Help with OMIM disease categories, filtering, etc

Question

[Wayne]

Hello all,

I'm attempting to compile a list of all immunology related diseases - defined as a disease caused by or related to the immune system (auto immunity, or immunodeficiency).

I'm using OMIM currently and trying to filter down their genemap dump of all pathologies, The list however, is way too long to go through manually and I cant figure out a good way to filter just based on reg/ex out what I need.

Does anyone know how to filter OMIM down by sub categories under the diseases , or by what cells they effect, or anything like this.

I'm wiling to try other databases too if they seem like a better idea. Any help would be awesome!

Thanks!

Answer 1

[EagleEye]

Register and download:

http://www.omim.org/downloads

You will have file called 'morbidmap' where you can grep (<phene mapping key>) the functions related to the diseases.

For the file morbidmap, the fields are, in order:

1. Disorder, <disorder MIM no.> (<phene mapping key>)
2. Gene/locus symbols
3. Gene/locus MIM no.
4. cytogenetic location

OR you can also try with this file genemap2.txt

[Wayne]

Thanks so much for responding

Ok so I noticed this key... where is the list of phenotype keys and values? I have genemap2 downloaded ... it has disorder and comments... but not any kind of classification system or enough detail that I need. I feel like I'm missing a "phenotype file"

Answer 2

[Pierre Lindenbaum]

I'm attempting to compile a list of all immunology related diseases

Using the disease ontology and the following xslt stylesheet https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/do/do_children.xsl, get all the child terms under DOID:2914 (immune system disease in http://disease-ontology.org/)

$ curl "http://www.berkeleybop.org/ontologies/doid.owl" | \

xsltproc --stringparam ID "DOID:2914" do_children.xsl -

#ID   LABEL   URI   DESCRIPTION
DOID:2914   immune system disease   http://purl.obolibrary.org/obo/DOID_7  A disease of anatomical entity that is located_in the immune system.
DOID:0060056    hypersensitivity reaction disease   http://purl.obolibrary.org/obo/DOID_2914 
DOID:1205   hypersensitivity reaction type I disease    http://purl.obolibrary.org/obo/DOID_0060056  An immune system disease that is an exaggerated immune response to allergens, such as insect venom, dust mites, pollen, pet dander, drugs or some foods.
DOID:3044   food allergy    http://purl.obolibrary.org/obo/DOID_1205  A hypersensitivity reaction type I disease that is an abnormal response to a food, triggered by the body's immune system.
DOID:0060057    gluten allergic reaction    http://purl.obolibrary.org/obo/DOID_3044 
DOID:3660   wheat allergic reaction http://purl.obolibrary.org/obo/DOID_3044 
DOID:4376   milk allergic reaction  http://purl.obolibrary.org/obo/DOID_3044  A food allergy that results in adverse immune reaction to one or more of the proteins in cow's milk and/or the milk of other animals, which are normally harmless to the non-allergic individual.
DOID:4377   egg allergy http://purl.obolibrary.org/obo/DOID_3044  A food allergy that is an allergy or hypersensitivity to dietary substances from the yolk or whites of eggs, causing an overreaction of the immune system which may lead to severe physical symptoms.
DOID:4378   peanut allergic reaction    http://purl.obolibrary.org/obo/DOID_3044  A food allergy that is an allergy or hypersensitivity to dietary substances from peanuts causing an overreaction of the immune system which in a small percentage of people may lead to severe physical symptoms.
(...)