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Protocols 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




No version available


  • person_outline Chunlei Wu <>

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Publications for citations


Cross linking BioThings APIs through JSON LD to facilitate knowledge exploration

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. […]


Resources for Interpreting Variants in Precision Genomic Oncology Applications

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 […]


Genome wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia associated loci

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, […]


CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer

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 […]

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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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