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