Thursday, April 18, 2013

#ACSNola talk: "Open PHACTS: meaningful linking of preclinical drug discovery knowledge"

Half a year ago I submitted this abstract for the #ACSNola meeting last week (and as in the slides, I stress that is a large community effort involving not only academic groups but also many pharma companies):

Open PHACTS: meaningful linking of preclinical
drug discovery knowledge

E. Willighagen, C. Brenninkmeijer, C. Evelo,
L. Harland, A. Gray, C. Goble, A. Waagmeester,
A. Williams

Recently, semantic web technologies have been
adopted by the life sciences community for this
purpose. However, while these new technologies
provide us with methods, they do not provide us
with an exact solution. Open PHACTS uses these
methods to solve problems in linking preclinical
knowledge from databases like Uniprot, ChEMBL,
and WikiPathways. Problems that are discusses
and for which our solutions will be presented
include: 1. approaches to map data between the
databases using the Vocabulary of Interlinked
Dataset, including identifier mapping with
BridgeDBappropriate choices of mapping
predicates, and ontologies to cover provenance,
such as the Provenance Authoring and Versioning
ontology; 2. deal with different units for
experimental data using the Quantities, Units,
Dimensions and Data (QUDT) ontology for (on the
fly) quantity conversion; and 3. how all this
is linked to user-oriented graphical user

I have now uploaded the slides:

Also note the associate partnership program: it is not too late to join the 40 other associate partners and team up with Open PHACTS!