Best way to filter a list of diseases by those relating to the immune system?

Question

[psyc_biostars]

I have a list of diseases which I got from GWAS Catalog associations. However, I want to be able to filter these out systematically (via R), leaving only diseases related to the immune system.

Does anyone have any suggestions for how to do this? I thought it might be an idea to get a list of all immune diseases and all immune cell types, and to keep any entry that mentions those terms.

[Ram]

Please add more relevant tags. Is R really the only relevant tag here?

Answer 1

[Pierre Lindenbaum]

GWAS use the Experimental Factor Ontology https://www.ebi.ac.uk/ols/ontologies/efo . There is an associated OWL file for download . I've got a tool that performs a very basic scan over all the simple children of a given term. For immune system disease I get the following terms that you can use to 'grep' the database.

	http://www.ebi.ac.uk/efo/EFO_0003898 ankylosing spondylitis
	http://www.ebi.ac.uk/efo/EFO_0000783 myositis
	http://www.ebi.ac.uk/efo/EFO_1001806 macrophage activation syndrome
	http://www.ebi.ac.uk/efo/EFO_1001807 malacoplakia
	http://www.ebi.ac.uk/efo/EFO_1000719 juvenile dermatitis herpetiformis
	http://www.orpha.net/ORDO/Orphanet_602 Distal myopathy, Nonaka type
	http://www.orpha.net/ORDO/Orphanet_2841 Familial benign chronic pemphigus
	http://www.ebi.ac.uk/efo/EFO_0005676 Autoimmune Hepatitis
	http://www.ebi.ac.uk/efo/EFO_0009313 Linear IgA Dermatosis
	http://www.ebi.ac.uk/efo/EFO_0000540 immune system disease
	http://www.ebi.ac.uk/efo/EFO_0009553 HIV-associated cancer
	http://www.ebi.ac.uk/efo/EFO_0007460 reactive arthritis
	http://www.ebi.ac.uk/efo/EFO_0007382 multiple chemical sensitivity
	http://www.ebi.ac.uk/efo/EFO_0007220 congenital toxoplasmosis
	http://www.orpha.net/ORDO/Orphanet_1839 Hereditary mucoepithelial dysplasia
	http://www.ebi.ac.uk/efo/EFO_1001165 Schnitzler syndrome
	http://www.ebi.ac.uk/efo/EFO_1000870 CNS demyelinating autoimmune disease
	http://www.ebi.ac.uk/efo/EFO_0000706 spondyloarthropathy
	http://www.ebi.ac.uk/efo/EFO_0000676 psoriasis
	http://www.ebi.ac.uk/efo/EFO_1000747 parapsoriasis
	http://www.orpha.net/ORDO/Orphanet_79477 Griscelli disease type 2
	http://www.orpha.net/ORDO/Orphanet_83617 Agammaglobulinemia - microcephaly - craniosynostosis - severe dermatitis
	http://www.ebi.ac.uk/efo/EFO_1000749 pemphigus
	http://www.ebi.ac.uk/efo/EFO_0006812 autoimmune thyroid disease
	http://www.orpha.net/ORDO/Orphanet_314 Erythroderma desquamativum
	http://www.ebi.ac.uk/efo/EFO_0006813 atrophic thyroiditis
	http://www.ebi.ac.uk/efo/EFO_0005846 cryoglobulinemia
	http://www.ebi.ac.uk/efo/EFO_0005687 fibromyalgia
	http://www.ebi.ac.uk/efo/EFO_0003063 polymyositis
	http://www.ebi.ac.uk/efo/EFO_0002498 aggressive insulitis
	http://www.ebi.ac.uk/efo/EFO_0008598 autoimmune bullous skin disease
	http://www.ebi.ac.uk/efo/EFO_0009651 rag2 deficiency
	http://www.orpha.net/ORDO/Orphanet_183770 Rare genetic immune disease
	http://www.orpha.net/ORDO/Orphanet_183494 Genetic immune deficiency with skin involvement
	http://www.ebi.ac.uk/efo/EFO_1002004 drug hypersensitivity syndrome
	http://www.ebi.ac.uk/efo/EFO_1002003 hypersensitivity reaction disease
	http://www.ebi.ac.uk/efo/EFO_1001994 Scleroderma Polymyositis Overlap Syndrome
	http://www.ebi.ac.uk/efo/EFO_1001995 Sclerodermatomyositis
	http://www.ebi.ac.uk/efo/EFO_1001511 monogenic diabetes
	http://www.ebi.ac.uk/efo/EFO_1001115 POEMS syndrome
	http://www.ebi.ac.uk/efo/EFO_1001039 Melkersson-Rosenthal syndrome
	http://www.ebi.ac.uk/efo/EFO_1001316 Eosinophilia-Myalgia Syndrome
	http://www.ebi.ac.uk/efo/EFO_0002502 benign insulitis
	http://www.orpha.net/ORDO/Orphanet_302 Epidermodysplasia verruciformis
	http://www.ebi.ac.uk/efo/EFO_0010647 STAT3 gain of function
	http://www.ebi.ac.uk/efo/EFO_0009538 chronic inflammatory demyelinating polyneuropathy
	http://www.ebi.ac.uk/efo/EFO_0008602 paraneoplastic pemphigus
	http://www.ebi.ac.uk/efo/EFO_0005297 Granulomatosis with Polyangiitis
	http://www.ebi.ac.uk/efo/EFO_0007433 phagocyte bactericidal dysfunction
	http://www.ebi.ac.uk/efo/EFO_0007284 geotrichosis
	http://www.ebi.ac.uk/efo/EFO_0005140 autoimmune disease
	http://www.ebi.ac.uk/efo/EFO_1000691 epidermolysis bullosa acquisita
	http://www.ebi.ac.uk/efo/EFO_1001264 Anemia, Hemolytic, Autoimmune
	http://www.ebi.ac.uk/efo/EFO_1001341 Heavy Chain Disease
	http://www.ebi.ac.uk/efo/EFO_0007160 autoimmune thrombocytopenic purpura
	http://www.ebi.ac.uk/efo/EFO_1000297 Histiocytic and Dendritic Cell Neoplasm
	http://www.ebi.ac.uk/efo/EFO_1001221 twin-to-twin transfusion syndrome
	http://www.ebi.ac.uk/efo/EFO_1000771 subcorneal pustular dermatosis
	http://www.ebi.ac.uk/efo/EFO_1001860 thymus hyperplasia
	http://www.ebi.ac.uk/efo/EFO_1001982 Antisynthetase syndrome
	http://www.ebi.ac.uk/efo/EFO_1001820 oroficial granulomatosis
	http://www.orpha.net/ORDO/Orphanet_906 Wiskott-Aldrich syndrome
	http://www.ebi.ac.uk/efo/EFO_1001988 Juvenile Polymyositis
	http://www.orpha.net/ORDO/Orphanet_179 Birdshot chorioretinopathy
	http://www.orpha.net/ORDO/Orphanet_379 Chronic granulomatous disease
	http://www.ebi.ac.uk/efo/EFO_0007208 Churg-Strauss syndrome
	http://www.ebi.ac.uk/efo/EFO_0009706 latent autoimmune diabetes in adults
	http://www.ebi.ac.uk/efo/EFO_1001819 orbital myositis
	http://www.orpha.net/ORDO/Orphanet_279943 Hereditary neutrophilia
	http://www.orpha.net/ORDO/Orphanet_2314 Autosomal dominant hyper-IgE syndrome
	http://www.ebi.ac.uk/efo/EFO_0007200 cerebral toxoplasmosis
	http://www.ebi.ac.uk/efo/EFO_0007323 inclusion body myositis
	http://www.ebi.ac.uk/efo/EFO_0007322 idiopathic CD4-positive T-lymphocytopenia
	http://www.ebi.ac.uk/efo/EFO_0007371 Miller Fisher syndrome
	http://www.ebi.ac.uk/efo/EFO_1000680 mucous membrane pemphigoid
	http://www.ebi.ac.uk/efo/EFO_1001494 psoriasis vulgaris
	http://www.ebi.ac.uk/efo/EFO_0007292 Guillain-Barre syndrome
	http://www.ebi.ac.uk/efo/EFO_1000684 dermatitis herpetiformis
	http://www.ebi.ac.uk/efo/EFO_1001016 leukostasis
	http://www.ebi.ac.uk/efo/EFO_1001856 Susac Syndrome
	http://www.ebi.ac.uk/efo/EFO_1000965 Henoch-Schoenlein purpura

view raw biostar441624.txt hosted with ❤ by GitHub

[psyc_biostars]

Great resource, thank you - what is the tool that you use to do this?

[Pierre Lindenbaum]

https://github.com/lindenb/jsandbox/blob/master/src/sandbox/tools/owl/OWLTool.java