BioPortal: ontologies and integrated data resources at the click of a mouse

Abstract

Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. Thus, BioPortal not only provides investigators, clinicians, and developers ‘one-stop shopping’ to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.

Optimizing Similarity Computations for Ontology Matching - Experiences from GOMMA

“…Thus, after this preprocessing, a concept has a set of sorted token vectors (stvs) representing the n-grams of their string attribute values as integers. For example, the trigrams of c 2 are represented as { [9,10], [11,12,13,14,15,16,17]}.…”

“…Mappings (alignments) between ontologies are important for many life science applications and are increasingly provided in platforms such as BioPortal [13]. New mappings are typically determined semi-automatically with the help of ontology match systems such as GOMMA (Generic Ontology Matching and Mapping Management) [10] utilizing different matchers to evaluate the linguistic and structural similarity of concepts [3].…”

Curating gene variant databases (LSDBs): Toward a universal standard

“…Free text seems simplest to implement, but providing specific choices from ontologies and controlled vocabularies enhances standardization and makes queries easier. Suitable ontologies and terms can be found using Bioportal (http://bioportal.bioontology.org/) [Noy et al, 2009]. Make sure that you give a detailed legend and some example entries.…”

The Distributed Ontology, Modeling and Specification Language – DOL

“…-modular and distributed ontologies are specially supported, -ontologies can not only be aligned (as in BioPortal [37] and NeON [14]), but also combined along alignments, -logical links between ontologies (interpretation of theories, conservative extensions etc.) are supported, -support for a variety of ontology languages (OWL, RDF, Common Logic, first-order logic; planned: UML, relational database schemas, F-logic, distributed description logics, and more), -ontologies can be translated to other ontology languages, and compared with ontologies in other languages, -heterogeneous ontologies involving several languages can be built, -ontology languages and ontology language translations are first-class citizens and are available on the Web as linked data.…”