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

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(HTP Evidence Codes)
(HTP Evidence Codes)
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*New HTP paper google spreadsheet for potential HTP papers annotated using the GO:Sheet laballed:"Over_40_per_evidencecode"
 
*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://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.
 
*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 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.

Revision as of 01:48, 14 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

  • We need to have groups properly captured in the Assigned By field of output GPAD files
  • All current and future Noctua curators who are associated with one or more curation groups need to fill out the groups field in their entry in the users.yaml file
  • Full path: https://github.com/geneontology/go-site/blob/master/metadata/users.yaml
  • Groups are entered as URLs, e.g. http://www.wormbase.org, in single quotes
  • If curators belong to multiple annotation groups, the first group will be considered the default
  • To change groups in Noctua, select from the drop-down list next to the curator name in the upper right of the tool

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:
 (8) EcoCyc
 (7) EcoliWiki
 (7) MGI
 (7) PseudoCAP
 (3) RGD
 (2) GR
 (1) SynGO
  • 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

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 (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 32
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 spread sheet.

Minutes

  • On call:

Ontology Term Requests - Reminder

Noctua -Infrastructure

Annotation Attribution

Annotation QC

Direct Annotation to High Level Terms

Transport

Signaling Project

HTP Evidence Codes