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| | [[WormBase-Caltech_Weekly_Calls_April_2016|April]] | | [[WormBase-Caltech_Weekly_Calls_April_2016|April]] |
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| | + | [[WormBase-Caltech_Weekly_Calls_May_2016|May]] |
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| − | == May 5, 2015 ==
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| | | | |
| − | === Tissue enrichment tool === | + | == June 2, 2016 == |
| − | * Some slight modifications have been made
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| − | * Raymond/Juancarlos request testing
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| − | * Made adjustments to gene name handling
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| − | * Tool could go live for the next release
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| − | * Data will remain frozen at WS252
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| | | | |
| − | === Gene summaries === | + | === Topic 1 === |
| − | * Paul asked Norbert about gene descriptions
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| − | * FB has been getting good community response for contributing gene descriptions
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| − | * Automation still sounds like the right way to go
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| − | * Ranjana will look at summaries at other MOD sites
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| − | | |
| − | === Phenotype display ===
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| − | * MGI/MGD had a graph display of phenotype ontology (Paul S.)
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| − | * Made phenotype ontology slim for the summary heatmaps
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| − | * How do all of the MODs display phenotypes?
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| − | | |
| − | === Progress reports ===
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| − | * Curators can write a paragraph on innovation
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| − | ** Community curation (report numbers)
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| − | ** WOBr
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| − | ** SObA
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| − | ** Automated descriptions
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| − | ** Micropublications
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| − | | |
| − | === Curation pipeline comparisons ===
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| − | * Would be nice to compare how MODs prioritize curation, triage papers, etc.
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| − | * How many MODs curate paper-by-paper (for all datatypes at once) vs. our method, by datatype?
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| − | ** WB & MGI curate by datatype, most others by paper (for all datatypes)
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| − | * How are all MODs doing in terms of paper coverage?
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| − | ** Do we need more manual effort, more automation? How much, given cost of each?
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| − | | |
| − | === SPELL ===
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| − | * SGD uses SPELL but does not develop
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| − | | |
| − | | |
| − | == May 12, 2016 ==
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| − | | |
| − | ===Communication tools for umod teams===
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| − | *Mike Cherry set up Stanford umod-project- email lists for the different umod groups, PIs, software developers, and curators
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| − | **umod-project-curation@lists.stanford.edu
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| − | **https://mailman.stanford.edu/mailman/listinfo/umod-project-curation
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| − | **note: if you signup for a digest, you will receive e-mails from the list on a different time scale than people who didn't choose 'digest'
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| − | *Slack is back, download the app and look umod-project. You can also visit https://umod-project.slack.com/.
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| − | **Browse the channels and join the ones that you want.
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| − | **Create any new channel, it seems there is no limit to the channels that can be created.
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| − | *Suzi Lewis will be setting up a github account for project tracking and wiki pages
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| − | | |
| − | === Human Disease working group meeting ===
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| − | * Next Monday and Tuesday, in Kerckhoff 024
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| − | * Curators will review data models for human disease at each site
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| − | * Brainstorming session for future plans
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| − | * Possibility of molecule-disease interactions ("exacerbated by", "ameliorated by")
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| − | | |
| − | === Metabolomics ===
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| − | * Wen came across metabolic profiling papers while looking for proteomics papers
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| − | * Wen will send to Karen, who is managing metabolites as part of molecule class
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| − | * BIGG database, a new metabolite database (http://bigg.ucsd.edu/)
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| − | | |
| − | === Progress Report ===
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| − | * Send Paul progress report blurbs in next week (by Thursday)
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| − | | |
| − | === Cross MOD call ===
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| − | * Reviewed FlyBase and Rat Genome Database this week
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| − | * Will review SGD and MGI next week
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| − | * Suzi Lewis asking about Intermine instances; what can Mine do that the Base cannot, and vice versa?
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| − | * Other MODs have more fully functional and fully populated InterMine instances
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| − | * Agenda and Minutes: http://bit.ly/1NXuBVD
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| − | * Schedule and Topic signup: http://bit.ly/243UNL2
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| − | | |
| − | === FraqMine/SimpleMine ===
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| − | * http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/fraqmine.cgi
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| − | * We want to make the tool available to users, maybe under Tools menu
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| − | * Will need to discuss with Todd (Paul sending email)
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| − | | |
| − | === Micropublications ===
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| − | *BioCADDIE developers are currently working on indexing datasets requested by the NIH for inclusion in a June 30 Prototype test. After then they will reach out to us to look into the WormData (micropublication) indexing.
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| − | | |
| − | | |
| − | == May 19, 2016 ==
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| − | | |
| − | === Dead genes in FraqMine? ===
| |
| − | * User asked for gene IDs for dead genes from list of sequence IDs
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| − | * FraqMine/SimpleMine does not currently accept/return dead genes
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| − | * Juancarlos will make changes to script to add an additional column indicating that a gene is dead, after Wen changes the source files to include the data
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| − | | |
| − | === Community curation request delay ===
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| − | * Currently we wait 3 months before sending additonal community curation requests to authors
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| − | * Considering making delay only 1 month or less; opinions?
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| − | * Most annotations come within a week of a request
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| − | * One month is probably good
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| − | * Should we send list of alleles to lab heads with annotated phenotypes?
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| − | * Show community curated alleles/annotations on WB homepage?
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| − | * Show top 20 community curators on WB homepages?
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| − | * Make use of the "Activity" widget on homepage? Replace random page with community contributions?
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| − | | |
| − | === Citace upload ===
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| − | * June 28th, 10am
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| − | | |
| − | === uMOD Phenotype call ===
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| − | * Today 11am Pacific
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| − | * Join BlueJeans call: https://bluejeans.com/626771895
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| − | * To be discussed at NHGRI meeting next Monday & Tuesday
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| − | | |
| − | === Distinctions between Human Disease curation and Phenotype curation? ===
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| − | * WB and other MODs have been curating phenotype and human disease separately
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| − | * Some consider phenotypes and disease as the same (Monarch perspective)
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| − | * We should consider the extent to which these overlap and are distinct
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| − | | |
| − | === Human Disease meeting ===
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| − | * People are looking for commonalities
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| − | * Disease Ontology is a good starting point of commonality
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| − | * Agreement to curate experimental models
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| − | * UMOD Disease portal: search for a gene and get links to each individual MOD
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| − | * DBs should serve a disease data file
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| − | ** WB has gene-disease association file
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| − | * Sources of disease files: OMIM, Medic(?), etc.
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| − | * MIM-to-gene file
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| − | * Query tools: what should they look like? What kind of results?
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| − | ** Simple table views as results
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| − | * UMOD disease detail report page ideas
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| − | * Want to consider relations to molecules/chemicals ("modifiers")
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| − | ** Exacerbates, ameliorates, is a therapeutic for
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| − | * Drug-induced models
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| − | * Disease strains/genotypes, how to handle
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| − | * Should disease curation expand to capturing alleles/genotypes/strains?
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| − | ** We can, going forward
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| − | | |
| − | === Objectifying Genotypes ===
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| − | * Increasingly, we are encountering needs to objectify genotypes
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| − | * We have strain objects, although strains are not always specified in papers
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| − | * We could potentially create strain objects that are named according to a paper ID
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| − | * This would enable us to capture certain phenotype and genetic interaction annotations
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| − | * We need to consider a strain's phenotype in relation to a control strain
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| − | * We already annotate phenotypes to transgenes while specifying the gene (in the transgene) that causes the phenotype
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| − | * It will be good for WB cuartors to hear from other MODs about how they handle this
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| − | * We can reconvene after today's phenotype call and focus on this discussion for future cross-MOD calls
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| − | * Created a wiki page for the in-house discussion, will bring in other mods once we have a clear understanding of what we want to do and what we need
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| − | | |
| − | | |
| − | == May 26, 2016 ==
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| − | | |
| − | === Gene Name Changes widget on WB homepage ===
| |
| − | * Should go live for WS253 (this weekend)
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| − | * Will display changes to gene names
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| − | * Will make a blog post to announce
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| − | | |
| − | === UMOD call next week: Phenotype curation ===
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| − | * Will discuss data associations made at each MOD
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| − | * Will discuss genetic entities annotated with phenotypes (genotypes, alleles, RNAi reagents)
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| − | * Will discuss use of phenotype ontologies vs. entity-quality PATO annotations
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| − | * Should consider/dicsuss environment/condition
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| − | * Chris will contact other presenters with topic guide
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| − | | |
| − | === UMOD weekly curator call ===
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| − | * Could be a forum for summarizing working group discussions
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| − | | |
| − | === Biological Ontologies & BioCreative meeting ===
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| − | * http://icbo.cgrb.oregonstate.edu/
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| − | * August 1-4, 2016
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| − | * Oregon State University
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| − | * Chris Mungall will give tutorial on ontology development
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| − | * Raymond has been in contact with Chris about cell ontology
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| − | * Raymond has been trying to "owl-ize" the anatomy ontology
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| − | * We could gain advantages by using OWL format for our ontologies
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| − | * We want to understand OWL and Protege
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| − | * We'll want to create a UMOD ontology working group
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| − | | |
| − | === TAGC coloring book ===
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| − | * Have worm facts incorporated
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| − | * Need to include rat info
| |
| − | * Cost depends on publisher
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| − | * Up to 30 pages, currently
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| − | * Including data for 7 MODs
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| − | | |
| − | === NHGRI meeting ===
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| − | * NIH people are happy about UMOD collaboration
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| − | * Question: what are we NOT going to do?
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| − | * What needs fundraising? e.g. neural circuits, metabolite curation
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| − | * Short term: create working groups and discuss
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| − | * Micropublications, GSA pipeline, author interactions/community annotation, toxicology; new ventures to think about as UMOD
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| − | * WB curators can develop it and then share with others
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| − | * Do MODs curate from bio-archives (preprints)? No, only peer-reviewed articles
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| − | | |
| − | === Micropublications ===
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| − | * BioCaddie trying to develop new DataMed, data indexing
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| − | * Micropublications could be indexed by DataMed and/or PubMed
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| − | * What are requirements for PubMed? Need to collect some minimum number of publications (~50-100?) intitally
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| − | * Indexing by Google Scholar?
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| − | * 3-year projection; where do we want it to be?
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| − | | |
| − | === Curation methods ===
| |
| − | * How to various MODs curate? by paper vs. by datatype?
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| − | * Will we need to move to a paper-by-paper curation approach? Not necessarily
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| − | * What is the curation tool of the future? Needs to be flexible
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| − | * How many core yet independent databases will be in use?
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| − | * Over time we may migrate over to some other system
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| − | | |
| − | === WS253 in Datomic ===
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| − | * Datomic query tool available
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