Chemical entities, reactions, methods and materials.
Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds.
RXNO is the name reaction ontology. It contains more than 500 classes representing organic reactions such as the Diels–Alder cyclization.
An ontology for glycans based on GlyTouCan, but organized by subsumption.
The chemical information ontology (cheminf) describes information entities about chemical entities. It provides qualitative and quantitative attributes to richly describe chemicals.
MOP is the molecular process ontology. It contains the molecular processes that underlie the name reaction ontology RXNO, for example cyclization, methylation and demethylation.
CHEBI provides a distinct role hierarchy. Chemicals in the structural hierarchy are connected via a 'has role' relation. CHIRO provides links from these roles to useful other classes in other ontologies. This will allow direct connection between chemical structures (small molecules, drugs) and what they do. This could be formalized using 'capable of', in the same way Uberon and the Cell Ontology link structures to processes.
CHMO, the chemical methods ontology, describes methods used to
The PSI-Mass Spectrometry (MS) CV contains all the terms used in the PSI MS-related data standards. The CV contains a logical hierarchical structure to ensure ease of maintenance and the development of software that makes use of complex semantics.
The PMD Core Ontology (PMDco) is a comprehensive framework for representing knowledge that encompasses fundamental concepts from the domains of materials science and engineering (MSE). The PMDco has been designed as a mid-level ontology to establish a connection between specific MSE application ontologies and the domain neutral concepts found in established top-level ontologies. The primary goal of the PMDco is to promote interoperability between diverse domains.
A data model for managing information about chemical entities, ranging from atoms through molecules to complex mixtures.
The Potential Drug-drug Interaction and Potential Drug-drug Interaction Evidence Ontology
EMMO is a multidisciplinary effort to develop a standard representational framework (the ontology) for applied sciences. It is based on physics, analytical philosophy and information and communication technologies. It has been instigated by materials science to provide a framework for knowledge capture that is consistent with scientific principles and methodologies. (from GitHub)
The eNanoMapper project (https://www.enanomapper.net/), NanoCommons project (https://www.nanocommons.eu/) and ACEnano project (http://acenano-project.eu/) are creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. This ontology is an application ontology targeting the full domain of nanomaterial safety assessment. It re-uses several other ontologies including the NPO, CHEMINF, ChEBI, and ENVO.
Voc4Cat is a [SKOS](https://www.w3.org/TR/2009/REC-skos-reference-20090818/) vocabulary for the catalysis disciplines. The vocabulary was created in the [NFDI4Cat](http://www.nfdi4cat.org/) initiative. The first collection of terms was published in June 2023 with a focus on photo catalysis. Our goal is to continuously extend the vocabulary to other areas of catalysis and related disciplines like chemical engineering or materials science.
PROCO (PROcess Chemistry Ontology) is a formal ontology that aims to standardly represent entities and relations among entities in the domain of process chemistry.
NFDI-MatWerk aims to establish a digital infrastructure for Materials Science and Engineering (MSE), fostering improved data sharing and collaboration. This repository provides comprehensive documentation for NFDI MatWerk Ontology (MWO) v3.0.0, a foundational framework designed to structure research data and enhance interoperability within the MSE community.
An ontology of physico-chemical processes, i.e. physico-chemical changes occurring in course of time.
Linked-data framework for connecting species in chemical kinetic reaction mechanisms with quantum calculations. A mechanism can be constructed from thermodynamic, reaction rate, and transport data that has been obtained either experimentally, computationally, or by a combination of both. In order to implement this approach, two existing ontologies, namely OntoKin, for representing chemical kinetic reaction mechanisms, and OntoCompChem, for representing quantum chemistry calculations, are extended. (from https://nfdi4cat.org/services/ontologie-sammlung/)
Represents chemical kinetic reaction mechanisms.
Allotrope Merged Ontology Suite: Allotrope Merged Ontology Suite. A ontology listed in Bioregistry, OLS (EMBL-EBI), TIB Terminology Service.
An ontology developed as part of the Chemical Analysis Metadata Project (ChAMP) as a resource to semantically annotate standards developed using the ChAMP platform. (source: CAO ontology)
Chemical Substance Domain Ontology: A ontology listed in Discovered via prefix.cc.
Electrochemistry Domain Ontology: A ontology listed in Discovered via prefix.cc.
Represent chemical entities having particular CHEBI roles
MDS-Onto is a domain (low) level ontology that describes terms in Materials Data Science.
OntoSpecies is an ontology developed for representing chemical species.
An ontology of physico-chemical methods and properties.
OntoChemExp is an ontology developed for representing chemical experiments.
An ontology defined for representing the processes, business and geospatial information of a chemical plant
An ontology developed for representing chemical synthesis procedures, specifically for Metal-Organic Polyhedra (MOPs). This is object graph mapper (OGM) version.
OntoCrystal is an ontology developed for representing crystal structure information
OntoHPLC is an ontology developed for expressing a high performance liquid chromatography.
An ontology developed for representing Metal-Organic Polyhedra (MOPs). This is object graph mapper (OGM) version.
An ontology developed for describing reaction experiment.
The Vibration Spectroscopy Ontology defines technical terms with which research data produced in vibrational spectroscopy experiments can be semantically enriched, made machine readable and FAIR.
The Crystallographic Defect Core Ontology (CDCO) defines the common terminology shared across all types of crystallographic defects, providing a unified framework for data integration in materials science.
Gelmat is an ontology for sol-gel materials. It extends the Polymat ontology (Dembska, Held, Schindler; DLR/Hereon) with classes for sol-gel synthesis routes, gel types, surface modification, drying methods, characterisation methods, process parameters, and material properties. Covers all major sol-gel derived material classes including silica, organosilica, organic, carbon, and composite aerogels.
A crystallography domain ontology based on EMMO and the CIF core dictionary. It is implemented as a formal language. (from https://nfdi4cat.org/services/ontologie-sammlung/)
SSO describes structural analysis models, their materials and constitutive behaviours, and the calibration events that update those behaviours against measured data.
A version of the Materials Data Vocabulary structured as Simple Knowledge Organization System (SKOS). The XML was originally created by the TemaTres software. This vocabulary describes the applicability to material science of records in the NIST Materials Resource Registry (NMRR - https://materials.registry.nist.gov/). The NMRR allows for the registration of materials resources, bridging the gap between existing resources and the end users.
Domain ontology for thin-film solar cells and related tandem solar cells. Contains relevant terms and concepts from BFO, IAO, UO, PATO, OBI, CHMO.
PolyMat is a domain ontology designed for polymer membrane research and tailored for immediate integration within Electronic Laboratory Notebooks (ELNs), facilitating efficient documentation of laboratory experiments and advancing the domain's FAIRification process.
Rhea is an expert-curated knowledgebase of chemical and transport reactions of biological interest. Enzyme-catalyzed and spontaneously occurring reactions are curated from peer-reviewed literature and represented in a computationally tractable manner by using the ChEBI (Chemical Entities of Biological Interest) ontology to describe reaction participants.
The Wet-Chemical Syntheses (WeChemSyn) Ontology (WCSO) provides a semantic framework for the structured representation of knowledge related to the wet-chemical syntheses of (nano) particles. Developed at the Bundesanstalt für Materialforschung und -prüfung (BAM) / Federal Institute for Materials Research and Testing in Berlin, Germany, WCSO supports the formalization and integration of data related to wet-chemical synthesis across experimental workflows, processes, and material properties.
ChEMBL is a database of bioactive compounds, their quantitative properties and bioactivities (binding constants, pharmacology and ADMET, etc). The data is abstracted and curated from the primary scientific literature.
OntoRXN is an ontology for the description of reaction networks as undirected graphs characterized by energies.
Concepts for a physical or chemical substance that is used to create a manifestation.
Concepts for the physical form of the material on which the content of the resource is stored.
Browse all 99 in the catalog →
The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and clinical investigations. The ontology will represent the design of an investigation, the protocols and instrumentation used, the material used, the data generated and the type analysis performed on it. Currently OBI is being built under the Basic Formal Ontology (BFO).
The MHC Restriction Ontology is an application ontology capturing how Major Histocompatibility Complex (MHC) restriction is defined in experiments, spanning exact protein complexes, individual protein chains, serotypes, haplotypes and mutant molecules, as well as evidence for MHC restrictions.
An ontology of units of measurement, used across OBO Foundry ontologies to annotate quantitative values with standard units.
COB brings together key terms from a wide range of OBO projects to improve interoperability.
The Ontology of Adverse Eventsy (OAE) is a biomedical ontology in the domain of adverse events. OAE aims to standardize adverse event annotation, integrate various adverse event data, and support computer-assisted reasoning. OAE is a community-based ontology. Its development follows the OBO Foundry principles. Vaccine adverse events have been used as an initial testing use case. OAE also studies adverse events associated with the administration of drug and nutritional products, the operation of surgeries, and the usage of medical devices, etc.
An ontology for modeling and understanding of pharmacokinetics in biological systems.
An ontology to support comparative effectiveness researchers studying claims data.
The Sequence Ontology (SO) is a structured controlled vocabulary for the parts of a genomic annotation. It provides a common set of terms and definitions to facilitate the exchange, analysis and management of genomic data.
The Pathway Ontology captures information on biological networks, the relationships between netweorks and the alterations or malfunctioning of such networks within a hierarchical structure. The five main branches of the ontology are: classic metabolic pathways, regulatory, signaling, drug, and disease pathwaysfor complex human conditions.
A structured controlled vocabulary for cross-linking reagents used with proteomics mass spectrometry.
The Molecular Interactions (MI) ontology forms a structured controlled vocabulary for the annotation of experiments concerned with protein-protein interactions. MI is developed by the HUPO Proteomics Standards Initiative.
The BioAssay Ontology (BAO) describes chemical biology screening assays and their results including high-throughput screening (HTS) data for the purpose of categorizing assays and data analysis.
The Proteomics Standards Initiative modification ontology (PSI-MOD) aims to define a concensus nomenclature and ontology reconciling, in a hierarchical representation, the complementary descriptions of residue modifications.
The upper level ontology upon which OBO Foundry ontologies are built.
The Bioregistry is integrative meta-registry of biological databases, ontologies, and nomenclatures that is backed by an open database.
Ontologies that aim to provide semantic specifications for units of measure, quantity kind, dimensions and data types.
An ontology of phenotypes covering microbes
The semanticscience integrated ontology (SIO) provides a simple, integrated upper level ontology (types, relations) for consistent knowledge representation across physical, processual and informational entities.
An ontology that represents the basic knowledge of physical, chemical and functional characteristics of nanotechnology as used in cancer diagnosis and therapy.
The Enzyme Nomenclature (also known as the Enzyme Commission Code) is a species-agnostic controlled vocabulary for specific enzymes and an associated hierarchical classification into 7 main categories. The Enzyme Nomenclature is maintained by the [Nomenclature Committee](https://iubmb.org/about/committees/nomenclature-committee/) of the International Union of Biochemistry and Molecular Biology (IUBMB). A detailed history of the nomenclature since the 1950s can be found [here](https://iubmb.qmul.ac.uk/enzyme/history.html).
An ontology to support the interoperability of biodiversity data, including data on museum collections, environmental/metagenomic samples, and ecological surveys.
OVAE is a biomedical ontology in the area of vaccine adverse events. OVAE is an extension of the community-based Ontology of Adverse Events (OAE).
The goal of the Systems Biology Ontology is to develop controlled vocabularies and ontologies tailored specifically for the kinds of problems being faced in Systems Biology, especially in the context of computational modeling. SBO is a project of the BioModels.net effort.
The Anatomical Therapeutic Chemical (ATC) classification system, divides active substances into different groups according to the organ or system on which they act and their therapeutic, pharmacological and chemical properties. Drugs are classified in groups at five different levels; Drugs are divided into fourteen main groups (1st level), with pharmacological/therapeutic subgroups (2nd level). The 3rd and 4th levels are chemical/pharmacological/therapeutic subgroups and the 5th level is the chemical substance.
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