WBConfCall 2014.09.03-Agenda and Minutes

Agenda

Adding worm disease models/data to the Monarch Initiative website

(From Ranjana)

• http://monarchinitiative.org/ : connects phenotypes, diseases, models, and genes for translational research across species (People involved: Melissa Haendel, Chris Mungall, Suzi Lewis, Nicole Washington and others)
• Last time I spoke to them, seems like they were still working on a lot of stuff; today, got a very enthusiastic response from Chris and Nicole about including worm disease model data
• Pointed them to our gene-disease association file, on the FTP site:ftp://ftp.sanger.ac.uk/pub/wormbase/releases/WS245/ONTOLOGY/disease_association.WS245.wb, however this is incomplete since it doesn't have the disease model descriptions, and the manually curated OMIM connections, so also sent them the WS245 caltech manual curations file
• Will wait to see whether they can work with the above files or would they need something else
• Link to monarchinitiative.org from WormBase? Possibly from the DO term page? there is documentation at http://monarchinitiative.org/page/services and http://monarchinitiative.org/docs/files/api-js.html?
• A page example for Parkinson's Disease: http://monarchinitiative.org/disease/DOID_14330, from here one can go to the different tabs for Models, Genes, Compare, etc.

Model change requests

• Wen and Daniela: model changes to #Qualifier so that we can combine life stage with anatomy term in expression pattern annotation. We hope these changes can be included in WS246 models.wrm. We just need to add Life_stage and Anatomy_term fields to #Qualifier.

#Qualifier    Certain Text
              Uncertain Text   
              Partial Text  
              Anatomy_term ?Anatomy_term //Added by Wen and Daniela                
              Life_stage  ?Life_stage //Added by Wen and Daniela

• Ranjana: Addition of a new tag, 'Automated_description' to 'Structured_description' under ?Gene.

--James and I are working on a project here at Caltech, which will generate completely automated descriptions for genes based on data already curated in WormBase. Currently these data are: Orthology/Homology and the GO annotations for Process, Function and Cell component. Since this is a significant departure from the way the human written ones were generated, I'd like to request a new tag 'Automated_description' under 'Structured_description' in the Gene class for WS246.

?Gene

Structured_description	Provisional_description
                       Concise_description            
                       Automated_description  <--New tag