Annotation Conf. Call 2017-11-14

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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 Done?
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
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!

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
    • Note that gene products that are part of the pathway should also have an annotation to the pathway
    • One of the main conceptual issues here is that gene products that are part of the signaling pathway should not be annotated to cAMP biosynthetic process, as the process they are involved in here is signaling not biosynthesis
  • If gene products are annotated that are not part of the G-protein-coupled receptor signaling pathway, these annotations should be brought to an annotation call for review
  • Report progress of review or issues in the associated 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.