Project:
Rephetio: Repurposing drugs on a hetnet [rephetio]

Publication:
KaBOB: ontology-based semantic integration of biomedical databases

KaBOB Knowledgebase


Larry Hunter just gave a talk here where he highlighted his group's work developing KaBOB:
http://www.biomedcentral.com/1471-2105/16/126/abstract

Some of the work that they've done may help with processing of external databases. They unify some of the drug/target concepts in DrugBank and PharmGCB, for example, by developing abstract representations of genes, gene products, variants, etc.

Thanks for the recommendation [1]. Unless there is a specific contribution that this resource could immediately provide, I am wary to invest significant time in understanding and integrating it.

For example, do we want to introduce a dependency on a 1,665 line java package to parse a DrugBank record, when we can retrieve the small subset of information we require with much simpler scripts.

My initial sense is that while this study tackles some important problems in biodata integration, there isn't a readily available way to easily retrieve and incorporate the unified vocabularies. It would be great to get feedback from the authors, in case I am wrong.

 
Status: Declined
Labels
  resource
Views
132
Cite this as
Casey Greene, Daniel Himmelstein (2015) KaBOB Knowledgebase. Thinklab. doi:10.15363/thinklab.d66
License

Creative Commons License

Share