What Is The Best Way To Interact Programmatically With Omim?

Question

[Nico Adams]

Dear All,

I am currently developing an ontology for a particular type of Mendelian Disease and I would like to map the terms in my ontology to corresponding OMIM terms. The first step of doing this would be to get hold of OMIM terms. What is the best way to go about this in your experience?

I can, of course, always download and parse the flat text file, but was wondering whether anybody knows of a better way!

Thanks for your help!

Answer 1

[Pierre Lindenbaum]

You can search for an OMIM record using NCBI-ESearch and retrieve a structured/XML version of the record via NCBI-EFetch: e.g to retrieve http://www.ncbi.nlm.nih.gov/omim/147670 ( INSR , omim-id= 147670 )

http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=omim&id=147670&retmode=xml&rettype=full

http://www.ncbi.nlm.nih.gov
/dtd/NCBI_Mim.dtd">
<Mim-entries>
<Mim-entry>
  <Mim-entry_mimNumber>147670</Mim-entry_mimNumber>
  <Mim-entry_mimType value="star">1</Mim-entry_mimType>
  <Mim-entry_title>INSULIN RECEPTOR; INSR</Mim-entry_title>
  <Mim-entry_copyright>Copyright (c) 1966-2010 Johns Hopkins University</Mim-ent>
  <Mim-entry_symbol>INSR</Mim-entry_symbol>
  <Mim-entry_locus>19p13.2</Mim-entry_locus>
  <Mim-entry_seeAlso>
    <Mim-cit>
      <Mim-cit_number>25</Mim-cit_number>
      <Mim-cit_author>Elbein</Mim-cit_author>
      <Mim-cit_others>et al.</Mim-cit_others>
      <Mim-cit_year>1986</Mim-cit_year>
    </Mim-cit>
    <Mim-cit>
      <Mim-cit_number>27</Mim-cit_number>
      <Mim-cit_author>Ferrannini</Mim-cit_author>
(...)

[Nico Adams]

Wonderful. Thanks Pierre!

Answer 2

[Chris Maloney]

As mentioned in Is Omim No Longer Available As Structured Data?, NCBI no longer serves OMIM data through efetch. The way to access OMIM now is through their API.

Answer 3

[onemoreuser]

How do I get the OMIM id?

[LLTommy]

Well, short question so you get a short answer: I am pretty sure that EBI's Ontology Lookup Service could help you.