How to cite this record
FAIRsharing.org: DataMed; DataMed; DOI: https://doi.org/10.25504/FAIRsharing.v5q4zc;
Last edited: March 8, 2021, 11:41 a.m.; Last accessed: Oct 17 2021 1:57 a.m.
Publication for citation
DataMed - an open source discovery index for finding biomedical datasets.
Chen X,Gururaj AE,Ozyurt B,Liu R,Soysal E,Cohen T,Tiryaki F,Li Y,Zong N,Jiang M,Rogith D,Salimi M,Kim HE,Rocca-Serra P,Gonzalez-Beltran A,Farcas C,Johnson T,Margolis R,Alter G,Sansone SA,Fore IM,Ohno-Machado L,Grethe JS,Xu H; J Am Med Inform Assoc ;
2018;
10.1093/jamia/ocx121 ;
Edits to 'https://fairsharing.org/FAIRsharing.v5q4zc' by 'The FAIRsharing Team' at 11:41, 08 Mar 2021 (approved):
'related_databases' has been modified:
Before:
Mouse Phenome Database
WormBase
Cell Image Library
ArrayExpress
PeptideAtlas
NeuroMorpho.Org
Rat Genome Database
Gene Expression Omnibus
Sequence Read Archive
Database of Genotypes and Phenotypes
Dryad
ClinicalTrials.gov
The Cardiovascular Research Grid
GeneNetwork
RCSB Protein Data Bank
The Cancer Imaging Archive
UniProt Knowledgebase
Biological Magnetic Resonance Databank
VectorBase
Electron Microscopy Data Bank
ProteomeXchange
NeuroVault
Nuclear Receptor Signaling Atlas
Immunology Database and Analysis Portal
NIDDK Central Repository
Metabolomics Workbench
NCBI BioProject
Library of Integrated Network-Based Cellular Signatures Data Portal
National Sleep Research Resource
ClinVar
Gemma
Inter-university Consortium for Political and Social Research
Omics Discovery Index
DataCite Repository
GTEx Portal
Center for Expanded Data Annotation and Retrieval Workbench
National Cancer Institute's Genomic Data Commons
Neuroimaging Informatics Tools and Resources Collaboratory Image Repository
After:
Mouse Phenome Database
WormBase
Cell Image Library
ArrayExpress
PeptideAtlas
NeuroMorpho.Org
Rat Genome Database
Gene Expression Omnibus
Sequence Read Archive
Database of Genotypes and Phenotypes
Dryad
ClinicalTrials.gov
The Cardiovascular Research Grid
GeneNetwork
RCSB Protein Data Bank
The Cancer Imaging Archive
UniProt Knowledgebase
Biological Magnetic Resonance Databank
VectorBase
Giga Science Database
Electron Microscopy Data Bank
ProteomeXchange
NeuroVault
Coherent X-ray Imaging Data Bank
Nuclear Receptor Signaling Atlas
Immunology Database and Analysis Portal
NIDDK Central Repository
Metabolomics Workbench
NCBI BioProject
Library of Integrated Network-Based Cellular Signatures Data Portal
National Sleep Research Resource
ClinVar
Gemma
Zenodo
MorphoBank
Inter-university Consortium for Political and Social Research
Omics Discovery Index
UK Data Archive
DataCite Repository
Australian Data Archive
GTEx Portal
Center for Expanded Data Annotation and Retrieval Workbench
National Cancer Institute's Genomic Data Commons
Neuroimaging Informatics Tools and Resources Collaboratory Image Repository
Added:
Giga Science Database
Coherent X-ray Imaging Data Bank
Zenodo
MorphoBank
UK Data Archive
Australian Data Archive
Removed:
Edits to 'https://fairsharing.org/FAIRsharing.v5q4zc' by 'The FAIRsharing Team' at 11:35, 08 Mar 2021 (approved):
'organizations' has been modified:
Before:
National Institutes of Health (NIH), Bethesda, MD, USA|https://www.nih.gov/|Funds
After:
National Institutes of Health (NIH), Bethesda, MD, USA|https://www.nih.gov/|Funds
biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) Consortium|https://datamed.org/|Maintains
Added:
biomedical and healthCAre Data Discovery Index Ecosystem (bioCADDIE) Consortium|https://datamed.org/|Maintains
Removed:
'standardsImplemented' has been modified:
Before:
Schema.org
DatA Tag Suite
After:
Schema.org
DatA Tag Suite
Bioschemas
Added:
Bioschemas
Removed:
'related_databases' has been modified:
Before:
After:
Mouse Phenome Database
WormBase
Cell Image Library
ArrayExpress
PeptideAtlas
NeuroMorpho.Org
Rat Genome Database
Gene Expression Omnibus
Sequence Read Archive
Database of Genotypes and Phenotypes
Dryad
ClinicalTrials.gov
The Cardiovascular Research Grid
GeneNetwork
RCSB Protein Data Bank
The Cancer Imaging Archive
UniProt Knowledgebase
Biological Magnetic Resonance Databank
VectorBase
Electron Microscopy Data Bank
ProteomeXchange
NeuroVault
Nuclear Receptor Signaling Atlas
Immunology Database and Analysis Portal
NIDDK Central Repository
Metabolomics Workbench
NCBI BioProject
Library of Integrated Network-Based Cellular Signatures Data Portal
National Sleep Research Resource
ClinVar
Gemma
Inter-university Consortium for Political and Social Research
Omics Discovery Index
DataCite Repository
GTEx Portal
Center for Expanded Data Annotation and Retrieval Workbench
National Cancer Institute's Genomic Data Commons
Neuroimaging Informatics Tools and Resources Collaboratory Image Repository
Added:
Mouse Phenome Database
WormBase
Cell Image Library
ArrayExpress
PeptideAtlas
NeuroMorpho.Org
Rat Genome Database
Gene Expression Omnibus
Sequence Read Archive
Database of Genotypes and Phenotypes
Dryad
ClinicalTrials.gov
The Cardiovascular Research Grid
GeneNetwork
RCSB Protein Data Bank
The Cancer Imaging Archive
UniProt Knowledgebase
Biological Magnetic Resonance Databank
VectorBase
Electron Microscopy Data Bank
ProteomeXchange
NeuroVault
Nuclear Receptor Signaling Atlas
Immunology Database and Analysis Portal
NIDDK Central Repository
Metabolomics Workbench
NCBI BioProject
Library of Integrated Network-Based Cellular Signatures Data Portal
National Sleep Research Resource
ClinVar
Gemma
Inter-university Consortium for Political and Social Research
Omics Discovery Index
DataCite Repository
GTEx Portal
Center for Expanded Data Annotation and Retrieval Workbench
National Cancer Institute's Genomic Data Commons
Neuroimaging Informatics Tools and Resources Collaboratory Image Repository
Removed:
'supportLinks' has been modified:
Before:
After:
contact form|https://datamed.org/about.php
help|https://datamed.org/help.php
online documentation|https://github.com/biocaddie
Added:
contact form|https://datamed.org/about.php
help|https://datamed.org/help.php
online documentation|https://github.com/biocaddie
Removed:
'description' has been modified:
Before: DataMed is a prototype biomedical data search engine. Its goal is to discover data sets across data repositories or data aggregators. In the future it will allow searching outside these boundaries. DataMed supports the NIH-endorsed FAIR principles of Findability, Accessibility, Interoperability and Reusability of datasets with current functionality assisting in finding datasets and providing access information about them.
The data repositories covered in this initial release have been selected by the bioCADDIE team and represent only a small sample of biomedical data. Many highly relevant data sets have not yet been indexed. Please provide suggestions on data repositories that DataMed should cover.
The translation of user queries into structured data used in the search is being refined. Advanced search allows users to structure their queries. Some DataMed search features are not yet available for all data. Please provide feedback about the quality of search results.
DataMed indexes the core metadata available for most datasets, but it offers enhanced search functions when repositories provide additional metadata. The Data Tag Suite (DATS) metadata specification has evolved with input from the community and will include a schema.org annotated serialization.
You can use the web interface and provide us feedback here about your search experience. This is a prototype in development and your valuable suggestions and comments will help us to make the system better.
After: DataMed is a prototype biomedical data search engine. Its goal is to discover data sets across data repositories or data aggregators. In the future it will allow searching outside these boundaries. DataMed supports the NIH-endorsed FAIR principles of Findability, Accessibility, Interoperability and Reusability of datasets with current functionality assisting in finding datasets and providing access information about them.
The data repositories covered in this initial release have been selected by the bioCADDIE team and represent only a small sample of biomedical data. DataMed indexes the core metadata available for most datasets, but it offers enhanced search functions when repositories provide additional metadata.
'onto_disciplines' has been modified:
Before:
Biomedical Science
After:
Biomedical Science
Data Integration
Added:
Data Integration
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'dataProcesses' has been modified:
Before:
After:
Submit Repository, data curation, https://datamed.org/submit_repository.php
Advanced Search, data access, https://datamed.org/advanced.php
Added:
Submit Repository, data curation, https://datamed.org/submit_repository.php
Advanced Search, data access, https://datamed.org/advanced.php
Removed:
'publications' has been modified:
Before:
After:
DataMed - an open source discovery index for finding biomedical datasets.|Chen X,Gururaj AE,Ozyurt B,Liu R,Soysal E,Cohen T,Tiryaki F,Li Y,Zong N,Jiang M,Rogith D,Salimi M,Kim HE,Rocca-Serra P,Gonzalez-Beltran A,Farcas C,Johnson T,Margolis R,Alter G,Sansone SA,Fore IM,Ohno-Machado L,Grethe JS,Xu H|J Am Med Inform Assoc|2018
Added:
DataMed - an open source discovery index for finding biomedical datasets.|Chen X,Gururaj AE,Ozyurt B,Liu R,Soysal E,Cohen T,Tiryaki F,Li Y,Zong N,Jiang M,Rogith D,Salimi M,Kim HE,Rocca-Serra P,Gonzalez-Beltran A,Farcas C,Johnson T,Margolis R,Alter G,Sansone SA,Fore IM,Ohno-Machado L,Grethe JS,Xu H|J Am Med Inform Assoc|2018
Removed:
'accessPoints' has been modified:
Before:
After:
REST|https://datamed.org/APIDoc.php|API Documentation
Added:
REST|https://datamed.org/APIDoc.php|API Documentation
Removed:
Edits to 'https://fairsharing.org/FAIRsharing.v5q4zc' by 'The FAIRsharing Team' at 13:23, 24 Oct 2019 (approved):
'onto_domains' has been modified:
Before:
After:
FAIR
Added:
FAIR
Removed:
Edits to 'https://fairsharing.org/FAIRsharing.v5q4zc' by 'The FAIRsharing Team' at 17:30, 02 Feb 2018 (approved):
'miriam_url' has been modified:
Before: None
After:
DataMed
