Difference between revisions of "WormBase-Caltech Weekly Calls"
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[[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]] | [[WormBase-Caltech_Weekly_Calls_2011|2011 Meetings]] | ||
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+ | [[WormBase-Caltech_Weekly_Calls_January_2011|January]] | ||
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SVM paper done | SVM paper done | ||
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+ | == February 2, 2012 == | ||
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+ | EPIC data into WormBase | ||
+ | *Daniela spoke to John Murray | ||
+ | *Need to modify model and display for data | ||
+ | *3D movies as ?Movie objects | ||
+ | |||
+ | |||
+ | Endrov | ||
+ | *Tom Burglin and student Johan developed Endrov.net | ||
+ | *May be able to incorporate Endrov visualizations of Blender model and cell lineage into WormBase website? | ||
+ | *Need to talk to Todd and Web team | ||
+ | |||
+ | |||
+ | Elsevier legal issues | ||
+ | *Science-direct website links to-and-from WormBase website | ||
+ | *Daniela still working with contacts at MGI (Mouse Genomics Institute/Jackson Labs) & Elsevier | ||
+ | *MGI already has established links with Elsevier |
Revision as of 17:53, 2 February 2012
Contents
2012 Meetings
January 5, 2012
Interactions patch
- One large scale paper omitted from upload
- Patch sent in; all OK
Integration of 3rd party data
- BioGRID, Gene Orienteer, Interolog database, etc.
- Gene Orienteer
- May only want interactions above a threshold
- Interolog database
- Get gene pages linked to their database
- Display data on gene pages, but keep display distinct?
- FlyBase links out to BioGRID, Interolog
- modEncode Transcription Regulatory Network display/diagrams?
New site release with WS230?
- About 2 months
Textpresso Interaction Sentences
- Now have sentences associated with interactions
- Need to discuss what sentences should be kept as adequate evidence of interaction and placed in remarks
- See if Textpresso can pull out paragraphs (or +/- 4 sentences?) for each sentence to see context
- Can we devise some automation to handle interaction updates?
January 12, 2012
SVM
- Genetic Interaction SVM
- How well does it work?
- Do we have sentences?
- Kimberly will follow up with Xiaodong
- For HIV papers?
Human Diseases Connections
- Should be on new gene pages
- Browse function not yet fully functional
- Search with autocomplete available
- Table from 2000 Review, human/C. elegans orthologs and diseases - put on website?
- Indexed ACEDB data used for searches; create table from indexed data?
- Textpresso pipeline flags relevant disease papers; can info be added to database?
- ?Human_disease model vs tag in ?Gene model?
- Similar discussion to ?Process model discussion
- Let's propose a ?Human_disease model; see what objections/suggestions anyone has (EBI?)
- Will follow the OBO/NCBI human disease ontology
Gloworm links
- Raymond made links from Anatomy pages to Gloworm site
- Can view movie relevant to Anatomy object at Gloworm
- Gloworm seems to only work on Macs (firewalled on Windows, doesn't work at all on Linux)
- Can we add an Apple symbol/logo next to Gloworm links on new site?
- Logo difficult, but we could add a text caveat
- New window opens with links; users should see error and be able to send Bill Mohler a message
Ontology Searches
- Status?
- Gary and Karen talking about fixing/cleaning up Phenotype Ontology
- Would be useful to have a filter on ontology searches
- Phenotype search available now, but no filters
- New search features not likely to be made in near future
- Intermine may be better tool for this
Genetic Interactions
- Rose discussed genetic interaction ontology with BioGRID et al in December
- BioGRID will stick with older terms (at least for now) as SGD and Entrez Gene need to also be on board
- Chris will review older 'Genetic' interactions with new terms as a proof of concept
- Can send results to BioGRID, SGD, and Entrez Gene
GSA markup
- Flybase wants authors to take care of all markup QC
- Pipeline: Author QC -> DJS -> Flybase check
- Flybase has minimal QC Fast service
- Michael added an 'UNDO' button for QC Fast
- Remove author ability to add links?
SVM Computers in Church 63
- SVM papers still in review (long process)
- Need to wait until SVM paper accepted before moving those computers
January 19, 2012
Parsing Legacy data into database
- Need some model changes to get the data in
- Model changes would be to:
- Add an Ease_of_scoring (ES) tag to #Phenotype_info, and
- Add a Mating_efficiency tag under ?Variation
Rescue_by_transgene tag
- If a transgene rescues an allele, it is placed under Rescue_by_transgene tag in the ?Variation class
- Move Rescue_by_transgene tag to #Phenotype_info in context of an Allele/Variation
- Can we display the transgene summary (i.e. genotype) in the Variation page? Yes
Changing author names in abstracts
- Changing the text/authors of an abstract was decided to be not allowed
- Is this a work issue or just a policy issue?
- Both, but most importantly a policy issue
- We get asked to make many changes to abstracts (sometimes content)
- It was decided (for fairness) that we wouldn't make any changes
- Polls were already taken at International meeting; consensus is that no changes will be made
- Formalize an 'Erratum' remark; Author(s) can submit?
- Authors need to login, verify their identity and authorship before being able to make an Erratum comment
- Occasionally we may need to verify/resolve issues; that's OK
SPELL download
- Users can download all (gene-centric, WormBase-parsed) SPELL data
- Wen wants to place the entire SPELL download on the FTP site
- Wen can send it to Todd
RNAi probe mappings
- EBI will eventually take over RNAi probe mappings to genome
- EBI already maps genomic coordinates to genes
- If EBI can take over the first step of mapping, we can develop an RNAi OA
- Ideally, curators could submit: PCR product names (e.g. sjj_W02C12.3), raw DNA sequence, primers
- Maybe EBI only wants DNA text? Need to check with them
ePCR
- Old script
- Any newer scripts available? Substitution?
SVM paper accepted
- Computers in Church 63 may be able to be moved
- Michael and Yuling need to check the data on them
- Need to touch base with Ruihua to ensure the computers can be moved
January 26, 2012
Luke Hutchison talking
SPELL server hanging on Amazon
- Raymond working on fixing
Interaction Model
- New ?Interaction model proposal consolidates current ?YH, ?Gene_regulation, and ?Interaction classes
- Various changes will be made to current version
SVM paper done
February 2, 2012
EPIC data into WormBase
- Daniela spoke to John Murray
- Need to modify model and display for data
- 3D movies as ?Movie objects
Endrov
- Tom Burglin and student Johan developed Endrov.net
- May be able to incorporate Endrov visualizations of Blender model and cell lineage into WormBase website?
- Need to talk to Todd and Web team
Elsevier legal issues
- Science-direct website links to-and-from WormBase website
- Daniela still working with contacts at MGI (Mouse Genomics Institute/Jackson Labs) & Elsevier
- MGI already has established links with Elsevier