Knowledge from Gene
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6.4 years ago
BioICoder ▴ 40

Hello everyone,

I have a bunch of gene names (over 80 genes) and my goal is find some knowledge in regards to those genes such as OMIM ID, Mood of Inheritance and their characteristics, gene functions and etc. I could find a number of those knowledge from OMIM but I couldn't find a good tutorial the describe OMIM API well. I preferred doing that using Python language or else is there a tool that can find those knowledge and also allow batch input?

Thank you so much in advance.

python OMIM • 1.4k views
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6.4 years ago

MyGene has a pretty good and easy to use python API that yields tons of stuff - database IDs, function, etc. You can iterate through your gene names easily enough in Python to get all the info you'd want for each gene. They also let you try their API online, so you can try that to see if the info you need is available.

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Although I couldn't extract all the info I needed but its very helpful and it uses simple python syntax which is also plus, thanks for sharing!

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What info is it missing that you'd want?

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Mood of inheritance and characteristics, and gene function!

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Do you mean mode of inheritance? And which characteristics? For function, you can run the gene ID through uniprot to get a summary of the function. It's the best way to get generalized functions that I've found. This post should should probably get you started, but the uniprot API site will of course also be helpful. This pdf has some commands for python that should also point you in the right direction (particularly the last 2 pages, which show how to get JSON requests from a query). Opening the request in a browser will give you a good idea of how the data will be returned so that you can parse it properly to get the function.

For example, here's the webpage for CDK2. And here's how that info is returned in xml format (but you can change the extension to basically whatever you want to determine how you want to parse it - XML, txt, etc are all valid).

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