The omics discovery REST interface | Zendy

Gaurhari Dass | Zendy; Manh-Tu Vu | Zendy; Pan Xu | Zendy; Enrique Audain | Zendy; MarcPhillip Hitz | Zendy; Björn Grüning | Zendy; Henning Hermjakob | Zendy; Yasset PérezRiverol | Zendy

AI Assistant Blog Pricing

Home ZAIA Blog

Open Access

The omics discovery REST interface

Author(s) -

Gaurhari Dass,

Manh-Tu Vu,

Pan Xu,

Enrique Audain,

MarcPhillip Hitz,

Björn Grüning,

Henning Hermjakob,

Yasset PérezRiverol

Publication year - 2020

Publication title -

nucleic acids research

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 9.008

H-Index - 537

eISSN - 1362-4954

pISSN - 0305-1048

DOI - 10.1093/nar/gkaa326

Subject(s) - python (programming language) , metadata , interface (matter) , search engine indexing , genomics , biology , proteomics , dissemination , omics , tracing , annotation , computer science , computational biology , bioinformatics , information retrieval , world wide web , genome , gene , genetics , pulmonary surfactant , telecommunications , biochemistry , gibbs isotherm , operating system

The Omics Discovery Index is an open source platform that can be used to access, discover and disseminate omics datasets. OmicsDI integrates proteomics, genomics, metabolomics, models and transcriptomics datasets. Using an efficient indexing system, OmicsDI integrates different biological entities including genes, transcripts, proteins, metabolites and the corresponding publications from PubMed. In addition, it implements a group of pipelines to estimate the impact of each dataset by tracing the number of citations, reanalysis and biological entities reported by each dataset. Here, we present the OmicsDI REST interface (www.omicsdi.org/ws/) to enable programmatic access to any dataset in OmicsDI or all the datasets for a specific provider (database). Clients can perform queries on the API using different metadata information such as sample details (species, tissues, etc), instrumentation (mass spectrometer, sequencer), keywords and other provided annotations. In addition, we present two different libraries in R and Python to facilitate the development of tools that can programmatically interact with the OmicsDI REST interface.

The content you want is available to Zendy users.

Already have an account? Click here to sign in.

Having issues? You can contact us here

Accelerating Research