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Ontology generation software tools | Biomedical text mining

SPANG
Desktop

SPANG

Generates typical SPARQL queries according to specified arguments. SPANG has…

Generates typical SPARQL queries according to specified arguments. SPANG has unique features for querying RDF datasets. It can call SPARQL template libraries constructed in a local system or…

Slimmer
Desktop

Slimmer

Assists user in reducing ontologies. Slimmer is a tool that helps in working of…

Assists user in reducing ontologies. Slimmer is a tool that helps in working of ontology: especially in the selection of part and the removal of part of an ontology.

OBI
Terminology

OBI Ontology for Biomedical Investigations

Provides terms with precisely defined meanings to describe all aspects of how…

Provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation…

GBOL
Terminology

GBOL Genome Biology Ontology Language

Provides the means to describe computationally inferred genome annotations of…

Provides the means to describe computationally inferred genome annotations of biological objects typically found in a genome sequence annotation data file. GBOL is modular in design, extendible and…

Brain
Desktop

Brain

A Java software library facilitating the manipulation and creation of…

A Java software library facilitating the manipulation and creation of ontologies and knowledge bases represented with the Web Ontology Language (OWL). Brain aims at bridging the gap between graphical…

OnEX
Web

OnEX Ontology Evolution Explorer

A system for exploring ontology changes. Currently, OnEX provides access to…

A system for exploring ontology changes. Currently, OnEX provides access to about 520 versions of 16 well-known life science ontologies. The system is based on a three-tier architecture including an…

T-GROWLer
Desktop

T-GROWLer

An ontology-based workflow pattern extractor. TGROWLeR system abstracts general…

An ontology-based workflow pattern extractor. TGROWLeR system abstracts general patterns from workflow sequences previously extracted from texts. It comprises two modules (a workflow extractor and a…

DOG4DAG
Desktop

DOG4DAG Dresden Ontology Generator for Directed Acyclic Graphs

An ontology generation plugin for both Protégé 4.1 and OBO-Edit 2.1. DOG4DAG…

An ontology generation plugin for both Protégé 4.1 and OBO-Edit 2.1. DOG4DAG allows for term generation, sibling generation, definition generation, and relationship induction. By integrating it…

ODP
Desktop

ODP Ontology Design Patterns

Offers a collection of well documented and tested ontology design patterns…

Offers a collection of well documented and tested ontology design patterns (ODPs), including examples from the biological knowledge domain, implemented in web ontology language (OWL). ODP is a…

OTO
Web

OTO Ontology Term Organizer

A user-friendly, web-based, consensus-promoting, open source application for…

A user-friendly, web-based, consensus-promoting, open source application for organizing domain terms by dragging and dropping terms to appropriate locations. The application is designed for users…

OWL API
Desktop

OWL API

A high level application programming interface (API) for working with OWL…

A high level application programming interface (API) for working with OWL ontologies. The OWL API is closely aligned with the OWL 2 structural specification. The OWL API supports parsing and…

IMGT-ONTOLOGY
Terminology

IMGT-ONTOLOGY

Allows scientists and clinicians to use, for the first time, identical terms…

Allows scientists and clinicians to use, for the first time, identical terms with the same meaning in immunogenetics. IMGT-ONTOLOGY provides a semantic repository that will improve interoperability…

OWL2Perl
Desktop

OWL2Perl

A Perl framework that generates Perl modules based on OWL class definitions.…

A Perl framework that generates Perl modules based on OWL class definitions. These modules can then be used by other software applications to create resource description framework (RDF) data…

CODEX
Web

CODEX Complex Ontology Diff EXplorer

Allows determining semantic changes between two versions of an ontology, which…

Allows determining semantic changes between two versions of an ontology, which users can interactively analyze in multiple ways. CODEX consists of a web front-end, a web service interface and a…

OBO Converter
Desktop

OBO Converter

A Java tool to convert files from OBO format to Web Ontology Language (OWL)…

A Java tool to convert files from OBO format to Web Ontology Language (OWL) (and vice versa) that can also be used as a Protégé Tab plug-in. It uses the OBO to OWL mapping provided by the National…

OBO Explorer
Desktop

OBO Explorer

A graphical editor for bio-ontologies that makes use of the Protégé platform…

A graphical editor for bio-ontologies that makes use of the Protégé platform and the OBO to OWL Converter tab. Together, these components allow the user to work with Open Biomedical Ontologies in…

OBO-Edit
Desktop

OBO-Edit

An open source, platform-independent ontology editor developed and maintained…

An open source, platform-independent ontology editor developed and maintained by the Gene Ontology Consortium. Implemented in Java, OBO-Edit uses a graph-oriented approach to display and edit…

ONTO-PERL
Desktop

ONTO-PERL

An OBO-centered PERL API that provides a turnkey service to help…

An OBO-centered PERL API that provides a turnkey service to help bio-ontologists handle ontologies, do data exploration and perform mining. This API significantly extends the repertoire of available…

SPARQLGraph
Web

SPARQLGraph

A web-based platform for querying biological Semantic Web databases in a…

A web-based platform for querying biological Semantic Web databases in a graphical way. SPARQLGraph offers an intuitive drag & drop query builder, which converts the visual graph into a query and…

WebProtégé
Desktop
Web

WebProtégé

A free, open-source ontology editor and framework for building intelligent…

A free, open-source ontology editor and framework for building intelligent systems. Protégé is supported by a strong community of academic, government, and corporate users, who use Protégé to…

Sbmlharvester
Desktop

Sbmlharvester

Converts Systems Biology Markup Language (SBML) models into OWL. Sbmlharvester…

Converts Systems Biology Markup Language (SBML) models into OWL. Sbmlharvester allows to check SBML model structure and complex by querying across biomedicals ontologies and models. The software…

dbxobo
Desktop

dbxobo

Indexes an ontology in OBO format, and builds EMBOSS B+tree format index files.…

Indexes an ontology in OBO format, and builds EMBOSS B+tree format index files. These indexes allow access of flat files larger than 2Gb. Related application dbxedam provides additional index fields…

ontogetup
Desktop

ontogetup

Gets ontology of one or more terms by id of child. ontogetup finds ontology…

Gets ontology of one or more terms by id of child. ontogetup finds ontology terms matching a query. All parents of the term, related to the term by 'is_a' (class/subclass) relationships,…

DBonto
Dataset

DBonto

Develops next generation semantics-aware data management systems that are based…

Develops next generation semantics-aware data management systems that are based on a synthesis of ontological reasoning and database management principles. DBonto incorporate techniques from many…

Orymold
Desktop

Orymold

Permits contextual management of gene expression data. Orymold accepts new…

Permits contextual management of gene expression data. Orymold accepts new terms in the ontology and thus rapidly molds it to accept new data. It is able to include macro and microscopic pictures of…

COBrA
Desktop

COBrA

A Java-based ontology editor for bio-ontologies that distinguishes itself from…

A Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and…

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