WormBase-Caltech Weekly Calls
From WormBaseWiki
Contents
Previous Years
2017 Meetings
March 2, 2017
Expression Cluster SVM
- Started curating expression clusters in 2007
- Had been using text pattern match to identify expression cluster papers
- Now with more papers for positive and negative training set, shifting to SVM identification
- 540 positive papers, 900 negative papers for training
- Wen received first batch, roughly ~70% precision, possibly ~80-90% recall
- Wen reviewed papers from WormEXP (http://wormexp.zoologie.uni-kiel.de/wormexp/)
Karen's SBIR grant
- Looks like it will get funded
- Karen will need to become part time at WormBase (needs to be more than half time on SBIR)
- Paul put in a request for posting another curator position
- If anyone has ideas about a potential (part-time or full-time) curator, let Paul know
- Will need to consider re-allocation of curation responsibilities
- Molecule curation in maintenance mode, may require updating of mapping terms with our internal IDs
- Ranjana: want to incorporate molecules in disease curation for WB/AGR, can offer to take over maintenance
- Do other AGR members curate molecules? In some cases yes; don't capture metabolites
- Transgene curation could be distributed
- Karen will be working on more automated curation of transgenes from papers; maybe also for molecules
Metabolomics
- What would we like to see in WB for metabolomics?
- Marian Walhout lab created the WormFlux database (http://wormflux.umassmed.edu/)
- WB enzyme gene pages link out to respective gene pages on WormFlux
- How are enzymatic pathways represented in GO, or by phenotype info? What's the cross-talk?
Pathway representation
- What are the best ways to capture empirical evidence as support for pathway models?
- Want clear, granular evidence for each assertion in a model, but need to accommodate probabilistic statements
- How can micropublications be used to fill in the gaps?
SObA GO on human data
- What would be a good set of genes to test?
- If we omit IEAs (most from mouse), are we left with substantial data for human genes?
March 9, 2017
Expression widget via Datomic
- Sibyl is working on delivering the Expression widget from Datomic
- Issue with gene expression "mountain" data
- AcePerl script/query underlying the data, may be incorrect and needs an update
Human GO SObA graph
- Working SObA graph for human gene ontology data:
- Running off GOLR server for now
- Would be great to have a SObA widget on AGR portal
- Will need to get widgets working on AGR portal
- Will be good to have, for now, a stand alone version
AGR update
- SAB meeting on Tuesday (two days ago)
- Positive feedback
AGR database
- Although official database has not been chosen, most portal processes are running just on memory, need to start storing things in a database
- The database used may be the stepping stone for eventual database migration for AGR
AGR Curator calls
- Karen asking about purpose of curator calls going forward
- Have covered a good number of topics, a few still yet to be covered: synteny browser, person curation
- Possibly have discussions about the functions of different (and possibly new) working groups
- Can revisit curation procedures
- Should curator calls happen independently of AGR to share thoughts and methods about curation
Methods in Molecular Biology chapter update
- Have received drafts for most sections
- Working on making them consistent and making figures legible
March 16, 2017
Funding opportunities
- Could we focus on curation for disease genes and work with other groups?
- Maybe work with GO
- What diseases would rely more on worm research than others?
- Lots of disease models on neurodegeneration diseases testing herbal treatments and compounds to treat
- Parasitic nematode research? May not work out
- Really want to focus on what worm research informs about human disease
- What are the studies that focus on orthology to human disease genes?
- If some funding is cut, there will likely be refunding in a targeted manner (e.g. Alzheimer's research)
- Can we do Textpresso search for funding agencies?
- Much more funding is going to military research; could look at what could apply (Tropical diseases, responses to pathogen, etc.)
IWM swag
- Still have tattoos from last years TAGC meeting
- WormBase piggy bank?
Human GO SObA
- Server that Raymond used originally is not appropriate
- Will require some reworking of the backend code
- Might be ready after the Biocuration meeting
- Could use in AGR disease pages, showing enriched GO terms (from genes implicated in the disease)
- Could have (instead of enriched terms) a graph of all gene annotations merged
- What is a reasonably sized list of items to manage in the human mind? 7 +/- 3? 20?
- Can define a cutoff at which point using SObA is helpful
Micropublications
- Deadline for grant rebuttal?
- Organization name at IWM will be: Micropublication biology
- Each micropublication is intended as a curatable unit
- Shohei Mitani wants, for example, to submit 100 knockout phenotypes; should be 100 micropublications
- Tim concerned that 100 micropubs is too much, but that is probably OK
- Want to generate a "narrative" from multiple individual micropubs
- Can DOI's be part of another DOI? Are relationships between DOI's allowed?
AGR communication and data pipeline
- Discussion about number of calls and modes of communication
- There was concern about data pipeline demands becoming overwhelming, e.g. loading data for Intermine as well as AGR portal
- There are questions about which database will be used as an interim database, which could possibly become the standard database
- AGR members like the Datomic techonology, but are concerned about the non-open-source aspect
- Should we have an all-hands call once a month (or every two weeks) where working groups could present and discuss issues? Yes, Kimberly will email Stacia about this idea
- AGR PI's were in favor of having a technical meeting face-to-face; disease working group face-to-face meeting worked well
- There may be AGR working group meetings at Biocuration meeting
March 23, 2017
Biocuration meeting
- Mary Ann (or someone who is available) will present the micropublications poster
- Can share posters here: https://f1000research.com/channels/biocuration
Person curation AGR curator call
- Person curation is topic of next AGR curator call (April 12th)
- Cecilia can present on person curation (persons, paper-person connections)
- Karen can help
- Could discuss authors vs. persons in WormBase
- Chris can discuss experience with online chat service
Potential AGR all-hands call on April 5th
- Stacia Engel will let people know
- Would have short presentations from working groups
Karen part time as of April 1st
- Grant came through (congratulations!), so Karen will be part time as of Apr 1
- Someone should take over transgene and molecule curation
- Transgenes
- Relevant curators already have training on how to curate
- How much of these curation processes are on auto-pilot?
- CGC sends strain info (with trangenes) to Mary Ann
- Can we automate the transgene-strain connections coming from CGC?
- Mary Ann can take over manual transgene curation
- Could have summer student (undergard or high school) to help?
- Molecules
- Ranjana, Wen, & Chris can take over molecule curation
- Should we automate the dumping process? Wen will take over dumping the data
Micropublications
- Minipublication from Tim Schedl's lab
- Narrative of multiple micropublications
- Requesting a DOI for each individual data set
- Need a process to submit everything at once (through forms)
- Grad student submitting 2 allele-phenotypes and 2 expression patterns
- Working on grant rebuttal
- Need to demonstrate sustainability of micropublication process; persistence if funding goes away? how does the pipeline scale?
- How much will the data be used?
- What is the setup cost for Xenbase (or other database)? Setting up the forms initially, processing data and having reviewers longer term
- Request submitters to suggest reviewers; also have a pool of willing reviewers
- Submitters can be included in reviewer pool
March 30, 2017
Biocuration meeting
- Received good feedback from meeting
- Micropublication poster won poster prize (go Daniela!)
- Lots of precision medicine
- Great keynote talks
- Disease meeting at Biocuration meeting
- Discussed layout for gene report page for AGR 0.6
- Need to clarify association type
- Good feedback about automated decriptions talk
- SGD outreach (Kevin MacPherson)
- Systematically posting blogs posts and twitter
- Write articles
- Yeast research blog posts
- First of the month webinars
- For WormBase outreach, we could write articles, news & views
- Can post blogs about worm researcher's work
- Community write articles?
- Newsletter (used to send out hardcopies), bring back? People used to feel like it was spamming
- We can have Facebook page (Google + ?)
- We need public education, can/should be fun content
- Sarah Torres willing to post things on social media, but we need to send her the content
- Ask Barbara Perry about writing/editing some articles? Two person job, writing and editing
- Create content for lay public
- Random Twitter posts putting some people off
- Would be good to have someone tweeting hot topics from worm meetings
- Phenotypes
- From Melissa Haendel, try INCA(?) instead of using EQ/post-composed terms?
- Curating pratices; better (or more fun) than WormBase?
- PDF highlighting tools
Micropublications
- Grant review: Questions about sustainability, high throughput data, and how people will use the data
- Minipublications as small narratives
IWM
- Paul giving brief plenary talk about WormBase
- We could wear some identifiable WormBase gear
- Hats, ties, bowties, ascots, scarfs, t-shirts, ribbon?
Textpresso Central
- Ready for the public
- C. elegans corpus updated weekly
- "Data not shown" pipeline working for Daniela
