Difference between revisions of "Annotation Conf. Call 2017-11-28"

From GO Wiki
Jump to: navigation, search
(Signaling Project)
(Wnt signaling pathway)
 
(26 intermediate revisions by 2 users not shown)
Line 9: Line 9:
 
**groups
 
**groups
 
**orcid (uri)
 
**orcid (uri)
*'''ACTION:''' Berkeley will be providing a one-time report that indicates where users have edit permission in Noctua but don't have an orcid or group associated with them
+
*'''ACTION:''' Berkeley will be providing a report that indicates where users have edit permission in Noctua but don't have an orcid or group associated with them
  
 
== Annotation Review ==
 
== Annotation Review ==
Line 18: Line 18:
 
***Zebrafish
 
***Zebrafish
 
***C. elegans
 
***C. elegans
 +
****GO:0007194 negative regulation of adenylate cyclase activity
 +
****We've annotated a phospholipase C to this term and it is believed to reduce adenylate cyclase activity via competitive binding of an adenylate cyclase activator, Ha-Ras.
 
***Drosophila
 
***Drosophila
 +
****Gprk2 seems to be required for maintaining cellular cAMP levels and for Hh signaling, but does not act via Smoothened or G-proteins. Could be regulating AC directly or indirectly.
 
***Mouse
 
***Mouse
 +
==== Wnt signaling pathway ====
 +
*[https://docs.google.com/spreadsheets/d/1WJHkgtXLvPizEJt5Sce8mFeH9AI_JUAtQa0pVOmAH_w/edit#gid=0 beta-catenin annotations to review]
 +
**DNA binding
 +
**Upgrade to canonical Wnt signaling
 +
*[https://docs.google.com/spreadsheets/d/1YONqkh9AzvX-H-othzE0Ps0agAo25t3uCnWty5GQ6o4/edit#gid=0 annotations to receptor ligand activity]
 +
**Wild-type function vs disease state
 +
**Annotation extensions to capture where receptor ligand activity occurs
 +
***has_start_location, has_end_location
 +
**More work may be done on the receptor ligand activity branch of the MF
 +
**We will also be examining the MF term 'signal transducer activity' to see if it is really needed
 +
 +
=== Ontology Development ===
 +
==== Synaptic vesicle endocytosis ====
 +
*[https://github.com/geneontology/go-annotation/issues/1697 Please review annotations: 'synaptic vesicle endocytosis GO:0048488' and child terms]
 +
==== Protein import into the nucleus ====
 +
*[https://github.com/geneontology/go-annotation/issues/1700 Annotation review : protein import into the nucleus]
 +
 +
== HTP Evidence Codes ==
 +
*New HTP paper google spreadsheet for potential HTP papers annotated using the GO:Sheet laballed:"Over_40_per_evidencecode"
 +
https://docs.google.com/spreadsheets/d/11xExGJfj_39xPQUGkam3Xvtd6dtZ5DfANXhM2ZtDYB0/edit?ts=58d39700#gid=2144791301
 +
*https://github.com/geneontology/go-annotation/issues/1655
 +
*Generated by splitting out the experimental evidence codes and collating the papers with >40 lines of annotation per paper/per evidence code.
 +
*For most contributors, I have been able to do this directly from the GAF they submit to the GOC so that any DB-specific refs are included and any other sources that are incorporated into the anointed set.
 +
*For a few others, indicated on the sheet, had to download them from QuickGO.
 +
*Note: As they have been separated on evidence code, same paper may feature on separate lines.
 +
*Note: Only equivalent evidence codes to HTPs looked at (EXP, IDA, IEP, IGI, IMP).
 +
 +
 +
*Summary of lines in "Over_40_per_evidencecode"
 +
{| {{Prettytable}} class='sortable'
 +
! Source
 +
! Publications
 +
! Done?
 +
! Summary of Action
 +
|-
 +
| AgBase
 +
| 29
 +
|-
 +
| ARUK-UC
 +
| 2
 +
|-
 +
| BHF-UCL
 +
| 19
 +
|-
 +
| dictyBase
 +
| 9
 +
| Y
 +
|-
 +
| Ecoliwiki
 +
| 9
 +
|-
 +
| FlyBase
 +
| 62
 +
|-
 +
| MGI
 +
| 32
 +
|-
 +
| MTBBASE
 +
| 10
 +
|-
 +
| ParkinsonsUK-UCL
 +
| 5
 +
|-
 +
| PomBase
 +
| 9
 +
| Y
 +
|-
 +
| RGD
 +
| 2
 +
|-
 +
|SGD
 +
| 43
 +
|-
 +
| TAIR
 +
| 84
 +
|-
 +
| UniProt
 +
| 88
 +
|-
 +
| WB
 +
| 16
 +
| Y
 +
| 5 -> HTP code; 7 -> UniProt; 4 -> no change in evidence code, but will review annotations generally
 +
|-
 +
| ZFIN
 +
| 24
 +
| Y
 +
|-
 +
|}
 +
 +
*It would be great if each group could go over these (may take some time) and indicate if the paper/experiment was HTP and what action was taken on the spreadsheet.
 +
*[https://docs.google.com/document/d/1_T5FarM7eddFqO7DWooP5UOx1vw4H6lBMktGc62uFIY/edit#heading=h.h26ct5b5pki0 More concise version of HTP guidelines]. Please use and give feedback!
 +
 +
*Instructions for updating evidence codes in Protein2GO
 +
**First, send the request to goa@ebi.ac.uk, not to Tony directly.
 +
**Second, clearly list the PMID you like to have updated.
 +
**Finally, list the specific HTP ECO code you would like to use for the  annotations from the PMID you listed.
 +
**Note that not all annotations from a given paper will need to be switched to an HTP code, only those for which the group specifies the evidence code to switch.
  
 
= Minutes =
 
= Minutes =
*On call:
+
*On call: Edith, George, Giulia, Harold, Helen, Karen, Kimberly, Midori, Pascale, Paul T., Penelope, Petra, Ruth, Sabrina, Shur-Jen, Stan, Tanya
 +
 
 +
== Infrastructure ==
 +
=== users.yaml file ===
 +
*[http://skyhook.berkeleybop.org/snapshot/metadata/users-and-groups-report.txt Link to users.yaml QC report]
 +
*'''AI:''' Curators need to check if they are listed in the report and update their groups and uris, as needed.
 +
*Please contact Kimberly or Seth if you need help with this.  Thx.
 +
*Please keep in mind that the report is generated as part of the new build and a new attempt is made every night.
 +
*This means that 1) if the load fails the report may not be there (which is a good thing) and 2) there will times every day during regeneration when the report is not yet there.
 +
 
 +
== Annotation Review ==
 +
=== Signaling Project ===
 +
==== adenylate cyclase-activating G-protein coupled receptor signaling pathway ====
 +
*[https://github.com/geneontology/go-annotation/issues/1691 Review annotation for GPCR]
 +
*We discussed cases where it didn't appear that annotations wrt regulation of cAMP signaling or regulation of adenylate cyclase could not be re-housed to adenylate cyclase-activating GPCR signaling pathway
 +
*'''AI:''' Harold created regulation terms for regulation of the signaling pathway.  See: [https://github.com/geneontology/go-ontology/issues/14664 NTR 'regulation of adenylate cyclase-activating G protein coupled receptor signaling pathway]
 +
*Other cases still under discussion:  regulation of adenylate cyclase activity by competitive binding to an activator and regulation of cAMP signaling but via an uncharacterized pathway
 +
*We need to consider if we can make a more informative statement if not one about the precise signaling pathway affected by a mutation.
 +
*'''AI:''' [https://github.com/geneontology/go-annotation/issues/1712 Review annotations to 'cAMP biosynthetic process']
 +
*'''AI:''' We need to confirm how we are going to annotate regulation.  Direct regulation = activator or inhibitor.  What about indirect regulation?
 +
 
 +
==== Wnt signaling pathway ====
 +
*[https://docs.google.com/spreadsheets/d/1WJHkgtXLvPizEJt5Sce8mFeH9AI_JUAtQa0pVOmAH_w/edit#gid=0 beta-catenin annotations to review]
 +
**DNA binding
 +
**Upgrade to canonical Wnt signaling
 +
*[https://docs.google.com/spreadsheets/d/1YONqkh9AzvX-H-othzE0Ps0agAo25t3uCnWty5GQ6o4/edit#gid=0 annotations to receptor ligand activity]
 +
**'''AI:''' Review annotation of MAPT to 'receptor ligand activity '[https://github.com/geneontology/go-annotation/issues/1713 . Wild-type function vs disease state]
 +
**Annotation extensions for 'receptor ligand activity' will be reviewed on an upcoming call, as will 'signal transducer activity'
 +
 
 +
=== Ontology Development ===
 +
==== Synaptic vesicle endocytosis ====
 +
*[https://github.com/geneontology/go-annotation/issues/1697 Please review annotations: 'synaptic vesicle endocytosis GO:0048488' and child terms]
 +
'''AI:''' Barbara has made the proposed changes to 'synaptic vesicle exocytosis' parent and will create the more specific child terms.
 +
==== Protein import into the nucleus ====
 +
*[https://github.com/geneontology/go-annotation/issues/1700 Annotation review : protein import into the nucleus]
 +
'''AI:''' Please continue to review annotations to the more specific children of 'protein import into the nucleus' and re-house to the more general parent term whenever possible.
 +
 
 +
 
 +
== HTP Evidence Codes ==
 +
'''AI:''' Please continue to review papers and upgrade evidence codes to HTP codes when appropriate.
 +
*For some groups, this may take some time to trickle down into their respective databases, but that is okay as long as the process has been started.
  
  
  
 
[[Category: Annotation Working Group]]
 
[[Category: Annotation Working Group]]

Latest revision as of 16:22, 28 November 2017

Meeting URL

Agenda

Infrastructure

users.yaml file

  • users.yaml file is used to store curator metadata and will also be used for proper annotation attribution (i.s. Assigned by) in the GPAD outputs from Noctua
  • ACTION: One curator from each curation site should review entries in users.yaml file to fill in information for:
    • groups
    • orcid (uri)
  • ACTION: Berkeley will be providing a report that indicates where users have edit permission in Noctua but don't have an orcid or group associated with them

Annotation Review

Signaling Project

adenylate cyclase-activating G-protein coupled receptor signaling pathway

  • Review of cAMP-related signaling and biosynthesis terms and annotations
    • Questions about existing annotations that could not be immediately re-housed:
      • Zebrafish
      • C. elegans
        • GO:0007194 negative regulation of adenylate cyclase activity
        • We've annotated a phospholipase C to this term and it is believed to reduce adenylate cyclase activity via competitive binding of an adenylate cyclase activator, Ha-Ras.
      • Drosophila
        • Gprk2 seems to be required for maintaining cellular cAMP levels and for Hh signaling, but does not act via Smoothened or G-proteins. Could be regulating AC directly or indirectly.
      • Mouse

Wnt signaling pathway

  • beta-catenin annotations to review
    • DNA binding
    • Upgrade to canonical Wnt signaling
  • annotations to receptor ligand activity
    • Wild-type function vs disease state
    • Annotation extensions to capture where receptor ligand activity occurs
      • has_start_location, has_end_location
    • More work may be done on the receptor ligand activity branch of the MF
    • We will also be examining the MF term 'signal transducer activity' to see if it is really needed

Ontology Development

Synaptic vesicle endocytosis

Protein import into the nucleus

HTP Evidence Codes

  • New HTP paper google spreadsheet for potential HTP papers annotated using the GO:Sheet laballed:"Over_40_per_evidencecode"

https://docs.google.com/spreadsheets/d/11xExGJfj_39xPQUGkam3Xvtd6dtZ5DfANXhM2ZtDYB0/edit?ts=58d39700#gid=2144791301

  • https://github.com/geneontology/go-annotation/issues/1655
  • Generated by splitting out the experimental evidence codes and collating the papers with >40 lines of annotation per paper/per evidence code.
  • For most contributors, I have been able to do this directly from the GAF they submit to the GOC so that any DB-specific refs are included and any other sources that are incorporated into the anointed set.
  • For a few others, indicated on the sheet, had to download them from QuickGO.
  • Note: As they have been separated on evidence code, same paper may feature on separate lines.
  • Note: Only equivalent evidence codes to HTPs looked at (EXP, IDA, IEP, IGI, IMP).


  • Summary of lines in "Over_40_per_evidencecode"
Source Publications Done? Summary of Action
AgBase 29
ARUK-UC 2
BHF-UCL 19
dictyBase 9 Y
Ecoliwiki 9
FlyBase 62
MGI 32
MTBBASE 10
ParkinsonsUK-UCL 5
PomBase 9 Y
RGD 2
SGD 43
TAIR 84
UniProt 88
WB 16 Y 5 -> HTP code; 7 -> UniProt; 4 -> no change in evidence code, but will review annotations generally
ZFIN 24 Y
  • It would be great if each group could go over these (may take some time) and indicate if the paper/experiment was HTP and what action was taken on the spreadsheet.
  • More concise version of HTP guidelines. Please use and give feedback!
  • Instructions for updating evidence codes in Protein2GO
    • First, send the request to goa@ebi.ac.uk, not to Tony directly.
    • Second, clearly list the PMID you like to have updated.
    • Finally, list the specific HTP ECO code you would like to use for the annotations from the PMID you listed.
    • Note that not all annotations from a given paper will need to be switched to an HTP code, only those for which the group specifies the evidence code to switch.

Minutes

  • On call: Edith, George, Giulia, Harold, Helen, Karen, Kimberly, Midori, Pascale, Paul T., Penelope, Petra, Ruth, Sabrina, Shur-Jen, Stan, Tanya

Infrastructure

users.yaml file

  • Link to users.yaml QC report
  • AI: Curators need to check if they are listed in the report and update their groups and uris, as needed.
  • Please contact Kimberly or Seth if you need help with this. Thx.
  • Please keep in mind that the report is generated as part of the new build and a new attempt is made every night.
  • This means that 1) if the load fails the report may not be there (which is a good thing) and 2) there will times every day during regeneration when the report is not yet there.

Annotation Review

Signaling Project

adenylate cyclase-activating G-protein coupled receptor signaling pathway

  • Review annotation for GPCR
  • We discussed cases where it didn't appear that annotations wrt regulation of cAMP signaling or regulation of adenylate cyclase could not be re-housed to adenylate cyclase-activating GPCR signaling pathway
  • AI: Harold created regulation terms for regulation of the signaling pathway. See: NTR 'regulation of adenylate cyclase-activating G protein coupled receptor signaling pathway
  • Other cases still under discussion: regulation of adenylate cyclase activity by competitive binding to an activator and regulation of cAMP signaling but via an uncharacterized pathway
  • We need to consider if we can make a more informative statement if not one about the precise signaling pathway affected by a mutation.
  • AI: Review annotations to 'cAMP biosynthetic process'
  • AI: We need to confirm how we are going to annotate regulation. Direct regulation = activator or inhibitor. What about indirect regulation?

Wnt signaling pathway

Ontology Development

Synaptic vesicle endocytosis

AI: Barbara has made the proposed changes to 'synaptic vesicle exocytosis' parent and will create the more specific child terms.

Protein import into the nucleus

AI: Please continue to review annotations to the more specific children of 'protein import into the nucleus' and re-house to the more general parent term whenever possible.


HTP Evidence Codes

AI: Please continue to review papers and upgrade evidence codes to HTP codes when appropriate.

  • For some groups, this may take some time to trickle down into their respective databases, but that is okay as long as the process has been started.