WormBase-Caltech Weekly Calls
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- 1 Previous Years
- 2 2018 Meetings
GoToMeeting link: https://www.gotomeet.me/wormbase1
May 3, 2018
- Wen was working on simplification of SimpleMine output
- Considering removing general terms in an ontology when more specific terms exist
- Concern that we would be removing information; will keep terms
- Topics in SPELL need some organization, possibly trimming
- We could create a graph (SObA) display of topics (based on GO process)
SPELL problem with WS265
- Wen had to debug; SPELL has limit of how many genes can be processed per data set (46,340)
- Wen trying to accommodate, deleting some genes from data set that had no expression (kludge)
- Wen will write to Matt Hibbs to ask how to deal with
- Will Alliance work together on a system to analyze large scale expression data?
- Will arrive at 10am
- Skype calls with remote curators
- Curators will send group Skype handle and requested time to talk
May 10, 2018
ECO terms for genome editing
- Asking group's feedback on ECO terms for genome editing (Daniela)
- What would be used for fly-enhancer trap experiment?
- Genomically encoded GFP, for example
- ECO: GFP localization
- ECO term, example: Fluorescent protein transcript localization evidence
- Single copy transgene? Endogenous locus?
- Whether it is CRISPR or not may not be relevant
- May request ECO terms that capture distinct types of transgenes evidence
- Will use generic term for now
- Do other MODs use ECO?
- May want to capture endogenous/non-endogenous, multi-copy/single-copy distinctions
- Many of these features are captured in the transgene and construct objects already; specific ECO code redundant?
- Significant involvement in Alliance
- Interest in micropublications; will push a pilot
- June 19, moving from older DB to Postgres
- Investigating automation for some curation processes
- Students review which papers to include; acquire PDF
- Curate paper-by-paper
- Supplement request for year 3, due soon (May 15)
- Formal report from NHGRI, 18-month plan looks good
- Further future plans (from NHGRI perspective) aren't quite clear
- Software infrastructure?
- Central- vs. MOD-control of resources questions
- Likely will have to write a NIH proposal in Fall or Winter
- How much is Alliance going to handle human variants?
- NHGRI interested in metabolomics; Alliance plans?
- Had help desk question about phenotypic screens in organisms other than worms, flies, yeast, bacteria
- There have been human cell line phenotypic screens (e.g. siRNA/shRNA); who curates these, if anyone?
- Also, induced pluripotent stem cell experiments
- Issue came up about assigning unique WBStrain IDs
- Can use a nightly nameserver dump from Hinxton to populate Postgres/OA
- Will need to clean up existing strains in Postgres
- Also, considering unique IDs for genotypes
- Mechanics of naming and managing naming of objects
- Nightly syncing (cronjob) to nameserver
- Ideally, we would have instant updates; Hinxton firewall prevents direct access; Matt working on establishing a separate nameserver location to gain direct access
- Strain names (at least historically) have been updated quarterly from CGC file
- Curators need mechanism to create and use strain (and variation) names right away
- Current system requires manual denormalization step; has worked so far
May 17, 2018
- Create a strain OA? Central curation tool for strain data?
- Would need to maintain synchrony with CGC and Hinxton
- Postgres/Tazendra variation adding CGI: http://tazendra.caltech.edu/~azurebrd/cgi-bin/forms/generic.cgi?action=TempVariationObo
- Will add similar link for Strains, adding info to obo_name_strain and obo_data_strain as well as a tempfile, which will those objects in postgres when the nightly_geneace.pl updates the OA strain info
- Who will present? Present what?
- We can generate a central document with stats to give to SAB
- Ask SAB for opinions and guidance?
- Would be good to assess current efforts and priorities, ask if we should stay the course or make modifications to our approach