WormBase-Caltech Weekly Calls
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- 1 Previous Years
- 2 2019 Meetings
- 2.1 October 3, 2019
- 2.2 October 10, 2019
- 2.3 October 17, 2019
GoToMeeting link: https://www.gotomeet.me/wormbase1
October 3, 2019
SObA comparison graphs
- Raymond and Juancarlos have worked on a SObA-graph based comparison tool to compare two genes for ontology-based annotations
- Prototype 1
- Prototype 2
- What information does a user most care about?
- What terms (nodes) are annotated to gene 1 and what terms to gene 2
- For a given term, what is the relative number of annotations between gene 1 and gene 2.
- For a given node, what is the relative number of annotations each gene has to the total annotations of that gene.
- # 3 is actually what we applied to size the nodes in the single-gene version of SObA. Thus, not surprisingly, I think it is important.
- Generally people like Prototype 2 as a default view; we could possibly have a toggle to see the other view
- In either case users need a good legend and/or documentation
- Jae, it would be good if a user could specifically highlight nodes specific to each gene and gray-out or de-emphasize the common nodes
Germ line discussion
- Currently, the anatomy ontology has "germ line" as a type of "Cell" and a type of "Tissue", and "germ cell" as a type of "germ line"
- Chris would like to (1) remove "germ line" from under "Cell" and leave it under "Tissue" and (2) move "germ cell" out from under "germ line" and place directly under "Cell"
- Chris will update pull request to include a change to move "germline precursor cell" out from under "germ line" and place it under "Cell" (done)
Script to remove blank entries from Postgres
- Chris stumbled across several entries in the OA that were blank (empty strings) or consisted of only whitespace, some of which were causing errors upon upload to ACEDB
- Juancarlos has written a script to look for all such entries; 66 tables have them on sandbox (likely same on live OA)
- Does anyone object to removing these entries throughout Postgres?
- Juancarlos will remove all the empty fields identified by his script
October 10, 2019
- Held in Bar Harbor, Maine (organized by JAX, including MGI's Sue Bello and Cindy Smith)
- Dates: Sunday May 17th to Wednesday May 20th, 2020
- Will have 3rd POTATO workshop
- Meeting website
- Key Dates
- October 31, 2019 - Paper Submission Deadline
- January 24, 2020 - Abstract and Workshop Submission Deadline
- March 6, 2020 - Notification of Acceptance
- April 6, 2020 - Early Bird Registration Ends
- May 8, 2020 - Registration Deadline
- Academic ISB Member, early bird registration fee is $250
- Author First Pass form paper, submitting to Database, biocuration issue (managed by biocuration group); authors have an opportunity to present at Biocuration conference
- International Conference on Biomedical Ontologies
- Meeting website
- Held in Bozen-Bolzano, Italy
- 16 - 19 September 2020
SObA comparison tool
- Prototype #1 updated
Textpresso derived paper connections
- For example for strains and constructs, maybe anatomy terms?
- May want to flag Textpresso predictions (as opposed to manually connected)
- Couple of options:
- 1) At time of build, populate the papers (in ACEDB/Datomic) into a 'Putative_reference' tag and display in a distinct 'Putative references' widget
- 2) Not part of database build, but make associations live (using RESTful API to link out to Textpresso and submit search with URL) using Textpresso with links to Textpresso and Textpresso results, giving users chance to see context of matches in sentences at the Textpresso site
- A link to Textpresso could be done regardless of other approaches; low-hanging fruit?
- Do a diff so that Textpresso pulls up only additional papers (not already associated)?
- 3) Could populate WB page with connections made through a Textpresso API call (could cache results? maybe, but might as well choose 1st option?)
- Transgene pipeline:
- Arun wrote script, matching transgene names (using regex; Is and Si transgenes) to papers, automatically populate OA
- Another script, captures Ex transgenes as well, automatically connects to construct objects
- WB only displays verified papers; unverified (predicted) associations are not dumped
- Could integrate author verification as part of AFP pipeline, even for older papers? Would we want to re-request AFP results for authors that have already replied in the past? Probably not
- Could embed AFP predictions in WB display with link to AFP form for authors (and others?) to verify, via logged-in users? Or via a validation token sent via email?
- Chris will make GitHub ticket to ask WB web team to add a link to Textpresso search from References widget on respective page; will require a Textpresso URL constructor
- Can apply to: genes, transgenes, constructs, strains, alleles, AFP-vetted entities
October 17, 2019
Alliance All Hands Face-to-Face
- Flights: has everyone already booked? No, not yet
- Any coordination of flights from Pasadena/LA?
- Ranjana and Valerio got a direct flight from Burbank to Boston on Sunday for premeetings
SObA Comparison Tool
- Prototype discussed last week, updated with feedback from prior discussions
- Would this be a stand-alone tool discoverable under the Tools menu?
- Possibly; could be a gene page widget, but may be out of place
- Stand-alone tool probably makes more sense
- Life stage graph doesn't specify expression pattern vs. expression cluster; pretty much only expression patterns (no clusters)
- Raymond intending to share progress on SObA at December Alliance All-Hands Face-to-Face
- For example, share GO SObA graph for other species
- Will need to be dependent on a SOLR server with all species data
- Raymond has run into problems trying to setup his own SOLR server
- Raymond asked Seth Carbon if we could us GO server, but he prefers not
- Appear to be software versioning issues, possible memory issues
"all stages Ce" life stage
- Currently used to annotate that RNA was collected from, or a gene was observed to be expressed during, all C. elegans life stages