Teleost Anatomy OntologyTeleost taxonomyNIFSTDNCI ThesaurusHuman diseaseBiomedical Resource OntologyExperimental Factor OntologyPRotein Ontology (PRO)Xenopus anatomy and developmentAfrican Traditional MedicineOntology of Clinical Research (OCRe)Ontology of Physics for BiologyOntology for Biomedical InvestigationsVaccine OntologyBiomedical Resource OntologyOntology of Clinical Research (OCRe)Experimental Factor OntologyBasic Vertebrate AnatomyNanoParticle OntologyPhysico-chemical methods and propertiesOntology of Clinical Research (OCRe)NIFSTDExperimental Factor Ontology
Subscribe to updates| Ontology Name: | NCBI organismal classification |
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| Ontology Id: | 1132 |
| BioPortal PURL: | http://purl.bioontology.org/ontology/NCBITaxon |
| Format: | OBOF |
| Categories: |
Taxonomic Classification
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| Groups: |
Unified Medical Language System
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| Contact: | NCBI information, info@ncbi.nlm.nih.gov |
| Home Page: | http://www.ncbi.nlm.nih.gov/Taxonomy/taxonomyhome.html/ |
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| Description: | A taxonomic classification of living organisms and associated artifacts for their controlled description within the context of databases. |
| Version Number | Release Date | Ontology File | Visualize | Download Diff File |
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| 1.2 | 10/27/2008 | Download Ontology | Explore |
| Electrophysiology Ontology | |
| The Electrophysiology (EP) Ontology is part of Project 2 of the Cardiovascular Research Grid (CVRG), an NHLBI funded effort to develop a national infrastructure for managing, sharing, and analyzing a broad range of cardiac data. The EP Ontology will contain terms for describing single-channel electrophysiological experiments and data obtained using voltage-clamp, current clamp and fluorescence imaging techniques applied at the cell level and multi-channel fluorescence imaging techniques applied at the cell, tissue and whole heart levels. | |
| People: | Dr. Raimond L. Winslow, Stephen J. Granite |
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| Institution: | The Johns Hopkins University |
| Homepage: | http://www.cvrgrid.org |
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| NCBO Annotator | |
| A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the NCBO Resource Index to create an ontology index of these resources. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards. | |
| People: | Clement Jonquet |
| Institution: | Stanford University |
| Homepage: | http://www.bioontology.org/annotator-service |
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| NCBO Resource Index | |
| The NCBO Resource Web service 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 resources related to particular ontology concepts. The annotations are generated using the NCBO Annotator and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. The NCBO Resources web service uses a concept recognizer (currently provided by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand these using ontology is_a relations in the ontology. The system's indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. Researchers can then search biomedical data sources using ontology concepts. | |
| People: | Clement Jonquet |
| Institution: | Stanford University |
| Homepage: | http://www.bioontology.org/resources-index |
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| Review By sgranite From Project Electrophysiology Ontology |
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| Widget Description | Widget Demonstration |
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Type a term in NCBI organismal classification and jump to it in BioPortalGet Code |
Step 2: Follow the Instructions
For more help visit NCBO Widget Wiki |
Fill in a field in your form with a term from NCBI organismal classificationGet Code |
Example 1 (start typing the term name to get its full URI)
Example 2 (get the ID for a term) Example 3 (get the preferred name for a term) Step 2: Follow the Instructions
Examples:
For more help visit NCBO Widget Wiki |
Get RSS feed for changes in NCBI organismal classificationGet Code |
Step 2: Follow the InstructionsCopy the code below and paste it to your HTML page Referencing an ontology in your widgetsFor more help visit NCBO Widget Wiki |
Visualize NCBI organismal classificationGet Code |
Step 2: Follow the InstructionsCopy the code below and paste it to your HTML page
If you want the visualization to be focused on a particular term in the ontology, you can add the term id to the parameters above. For example, to have the widget focus on Melanoma in NCI Thesaurus, replace the following line in the snippet above:
For more help visit NCBO Widget Wiki |
Display tree widget for NCBI organismal classificationGet Code |
Step 2: Follow the InstructionsCopy the code below and paste it to your HTML page
You can also leave the ontology parameter blank to get a list of all ontologies:
For more help visit NCBO Widget Wiki |
BioPortal calculates the metrics on the salient properties of the ontology, including statistics and quality-control and quality-assurance metrics. Each ontology may have all, some, or no values filled in for its metrics and only metrics for the most recent version are reflected. The metrics currently do not distinguish between the terms defined directly in this ontology and imported terms (for OWL) or referenced terms (for OBO). See metrics descriptions
| Number of classes: | 513248 |
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| Number of individuals: | 0 |
| Number of properties: | 6 |
| Maximum depth of the class hierarchy: | 41 |
| Maximum number of siblings in the class hierarchy: | 10010 |
| Average number of siblings in the class hierarchy: | 1 |
| Classes with a single subclass: |
37985 / 513248 (7.40%) of classes have only one subclass (details)Classes with a single subclassNCBITaxon:100008 |
| Classes with large number of subclasses: |
2581 / 513248 (0.50%) of classes have more than 25 subclasses (details)Classes with large number of subclassesNCBITaxon:293275 (201 subclasses) |
| Classes with no author: | |
| Classes with no definition: |
| Version | Base Version | Created | Created By | Ontology File | Visualize |
|---|---|---|---|---|---|
| 1.0 | 1.2 | 10/24/2009 | NCBI information, nfo@ncbi.nlm.nih.gov | Download View | Explore |
| Version | Base Version | Created | Created By | Ontology File | Visualize |
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| 1.2.1 beta | 1.2 | 08/10/2010 | Sridevi Polavaram, spolavar@gmail.com | Download View | Explore |
| 1.2 beta | 1.2 | 08/09/2010 | Sridevi Polavaram, spolavar@gmail.com | Download View | Explore |
| Version | Base Version | Created | Created By | Ontology File | Visualize |
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| 1.2.2 | 1.2 | 08/15/2010 | Sridevi Polavaram, spolavar@gmail.com | Download View | Explore |
| Version | Base Version | Created | Created By | Ontology File | Visualize |
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| 1.0 | 1.2 | 05/07/2010 | Sridevi Polavaram, spolavar@gmail.com | Download View | Explore |
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