One of our project used to query OMIM data as XML through NCBI's efetch utility, as described here for example:
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...)?
If you go to the NCBI webpage for OMIM, this is clearly stated:
NCBI is implementing changes to help you find current content in OMIM based on resources at NCBI, and then directing you to omim.org. Please be aware that you will leave NCBI to view OMIM records. Access to full records from NCBI (e.g. web, ftp, eutils) will no longer be supported.
Sadly it looks like access control to the full OMIM data has been made more restricted by moving it to a separate site run by Johns Hopkins University. From the looks of it you can obtain the same flatfiles as you used to be able to get from the NCBI FTP site. However, I see no sign of web services. Their help pages make no mention of XML.
This is unfortunate. To summarise for anyone interested:
Esearch returns IDs (in this case, 601228).
Efetch returns the error:
curl http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=omim&id=601228 # Database: omim - is not supported
Esummary returns a brief XML document:
curl http://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=omim&id=601228 <?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE eSummaryResult PUBLIC "-//NLM//DTD eSummaryResult, 29 October 2004//EN" "http://www.ncbi.nlm.nih.gov/entrez/query/DTD/eSummary_041029.dtd"> <eSummaryResult> <DocSum> <Id>601228</Id> <Item Name="Oid" Type="String">%601228</Item> <Item Name="Title" Type="String">POLYPOSIS SYNDROME, HEREDITARY MIXED, 1; HMPS1</Item> <Item Name="AltTitles" Type="String">COLORECTAL CANCER, SUSCEPTIBILITY TO, 4, INCLUDED; CRCS4, INCLUDED</Item> <Item Name="Locus" Type="String">15q15.3-q22.1</Item> </DocSum> </eSummaryResult>
So answer to the question is "no, it isn't."
I've been waiting for this since July 2011. https://twitter.com/OmimOrg/status/90770519841980416
@yokofakun[?] @mrrizkalla and we have an web API in the wings, not quite ready to open it up yet . omim.org (@OmimOrg)
The omim.org download page indicates that the data is copyrighted by the JHU, and they make you agree not to redistribute it if you want to download it. That might be part of the reason they don't make it available through an API. But why would they feel the need to control it like this, I wonder.