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| | [[WormBase-Caltech_Weekly_Calls_August_2016|August]] | | [[WormBase-Caltech_Weekly_Calls_August_2016|August]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_September_2016|September]] |
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| − | == September 1, 2016 ==
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| − | === Working group discussions === | + | == October 6, 2016 == |
| − | * More clear about issues surrounding orthology sets
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| − | * ZFIN has protein curation that may be becoming a bit out of date
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| − | | |
| − | === Single-cell RNA profiling ===
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| − | * We've been curating some data, but not clear how to display the data
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| − | * Some data sets, like tiling arrays, might conclude genes that are expressed in a cell/tissue
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| − | * Genes that are detected at convincing levels (present call) in cell/tissue
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| − | * Should we display expression data that we do not (or cannot) update differently from other data
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| − | * Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not
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| − | * Could capture quantitative assessments; transcripts per million, etc.
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| − | * Should we provide an analysis of raw data to users to perform their own comparative analyses
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| − | * Bob Goldstein's group prepared software tools in their paper; could we make use of them?
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| − | * Big question: how do we handle divergent (expression) data?
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| − | * David (Angeles) working on an expression data analysis pipeline
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| − | * Single-cell RNA-Seq data: should it be merged with expression pattern data? Ideally, yes
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| − | * There's difficulty in reconciling small and large datasets (or different data types)
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| − | * Would we want to apply some type of weighting to each type of evidence for a gene-anatomy association, for example
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| − | * In general for expression, it would be great to consolidate data to directly connect genes to anatomy/life stage
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| − | | |
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| − | == September 8, 2016 ==
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| − | | |
| − | === TransgeneOme import (Daniela) ===
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| − | * adding a Community_curator tag or Curator tag in the Expression model to acknowledge the community curators that annotated/will annotate the data.
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| − | * for the records- documentation on the import here: http://wiki.wormbase.org/index.php/TransgeneOme_import
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| − | * Daniela and Juancarlos worked on parsing large JSON import
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| − | * Data is dynamic: people can add images and annotations; will be updated every WormBase release
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| − | * Do we want to import the person that created the annotation via the TransgeneOme project?
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| − | ** Maybe, but should be free text instead of a modeled tag for WBPersons (Raymond)
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| − | ** It is likely sufficient to point WB users to the TransgeneOme annotation, without explicitly referencing the contributor
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| − | | |
| − | === Phenotype assay model proposal (Chris) ===
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| − | * Trying to create a model that can accommodate complex genotypes and make querying phenotype experimental data easier
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| − | * Want to co-opt an existing, unused model ?Phenotype_assay to encapsulate details of an experiment
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| − | * Proposal is to pull several tags from ?RNAi and #Phenotype_info into the ?Phenotype_assay class
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| − | * Remaining tags in ?RNAi could be used to hold RNAi mapping information
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| − | * 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)
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| − | * Maybe should keep penetrance, quality and EQ annotations in #Phenotype_info so as to provide detail for each phenotype when multiple phenotypes are used
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| − | * 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
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| − | | |
| − | | |
| − | == September 15, 2016 ==
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| − | | |
| − | === Strain curation with disease ===
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| − | * People create transgenic strains for modeling human disease
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| − | * We currently only curate strains in CGC (where we get our strain list)
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| − | * Other strains have been added via direct communication with Mary Ann
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| − | * Ranjana would like to capture strains affecting human disease from the literature
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| − | * Many strains not available in WormBase
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| − | * Is it worth curating these other strains? Yes; one concern that we would be diluting the quality of existing strains
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| − | * Big concern is whether or not the strain(s) are available
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| − | * (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)
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| − | * (Raymond) We could just capture genotype as free text
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| − | * Would be best to curate the strains, regardless of availability
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| − | * Ranjana will send some example papers/strains to Mary Ann and they will discuss
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| − | * 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).
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| − | | |
| − | === WormBase header changes ===
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| − | * Miyuki has been working on new WormBase header; requests feedback
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| − | * Available on staging
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| − | | |
| − | === Tissue enrichment analysis ===
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| − | * Tool is live and ready to use
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| − | * Raymond has added a link to the tool on the Tools page
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| − | * Raymond will submit a ticket to put on the main Tools dropdown
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| − | | |
| − | | |
| − | == September 22, 2016 ==
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| − | | |
| − | === GOC meeting at USC, November 4-6, Noctua Workshop, November 7 ===
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| − | *Next GO Consortium meeting is in early November at USC
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| − | *The consortium meeting will run from Friday, 11/4 - Sunday, 11/6
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| − | *Noctua/LEGO workshop will be on Monday, 11/7 (9am - 3pm)
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| − | *[http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Logistics Meeting Logistics Page]
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| − | **We will need to add all WB curators to the attendees table
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| − | *[http://wiki.geneontology.org/index.php/2016_Los_Angeles_GOC_Meeting_Agenda Meeting Agenda - in progress]
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| − | * People interested in going to the consortium meeting or the workshop should register or let Kimberly know
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| − | * Kimberly can setup accounts for people to try Noctua trial curation
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| − | | |
| − | === Display of top community curators ===
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| − | * Sibyl has setup a widget for the homepage and submit data page displaying top 20 community curators
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| − | * Chris has compiled numbers from phenotype community annotations
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| − | * We want to gather community annotations from other forms as well (historically and from newer forms)
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| − | | |
| − | === Intellectual Lineage ===
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| − | * Will display on person page
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| − | * There exist "unknown" relationships; can we update those to known relationships?
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| − | * We can email both parties of each unknown relationship asking about the nature of the relationship
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| − | | |
| − | === Gene Ontology development ===
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| − | * There may be a need for an additional ontology developer/editor
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| − | * There's an accumulation of GitHub tickets requesting new terms/edits
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| − | * It's not clear how the ontology will evolve in light of LEGO curation
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| − | | |
| − | === Tables in PDF ===
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| − | * Some tables have been converted from Excel to PDF
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| − | * PDF tables are difficult to parse
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| − | * We can/should ask authors for original Excel spreadhseet
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| − | | |
| − | === Metabolomics efforts ===
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| − | * PIs working on grants to study metabolomics in accumulated mutation lines
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| − | * Want to contribute data to WormCyc
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| − | * BioCyc doesn't use same standard vocabularies that WormBase does (e.g. ChEBI)
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| − | | |
| − | === AGR Portal use cases ===
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| − | * Working group had started working on a gene page, but have made a new use case for general search
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| − | * The draft use case would describe searching with general text to find matches to genes, diseases, GO terms, and orthology groups
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| − | * Next will try to work out a use case for arriving at a gene comparison page, e.g. starting with a human gene
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| − | * Would probably be good to break into smaller groups of 2-3 people to independently work on different use cases
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| − | * Starting simple is good, even if the added value isn't immediately clear
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| − | | |
| − | | |
| − | == September 29, 2016 ==
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| − | | |
| − | === AGR Portal Use Case update ===
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| − | * Use case working group now working on a gene/gene-product comparison page for all genes in an orthology group/PANTHER family or subfamily
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| − | * Plan is to display information for genes side-by-side for each data type
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| − | * First data types would include gene descriptions, gene ontology annotations, and disease associations
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| − | * For GO terms many would like to see the "ribbon" display with GO slim terms or context-specific terms
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| − | * 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
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| − | * Could be useful to use SObA logic in selecting terms to show in ribbon
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| − | * Would be nice to display the genes according to species or listed by their relationships within a phylogenetic tree, for each data type
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| − | * Highlighting commonalities between genes in the group would be nice
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| − | | |
| − | === Intellectual lineage display ===
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| − | * Juancarlos working on display of the lineage on WBPerson pages in a widget
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| − | * Data will be pulled from ACEDB and used to generate display
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| − | * Performing necessary calculations was crashing the machine
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| − | * Want to scale the display based on number of connections
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| − | | |
| − | === Changes to Disease Term OA ===
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| − | * 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.
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| − | * Changes incorporate information for strains, genotypes, treatments like drugs etc.
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| − | * There's still a question about how to encapsulate the information from a single annotation
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| − | * 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.
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| − | * Modeling can be done once more trial curation is done, some AGR modeling decisions to be made
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| − | * Could curate and store data in OA for now, holding it until we have an appropriate data model and display pipeline
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| − | * Want to capture strain, drug treatment, conditions, etc.
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| − | * How do we connect disease-relevant genetic interactions to the disease or disease models?
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| − | * Disease group working out standards for disease model curation
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| − | * Ranjana will email interaction curators when she needs to, in these cases
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| − | | |
| − | === Noctua/LEGO ===
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| − | * Can we annotate details of experiment in Noctua? It's not clear
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| − | * Noctua has predominantly been used in the context of GO annotations
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| − | * Kimberly happy to demo Noctua in group meeting or individual Skype session
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