Standards > model/format > bsg-s000078


ready Investigation Study Assay Tabular

Abbreviation:ISA-Tab


Recommended
General Information
General-purpose ISA-Tab file format - an extensible, hierarchical structure that focuses on the description of the experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships).

How to cite this record FAIRsharing.org; DOI: https://doi.org/10.25504/FAIRsharing.53gp75; Last edited: Feb. 22, 2018, 1:59 p.m.; Last accessed: Feb 24 2018 4:04 a.m.



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Record updated: Nov. 21, 2017, 11:27 a.m. by The FAIRsharing Team.



Access / Retrieve Data

Conditions of Use





Publications

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level.

Rocca-Serra P, Brandizi M, Maguire E, Sklyar N, Taylor C, Begley K, Field D, Harris S, Hide W, Hofmann O, Neumann S, Sterk P, Tong W, Sansone SA.
Bioinformatics 2010

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MetaboLights—an open-access general-purpose repository for metabolomics studies and associated meta-data

Haug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Rocca-Serra P, Maguire E, González-Beltrán A, Sansone SA, Griffin JL, Steinbeck C.
Nucleic Acid Research 2013

View Paper (PubMed) View Paper (DOI)

OntoMaton: a bioportal powered ontology widget for Google Spreadsheets

Eamonn Maguire, Alejandra Gonzalez-Beltran, Trish Whetzel, Susanna-Assunta Sansone, Philippe Rocca-Serra
Bioinformatics 2012

View Paper (PubMed) View Paper (DOI)


Implementing Databases (9)
Stem Cell Discovery Engine
Comparison system for cancer stem cell analysis

MetaboLights
MetaboLights is a database for Metabolomics experiments and derived information. The database is cross-species, cross-technique and covers metabolite structures and their reference spectra as well as their biological roles, locations and concentrations, and experimental data from metabolic experiments. We offer user-submission tools and have strong reporting capabilities. We will utilise and further develop de-facto standard formats where various components are encapsulated, such as the encoded spectral and chromatographic data, and associated information about the chemical structure, as well as metadata describing assays and the study as a whole. We are dedicated to collaborate closely with major parties in world-wide metabolomics communities, such as the Metabolomics Society and the associated Metabolomics Standards Initiative (MSI).

Golm Metabolome Database
The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discovery of novel metabolic biomarkers.

Giga Science Database
GigaDB primarily serves as a repository to host data and tools associated with articles in GigaScience; however, it also includes a subset of datasets that are not associated with GigaScience articles. GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support an article or study.

Stem Cell Commons
The Stem Cell Commons were initiated by the Harvard Stem Cell Institute to develop a community for stem cell bioinformatics. This open source environment for sharing, processing and analyzing stem cell data brings together stem cell data sets with tools for curation, dissemination and analysis. Standardization of the analytical approaches will enable researchers to directly compare and integrate their results with experiments and disease models in the Commons.

FAIRDOMHub
The FAIRDOMHub is a publicly available resource build using the SEEK software, which enables collaborations within the scientific community. FAIRDOM will establish a support and service network for European Systems Biology. It will serve projects in standardizing, managing and disseminating data and models in a FAIR manner: Findable, Accessible, Interoperable and Reusable. FAIRDOM is an initiative to develop a community, and establish an internationally sustained Data and Model Management service to the European Systems Biology community. FAIRDOM is a joint action of ERA-Net EraSysAPP and European Research Infrastructure ISBE.

Genetic and Genomic Information System
GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, markers, polymorphisms, germplasms, phenotypes and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest. GnpIS is used by both large international projects and plant science departments at the French National Institute for Agricultural Research. It is regularly improved and released several times per year. GnpIS is accessible through a web portal and allows to browse different types of data either independently through dedicated interfaces or simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools.

Microenvironment Perturbagen LINCS Center image server
The MEP LINCS project contributes to the development of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) program by developing a dataset and computational strategy to elucidate how microenvironment (ME) signals affect cell intrinsic intracellular transcriptional- and protein-defined molecular networks to generate experimentally observable cellular phenotypes measured by high-content imaging.

NCI Center for Strategic Scientific Initiatives Data Coordinating Center
The CSSI Data Coordinating Center (DCC) provides the greater Cancer Research and Biomedical Research communities access to the data from a myriad of projects that have been supported by CSSI -- serving as a permanent repository for these and related investigations. The DCC allows users in the community to download the metadata and data from these investigations in the ISA-TAB format. The DCC also allows any user to upload and download the metadata and data associated with investigations. The DCC has a graphical user interface allowing users to easily visualize the content within the data archives

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