Search Results for "ontology"
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113 projects for "ontology" with 1 filter applied:
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clusterProfiler
A universal enrichment tool for interpreting omics data
clusterProfiler is an R/Bioconductor package that provides a unified workflow for functional enrichment analysis to interpret high-throughput omics results. It supports both over-representation analysis and gene set enrichment analysis, letting you work with unranked gene lists or ranked statistics from differential pipelines. The package connects to multiple knowledge bases—such as Gene Ontology, KEGG, Reactome, Disease Ontology, MeSH and others—through a consistent interface so you can query... -
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AtomicServer
An open source headless CMS / real-time database
Create, share, fetch, and model Atomic Data! AtomicServer is a lightweight, yet powerful CMS / Graph Database. Atomic Data is a modular specification for sharing, modifying, and modeling graph data. It combines the ease of use of JSON, the connectivity of RDF (linked data), and the reliability of type-safety. Atomic Data uses links to connect pieces of data, and therefore makes it easier to connect datasets to each other - even when these datasets exist on separate machines. -
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UnBBayes
Framework & GUI for Bayes Nets and other probabilistic models.
UnBBayes is a probabilistic network framework written in Java. It has both a GUI and an API with inference, sampling, learning and evaluation. It supports Bayesian networks, influence diagrams, MSBN, OOBN, HBN, MEBN/PR-OWL, PRM, structure, parameter and incremental learning. Please, visit our wiki (https://sourceforge.net/p/unbbayes/wiki/Home/) for more information. Check out the license section (https://sourceforge.net/p/unbbayes/wiki/License/) for our licensing policy. -
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AminePlatform
Amine is a Multi-Layer Platform for the dev. of Intelligent Systems
Amine is an Artificial Intelligence Multi-Layer Java Open Source Platform dedicated to the development of various kinds of Intelligent Systems and Agents (Knowledge-Based, Ontology-Based, Conceptual Graph -CG- Based, NLP, Reasoning and Learning, Natural Language Processing, etc.). Ontology, KB can be created and manipulated with various processes. CG theory is used as the main knowledge representation language. Amine provides two languages: PROLOG+CG which extends PROLOG with CG and Amine... -
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Flora-2 is a powerful knowledge representation and reasoning system designed for building knowledge-intensive applications. It is based on F-logic, HiLog, Transaction Logic, and also supports defeasible reasoning. Applications include intelligent agents, Semantic Web, ontology management, and more. If you use Flora-2 and like it, please acknowledge it in your project!
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Mimosa is a modeling and simulation platform, covering the process from building conceptual models to running the simulations. The specification uses ontologies and an extensible set of formalisms for the dynamics. The simulation kernel is based on DEVS.
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DODDLE-OWL
a Domain Ontology rapiD DeveLopment Environment – OWL extension
DODDLE-OWL is a domain ontology development tool for the Semantic Web. DODDLE-OWL makes reuse of existing ontologies and supports the semi-automatic construction of taxonomic and other relationships in domain ontologies from documents. -
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A key goal for NEMO is the development of a formal logic (“ontology”) to support data sharing, logic-based queries and mapping/integration of patterns across data from different labs, different experiment paradigms, and different modalities (EEG/MEG)
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SW-DLP: Developing ontoLogy by Profiling
a tool for easing the ontologies editing and evolution (Semantic Web)
The DLP tool was ideated and developed by: Dr. Luca Mazzola, MsC. Patrick Kapahnke, and PD Dr. Matthias Klusch at the German Research Center for Artificial Intelligence DFKI GmbH (http://www.dfki.de ) in Saarbrücken, Germany. Copyright: DFKI, 2017, licence GLP see https://www.gnu.org/licenses/gpl-3.0.en.html For bug reports, technical problems and feature requests please contact: Luca Mazzola: luca.mazzola@dfki.de or mazzola.luca@gmail.com Patrick Kapahnke: patrick.kapahnke@dfki.de -
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Taxoblast
Taxoblast is a pipeline to identify contamination in genomic sequence
... for the entire scaffold, taking into account the taxonomic ontology. Scaffolds that exclusively match potential contaminants may be safely removed while sequences matching partially contaminants and partially the target organism may constitute horizontal transfers or assembly artifacts and need to be examined manually. -
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Gellish - A Product Modeling Language
Formalized English (o.a.) for standardized information exchange
Formal English (Formal Dutch, etc.) are members of the Gellish family of computer interpretable languages for modeling products and processes and their properties as well as for knowledge representation, modeling of requirements and for modeling definitions. The project is intended for further development of Formal English and its Taxonomic Dictionary-Ontology. Software tools for supporting implementations are developed as a https://github.com/ project. The 2008 version of the taxonomic... -
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SmartSlog (Smart Space Ontology) is a software/application development kit (SDK or ADK) for programming Smart-M3 agents (Knowledge Processors, KPs) that consume/produce smart space content according with its high-level ontological representation. SmartSlog applies the code generation approach: given an OWL ontology description, the ontology programming library is produced. The latter provides API to access the smart space via a Smart-M3 Semantic Information Broker (SIB) and data structures...
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A Java interface and implementation for the W3C Web Ontology Language (OWL), used to represent Semantic Web ontologies. The API is focused towards OWL 2 and offers an interface to inference engines and validation functionality.
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VIVO
Semantic researcher networking
VIVO is a semantic web project built on the Jena semantic web framework, and is an application to facilitate the discovery of researchers and collaborators across the country and internationally. -
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OntoMetriCalc
A Java API for measuring OWL ontologies
OntoMetriCalc (Ontology Metrics Calculator) is a Java API for measuring OWL ontologies based on Jena. -
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S-Match
S-Match is a semantic matching framework.
..., ontology evolution and alignment, peer-to-peer information sharing, digital libraries integration, web service composition, agent communication, and query answering on the web. S-Match is extendable to host new algorithms. -
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TDD MAS Toolkit
A set of powerful tools to perform TDD on MAS based on JADE
The TDD MAS Toolkit provides a set of tools to perform Test Driven Development of MAS based on Jade. The toolkit allows developers to set up simulation based and test case scenario based testing, providing powerful insights of the MAS under construction and assuring that the interation protocols and agent interaction in general are been enacted as expected. -
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[DEPRECATED] Gene Ontology
The DEPRECATED legacy location of the GO, see http://geneontology.org
The DEPRECATED legacy of the Gene Ontology project on SourceForge. Please see http://geneontology.org for current software and downloads. -
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Geoportal Server is a standards-based, open source product that enables discovery and use of geospatial resources including data and services.
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A consumer API that can process the response of an ontology evaluation web service provider.
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ONTODerm is a specialty specific ontology for dermatology to integrate dermatology with medical software systems.
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ontocomp
OntoComP is a Protégé 4 plug-in for completing OWL ontologies
OntoComP is a Protégé 4 plug-in for completing OWL ontologies. It enables the user to check whether an OWL ontology contains "all relevant information" about the application domain, and extends the ontology appropriately if this is not the case. It achieves this by asking the user questions of the form "are instances of classes C1 and C2 also instances of class C3?". If the user confirms such a question, then a new axiom of the application domain that does not follow from the ontology has been... -
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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
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Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.