WormBase-Caltech Weekly Calls September 2016

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September 1, 2016

Working group discussions

  • More clear about issues surrounding orthology sets
  • ZFIN has protein curation that may be becoming a bit out of date

Single-cell RNA profiling

  • We've been curating some data, but not clear how to display the data
  • Some data sets, like tiling arrays, might conclude genes that are expressed in a cell/tissue
  • Genes that are detected at convincing levels (present call) in cell/tissue
  • Should we display expression data that we do not (or cannot) update differently from other data
  • Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not
  • Could capture quantitative assessments; transcripts per million, etc.
  • Should we provide an analysis of raw data to users to perform their own comparative analyses
  • Bob Goldstein's group prepared software tools in their paper; could we make use of them?
  • Big question: how do we handle divergent (expression) data?
  • David (Angeles) working on an expression data analysis pipeline
  • Single-cell RNA-Seq data: should it be merged with expression pattern data? Ideally, yes
  • There's difficulty in reconciling small and large datasets (or different data types)
  • Would we want to apply some type of weighting to each type of evidence for a gene-anatomy association, for example
  • In general for expression, it would be great to consolidate data to directly connect genes to anatomy/life stage

September 8, 2016

TransgeneOme import (Daniela)

  • adding a Community_curator tag or Curator tag in the Expression model to acknowledge the community curators that annotated/will annotate the data.
  • for the records- documentation on the import here: http://wiki.wormbase.org/index.php/TransgeneOme_import
  • Daniela and Juancarlos worked on parsing large JSON import
  • Data is dynamic: people can add images and annotations; will be updated every WormBase release
  • Do we want to import the person that created the annotation via the TransgeneOme project?
    • Maybe, but should be free text instead of a modeled tag for WBPersons (Raymond)
    • It is likely sufficient to point WB users to the TransgeneOme annotation, without explicitly referencing the contributor

Phenotype assay model proposal (Chris)

  • Trying to create a model that can accommodate complex genotypes and make querying phenotype experimental data easier
  • Want to co-opt an existing, unused model ?Phenotype_assay to encapsulate details of an experiment
  • Proposal is to pull several tags from ?RNAi and #Phenotype_info into the ?Phenotype_assay class
  • Remaining tags in ?RNAi could be used to hold RNAi mapping information
  • Remaining rags in #Phenotype_info can be used to describe the nature of an allele in the context of a phenotype, or nature of phenotype (Ease of scoring)
  • Maybe should keep penetrance, quality and EQ annotations in #Phenotype_info so as to provide detail for each phenotype when multiple phenotypes are used
  • It is currently difficult to recreate a phenotype annotation made by a curator using the OA, as so much experimental detail is captured exclusively in the hash

September 15, 2016

Strain curation with disease

  • People create transgenic strains for modeling human disease
  • We currently only curate strains in CGC (where we get our strain list)
  • Other strains have been added via direct communication with Mary Ann
  • Ranjana would like to capture strains affecting human disease from the literature
  • Many strains not available in WormBase
  • Is it worth curating these other strains? Yes; one concern that we would be diluting the quality of existing strains
  • Big concern is whether or not the strain(s) are available
  • (Raymond) Two aspects of strain curation: 1) strains that are available (e.g. from CGC) 2) carrier of genotype to use for other curation (like disease)
  • (Raymond) We could just capture genotype as free text
  • Would be best to curate the strains, regardless of availability
  • Ranjana will send some example papers/strains to Mary Ann and they will discuss
  • We could create links from strains in WB to the CGC (or state that people should write directly to the source lab; might be problematic).

WormBase header changes

  • Miyuki has been working on new WormBase header; requests feedback
  • Available on staging

Tissue enrichment analysis

  • Tool is live and ready to use
  • Raymond has added a link to the tool on the Tools page
  • Raymond will submit a ticket to put on the main Tools dropdown

September 22, 2016

GOC meeting at USC, November 4-6, Noctua Workshop, November 7

  • Next GO Consortium meeting is in early November at USC
  • The consortium meeting will run from Friday, 11/4 - Sunday, 11/6
  • Noctua/LEGO workshop will be on Monday, 11/7 (9am - 3pm)
  • Meeting Logistics Page
    • We will need to add all WB curators to the attendees table
  • Meeting Agenda - in progress
  • People interested in going to the consortium meeting or the workshop should register or let Kimberly know
  • Kimberly can setup accounts for people to try Noctua trial curation

Display of top community curators

  • Sibyl has setup a widget for the homepage and submit data page displaying top 20 community curators
  • Chris has compiled numbers from phenotype community annotations
  • We want to gather community annotations from other forms as well (historically and from newer forms)

Intellectual Lineage

  • Will display on person page
  • There exist "unknown" relationships; can we update those to known relationships?
  • We can email both parties of each unknown relationship asking about the nature of the relationship

Gene Ontology development

  • There may be a need for an additional ontology developer/editor
  • There's an accumulation of GitHub tickets requesting new terms/edits
  • It's not clear how the ontology will evolve in light of LEGO curation

Tables in PDF

  • Some tables have been converted from Excel to PDF
  • PDF tables are difficult to parse
  • We can/should ask authors for original Excel spreadhseet

Metabolomics efforts

  • PIs working on grants to study metabolomics in accumulated mutation lines
  • Want to contribute data to WormCyc
  • BioCyc doesn't use same standard vocabularies that WormBase does (e.g. ChEBI)

AGR Portal use cases

  • Working group had started working on a gene page, but have made a new use case for general search
  • The draft use case would describe searching with general text to find matches to genes, diseases, GO terms, and orthology groups
  • Next will try to work out a use case for arriving at a gene comparison page, e.g. starting with a human gene
  • Would probably be good to break into smaller groups of 2-3 people to independently work on different use cases
  • Starting simple is good, even if the added value isn't immediately clear

September 29, 2016

AGR Portal Use Case update

  • Use case working group now working on a gene/gene-product comparison page for all genes in an orthology group/PANTHER family or subfamily
  • Plan is to display information for genes side-by-side for each data type
  • First data types would include gene descriptions, gene ontology annotations, and disease associations
  • For GO terms many would like to see the "ribbon" display with GO slim terms or context-specific terms
  • Would be good if ribbon content was dynamically generated (rather than a predetermined set of terms), to reflect the nature of genes in an orthology group
  • Could be useful to use SObA logic in selecting terms to show in ribbon
  • Would be nice to display the genes according to species or listed by their relationships within a phylogenetic tree, for each data type
  • Highlighting commonalities between genes in the group would be nice

Intellectual lineage display

  • Juancarlos working on display of the lineage on WBPerson pages in a widget
  • Data will be pulled from ACEDB and used to generate display
  • Performing necessary calculations was crashing the machine
  • Want to scale the display based on number of connections

Changes to Disease Term OA

  • This OA will be used when information about the disease model cannot be curated to a C. elegans gene, e.g. when a human gene was put into the worm.
  • Changes incorporate information for strains, genotypes, treatments like drugs etc.
  • There's still a question about how to encapsulate the information from a single annotation
  • Separate annotations will be made if a second paper uses the same disease model (described in the paper being curated) and adds a treatment to it to show amelioration or exacerbation of disease; separate annotation means a different row with a different PGID in the OA.
  • Modeling can be done once more trial curation is done, some AGR modeling decisions to be made
  • Could curate and store data in OA for now, holding it until we have an appropriate data model and display pipeline
  • Want to capture strain, drug treatment, conditions, etc.
  • How do we connect disease-relevant genetic interactions to the disease or disease models?
  • Disease group working out standards for disease model curation
  • Ranjana will email interaction curators when she needs to, in these cases


  • Can we annotate details of experiment in Noctua? It's not clear
  • Noctua has predominantly been used in the context of GO annotations
  • Kimberly happy to demo Noctua in group meeting or individual Skype session