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| − | == July 9, 2015 ==
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| − | === Expression Pattern ===
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| − | * Certain/uncertain qualifiers not annotated before some date
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| − | * ~3,000 ?Expr_pattern objects without that annotation/tag
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| − | * Daniela work on bringing up to date, hopefully won't take long
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| − |
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| − | === Expression Clusters to Anatomy & Life Stage annotations ===
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| − | * Many large scale datasets with tissue-specific expression data
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| − | * Much of what is in SPELL is not annotated to ?Anatomy or ?Life_stage terms
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| − | * A goal: make expression data queryable via ?Anatomy terms/pages
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| − | * Wen will make the model change proposal
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| − | * We may not want to show explicitly in widget
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| − | * There is a need for a condensed display of expression data (per gene)
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| − | * Some datasets, like the EPIC data, explicitly mention each embryonic cell name
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| − | * Need for a condensed ontology browser per gene/anatomy and gene/life stage
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| − |
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| − | === Proteomic analysis ===
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| − | * Encyclopedia of Proteomic Dynamics, contacted Wen to share data
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| − | * Wen will meet/discuss with group soon to determine what the goals are
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| − | * It isn't clear what format the data has
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| − | * Should include Gary Williams on discussions as he already processes Mass Spectrometry data
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| − |
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| − | === External Databases ===
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| − | * To what extent can we take care of the data and display of other lab/publication databases
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| − | * Many authors want to share and make links to their database/website via WormBase
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| − | * What is the best way to handle large scale dataset sharing requests that don't necessarily (for the time being) fit our data model
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| − | * We can take advantage of the "External Links" display on WBPaper pages to link out the the external databases affiliated with the paper, including a link to our FTP site with shared data files, maybe?
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| − | * At least a stop gap measure until we can properly model the data
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| − |
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| − | === Cis-regulatory site nomenclature? ===
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| − | * Barbara Meyer's lab published many "rex" (Recruitment Elements on X) sites, numbered sequentially
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| − | * Tim Schedl wondering about others' thoughts/opinions on how to, possibly, standardize the names of cis-regulatory elements
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| − | * Could be like gene names, without dash, e.g. "rex1", "rex2"
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| − | * We may want to try "WBsf-" prefix, on all element names like "WBsf-rex1", although may be only used in-house
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| − |
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| − | === Phenotypes ===
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| − | * Were there any conclusions about phenotype lookup from the Allele-Phenotype form?
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| − | * Chris spoke with Harald Hutter and others at the meeting about how to improve the lookup for phenotypes
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| − | * Would be good to provide an explicit option to see phenotypes of related (or allele-affiliated) genes, perhaps by shared GO-term annotation
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| − | * Need to think more on how to best compress display of phenotypes on gene pages as well
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| − | * We do already provide links to the Variation and Gene pages (with Phenotypes displayed) in the term information box of the form
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| − |
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| − |
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| − | == July 16, 2015 ==
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| − | === Anatomy term page expression ===
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| − | * Raymond and Juancarlos are working on a display of genes that may be exclusively expressed in that anatomy object
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| − |
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| − | === Construct/Transgene curation ===
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| − | * Karen trying to make the curation of constructs & transgenes easier
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| − | * May consider merging the transgene and construct OA's
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| − | * Possibly add a construct/transgene request functionality in other OA's
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| − | ** Would those need multiple input fields?
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| − | ** Karen would take care of the details
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| − |
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| − | === Molecule model ===
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| − | * Exogenous/endogenous tags issue
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| − | * Scraping data from external chemical databases versus adding biologically relevant data from papers
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| − | * We pull data from, e.g. CHEBI, but not all molecules fall under their purview, e.g. proteins
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| − |
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| − | === Micropublication ===
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| − | * Promotion and outreach
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| − | * Micropublications discoverable in PubMed?
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| − | * Publisher = WormBase? Caltech?
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| − | * Minimal standards for publication?
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| − |
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| − |
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| − | == July 23, 2015 ==
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| − | === Worm model for autism ===
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| − | * Would want to take human variations implicated in autism; look for orthologous genes in C. elegans/nematodes and find/make synonymous mutations
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| − | * Prioritize based on worm phenotypes
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| − | * Generally applies to human disease variants
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| − |
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| − | === Database Migration ===
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| − | * Thomas Down leaving WormBase in September
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| − | * Moving ahead with Datomic
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| − | * Good starting use-case for Datomic is querying Datomic-version of GeneACE
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| − | * Need to make sure documentation for migration to Datomic is available and comprehensible
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| − | * Point-people at each site: Sibyl @ OICR, Juancarlos @ Caltech
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| − | * Now need to work out the mechanics of curating into Datomic
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| − |
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| − | === WormBase ParaSite ===
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| − | * Reciprocal searches (WB <-> PS) are working well
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| − |
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| − | === Microarray datasets & modSeek ===
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| − | * Some earlier datasets were re-processed (log-transformed, or re-annotated into original replicates instead of averaged results)
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| − | * Need to try out different methods of processing raw-data (WB usually only takes in processed data)
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| − | * One pipeline can feed data into SPELL and modSeek
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| − | * It's difficult to establish/determine gold standards for assessing process performance
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| − |
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| − | === WormBook chapter reviewers ===
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| − | * Send reviewer suggestions to Paul ASAP
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| − |
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| − | === C. elegans proteome in UniProt ===
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| − | * Not a complete correspondence between WormBase and UniProt
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| − | * Cases: UniProt has entry for a protein that differs by one or two amino acids from WormBase
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| − | ** Made from translations of what cDNAs etc. have been submitted
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| − | ** Partial data, e.g. partial cDNAs translated
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| − | * Anything we can do to achieve greater consistency?
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| − | * Protein data sets are important
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| − | * Hinxton can use disrepancies as a flag to check on the gene/protein models
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| − | * Would be good to have more reciprocal linkage between UniProt and WormBase
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| − | * AVR-15, UniProt have two additional entries compared to Wormbase, differing in only 1 or 2 amino acids
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| − | * Should we pick up different entries from UniProt and store/display the data; how to reconcile?
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| − | * Possible use case: enter a UniProt ID into the BLAST/BLAT tool to identify WormBase matches
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| − |
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| − | === Gene Orienteer Data ===
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| − | * Sibyl and Xiaodong looking at data and scripts from Gene Orienteer
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| − |
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| − | === Precanned queries for exclusive expression ===
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| − | * Raymond & Juancarlos working on final details
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| − | * Intent is to display genes that may be specifically/exclusively expressed in e.g. an anatomy term
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| − |
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| − | === Embryonic developmental timing ===
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| − | * Sulston, Murray timing data sets for wild type embryonic cell division timing
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| − | * Mutant data sets are coming in as well
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| − |
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| − | === Genetic Interaction Ontology (GIO) ===
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| − | * Latest version of the GIO complete
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| − | * Juancarlos and Chris built a "genetic interaction calculator" to determine interaction types from quantitative phenotype inequalities
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| − | ** http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/gi_calculator.cgi
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| − | * Sending out to other MODs, etc.
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| − | * Seems that although there is buy in conceptually, most curators can't afford the time for such detailed curation
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| − |
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| − | === Phenotype (ontology) display ===
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| − | * Problems with display of phenotypes (and other annotations) on WormBase, as pointed out by several people at the IWM
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| − | * Karen would like to start creating allele concise descriptions
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| − | * We need compact, intelligently ordered annotation lists, not just alphabetical lists of ontology annotations
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| − | * It would be good to show ancestors for relatedness and order
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| − | * Chris working on Python script to display all annotations in the context of the entire ontology
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| − | * We will need to see if this approach is feasible/beneficial
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| − |
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| − | === PATO-style EQ (Entitiy-Quality) phenotype annotations ===
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| − | * It is clear that some phenotype annotations require details, e.g. "drug sensitivity" annotations should have the drug involved
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| − | ** This drug/molecule annotation should be present in the details if not directly in the term itself
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| − | * Raises the issue of a number of cases where we need PATO-style EQ annotations, not just explicit phenotype terms for all possible scenarios
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| − | * This would be helpful in annotating embryonic timing and identity phenotype datasets
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| − |
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| − |
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| − | == July 30, 2015 ==
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| − |
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| − | === Wen Chen helped Wen Chen ===
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| − | * Wen Chen (lab) has list of genes to analyze
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| − | * Wen Chen (WB) helped process the list
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| − | * Would be good to have a simple CGI to process a list of genes in a variety of ways
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| − | ** http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/fraqmine.cgi
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| − | ** For GeneTissueLifeStage and GeneConciseDescription more datatypes easily slotted in if curator makes a file
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| − | * Is this redundant with WormMine?
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| − | ** Not for data that doesn't exist (in WormMine) yet; more agile: could be up and running within a matter of days
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| − |
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| − | === Interconnections between WormBase and FlyBase ===
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| − | * We could create more inter-connectivity between the two databases
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| − | * Sharing concise descriptions of genes
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| − | * Would be good for FlyBase and WB curators (Xiaodong?) to talk about where the links should exist at each site
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| | == August 6, 2015 == | | == August 6, 2015 == |
