WormBase-Caltech Weekly Calls

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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?