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All notes

181 notes across 22 sections. Every note follows the same shape: what it is, key concepts, how you would use it, the angle on large language models, pitfalls, and a verdict.

History & Foundations

Operational Ontologies

  • The Palantir Ontology — Palantir’s Ontology is the operational layer at the centre of Foundry’s architecture.

Criticism

Upper-level Ontologies

  • BFO (Basic Formal Ontology) — BFO is a small upper-level ontology intended to support information retrieval, analysis, and integration across scientific and other domains.
  • DBpedia Ontology (DBO) — The DBpedia Ontology is described as the heart of DBpedia: a shallow, cross-domain ontology that began from commonly used Wikipedia infoboxes and evolved…
  • DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering) — DOLCE is a foundational ontology developed and maintained by the ISTC-CNR Laboratory for Applied Ontology.
  • GFO (General Formal Ontology) — The General Formal Ontology is a top-level ontology for conceptual modeling under continuing development by Onto-Med.
  • gist — gist is Semantic Arts’ minimalist, domain-independent upper ontology for enterprise use.
  • gUFO — gUFO is a lightweight implementation of the Unified Foundational Ontology for Semantic Web OWL 2 DL applications.
  • SUMO (Suggested Upper Merged Ontology) — SUMO and its domain ontologies are presented as a large free formal ontology used in search, linguistics, and reasoning.
  • YAMATO (Yet Another More Advanced Top-level Ontology) — YAMATO is a foundational ontology built and maintained by Riichiro Mizoguchi, first created in 1999 and subsequently revised several times.

Mid-level Ontologies

  • Common Core Ontologies (CCO) — CCO is a suite of eleven ontologies containing logically defined generic terms and relations intended to cover entities across domains.
  • MILO (Mid-Level Ontology) — MILO is a formal ontology intended to bridge SUMO’s abstract content and the richer detail of domain ontologies.

Cross-domain Ontologies

  • Billion Triple Challenge (BTC) 2019 Dataset — BTC 2019 is an open dataset produced by an LDspider crawl of RDF/XML, Turtle, and N-Triples documents from 12 December 2018 to 11 January 2019.
  • ConceptNet — ConceptNet is a freely available, open multilingual semantic network intended to help computers understand word meanings.
  • Cyc — Cyc is presented as an enterprise machine-reasoning AI platform that uses codified human common sense and knowledge rather than patterns and statistics.
  • DBpedia — DBpedia presents itself as global, unified access to knowledge graphs and as a major Linked Open Data resource built from Wikipedia-language editions and…
  • Freebase — Freebase was a data-sharing project that ran from 2007 to 2015; its API has been shut down.
  • KBpedia — KBpedia is an open-source knowledge graph that integrates seven public knowledge bases into one computable structure for data interoperability and…
  • MindNet — MindNet is a Microsoft Research knowledge-representation project that automatically builds semantic networks from dictionaries, encyclopedias, and free text.
  • Mosaic Knowledge Graphs — The fetched source identifies an archived page titled “Mosaic Knowledge Graphs.” It contains Wayback Machine capture metadata rather than the archived…
  • NELL ontology and knowledge base — This archived Linked Data server publishes the ontology and knowledge base produced by NELL, the Never-Ending Language Learning project in Carnegie Mellon’s…
  • OWL-Time (Time Ontology) — OWL-Time is an OWL 2 DL ontology for describing temporal properties of resources.
  • SENSUS — The fetched source does not describe SENSUS: the requested URL redirected to the USC Information Sciences Institute Natural Language Group home page.
  • Wikidata — Wikidata is a free, open knowledge base readable and editable by both humans and machines.
  • YAGO — YAGO is a large semantic knowledge base jointly developed by the Max Planck Institute for Informatics and Télécom ParisTech.

Domain Ontologies

  • Built Environment Ontology Lookup Service (BE-OLS) — BE-OLS is a platform for discovering, exploring, and evaluating built-environment ontologies.
  • CIDOC CRM (Conceptual Reference Model) — CIDOC CRM is a formal ontology and information-integration framework for cultural heritage documentation.
  • CLARIAH/awesome-humanities-ontologies — A curated directory of ontologies, vocabularies, terminologies, and taxonomies for modelling and publishing Humanities datasets as Linked Data.
  • D3FEND — The fetched page is the MITRE D3FEND ontology-resource hub, distributing the entire current D3FEND model.
  • Digital Buildings Ontology (DBO) — Digital Buildings is an Apache-licensed schema and toolset for representing structured information about buildings and installed equipment.
  • FIBO — The Financial Industry Business Ontology (FIBO) defines financial-business things and the relationships among them so that finance data can carry shared…
  • Food Ontology — This is an RDF/XML OWL ontology for foods, drinks, meals, and meal courses, derived from and substantially modifying a DAML wine ontology.
  • FoodOn — FoodOn is a controlled vocabulary and ontology for naming food-bearing parts of animals, plants, and fungi, derived food products, and production processes.
  • Gene Ontology (GO) — The Gene Ontology Resource is a knowledgebase and bioinformatics initiative for computationally representing how genes encode biological functions from…
  • Geographical Entity Ontology — The Geographical Entity Ontology is an ontology of geographical entities implemented in OWL 2 and based on Basic Formal Ontology (BFO).
  • GoodRelations — GoodRelations is a Web vocabulary for publishing detailed product and service information in a form that search engines, mobile applications, and browser…
  • Liquid-Legal-Institute/Legal-Ontologies — A curated list of selected resources, methods, and tools for legal ontologies, data schemes, and knowledge graphs.
  • OBO Foundry — The Open Biological and Biomedical Ontology Foundry is a community effort to develop interoperable ontologies for the biological sciences.
  • Open Energy Ontology (OEO) — The OEO is an open domain ontology for the energy-system-analysis context and part of the Open Energy Family.
  • Product Types Ontology — The Product Types Ontology provides GoodRelations-compatible class definitions for product or service types that have entries in English Wikipedia.
  • PROV-O — PROV-O is the W3C Recommendation that expresses the PROV Data Model in OWL 2, providing classes, properties, and restrictions for representing and exchanging…
  • rNews — rNews is an IPTC-approved standard for embedding news-specific metadata in HTML documents.
  • SIOC (Semantically Interlinked Online Communities) — SIOC is an ontology of terms for describing online communities on the Web of Data.
  • Uberon — Uberon is an integrated cross-species ontology of anatomical structures in animals.
  • Unified Cyber Ontology (UCO) — Unified Cyber Ontology (UCO) is a community-developed ontology/model intended to provide a consistent foundation for standardized information representation…
  • vCard Ontology — A W3C Interest Group Note mapping vCard RFC 6350 to RDF/OWL for describing people and organizations with Semantic Web techniques.
  • Wine Ontology — The Wine Ontology is an example OWL ontology derived from the DAML Wine ontology, with substantial changes to its region relations.

Ontologies and Vocabularies

  • BARTOC (Basel Register of Thesauri, Ontologies & Classifications) — BARTOC is a site that unites information about terminologies and terminology registries.
  • BioPortal — NCBO BioPortal presents itself as a comprehensive repository of biomedical ontologies that is free and open to all users without login.
  • DBpedia Archivo — DBpedia Archivo is an ontology archive that automatically discovers OWL ontologies on the web, checks them every eight hours, and persistently archives changed…
  • KBS/Ontology Projects Worldwide — This is an alphabetically indexed directory of knowledge-base, ontology, knowledge-representation, and related projects and groups.
  • Linked Open Vocabularies — Linked Open Vocabularies (LOV) is a catalog containing 910 vocabularies in the fetched page.
  • Lists of ontologies — This W3C Wiki page is a directory of ontology-listing pages that map themes such as people or products to ontology URIs.
  • Ontology List — Ontology List is an archived, categorized directory of ontology and vocabulary names, with short descriptions for some entries.
  • Ontology Lookup Service (OLS) — The rendered Ontology Lookup Service page is a browsable catalog of ontologies, prominently including OBO Foundry resources and many scientific and biomedical…
  • OntologyDesignPatterns.org — OntologyDesignPatterns.org is a Semantic Web portal dedicated to ontology design patterns and run by ODPA.
  • prefix.cc — prefix.cc describes itself as a namespace lookup service for RDF developers.
  • Protege Ontology Library — A Protege Wiki page for the Protege Ontology Library.
  • The Linked Open Data Cloud — The Linked Open Data Cloud site hosts a diagram of datasets published in Linked Data format, organized into domain subclouds.

Vocabularies

  • DCMI Metadata Terms — DCMI Metadata Terms is the authoritative specification of metadata terms maintained by the Dublin Core Metadata Initiative.
  • Dublin Core Metadata Element Set — The Dublin Core Metadata Element Set 1.1 is a vocabulary of fifteen broad, generic properties for describing many kinds of resources.
  • IMI (Infrastructure for Multilayer Interoperability) Core Vocabulary — IMI is a Common Vocabulary Framework for describing shared terms and their relationships to improve interoperability in open data and Digital Government.
  • Open Graph protocol — The Open Graph protocol is a metadata vocabulary that lets a web page be represented as a rich object in a social graph.
  • RDF Schema (RDFS) 1.1 — RDF Schema 1.1 is a W3C data-modeling vocabulary and semantic extension for RDF.
  • Schema.org Schemas — This Schema.org page is the development-version view of the full schema hierarchy.
  • SKOS (Simple Knowledge Organization System) — SKOS is a W3C Recommendation defining a common data model for sharing and linking knowledge organization systems such as thesauri, classification schemes,…

Languages

  • Common Logic (CL) — Common Logic is an ISO-published framework for a family of first-order-logic-based languages intended to exchange and transmit knowledge between computer…
  • HDT — HDT (Header, Dictionary, Triples) is a compact data structure and binary serialization format for RDF.
  • JSON-LD — JSON-LD (“JavaScript Object Notation for Linked Data”) is a W3C Recommendation for encoding linked data in JSON while retaining a form similar to traditional…
  • Loom — Loom is a knowledge-representation language and environment for constructing intelligent applications, developed at USC’s Information Sciences Institute.
  • N-Quads — N-Quads is a W3C RDF serialization with the .nq extension and application/n-quads media type.
  • N-Triples — N-Triples is a line-based plain-text serialization for RDF graphs and a subset of Turtle.
  • Nanotation — Nanotation is described as a mechanism for using “digital sentences” to enhance blog posts, forum discussions, tweets and other micro-blog posts, HTML, and…
  • Notation3 — Notation3 (N3) is a compact, non-XML serialization for RDF models designed for human readability.
  • OBO Format (OBOF) — This is the working-draft specification for OBO Flat File Format 1.4, providing a BNF grammar and a mapping to OWL 2 DL.
  • Ontology language — Ontology languages are formal, usually declarative languages for constructing ontologies and encoding domain knowledge.
  • OWL 2 Web Ontology Language — OWL 2 is a W3C ontology language for the Semantic Web with formally defined meaning, representing classes, properties, individuals, and data values in Semantic…
  • RDF (Resource Description Framework) 1.1 — RDF is a W3C method for describing and exchanging graph data, originally designed as a metadata data model.
  • RDF* — The fetched source is the RDF-star community landing page, describing RDF-star (formerly RDF*) as part of the RDF-DEV community group.
  • RDF/XML — RDF/XML is a W3C-defined syntax for serializing an RDF graph as an XML document.
  • RDFa — RDFa, or Resource Description Framework in Attributes, is a W3C Recommendation that adds attributes to HTML, XHTML, and XML-based documents so they can carry…
  • TriG — TriG is a plain-text serialization format for RDF graphs, named graphs, and RDF datasets.
  • TriX — TriX (“Triples in XML”) is an XML serialization for RDF graphs, Named Graphs, and RDF Datasets.
  • Turtle — Turtle (Terse RDF Triple Language) is a syntax and .ttl file format for expressing RDF graphs.

Logics

  • Description Logic Complexity Navigator — A web navigator maintained by Evgeny Zolin for complexity results about reasoning in Description Logics.
  • Description Logics (DLs) — Description logics are a family of formal knowledge-representation languages, generally more expressive than propositional logic and less expressive than…
  • F-Logic — F-Logic (frame logic) is a knowledge-representation and ontology language combining conceptual modeling and object/frame-oriented features with declarative…

Querying

  • [protege-user] which is the best query language for owl ontologies? — A 2016 Protege-user mailing-list reply comparing DL Query, SPARQL, and SQWRL for querying OWL ontologies.
  • DL Query (class expression) — The DL Query tab is a Protégé Desktop feature for searching a classified ontology with class expressions based on Manchester OWL syntax.
  • SPARQL 1.1 — SPARQL 1.1 Query Language is a W3C Recommendation defining the syntax and semantics of queries over RDF graphs.
  • SPARQL* — The fetched page is the community home for RDF-star, formerly RDF*, within the RDF-DEV community group.
  • SPARQL-DL — SPARQL-DL is a substantial subset of SPARQL with semantics based directly on OWL-DL entailment.
  • SPARQL-OWL algorithm — This paper presents a sound and complete query-answering algorithm for SPARQL’s OWL 2 Direct Semantics entailment regime.

Rule and Schema Definition

  • LinkML — LinkML is the Linked Data Modeling Language, a flexible language for authoring data schemas in YAML.
  • SHACL (Shapes Constraint Language) — SHACL is a W3C Recommendation for describing RDF graphs through constraints on their content, structure, and meaning.
  • ShEx (Shape Expressions) — Shape Expressions (ShEx) is a data-modeling language for describing and validating RDF graphs.
  • SPIN (SPARQL Inferencing Notation) — SPIN is a W3C Member Submission for representing SPARQL rules and constraints on Semantic Web models, described by its site as a de-facto industry standard.
  • SWRL (Semantic Web Rule Language) — SWRL is a 2004 W3C Member Submission proposing a rule language that combines OWL DL/OWL Lite with Unary/Binary Datalog RuleML.

Reasoners

  • CEL — CEL is a lightweight description-logic reasoner aimed at large-scale biomedical ontologies.
  • cwm — cwm is a general-purpose Semantic Web data processor and forward-chaining reasoner for querying, checking, transforming, and filtering information.
  • ELK — ELK is a Java-based ontology reasoner for the OWL 2 EL profile.
  • FaCT++ — FaCT++ is presented as a new generation of the FaCT OWL-DL reasoner.
  • HermiT — HermiT is an open-source reasoner for OWL ontologies, based on a hypertableau calculus and released under the LGPL.
  • Hoolet — Hoolet is a prototype OWL-DL reasoner that translates an ontology into first-order axioms and sends them to a first-order prover for consistency checking.
  • HyLAR — HyLAR is a hybrid, location-agnostic, rule-based incremental reasoner for the Web.
  • jcel — jcel is a Java reasoner for description logics in the EL family, described specifically as an EL+ / OWL 2 EL reasoner.
  • Openllet — Openllet is an open-source, Java-based OWL 2 DL reasoner.
  • OWL-RL — OWL-RL is a simple RDFLib-based implementation of the OWL 2 RL profile plus basic RDFS inference.
  • Pellet 2 — Pellet is an open-source, pure-Java OWL 2 DL reasoner.
  • pyfactxx — pyfactxx provides Python bindings that connect the C++ FaCT++ reasoner to RDFLib.
  • Racer — Racer is a freely available knowledge-representation system implementing an optimized tableau calculus for the description logic SHIQ(D).
  • Whelk — Whelk is an OWL reasoner based on the algorithm implemented by ELK.

Ontology Editors

  • A List of Ontology Engineering Tools (Ontology Editors) — This is an archived directory of ontology-engineering tools and their websites.
  • Apollo — Apollo was a Java-based, user-friendly knowledge-modeling application designed for varied knowledge-representation needs.
  • Eddy — Eddy is a cross-platform graphical editor for specifying and visualizing Graphol ontologies.
  • ELOT — ELOT is a literate ontology-engineering environment in which one plain-text Org notebook is both the ontology source and its documentation.
  • Fluent Editor — Fluent Editor is an ontology editor centered on Controlled Natural Language, especially a restricted form of English intended to reduce ambiguity and…
  • Knoodl — Knoodl was presented as a cloud-hosted Distributed Information Management System combining semantic and traditional information-management technology.
  • List of ontology editors — The fetched page defines ontology editors as applications that assist with creating or manipulating ontologies, commonly through one or more ontology languages.
  • OntoME — OntoME is an ontology management environment for object-oriented structured data models.
  • OntoStudio — OntoStudio X is a lightweight, Excel-based IDE for building explainable knowledge systems with OntoBroker’s Java API and ObjectLogic capabilities.
  • OWLGrEd — OWLGrEd presents itself as a graphical ontology editor intended to make ontologies easier to see and edit.
  • Protégé — Protégé is a free, open-source OWL ontology editor for building and managing ontologies.
  • SWOOP — SWOOP v2.3 beta 3 is an OWL ontology browser and editor built around a standard web-browser UI paradigm, including an address bar, history, bookmarks, and…
  • TopBraid Composer — The fetched source does not identify or describe TopBraid Composer.
  • VocBench — VocBench is a free, open-source, web-based platform for multilingual collaborative management of OWL ontologies, SKOS/SKOS-XL thesauri, OntoLex-lemon lexicons,…
  • WebODE — WebODE is an extensible ontology-engineering suite built around an application server and a shared ontology access service.

Ontology Utilities

  • LODE — LODE 2.0 is an open-source service that extracts entities and textual definitions from semantic artifacts and renders browsable, linked HTML documentation.
  • OAK — Ontology Access Kit (OAK) is documented as a toolkit for working with ontologies through both Python and a command line.
  • obonet — obonet is a lightweight Python package for reading OBO-serialized ontologies into a NetworkX MultiDiGraph.
  • OnToology — OnToology automates part of collaborative ontology development for a GitHub repository containing OWL files.
  • Ontospy — Ontospy is a lightweight Python library and command-line tool for inspecting vocabularies encoded in RDF-family languages.
  • owl-cli — This repository now documents Cool RDF, the project formed by merging and updating the former owl-cli and turtle-formatter.
  • OWLTools — OWLTools is a Java library and command-line toolkit that simplifies common OWLAPI operations, especially work with annotation properties and connections…
  • pyLODE — pyLODE is a Python reimplementation of LODE that parses OWL/RDF with RDFLib and generates human-readable, static HTML ontology documentation.
  • pyontutils — pyontutils is a collection of Python utilities for maintaining ontologies in Git and making them available through SciGraph.
  • ROBOT — ROBOT is a tool for working with Open Biomedical Ontologies, available as a command-line program or as a library for JVM languages.
  • Tarql — Tarql is a Java command-line tool, based on Apache ARQ, that converts CSV files to RDF using SPARQL 1.1 syntax.
  • VocPrez — VocPrez is an archived, read-only web delivery system for RDF vocabularies formulated in SKOS.
  • WebVOWL — WebVOWL is a browser UI for presenting ontology visualizations, with OWL2VOWL providing the conversion backend.
  • WIDOCO — WIDOCO (WIzard for DOCumenting Ontologies) generates enriched, customizable, human-readable ontology documentation through a GUI wizard or command line.
  • yamlpyowl — yamlpyowl reads ontologies—including individuals and SWRL rules—written in YAML and represents them as Python objects through owlready2.

OWL-aware libraries

  • Apache Jena Ontology API — The Jena Ontology API is a Java programming interface for working with RDF-backed RDFS and OWL ontologies.
  • FunOWL — FunOWL is a pure-Python implementation of OWL 2 Functional-Style Syntax with a Pythonic API that stays close to the raw OWL functional model.
  • Horned OWL — Horned OWL is a Rust library for processing and manipulating OWL documents inside Rust applications.
  • ontor — ontor (ONTology editOR) is a Python library built on Owlready2 for creating, editing, extending, debugging, visualizing, and reasoning over OWL2 ontologies.
  • OPPL — OPPL is an abstract formalism for manipulating ontologies written in OWL.
  • OWL API — The fetched site is the owlcs-maintained project landing page for the OWL API.
  • Owlish — Owlish is a Rust library providing OWL 2 data structures for building and working with ontologies.
  • Owlready2 — Owlready2 is an LGPLv3 package for ontology-oriented programming in Python.
  • Tawny-OWL — Tawny-OWL is a Clojure domain-specific language for constructing OWL ontologies in an evaluative, functional, fully programmatic environment, implemented…

Alignment & Matching

  • AgreementMakerLight (AML) — AgreementMakerLight is an automated, efficient ontology-matching system with a flexible, extensible framework.
  • Alignment API — The Alignment API is a Java API and implementation for expressing and sharing ontology alignments.
  • LogMap — LogMap is a highly scalable ontology matching system with built-in reasoning and inconsistency-repair capabilities.
  • OntoAligner — OntoAligner is a modular Python toolkit for matching entities across two ontologies or knowledge graphs.
  • OntoEMMA — OntoEMMA is an ontology matcher for generating alignments between knowledgebases.
  • Ontology Matching — Ontology Matching is an information repository devoted to methods for finding correspondences between semantically related entities in different ontologies.

Machine Learning

  • Do Language Models Replace Ontologies? — The live argument about whether large language models make hand-built ontologies unnecessary, obsolete the labour of building them, or increase their value.
  • OntoLearner — OntoLearner is a modular, extensible Python framework for semi-automatic ontology construction and enrichment.

Datastore

  • SciGraph — SciGraph represents ontologies and ontology-encoded data as a Neo4j property graph.

Communities