrieve it with a protein complex search.."<br />
<br />
Harold: I just think it's wrong. Don't think most biologists would agree that <br />
these complexes with other components are protein complexes<br />
DOS: Agree. Don't like the loss of expressiveness either.<br />
<br />
Discussion of compromise proposals - renaming or synonyms on protein complex?<br />
<br />
Proposal:<br />
<br />
macromolecular complex: update definition to say it contains at least one protein; <br />
make ‘protein-containing complex’ a synonym of this term <br />
and suggest to Val to consider tweaking the search tool at PomBase? <br />
<br />
protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, <br />
if you are looking for a more general term please consider using the parent ‘macromolecular complex’”<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
Please read ahead of meeting, I needed a little time to wrap my head around this. (Tanya)<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
Discussion is ongoing and recorded in the GH ticket above.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David oshttps://wiki.geneontology.org/index.php?title=Ontology_meeting_2016-08-25&diff=61611Ontology meeting 2016-08-252016-08-26T15:39:13Z<p>David os: /* Modified proteins */</p>
<hr />
<div>Attendees: Paola, David H, David OS, Harold, Judy, Tanya, Chris, Jim, Melanie<br />
<br />
Regrets:<br />
<br />
Minutes: Paola<br />
<br />
<br />
===xref error===<br />
<br />
These keep coming in at commit:<br />
<br />
:: ERROR: valid-id-space: bad xref: :develops_from Line: xref: :develops_from<br />
<br />
:: ERROR: valid-id-space: bad xref: :part_of Line: xref: :part_of<br />
<br />
Chris: solution: svn update the whole ontology directory and they should be gone forever (or possibly appear just once again).<br />
<br />
===TG freeform===<br />
<br />
Following up on last week's discussion (see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#TG_freeform), these were the action items:<br />
<br />
"FreeForm is currently broken so needs to be closed down. But could still be useful if fixed, e.g. for protein complexes (better for Birgit to add). AI: Chris to post ticket detailing problems and to look into whether there is some easy way to fix."<br />
<br />
Chris - could you update us please? In the meantime, shall I (Paola) send another reminder to go-consortium NOT to use the tool?<br />
<br />
We opened a ticket on the TG tracker for Chris to see how easy it is to turn TGFF off (https://github.com/geneontology/termgenie/issues/94).<br />
<br />
AI: Paola to email go-consortium reminding not to use TGFF, and stating that we may close it down soon (refer to the ticket above). DONE<br />
<br />
===Daily report of terms and stats===<br />
<br />
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats<br />
<br />
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?<br />
<br />
Ticket: https://github.com/geneontology/go-site/issues/217<br />
<br />
===Metadata update===<br />
<br />
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md<br />
<br />
Chris: general plan is to move everything to yaml including metadata. All agree that’s a good plan.<br />
<br />
===Modified proteins===<br />
<br />
There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC.<br />
[[https://github.com/geneontology/go-ontology/issues/12582]]<br />
[[https://github.com/geneontology/go-ontology/issues/12580]]<br />
[[https://github.com/geneontology/go-ontology/issues/12522]]<br />
<br />
Editors will further discuss the topic, and will then formulate a proposal to present to the wider group.<br />
Preliminary plan:<br />
1. Merge all the terms for modified protein binding (e.g. gylcosylated protein binding) into 'protein binding'<br />
2. Add comment to 'protein binding': Please do not annotate to this term when it is known that binding is to a protein modification (e.g. to the oligosaccharide component of glycoprotein). In these case, please instead annotate to the an appropriate term for the bound structure (e.g. polysaccharide binding)<br />
<br />
===Protein complexes===<br />
<br />
https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346<br />
<br />
Val says "many people use the "protein complex" term, and would expect that to retrieve complexes like the ribosome and the spliceosome and telomerase (I suspect)<br />
<br />
Is it possible to define a protein complex as a complex which has only proteins, or protein and RNA components?<br />
<br />
so <br />
protein complex<br />
--ribonucleoprotein complex<br />
<br />
Would that be crazy? then everything can go under protein complex, unless we know that it has an RNA component, then it moves down...<br />
<br />
This way people will retrieve all protein complexes with the protein complex term.<br />
<br />
Similarly <br />
protein-DNA complex (telosome), which is currently not retrieved by a "protein complex" search. I doubt there are any biologists who would not describe the telosome as a 'protein complex'<br />
https://en.wikipedia.org/wiki/Shelterin<br />
<br />
but you would not currently retrieve it with a protein complex search.."<br />
<br />
Proposal:<br />
<br />
macromolecular complex: update definition to say it contains at least one protein; <br />
make ‘protein-containing complex’ a synonym of this term <br />
and suggest to Val to consider tweaking the search tool at PomBase? <br />
<br />
protein complex: add user friendly comment along the lines of “these are complexes containing *only* proteins, <br />
if you are looking for a more general term please consider using the parent ‘macromolecular complex’”<br />
<br />
===FAO update===<br />
<br />
* FAO now has a home on github<br />
* We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain<br />
* See Inferences Changes Report for: 2016-08-24 - e.g.<br />
<br />
<pre><br />
[Term]<br />
+id: GO:0075251 ! uredospore formation<br />
+is_a: GO:0044711 {is_inferred="true"} ! single-organism biosynthetic process<br />
</pre><br />
<br />
===New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)===<br />
Please read ahead of meeting, I needed a little time to wrap my head around this. (Tanya)<br />
<br />
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]<br />
<br />
Discussion is ongoing and recorded in the GH ticket above.<br />
<br />
<br />
[[Category:Ontology]]<br />
[[Category:Meetings]]</div>David os