Search Results for "ontology"
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Showing 250 open source projects for "ontology"
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Common Core Ontologies
The Common Core Ontology Repository
The Common Core Ontologies (CCO) comprise twelve ontologies that are designed to represent and integrate taxonomies of generic classes and relations across all domains of interest. CCO is a mid-level extension of Basic Formal Ontology (BFO), an upper-level ontology framework widely used to structure and integrate ontologies in the biomedical domain (Arp, et al., 2015). BFO aims to represent the most generic categories of entity and the most generic types of relations that hold between them... -
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Schema.DTS
JSON-LD TypeScript types for Schema vocabulary
... practices. The repository also contains a generator tool that can pull ontology definitions and emit TypeScript definitions in bulk, ensuring the typings stay up to date and maintain consistency. It supports scenarios such as nested objects, graphs of entities, and action types with input/output constraints, which makes it suitable for rich metadata authoring and linked-data workflows. While it is maintained by Google, it is not an officially supported Google product. -
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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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QFramework
Unity3D System Design Architecture
QFramework is to provide a set of simple, powerful, easy-to-use, SOLID principles, support domain-driven design (DDD), event-driven, data-driven, layered, MVC, CQRS, modular, easy-to-extend architecture, her source code is only Up to line 800, you can completely save it in your notes app. Presentation layer: ViewController layer. The IController interface is responsible for the performance when receiving input and state changes. In general, MonoBehaviour is the presentation layer. System... -
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Eddy
An editor for the specification of Graphol ontologies
... functionalities which prevents ontology designers from constructing invalid Graphol expressions: feedback on the validity of the expression is given through color coding diagram elements. Eddy also supports the standard profiles of OWL 2, i.e. OWL 2 QL, OWL 2 RL, and OWL 2 EL (to appear). Moreover, to support interaction with third-party tools such as OWL 2 reasoners and editors like Protégé, Eddy is able to export the produced Graphol ontology into an OWL 2 ontology. -
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... ontology files for nouns, verbs, adjectives, adverbs. Stand-alone or server modes. LINUX ( 64 bit) and Windows (Visual Studio 10) and Mac/iOS. See BrilligUnderstanding.com for our home website. See github.com/chatscriptnlp/ChatScriptNLP for git accessible form (which also has fixes as needed prior to next full release cycle)
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GOBU
Gene Browsing Utility
Gene Ontology Browsing Utility (hereinafter, GOBU, pronounced as "go-boo") is a browsing and manipulating tool for Post-Pipeline genetic data, especially useful for data with GO annotations. With help of GOBU, we expect biologists and their cooperating technicians can pay less effort on common programming stuff. At the same time, GOBU provides an Extendable Architecture which guarantees the possibility of 1. Arbitrary Data Description, 2. Data Integration, and 3. Extendable User Interface. -
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TRAK Metamodel
Tuples (triples) for TRAK architecture viewpoints and views
The definition of the metamodel for TRAK (defines allowed AD elements and relationships i.e. tuples/ triples for the TRAK viewpoints and views). TRAK is a general systems-thinkers'/system engineering enterprise architecture framework. It is simple, user-friendly, pragmatic and not limited to IT. 100% triple-centric and semantically-sound. Forms basis for RDF + OWL ontology description - see https://trakmetamodel.sourceforge.io/vocab/TRAK_metamodel.html. Each TRAK metamodel element now has its... -
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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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MELO
Machine Executable Language Ontology (MELO)
This project is intended to fill the gap between the semantic web and the mainstream of software engineering, especially to integrate the semantic web with programming languages, and find an ontological representation of programming languages, including abstract syntax code execution, and global interoperability in execution environments. The machine executable language is modelled in OWL 2 DL using OWL API in C++ developed in this project. -
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DeeProtGO
DeeProtGO is a deep learning model for predicting GO terms of proteins
This project contains the source code of DeeProtGO as well as an example of its use when predicting GO terms of the biological process sub-ontology for eukaryotic proteins. -
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GENET-CNV
Integrated DNA copy number variation and gene expression analysis
The Boolean implication networks outperformed Bayesian networks, Pearson’s correlation networks, and other Boolean networks in constructing genome-scale co-expression networks evaluated with comprehensive biological pathways and Gene Ontology in MSigDB. References: Guo NL, Wan YW. Pathway-based identification of a smoking associated 6-gene signature predictive of lung cancer risk and survival. Artificial Intelligence in Medicine 2012 Jun;55(2):97-105. Ye Q, Singh S, Qian PR, Guo NL... -
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simpleowlapi
A light-weight wrapper for the OWLAPI
simpleOWLAPI is a light-weight wrapper for the OWLAPI that enables faster programmatic development of OWL ontologies with more concise code using the power of the Manchester OWL Syntax and related parsers. The wrapper does not make use of all the features of the more powerful OWLAPI. Rather, it is designed specifically for rapid and concise ontology construction in workflows involving semantic data engineering. It can also be used in contexts such as educational and demonstration settings... -
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The Kinetic Simulation Algorithm Ontology (KiSAO; http://co.mbine.org/standards/kisao) is an ontology of algorithms for simulating and analyzing biological models, as well as the characteristics of these algorithms, their input parameters, and their outputs. In addition, KiSAO captures relationships among algorithms, their parameters, and their outputs. Development of KiSAO has moved to https://github.com/SED-ML/KiSAO/.
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Product Design Requirement Ontology Model (PDROM) provides rich requirement semantics. The model supports a new level of engineering requirement storage and analysis by addressing different facets of requirement specifications. PDROM consists of two main parts: (I) Part I is for requirement representation and description of a requirement and (ii) Part II is to support requirement generation and links between product requirements and design rational.
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Fun4Me
A package for functional annotation for metagenomes
This package includes a few programs for rapid functional annotation for metagenomic sequences, including, 1) Gene prediction by FragGeneScan; 2) Similarity search by RAPSearch2; 3) Functional annotation in GO (Gene Ontology) and EC (Enzyme Commission) based on similarity search results; 4) From EC to metabolic pathway reconstruction by MinPath. Inputs: Just sequencing reads (or assemblies) Outputs: Protein-coding genes (or gene fragments); similarity search; functional annotations... -
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The presented tool, called ONTOOL, allows for creating UML class diagrams on the basis of the selected OWL domain ontologies, and verifying if the diagrams are compliant with the ontologies. ONTOOL additionally allows for normalizing any syntactically correct and consistent ontology expressed in OWL. ONTOOL has been tested with a number of test cases, and empirically evaluated through conducting an experiment. The tool has been implemented as a proof of concept of the methods proposed...
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ART JADE
ART Ontology and Protocols in JADE
Ontology and Protocols of Agent Reputation and Trust testbed using JADE platform. -
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MoPAC
The Modular Pipeline for the Analysis of CRISPR screens
To facilitate the comparison of gene essentialities in two or more cell samples, we propose MoPAC (Modular Pipeline for Analysis of CRISPR screens), a Shiny-driven interactive tool for differential essentiality analysis in CRISPR/Cas9 screens. For installation and usage instructions please refer to the wiki page. -
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UFO-Cytoscape
Ontology-based semantic similarity calculation and visualization
Motivation: Biomedical ontologies have been growing quickly and proven to be useful in many biomedical applications. The use of this data is mainly based on semantic similarity calculation between ontology terms and between annotated biomedical entities. Many semantic similarity measures have been proposed for such calculation. Results: A number of tools have been developed on different platforms for ontology visualization and semantic similarity calculation. However, these tools have... -
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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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This is a Python-based efficient implementation of several semantic similarity measures. The target is to enable fast and easy calculation of similarity between proteins and genes using the Gene Ontology (GO).