LEGO October 10, 2016: Difference between revisions
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==Software Updates== | ==Software Updates== | ||
*Monday morning - no existing models visible after login | *Monday morning - no existing models visible after login | ||
*AmiGO build? If so, could there be a message displayed on the tool? | |||
===GAF/GPAD Updates=== | ===GAF/GPAD Updates=== | ||
Line 11: | Line 12: | ||
===GPI Files=== | ===GPI Files=== | ||
*Review specifications | *Review specifications | ||
**Groups will need to start submitting these files routinely, but there are still a few aspects of the specifications that need to be clarified | **Groups will need to start submitting these files routinely, but there are still a few aspects of the specifications that need to be clarified and then documented on github, website | ||
**[https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-1_2.md Chris' gpad-gpi docs on github] | **[https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-1_2.md Chris' gpad-gpi docs on github] | ||
**[https://drive.google.com/drive/folders/0B8kRPmmvPJU3c2d3TUpTOWotZzg Kimberly's Google doc on gpi specs for website] | **[https://drive.google.com/drive/folders/0B8kRPmmvPJU3c2d3TUpTOWotZzg Kimberly's Google doc on gpi specs for website] | ||
**Contents of header - what's required, what's optional, format for tag value-pairs, format for free text | |||
***Required: | |||
****!gpi-version: 1.2 | |||
****!Date: 2016-10-10 | |||
***Other possible tag value-pairs: | |||
****!Project_name: WB | |||
****!Contact_email: help@wormbase.org | |||
****!URL: http://www.wormbase.org | |||
****!Release: WS256 | |||
***Other possible content: | |||
****Explanation of gpi file fields | |||
****Explanation of entities represented, e.g. Reference Proteome | |||
****Explanation of specific DB_xrefs included | |||
**Contents of file - what's required, what's optional, format | |||
***Required fields are indicated in github doc, website | |||
***Entities needed for curation should be included in gpi file | |||
***Clarification needed on: | |||
****Entity namespace in Column 1? - YES | |||
****DB Object Type - use SO terms (and IDs?) here? | |||
****Taxon prefix, i.e. 6239 or taxon:6239? | |||
****Parent IDs - always a gene? canonical protein and a gene? | |||
****DB_xrefs - are any DB_xrefs required? | |||
*****MODs should include xrefs from genes to UniProtKB GCRP (Gene-Centric Reference Proteome) accessions? Reciprocal? | |||
*****RNAcentral accessions for ncRNAs when possible | |||
*****Protein/macromolecular complexes? | |||
****Gene Product Properties - anything required? | |||
*****UniProtKB includes information on Swiss_Prot vs TrEMBL subset | |||
===Use of PRO Identifiers for Modified Forms of Proteins=== | |||
*The dictyBase annotation consistency exercise model was a good example of where we might like to be able to annotate to modified forms of proteins, e.g. GTP-bound Ras | |||
*For consistency, do we want to make this required? What/How would that be indicated in a template? | |||
*What work needs to be done with PRO to prepare for this if we decide to go that route? | |||
===Domain, Range Constraints for Relations in Noctua=== | |||
*Updates? | |||
*https://github.com/geneontology/noctua/issues/358 | |||
==Annotation== | |||
===Tuesday Annotation Calls=== | |||
*We will discuss the latest version of the dictyBase annotation consistency exercise on tomorrow's (2016-10-11) annotation call. | |||
*Will try to incorporate more LEGO discussion into Tuesday annotation calls. | |||
===Templates=== | |||
*Compile list of specific templates that would be useful to have. | |||
=Minutes= | |||
*On call: Chris, David, Giulia, Helen, Jim, Kimberly VA, Moni, Ruth, Sabrina, Seth, Stacia, Suzi | |||
==AmiGO build fails and Noctua== | |||
*When an AmiGO build fails, no models are visible on Noctua | |||
*Seth may be able to set up a 'Don't worry' message to explain what happened for tool users | |||
==Software Updates== | |||
===GAF/GPAD Updates=== | |||
*Reasoner can show all inferred relations in the graphical editor | |||
**These relations are not wrong, but we wouldn't normally have made them | |||
*Not all relations need to be shown, though | |||
*Next step is to work on the GAF output with the select relations | |||
*Models and desired GAF/GPAD output are being collected in the minerva repository on github | |||
*Some of our traditional annotation rules are violated with LEGO models | |||
**We will need to re-visit some of these rules to see if we need to change them | |||
***TAS for protein binding | |||
***IEP for cellular component | |||
===GPI File Specifications=== | |||
*Different specs available depending upon where you look | |||
*Just need to keep this as a markdown in github | |||
*website specs could be simplified with the more detailed specs available for developers | |||
*Required gpi fields: | |||
**!gpi-version: 1.2 | |||
**!Date: 2016-10-10 | |||
[[Category:LEGO]] | [[Category:LEGO]] |
Latest revision as of 16:44, 10 October 2016
Bluejeans URL - NOTE NEW MEETING TIME: 8:00am PST
https://bluejeans.com/969313231
Agenda
Software Updates
- Monday morning - no existing models visible after login
- AmiGO build? If so, could there be a message displayed on the tool?
GAF/GPAD Updates
GPI Files
- Review specifications
- Groups will need to start submitting these files routinely, but there are still a few aspects of the specifications that need to be clarified and then documented on github, website
- Chris' gpad-gpi docs on github
- Kimberly's Google doc on gpi specs for website
- Contents of header - what's required, what's optional, format for tag value-pairs, format for free text
- Required:
- !gpi-version: 1.2
- !Date: 2016-10-10
- Other possible tag value-pairs:
- !Project_name: WB
- !Contact_email: help@wormbase.org
- !URL: http://www.wormbase.org
- !Release: WS256
- Other possible content:
- Explanation of gpi file fields
- Explanation of entities represented, e.g. Reference Proteome
- Explanation of specific DB_xrefs included
- Required:
- Contents of file - what's required, what's optional, format
- Required fields are indicated in github doc, website
- Entities needed for curation should be included in gpi file
- Clarification needed on:
- Entity namespace in Column 1? - YES
- DB Object Type - use SO terms (and IDs?) here?
- Taxon prefix, i.e. 6239 or taxon:6239?
- Parent IDs - always a gene? canonical protein and a gene?
- DB_xrefs - are any DB_xrefs required?
- MODs should include xrefs from genes to UniProtKB GCRP (Gene-Centric Reference Proteome) accessions? Reciprocal?
- RNAcentral accessions for ncRNAs when possible
- Protein/macromolecular complexes?
- Gene Product Properties - anything required?
- UniProtKB includes information on Swiss_Prot vs TrEMBL subset
Use of PRO Identifiers for Modified Forms of Proteins
- The dictyBase annotation consistency exercise model was a good example of where we might like to be able to annotate to modified forms of proteins, e.g. GTP-bound Ras
- For consistency, do we want to make this required? What/How would that be indicated in a template?
- What work needs to be done with PRO to prepare for this if we decide to go that route?
Domain, Range Constraints for Relations in Noctua
Annotation
Tuesday Annotation Calls
- We will discuss the latest version of the dictyBase annotation consistency exercise on tomorrow's (2016-10-11) annotation call.
- Will try to incorporate more LEGO discussion into Tuesday annotation calls.
Templates
- Compile list of specific templates that would be useful to have.
Minutes
- On call: Chris, David, Giulia, Helen, Jim, Kimberly VA, Moni, Ruth, Sabrina, Seth, Stacia, Suzi
AmiGO build fails and Noctua
- When an AmiGO build fails, no models are visible on Noctua
- Seth may be able to set up a 'Don't worry' message to explain what happened for tool users
Software Updates
GAF/GPAD Updates
- Reasoner can show all inferred relations in the graphical editor
- These relations are not wrong, but we wouldn't normally have made them
- Not all relations need to be shown, though
- Next step is to work on the GAF output with the select relations
- Models and desired GAF/GPAD output are being collected in the minerva repository on github
- Some of our traditional annotation rules are violated with LEGO models
- We will need to re-visit some of these rules to see if we need to change them
- TAS for protein binding
- IEP for cellular component
- We will need to re-visit some of these rules to see if we need to change them
GPI File Specifications
- Different specs available depending upon where you look
- Just need to keep this as a markdown in github
- website specs could be simplified with the more detailed specs available for developers
- Required gpi fields:
- !gpi-version: 1.2
- !Date: 2016-10-10