Difference between revisions of "WormBase-Caltech Weekly Calls"
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Nematode Textpresso | Nematode Textpresso |
Revision as of 18:49, 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
- Can AMIGO 2 query information across multiple ontologies (DO, GO, WPO, etc.)? Don't know yet, but would be useful
- Term-enrichment functionality? Not currently available through AMIGO
Transposons
- Paul Davis, Juancarlos, Kimberly have uploaded ~300 transposon genes
- Each has ~2 line description
Brugia Concise Descriptions
- What kind of information could we use for scripted descriptions?
- Collecting what type of info we have currently
Protein-2-GO
- Hopefully WormBase can integrate by early next year
CCC form 2.0
- Kimberly and Juancarlos have been working on
- Specs put together this week
- Form can communicate with Protein-2-GO
- Should have something next year
Nematode Textpresso
- Textpresso 2.5 vs 2.0 changes
- Free up disk space
- Will then move data over (from Brama) to Textpresso-Dev
- Should be done before SAB meeting
- Once public, we can ask other groups what types of ontologies would be helpful
GO-linking tool
- Figures are now linkable
Converting OBO files into ACE files
- Daniela will work with Juancarlos
Curation Status Form
- Almost ready to be live on Tazendra
- Need to check the newest SVM results on *.main vs *.concat
- Documentation on Wiki: http://wiki.wormbase.org/index.php/New_2012_Curation_Status
- Do Paper Editor modifications (e.g. False Positive flagging) transfer to the Curation Status tool? No, if you have entered data, contact Juancarlos about how you want it transferred
- We need to discuss consolidation/coordination of functionality across the various CGIs
Allele curation
- Curation prioritization: Genes that haven't been described (e.g. no phenotype)
- Exclude large-scale results?
- RNAi results? Ignore, consider, compare?
- Null alleles (or putative nulls) are important
Legacy alleles
- Karen transferring descriptions from C. elegans I, II, into database
- Down to ~430 legacy alleles in queue
- Community/expert input on reference alleles, etc.
- Still missing some info as it doesn't fit in data model
- Concise descriptions of alleles/variations? Scripted to pull some standard info
- Allelic series info has been going into Remark, although maybe not optimal (series of phenotypes?)
Parasitic Strains from Peter Hunt
- Karen put info in for parasitic nematode strains
- Incorporating drug-resistance/sensitivity effects on different parasite strains
- Phenotype: drug resistance ; cross-referenced to drug name (or drug class name) via chemical ontology
- Chemical classes; chemical SLIM ontology terms
Molecule Site-of-Action
- Currently, site-of-action data restricted to genes
- Calcium ion (molecule) site of action data came in through Author First Pass
- How to curate without major model revisions?
- Static WormBase page? Uncuratable, yet interesting data?
- Uncuratable class?
- Site-of-action tag for molecule class/model?
- Process page info?
Phenotype-enrichment
- Information richness/quality when calculating enrichment of GO or Phenotype terms
- Disregard/de-emphasize low-resolution terms? E.g. lethality, growth, sick, etc.
- What is informative?