Annotation Conf. Call 2017-11-14: Difference between revisions
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**GO:0030818 negative regulation of cAMP biosynthetic process | **GO:0030818 negative regulation of cAMP biosynthetic process | ||
*If gene products that are '''part of''' the G-protein-coupled receptor signaling pathway are annotated to any of the above terms, these annotations should be removed | *If gene products that are '''part of''' the G-protein-coupled receptor signaling pathway are annotated to any of the above terms, these annotations should be removed | ||
*If gene products are annotated that are '''not''' '''part of''' the G-protein-coupled receptor signaling pathway | **Note that gene products that are '''part of''' the pathway should also have an annotation to the pathway | ||
*If gene products are annotated that are '''not''' '''part of''' the G-protein-coupled receptor signaling pathway, these annotations should be brought to an annotation call for review | |||
*Report progress of review or issues in [https://github.com/geneontology/go-annotation/issues/1691 the associated github ticket] | *Report progress of review or issues in [https://github.com/geneontology/go-annotation/issues/1691 the associated github ticket] | ||
Revision as of 11:18, 15 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
- Next call: Wednesday, November 22nd at 8am PST
- Attribution with GO-CAM exports to GOC annotation files
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:
(7) PseudoCAP (Fiona Brinkman) (2) GR (Pankaj)
- 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
- SET1
- A) GO:0007189 adenylate cyclase-activating G protein coupled receptor signaling pathway
- Total annotations: 955 (direct)
- 1 InterPro
- 100 EXP
- -> No action needed from curators
- B) GO:0010579 positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway
- Total annotations: 105 (direct)
- 2 InterPro: InterPro:IPR000497, InterPro:IPR001413
- 29 EXP
- -> No action needed from curators
- C) GO:0030819 positive regulation of cAMP biosynthetic process
- Total annotations: 385 (direct)
- -> 493/761 are *also* annotated to G-protein coupled receptor activity (GO:0004930) according to the matrix
- 0 InterPro
- 104 EXP
- -> These annotations should be reviewed and moved to 'adenylate cyclase-activating G protein coupled receptor signaling pathway' if appropriate
- D) GO:0043950 positive regulation of cAMP-mediated signaling
- Total annotations: 109
- 0 InterPro
- 22 EXP
- -> These annotations should be reviewed and moved to 'adenylate cyclase-activating G protein coupled receptor signaling pathway' if appropriate (most should)
- Terms A and B have been merged. https://github.com/geneontology/go-ontology/issues/14547
- Annotations to terms C and D should be reviewed; a quick look indicated that most could be annotated to term A
- Once the clean up is done we will be able to make a decision as to what to do with terms C and D. They may need to remain in the ontology, with curator notes to consider annotating to term A.
- 'positive regulation of cAMP biosynthetic process’ could probably be merged with ‘adenlyate cyclase activity’ (to be confirmed once annotations are reviewed)
- 'positive regulation of cAMP-mediated signaling’ could probably be merged with GO:0007189 adenylate cyclase-activating G protein coupled receptor signaling pathway
- SET2
- A) GO:0007193 adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway
- Total annotations: 301
- 0 InterPro
- 40 EXP
- -> No action needed from curators
- B) GO:0007194 negative regulation of adenylate cyclase activity
- Total annotations: 563
- 0 InterPro
- 30 EXP, mostly GPCRs
- -> These annotations should be reviewed and moved to 'adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway' if appropriate
- Perhaps there is ‘direct’ negative regulation of ACA activity’, let’s see when we review the annotations.
- C) GO:0030818 negative regulation of cAMP biosynthetic process
- Total annotations: 144
- 0 InterPro
- 32 EXP, mostly GPCRs
- -> These annotations should be reviewed and moved to 'adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway' if appropriate
- There is no ‘B’ term equivalent in this list (negative regulation of ACA .. etc)
- Annotations to terms B and C should be reviewed; a quick look indicated that most could be annotated to term A
- Again, once the clean up is done we will be able to make a decision as to what to do with these terms.
- Again perhaps this term sould be merged into 'adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway’
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 |
---|---|
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 | 88 |
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 spreadsheet.
- More concise version of HTP guidelines. Please use and give feedback!
Protein Complexes Working Group
- Birgit is spearheading this working group
- Doodle poll
- First meeting, Thursday, November 30th, 8am PST (11am EST, 4pm UMT)
- Use the same Zoom as for the annotation calls
Minutes
- On call: Edith, George, Harold, Helen, Judy, Karen, Kimberly, Liz, Pascale, Paul T., Penelope, Petra, Rob, Ruth, Sabrina, Sage, Shur-Jen, Stacia, Stan, Suzi, Tanya, Terry
Ontology Term Requests - Reminder
Noctua -Infrastructure
Annotation Attribution
- ACTION: One curator from each MOD should review entries in users.yaml file to fill in information for:
- Groups
- Note that the group for GO_Central curation (i.e. PAINT) is http://geneontology.org
- ORCID
- Unless you are curating for PAINT, you don't need to add this URL as a group
- Groups
- ACTION: Check with Chris and Seth about the reason for ORCID in two fields:
- URI
- accounts
- ACTION: Check with Chris and Seth about ORCIDs for groups/projects
Annotation QC
Direct Annotation to High Level Terms
Transport
- Nearly all groups have updated their direct annotations to 'transport'. Thank you!!
- InterPro has updated their mappings
- SwissProt keyword mappings have also been updated
- 'Transport' will now be added to the 'do_not_annotate' subset
- ACTION: Determine if there is a way to query over all mappings files to see if high level terms are used there.
- ACTION: Consult with Val for the next high level term to review.
Signaling Project
- ACTION: Curators need to check annotations to:
- GO:0030819 positive regulation of cAMP biosynthetic process
- GO:0043950 positive regulation of cAMP-mediated signaling
- GO:0007194 negative regulation of adenylate cyclase activity
- GO:0030818 negative regulation of cAMP biosynthetic process
- If gene products that are part of the G-protein-coupled receptor signaling pathway are annotated to any of the above terms, these annotations should be removed
- Note that gene products that are part of the pathway should also have an annotation to the pathway
- If gene products are annotated that are not part of the G-protein-coupled receptor signaling pathway, these annotations should be brought to an annotation call for review
- Report progress of review or issues in the associated github ticket
HTP Evidence Codes
- ACTION: Please check the Google spreadsheet that Helen has put together and indicate whether the flagged papers and corresponding annotations are indeed high throughput
- If yes, then the evidence codes for the HTP annotations will need to be updated to the new codes.
- ACTION: George will check with Tony about whether he'd like an SOP for updating evidence codes in Protein2GO since there may be many that need revision.