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OmicsDI specifications

Information


Unique identifier OMICS_18209
Name OmicsDI
Alternative name Omics Discovery Index
Restrictions to use None
Community driven No
Data access Browse, Application programming interface
User data submission Not allowed
Maintained Yes

Maintainers


  • person_outline Yasset Perez-Riverol
  • person_outline Henning Hermjakob
  • person_outline Andrey Zorin
  • person_outline Gaurhari Dass
  • person_outline Mihai Glonț

Publications for Omics Discovery Index

OmicsDI citations

 (6)
library_books

A lost opportunity for science: journals promote data sharing in metabolomics but do not enforce it

2017
Metabolomics
PMCID: 5808091
PMID: 29479297
DOI: 10.1007/s11306-017-1309-5

[…] There are now > 750 metabolomics studies indexed on MetabolomeXchange (http://www.metabolomexchange.org/) and > 1300 on OmicsDI (Perez-Riverol et al. ). These studies with data publicly available in dedicated repositories [MetaboLights (Haug et al. ), Metabolomics Workbench (Sud et al. ), MetaPhen (Carroll et al. ), Me […]

library_books

BioModels: expanding horizons to include more modelling approaches and formats

2017
Nucleic Acids Res
PMCID: 5753244
PMID: 29106614
DOI: 10.1093/nar/gkx1023

[…] An effective search is critical to any repository that seeks to encourage model dissemination and reuse. The upgraded search system, based on the Omics Discovery Index () and the EBI search engine (), retains the in-depth capabilities of the previous system whilst offering a streamlined experience for end users in terms of speed and ease of use […]

library_books

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets

2017
Proteomics
PMCID: 5707441
PMID: 28792687
DOI: 10.1002/pmic.201700244

[…] In conclusion, it is important to note that, at the moment of writing, several popular resources and tools are already using OLS Client as annotation source, including resources such as IntAct, OmicsDI, BioModels, and the Reactome Pathway Annotation Tool, or stand‐alone tools (which use OLS Dialog on top) such as PeptideShaker, the Laboratory Information Management System (LIMS) colims (http […]

library_books

DATS, the data tag suite to enable discoverability of datasets

2017
Sci Data
PMCID: 5460592
PMID: 28585923
DOI: 10.1038/sdata.2017.59

[…] search (ICPSR), the world's largest archive of digital social science data and one of the NIH-supported repositories (https://www.nlm.nih.gov/NIHbmic/nih_data_sharing_repositories.html); the NIH BD2K OmicsDI, a data discovery index for proteomics, genomics and metabolomics datasets; the NIH Federal Interagency Traumatic Brain Injury Research (FITBIR, https://fitbir.nih.gov), an informatics system […]

library_books

The EBI search engine: EBI search as a service—making biological data accessible for all

2017
Nucleic Acids Res
PMCID: 5570174
PMID: 28472374
DOI: 10.1093/nar/gkx359

[…] of the EBI Search API (Application Programming Interface) to create complex views of inter-related data, thus allowing users to combine and create different views. Examples of this can be seen on the OmicsDI (http://www.omicsdi.org/) portal that integrates 11 data sources relating to transcriptomics, genomics, proteomics and metabolomics; the EBI Metagenomics portal is another example that provide […]

library_books

The ProteomeXchange consortium in 2017: supporting the cultural change in proteomics public data deposition

2016
Nucleic Acids Res
PMCID: 5210636
PMID: 27924013
DOI: 10.1093/nar/gkw936

[…] ‘omics data sets is a key area where easy public accessibility of data sets will accelerate progress in the field. In this context, the PX partners are actively contributing to the recently developed OmicsDI (Omics Discovery Index) portal (http://www.omicsdi.org). The objective of OmicsDI is to provide a centralized access point to omics data sets coming from different omics approaches including g […]

Citations

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OmicsDI institution(s)
European Molecular Biology Laboratory, EMBL-European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridge, UK; Department of Physiology and Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; Department of Medicine, Division of Cardiology, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA; State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Lifeomics, National Center for Protein Sciences (The PHOENIX Center, Beijing), Beijing, China
OmicsDI funding source(s)
Supported by US NIH BD2K grant U54 GM114833, EMBL core funding, the Wellcome Trust (grant number WT101477MA) and EMBL core funding.

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