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Associated diseases

Associated diseases specifications


Unique identifier OMICS_17137
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License Apache License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


  • Primates
    • Homo sapiens



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  • person_outline Chunlei Wu <>

Additional information

Publications for in pipelines

PMCID: 5796402
PMID: 29390967
DOI: 10.1186/s12859-018-2041-5

[…] nes which the variant might affect as well as available drugs targeting these affected genes, he would have to query multiple biothings apis, e.g. which contains wikipathways information, which contains variant annotation information, as well as which contains drug annotation information. thus, a typical workflow would involve the following steps (fig. ):quer […]

PMCID: 5796402
PMID: 29390967
DOI: 10.1186/s12859-018-2041-5

[…] to retrieve all uniprot ids related to these wikipathways ids.query to retrieve the drug objects associated to the target proteins, using the uniprot ids found in step f.fig. 2, query to retrieve the annotation objects for variant “chr6:g.26093141g > a” and “chr12:g.111351981c > t”., parse the annotation objects to get the ncbi gene ids related […]

To access a full list of citations, you will need to upgrade to our premium service. in publications

PMCID: 5796402
PMID: 29390967
DOI: 10.1186/s12859-018-2041-5

[…] alone is not sufficient for rich integrative queries across apis., here, we have implemented json for linking data (json-ld) technology on the biothings apis that we have developed,, and json-ld provides a standard way to add semantic context to the existing json data structure, for the purpose of enhancing the interoperability between apis. […]

PMCID: 5610688
PMID: 28975082
DOI: 10.3389/fonc.2017.00214

[…] of variants., while evalutation of each database by both clinical and informatics team members, databases marked with “a” are maintained, recently (or continuously) updated, and curated. the database includes both civic and cancer genome interpreter data. the last column in the table notes bulk access approaches as these are relevant when including databases […]

PMCID: 5333373
PMID: 28240266
DOI: 10.1038/ncomms14519

[…] analyses to characterize the properties of sqtl snps., we functionally annotated 1,539 sqtl and 48,068 non-sqtl snps by using snpeff. information of snpeff annotation was collected by using ( and variant effect predictor (vep). according to these annotations, snps were classified into the following categories: nonsense, readthrough, start-loss, […]

PMCID: 5367263
PMID: 28138153
DOI: 10.1038/ng.3774

[…] and variant synonyms are determined by curators, reviewed by editors and stored in a standardized format (for example, hgvs) for each variant. additional variant information is imported through the annotation api, providing links to complementary resources and variant annotations such as clinvar, cosmic and exac. each variant is associated with a single gene, and each gene view […]

To access a full list of publications, you will need to upgrade to our premium service. institution(s)
Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Biomedical Informatics and Medical Education, The University of Washington, Seattle, WA, USA; McDonnell Genome Institute, Washington University School of Medicine, St. Louis, MO, USA; Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA; The Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA, USA; Center for Research in Biological Systems, University of California San Diego, La Jolla, CA, USA; Lawrence Berkeley National Laboratory, Berkeley, CA, USA funding source(s)
Supported by the US National Institute of Health (grants U01HG008473, GM083924 and U54GM114833, U01HG006476, and K22CA188163); by the Scripps Translational Science Institute with an NIH-NCATS Clinical and Translational Science Award (CTSA; 5 UL1 TR001114). reviews

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