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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)

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 be ready soon

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?