Search Results for "ontologies"

obo An umbrella organization for ontologies and structured shared controlled vocabularies for use across all biological and biomedical domains

The Systems Biology Ontology project (SBO) goal is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. !!!! Important Announcement !!!! We have moved the curation and development of Systems Biology Ontology (SBO) to a git-hub repository https://github.com/EBI-BioModels/SBO. Hence, this SourceForge SBO project has also been retired.

Ontologies, which are made up by standardized and defined controlled vocabulary terms and their inter-relationships, are comprehensive and readily searchable repositories for knowledge in a given domain

SemaRule Navigator is an Integrated Suite of Open-Source and Free-License Software, placing Semantic and Text Analysis Technologies in the toolbox of Researchers, Students, and Enterprises.

The Shrimp suite provides interactive visualizations of graph-based data. Creole (Eclipse plug-in) visualizes Java source code. Jambalaya (Protege plug-in) visualizes ontologies (including OWL), & Stand-Alone Shrimp visualizes RSF/GXL/PRJ/PPRJ files.

NOTE: please refer to OPPL 2. OPPL is a preprocessor language that allows users to define macros for altering OWL ontologies. The syntax is very simple and intuitive, offering a very abstract and high level "scripting" language, for example for int

Protege is a free, open-source platform that provides a suite of tools to construct domain models and knowledge-based applications with frame-based and Semantic Web ontologies.

OntoCardio is an initiative to build ontologies for the legacy Cardio Database (Resource of bioinformation on cardiovascular diseases). SMI's Protege and its OWL plug-in has been adopted as the ontology construction and programming framework.

Danaides stores meta-data from biological banks in a graph databases as well as OBO formatted ontologies. It also provides a web query interface to parse ontologies or extract nodes based on ontology requirements. Example: Get all known elements that are in family of Fish (species ontology) AND a RNA (sequence ontology).

A biological data warehouse that locally stores and integrates biological sequences, molecular interactions, homology information, functional annotations of genes, and biological ontologies. Website: http://bioinformatics.ubc.ca/atlas

The OBO-Annotator is a semantic NLP tool that is designed to give its end-users a great deal of flexibility to combine any number of OBO ontologies from the OBO foundry regardless of their format and use them to annotate text-bases.