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ArrayExpress update—from an archive of functional genomics experiments to the atlas of gene expression
TLDR
This update describes the ArrayExpress developments over the last two years and describes the new summary database and meta-analytical tool of ranked gene expression across multiple experiments and different biological conditions.
ArrayExpress update—an archive of microarray and high-throughput sequencing-based functional genomics experiments
TLDR
The ArrayExpress Archive is one of the three international public repositories of functional genomics data supporting publications and provides queries based on technology and sample attributes such as disease, cell types and anatomy.
Modeling sample variables with an Experimental Factor Ontology
TLDR
The application of reference ontologies to data is a key problem, and this work presents guidelines on how community ontologies can be presented in an application ontology in a data-driven way.
ArrayExpress update—trends in database growth and links to data analysis tools
The ArrayExpress Archive of Functional Genomics Data (http://www.ebi.ac.uk/arrayexpress) is one of three international functional genomics public data repositories, alongside the Gene Expression
Expression Atlas update—a database of gene and transcript expression from microarray- and sequencing-based functional genomics experiments
TLDR
The new version of Expression Atlas introduces the concept of ‘baseline’ expression, i.e. gene and splice variant abundance levels in healthy or untreated conditions, such as tissues or cell types, in order to maximize the biological value provided to the user.
Disease Ontology 2015 update: an expanded and updated database of human diseases for linking biomedical knowledge through disease data
TLDR
The current version of the Human Disease Ontology (DO), a biomedical resource of standardized common and rare disease concepts with stable identifiers organized by disease etiology, is moving to a multi-editor model utilizing Protégé to curate DO in web ontology language.
Modeling biomedical experimental processes with OBI
TLDR
It is demonstrated 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 Ontology for Biomedical Investigations
TLDR
The state of OBI and several applications that are using it are described, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources.
Gene Expression Atlas at the European Bioinformatics Institute
The Gene Expression Atlas (http://www.ebi.ac.uk/gxa) is an added-value database providing information about gene expression in different cell types, organism parts, developmental stages, disease
Open Targets: a platform for therapeutic target identification and validation
TLDR
The Open Targets Validation Platform is designed to support identification and prioritization of biological targets for follow-up and provides evidence about the association of known and potential drug targets with diseases.
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