Main Page

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.

NCBO Links	Shared Materials	NCBC Links
Home page	Public Requirements	Home page of National Centers for Biomedical Computing
FAQ	Shared Materials	NCBC Software and Data Integration Working Group (SDIWG) and Centers Discussion
Dissemination
News, Events and Publications	Evaluation Activities	NCBC Scientific Ontologies Working Group

Software

• BioPortal:Main_Page - Main page for accessing BioPortal
• SPARQL BioPortal early access to the beta version.
• BioPortal Help - Help text for BioPortal Web site
• 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.

User Support Documentation

• Help - General BioPortal help documentation.
• BioPortal UI URLs - Documentation on how to link back to BioPortal UI pages
• NCBO REST services - Documentation on how to use BioPortal functionality as Web services
• View_Extraction - Documentation on how to extract subtree views from ontologies
• 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
• Code samples - Sample code for common tasks with BioPortal Web services
• BioPortal Virtual Machine Appliance - Contains BioPortal, Annotator, and Resource Index.
• 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

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

Research projects and Prototypes

• RDF Triple Stores - Notes, learning and how-tos regarding uploading data to various triple stores (Nipun Bhatia)
• Path to Root - Project for consuming the path to root and other OBS rest services (Nipun Bhatia)
• PURL Server - Instructions on how to set-up a PURL server and create Master-Slave architecture for redundancy (Nipun Bhatia)
• Ontology Recommender Web service - Documentation & information about the NCBO Ontology Recommender (Clement Jonquet)
• Annotation Summarizer - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal (Rob Tirrell)
• Lexicon Builder - Project for creating a service that allows building of custom lexicons from bioportal ontologies. (Gautam Parai)
• Medline Analysis - Project for applying natural language processing methods on Medline to analyze the frequency and syntactic type distribution of ontology terms. (Rong Xu)
• 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)