WormBase-Caltech Weekly Calls
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September 4, 2014
I need to leave at 5.30pm (ermm, 9.30am CA time?) Mary Ann
- Automated descriptions to go in for WS245
New Upload Schedule
- Delayed a couple weeks compared to original schedule
- Official citace upload to Hinxton on October 10th
- We can/should upload our data Wednesday before SAB trip (October 1st) to Hinxton
- Wen needs queries to include in Citace Upload summary by October 1st
- Upload contingent on models freeze
Data submission as part of publication process
- eLife considering micro-publication, addendums to papers (individual add-on experimental results)
- Can certain data be required to publish? Sequence info, etc. ?
- Could there be a pilot with a specific publisher (like GSA markup)?
- Use RDF (Resource Description Framework) triples
- Checking individual statements/sentences from literature for data presence/absence in database
- Life_stage and Anatomy_term
- Adding to enable annotation of EPIC data
- Couples (or attempts to) time-and-space (life_stage-and-anatomy) annotation of expression pattern
- Can ambiguities be captured?
- This approach (bit of a kludge) introduces some denormalization (normalization can be automated later)
- Setting up connection to Minerva
- Juancarlos working with Seth, Chris, Heiko to debug setup
- Would be good (necessary?) to establish a working protocol for collaboration
- Raymond's LEGO-like approach to curating anatomy function
- Annotate a phenotype by annotating relevant DB objects, e.g. anatomy term, GO term, etc. as well as context/condition
- Use minimal relationships (relationship ontologies complicated and difficult to use)
September 11, 2014
- Can we start putting together a more detailed agenda, at least for Caltech?
- Would be good to decide on our talk topics so we can begin putting our presentation(s) together.
- Curation Stats numbers spreadsheet
- Good to capture amount of time (FTEs) on curation, but also software development, curation tools, pipelines, data modeling, help desk, fixing old data
- Would be good to have a rough breakdown of every curator's FTE breakdown
- Allocation of resources
- Ontology development; how much time is spent? Is it worth it?
- What tools do we have, or could we develop, that could substantially improve efficiency/effectiveness of curation? Example: sequence generation tool
- What are considerations for future database migration? We should account for migration delays to curation, etc.
- The curation database (like Postgres now) may or may not be the same database that drives the website
- Are our curation pipelines capturing sufficient detail (or too much, unnecessary detail)?
- Is it worth capturing negative data?
SAB Talk Proposals
- Nomenclature - not stats, but what we do, how it's done, communication etc Mary Ann