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| | [[WormBase-Caltech_Weekly_Calls_November_2012|November]] | | [[WormBase-Caltech_Weekly_Calls_November_2012|November]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_December_2012|December]] |
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| − | = December 6, 2012 =
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| − | Concise descriptions
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| − | *Concise descriptions tool as a pilot for community annotation
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| − | *How can concise descriptions be generated on an automated basis?
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| − | *Prioritize with genes with little to no known information
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| − | *Focus on genes in other species
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| − | *GBrowse-visible description (30 character limit)
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| − | *Complex gene information will still be best handled manually
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| − | *''Brugia malayi'' good starting point; Also, ''Pristionchus'' and ''C. briggsae''
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| − | *Ralf Sommer would help generate concise descriptions
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| − | *Working with ''Brugia'' community already
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| − | *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?
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| − | *Use GO annotations in automated fashion?
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| − | *Parasitic worm vs. Free-living worm descriptions (host, drugs, species-specific genes, etc.)
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| − | *30-character controlled vocabulary for genes?
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| − | *Annotate (and then display) based on drug sensitivity, resistance, no effect? Show "potential" drug interactions?
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| − | *Icons on genes indicating drug interaction, for example
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| − | | |
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| − | PAINT meeting
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| − | *Ranjana going to next week
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| − | *PAINT: Panther tree-based transfer of GO annotations across species
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| − | *Orthologs/paralogs adopt annotations
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| − | AMIGO update
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| − | *Can display our ontologies now
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| − | *User interface may take some time
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| − | *Would be best if Raymond could work with a programmer (Juancarlos?)
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| − | | |
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| − | Remark field display issues
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| − | *Todd commented that he would like the "Remark" and "Summary" fields to display similar type of info across all pages/objects/data-types
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| − | *Transgene curation (and others?) may need adjustment to what goes in the "Summary" and "Remark" field
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| − | *May create new tag to accommodate info?
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| − | | |
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| − | Upload
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| − | *Data upload will be Dec 20th
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| − | *Database build will happen second week of Janurary
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| − | | |
| − | | |
| − | = December 13, 2012 =
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| − | | |
| − | PAINT Meeting
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| − | *Looking at whole tree of all genes across all species
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| − | *Applying gene (GO) annotations across all species
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| − | *Broad perspective
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| − | *Annotations help PAINT, PAINT helps annotations
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| − | *"Viewing the tree"
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| − | *GO annotations can be applied/dragged onto most recent common ancestor, and PAINT fills the annotation in to all genes in between
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| − | *Feature requests discussed
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| − | *Subfamilies/subclades color-coded for easier viewing
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| − | *Annotation matrix to view along with tree
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| − | *Molecular functions most readily conserved; processes less so (cell component intermediate)
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| − | *Reliability/prioritization of annotations: molecular function -> cell component -> biological process
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| − | *How much is rule-based? How is Quality Control handled/established?
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| − | *Liberal vs Conservative annotations; try to back up with literature
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| − | *"Triangulation" tools
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| − | *Good rules could replace manual annotation with automated annotation
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| − | *Automatic quality-control e-mailing
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| − | *Sample annotating of gene families
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| − | **Nitric oxide synthase
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| − | **Some transcription factors
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| − | **Some enzymes
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| − | *Panther trees describe relationships between genes, but really use proteins to make associations
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| − | *Duplications? How to annotate? Tricky; requires some literature searching
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| − | *Key annotations: species-specific genes/proteins for (relatively) sparsely annotated species; identifying unknowns, high value annotations
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| − | | |
| − | | |
| − | WormBase GO progress report | |
| − | *Kimberly working on; will send out to relevant people
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| − | | |
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| − | Common GO Annotation Tool
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| − | *Uniprot tool: Protein-2-GO?
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| − | *Adopt aspects of the WormBase Ontology Annotator
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| − | *Some MODs are heavily embedded in an in-house tool
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| − | *Good to have a general common tool for all data types
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| − | | |
| − | | |
| − | AMIGO 2 Ontology Browser
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| − | *Would like to develop feedback cycle of use/development
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| − | *Versioning issues
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| − | *Branching off of current AMIGO 2
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| − | *Seth wouldn't want anatomy or phenotype terms showing up in his ontologies
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| − | | |
| − | | |
| − | = December 20, 2012 =
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| − | | |
| − | | |
| − | SPELL
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| − | *Athena updated to Ubuntu 4, not compatible with old Ruby
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| − | *SPELL still runs on older Ruby/Rails
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| − | *Difficulty updating code to accommodate OS change
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| − | *Currently building database on Athena and migrating to other machine
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| − | *Will continue running the older Ubuntu OS for now
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| − | *Front end is Ruby, back end is Java; maybe somehow ditch Ruby layer
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| − | *Proficient Ruby programmer could (maybe) upgrade the SPELL code appropriately
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| − | *What are other MODs (SGD?) doing? How can we emulate that?
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| − | *Also: there are some queries we would like to be able to perform that SPELL doesn't currently provide
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| − | **Develop another interface/query functionality?
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| − | **Use intermine? Intermine does not have good microarray data module
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| − | **Integration with other data types
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| − | **Query example: Find genes that have similar expression profile and physical interaction?
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| − | *Will try to contact Matthew Hibbs for update
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| − | *Do Matt et al have description of the API that we could look at, use?
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| − | | |
| − | | |
| − | AMIGO 2
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| − | *Juancarlos and Raymond still working on
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| − | *Juancarlos communicating with Seth
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| − | *Need to work out smooth architectural design so Juancarlos can work on code at our end, we can test locally
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| − | *AMIGO/Seth wants to move to Git version system
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| − | *Next, get at annotation info/files so that annotation data can be attached/linked to the ontology terms
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| − | *Seth said in ~month transitioning to new/stable version of software
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| − | | |
| − | | |
| − | Process Pages
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| − | *Karen and JD working on
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| − | *Karen explained what should be displayed, where and how on the page
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| − | *Mark Perry had worked on/developed display stuff for Molecules
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| − | *Should be complete for SAB meeting
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| − | | |
| − | | |
| − | Images on Staging
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| − | *Images are not displaying on the staging site
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| − | *Daniela will generate a GitHub ticket
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| − | | |
| − | | |
| − | Disease Ontology
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| − | *DO terms going to citace/ACEDB for upload
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| − | *Upgrading OBO files as well?
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| − | *Now we make the OBO files generally available to community
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| − | *Curation will produce association files (connecting terms to genes)
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| − | *Association files in GAF format? (AMIGO-useable format)
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| − | | |
| − | | |
| − | WormBase Ontology Browser
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| − | *What are the specs/features we want for an ontology/DAG browser?
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| − | *Have we settled on AMIGO? Yes, pretty much
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| − | *Can it handle Phenotype ontology, etc. (non-GO ontologies)?
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| − | *AMIGO 2 is more pliable than older AMIGO for these types of ontologies
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| − | *AMIGO 2 Documentation already put together by AMIGO 2 developers;
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| − | *Raymond has been and will document WormBase specific integration efforts
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| − | *Intermine doesn't have an ontology browser functionality
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| − | *Write grant?
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| − | *National Center for Biomedical Ontologies: do they have a preferred web app/display?
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| − | *Querying ontologies with integrated annotation/association data (e.g.), not available
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| − | *Can AMIGO 2 query information across multiple ontologies (DO, GO, WPO, etc.)? Don't know yet, but would be useful
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| − | *Term-enrichment functionality? Not currently available through AMIGO
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| − | | |
| − | | |
| − | Transposons
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| − | *Paul Davis, Juancarlos, Kimberly have uploaded ~300 transposon genes
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| − | *Each has ~2 line description
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| − | | |
| − | | |
| − | Brugia Concise Descriptions
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| − | *What kind of information could we use for scripted descriptions?
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| − | *Collecting what type of info we have currently
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| − | | |
| − | | |
| − | Protein-2-GO
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| − | *Hopefully WormBase can integrate by early next year
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| − | | |
| − | | |
| − | CCC form 2.0
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| − | *Kimberly and Juancarlos have been working on
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| − | *Specs put together this week
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| − | *Form can communicate with Protein-2-GO
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| − | *Should have something next year
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| − | | |
| − | Nematode Textpresso
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| − | *Textpresso 2.5 vs 2.0 changes
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| − | *Free up disk space
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| − | *Will then move data over (from Brama) to Textpresso-Dev
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| − | *Should be done before SAB meeting
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| − | *Once public, we can ask other groups what types of ontologies would be helpful
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| − | | |
| − | | |
| − | GO-linking tool
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| − | *Figures are now linkable
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| − | | |
| − | | |
| − | Converting OBO files into ACE files
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| − | *Daniela will work with Juancarlos
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| − | | |
| − | | |
| − | Curation Status Form
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| − | *Almost ready to be live on Tazendra
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| − | *Need to check the newest SVM results on *.main vs *.concat
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| − | *Documentation on Wiki: http://wiki.wormbase.org/index.php/New_2012_Curation_Status
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| − | *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
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| − | *We need to discuss consolidation/coordination of functionality across the various CGIs
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| − | | |
| − | | |
| − | Allele curation
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| − | *Curation prioritization: Genes that haven't been described (e.g. no phenotype)
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| − | *Exclude large-scale results?
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| − | *RNAi results? Ignore, consider, compare?
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| − | *Null alleles (or putative nulls) are important
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| − | | |
| − | | |
| − | Legacy alleles
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| − | *Karen transferring descriptions from C. elegans I, II, into database
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| − | *Down to ~430 legacy alleles in queue
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| − | *Community/expert input on reference alleles, etc.
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| − | *Still missing some info as it doesn't fit in data model
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| − | *Concise descriptions of alleles/variations? Scripted to pull some standard info
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| − | *Allelic series info has been going into Remark, although maybe not optimal (series of phenotypes?)
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| − | | |
| − | | |
| − | Parasitic Strains from Peter Hunt
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| − | *Karen put info in for parasitic nematode strains
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| − | *Incorporating drug-resistance/sensitivity effects on different parasite strains
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| − | *Phenotype: drug resistance ; cross-referenced to drug name (or drug class name) via chemical ontology
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| − | *Chemical classes; chemical SLIM ontology terms
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| − | | |
| − | | |
| − | Molecule Site-of-Action
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| − | *Currently, site-of-action data restricted to genes
| |
| − | *Calcium ion (molecule) site of action data came in through Author First Pass
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| − | *How to curate without major model revisions?
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| − | *Static WormBase page? Uncuratable, yet interesting data?
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| − | *Uncuratable class?
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| − | *Site-of-action tag for molecule class/model?
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| − | *Process page info?
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| − | | |
| − | | |
| − | Phenotype-enrichment
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| − | *Information richness/quality when calculating enrichment of GO or Phenotype terms
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| − | *Disregard/de-emphasize low-resolution terms? E.g. lethality, growth, sick, etc.
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| − | *What is informative?
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