Annotation Conf. Call 2017-09-12: Difference between revisions

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[https://github.com/geneontology/go-annotation/projects/4  github/go-annotation Signaling Projects page]
[https://github.com/geneontology/go-annotation/projects/4  github/go-annotation Signaling Projects page]


* JAK/STAT
* JAK/STAT - Giulia (Ruth away)
**[https://docs.google.com/spreadsheets/d/1H6ZCHAxd5YSpj-UaUzkJ6ssF2FXj9hT8kkT5qGaS1lY/edit#gid=683337807 Google spreadsheet with annotation and ontology analysis]
**Thinking about how to define the beginning of the pathway and its components
**How is the pathway regulated?
**Review annotations - Annotation and Ontology Issues:
***Some members of the pathway have regulation terms and some regulators are annotated directly to the pathway
***Many cases with no MF terms
***Tickets: [https://github.com/geneontology/go-ontology/issues/14164 positive regulation of TF dimerization activity #14164], [https://github.com/geneontology/go-ontology/issues/14165 positive regulation of STAT transcription factor activity #14165], [https://github.com/geneontology/go-ontology/issues/14166 tyrosine dephosphorylation of STAT protein #14166], [https://github.com/geneontology/go-ontology/issues/14167 JAK/STAT pathway #14167]
**Working on GO-CAM model
* GPCR
* GPCR
* MAPK - David, Sabrina
* MAPK - David, Sabrina
* Wnt - Helen (Kimberly away)
* Wnt - Helen (Kimberly away)
**receptor ligand activity #14120 https://github.com/geneontology/go-ontology/issues/14120
**[https://drive.google.com/drive/folders/0B7bEr6HANSlGM05zSU90VndEYTA  Canonical Wnt Signaling folder] with various analysis, docs
**[https://github.com/geneontology/go-ontology/issues/14120 receptor ligand activity #14120]
***receptor agonist activity (GO:0048018) re-named 'receptor ligand activity' and new definition (http://amigo.geneontology.org/amigo/term/GO:0048018). Relationships to ‘signal transduction' & 'receptor activator activity' removed.
***receptor agonist activity (GO:0048018) re-named 'receptor ligand activity' and new definition (http://amigo.geneontology.org/amigo/term/GO:0048018). Relationships to ‘signal transduction' & 'receptor activator activity' removed.
*** Kimberly has checked usage of receptor agonist activity in curation corresponds to ligand as defined above and looking at documenting criteria for using this term.
*** Kimberly has checked usage of receptor agonist activity in curation corresponds to ligand as defined above and looking at documenting criteria for using this term.
**Review of 'receptor activator activity'
**Review of 'receptor activator activity'
***Inconsistent use. ~20 experimental annotations https://docs.google.com/spreadsheets/d/15HcC6LFgOhA-BdQHvKMRjk3e-uIaGvitD5xH8Qzdkpk/edit#gid=233101787, different activities/processes have been annotated with this term. Will make a ticket.
***Inconsistent use. [https://docs.google.com/spreadsheets/d/15HcC6LFgOhA-BdQHvKMRjk3e-uIaGvitD5xH8Qzdkpk/edit#gid=233101787 Google spread sheet of ~20 experimental annotations] - different activities/processes have been annotated with this term. Will ask curators to review.
**Review annotations of beta-catenin to DNA binding terms. Will make a ticket.
**Review annotations of beta-catenin to DNA binding terms. Will ask curators to review.
**Tickets: for merging ‘frizzled-2 binding’ with ‘frizzled binding’ https://github.com/geneontology/go-ontology/issues/14182, and moving 'smoothened binding' from under 'frizzled binding' https://github.com/geneontology/go-ontology/issues/14182.
**Tickets: for merging ‘frizzled-2 binding’ with ‘frizzled binding’ https://github.com/geneontology/go-ontology/issues/14182, and moving 'smoothened binding' from under 'frizzled binding' https://github.com/geneontology/go-ontology/issues/14182.
**Collecting publications for documentation to illustrate term use and assays https://docs.google.com/document/d/1S6pjVaSpqwDHB3Q-2JBf35BrgOD-Z9z3w8WjijWvjw8/edit
**Collecting publications for documentation to illustrate term use and assays https://docs.google.com/document/d/1S6pjVaSpqwDHB3Q-2JBf35BrgOD-Z9z3w8WjijWvjw8/edit
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*Review [http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Meeting_Agenda Meeting Agenda]
*Review [http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Meeting_Agenda Meeting Agenda]
*GOC Meeting dinner
**The attendants should all have received an email with a link to a Google form to select their choice of food. Please complete the form by next Friday (22nd of September).


= Minutes =  
= Minutes =  
*On call:
*On call:Helen, Giulia, Edith, Kevin, Petra, David H, Stan, Midori, Sage, Rob, Tanya, Judy, Karen, Stacia, Shur-Jen, Harold





Latest revision as of 11:35, 12 September 2017

Meeting URL

Agenda

Update on Signaling Projects

github/go-annotation Signaling Projects page

Cambridge GO Meeting

  • GOC Meeting dinner
    • The attendants should all have received an email with a link to a Google form to select their choice of food. Please complete the form by next Friday (22nd of September).

Minutes

  • On call:Helen, Giulia, Edith, Kevin, Petra, David H, Stan, Midori, Sage, Rob, Tanya, Judy, Karen, Stacia, Shur-Jen, Harold