Difference between revisions of "WormBase-Caltech Weekly Calls"
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*Would like to institute stable identifiers across releases, so the plan is to call these objects, '
*Would like to institute stable identifiers across releases, so the plan is to call these objects, ':<number>' so then the above identifier would become '':00000004"
*'WBDisease_annotation:00000004' too long for acedb?
Revision as of 20:58, 26 June 2019
- 1 Previous Years
- 2 2019 Meetings
- 2.1 June 6, 2019
- 2.2 June 13, 2019
- 2.3 June 27th, 2019
GoToMeeting link: https://www.gotomeet.me/wormbase1
June 6, 2019
New SObA graphs
- May put graphs within existing widgets, but don't need to rush to get that ready for IWM
Phenotype association file format
- May be best to leave the format as is
- There are problems; paper IDs keep switching columns
- Would need to revisit the reasoning for why we do it that way
- When will the Alliance produce a similar/replacement file? Not sure
- Sent out 1140 emails on May 30
- Since have received 374 annotations from 54 papers (42 requested, 12 additional)
- 21 papers flagged as not having phenotypes
- Of 1140 papers emailed about, 35 emails bounced, and have received some flagging or curation on 63 (63/1105 = ~6% response rate), in first week
June 13, 2019
- Coordinating transportation of swag boxes to Pauley Pavilion
- Workshop on Saturday June 22, from 1pm to 2:30pm
- Saturday morning micropublication breakfast 7:30 - 8:30am
- Presenters: it may be best to present as use cases rather than a research project
- Chris will cover SimpleMine for Wen
- Chris: won't do live demo; only screenshots, maybe some video
- Paul's lab will do marathon bibs to show lab affiliation and graphical abstract
- Paul's talk
- Cover Alliance
- New features
- SObA (for new data)
- Complete for protein-protein interactions
- RNASeq tools
- Updated automated gene concise descriptions?
- Phenotype community curation
- Chris will send Paul numbers on: top community curators, overall stats (number of annotations, papers, curators)
- Author First Pass
- Paul attended
- Alliance publicity was discussed
- SAB likes the Alliance orthology features
- Working on topics: displaying papers and data
- Pathways: discussion about best approach
- Metabolic engineering
- Meta data about RNASeq data
- SPELL tool, basically only tool of its kind available; need new tools
- Species-specific proteins: how best to find them? HMMs (Jackhammer)?
- Progress being made within the Alliance to update the automated concise gene descriptions
- We will still accept manually written descriptions and display them in parallel with automated descriptions
- If people are requesting manually written gene descriptions, they could submit a microreview
- Concern was expressed about how to handle a really high throughput of submissions:
- Daniela: Working towards automating as much of the processing pipeline as possible
- Raymond: The throughput will be handled appropriately depending on demand; priority scheme will help
- Not getting lots of submissions yet, probably won't be inundated in the near future
- Karen: tools are still being developed; the platform is not being advertised as much as it could be; will ramp up outreach and communication once tools are in place to handle more submissions
- Karen: Micropublications team will reach out to curators to help build submission forms for respective data types
Undiagnosed Disease Network data
- Andy Golden will meet with Ranjana and Chris at IWM to discuss
- Andy asked about protocol pages at WormBase?
- Paul: Bioprotocols and Protocols IO
- Maybe we could interface with those existing resources to link to relevant protocols from WormBase (and WormBook)
June 27th, 2019
- Impressions, analysis, feedback from Users etc etc
Giving disease model annotations a stable identifier
- Currently disease model annotations get a temporary ID at the time of dump,
Disease_model_annotation : "00000004" Disease_term "DOID:0050833" Disease_of_species "Homo sapiens" Variation "WBVar00275555" Disease_relevant_gene "WBGene00011559" Inferred_gene "WBGene00011559" Association_type "is_implicated_in" Evidence_code "IMP" Genetic_sex "hermaphrodite" Paper_evidence "WBPaper00035924" Database "OMIM" "gene" "613891 " Database "OMIM" "disease" "258900" Curator_confirmed "WBPerson324" Date_last_updated "2017-04-24"
- Would like to institute stable identifiers across releases, so the plan is to call these objects, 'WBDisease_annotation:<number>' so then the above identifier would become WBDisease_annotation:00000004"
- ID convention--is underscore allowed?
- Is 'WBDisease_annotation:00000004' too long for acedb?