WormBase-Caltech Weekly Calls
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2012 Meetings
April 12, 2012
RNAi OA
- OA almost ready to go live
- Testing now with test curation
- Should go live next week for official curation
New Website
- Most problems are being fixed in a timely manner
- Curators can now edit links and add custom widgets
- Issues (tracked on GitHub) being dealt with quickly
BioCurator Meeting
- Good meeting, bigger than before
- Common themes: data standards, how to educate users of database materials and how to use it (and think critically)
- How can MODs work better with journals and PubMed to solve the 'triage' problem?
- Streamlining the paper acquisition/curation process
- MODs should ask NLM to take the burden of retrieving PDFs
- Get lawyers involved to make available?
- Publishers tend to be lax on text mining rules, maybe will evolve into an easier process
- Maybe write a grant for research project as a proof-of-principle that triage can be done in an effective/efficient manner
- May ask ISB (Int Society Biocurators) for help with this
- Sequence and protein curation: tools, databases (topic-specific; pathways, cancer, etc.)
- GeneWiki for human gene annotation
- One page for each gene; already have ~10,000 articles
- ~Dozen editors, credibility of authors checked (?)
- Reasonably satisfied with coverage of human disease genes
- Whole-genome sequencing of individuals
- Newly identified genetic disorder
- VAST instead of BLAST
- Tool to identify primers from papers and map them to the genome automatically
- Intermine discussed
- Comparable to WormMart
- Object-oriented database
- Performs similar to WormBase
- Many pre-canned queries
- Advanced search Query-builder available
- MODs switched over to Intermine from BioMart
- WormMart - Will Spooner tried to provide queries that are more natural
- We can work to build an interface on top of Intermine, etc.
- Todd has made progress with getting Intermine for WormBase
- Lot's of specialized talks, reduced the productivity (compared to BioCreative meeting)
- Curators explaining their curation pipeline
- Textpresso still popular ;)
- Six out of seven MODs using Textpresso
- Discussed text mining in particular applications (eg. CCC)
- Textpresso only tool using full-text for mining
- Pete from FlyBase: SVM results are deteriorating (similar to WormBase)
- Start training from scratch; hopefully get better recall/precision numbers
- Natural language processing on figure legends/captions
- Tries to find text in the body that relates to figure
- Possible collaboration with Texpresso
- NLP research group in Germany
- 'Actor', 'agent' etc. and relationships (RDF triplets)
- Doug Howe (ZFIN), zebrafish corpus small enough, doesn't need Textpresso
- Julio Collado-Vides, Textpresso for E. coli fell apart, but trying to get back together
Paul will meet someone from Elsevier
- Image curation/ rights issues
Genetic Interaction ontology
- SGD on board with ontology so far; performing trial curation
- FlyBase interested in using as well; will meet with Chris and Rose in May to discuss
April 19, 2012
Interaction object displays on WormBase website
- Chris and Maher will sort out on GitHub
- Chris will map data from old tags to new tags and suggest display changes for new data types where necessary
- One issue to deal with is the complex objects with multiple Interaction_types (and intended to be separate objects)
Interaction model and intragenic suppression
- We need to make some modifications to the new Interaction model if we want to accommodate intragenic suppression (or other intragenic) events
- Proposed change is to:
- Make each allele a separate object
- Move the Variation (and Transgene) tag out of the Interactor_info hash and into the main Interaction model under the Interactor tag
- Add a Cis_intragenic_suppression and a Trans_intragenic_suppression tag under the Interaction_type tag (perhaps also intragenic_enhancement?)
- With these changes:
- Each variation (and transgene) can be listed as an interactor with Interactor_info indicating Affected, Effector, or Non_directional
- Genes associated with intragenic, interacting variations will display (in Cytoscape view) as interacting with itself via a Genetic Interaction'
- Mary Ann can then indicate/curate the flanking sequences for each allele
Life_stage objects still dump as names, not IDs
- This is because ACEDB only handles names, not IDs
- Daniela is in charge of this class; we can discuss with her when she's back
- We likely want to change to a system where we use only IDs in .ACE objects
URL Constructors for GSA markup
- Todd has taken care of much of the issue of URL construction for GSA marked-up papers
- Karen will send Todd examples of Anatomy_term/Anatomy_name links that need to be checked
- GSA papers will need to be rechecked to ensure that all links are working
Network outages
- Various office network ports are non-functional as of yesterday
- IMSS/Network admins aware of issue and working on it
Interaction and Gene_regulation objects for next upload
- Conversion scripts will need to be run again to convert objects to new model format
- Chris will look into whether or not the mapping files (needed to update Gene_regulation objects) will need to be updated for the newest data
- Xiaodong will dump Gene_regulation objects out of the OA using the old dumping script
