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.

Chemical biology databases: from aggregation, curation to representation

“…For example, Linked data was created by the Linked Open Drug Data (LODD) task force of the World Wide Web Consortium (W3C) Health Care and Life Science Interest Group (HCLS IG). Endeavors such as Bio2RDF, Chem2Bio2RDF [38] and OpenPHACTS [39] represent additional efforts to formalize and integrate biology and chemical-biology data using semantic-web technologies. BARD has an extensive 'plug in' architecture to facilitate the deployment of community-developed computational algorithms.…”

API-centric Linked Data integration: The Open PHACTS Discovery Platform case study

“…LDA endpoints are characterized by whether they return data about a single resource, or a list of resources of the same type. 8 For a full list of available datasources with VoID descriptions, see https://github.com/openphacts/ops-platform-setup/tree/ master/data-sources 9 http://www.youtube.com/watch?v=8XV0kC7PuSU 10 The URL for getting information on the compound Sorafenib is as follows: https://beta.openphacts.org/1. 3/compound?uri=http%3A%2F%2Fwww.conceptwiki.org% 2Fconcept%2F38932552-111f-4a4e-a46a-4ed1d7bdf9d5&app_id= 0e939a76&app_key=1004d9ef5f4ee1ab0bbfc02b623cb955.…”

“…The Open PHACTS Discovery Platform provides integrated access to 11 Linked Data sets covering information about chemistry, pathways, and proteins 8 . Here, we describe version 1.3 of the platform, this is an update from the version 1.2 released in April 2013.…”

“…In contrast, this paper focuses on the role of APIs with respect to the data integration approach and its relationship to standard Linked Data application design. The API to the platform is itself a consequence of a requirements gathering process focused on business questions from a number of pharmaceutical companies and academic institutions [8].…”

Using the BioAssay Ontology for Analyzing High-Throughput Screening Data

“…Open PHACTS has defined a set of scientifically relevant competency questions around compound-target, and compound-target-disease and pathway relationships that the platform will aim to answer. 6 This work is part of the Open PHACTS project with the aim to develop annotation and analysis tools within the pharmaceutical and biotechnology industry, as well as public databases (e.g., PubChem and ChEMBL). The in-house assays are annotated manually from protocols with high granularity to cover specifications that can be used to identify technology artifacts and tool compounds and to support future assay design and screening campaign development.…”