Difference between revisions of "WormBase-Caltech Weekly Calls"
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*AMIGO 2 Documentation already put together by AMIGO 2 developers; | *AMIGO 2 Documentation already put together by AMIGO 2 developers; | ||
*Raymond has been and will document WormBase specific integration efforts | *Raymond has been and will document WormBase specific integration efforts | ||
+ | *Intermine doesn't have an ontology browser functionality | ||
+ | *Write grant? | ||
+ | *National Center for Biomedical Ontologies: do they have a preferred web app/display? | ||
+ | *Querying ontologies with integrated annotation/association data (e.g.), not available |
Revision as of 17:29, 20 December 2012
2012 Meetings
December 6, 2012
Concise descriptions
- Concise descriptions tool as a pilot for community annotation
- How can concise descriptions be generated on an automated basis?
- Prioritize with genes with little to no known information
- Focus on genes in other species
- GBrowse-visible description (30 character limit)
- Complex gene information will still be best handled manually
- Brugia malayi good starting point; Also, Pristionchus and C. briggsae
- Ralf Sommer would help generate concise descriptions
- Working with Brugia community already
- Could we select what type of GBrowse description is visible (potential drug targets, molecular function (GO term?), secreted proteases, resistance locus, etc.)? Using radio buttons, for example?
- Use GO annotations in automated fashion?
- Parasitic worm vs. Free-living worm descriptions (host, drugs, species-specific genes, etc.)
- 30-character controlled vocabulary for genes?
- Annotate (and then display) based on drug sensitivity, resistance, no effect? Show "potential" drug interactions?
- Icons on genes indicating drug interaction, for example
PAINT meeting
- Ranjana going to next week
- PAINT: Panther tree-based transfer of GO annotations across species
- Orthologs/paralogs adopt annotations
AMIGO update
- Can display our ontologies now
- User interface may take some time
- Would be best if Raymond could work with a programmer (Juancarlos?)
Remark field display issues
- Todd commented that he would like the "Remark" and "Summary" fields to display similar type of info across all pages/objects/data-types
- Transgene curation (and others?) may need adjustment to what goes in the "Summary" and "Remark" field
- May create new tag to accommodate info?
Upload
- Data upload will be Dec 20th
- Database build will happen second week of Janurary
December 13, 2012
PAINT Meeting
- Looking at whole tree of all genes across all species
- Applying gene (GO) annotations across all species
- Broad perspective
- Annotations help PAINT, PAINT helps annotations
- "Viewing the tree"
- GO annotations can be applied/dragged onto most recent common ancestor, and PAINT fills the annotation in to all genes in between
- Feature requests discussed
- Subfamilies/subclades color-coded for easier viewing
- Annotation matrix to view along with tree
- Molecular functions most readily conserved; processes less so (cell component intermediate)
- Reliability/prioritization of annotations: molecular function -> cell component -> biological process
- How much is rule-based? How is Quality Control handled/established?
- Liberal vs Conservative annotations; try to back up with literature
- "Triangulation" tools
- Good rules could replace manual annotation with automated annotation
- Automatic quality-control e-mailing
- Sample annotating of gene families
- Nitric oxide synthase
- Some transcription factors
- Some enzymes
- Panther trees describe relationships between genes, but really use proteins to make associations
- Duplications? How to annotate? Tricky; requires some literature searching
- Key annotations: species-specific genes/proteins for (relatively) sparsely annotated species; identifying unknowns, high value annotations
WormBase GO progress report
- Kimberly working on; will send out to relevant people
Common GO Annotation Tool
- Uniprot tool: Protein-2-GO?
- Adopt aspects of the WormBase Ontology Annotator
- Some MODs are heavily embedded in an in-house tool
- Good to have a general common tool for all data types
AMIGO 2 Ontology Browser
- Would like to develop feedback cycle of use/development
- Versioning issues
- Branching off of current AMIGO 2
- Seth wouldn't want anatomy or phenotype terms showing up in his ontologies
December 20, 2012
SPELL
- Athena updated to Ubuntu 4, not compatible with old Ruby
- SPELL still runs on older Ruby/Rails
- Difficulty updating code to accommodate OS change
- Currently building database on Athena and migrating to other machine
- Will continue running the older Ubuntu OS for now
- Front end is Ruby, back end is Java; maybe somehow ditch Ruby layer
- Proficient Ruby programmer could (maybe) upgrade the SPELL code appropriately
- What are other MODs (SGD?) doing? How can we emulate that?
- Also: there are some queries we would like to be able to perform that SPELL doesn't currently provide
- Develop another interface/query functionality?
- Use intermine? Intermine does not have good microarray data module
- Integration with other data types
- Query example: Find genes that have similar expression profile and physical interaction?
- Will try to contact Matthew Hibbs for update
- Do Matt et al have description of the API that we could look at, use?
AMIGO 2
- Juancarlos and Raymond still working on
- Juancarlos communicating with Seth
- Need to work out smooth architectural design so Juancarlos can work on code at our end, we can test locally
- AMIGO/Seth wants to move to Git version system
- Next, get at annotation info/files so that annotation data can be attached/linked to the ontology terms
- Seth said in ~month transitioning to new/stable version of software
Process Pages
- Karen and JD working on
- Karen explained what should be displayed, where and how on the page
- Mark Perry had worked on/developed display stuff for Molecules
- Should be complete for SAB meeting
Images on Staging
- Images are not displaying on the staging site
- Daniela will generate a GitHub ticket
Disease Ontology
- DO terms going to citace/ACEDB for upload
- Upgrading OBO files as well?
- Now we make the OBO files generally available to community
- Curation will produce association files (connecting terms to genes)
- Association files in GAF format? (AMIGO-useable format)
WormBase Ontology Browser
- What are the specs/features we want for an ontology/DAG browser?
- Have we settled on AMIGO? Yes, pretty much
- Can it handle Phenotype ontology, etc. (non-GO ontologies)?
- AMIGO 2 is more pliable than older AMIGO for these types of ontologies
- AMIGO 2 Documentation already put together by AMIGO 2 developers;
- Raymond has been and will document WormBase specific integration efforts
- Intermine doesn't have an ontology browser functionality
- Write grant?
- National Center for Biomedical Ontologies: do they have a preferred web app/display?
- Querying ontologies with integrated annotation/association data (e.g.), not available