BioStudies
Names
More detailed information about this field from each metasource.
BioStudies
metasource: Fairsharing.org
version: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: BioStudies; editing status 2020-12-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CF7B last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
biostudies
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Names
More detailed information about this field from each metasource.
BioStudies
metasource: Fairsharing.orgversion: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: BioStudies; editing status 2020-12-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CF7B last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
biostudies
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
Names
More detailed information about this field from each metasource.
BioStudies
metasource: Fairsharing.orgversion: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
metasource: re3data.org
version: re3data.org: BioStudies; editing status 2020-12-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CF7B last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
biostudies
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.
Description
More detailed information about this field from each metasource.
The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database can accept a wide range of types of studies described via a simple format. It also enables manuscript authors to submit supplementary information and link to it from the publication.
metasource: Fairsharing.orgversion: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
ArrayExpress (https://www.ebi.ac.uk/arrayexpress) is an archive of functional genomics data at EMBL-EBI, established in 2002, initially as an archive for publication-related microarray data and was later extended to accept sequencing-based data. Over the last decade an increasing share of biological experiments involve multiple technologies assaying different biological modalities, such as epigenetics, and RNA and protein expression, and thus the BioStudies database (https://www.ebi.ac.uk/biostudies) was established to deal with such multimodal data. Its central concept is a study, which typically is associated with a publication. BioStudies stores metadata describing the study, provides links to the relevant databases, such as European Nucleotide Archive (ENA), as well as hosts the types of data for which specialized databases do not exist. With BioStudies now fully functional, we are able to further harmonize the archival data infrastructure at EMBL-EBI, and ArrayExpress is being migrated to BioStudies. In future, all functional genomics data will be archived at BioStudies. The process will be seamless for the users, who will continue to submit data using the online tool Annotare and will be able to query and download data largely in the same manner as before. Nevertheless, some technical aspects, particularly programmatic access, will change. This update guides the users through these changes.
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
The BioStudies database holds descriptions of biological studies, links to data from these studies in other databases at EMBL-EBI or outside, as well as data that do not fit in the structured archives at EMBL-EBI. The database accepts submissions via an online tool, or in a simple tab-delimited format. It also enables authors to submit supplementary information and link to it from the publication.
metasource: re3data.orgversion: re3data.org: BioStudies; editing status 2020-12-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CF7B last accessed: 2022-11-04
Webpage:
https://www.ebi.ac.uk/biostudies/Webpage
More detailed information about this field from each metasource.
https://www.ebi.ac.uk/biostudies/
metasource: Fairsharing.orgversion: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: re3data.org
version: re3data.org: BioStudies; editing status 2020-12-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CF7B last accessed: 2022-11-04
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
https://www.ebi.ac.uk/biostudies
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Licence:
Name: EMBL-EBI Terms of UseLicence name
More detailed information about this field from each metasource.
EMBL-EBI Terms of Use
metasource: Fairsharing.orgversion: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
CC
metasource: re3data.orgversion: re3data.org: BioStudies; editing status 2020-12-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CF7B last accessed: 2022-11-04
Licence URL
More detailed information about this field from each metasource.
http://www.ebi.ac.uk/about/terms-of-use
metasource: Fairsharing.orgversion: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
https://www.ebi.ac.uk/about/terms-of-use
metasource: re3data.orgversion: re3data.org: BioStudies; editing status 2020-12-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CF7B last accessed: 2022-11-04
Publications:
Publications
More detailed information about this field from each metasource.
The BioStudies database-one stop shop for all data supporting a life sciences study
PMID: 29069414
metasource: Fairsharing.org
version: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The BioStudies database
PMID: 26700850
metasource: Fairsharing.org
version: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gkaa1062
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkx965
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Publications
More detailed information about this field from each metasource.
The BioStudies database-one stop shop for all data supporting a life sciences study
PMID: 29069414
metasource: Fairsharing.org
version: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
The BioStudies database
PMID: 26700850
metasource: Fairsharing.org
version: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
http://dx.doi.org/10.1093/nar/gkaa1062
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://dx.doi.org/10.1093/nar/gkx965
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
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The BioStudies database-one stop shop for all data supporting a life sciences study
PubMed citations: 34.
34 articles citing: The BioStudies database-one stop shop for all data supporting a life sciences study
Ecosystem-specific microbiota and microbiome databases in the era of big data. PMID:35842686
Data Mining, Quality and Management in the Life Sciences. PMID:35507257
Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. PMID:35382863
Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis. PMID:34492007
Current Approaches for Advancement in Understanding the Molecular Mechanisms of Mycotoxin Biosynthesis. PMID:34360643
A general role for TANGO1, encoded by MIA3, in secretory pathway organization and function. PMID:34350936
BRCA2 binding through a cryptic repeated motif to HSF2BP oligomers does not impact meiotic recombination. PMID:34326328
The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing. PMID:34048576
A native conjugative plasmid confers potential selective advantages to plant growth-promoting Bacillus velezensis strain GH1-13. PMID:33990691
A community resource for paired genomic and metabolomic data mining. PMID:33589842
A Semi-automated Organoid Screening Method Demonstrates Epigenetic Control of Intestinal Epithelial Differentiation. PMID:33575256
Data-deposition protocols for correlative soft X-ray tomography and super-resolution structured illumination microscopy applications. PMID:33490973
Reproducible image handling and analysis. PMID:33480052
A digital 3D reference atlas reveals cellular growth patterns shaping the Arabidopsis ovule. PMID:33404501
Pairing of segmentation clock genes drives robust pattern formation. PMID:33361814
From ArrayExpress to BioStudies. PMID:33211879
CEN-tools: an integrative platform to identify the contexts of essential genes. PMID:33073517
Setting the stage for next-generation risk assessment with non-animal approaches: the EU-ToxRisk project experience. PMID:32886186
The EU-ToxRisk method documentation, data processing and chemical testing pipeline for the regulatory use of new approach methods. PMID:32632539
Dynamic rewiring of the human interactome by interferon signaling. PMID:32539747
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources. PMID:32429287
Effect of Vectashield-induced fluorescence quenching on conventional and super-resolution microscopy. PMID:32296095
A Scanning Electron Micrograph-based Resource for Identification of Loci Involved in Epidermal Development in Tomato: Elucidation of a New Function for the Mixta-like Transcription Factor in Leaves. PMID:32169962
A comparative study of machine learning algorithms for predicting acute kidney injury after liver cancer resection. PMID:32140301
Supervised Machine Learning Predictive Analytics For Triple-Negative Breast Cancer Death Outcomes. PMID:31802913
In Silico Toxicology Data Resources to Support Read-Across and (Q)SAR. PMID:31244651
Biomedical Image Processing with Containers and Deep Learning: An Automated Analysis Pipeline: Data architecture, artificial intelligence, automated processing, containerization, and clusters orchestration ease the transition from data acquisition to insights in medium-to-large datasets. PMID:31094000
Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network. PMID:30667172
A data citation roadmap for scientific publishers. PMID:30457573
The European Bioinformatics Institute in 2018: tools, infrastructure and training. PMID:30445657
A call for public archives for biological image data. PMID:30377375
ArrayExpress update - from bulk to single-cell expression data. PMID:30357387
The 2018 Nucleic Acids Research database issue and the online molecular biology database collection. PMID:29316735
The European Bioinformatics Institute in 2017: data coordination and integration. PMID:29186510 -
The BioStudies database
PubMed citations: 13.
13 articles citing: The BioStudies database
Data Mining, Quality and Management in the Life Sciences. PMID:35507257
Sharing Biomedical Data Obtained Through Government-Funded Research and Development Projects in Korea. PMID:34788906
From ArrayExpress to BioStudies. PMID:33211879
Systems analysis of RhoGEF and RhoGAP regulatory proteins reveals spatially organized RAC1 signalling from integrin adhesions. PMID:32203420
Determining cellular CTCF and cohesin abundances to constrain 3D genome models. PMID:31205001
A data citation roadmap for scholarly data repositories. PMID:30971690
MECP2 variation in Rett syndrome-An overview of current coverage of genetic and phenotype data within existing databases. PMID:29704307
Opportunities and Challenges in Building a Spatiotemporal Multi-scale Model of the Human Pancreatic β Cell. PMID:29570991
Europe PMC in 2017. PMID:29161421
The Image Data Resource: A Bioimage Data Integration and Publication Platform. PMID:28775673
Preparing for Preprints. PMID:27908933
SSBD: a database of quantitative data of spatiotemporal dynamics of biological phenomena. PMID:27412095
Image data in need of a home. PMID:26700853 - http://dx.doi.org/10.1093/nar/gkaa1062
- http://dx.doi.org/10.1093/nar/gkx965
Tags:
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protocol
metasource: Fairsharing.org
version: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
study design
metasource: Fairsharing.org
version: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
microarray data and other gene expression databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
biomedical science
metasource: re3data.org
version: re3data.org: BioStudies; editing status 2020-12-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CF7B last accessed: 2022-11-04
experimental design and studies
metasource: bio.tools
version: extracted_at: 2022-11-04T11:32:12.196036
Tags
More detailed information about this field from each metasource.
protocol
metasource: Fairsharing.orgversion: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
study design
metasource: Fairsharing.orgversion: FAIRsharing.org: BioStudies; BioStudies; DOI: https://doi.org/10.25504/FAIRsharing.mtjvme; Last edited: Feb. 8, 2021, 8:55 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
microarray data and other gene expression databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
biomedical science
metasource: re3data.orgversion: re3data.org: BioStudies; editing status 2020-12-22; re3data.org - Registry of Research Data Repositories. http://doi.org/10.17616/R3CF7B last accessed: 2022-11-04
experimental design and studies
metasource: bio.toolsversion: extracted_at: 2022-11-04T11:32:12.196036
protocol study design microarray data and other gene expression biomedical science experimental design and studies
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