The Semantic Web and Drug Discovery was a recent topic at the San Diego Informatics Lunch forum. This is an informal get-together of bioinformatics and cheminformatics practitioners to share ideas and discuss how different technologies can be applied in our disciplines.
The topic arose because although the Semantic Web has been talked about for nearly 10 years now, there seems to be little visible progress (outside of academia) with respect to applying those technologies to drug discovery.
A few definitions are required before we proceed further. The Semantic Web (also known as the web of data) is a set of technologies used to make data available in a universally accessible format. Assertions like “A phosphorylates B” are represented as Subject-Verb-Object “triples” in RDF (resource description framework). Relationships between attributes can be grouped and formalized through an ontology which allows one to express concepts like:
- Genes have: Entrez-Gene IDs, Sequences, Descriptions
- Genes belong to biological networks
- Genes have cellular components, molecular, and biological functions.
These networks of assertions can be mined for new relationships using reasoning engines, and queried using a SQL-like language called SPARQL. You can read more about the Semantic Web at the Wikipedia article on the subject.
Ben Good of the Genomics Institute of the Novartis Foundation (GNF) spoke about the his experiences with curating the GeneWiki and most recently in automatically tweeting changes to the GeneWiki via @GeneWikiPulse.
We also discussed the work of Carlos Zamudio towards establishing standards for expressing bioassay data.
Part of the challenge in working in an historically closed-mouth industry, is that it’s often difficult to get pharmaceutical companies to discuss how they are using (or plan to use) semantic web technologies. And many of these types of scenarios may never see the light of day. That said, the W3C established a working group for health care and life sciences which described a number of the scenarios in which semantic web technologies could be used in pharmaceutical and life sciences companies.
- Case Study: Applying the Semantic Web to Internal Compound Repurposing
- Use Case: Drug Ontology Project for Elsevier (DOPE)
- Case Study: Composing a Safer Drug Regimen for each Patient with Semantic Web Technologies
In addition, the ISCB has a yearly conference on the subject called CSHALS — Conference on Semantics in Healthcare and Life Sciences.
Bill Smith placed a question on Quora to help continue the conversation offline.