Controlled vocabularies are increasingly used by databases to describe genes and gene products because they facilitate identification of similar genes within an organism or among different organisms. One of The Arabidopsis Information Resource's goals is to associate all Arabidopsis genes with terms developed by the Gene Ontology Consortium that describe the molecular function, biological proce...

This paper focuses on the use of controlled vocabularies (CVs) and ontologies especially in the area of proteomics, primarily related to the work of the Proteomics Standards Initiative (PSI). It describes the relevant proteomics standard formats and the ontologies used within them. Software and tools for working with these ontology files are also discussed. The article also examines the "mappin...

The Immune Epitope Database (IEDB) project incorporates independently developed ontologies and controlled vocabularies into its curation and search interface. This simplifies curation practices, improves the user query experience and facilitates interoperability between the IEDB and other resources. While the use of independently developed ontologies has long been recommended as a best practice...

The Gene Ontology (GO) project (http://www. geneontology.org/) provides structured, controlled vocabularies and classi®cations that cover several domains of molecular and cellular biology and are freely available for community use in the annotation of genes, gene products and sequences. Many model organism databases and genome annotation groups use the GO and contribute their annotation sets to...

We present a novel controlled vocabulary for the classification of Educational Resource Type and Media type that has been developed within the mEducator Best Practice Network, and discuss the rationale behind its design and its SKOS implementation. Several available controlled vocabularies were analyzed, but none was found entirely satisfactory for the project's purposes. Although the driving m...

Controlled vocabularies enhance precision and recall but sometimes they achieve this at the expense of imposing a prescribed terminology and a homogeneous worldview upon a heterogeneous user community. Folksonomies allow end-users the freedom to describe content any way they want, but in doing so they create meta noise which diminishes precision and recall. This paper presents an alternative mo...

The concept of Linked Data has made its entrance in the cultural heritage sector due to its potential use for the integration of heterogeneous collections and deriving additional value out of existing metadata. However, practitioners and researchers alike need a better understanding of what outcome they can reasonably expect of the reconciliation process between their local metadata and establi...

Pathbase (http://www.pathbase.net) is a web accessible database of histopathological images of laboratory mice, developed as a resource for the coding and archiving of data derived from the analysis of mutant or genetically engineered mice and their background strains. The metadata for the images, which allows retrieval and interoperability with other databases, is derived from a series of orth...

The Spatial Information Services Stack Vocabulary Service (SISSVoc) is a Linked Data API for publishing vocabularies. SISSVoc provides a RESTful interface via a set of URI patterns that are aligned with SKOS. This provides a standard web interface to any controlled vocabulary structured using, or decorated with, SKOS classes and properties. It can be consumed via web clients as human-readable r...

"-Omics" is a current suffix for numerous types of large-scale biological data generation procedures, which naturally demand the development of novel algorithms for data storage and analysis. With next generation genome sequencing burgeoning, it is pivotal to decipher a coding site on the genome, a gene's function, and information on transcripts next to the pure availability of sequence informa...