Difference between revisions of "Main Page"

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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.
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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project funding has ended, documentation for some projects or project details (n.b., NCBO BioPortal details) may be out of date.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
  
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{| class="wikitable"
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Please visit our [http://www.bioontology.org main site] for more information about NCBO.
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|-
 
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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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|-
 
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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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=== Ontology Development Area ===
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__TOC__
  
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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:
  
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*[[BRO:Main_Page]] - Biomedical Resource Ontology
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* [https://bioportal.bioontology.org BioPortal] - A web-based application for accessing and sharing biomedical ontologies
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*[[PATO:Main_Page]] - An ontology of phenotypic qualities
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* [https://data.bioontology.org/ BioPortal REST API] - A RESTful API to access BioPortal content
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*[[RO:Main_Page]] - OBO Relations ontology
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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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*[[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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*[[NPO:Main_Page]] - NanoParticle Ontology
 
  
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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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Please refer to our [[BioPortal_Release_Notes|release notes]] page for change logs.
  
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=== Software ===
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== Documentation ==
  
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*[http://bioportal.bioontology.org Bioportal:Main_Page] - Main page for accessing Bioportal
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* [[BioPortal Help|BioPortal]] - get help with the user interface and instructions for commonly performed tasks
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*[[OboInOwl:Main_Page]] - Mapping between OBO and OWL formats
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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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*[[Phenote:Main_Page]] - A Phenotype Annotation Tool using Ontologies
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* [[:Category:NCBO_Virtual_Appliance|BioPortal Virtual Appliance]] - read a getting started guide and installation instructions
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*[[NCBO-OOR Development]] - Documentation on how the Open Ontology Repository community can customize and advance BioPortal capabilities.
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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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* [[NCBO_Developer_Documentation|Developer documentation]]
  
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=== How to's ===
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=== Mail Support ===
  
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* [[NCBO REST services]] - Documentation on how to use BioPortal functionality as Web services
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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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* [[BioPortal UI URLs]] - Documentation on how to link back to BioPortal UI pages
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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://www.bioontology.org/wiki/index.php/SampleCodeCookbook Code samples] - Sample code for common tasks with BioPortal Web services
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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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* [[Annotator Web service]] - Documentation & information about the NCBO Annotator
 
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* [[Resource Index]] - Documentation & information about the annotation-based NCBO biomedical Resources 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)
 
  
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=== Research projects and Prototypes ===
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== Ontology Development Projects ==
  
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*[[RDF Triple Stores]] - Notes, learning and how-tos regarding uploading data to various triple stores
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These are some of the ontology development projects that NCBO participated in:
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*[[Path to Root]] - Project for consuming the path to root and other OBS rest services
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*[[Annotation Summarizer]] - Project utilizing OBS REST services to derive information from datasets referencing ontologies in BioPortal
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* [http://bioportal.bioontology.org/ontologies/BRO Biomedical Resource Ontology]
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*[[PURL Server]] - Instructions on how to set-up a PURL server and create Master-Slave architecture for redudancy
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* [http://bioportal.bioontology.org/ontologies/TMO Translational Medicine Ontology]  
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*[[Lexicon Builder]] - Project for creating a service that allows building of custom lexicons from bioportal ontologies.
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* [[NPO:Main_Page|NanoParticle Ontology]]  
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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.
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* [http://bioportal.bioontology.org/ontologies/PATO Phenotypic Quality 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.
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* [[RO:Main_Page|OBO Relations Ontology]]
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* [[Ontology Recommender Web service]] - Documentation & information about the NCBO Ontology Recommender
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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 20:22, 29 March 2024

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:

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