Annotation Conf. Call 2017-11-28: Difference between revisions
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= Agenda = | = Agenda = | ||
== Infrastructure == | |||
=== users.yaml file === | |||
*[https://github.com/geneontology/go-site/blob/master/metadata/users.yaml 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 ==== | |||
*[https://github.com/geneontology/go-annotation/issues/1691 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 ==== | |||
*[https://docs.google.com/spreadsheets/d/1WJHkgtXLvPizEJt5Sce8mFeH9AI_JUAtQa0pVOmAH_w/edit#gid=0 beta-catenin annotations to review] | |||
**DNA binding | |||
**Upgrade to canonical Wnt signaling | |||
*[https://docs.google.com/spreadsheets/d/1YONqkh9AzvX-H-othzE0Ps0agAo25t3uCnWty5GQ6o4/edit#gid=0 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 | |||
== Signaling Project == | === Ontology Development === | ||
*Review of cAMP- | ==== Synaptic vesicle endocytosis ==== | ||
*[https://github.com/geneontology/go-annotation/issues/1697 Please review annotations: 'synaptic vesicle endocytosis GO:0048488' and child terms] | |||
==== Protein import into the nucleus ==== | |||
*[https://github.com/geneontology/go-annotation/issues/1700 Annotation review : 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://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? | |||
! Summary of Action | |||
|- | |||
| 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 | |||
| Y | |||
| 5 -> HTP code; 7 -> UniProt; 4 -> no change in evidence code, but will review annotations generally | |||
|- | |||
| 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! | |||
*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. | |||
= Minutes = | |||
*On call: Edith, George, Giulia, Harold, Helen, Karen, Kimberly, Midori, Pascale, Paul T., Penelope, Petra, Ruth, Sabrina, Shur-Jen, Stan, Tanya | |||
== Infrastructure == | |||
=== users.yaml file === | |||
*[http://skyhook.berkeleybop.org/snapshot/metadata/users-and-groups-report.txt Link to users.yaml QC report] | |||
*'''AI:''' Curators need to check if they are listed in the report and update their groups and uris, as needed. | |||
*Please contact Kimberly or Seth if you need help with this. Thx. | |||
*Please keep in mind that the report is generated as part of the new build and a new attempt is made every night. | |||
*This means that 1) if the load fails the report may not be there (which is a good thing) and 2) there will times every day during regeneration when the report is not yet there. | |||
== Annotation Review == | |||
=== Signaling Project === | |||
==== adenylate cyclase-activating G-protein coupled receptor signaling pathway ==== | |||
*[https://github.com/geneontology/go-annotation/issues/1691 Review annotation for GPCR] | |||
*We discussed cases where it didn't appear that annotations wrt regulation of cAMP signaling or regulation of adenylate cyclase could not be re-housed to adenylate cyclase-activating GPCR signaling pathway | |||
*'''AI:''' Harold created regulation terms for regulation of the signaling pathway. See: [https://github.com/geneontology/go-ontology/issues/14664 NTR 'regulation of adenylate cyclase-activating G protein coupled receptor signaling pathway] | |||
*Other cases still under discussion: regulation of adenylate cyclase activity by competitive binding to an activator and regulation of cAMP signaling but via an uncharacterized pathway | |||
*We need to consider if we can make a more informative statement if not one about the precise signaling pathway affected by a mutation. | |||
*'''AI:''' [https://github.com/geneontology/go-annotation/issues/1712 Review annotations to 'cAMP biosynthetic process'] | |||
*'''AI:''' We need to confirm how we are going to annotate regulation. Direct regulation = activator or inhibitor. What about indirect regulation? | |||
==== Wnt signaling pathway ==== | |||
*[https://docs.google.com/spreadsheets/d/1WJHkgtXLvPizEJt5Sce8mFeH9AI_JUAtQa0pVOmAH_w/edit#gid=0 beta-catenin annotations to review] | |||
**DNA binding | |||
**Upgrade to canonical Wnt signaling | |||
*[https://docs.google.com/spreadsheets/d/1YONqkh9AzvX-H-othzE0Ps0agAo25t3uCnWty5GQ6o4/edit#gid=0 annotations to receptor ligand activity] | |||
**'''AI:''' Review annotation of MAPT to 'receptor ligand activity '[https://github.com/geneontology/go-annotation/issues/1713 . Wild-type function vs disease state] | |||
**Annotation extensions for 'receptor ligand activity' will be reviewed on an upcoming call, as will 'signal transducer activity' | |||
=== Ontology Development === | |||
==== Synaptic vesicle endocytosis ==== | |||
*[https://github.com/geneontology/go-annotation/issues/1697 Please review annotations: 'synaptic vesicle endocytosis GO:0048488' and child terms] | |||
'''AI:''' Barbara has made the proposed changes to 'synaptic vesicle exocytosis' parent and will create the more specific child terms. | |||
==== Protein import into the nucleus ==== | |||
*[https://github.com/geneontology/go-annotation/issues/1700 Annotation review : protein import into the nucleus] | |||
'''AI:''' Please continue to review annotations to the more specific children of 'protein import into the nucleus' and re-house to the more general parent term whenever possible. | |||
== HTP Evidence Codes == | |||
'''AI:''' Please continue to review papers and upgrade evidence codes to HTP codes when appropriate. | |||
*For some groups, this may take some time to trickle down into their respective databases, but that is okay as long as the process has been started. | |||
[[Category: Annotation Working Group]] | [[Category: Annotation Working Group]] |
Latest revision as of 19:22, 28 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 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
- 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
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 | ||
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 | Y | 5 -> HTP code; 7 -> UniProt; 4 -> no change in evidence code, but will review annotations generally |
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!
- 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.
Minutes
- On call: Edith, George, Giulia, Harold, Helen, Karen, Kimberly, Midori, Pascale, Paul T., Penelope, Petra, Ruth, Sabrina, Shur-Jen, Stan, Tanya
Infrastructure
users.yaml file
- Link to users.yaml QC report
- AI: Curators need to check if they are listed in the report and update their groups and uris, as needed.
- Please contact Kimberly or Seth if you need help with this. Thx.
- Please keep in mind that the report is generated as part of the new build and a new attempt is made every night.
- This means that 1) if the load fails the report may not be there (which is a good thing) and 2) there will times every day during regeneration when the report is not yet there.
Annotation Review
Signaling Project
adenylate cyclase-activating G-protein coupled receptor signaling pathway
- Review annotation for GPCR
- We discussed cases where it didn't appear that annotations wrt regulation of cAMP signaling or regulation of adenylate cyclase could not be re-housed to adenylate cyclase-activating GPCR signaling pathway
- AI: Harold created regulation terms for regulation of the signaling pathway. See: NTR 'regulation of adenylate cyclase-activating G protein coupled receptor signaling pathway
- Other cases still under discussion: regulation of adenylate cyclase activity by competitive binding to an activator and regulation of cAMP signaling but via an uncharacterized pathway
- We need to consider if we can make a more informative statement if not one about the precise signaling pathway affected by a mutation.
- AI: Review annotations to 'cAMP biosynthetic process'
- AI: We need to confirm how we are going to annotate regulation. Direct regulation = activator or inhibitor. What about indirect regulation?
Wnt signaling pathway
- beta-catenin annotations to review
- DNA binding
- Upgrade to canonical Wnt signaling
- annotations to receptor ligand activity
- AI: Review annotation of MAPT to 'receptor ligand activity '. Wild-type function vs disease state
- Annotation extensions for 'receptor ligand activity' will be reviewed on an upcoming call, as will 'signal transducer activity'
Ontology Development
Synaptic vesicle endocytosis
AI: Barbara has made the proposed changes to 'synaptic vesicle exocytosis' parent and will create the more specific child terms.
Protein import into the nucleus
AI: Please continue to review annotations to the more specific children of 'protein import into the nucleus' and re-house to the more general parent term whenever possible.
HTP Evidence Codes
AI: Please continue to review papers and upgrade evidence codes to HTP codes when appropriate.
- For some groups, this may take some time to trickle down into their respective databases, but that is okay as long as the process has been started.