WormBase-Caltech Weekly Calls January 2012

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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

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