LEGO October 10, 2016: Difference between revisions
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***TAS for protein binding | ***TAS for protein binding | ||
***IEP for cellular component | ***IEP for cellular component | ||
===GPI File Specifications=== | |||
*Different specs available depending upon where you look | |||
Revision as of 11:17, 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
- Other possible tag value-pairs:
- !Date: 20161010
- !Project_name: WB
- !Contact_email: help@wormbase.org
- !URL: http://www.wormbase.org
- !WB_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?
- 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, Ruth, Sabrina, Seth, 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