Annotation Conf. Call 2017-11-28: Difference between revisions

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=== Ontology Development ===
=== Ontology Development ===
== 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"
{| {{Prettytable}} class='sortable'
! 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.
*[https://docs.google.com/document/d/1_T5FarM7eddFqO7DWooP5UOx1vw4H6lBMktGc62uFIY/edit#heading=h.h26ct5b5pki0 More concise version of HTP guidelines]. Please use and give feedback!


= Minutes =
= Minutes =

Revision as of 11:28, 27 November 2017

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 one-time 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

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

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!

Minutes

  • On call:
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