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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)