|
|
Line 1: |
Line 1: |
− | ==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
| |