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
- Review of cAMP-related signaling and biosynthesis terms and annotations
- Questions about existing annotations that could not be immediately re-housed:
- Zebrafish
- C. elegans
- Drosophila
- Mouse
- Questions about existing annotations that could not be immediately re-housed:
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://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: