Susanna-Assunta Sansone

ArrayExpress—a public repository for microarray gene expression data at the EBI

ArrayExpress is a public repository for microarray data that supports the MIAME (Minimum Informa-tion About a Microarray Experiment) requirements and stores well-annotated raw and normalized data. As of November 2004, ArrayExpress contains data from ∼12 000 hybridizations covering 35 species. Data can be submitted online or directly from local databases or LIMS in a standard format, and password-protected access to prepublication data is provided for reviewers and authors. The data can be retrieved by accession number or queried by vari-ous parameters such as species, author and array platform. A facility to query experiments by gene and sample properties is provided for a growing subset of curated data that is loaded in to the ArrayExpress data warehouse. Data can be visualized and analysed using Expression Profiler, the integrated data analysis tool. ArrayExpress is available at http://www.ebi.ac.uk/arrayexpress.

The FAIR Guiding Principles for scientific data management and stewardship

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, the FAIR Principles put specific emphasis on enhancing the ability of machines to automatically find and use the data, in addition to supporting its reuse by individuals. This Comment is the first formal publication of the FAIR Principles, and includes the rationale behind them, and some exemplar implementations in the community.

ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression

ArrayExpress http://www.ebi.ac.uk/arrayexpress consists of three components: the ArrayExpress Repository—a public archive of functional genomics experiments and supporting data, the ArrayExpress Warehouse—a database of gene expression profiles and other bio-measurements and the ArrayExpress Atlas—a new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions. The Repository contains data from over 6000 experiments comprising approximately 200 000 assays, and the database doubles in size every 15 months. The majority of the data are array based, but other data types are included, most recently—ultra high-throughput sequencing transcriptomics and epigenetic data. The Warehouse and Atlas allow users to query for differentially expressed genes by gene names and properties, experimental conditions and sample properties, or a combination of both. In this update, we describe the ArrayExpress developments over the last two years.

Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project

The Minimum Information for Biological and Biomedical Investigations (MIBBI) project aims to foster the coordinated development of minimum-information checklists and provide a resource for those exploring the range of extant checklists.

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

MetaboLights (http://www.ebi.ac.uk/metabolights) is the first general-purpose, open-access repository for metabolomics studies, their raw experimental data and associated metadata, maintained by one of the major open-access data providers in molecular biology. Metabolomic profiling is an important tool for research into biological functioning and into the systemic perturbations caused by diseases, diet and the environment. The effectiveness of such methods depends on the availability of public open data across a broad range of experimental methods and conditions. The MetaboLights repository, powered by the open source ISA framework, is cross-species and cross-technique. It will cover metabolite structures and their reference spectra as well as their biological roles, locations, concentrations and raw data from metabolic experiments. Studies automatically receive a stable unique accession number that can be used as a publication reference (e.g. MTBLS1). At present, the repository includes 15 submitted studies, encompassing 93 protocols for 714 assays, and span over 8 different species including human, Caenorhabditis elegans, Mus musculus and Arabidopsis thaliana. Eight hundred twenty-seven of the metabolites identified in these studies have been mapped to ChEBI. These studies cover a variety of techniques, including NMR spectroscopy and mass spectrometry.

Modeling biomedical experimental processes with OBI

BackgroundExperimental descriptions are typically stored as free text without using standardized terminology, creating challenges in comparison, reproduction and analysis. These difficulties impose limitations on data exchange and information retrieval.ResultsThe Ontology for Biomedical Investigations (OBI), developed as a global, cross-community effort, provides a resource that represents biomedical investigations in an explicit and integrative framework. Here we detail three real-world applications of OBI, provide detailed modeling information and explain how to use OBI.ConclusionWe demonstrate how OBI can be applied to different biomedical investigations to both facilitate interpretation of the experimental process and increase the computational processing and integration within the Semantic Web. The logical definitions of the entities involved allow computers to unambiguously understand and integrate different biological experimental processes and their relevant components.AvailabilityOBI is available at http://purl.obolibrary.org/obo/obi/2009-11-02/obi.owl

The metabolomics standards initiative (MSI)

In 2005, the Metabolomics Standards Initiative has been formed. An outline and general introduction is provided to inform about the history, structure, working plan and intentions of this initiative. Comments on any of the suggested minimal reporting standards are welcome to be sent to the open email list Msi-workgroups-feedback@lists.sourceforge.net

Summary recommendations for standardization and reporting of metabolic analyses.

The Standard Metabolic Reporting Structures (SMRS) working group outlines its vision for an open,community-driven specification for the standardization and reporting of metabolic studies.The Standard Metabolic Reporting Structures (SMRS) working group outlines its vision for an open,community-driven specification for the standardization and reporting of metabolic studies.

The MGED Ontology: a resource for semantics-based description of microarray experiments

MOTIVATION The generation of large amounts of microarray data and the need to share these data bring challenges for both data management and annotation and highlights the need for standards. MIAME specifies the minimum information needed to describe a microarray experiment and the Microarray Gene Expression Object Model (MAGE-OM) and resulting MAGE-ML provide a mechanism to standardize data representation for data exchange, however a common terminology for data annotation is needed to support these standards. RESULTS Here we describe the MGED Ontology (MO) developed by the Ontology Working Group of the Microarray Gene Expression Data (MGED) Society. The MO provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to hybridize the RNA and analyze the data. The MO was developed to provide terms for annotating experiments in line with the MIAME guidelines, i.e. to provide the semantics to describe a microarray experiment according to the concepts specified in MIAME. The MO does not attempt to incorporate terms from existing ontologies, e.g. those that deal with anatomical parts or developmental stages terms, but provides a framework to reference terms in other ontologies and therefore facilitates the use of ontologies in microarray data annotation. AVAILABILITY The MGED Ontology version.1.2.0 is available as a file in both DAML and OWL formats at http://mged.sourceforge.net/ontologies/index.php. Release notes and annotation examples are provided. The MO is also provided via the NCICBs Enterprise Vocabulary System (http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do). CONTACT Stoeckrt@pcbi.upenn.edu SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.

The Metabolomics Standards Initiative

In 2005, the Metabolomics Standards Initiative has been formed. An outline and general introduction is provided to inform about the history, structure, working plan and intentions of this initiative. Comments on any of the suggested minimal reporting standards are welcome to be sent to the open email list Msi-workgroups-feedback@lists.sourceforge.net