Toward interoperable bioscience data

Sansone, Susanna-Assunta; Rocca-Serra, Philippe; Field, Dawn; Maguire, Eamonn; Taylor, Chris; Hofmann, Oliver; Fang, Hong; Neumann, Steffen; Tong, Weida; Amaral‐Zettler, Linda; Begley, Kimberly; Booth, Tim; Bougueleret, Lydie; Burns, Gully A. P. C.; Chapman, Brad; Clark, Tim W.; Coleman, Lisa; Copeland, Jay; Das, Sudeshna; Daruvar, Antoine de; Matos, Paula de; Dix, Ian; Edmunds, Scott; Evelo, Chris T.; Forster, Mark K.; Gaudet, Pascale; Gilbert, Jack A.; Goble, Carole; Griffin, Julian L.; Jacob, Daniel; Kleinjans, Jos; Harland, Lee; Haug, Kenneth; Hermjakob, Henning; Sui, Shannan Ho; Laederach, Alain; Liang, Shuang; Marshall, Stephen; McGrath, Annette; Merrill, Emily; Reilly, Dorothy; Roux, Magali; Shamu, Caroline E.; Shang, Catherine A.; Steinbeck, Christoph; Trefethen, Anne; Williams‐Jones, Bryn; Wolstencroft, Katy; Xenarios, Ioannis; Hide, Winston

doi:10.1038/ng.1054

Cited by 375 publications

(319 citation statements)

References 30 publications

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“…ToxBank uses the Investigation/Study/Assay (ISA) infrastructure open source desktop software suite. [33] Ontologies and a domain-specific ToxBank keyword hierarchy are used to enrich datasets by adding enough experimental metadata to make the archives comprehensible and reusable. [16] The ISA2RDF tool developed by ToxBank builds on the ISA-Tab framework and facilitates conversion of investigation meta-data into the semantic web standard RDF format.…”

Section: Toxbankmentioning

confidence: 99%

“…Investigational data generated by the research program is prepared and reviewed by SEURAT-1 investigators using the ISAcreator [33] tool to enter the experimental design, with the steps of the investigation each linked to SEURAT-1 protocols as well as to any raw or processed data. This ensures the data is in a defined and standardized format agreed across the cluster.…”

Section: Design Of the Toxbank Data Warehousementioning

confidence: 99%

“…[33] It is being used to represent the diverse types of experimental data within the TBDW. Data access and upload procedures are defined by an investigation API.…”

Section: Toxbank Data Warehouse Architecture and Technologiesmentioning

confidence: 99%

“…The ISA2RDF tool developed by ToxBank builds on the SPECIAL ISSUE Figure 3. Screen captures of the ToxBank Data Warehouse graphical user interface for uploading, searching, browsing, and downloading cluster protocols and data (currently in the beta-testing phase), along with the ISAcreator software [33] for preparing an investigation dataset. Links to compound and biomaterials information in the ToxBank wiki (wiki.toxbank.net) are provided for all protocols and data sets.…”

Section: Toxbank Data Warehouse Architecture and Technologiesmentioning

confidence: 99%

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The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing

Kohonen

Benfenati

Bower

et al. 2013

Molecular Informatics

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The aim of the SEURAT‐1 (Safety Evaluation Ultimately Replacing Animal Testing‐1) research cluster, comprised of seven EU FP7 Health projects co‐financed by Cosmetics Europe, is to generate a proof‐of‐concept to show how the latest technologies, systems toxicology and toxicogenomics can be combined to deliver a test replacement for repeated dose systemic toxicity testing on animals. The SEURAT‐1 strategy is to adopt a mode‐of‐action framework to describe repeated dose toxicity, combining in vitro and in silico methods to derive predictions of in vivo toxicity responses. ToxBank is the cross‐cluster infrastructure project whose activities include the development of a data warehouse to provide a web‐accessible shared repository of research data and protocols, a physical compounds repository, reference or “gold compounds” for use across the cluster (available via wiki.toxbank.net), and a reference resource for biomaterials. Core technologies used in the data warehouse include the ISA‐Tab universal data exchange format, REpresentational State Transfer (REST) web services, the W3C Resource Description Framework (RDF) and the OpenTox standards. We describe the design of the data warehouse based on cluster requirements, the implementation based on open standards, and finally the underlying concepts and initial results of a data analysis utilizing public data related to the gold compounds.

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Section: Toxbankmentioning

confidence: 99%

Section: Design Of the Toxbank Data Warehousementioning

confidence: 99%

“…[33] It is being used to represent the diverse types of experimental data within the TBDW. Data access and upload procedures are defined by an investigation API.…”

Section: Toxbank Data Warehouse Architecture and Technologiesmentioning

confidence: 99%

Section: Toxbank Data Warehouse Architecture and Technologiesmentioning

confidence: 99%

See 2 more Smart Citations

The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing

Kohonen

Benfenati

Bower

et al. 2013

Molecular Informatics

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“…The underlying architecture and semantics of those tools is compatible with international data formatting standards [12].…”

Section: Solutions For Collaborative Discoverymentioning

confidence: 99%

Services Design in a Collaborative Network for Multidisciplinary Research Projects

Krestyaninova

Tammisto

2012

IFIP Advances in Information and Communication Technology

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Abstract. Providing information management services for multi-disciplinary research projects presents scientific, technological and communication challenges: constant change of themes and objects of scientific studies, entangled privacy and ownership requirements along with rapidly evolving methods of analysis and ways to look at data call for a highly dynamic communication and data service. We will present a case study of a collaborative network (simbioms.org). SIMBioMS, founded in 2005, develops open source software and provides data management services in biomedical research through four academic organisations and one company.

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Data Integration

Goble¹,

Wolstencroft²

2004

Dictionary of Bioinformatics and Computational Biology

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Toward interoperable bioscience data

Cited by 375 publications

References 30 publications

The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing

The ToxBank Data Warehouse: Supporting the Replacement of In Vivo Repeated Dose Systemic Toxicity Testing

Services Design in a Collaborative Network for Multidisciplinary Research Projects

Data Integration

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