Gene to OMIM phenotype

A couple of weeks ago, I wrote a post on identifying OMIM phenotypes that are associated with a gene of interest. I thought I solved the problem by using one of my favourite R packages (biomaRt) but alas. For example, I could not find any OMIM IDs associated with the TTN gene using biomaRt. In the end, I resorted to using the OMIM API through a small R package I wrote called romim.

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Gene to OMIM Morbid Map

Update 2017 May 10th: I realised that this approach doesn't work for all genes, unfortunately. For example, the gene TTN (which is an HGNC approved gene symbol) is associated with 600334, 603689, 604145, 608807, 611705, and 613765 but biomaRt returns an NA. Please refer to an updated post.

I was interested in the number of Online Mendelian Inheritance in Man (OMIM) disorders a particular gene was associated with, which in this case was FGFR2. Once again it was biomaRt to the rescue. OMIM is a collection of genes and disorders, and the morbid map refers to the disorders. This post is on looking up the OMIM morbid IDs for FGFR2.

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Getting started with the OMIM API

Updated 2016 September 15th: I've made this into an R package, which is available at my GitHub repository

A short post on utilising the OMIM API via some wrapper functions I wrote in R. A wrapper, as explained in the Wikipedia article, is simply a subroutine that calls another subroutine. If you plan on using the OMIM API, first register for your very own API key. After you submit the form you will get an email with the key, along with this message:

The API key will be activated within TWO hours, trying to use it before then will result in a error. It is for your own use, we ask that you do not share it with others.

So if you haven't already registered, stop reading now, and submit the form.

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OMIM IDs to gene coordinates

A post on linking OMIM IDs to gene coordinates using biomaRt; this provides a way of representing OMIM IDs on the genome. For those unfamiliar with OMIM, here's the description from the OMIM FAQ:

Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with particular focus on the molecular relationship between genetic variation and phenotypic expression.

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