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| | [[WormBase-Caltech_Weekly_Calls_May_2012|May]] | | [[WormBase-Caltech_Weekly_Calls_May_2012|May]] |
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| − | | + | [[WormBase-Caltech_Weekly_Calls_June_2012|June]] |
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| − | == June 7, 2012 ==
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| − | Midbuild
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| − | *Wen needs all .ace files ready to test the midbuild
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| − | *Chris will send modified WS232 models.wrm to Wen
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| − | **Chris will add all model changes proposed for WS233
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| − | **?Interaction model "Rearrangement" tag needs an XREF and ?Rearrangement model needs an "Interactor" tag
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| − | | |
| − | | |
| − | New Interaction OA
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| − | *Curators should take a look at the new Interaction OA on the sandbox (mangolassi) and notify Juancarlos, Chris, and/or Xiaodong of any problems
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| − | *All interactions, including Yeast-Two-Hybrid and Yeast-One-Hybrid experiments, are in the new OA
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| − | | |
| − | | |
| − | Paper pipeline for other species
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| − | *Kimberly will update pipeline to include papers from other species
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| − | *Papers can go through data tagging pipeline (SVM etc.)
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| − | *Images could be captured from cooperating journals
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| − | *Are PDFs available?
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| − | *~1600 papers for Brugia malayi, for example
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| − | *Mapping to genomes will be an issue (e.g. RNAi)
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| − | *We would want an automated curation mechanism in place for non-core species
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| − | | |
| − | == June 14, 2012 ==
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| − | | |
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| − | Mock Upload
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| − | *Everything was OK
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| − | *Wen will leave files in the same directories, so curators will need to overwrite or replace if you want a new file
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| − | *Ghost objects? Allele-phenotype didn't have correct life stages; fixed
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| − | | |
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| − | Anatomy terms
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| − | *Juancarlos changed obsolete anatomy terms to red text in the Term Info section of the OA
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| − | *We will update the anatomy terms somewhat periodically
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| − | *Some terms get deprecated; if a term gets deleted, a replacement needs to be found
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| − | *Merges can be dealt with more automatically
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| − | *Raymond will periodically check for "floating" anatomy terms
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| − | *Update went smoothly
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| − | *Not many 'obsolete' terms being used
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| − | *Many subsumed terms
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| − | *Paper-anatomy term associations in Citace Minus; Raymond will take care of them
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| − | *Kimberly uses legacy data for anatomy term associations to papers
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| − | *Cell/Cell-Group issues
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| − | | |
| − | | |
| − | Interaction OA
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| − | *Interaction OA and dumper script essentially finished
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| − | *Curators should check the OA on the sandbox once more before we make it live
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| − | *Interaction summary vs. Remark
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| − | **Interaction summary is for biological info/summary
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| − | **Remark is more for technical details
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| − | **We will ask Juancarlos if Remark data from old Interaction objects can be transferred to Interaction_summary field/table
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| − | *Make Interaction type unique (single ontology field)
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| − | *Move the "Phenotype" field to the first TAB
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| − | *Error checks
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| − | **5 Fatal errors (Interaction does not get dumped) if the following are not satisfied
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| − | ***1) There are at least two interactors
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| − | ***2) There is a reference
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| − | ***3) The Interactor types are compatible
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| − | ***4) There is an Interaction ID
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| − | ***5) There is an Interaction type
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| − | **1 Non-fatal error (Interaction gets dumped but error is reported in error file on dump)
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| − | ***Interaction type and directionality of interactors
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| − | *Additional error check for Karen - duplicate interactions on multiple rows
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| − | *"Check Data" button, what is it doing now? Can it do all the same checks as the dumper?
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| − | | |
| − | | |
| − | | |
| − | == June 21, 2012 ==
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| − | | |
| − | | |
| − | First Pass Forms
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| − | *We get e-mails when first pass forms are complete, even if PDF is not ready
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| − | *Can we set up the system to hold off on e-mailing curators until the PDF is ready?
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| − | **Already for Author First Pass, not for Journal First Pass (GSA/DJS)
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| − | **Right now:
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| − | ***1) Paper gets accepted by GSA/DJS
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| − | ***2) Journal sends Author First Pass form to authors on paper
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| − | ***3) Journal submits XML of paper to us
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| − | ***4) Linking script runs on XML
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| − | ***5) Quality Control checks on linked XML performed
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| − | **Mary Ann would rather only get alerts after PDF is available
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| − | **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
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| − | *The form currently e-mails curators whenever data is changed; do we want updated alerts?
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| − | | |
| − | | |
| − | WormMart
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| − | *WormMart wasn't accessible from EBI
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| − | *Raymond removed software that affects firewalls; seems to have resolved the issue
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| − | | |
| − | | |
| − | Upload deadline June 28th, 2012
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| − | | |
| − | | |
| − | High School student volunteer
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| − | *Kristy (Yingjie) Ren from Diamond Bar High School
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| − | *Does she want lab experience only, or would she want to do some WormBase work?
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| − | *We should ask her
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| − | *Work study approach? We pay 20%, govt pays 80%; better situation?
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| − | | |
| − | | |
| − | | |
| − | == June 28, 2012 ==
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| − | | |
| − | | |
| − | Kristy Ren (summer high school student)
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| − | *Will come in tomorrow at 10am
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| − | *Ranjana, Raymond, Paul, Hillel, and Karen will speak to her
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| − | *Curation efforts may be better for college students (work study)
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| − | | |
| − | | |
| − | Itai Yanai paper
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| − | *Daniela curating expression pattern data
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| − | *Temporal expression patterns across 5 species during development
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| − | *Microarray data
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| − | *Itai wants to display his expression images in WormBase
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| − | *He should provide sequence names instead of gene names
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| − | *EBI will do mapping to genes
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| − | *Should original/raw data go into SPELL? Probably
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| − | *What do we do with images that Itai can submit?
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| − | *How do we capture/store/process original data, and what do we display/capture in database?
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| − | *If we get a spreadsheet of the data, place on FTP site
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| − | *Custom Agilent arrays
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| − | | |
| − | | |
| − | Upload tomorrow at 10am
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| − | *New models (WS233) in CitaceMinus
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| − | *Life_stage names have not been changed yet
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| − | | |
| − | | |
| − | Yeast Two Hybrid Experiments
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| − | *Need to update ~11,000 experiments in OA to "High throughput"
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| − | **Can use OA batch form (or possibly script to query multiple PGIDs)
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| − | *Requested original data from 2004 Li et al Science paper from Vidal group (Michael Calderwood)
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| − | *Many erroneous objects need to be fixed
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| − | **Some have only bait or only target
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| − | **Some interactions may be wrong
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| − | | |
| − | | |
| − | Grant Application
| |
| − | *Paul will submit a grant application in 3 months
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| − | *Paul will talk to PIs about big picture goals of the project
| |
| − | *What is the 5 year plan?
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| − | *30 pages total (short)
| |
| − | *What will we need to think through?
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| − | **Curation approach/process (incl. SVM)
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| − | **Gene expression
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| − | ***Generating images from digital expression data
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| − | **Gene regulation/interaction
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| − | **Physical interactions (Protein-Protein, Protein-Nucleic Acid)
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| − | **Function/GO
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| − | **Pathways/Processes
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| − | ***Work study student to curate pathways via WikiPathways (potential pilot)
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| − | ***Develop process pages for the website?
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| − | **Anatomy
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| − | **Other species
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| − | **Outreach
| |
| − | **Documentation
| |
| − | **Community Annotation
| |
| − | **Life stages
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| − | **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?
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| − | **Disease/drug discovery
| |
| − | *Want to determine ASAP what we may need to pilot or experiment with
| |
| − | *Website
| |
| − | **Ontology browsers/searches
| |
| − | **Process pages
| |
| − | **Molecule pages
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| − | | |
| − | | |
| − | Taking over genetics curation from EBI
| |
