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

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= Minutes =
= Minutes =
*On call: Edith, George, Giulia, Helen, Karen, Kimberly, Midori, Penelope, Petra, Ruth, Sabrina, Stan
*On call: Edith, George, Giulia, Helen, Karen, Kimberly, Midori, Penelope, Petra, Ruth, Sabrina, Shur-Jen, Stan, Tanya
[[Category: Annotation Working Group]]
[[Category: Annotation Working Group]]

Revision as of 08:02, 28 November 2017

Meeting URL



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://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
dictyBase 9 Y
Ecoliwiki 9
FlyBase 62
MGI 32
ParkinsonsUK-UCL 5
PomBase 9 Y
SGD 43
UniProt 88
WB 16 Y 5 -> HTP code; 7 -> UniProt; 4 -> no change in evidence code, but will review annotations generally
  • 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.


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