Dear bioinformaticians Do you know a database (or resource) containing information about genes, like GeneCards, PubMed which also includes patents. Or do you know databases with patents where information about gene of interest could be collected. I need to collect all available information about genes, including publications and patents.
•
written
by
juliadmtr •
Thank you, do you know whether I can access it programmatically (from R or Python)?
I have only used as a paid user (as an employee of a company). There is some freely accessible data, but if you need access to 'everything' it's only via the paid account. If you pay, you'll get 'dumps' of data which you can then explore through whatever means you find comfortable (R/python/SQL, etc). For my purposes, we built several BLAST databases to find DNA/RNA and protein sequences that were covered by IP.
What is the name of the tool? Is it the same lens.org?
There isn't really a tool - lens.org gives paid users text files that you can explore. The advantage this provides is that nearly all bio-patents aren't necessarily searchable by a gene name or sequence because this information exists in the patent as a non-vector based image (think jpg vs pdf). I guess lens.org goes to great length to extract this data and make sure it's correct. From my limited experience, it's an extremely valuable resource if you need to validate your IP against existing IP.
Some of the text files they give are in defined formats, such as a fasta, that can easily be passed to existing tools, like BLAST, for ease of use.
Log in to answer this question.
I am interested to get this information programmatically in R or Python.
You could also use https://patents.google.com