We have just released the latest version of the Open Targets Platform, release
These are some of the highlights.
Our favourite stats
One of the questions we get a lot from our users is: "Do you have information on biomarkers?".
Biomarker is a linguistic blend of two words: biological and marker.
According to the Biomarkers Definitions Working Group in the NIH, a biomarker is as “a characteristic that is objectively measured and evaluated as an indicator of normal biological processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention”.
We are happy to announce that we now incorporate a collection of genomic biomarkers of drug responses (sensitivity, resistance and toxicity) and their level of clinical significance from the Cancer Biomarkers database. For a given target implicated in cancer, e.g. PTEN, you will find:
- Biomarker e.g. PTEN deletion
- Disease e.g. prostate adenocarcinoma
- Drug e.g. everolimus (MTOR inhibitor)
- Association e.g responsive
- Evidence e.g. early trials
- Publication e.g. NCT01955668
These biomarkers are curated and maintained by several researchers and clinicians in the field of precision oncology, and classified by cancer type. Check Tamborero et al. 2018 for more details.
We have a new data source, PROGENy (a.ka. Pathway RespOnsive GENes) (Schubert et al (2018).
We now use PROGENy for the systematic comparison of pathway activities between normal cells and primary samples from The Cancer Genome Atlas (TCGA), and include in the Platform sample-level pathway activities inferred from RNA-seq for:
- 9,250 tumour samples
- 741 normal cells
- 14 tumour types e.g. bladder carcinoma
- 11 biochemical pathways e.g. JAK-STAT
Head to our Platform to explore the 30 diseasess associated with TP53 based on evidence curated from this new data source. You can also use our REST-API to retrieve all the associations based on PROGENy only. Email us if you want to know more.
New visualisations for drugs
Exploring drug information from our Platform has never been more pleasing to the eye.
Our new drug summary visuals give a quick overview of drugs that we use as evidence in target-disease associations. Check the drug evidence for SCN8A in unipolar depression or head to the profile pages of any target or disease, such as lung carcinoma, to start exploring these new visualisations.
GitBook is the new home for our docs
Have you ever felt baffled when exploring our help pages?
Perhaps you have searched for more details on our association score but found it difficult to navigate our docs and get help?
The good news is that our Open Targets Platform documentation is now on GitBook.
Why not search for 'scoring' to see how easy it is now to find all the important help you need?
If you want to suggest new FAQs or need further help, please email us.
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By the way, have you seen our latest video on Pathway information, part of our series Everything you always wanted to know about a drug target but were afraid to ask?
p.s. For more details on our latest release, check our release notes.