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BioPortal

RRID:SCR_002713 RRID Copied

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BioPortal (RRID:SCR_002713)

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Resource Information

URL: http://bioportal.bioontology.org/

Proper Citation: BioPortal (RRID:SCR_002713)

Description: Open repository of biomedical ontologies that provides access via Web browsers and Web services to ontologies. It supports ontologies in OBO format, OWL, RDF, Rich Release Format (RRF), Protege frames, and LexGrid XML. Functionality includes the ability to browse, search and visualize ontologies as well as to comment on, and create mappings for ontologies. Any registered user can submit an ontology. The NCBO Annotator and NCBO Resource Index can also be accessed via BioPortal. Additional features: * Add Reviews: rate the ontology according to several criteria and describe your experience using the ontology. * Add Mappings: submit point-to-point mappings or upload bulk mappings created with external tools. Notification of new Mappings is RSS-enabled and Mappings can be browsed via BioPortal and accessed via Web services. * NCBO Annotator: Tool that tags free text with ontology terms. NCBO uses the Annotator to generate ontology annotations, creating an ontology index of these resources accessible via the NCBO Resource Index. The Annotator can be accessed through BioPortal or directly as a Web service. The annotation workflow is based on syntactic concept recognition (using the preferred name and synonyms for terms) and on a set of semantic expansion algorithms that leverage the ontology structure (e.g., is_a relations). * NCBO Resource Index: The NCBO Resource Index is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data linked via ontology terms. A set of annotations is generated automatically, using the NCBO Annotator, and presented in BioPortal. This service uses a concept recognizer (developed by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand them using ontology is_a relations. * Web services: Documentation on all Web services and example code is available at: BioPortal Web services.

Abbreviations: BioPortal

Synonyms: BioPortal Knowledgebase

Resource Type: service resource, data repository, storage service resource, repository, ontology, controlled vocabulary, data or information resource

Defining Citation: PMID:19483092, PMID:21672956, PMID:18999306

Keywords: biomedical, thesaurus, ontology mapping, annotation, metadata standard, ontology repository, portal, web service, obo, owl, rdf, rrf protege frame, lexgrid xml

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Funding Agency: NIGMS

Availability: Open unspecified license, Acknowledgement requested, The community can contribute to this resource

Resource Name: BioPortal

Resource ID: SCR_002713

Alternate IDs: nif-0000-23346

Alternate URLs: https://www.force11.org/node/4646

This resource

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lists	Porifera Ontology
lists	EnvO
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lists	Semantic DICOM Ontology
lists	Time Event Ontology
lists	Variation Ontology
lists	Vertebrate Skeletal Anatomy Ontology
lists	Epoch Clinical Trial Ontology
lists	Gazetteer
lists	Human Disease Ontology
lists	Information Artifact Ontology
lists	NCBITaxon
lists	Amphibian Taxonomy Ontology
lists	Anatomic Pathology Lexicon
lists	HIV ontology
lists	International Classification of Primary Care - 2 PLUS
lists	Mathematical Modelling Ontology
lists	Nursing Interventions Classification
lists	Phylogenetic Ontology
lists	Bleeding History Phenotype Ontology
lists	Body System Terms from ICD11
lists	Synthetic Biology Open Language Visual Ontology
lists	Teleost Anatomy Ontology
lists	Teleost Taxonomy Ontology
lists	ECO
lists	Bioassay Ontology
lists	RightField
lists	Gene Ontology
lists	HGNC
lists	Interaction Ontology
lists	International Classification for Nursing Practice
lists	Spider Ontology
lists	Vertebrate Trait Ontology
lists	Mental Functioning Ontology
lists	Ascomycete Phenotype Ontology
lists	Beta Cell Genomics Ontology
lists	Biological Collections Ontology
lists	Chemical Methods Ontology
lists	Chemical Information Ontology
lists	Common Anatomy Reference Ontology
lists	Experimental Conditions Ontology
lists	Dictyostelium Discoideum Anatomy Ontology
lists	Fission Yeast Phenotype Ontology
lists	Fly Taxonomy
lists	FlyBase Controlled Vocabulary
lists	Hymenoptera Anatomy Ontology
lists	Influenza Ontology
lists	Lipid Ontology
lists	Kinetic Simulation Algorithm Ontology
lists	Malaria Ontology
lists	FMA
lists	Minimal Anatomical Terminology
lists	NEMO Ontology
lists	Ontology for Genetic Interval
lists	Ontology for Parasite LifeCycle
lists	Ontology of Adverse Events
lists	Ontology of Medically Related Social Entities
lists	Ontology of Vaccine Adverse Events
lists	Rat Strain Ontology
lists	Plant Environmental Conditions
lists	Plant Trait Ontology
lists	Population and Community Ontology
lists	RNA Ontology
lists	Rat Strain Ontology
lists	Subcellular Anatomy Ontology
lists	Software Ontology
lists	Suggested Ontology for Pharmacogenomics
lists	Vertebrate Taxonomy Ontology
lists	PharmGKB Ontology
lists	Physico-Chemical Process
lists	International Classification for Patient Safety
lists	Adverse Event Reporting Ontology
lists	Experimental Factor Ontology
lists	Mass Spectrometry Ontology
lists	Master Drug Data Base Clinical Drugs
lists	Medaka Fish Anatomy and Development Ontology
lists	Medical Diagnostic Categories - Diagnosis Related Groups
lists	Medical Dictionary for Regulatory Activities
lists	Minimal Standard Terminology of Digestive Endoscopy
lists	Minimal Standard Terminology of Digestive Endoscopy - French
lists	Ontology of Physical Exercises
lists	Mosquito Gross Anatomy Ontology
lists	Systematized Nomenclature of Medicine - International Version
lists	Mosquito Insecticide Resistance Ontology
lists	Mouse Experimental Design Ontology
lists	Mouse Gross Anatomy and Development Ontology
lists	Systematized Nomenclature of Medicine - Clinical Terms
lists	Systems Chemical Biology and Chemogenomics Ontology
lists	Mouse Pathology Ontology
lists	NIF Cell Ontology
lists	NHS Quality Indicators
lists	Neural-Immune Gene Ontology
lists	Ontology of Physics for Biology
lists	Cell Type Ontology
lists	Xenopus Anatomy Ontology
lists	SO
lists	Ontology of Pneumology
lists	Open Biological and Biomedical Ontologies Relationship Types
lists	Biomedical Resource Ontology
lists	MGED Ontology
lists	Pharmacovigilance Ontology
lists	PhenX Phenotypic Terms
lists	Bioinformatics Web Service Ontology
lists	SysMO JERM Ontology of Systems Biology for Micro-Organisms
lists	MeSH
lists	PATO
lists	BFO
lists	MPO
lists	PR
lists	Cereal Plant Development Ontology
lists	PhenomeBLAST Ontology
lists	VIVO
lists	Computer Assisted Brain Injury Rehabilitation Ontology
lists	Computer Retrieval of Information on Scientific Projects Thesaurus
lists	NIFSTD
lists	Cell Line Ontology
lists	Student Health Record Ontology
lists	Zebrafish Anatomical Ontology
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lists	Read Codes Clinical Terms Version 3
lists	Reference Sequence Annotation
lists	Regulation of Gene Expression Ontolology
lists	Neurobehavior Ontology
lists	Regulation of Transcription Ontology
lists	Reproductive Trait and Phenotype Ontology
lists	Skin Physiology Ontology
lists	Vaccine Ontology
lists	OMIM
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lists	Adult Mouse Anatomy Ontology
lists	Bone Dysplasia Ontology
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lists	Botryllus schlosseri anatomy and development ontology
lists	EDAM Ontology
lists	LexGrid
lists	RxNorm
lists	Breast Cancer Grading Ontology
lists	Breast Tissue Cell Lines Ontology
lists	SBO
lists	Resource of Asian Primary Immunodeficiency Diseases Phenotype Ontology
lists	Brucellosis Ontology
lists	Sleep Domain Ontology
lists	C. elegans Development Vocabulary
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lists	C. elegans Gross Anatomy Vocabulary
lists	Plant Ontology
lists	C. elegans Phenotype Vocabulary
lists	CPTAC Proteomics Pipeline Infrastructure Ontology
lists	Cancer Research and Management ACGT Master Ontology
lists	Cancer Chemoprevention Ontology
lists	Cell Behavior Ontology
lists	Cereal Plant Gross Anatomy Ontology
lists	Cardiac Electrophysiology Ontology
lists	Cerebrotendinous Xanthomatosis Ontology
lists	Cell Cycle Ontology
lists	Cell Culture Ontology
lists	Cerrado concepts and plant community dynamics
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lists	Clusters of Orthologous Groups Analysis Ontology
lists	Computational Neuroscience Ontology
lists	BIRNLex
lists	Computer-Based Patient Record Ontology
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lists	Drug Interaction Knowledge Base Ontology
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lists	BioModels Ontology
lists	Bilingual Ontology of Alzheimer
lists	BioPortal Metadata Ontology
lists	Biochemical Substructure Ontology
lists	Biodiversity Ontology
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lists	Leukocyte Surface Marker Ontology
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lists	AEO
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lists	Amino Acid Ontology
lists	Amphibian Gross Anatomy Ontology
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lists	Current Procedural Terminalogy Hierarchy
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lists	Disease core ontology applied to Rare Diseases
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lists	Galen Ontology
lists	Gene Expression Ontology
lists	Gene Ontology Extension
lists	General Formal Ontology
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lists	Genomic Clinical Decision Support Ontology
lists	GeoSpecies Ontology
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lists	Habronattus Courtship Ontology
lists	Health Indicator Ontology
lists	Health Level Seven Reference Implementation Model Version 3
lists	Human Developmental Anatomy Ontology abstract version 2
lists	Human Developmental Anatomy Ontology timed version
lists	Human Interaction Network Ontology
lists	Human Physiology Simulation Ontology
lists	Logical Observation Identifier Names and Codes
lists	IMGT-ONTOLOGY
lists	Image and Data Quality Assessment Ontology
lists	Immune Disorder Ontology
lists	Infectious Disease Ontology
lists	InterNano Nanomanufacturing Taxonomy
lists	Interaction Network Ontology
lists	International Classification of External Causes of Injuries
lists	International Classification of Diseases Version 10
lists	International Classification of Diseases Version 10 - Clinical Modification
lists	International Classification of Diseases Version 10 - Procedure Coding System
lists	MR dataset acquisition
lists	Maize Gross Anatomy Ontology
lists	Major Histocompatibility Complex Ontology
lists	Medical image simulation
lists	Menelas Project Top-Level Ontology
lists	Mental State Assessment
lists	Metagenome Sample Vocabulary
lists	Metagenome and Microbes Environmental Ontology
lists	MicroRNA Ontology
lists	Microbial Culture Collection Vocabulary
lists	Microbial Typing Ontology
lists	Minimal Information about any Sequence Controlled Vocabularies
lists	Minimal Information about any Sequence Ontology
lists	NIF Dysfunction Ontlogy
lists	NIF Subcellular Ontology
lists	NMR-Instrument Component of Metabolomics Investigations Ontology
lists	Name Reaction Ontology
lists	NanoParticle Ontology
lists	National Cancer Institute Thesaurus
lists	National Drug Data File
lists	National Drug File - Reference Terminology
lists	Natural Products Ontology
lists	Neglected Tropical Disease Ontology
lists	Neomark Oral Cancer Ontology version 3
lists	Neomark Oral Cancer Ontology version 4
lists	Neural Motor Recovery Ontology
lists	NeuroMorpho.Org species ontology
lists	NeuroMorpho.Org species ontology old
lists	Non-Randomized Controlled Trials Ontology
lists	Nursing Care Coordination Ontology
lists	Ontological Knowledge Base Model for Cystic Fibrosis
lists	Ontology for Drug Discovery Investigations
lists	Ontology for General Medical Science
lists	Ontology for Genetic Disease Investigations
lists	Ontology for Genetic Susceptibility Factor
lists	Ontology for MicroRNA Target Prediction
lists	Symptom Ontology
lists	Ontology for Newborn Screening Follow-up and Translational Research
lists	Ontology of Alternative Medicine French
lists	Ontology of Biological and Clinical Statistics
lists	Ontology of Clinical Research
lists	Ontology of Core Data Mining Entities
lists	Ontology of Data Mining Investigations
lists	Pediatric Terminology
lists	Ontology of Experimental Variables and Values
lists	Ontology of General Purpose Datatypes
lists	Ontology of Geographical Region
lists	Ontology of Glucose Metabolism Disorder
lists	Ontology of Homology and Related Concepts in Biology
lists	Ontology of Language Disorder in Autism
lists	Orphanet Rare Disease Ontology
lists	Parasite Experiment Ontology
lists	Pathogen Transmission Ontology
lists	Pathogenic Disease Ontology
lists	Pharmacogenomic Relationships Ontology
lists	Physico-Chemical Methods and Properties
lists	Plant Anatomy
lists	Syndromic Surveillance Ontology
lists	Plant Structure Development Stage
lists	Portfolio Management Application
lists	Protein Modification Ontology
lists	Protein-Protein Interaction Ontology
lists	Proteomics Data and Process Provenance Ontology
lists	Provenance Ontology
lists	QUDT
lists	Quantitative Imaging Biomarker Ontology
lists	Radiology Lexicon
lists	Robert Hoehndorf Version of MeSH
lists	Role Ontology
lists	STATistics Ontology
lists	Sage Bionetworks Synapse Ontology
lists	Sample Processing and Separation Techniques Ontology
lists	Santa Barbara Coastal Observation Ontology
lists	Semantic Types Ontology
lists	Semantic Web for Earth and Environment Technology Ontology
lists	Semanticscience Integrated Ontology
lists	Single-Nucleotide Polymorphism Ontology
lists	Situation-Based Access Control Ontology
lists	Taxonomic Rank Vocabulary
lists	Taxonomy for Rehabilitation of Knee Conditions
lists	Terminological and Ontological Knowledge Resources Ontology
lists	Tick Gross Anatomy Ontology
lists	Tissue Microarray Ontology
lists	Traditional Medicine Constitution Value Set
lists	Traditional Medicine Meridian Value Sets
lists	Traditional Medicine Other Factors Value Set
lists	Traditional Medicine Signs and Symptoms Value Set
lists	Translational Medicine Ontology
lists	Tribolium Ontology
lists	Units Ontology
lists	Units of Measurement Ontology
lists	Upper-Level Cancer Ontology
lists	Vertebrate Homologous Organ Group Ontology
lists	Veterans Health Administration National Drug File
lists	Vital Sign Ontology
lists	WHO Adverse Reaction Terminology
lists	Web-Service Interaction Ontology
lists	Wheat Trait Ontology
lists	XEML Environment Ontology
lists	suicideo
lists	suicideonto
lists	Pseudogene
lists	Terminology for the Description of Dynamics
lists	Gene Regulation Ontology
lists	UBERON
lists	CHEBI
lists	Cognitive Paradigm Ontology
lists	Emotion Ontology
lists	Clinical Measurement Ontology
lists	Measurement Method Ontology
lists	NCI Thesaurus
lists	Ontology for Biomedical Investigations
lists	Biological Pathways Exchange
is listed by	Biositemaps
is listed by	FORCE11
is related to	Provisional Cell Ontology
has parent organization	National Center for Biomedical Ontology
has parent organization	Stanford University; Stanford; California
is parent organization of	NCBO Annotator

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