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
** 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://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/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]
***[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

GOC Meetings Cambridge

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.