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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.  
 
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.  
 
Please visit our [http://www.bioontology.org Main Site] for more information and materials.
 
Please visit our [http://www.bioontology.org Main Site] for more information and materials.
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{| class="wikitable"
 
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! style="background:#efefef;" | NCBO Links
 
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! style="background:#efefef;" | Shared Materials
 
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! style="background:#efefef;" | NCBC Links
 
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| [http://www.bioontology.org/ Home page]
 
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| [[Public Requirements Redirect|Public Requirements]]
 
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| [http://www.bisti.nih.gov/ncbc/ Home page of National Centers for Biomedical Computing]
 
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|-
 
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| [http://www.bioontology.org/wiki/index.php/NCBO_FAQ FAQ]
 
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| [[Shared Materials]]
 
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| [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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|-
 
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| [http://www.bioontology.org/wiki/index.php/Dissemination_Wiki Dissemination]
 
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| [http://www.bioontology.org/wiki/index.php/News_Events_Publications News, Events and Publications]
 
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| [[Evaluation Activities]]
 
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| [http://wiki.na-mic.org/Wiki/index.php/SDIWG:_NCBC_Scientific_Ontologies NCBC Scientific Ontologies Working Group]
 
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|}
 
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=== Software ===
 
=== Software ===
 
*[http://bioportal.bioontology.org NCBO BioPortal] - Home page for BioPortal Web site
 
*[http://bioportal.bioontology.org NCBO BioPortal] - Home page for BioPortal Web site
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* [http://sparql.bioontology.org/ NCBO BioPortal SPARQL Endpoint] - Access BioPortal via SPARQL queries
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* [http://sparql.bioontology.org/ NCBO BioPortal SPARQL Endpoint] - Access BioPortal via SPARQL queries (obsolete)
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*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
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* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.
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* [http://www.bioontology.org/wiki/index.php/BioPortal_Release_Notes BioPortal Software Release Announcements]  
 
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
 
*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
  
 
=== User Support Documentation ===
 
=== User Support Documentation ===
 
*[[BioPortal Help]] - General BioPortal help documentation.  
 
*[[BioPortal Help]] - General BioPortal help documentation.  
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* [[NCBO REST Web services]] - Documentation on how to use BioPortal functionality as Web services
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* [http://www.bioontology.org/wiki/index.php/Using_NCBO_Technology_In_Your_Project Using NCBO Technology in Your Project] - Documentation on how to use NCBO Technology in your project
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* [http://www.bioontology.org/wiki/index.php/View_Extraction Ontology Subset Extraction Web service] - Documentation on how to extract subtree views from ontologies
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* [http://www.bioontology.org/wiki/index.php/BioPortal_Mappings_Service Term Mappings Web service] - Documentation & information about accessing term mapping data
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=== Technical Documentation ===
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* [http://www.bioontology.org/wiki/index.php/Ontology_Notes Term Proposal Web service] - Documentation & information about posting and accessing comments and new term proposals
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* [http://data.bioontology.org/documentation NCBO REST Web services] - Listing of all NCBO web services with usage documentation
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* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
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* [http://www.bioontology.org/wiki/index.php/SPARQL_BioPortal BioPortal SPARQL Endpoint] - BioPortal SPARQL documentation
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* [[Ontology Recommender Web service]] - Documentation & information about the NCBO Ontology Recommender
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* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance BioPortal Virtual Appliance] - Contains BioPortal, Annotator, and Resource Index.
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* [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources Index
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* [http://www.bioontology.org/wiki/index.php/NCBO_Developer_Documentation Developer Documentation] - Some documentation for developers
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* [[BioPortal UI URLs]] - Documentation on how to link back to BioPortal UI pages
 
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* [http://www.bioontology.org/wiki/index.php/SampleCodeCookbook Code samples] - Sample code for common tasks with BioPortal Web services
 
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* [http://www.bioontology.org/wiki/index.php/Category:NCBO_Virtual_Appliance#Population_Workflows BioPortal Virtual Machine Appliance] - Contains BioPortal, Annotator, and Resource Index.
 
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* ''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 Projects ===
 
=== Ontology Development Projects ===
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Below are links for ontology development projects that NCBO is involved in.
 
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*[[BRO:Main_Page]] - Biomedical Resource Ontology
 
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*[[TMO:]] - Translational Medicine Ontology
 
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*[[NPO:Main_Page]] - NanoParticle Ontology
 
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*[[PATO:Main_Page]] - An ontology of phenotypic qualities
 
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*[[RO:Main_Page]] - OBO Relations ontology
 
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*[[CARO:Main_Page]] - Reference anatomical ontology
 
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*[[CL:Main_Page]] - OBO Cell ontology
 
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*[[SO:Main_Page]] - Sequence 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
 
  
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=== Research projects and Prototypes ===
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These are some of the ontology development projects that NCBO has participated in:
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*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores (Nipun Bhatia)
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*[[Path to Root]] - Project for consuming the path to root and other OBS rest services (Nipun Bhatia)
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* [[BRO:Main_Page]] - Biomedical Resource Ontology
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*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redundancy (Nipun Bhatia)
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* [[TMO:]] - Translational Medicine Ontology
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*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal (Rob Tirrell)
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* [[NPO:Main_Page]] - NanoParticle Ontology
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*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies. (Gautam Parai)
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* [[PATO:Main_Page]] - An ontology of phenotypic qualities
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*[[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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* [[RO:Main_Page]] - OBO Relations ontology
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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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* [[CARO:Main_Page]] - Reference anatomical ontology
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* [[CL:Main_Page]] - OBO Cell ontology
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* [[SO:Main_Page]] - Sequence 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

Revision as of 18:16, 5 December 2016

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. Please visit our Main Site for more information and materials.

Software

User Support Documentation

Technical Documentation

Ontology Development Projects

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

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