Search Results for "ontologies"

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

...All EFO development and source code has been moved to https://github.com/EBISPOT/efo *** The Experimental Factor Ontology (EFO) available from http://www.ebi.ac.uk/efo is an application focused ontology modeling the experimental factors in ArrayExpress and constructing mappings to multiple existing domain specific ontologies. To submit new terms, features or report bugs please submit a ticket at the following: http://www.ebi.ac.uk/panda/jira/secure/CreateIssue!default.jspa

mx is a Ruby/Rails code base with broad application in evolutionary biology, it includes general functionality for matrix handling, sequence management, ontology construction, specimen handling, taxonomic catalogs, taxonomic descriptions and more

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

Ontology Design Patterns (ODPs) are well known and efficient modeling solutions for ontologies. This public catalog offers a collection of well documented and tested ODPs, including examples from the biological knowledge domain, implemented in OWL.

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

The Cell Cycle Ontology extends existing ontologies for cell cycle knowledge building a resource that integrates and manages knowledge about the cell cycle components and regulatory aspects in OBO, OWL, and other commonly used ontology representation

The ONTO-SPARQL library contains sparql-queries for loading OBO-ontologies, and for browsing and searching through them. The results of the queries are returned in XML or a HTML-interface. They can be used by end-users and programmers.

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.