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BioPortal

General Information

BioPortal is a library of biomedical ontologies and terminologies developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S), Open Biological and Biomedical Ontologies (OBO) format, and Protégé frames and Rich Release Format. BioPortal groups ontologies by domain to aid discoverability and allows users to browse, search and visualize the content of ontologies. BioPortal also provides ontology recommendation, text annotation, ontology mapping, and a reference index to resources like PubMed.

Homepage http://bioportal.bioontology.org/

Countries that developed this resource United States

Created in 2005

Taxonomic range

Not applicable

Subjects

How to cite this record FAIRsharing.org: BioPortal; BioPortal; DOI: https://doi.org/10.25504/FAIRsharing.4m97ah; Last edited: Dec. 16, 2020, 1:20 p.m.; Last accessed: Oct 20 2021 2:15 a.m.

Publication for citation BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Whetzel PL,Noy NF,Shah NH,Alexander PR,Nyulas C,Tudorache T,Musen MA; Nucleic Acids Res ; 2011; 10.1093/nar/gkr469;

This record is maintained by CEDAR Metadata Center (jgraybeal)

Record added: April 21, 2016, 8:30 p.m.
Record updated: Dec. 16, 2020, 1:19 p.m. by The FAIRsharing Team.

Show edit history

Edits to 'https://fairsharing.org/FAIRsharing.4m97ah' by 'The FAIRsharing Team' at 13:19, 16 Dec 2020 (approved):

	'supportLinks' has been modified:
		Before:
			FAQ|https://www.bioontology.org/wiki/BioPortal_FAQ
			contact form|https://bioportal.bioontology.org/feedback
			help|https://www.bioontology.org/wiki/BioPortal_Help
			online documentation|https://www.bioontology.org/wiki/BioPortal_Release_Notes
			online documentation|http://github.com/ncbo
			twitter|@bioontology
		After:
			FAQ|https://www.bioontology.org/wiki/BioPortal_FAQ
			contact form|https://bioportal.bioontology.org/feedback
			help|https://www.bioontology.org/wiki/BioPortal_Help
			online documentation|https://www.bioontology.org/wiki/BioPortal_Release_Notes
			online documentation|http://github.com/ncbo
			tess training|https://tess.elixir-europe.org/materials/browsing-the-enanomapper-ontology-with-bioportal-aberowl-and-protege
			twitter|@bioontology
		Added:
			tess training|https://tess.elixir-europe.org/materials/browsing-the-enanomapper-ontology-with-bioportal-aberowl-and-protege
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.4m97ah' by 'The FAIRsharing Team' at 13:19, 16 Dec 2020 (approved):

	'organizations' has been modified:
		Before:
			Stanford University Center for Biomedical Informatics Research, CA, USA|http://bmir.stanford.edu/|Maintains
			NIH Common Fund, USA|https://commonfund.nih.gov|Funds
		After:
			NIH Common Fund, USA|https://commonfund.nih.gov|Funds
			Stanford University Center for Biomedical Informatics Research, CA, USA|http://bmir.stanford.edu/|Maintains
			National Center for Biomedical Ontology (NCBO), Stanford, CA, USA|http://www.bioontology.org/|Maintains
		Added:
			National Center for Biomedical Ontology (NCBO), Stanford, CA, USA|http://www.bioontology.org/|Maintains
		Removed:

	'supportLinks' has been modified:
		Before:
			contact form|http://bioportal.bioontology.org/feedback
			help|http://bioportal.bioontology.org/help
			twitter|@bioontology
		After:
			FAQ|https://www.bioontology.org/wiki/BioPortal_FAQ
			contact form|https://bioportal.bioontology.org/feedback
			help|https://www.bioontology.org/wiki/BioPortal_Help
			online documentation|https://www.bioontology.org/wiki/BioPortal_Release_Notes
			online documentation|http://github.com/ncbo
			twitter|@bioontology
		Added:
			FAQ|https://www.bioontology.org/wiki/BioPortal_FAQ
			contact form|https://bioportal.bioontology.org/feedback
			help|https://www.bioontology.org/wiki/BioPortal_Help
			online documentation|https://www.bioontology.org/wiki/BioPortal_Release_Notes
			online documentation|http://github.com/ncbo
		Removed:
			contact form|http://bioportal.bioontology.org/feedback
			help|http://bioportal.bioontology.org/help

	'description' has been modified:
		Before: BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S), Open Biological and Biomedical Ontologies (OBO) format, and Prot?g? frames and Rich Release Format. BioPortal has a service-oriented architecture; the NCBO Web services provide the functionality found in BioPortal and these Web services can be incorporated into other software applications to access and use ontology content. BioPortal groups ontologies by domain to ease finding relevant ontologies and allows users to browse, search and visualize the content of ontologies. BioPortal also provides value-added features like ontology recommendation, text annotation, ontology mapping, and a reference index to resources like PubMed.
		After: BioPortal is a library of biomedical ontologies and terminologies developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S), Open Biological and Biomedical Ontologies (OBO) format, and Prot?g? frames and Rich Release Format. BioPortal groups ontologies by domain to aid discoverability and allows users to browse, search and visualize the content of ontologies. BioPortal also provides ontology recommendation, text annotation, ontology mapping, and a reference index to resources like PubMed.

	'onto_disciplines' has been modified:
		Before:
			Life Science
		After:
			Life Science
			Ontology and Terminology
		Added:
			Ontology and Terminology
		Removed:

	'dataProcesses' has been modified:
		Before:
			freely available for public use, data access, http://data.bioontology.org
		After:
			Advanced Search, data access, http://bioportal.bioontology.org/search?opt=advanced
			Browse Ontologies, data access, http://bioportal.bioontology.org/ontologies
			Search Classes, data access, http://bioportal.bioontology.org/search
			Annotate Text, data access, http://bioportal.bioontology.org/annotator
			Ontology Recommender, data access, http://bioportal.bioontology.org/recommender
			Browse Ontology Mappings, data access, http://bioportal.bioontology.org/mappings
		Added:
			Advanced Search, data access, http://bioportal.bioontology.org/search?opt=advanced
			Browse Ontologies, data access, http://bioportal.bioontology.org/ontologies
			Search Classes, data access, http://bioportal.bioontology.org/search
			Annotate Text, data access, http://bioportal.bioontology.org/annotator
			Ontology Recommender, data access, http://bioportal.bioontology.org/recommender
			Browse Ontology Mappings, data access, http://bioportal.bioontology.org/mappings
		Removed:
			freely available for public use, data access, http://data.bioontology.org

	'accessPoints' has been modified:
		Before:
		After:
			REST|http://data.bioontology.org/documentation|API Documentation
		Added:
			REST|http://data.bioontology.org/documentation|API Documentation
		Removed:

	'tools' has been modified:
		Before:
		After:
			OntoPortal Virtual Appliance|3.0|https://ontoportal.github.io/administration/
			NCBO Widgets||https://www.bioontology.org/wiki/NCBO_Widgets
		Added:
			OntoPortal Virtual Appliance|3.0|https://ontoportal.github.io/administration/
			NCBO Widgets||https://www.bioontology.org/wiki/NCBO_Widgets
		Removed:

Edits to 'https://fairsharing.org/FAIRsharing.4m97ah' by 'jgraybeal' at 20:35, 06 Jul 2017 (approved):

	'description' has been modified:
		Before: BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S), Open Biological and Biomedical Ontologies (OBO) format, Protg frames and Rich Release Format (http://bioportal.bioontology.org). BioPortal has a service-oriented architecture; the NCBO Web services provide the functionality found in BioPortal and these Web services can be incorporated into other software applications to access and use ontology content. BioPortal groups ontologies by domain to ease finding relevant ontologies and allows users to browse, search and visualize the content of ontologies.
		After: BioPortal is a Web portal that provides access to a library of biomedical ontologies and terminologies developed in Web Ontology Language (OWL), Resource Description Framework (RDF)(S), Open Biological and Biomedical Ontologies (OBO) format, and Protg frames and Rich Release Format. BioPortal has a service-oriented architecture; the NCBO Web services provide the functionality found in BioPortal and these Web services can be incorporated into other software applications to access and use ontology content. BioPortal groups ontologies by domain to ease finding relevant ontologies and allows users to browse, search and visualize the content of ontologies. BioPortal also provides value-added features like ontology recommendation, text annotation, ontology mapping, and a reference index to resources like PubMed.

In Collections

Systems Medicine

Open Science Prize

Support

General

FAQ	FAQ
contact form	Feedback Form
help	BioPortal Help
online documentation	Release Notes
online documentation	Github Repository
twitter	@bioontology

Additional Information

Contact

John Graybeal ORCID

TeSS training resources

Browsing the eNanoMapper ontology with BioPortal, AberOWL and Protégé

Tools

OntoPortal Virtual Appliance	https://ontoportal.github.io/administration/	3.0
NCBO Widgets	https://www.bioontology.org/wiki/NCBO_Widgets

Access / Retrieve Data

Conditions of Use

Data Access

Advanced Search	http://bioportal.bioontology.org/search?opt=advanced
Browse Ontologies	http://bioportal.bioontology.org/ontologies
Search Classes	http://bioportal.bioontology.org/search
Annotate Text	http://bioportal.bioontology.org/annotator
Ontology Recommender	http://bioportal.bioontology.org/recommender
Browse Ontology Mappings	http://bioportal.bioontology.org/mappings

REST Web Services

API Documentation

http://data.bioontology.org/documentation

Publications

BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Whetzel PL,Noy NF,Shah NH,Alexander PR,Nyulas C,Tudorache T,Musen MA
Nucleic Acids Res 2011

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

BioPortal Metadata

Models and Formats

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined

Related Databases

Implementing Policies

This record is not implemented by any policy.

Credit

Record Maintainer

This record is maintained by CEDAR Metadata Center (jgraybeal)

Funds

NIH Common Fund, USA (Government body)

Maintains

Stanford University Center for Biomedical Informatics Research, CA, USA (Lab)
National Center for Biomedical Ontology (NCBO), Stanford, CA, USA (Research institute) Lead

Grant Number(s)

U54-HG004028 (NIH Common Fund, USA)

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