Difference between revisions of "Annotation Conf. Call 2017-11-14"

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(Signaling Project)
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*If gene products that are '''part of''' the G-protein-coupled receptor signaling pathway are annotated to any of the above terms, these annotations should be removed  
 
*If gene products that are '''part of''' the G-protein-coupled receptor signaling pathway are annotated to any of the above terms, these annotations should be removed  
 
*If gene products are annotated  that are '''not''' '''part of''' the G-protein-coupled receptor signaling pathway are annotated to any of the above terms, these annotations should be brought to an annotation call for review
 
*If gene products are annotated  that are '''not''' '''part of''' the G-protein-coupled receptor signaling pathway are annotated to any of the above terms, these annotations should be brought to an annotation call for review
 +
*Report progress of review or issues in [https://github.com/geneontology/go-annotation/issues/1691 the association github ticket]
  
 
== HTP Evidence Codes ==
 
== HTP Evidence Codes ==

Revision as of 08:17, 15 November 2017

Meeting URL

Agenda

Ontology Term Requests - Reminder

  • Refresher on information required for term requests:
    • Term name
    • Parents
    • Term definition
    • Reference(s)
    • dbxrefs (e.g. GOC:kmv)
  • If you need help with parentage or definitions, the ontology editors can help with this, but please make a first-pass attempt at parentage and defs to help expedite the ticket.
  • Guideline for Contributing to the Ontology

Noctua -Infrastructure

Annotation Attribution

Assigned by Noctua example.png

Annotation QC

Direct Annotation to High Level Terms

Transport

  • 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?
      • Once you've checked the annotations, please remove yourself from the Assignee list on the ticket, so we know you've finished
    • Unresolved annotations according to group:
 (7) PseudoCAP (Fiona Brinkman)
 (2) GR (Pankaj)
  • 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

Signaling Project

  • Pascale:
    • Review cAMP-mediated GPCR signaling pathway annotations
  • SET1
    • A) GO:0007189 adenylate cyclase-activating G protein coupled receptor signaling pathway
    • Total annotations: 955 (direct)
    • 1 InterPro
    • 100 EXP
    • -> No action needed from curators
  • B) GO:0010579 positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway
    • Total annotations: 105 (direct)
    • 2 InterPro: InterPro:IPR000497, InterPro:IPR001413
    • 29 EXP
    • -> No action needed from curators
  • C) GO:0030819 positive regulation of cAMP biosynthetic process
    • Total annotations: 385 (direct)
    • -> 493/761 are *also* annotated to G-protein coupled receptor activity (GO:0004930) according to the matrix
    • 0 InterPro
    • 104 EXP
    • -> These annotations should be reviewed and moved to 'adenylate cyclase-activating G protein coupled receptor signaling pathway' if appropriate
  • D) GO:0043950 positive regulation of cAMP-mediated signaling
    • Total annotations: 109
    • 0 InterPro
    • 22 EXP
    • -> These annotations should be reviewed and moved to 'adenylate cyclase-activating G protein coupled receptor signaling pathway' if appropriate (most should)
  • Terms A and B have been merged. https://github.com/geneontology/go-ontology/issues/14547
  • Annotations to terms C and D should be reviewed; a quick look indicated that most could be annotated to term A
  • Once the clean up is done we will be able to make a decision as to what to do with terms C and D. They may need to remain in the ontology, with curator notes to consider annotating to term A.
  • 'positive regulation of cAMP biosynthetic process’ could probably be merged with ‘adenlyate cyclase activity’ (to be confirmed once annotations are reviewed)
  • 'positive regulation of cAMP-mediated signaling’ could probably be merged with GO:0007189 adenylate cyclase-activating G protein coupled receptor signaling pathway
  • SET2
    • A) GO:0007193 adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway
    • Total annotations: 301
    • 0 InterPro
    • 40 EXP
    • -> No action needed from curators
  • B) GO:0007194 negative regulation of adenylate cyclase activity
    • Total annotations: 563
    • 0 InterPro
    • 30 EXP, mostly GPCRs
    • -> These annotations should be reviewed and moved to 'adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway' if appropriate
    • Perhaps there is ‘direct’ negative regulation of ACA activity’, let’s see when we review the annotations.
  • C) GO:0030818 negative regulation of cAMP biosynthetic process
    • Total annotations: 144
    • 0 InterPro
    • 32 EXP, mostly GPCRs
    • -> These annotations should be reviewed and moved to 'adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway' if appropriate
    • There is no ‘B’ term equivalent in this list (negative regulation of ACA .. etc)
    • Annotations to terms B and C should be reviewed; a quick look indicated that most could be annotated to term A
    • Again, once the clean up is done we will be able to make a decision as to what to do with these terms.
    • Again perhaps this term sould be merged into 'adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway’

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
AgBase 29
ARUK-UC 2
BHF-UCL 19
dictyBase 9
Ecoliwiki 9
FlyBase 62
MGI 32
MTBBASE 10
ParkinsonsUK-UCL 5
PomBase 9
RGD 2
SGD 44
TAIR 84
UniProt 88
WB 16
ZFIN 24
  • 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!

Protein Complexes Working Group

Minutes

  • On call: Edith, George, Harold, Helen, Judy, Karen, Kimberly, Liz, Pascale, Paul T., Penelope, Petra, Rob, Ruth, Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Tanya, Terry

Ontology Term Requests - Reminder

Noctua -Infrastructure

Annotation Attribution

  • ACTION: One curator from each MOD should review entries in users.yaml file to fill in information for:
    • Groups
    • ORCID
    • Unless you are curating for PAINT, you don't need to add this URL as a group
  • ACTION: Check with Chris and Seth about the reason for ORCID in two fields:
    • URI
    • accounts
  • ACTION: Check with Chris and Seth about ORCIDs for groups/projects

Annotation QC

Direct Annotation to High Level Terms

Transport

  • Nearly all groups have updated their direct annotations to 'transport'. Thank you!!
  • InterPro has updated their mappings
  • SwissProt keyword mappings have also been updated
  • 'Transport' will now be added to the 'do_not_annotate' subset
  • ACTION: Determine if there is a way to query over all mappings files to see if high level terms are used there.
  • ACTION: Consult with Val for the next high level term to review.

Signaling Project

  • ACTION: Curators need to check annotations to:
    • GO:0030819 positive regulation of cAMP biosynthetic process
    • GO:0043950 positive regulation of cAMP-mediated signaling
    • GO:0007194 negative regulation of adenylate cyclase activity
    • GO:0030818 negative regulation of cAMP biosynthetic process
  • If gene products that are part of the G-protein-coupled receptor signaling pathway are annotated to any of the above terms, these annotations should be removed
  • If gene products are annotated that are not part of the G-protein-coupled receptor signaling pathway are annotated to any of the above terms, these annotations should be brought to an annotation call for review
  • Report progress of review or issues in the association github ticket

HTP Evidence Codes

  • ACTION: Please check the Google spreadsheet that Helen has put together and indicate whether the flagged papers and corresponding annotations are indeed high throughput
  • If yes, then the evidence codes for the HTP annotations will need to be updated to the new codes.
  • ACTION: George will check with Tony about whether he'd like an SOP for updating evidence codes in Protein2GO since there may be many that need revision.