title: Scientific competency questions as the basis for semantically enriched open pharmacological space development.
abstract: Molecular information systems play an important part in modern data-driven drug discovery. They do not only support decision making but also enable new discoveries via association and inference. In this review, we outline the scientific requirements identified by the Innovative Medicines Initiative (IMI) Open PHACTS consortium for the design of an open pharmacological space (OPS) information system. The focus of this work is the integration of compound-target-pathway-disease/phenotype data for public and industrial drug discovery research. Typical scientific competency questions provided by the consortium members will be analyzed based on the underlying data concepts and associations needed to answer the questions. Publicly available data sources used to target these questions as well as the need for and potential of semantic web-based technology will be presented.
authors.affiliation: Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, CH-4056 Basel, Switzerland.
authors.forename: Kamal
authors.initials: K
authors.lastname: Azzaoui
authors.forename: Edgar
authors.initials: E
authors.lastname: Jacoby
authors.forename: Stefan
authors.initials: S
authors.lastname: Senger
authors.forename: Emiliano Cuadrado
authors.initials: EC
authors.lastname: Rodríguez
authors.forename: Mabel
authors.initials: M
authors.lastname: Loza
authors.forename: Barbara
authors.initials: B
authors.lastname: Zdrazil
authors.forename: Marta
authors.initials: M
authors.lastname: Pinto
authors.forename: Antony J
authors.initials: AJ
authors.lastname: Williams
authors.forename: Victor
authors.initials: V
authors.lastname: de la Torre
authors.forename: Jordi
authors.initials: J
authors.lastname: Mestres
authors.forename: Manuel
authors.initials: M
authors.lastname: Pastor
authors.forename: Olivier
authors.initials: O
authors.lastname: Taboureau
authors.forename: Matthias
authors.initials: M
authors.lastname: Rarey
authors.forename: Christine
authors.initials: C
authors.lastname: Chichester
authors.forename: Steve
authors.initials: S
authors.lastname: Pettifer
authors.forename: Niklas
authors.initials: N
authors.lastname: Blomberg
authors.forename: Lee
authors.initials: L
authors.lastname: Harland
authors.forename: Bryn
authors.initials: B
authors.lastname: Williams-Jones
authors.forename: Gerhard F
authors.initials: GF
authors.lastname: Ecker
mesh_terms: D057225:Data Mining; D062126:Databases, Chemical / Q000592:standards; D062313:Databases, Pharmaceutical / Q000592:standards; D055808:Drug Discovery / Q000379:methods* / Q000592:standards; D017408:Guidelines as Topic; D007256:Information Systems / Q000592:standards; D051188:Knowledge Bases; D015394:Molecular Structure; D012660:Semantics; D013329:Structure-Activity Relationship; D018511:Systems Integration