Search Results for "ontology"
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Showing 399 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, by defining a small number of classes and relations. CCO then extends from BFO in the sense that every class in CCO is asserted to be a subclass of some class in BFO, and that CCO adopts the generic relations defined in BFO (e.g., has_part) (Smith and Grenon, 2004). ... -
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clusterProfiler
A universal enrichment tool for interpreting omics data
...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 different biological lenses without rewriting code. It is designed for breadth, covering coding and non-coding features and thousands of organisms by leveraging continuously updated annotations. Results are returned in tidy, manipulation-friendly structures and pair naturally with rich visualization functions (via companion tooling) to summarize pathways, terms, and gene–set relationships. -
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Schema.DTS
JSON-LD TypeScript types for Schema vocabulary
...Usage examples demonstrate how one can import types like Person, WithContext, or Graph and compose JSON-LD objects in a way that aligns with semantic-web and knowledge-graph 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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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
...Drawing features allow designers to comfortably edit ontologies in a central viewport area, while two lateral docking areas contains specifically-tailored widgets for editing, navigating and inspecting open diagrams. Eddy is equipped with design-time syntax validation 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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sourceforge-onto-architecture
Ontology architecture, technical vision.
**SourceForge Ontology Committee (SF-ONTO)** — это независимый технический комитет, занимающийся разработкой, валидацией и поддержкой онтологических стандартов для систем искусственного интеллекта. Миссия: > Создать открытую, верифицируемую и этически согласованную систему онтологических знаний для разработки безопасного и ответственного искусственного интеллекта. -
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...The technology behind Outfit7's mobile app Tom Loves Angela and ESL chatbots at Japan's SpeakGlobal. 3rd place winner Chatbot Battles 2012 and awarded best 15 minute conversation prize. 3rd place Loebner winner for 2013 and 1st place in 2014 and 2015. Also has useful 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. -
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TRAK Metamodel
Tuples (triples) for TRAK architecture 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 own web page - see https://trakmetamodel.sourceforge.io/metamodel/index.html -
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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 modules, and SYNERGY which is a visual activation/propagation based language. ... -
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Mathematical Modelling Ontology
Ontology of types of mathematical models, and their properties
The Mathematical Modelling Ontology (MAMO) is a classification of the types of mathematical models used mostly in the life sciences, their variables, relationships and other relevant features. -
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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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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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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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IndustrialMaintenanceOntology
OWL ontology that represents the core of industrial maintenance domain
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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 in courses, workshops and tutorials. In particular, the library can also be used in Jupyter notebooks using a Java kernel such as the IJava kernel. -
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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. Immune-Omics Networks of CD27, PD1, and PDL1 in Non-Small Cell Lung Cancer. ... -
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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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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 in the Doctoral Thesis: Małgorzata Sadowska, "Creating and validating UML class diagrams with the use of domain ontologies expressed in OWL 2", Wroclaw University of Science and Technology, 2020.
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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 (in GO and EC); metabolic pathways. -
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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.
