Annotation Conf. Call 2017-11-28

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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.