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) | ||
** | **[https://drive.google.com/drive/folders/0B7bEr6HANSlGM05zSU90VndEYTA Canonical Wnt Signaling folder] with various analysis, docs | ||
***receptor agonist activity (GO:0048018) re-named receptor ligand activity and new definition (http://amigo.geneontology.org/amigo/term/GO:0048018). | **[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. | |||
*** 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. | ***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 | **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 | ||
* Ca2+ (Penelope away) | * Ca2+ (Penelope away) | ||
== Cambridge GO Meeting == | == Cambridge GO Meeting == | ||
*Signalling workshop | |||
**confirm attendence http://wiki.geneontology.org/index.php/2017_Cambridge_GOC_Signalling_Workshop | |||
*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
- JAK/STAT - Giulia (Ruth away)
- 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: positive regulation of TF dimerization activity #14164, positive regulation of STAT transcription factor activity #14165, tyrosine dephosphorylation of STAT protein #14166, JAK/STAT pathway #14167
- Working on GO-CAM model
- GPCR
- MAPK - David, Sabrina
- Wnt - Helen (Kimberly away)
- Canonical Wnt Signaling folder with various analysis, docs
- 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.
- 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'
- Inconsistent use. 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 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.
- Collecting publications for documentation to illustrate term use and assays https://docs.google.com/document/d/1S6pjVaSpqwDHB3Q-2JBf35BrgOD-Z9z3w8WjijWvjw8/edit
- Ca2+ (Penelope away)
Cambridge GO Meeting
- Signalling workshop
- Review 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
- On call:Helen, Giulia, Edith, Kevin, Petra, David H, Stan, Midori, Sage, Rob, Tanya, Judy, Karen, Stacia, Shur-Jen, Harold