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Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, <br>
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Welcome to the '''National Center for Biomedical Ontology (NCBO) public wiki'''. This wiki provides user guides and technical documentation for software developed by NCBO.
dissemination events conducted by the NCBO and publically shared materials from the NCBO.
 
  
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Note that as the NCBO project funding has ended, documentation for some projects or project details (n.b., NCBO BioPortal details) may be out of date. Pease send email to the BioPortal Support List
  
=== NCBO Links ===
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Please visit our [http://www.bioontology.org main site] for more information about NCBO.
*[http://www.bioontology.org/ NCBO Home page]
 
*[http://www.bioontology.org/wiki/index.php/NCBO_FAQ NCBO FAQ]
 
*[[Meetings and Events]]
 
  
=== Shared Materials===
 
  
*[[Public Requirements Redirect|Public Requirements]]
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__TOC__
  
*[[Shared Materials]]
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== Software ==
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To follow is a list of software developed and maintained by NCBO:
  
*[[Evaluation Activities]]
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* [https://bioportal.bioontology.org BioPortal] - A web-based application for accessing and sharing biomedical ontologies
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* [https://data.bioontology.org/ BioPortal REST API] - A RESTful API to access BioPortal content
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* [[:Category:NCBO_Virtual_Appliance|BioPortal Virtual Appliance]] - Contains BioPortal and the BioPortal REST API, runs on Linux
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* [http://sparql.bioontology.org/ BioPortal SPARQL Endpoint] - Access BioPortal content via SPARQL queries ''(obsolete)''
  
=== NCBC Links ===
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Please refer to our [[BioPortal_Release_Notes|release notes]] page for change logs.
  
*[http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]
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== Documentation ==
  
*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:Software_and_Data_Integration_Working_Group NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion]
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* [[BioPortal Help|BioPortal]] - get help with the user interface and instructions for commonly performed tasks
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* [http://data.bioontology.org/documentation BioPortal REST API] - see a list of available endpoints with usage instructions
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* [[:Category:NCBO_Virtual_Appliance|BioPortal Virtual Appliance]] - read a getting started guide and installation instructions
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* [[Using_NCBO_Technology_In_Your_Project|Using NCBO technologies in your project]] - get ideas for how to employ NCBO technologies in your website or application
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* [[SKOSSupport|SKOS support]] - view the specifics of BioPortal's support for SKOS vocabularies
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* [[SPARQL_BioPortal|BioPortal SPARQL Endpoint]] - read about programmatic submission of SPARQL queries and the named graph structure
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* [[NCBO_Developer_Documentation|Developer documentation]]
  
*[http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]
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=== Mail Support ===
  
=== Ontology Development Area ===
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* [https://mailman.stanford.edu/mailman/listinfo/bioontology-support BioPortal Support List] - sign up to see and request community support for BioPortal
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* [https://mailman.stanford.edu/pipermail/bioontology-support/ BioPortal mailman email archives] - the usual mailman archive format for BioPortal support list
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* [http://ncbo-support.2288202.n4.nabble.com/ BioPortal nabble email archives] - BioPortal support email list archives in easier format to search and navigate
  
Below are wikis for some of the current OBO ontologies. Each wiki is housed on the bioontologies.org wiki, in its own partition (wikispace) of the main wiki
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== Ontology Development Projects ==
  
*[[PATO:Main_Page]] - An ontology of phenotypic qualities
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These are some of the ontology development projects that NCBO participated in:
 
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*[[RO:Main_Page]] - OBO Relations ontology
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* [http://bioportal.bioontology.org/ontologies/BRO Biomedical Resource Ontology]
 
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* [http://bioportal.bioontology.org/ontologies/TMO Translational Medicine Ontology]
*[[CARO:Main_Page]] - Reference anatomical ontology
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* [[NPO:Main_Page|NanoParticle Ontology]]  
 
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* [http://bioportal.bioontology.org/ontologies/PATO Phenotypic Quality Ontology]
*[[CL:Main_Page]] - OBO Cell ontology
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* [[RO:Main_Page|OBO Relations Ontology]]
 
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* [[CARO:Main_Page|Common Anatomy Reference Ontology]]
*[[SO:Main_Page]] - Sequence Ontology
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* [[CL:Main_Page|Cell Ontology]]
 
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* [[SO:Main_Page|Sequence Types and Features Ontology]]
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders
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* [[Disease:Main_Page|Disease Ontology]], and other ontologies pertaining to diseases and disorders
 
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* [[OCI:Main_Page|Ontology of Clinical Investigation]]
*[[CTO:Main_Page]] - Clinical Trial Ontology
 
 
 
Note that each ontology lives in its own wikispace which corresponds to the [[OBO:IDSpace]] of that ontology. Note for wiki editors: all wiki pages that are to be considered local to a particular ontology should be prefixed with that IDSpace.
 
 
 
=== Software Development Area ===
 
*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
 
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
 
*[[Bioportal:Main_Page]]
 

Latest revision as of 11:58, 3 January 2018

Welcome to the National Center for Biomedical Ontology (NCBO) public wiki. This wiki provides user guides and technical documentation for software developed by NCBO.

Note that as the NCBO project funding has ended, documentation for some projects or project details (n.b., NCBO BioPortal details) may be out of date. Pease send email to the BioPortal Support List

Please visit our main site for more information about NCBO.


Software

To follow is a list of software developed and maintained by NCBO:

Please refer to our release notes page for change logs.

Documentation

Mail Support

Ontology Development Projects

These are some of the ontology development projects that NCBO participated in: