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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project funding has ended, documentation for some projects or project details (n.b., NCBO BioPortal details) may be out of date.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/Dissemination_Wiki Dissemination]
 
|-
 
| [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]
 
|}
 
  
  
=== Software ===
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__TOC__
*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing BioPortal
 
*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
 
*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
 
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
 
  
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== Software ==
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To follow is a list of software developed and maintained by NCBO:
  
=== User Support Documentation ===
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* [https://bioportal.bioontology.org BioPortal] - A web-based application for accessing and sharing biomedical ontologies
* [[BioPortal UI URLs]] - Documentation on how to link back to BioPortal UI pages
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* [https://data.bioontology.org/ BioPortal REST API] - A RESTful API to access BioPortal content
* [[NCBO REST services]] - Documentation on how to use BioPortal functionality as Web services
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* [[:Category:NCBO_Virtual_Appliance|BioPortal Virtual Appliance]] - Contains BioPortal and the BioPortal REST API, runs on Linux
* [[View_Extraction]] - Documentation on how to extract subtree views from ontologies
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* [http://sparql.bioontology.org/ BioPortal SPARQL Endpoint] - Access BioPortal content via SPARQL queries ''(obsolete)''
* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Mappings] - Documentation & information about accessing term mapping data
 
* [[Ontology Notes]] - Documentation & information about posting and accessing comments and new term proposals submitted on ontologies
 
* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
 
* [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources Index
 
* [http://www.bioontology.org/wiki/index.php/SampleCodeCookbook Code samples] - Sample code for common tasks with BioPortal Web services
 
* ''Retired'' -> See [[BioPortal REST services]] for access to UMLS content. [[UMLS_REST_Services]] - Documentation on how to use our ''prototype'' UMLS services (NetKernel)
 
  
=== Ontology Development Area ===
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Please refer to our [[BioPortal_Release_Notes|release notes]] page for change logs.
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
 
*[[BRO:Main_Page]] - Biomedical Resource Ontology
 
*[[TMO:]] - Translational Medicine Ontology
 
*[[NPO:Main_Page]] - NanoParticle Ontology
 
*[[PATO:Main_Page]] - An ontology of phenotypic qualities
 
*[[RO:Main_Page]] - OBO Relations ontology
 
*[[CARO:Main_Page]] - Reference anatomical ontology
 
*[[CL:Main_Page]] - OBO Cell ontology
 
*[[SO:Main_Page]] - Sequence Ontology
 
*[[Disease:Main_Page]] - Disease Ontology, and other ontologies pertaining to diseases and disorders
 
*[[OCI:Main_Page]] - Ontology of Clinical Investigation
 
  
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== Documentation ==
  
=== Research projects and Prototypes ===
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* [[BioPortal Help|BioPortal]] - get help with the user interface and instructions for commonly performed tasks
*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores (Nipun Bhatia)
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* [http://data.bioontology.org/documentation BioPortal REST API] - see a list of available endpoints with usage instructions
*[[Path to Root]] - Project for consuming the path to root and other OBS rest services (Nipun Bhatia)
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* [[:Category:NCBO_Virtual_Appliance|BioPortal Virtual Appliance]] - read a getting started guide and installation instructions
*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redundancy (Nipun Bhatia)
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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
*[[Ontology Recommender Web service]] - Documentation & information about the NCBO Ontology Recommender (Clement Jonquet)
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* [[SKOSSupport|SKOS support]] - view the specifics of BioPortal's support for SKOS vocabularies
*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal (Rob Tirrell)
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* [[SPARQL_BioPortal|BioPortal SPARQL Endpoint]] - read about programmatic submission of SPARQL queries and the named graph structure
*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies. (Gautam Parai)
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* [[NCBO_Developer_Documentation|Developer documentation]]
*[[Medline Analysis]] - Project for applying natural language processing methods on Medline to analyze the frequency and syntactic type distribution of ontology terms. (Rong Xu)
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*[[MetaMap Installation]] - Project to install a custom MetaMap using the NCBO data in order to integrate it in the [[Annotator Web service]] workflow. (Tejaswi Tenneti)
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=== Mail Support ===
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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
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== Ontology Development Projects ==
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These are some of the ontology development projects that NCBO participated in:
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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]]  
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* [http://bioportal.bioontology.org/ontologies/PATO Phenotypic Quality Ontology]
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* [[RO:Main_Page|OBO Relations Ontology]]
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* [[CARO:Main_Page|Common Anatomy Reference Ontology]]
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* [[CL:Main_Page|Cell Ontology]]
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* [[SO:Main_Page|Sequence Types and Features Ontology]]
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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]]

Latest revision as of 12:58, 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: