Annotation Conf. Call 2017-10-24: Difference between revisions
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== GOC Meetings Cambridge == | == GOC Meetings Cambridge == | ||
*Review key action items from signaling workshop and GOC meeting | *Review key action items from signaling workshop and GOC meeting | ||
**[https://docs.google.com/document/d/1Y9_Mvqes3op36TPHgfaS7K5FHnGZLgUApghIFYyUKR8/edit GOC Cambridge 2017 Meeting Minutes] | |||
** Focus on annotation to signaling pathways | ** Focus on annotation to signaling pathways | ||
*** [https://drive.google.com/drive/u/0/folders/0B7bEr6HANSlGQmlCYm5VRHNMNW8 Folder on Google drive for signaling pathways working group] | |||
*** [https://docs.google.com/document/d/1wCzCkPL9ft20ZP5XnTn8IQAcxoFEduaBmzVWKN0hbU0/edit Signaling Workshop Meeting Minutes] | |||
*** [https://github.com/geneontology/go-annotation/issues/1597 How to name specific MAPK pathways] | |||
*** [https://github.com/geneontology/go-ontology/issues/14275 NTR: “receptor ligand agonist activity” and “receptor ligand antagonist activity”] | |||
*** [https://github.com/geneontology/go-ontology/issues/13912 MP cell surface receptor signaling pathway] | |||
** Adoption of expanded set of BP relations | ** Adoption of expanded set of BP relations | ||
** Review use of contributes_to and colocalizes_with | ** Review use of contributes_to and colocalizes_with | ||
** Noctua into full production mode | ** Noctua into full production mode | ||
*** Meetings on second and fourth Wednesdays at 8am PST to discuss issues | |||
** Representation of protein complexes, and their constituent members, in GO and GO-CAM models | |||
*** [https://drive.google.com/drive/u/0/folders/0B7bEr6HANSlGTTJfbXY4OUxUU1k Folder on Google drive for protein complexes working group] | |||
*** [https://github.com/geneontology/go-annotation/issues/1662 inferring MFs from annotations to complex portal IDs to individual complex participants] | |||
***[https://github.com/geneontology/go-annotation/issues/1661 Protein complex representation in Noctua] | |||
** Review HTP annotations | |||
*** [https://github.com/geneontology/go-annotation/issues/1655 Review HTP annotations] | |||
***[https://docs.google.com/document/d/1ScIeclAzUXMe-tU6n0lVfsSwMHpOeNb7uK8On9-iKXc/edit Draft of HTP guidelines] | |||
*** [https://docs.google.com/spreadsheets/d/11xExGJfj_39xPQUGkam3Xvtd6dtZ5DfANXhM2ZtDYB0/edit#gid=0 HTP data currently in GO] | |||
= Minutes = | = Minutes = | ||
*On call: | *On call: David H., Dmitry, Edith, Eric, George, Giulia, Harold, Jim, Karen, Kimberly, Li, Liz, Midori, Pascale, Paul T., Penelope, Petra, Robert, Rob N., Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Tanya, Terry, Val | ||
== Annotation QC == | |||
* Action Item: Need curators to review experimental annotations to 'transport' | |||
* Report back on any annotations that can't reasonably be transferred to a more granular term | |||
* We will continue to look at the PomBase list and prioritize additional flags and error checks | |||
== Ontology Updates == | |||
* Will merge DNA binding transcription factor activity into nucleic acid binding transcription factor activity | |||
* Goal: trying to more easily distinguish 'general' transcription factors (generally only described wrt pol II TFs) from specific, regulatory TFs | |||
* Pascale will tag groups/people if annotations need review | |||
* Pascale, Karen, Paul T. will discuss further | |||
== GOC Cambridge Meetings == | |||
=== Signaling Pathways === | |||
* Will follow-up on signaling workshop with items using the go-annotation tracker | |||
=== HTP Evidence Codes === | |||
* Helen will finish updating guidelines | |||
* How doe the HTP evidence codes map up to existing GO evidence codes? | |||
** They are in a separate branch, although still experimental. | |||
[[Category: Annotation Working Group]] | [[Category: Annotation Working Group]] |
Latest revision as of 11:57, 24 October 2017
Meeting URL
Agenda
Annotation QC
- Manual annotation to uninformative high-level terms is strongly discouraged
- See: improving specificity by banning high level terms #1648
- For example: direct annotation to 'transport' (GO:0006810) is one case where a more specific annotation can likely be made
- In AmiGO, there are 53 experimentally supported annotations to 'transport'.
- Can groups check these annotations to see if a more granular term is appropriate?
- Annotations according to group:
(8) EcoCyc (7) EcoliWiki (7) MGI (7) PseudoCAP (6) SGD (5) UniProt (4) BHF-UCL (3) RGD (3) TAIR (2) GR (1) SynGO
- PomBase has a list of >1300 high-level terms that have a 'do not manually annotate' flag
- The proposal is to work through this list so annotations are consistent amongst all GOC members
Ontology Updates
- Pascale:
- Transcription factor activity refactor
- Molecular Function terms describing 'transcription factors'
- See: Make parent term for transcription factor activity
- See: Transcription factor branch refactoring: overview of annotations of TFIIIC and TFIIB complexes
GOC Meetings Cambridge
- Review key action items from signaling workshop and GOC meeting
- GOC Cambridge 2017 Meeting Minutes
- Focus on annotation to signaling pathways
- Adoption of expanded set of BP relations
- Review use of contributes_to and colocalizes_with
- Noctua into full production mode
- Meetings on second and fourth Wednesdays at 8am PST to discuss issues
- Representation of protein complexes, and their constituent members, in GO and GO-CAM models
- Review HTP annotations
Minutes
- On call: David H., Dmitry, Edith, Eric, George, Giulia, Harold, Jim, Karen, Kimberly, Li, Liz, Midori, Pascale, Paul T., Penelope, Petra, Robert, Rob N., Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Tanya, Terry, Val
Annotation QC
- Action Item: Need curators to review experimental annotations to 'transport'
- Report back on any annotations that can't reasonably be transferred to a more granular term
- We will continue to look at the PomBase list and prioritize additional flags and error checks
Ontology Updates
- Will merge DNA binding transcription factor activity into nucleic acid binding transcription factor activity
- Goal: trying to more easily distinguish 'general' transcription factors (generally only described wrt pol II TFs) from specific, regulatory TFs
- Pascale will tag groups/people if annotations need review
- Pascale, Karen, Paul T. will discuss further
GOC Cambridge Meetings
Signaling Pathways
- Will follow-up on signaling workshop with items using the go-annotation tracker
HTP Evidence Codes
- Helen will finish updating guidelines
- How doe the HTP evidence codes map up to existing GO evidence codes?
- They are in a separate branch, although still experimental.