What’s the Answer? (OMIM API now available)

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This question was raised in the last month, and there was some discussion–but there’s been a big change in the options since, and I wanted to highlight that so people know:

Question: Is OMIM no longer available as structured data?

One of our project used to query OMIM data as XML through NCBI’s efetch utility, as described here for example:

[?]What is the best way to interact programmatically with OMIM?[?]

However, it seems the service has stopped functioning a few months ago. It now simply returns the following error:

Database: omim – is not supported

I can find no mention of an update to the API on NCBI’s website or anywhere else. At the same time, the pages accessible directly on OMIM’s website offer no link to structured data (XML or otherwise) and the downloadable file, while using some specific format to delimit fields, is still far from the flexibility of the former XML files (for example, it is impossible to retrieve metadata for each reference).

Is there currently any way to regain access to OMIM data in a structured, parsable format (XML…)?

There was a lot of discussion about the changes since OMIM at NCBI moved away from to its new spot at OMIM.org, but just this week I spotted a tweet from OMIM which directly answers the access issue now:

I’ve you’ve been waiting for the OMIM API access, check it out at the Help page.

3 thoughts on “What’s the Answer? (OMIM API now available)

  1. jozerffer

    I can’t seem to get it the url correct or there is something wrong between the server and me. i have the apikey and try the example given in the site. I try using google chrome v18 and firefox v12 bu it doesn’t work. This is the url that i have try “http://api.omim.org:8000/api/entry?mimNumber=100100&include=text&apiKey=my_api_key”.

    Please someone help me. I am in desperate to get it work. Thank you very much in advance.

  2. Mary Post author

    Hey jozerffer–I’ll contact them this morning and ask them to come over and help.

  3. François Schiettecatte

    I am the OMIM developer, I just checked the url you used with my API key and it works, did you wait 24 hours for your API key to activate? I checked the list of API users and I could not find your name.

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