We have developed the Open Targets Platform to provide summaries of the evidence for the involvement of a specific gene with a selected disease.
A new tool called LINK (LIterature coNcept Knowledgebase) has been developed that allows the exploration of half a billion relations between genes, diseases, drugs and key concepts extracted from PubMed abstracts using NLP (Natural Language Processing).
Once MEDLINE relaxed their license for obtaining and analysing publication data last year, we started looking for novel ways to mine their data. We wanted to exploit the biomedical knowledge often buried in the literature to help scientists generate new hypotheses for the identification of new drug targets. For this purpose, we have built Library, an open source ecosystem comprising:
Our pipeline annotates genes, diseases and drugs present in PubMed abstracts, and extracts key concepts.
DoRothEA (Discriminant Regulon Expression Analysis) is a research resource that can be used to search candidate TF-drug interactions in cancer.
Due to their location as downstream effectors of signalling pathways, aberrant activities in upstream driver genes (even if not mutated) will cause altered TF activities, thus proposing TFs as sensors of pathway dysregulation and alternative markers. Here we study the role of 127 TFs in drug sensitivity across ~1,000 cancer cell lines screened with 265 anti-cancer compounds from the GDSC. In our first approach we studied how the TF activity pattern of an individual affects drug response and mined for single TF-drug statistical interactions. In our second approach we screened for TFs whose activity patterns complement or improve well-established genomic markers in the prediction of drug response.
Please see Garcia-Alonso et al. for an explanation of the approach.
Open Targets is guided by the following principles:
We place in the public domain all our new informatics tools, experimental methods, platforms and the data generated by our projects as soon as is practical. We do not plan to seek patent protection for IP arising from Open Targets. However, we recognise that instances may arise where this is appropriate to support our mission. Therefore, Open Targets has a Joint Patent Committee with scientific and legal experts from all of our partners that reviews all potential publications (but not raw data) prior to submission.
In practice, this means: