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