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Ontology databases | Biomedical text mining

OBO Foundry
Dataset

OBO Foundry Open Biological and Biomedical Ontologies Foundry

Provides a collaborative experiment to establish a set of principles for…

Provides a collaborative experiment to establish a set of principles for ontology development. OBO aims to create a suite of orthogonal interoperable reference ontologies in the biomedical domain. In…

NeXO
Dataset

NeXO Network-extracted Ontology

Provides structured knowledge about the cellular components, processes, and…

Provides structured knowledge about the cellular components, processes, and functions encoded by genes. NeXO is a data-driven gene ontology (GO) inferred directly from omics data. It uses a…

Uberon
Terminology

Uberon

Represents body parts, organs and tissues in a variety of animal species, with…

Represents body parts, organs and tissues in a variety of animal species, with a focus on vertebrates. Uberon is an integrated cross-species ontology covering anatomical structures in animals. It has…

OLS
Dataset

OLS Ontology Lookup Service

A spin-off of the PRIDE project, which required a centralized query interface…

A spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup. The OLS provides a web service interface to query multiple ontologies from…

SBO
Dataset

SBO Systems Biology Ontology

Provides a set of controlled, relational vocabularies of terms commonly used in…

Provides a set of controlled, relational vocabularies of terms commonly used in Systems Biology. Systems Biology Ontology is a database that consists of seven orthogonal vocabularies defining: (i)…

Gene, Disease Features Ontology-based Overview System
Dataset

Gene, Disease Features Ontology-based Overview System Gendoo

Provides a repository of profiles diseases and genes associated with related…

Provides a repository of profiles diseases and genes associated with related drugs, biological phenomena and anatomy described with MeSH vocabulary. Gendoo includes more than 1700000 associations.…

OntoBrowser
Desktop

OntoBrowser

Provides an easy-to-use online collaborative solution for subject matter…

Provides an easy-to-use online collaborative solution for subject matter experts to map reported terms to preferred ontology (or code list) terms and facilitate ontology evolution. OntoBrowser…

PCOSKB
Dataset

PCOSKB

A manually curated knowledgebase on polycystic ovary syndrome (PCOS).…

A manually curated knowledgebase on polycystic ovary syndrome (PCOS). PCOS-related information available through scientific literature is cross-linked with molecular, biochemical and clinical…

Ontobee
Dataset

Ontobee

A linked data server designed for ontologies. Ontobee is aimed to facilitate…

A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences and presents…

ProbOnto
Dataset

ProbOnto

Provides information about probability distributions. ProbOnto is a knowledge…

Provides information about probability distributions. ProbOnto is a knowledge base built from a simple ontological model. The database contains uni- and multivariate distributions and alternative…

ontologyX
Desktop

ontologyX

A suite of R packages, consisting of ontologyIndex, ontologyPlot and…

A suite of R packages, consisting of ontologyIndex, ontologyPlot and ontologySimilarity, which together formes a consistent interoperable set of tools that is readily extensible with additional…

SO
Terminology

SO Sequence Ontology

Regroups a set of terms and relationships used to describe the features and…

Regroups a set of terms and relationships used to describe the features and attributes of biological sequence. SO includes different kinds of features which can be located on the sequence. It…

BAO
Terminology

BAO BioAssay Ontology

Standardizes, organizes and semantically defines biological assays and…

Standardizes, organizes and semantically defines biological assays and screening results. BAO provides a foundation for standardizing assay descriptions and endpoints. The ontology serves as a…

Ontodog
Web

Ontodog

A web system that generates an ontology view with customized annotation.…

A web system that generates an ontology view with customized annotation. Authors define ‘ontology community view’ as a whole or a portion of the ontology that maintains textual and logical term…

eNanoMapper…
Terminology

eNanoMapper ontology

Aims to develop a comprehensive ontology and annotated database for the…

Aims to develop a comprehensive ontology and annotated database for the nanosafety domain to address the challenge of supporting the unified annotation of nanomaterials. eNanoMapper ontology was…

Pre_GI
Dataset

Pre_GI Predicted Genomic Islands database

Stores prokaryotic genomic islands. Pre_GI is a database that contains more…

Stores prokaryotic genomic islands. Pre_GI is a database that contains more than 20 000 islands found in bacterial and archaeal chromosomes and plasmids. The concept of ‘island’ relevant to this…

BioPortal
Dataset

BioPortal

An open repository of biomedical ontologies that provides access via Web…

An open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protege frames. BioPortal functionality includes…

nmrCV
Terminology

nmrCV

Provides an OWL ontology for nuclear magnetic resonance (NMR) data inspired by…

Provides an OWL ontology for nuclear magnetic resonance (NMR) data inspired by mzML, the Proteomics Standard Initiatives’ (PSI) standard format established for mass spectrometry data. nmrCV is…

CIO
Desktop

CIO Confidence Information Ontology

Provides an ontology to capture confidence information about annotation…

Provides an ontology to capture confidence information about annotation assertions in a more systematic manner. The CIO is an ontology created to address the main points identified to provide clear…

ICEPO
Terminology

ICEPO Ion Channel ElectroPhysiology Ontology

An ontological framework to annotate the electrophysiological class of ion…

An ontological framework to annotate the electrophysiological class of ion channels. ICEPO is the translation of quantitative assertions extracted through text mining to a formal representation that…

EXPO
Desktop

EXPO

Defines over 200 concepts for creating semantic markup about scientific…

Defines over 200 concepts for creating semantic markup about scientific experiments, using the Web Ontology Language OWL. The ontology EXPO aims to formalise generic knowledge about scientific…

NCRO
Terminology

NCRO Non-Coding RNA Ontology

Aims to integrate genomic and sequence-based annotation with gene expression…

Aims to integrate genomic and sequence-based annotation with gene expression regulation, secondary and 3D structure information, protein interactions, and their inter-relationships. NCRO consists in…

ENVO
Terminology

ENVO Environment Ontology

A resource for the semantically controlled description of environmental…

A resource for the semantically controlled description of environmental entities. ENVO bridges multiple domains including biomedicine, natural and anthropogenic ecology, omics and socioeconomic…

EBI RDF…
Dataset

EBI RDF platform

Aims to bring together the efforts of a number of EMBL-EBI resources that…

Aims to bring together the efforts of a number of EMBL-EBI resources that provide access to their data using Semantic Web technologies. The EBI RDF platform provides a unified way to query across…

Aber-OWL
Dataset

Aber-OWL

Provides reasoning services for bio-ontologies. Aber-OWL consists of an…

Provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and…

MGED Ontology
Terminology

MGED Ontology Microarray Gene Expression Database Ontology

Provides terms for annotating all aspects of a microarray experiment from the…

Provides terms for annotating all aspects of a microarray experiment from the design of the experiment and array layout, through to the preparation of the biological sample and the protocols used to…

OMIT
Terminology

OMIT Ontology for MIcroRNA Target prediction

Encodes in a standardized manner miR domain knowledge. OMIT is a semi-automated…

Encodes in a standardized manner miR domain knowledge. OMIT is a semi-automated ontology which makes use of machine intelligence, considers miR domain-dependent and domain-independent…

SIO
Terminology

SIO Semanticscience Integrated Ontology) (Semanticscience Integrated Ontology

Provides classes and relations to describe and relate objects, processes and…

Provides classes and relations to describe and relate objects, processes and their attributes with specific extensions in the biomedical domain. SIO’s data concern spatial and temporal qualitative…

CogPO
Terminology

CogPO Cognitive Paradigm Ontology

Represents certain characteristics of the cognitive paradigms used in the fMRI…

Represents certain characteristics of the cognitive paradigms used in the fMRI and PET literature. CogPO is compliant with the Basic Formal Ontology (BFO), and harmonizes where possible with larger…

OntoNorm
Desktop

OntoNorm

An open source machine learning framework to automatically map concepts in an…

An open source machine learning framework to automatically map concepts in an ontology to text. OntoNorm maps the protein-protein interaction (PPI) relevant articles with corresponding interaction…

OBO
Dataset

OBO Open Biological Ontology

Develops a family of interoperable ontologies that are both logically…

Develops a family of interoperable ontologies that are both logically well-formed and scientifically accurate. OBO offers a table of ontologies, available in several formats, with details for each,…

MCO
Terminology

MCO Microbial Conditions Ontology

Aims to standardize the annotation of experimental conditions in microbial data…

Aims to standardize the annotation of experimental conditions in microbial data repositories. MCO provides growth conditions terms together with their definitions, synonyms, references, and…

MC Miner
Desktop

MC Miner Molecular Connections Miner

Allows users to mine information from a range of unstructured data sources to…

Allows users to mine information from a range of unstructured data sources to create structured outputs. MC Miner is a state-of-the-art text mining engine that provides data usable to develop custom…

MC Lexicon
Dataset

MC Lexicon Molecular Connection Lexicon

Provides thesaurus management system which can be employed to build and manage…

Provides thesaurus management system which can be employed to build and manage information systems. MC Lexicon provides a comprehensive list of application programming interfaces (APIs) for…

IDOBRU
Terminology

IDOBRU Brucellosis Ontology

Covers and crosses the biomedical domains of clinical care, public health and…

Covers and crosses the biomedical domains of clinical care, public health and biomedical research in the specific brucellosis field. Brucellosis Ontology (IDOBRU) is an extension ontology of the…

ontogetdown
Desktop

ontogetdown

Get ontology term(s) by parent id. ontogetdown finds ontology terms matching a…

Get ontology term(s) by parent id. ontogetdown finds ontology terms matching a query. All children of the term, related to the term by 'is_a' (class/subclass) relationships, are returned.…

edamdef
Desktop

edamdef

Finds EDAM ontology terms by definition. edamdef searches the definition of…

Finds EDAM ontology terms by definition. edamdef searches the definition of EDAM terms and returns matching terms. The input is read from the installed EDAM database. The ontology term output can be…

ontoget
Desktop

ontoget

Gets ontology terms. ontoget reads ontology terms matching a query. Optionally,…

Gets ontology terms. ontoget reads ontology terms matching a query. Optionally, the parents or children of the term, related to the term by 'is_a' (class/subclass) relationships, may also…

ontocount
Desktop

ontocount

Counts ontology terms. ontocount reads ontology entries and reports the number…

Counts ontology terms. ontocount reads ontology entries and reports the number of entries found.

edamisformat
Desktop

edamisformat

Finds EDAM ontology terms by “is_format_of” relation. edamisformat takes as…

Finds EDAM ontology terms by “is_format_of” relation. edamisformat takes as input data from the installed EDAM database. The search can be restricted to specified EDAM namespaces. The ontology…

ontogetsibs
Desktop

ontogetsibs

Gets one or more ontology terms by identifier with common parent. ontogetsibs…

Gets one or more ontology terms by identifier with common parent. ontogetsibs finds ontology terms matching a query. All siblings of the term relationships, are returned. The information may be…

ontotext
Desktop

ontotext

Gets ontology term(s) original full text. ontotext is an Emboss tool that reads…

Gets ontology term(s) original full text. ontotext is an Emboss tool that reads one or more complete ontology term entries from a database or a file and writes them to a text file. Optionally, the…

edamname
Desktop

edamname

Finds EDAM ontology terms by name. edamname searches the names and synonyms of…

Finds EDAM ontology terms by name. edamname searches the names and synonyms of EDAM terms and returns matching terms. The input is read from the installed EDAM database. The search can be restricted…

edamhasinput
Desktop

edamhasinput

Finds EMBRACE Data and Methods (EDAM) ontology terms by has_input relation.…

Finds EMBRACE Data and Methods (EDAM) ontology terms by has_input relation. edamhasinput searches the has_input relations of EDAM terms and returns matching terms. The input is read from the…

CiTO
Terminology

CiTO Citation Typing Ontology

Describes the nature of reference citations in scientific research articles and…

Describes the nature of reference citations in scientific research articles and other scholarly works, both to other such publications and also to Web information resources, and for publishing these…

OntoFox
Web

OntoFox Ontology Fetches ontology terms and axioms

Retrieves ontology terms and axioms. OntoFox supports ontology reuse by…

Retrieves ontology terms and axioms. OntoFox supports ontology reuse by following and extending the existing method MIREOT (Minimum Information to Reference an External Ontology Term). It provides…

LipidGO
Dataset

LipidGO

Provides information about lipid-related Gene Ontology (GO) terms and gene…

Provides information about lipid-related Gene Ontology (GO) terms and gene products. LipidGO is a platform that allows users to search by key words to obtain the list of GO terms and by GO accession…

CDAO
Terminology

CDAO Comparative Data Analysis Ontology

Provides semantic descriptions of data and transformations for evolutionary…

Provides semantic descriptions of data and transformations for evolutionary comparative analysis. CDAO is an open source repository which provides terms for continuous and discrete characters and a…

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