Difference between revisions of "WormBase-Caltech Weekly Calls"
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Revision as of 19:12, 28 June 2012
2012 Meetings
June 7, 2012
Midbuild
- Wen needs all .ace files ready to test the midbuild
- Chris will send modified WS232 models.wrm to Wen
- Chris will add all model changes proposed for WS233
- ?Interaction model "Rearrangement" tag needs an XREF and ?Rearrangement model needs an "Interactor" tag
New Interaction OA
- Curators should take a look at the new Interaction OA on the sandbox (mangolassi) and notify Juancarlos, Chris, and/or Xiaodong of any problems
- All interactions, including Yeast-Two-Hybrid and Yeast-One-Hybrid experiments, are in the new OA
Paper pipeline for other species
- Kimberly will update pipeline to include papers from other species
- Papers can go through data tagging pipeline (SVM etc.)
- Images could be captured from cooperating journals
- Are PDFs available?
- ~1600 papers for Brugia malayi, for example
- Mapping to genomes will be an issue (e.g. RNAi)
- We would want an automated curation mechanism in place for non-core species
June 14, 2012
Mock Upload
- Everything was OK
- Wen will leave files in the same directories, so curators will need to overwrite or replace if you want a new file
- Ghost objects? Allele-phenotype didn't have correct life stages; fixed
Anatomy terms
- Juancarlos changed obsolete anatomy terms to red text in the Term Info section of the OA
- We will update the anatomy terms somewhat periodically
- Some terms get deprecated; if a term gets deleted, a replacement needs to be found
- Merges can be dealt with more automatically
- Raymond will periodically check for "floating" anatomy terms
- Update went smoothly
- Not many 'obsolete' terms being used
- Many subsumed terms
- Paper-anatomy term associations in Citace Minus; Raymond will take care of them
- Kimberly uses legacy data for anatomy term associations to papers
- Cell/Cell-Group issues
Interaction OA
- Interaction OA and dumper script essentially finished
- Curators should check the OA on the sandbox once more before we make it live
- Interaction summary vs. Remark
- Interaction summary is for biological info/summary
- Remark is more for technical details
- We will ask Juancarlos if Remark data from old Interaction objects can be transferred to Interaction_summary field/table
- Make Interaction type unique (single ontology field)
- Move the "Phenotype" field to the first TAB
- Error checks
- 5 Fatal errors (Interaction does not get dumped) if the following are not satisfied
- 1) There are at least two interactors
- 2) There is a reference
- 3) The Interactor types are compatible
- 4) There is an Interaction ID
- 5) There is an Interaction type
- 1 Non-fatal error (Interaction gets dumped but error is reported in error file on dump)
- Interaction type and directionality of interactors
- 5 Fatal errors (Interaction does not get dumped) if the following are not satisfied
- Additional error check for Karen - duplicate interactions on multiple rows
- "Check Data" button, what is it doing now? Can it do all the same checks as the dumper?
June 21, 2012
First Pass Forms
- We get e-mails when first pass forms are complete, even if PDF is not ready
- Can we set up the system to hold off on e-mailing curators until the PDF is ready?
- Already for Author First Pass, not for Journal First Pass (GSA/DJS)
- Right now:
- 1) Paper gets accepted by GSA/DJS
- 2) Journal sends Author First Pass form to authors on paper
- 3) Journal submits XML of paper to us
- 4) Linking script runs on XML
- 5) Quality Control checks on linked XML performed
- Mary Ann would rather only get alerts after PDF is available
- We can add a note about whether or not the PDF is available to the First Pass list, so Mary Ann can sort on that parameter
- The form currently e-mails curators whenever data is changed; do we want updated alerts?
WormMart
- WormMart wasn't accessible from EBI
- Raymond removed software that affects firewalls; seems to have resolved the issue
Upload deadline June 28th, 2012
High School student volunteer
- Kristy (Yingjie) Ren from Diamond Bar High School
- Does she want lab experience only, or would she want to do some WormBase work?
- We should ask her
- Work study approach? We pay 20%, govt pays 80%; better situation?
June 28, 2012
Kristy Ren (summer high school student)
- Will come in tomorrow at 10am
- Ranjana, Raymond, Paul, Hillel, and Karen will speak to her
- Curation efforts may be better for college students (work study)
Itai Yanai paper
- Daniela curating expression pattern data
- Temporal expression patterns across 5 species during development
- Microarray data
- Itai wants to display his expression images in WormBase
- He should provide sequence names instead of gene names
- EBI will do mapping to genes
- Should original/raw data go into SPELL? Probably
- What do we do with images that Itai can submit?
- How do we capture/store/process original data, and what do we display/capture in database?
- If we get a spreadsheet of the data, place on FTP site
- Custom Agilent arrays
Upload tomorrow at 10am
- New models (WS233) in CitaceMinus
- Life_stage names have not been changed yet
Yeast Two Hybrid Experiments
- Need to update ~11,000 experiments in OA to "High throughput"
- Can use OA batch form (or possibly script to query multiple PGIDs)
- Requested original data from 2004 Li et al Science paper from Vidal group (Michael Calderwood)
- Many erroneous objects need to be fixed
- Some have only bait or only target
- Some interactions may be wrong
Grant Application
- Paul will submit a grant application in 3 months
- Paul will talk to PIs about big picture goals of the project
- What is the 5 year plan?
- 30 pages total (short)
- What will we need to think through?
- Curation approach/process (incl. SVM)
- Gene expression
- Generating images from digital expression data
- Gene regulation/interaction
- Physical interactions (Protein-Protein, Protein-Nucleic Acid)
- Function/GO
- Pathways/Processes
- Work study student to curate pathways via WikiPathways (potential pilot)
- Develop process pages for the website?
- Anatomy
- Other species
- Outreach
- Documentation
- Community Annotation
- Life stages
- Data retrieval/mining; querying?
- Website/database
- What we want to display and how?
- Advanced Queries; Ontology Browsers; Data integration
- Tools
- Host/pathogen interaction (collaborate with pathogen curator groups?)
- Behavior? Process oriented?
- Disease/drug discovery
- Want to determine ASAP what we may need to pilot or experiment with
- Website
- Ontology browsers/searches
- Process pages
- Molecule pages
Taking over genetics curation from EBI