HCLSIG/LODD/Neuropharmacology demo
Neuropharmacology demo
Goal
To quickly build a useable interface to explore linked data in the neuropharmacology domain, based on existing or forthcoming linked data resources.
Participants
- Matthias Samwald
- Claus Stie Kallesøe
Relation to TMO
The project will start out with a focus on preclinical research, but clinical aspects will probably be added at a later point. The translational medicine ontology can serve as a foundation.
Relevant datasource
- Pubchem Bioassay
- Allen Brain Atlas
- BioGPS (or maybe something similar)
- PDB
Exploring the linked data space
Searching with Sig.ma
Below are some curated query results obtained with DERI's Sig.ma service.
And some API examples (querying bio2rdf, chem2bio2rdf, dbpedia and the FU Berlin endpoints):
- raw HTML response for Citalopram
- JSON response for Citalopram
- RDF response for Citalopram (Note that the RDF output does not equal RDF sources, it is actually an RDF format for the Sig.ma response)
Pubchem Bioassay
Pubchem Bioassay has been RDFized by the Chem2Bio2RDF project: http://cheminfov.informatics.indiana.edu:8080/pubchem/ (only pubchem) http://cheminfov.informatics.indiana.edu:8890/sparql (all Chem2Bio2RDF resources)
A useful graph of the datasets in Chem2Bio2RDF.
Some of the data is not very semantically rich, e.g. on http://cheminfov.informatics.indiana.edu:8080/pubchem/page/pubchem_bioassay_interaction/136144, what exactly does "pubchem:outcome 2 (xsd:int)" mean?
Chem2Bio2RDF has also RDFized PharmGKB (note that this RDF version seem unrelated to the RDF version produced by the Dumontier Lab) The properties have no definitions.
Allen Brain Atlas
A new linked data representation of the Allen Brain Atlas will become available in the next months and will be hosted by the Allen Brain institute. Right now, we also have an outdated RDF conversion of the Allen Brain Atlas data created by Science Commons in 2007 for the first HCLS knowledge base demo. However, we probably want to wait until the fresh linked data representation becomes available to us.
PDB
PDB is listed both on Bio2RDF and Chem2Bio2RDF -- the RDF representations are not identical.
http://bio2rdf.org/pdb:2c64 -- PDB entry associated with the publication "Binding of rasagiline-related inhibitors to human monoamine oxidases: a kinetic and crystallographic analysis." (some relevant data seems missing)
http://cheminfov.informatics.indiana.edu:8080/uniprot/page/pdb/2C64 -- related representation of that PDB entry in Chem2Bio2RDF. Does not look very helpful either. Mabye this refers only to a reference to PDB that was actually derived from Uniprot.