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Welcome to the '''NCBO Public WIKI'''. This WIKI provides information about collaborative ontology development efforts, dissemination events conducted by the NCBO and publically shared materials from the NCBO.
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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.
Please visit our [http://www.bioontology.org Main Site] for more information and materials.
 
  
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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project funding has ended, documentation for some projects or project details (n.b., NCBO BioPortal details) may be out of date.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
  
{| class="wikitable"
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Please visit our [http://www.bioontology.org main site] for more information about NCBO.
|-
 
! style="background:#efefef;" | NCBO Links
 
! style="background:#efefef;" | Shared Materials
 
! style="background:#efefef;" | NCBC Links
 
|-
 
| [http://www.bioontology.org/ Home page]
 
| [[Public Requirements Redirect|Public Requirements]]
 
| [http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]
 
|-
 
| [http://www.bioontology.org/wiki/index.php/NCBO_FAQ FAQ]
 
| [[Shared Materials]]
 
| [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]
 
|-
 
| [http://www.bioontology.org/wiki/index.php/News_Events_Publications News, Events and Publications]
 
| [[Evaluation Activities]]
 
| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]
 
|}
 
  
  
=== Ontology Development Area ===
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__TOC__
  
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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== Software ==
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To follow is a list of software developed and maintained by NCBO:
  
*[[PATO:Main_Page]] - An ontology of phenotypic qualities
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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)''
  
*[[RO:Main_Page]] - OBO Relations ontology
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Please refer to our [[BioPortal_Release_Notes|release notes]] page for change logs.
  
*[[CARO:Main_Page]] - Reference anatomical ontology
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== Documentation ==
  
*[[CL:Main_Page]] - OBO Cell ontology
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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]]
  
*[[SO:Main_Page]] - Sequence Ontology
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=== Mail Support ===
  
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders
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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
  
*[[OCI:Main_Page]] - Ontology of Clinical Investigation
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== Ontology Development Projects ==
  
*[[NPO:Main_Page]] - NanoParticle Ontology
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These are some of the ontology development projects that NCBO participated in:
 
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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.
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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]  
 
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* [[NPO:Main_Page|NanoParticle Ontology]]  
=== Software Development Area ===
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* [http://bioportal.bioontology.org/ontologies/PATO Phenotypic Quality Ontology]
 
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* [[RO:Main_Page|OBO Relations Ontology]]
*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing Bioportal
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* [[CARO:Main_Page|Common Anatomy Reference Ontology]]
*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
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* [[CL:Main_Page|Cell Ontology]]
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
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* [[SO:Main_Page|Sequence Types and Features Ontology]]
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
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* [[Disease:Main_Page|Disease Ontology]], and other ontologies pertaining to diseases and disorders
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores
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* [[OCI:Main_Page|Ontology of Clinical Investigation]]
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services
 
*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal
 
*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redudancy
 
*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies.
 
*[[Medline Analysis]] - Project for applying natural language processing methods on Medline to analyze the frequency and syntactic type distribution of ontology terms.
 
*[[MetaMap Installation]] - Project to install a custom MetaMap using the NCBO data in order to integrate it in the [[Annotator Web service]] workflow.
 
 
 
=== Web services ===
 
 
 
* [[BioPortal REST services]] - Documentation on how to use BioPortal functionality as Web services
 
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
 
* [[Ontology Recommender Web service]] - Documentation & information about the NCBO Ontology Recommender
 
* [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources Index
 
* ''Retired'' -> See [[BioPortal REST services]] for access to UMLS content. [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)
 

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: