Annotation Conf. Call 2017-11-28

From GO Wiki
Jump to navigation Jump to search
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.

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?