Difference between revisions of "WormBase-Caltech Weekly Calls"
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*Data upload will be Dec 20th | *Data upload will be Dec 20th | ||
*Database build will happen second week of Janurary | *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 | ||
Revision as of 23:00, 17 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
