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Ontology Widgets

Ontology Name:	NCI Thesaurus
Ontology Id:	1032
Format:	OWL
Categories:
Groups:	Cancer Biomedical Informatics Grid Unified Medical Language System
Contact:	NCICB Support, ncicb@pop.nci.nih.gov
Home Page:	http://ncicb.nci.nih.gov/core/EVS
Publications Page:
Documentation Page:	http://nciterms.nci.nih.gov/NCIBrowser/Dictionary.do
Description:	A vocabulary for clinical care, translational and basic research, and public information and administrative activities.

Version Number	Release Date	Ontology File	Visualize
09.09	11/09/2009	Download Ontology	Explore
09.07	09/02/2009	Download Ontology	Explore
09.05d	12/08/2008	Download Ontology	Explore
08.12d	12/08/2008	Download Ontology	Explore
7.06D	08/22/2007	Download Ontology	Explore

Notes

Mappings

NCBO Annotator
A Web service that tags free text with ontology concepts. NCBO uses these Web services to annotate resources in the NCBO Resource Index to create an ontology index of these resources. This Web service can be accessed through BioPortal or used directly in your software. Currently, the annotation workflow is based on syntactic concept recognition (using concept names and synonyms) and on a set of semantic expansion algorithms that leverage the semantics in ontologies (e.g., is_a relations). Our service methodology leverages ontologies to create annotations of raw text and returns them using semantic web standards.
People:	Clement Jonquet
Institution:	Stanford University
Homepage:	http://www.bioontology.org/annotator-service

NCBO Resource Index
The NCBO Resource Web service is a system for ontology based annotation and indexing of biomedical data; the key functionality of this system is to enable users to locate biomedical data resources related to particular ontology concepts. The annotations are generated using the NCBO Annotator and presented through integration with BioPortal, enabling researchers to search for biomedical resources associated (annotated) with specific ontology terms. The NCBO Resources web service uses a concept recognizer (currently provided by the National Center for Integrative Biomedical Informatics, University of Michigan) to produce a set of annotations and expand these using ontology is_a relations in the ontology. The system's indexing workflow processes the text metadata of diverse resource elements such as gene expression data sets, descriptions of radiology images, clinical trial reports, and PubMed article abstracts to annotate and index them with concepts from appropriate ontologies. Researchers can then search biomedical data sources using ontology concepts.
People:	Clement Jonquet
Institution:	Stanford University
Homepage:	http://www.bioontology.org/resources-index

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Adding NCBO Widgets for NCI Thesaurus to Your Site

Step 1: Select a widget

Widget Description	Widget Demonstration
Type a term in NCI Thesaurus ontology and jump to it in BioPortal Get Code	Jump To: Step 2: Follow the Instructions Download the quick_jump.js file and put it on your server Copy the code below and paste it to your HTML page Note: If you would like to use Quick Jump across multiple ontologies: You can enter a comma-separated list of ontology ids: var BP_ontology_id = "1032,1089"; You cans set the variable to 'all' to search all ontologies in BioPortal: var BP_ontology_id = "all"; In the code that you just pasted, make sure to change the path to the quick_jump.js file to point to the location where you put the file (relative to your HTML file) For example, if you put the quick_jump.js file in the same directory as your HTML file, this is the code you would use: <script type="text/javascript"> var BP_ontology_id = "1032"; </script> <script src="quick_jump.js" type="text/javascript" charset="utf-8"> </script> For more help visit NCBO Widget Wiki
Fill in a field in your form with a term from NCI Thesaurus ontology Get Code	Example 1 (start typing the term name to get its full URI) Example 2 (get the ID for a term) Example 3 (get the preferred name for a term) Step 2: Follow the Instructions Download the form_complete.js file and put it on your server In the header for the page where you want the form field, include the form_complete.js file On your form, for the fields where you want to use the term-selection widget, specify the field's class in the following format: `bp_form_complete-{ontology_id_list}-{value}` For example, `bp_form_complete-1032-uri` will use NCI Thesaurus (ontology id is 1032) and will put the term URI in the field after the user selects the term from the pull-down list. Note: In addition to single ontology ids, you can use a list: `bp_form_complete-1032,1089-uri` OR use 'all' to search across all BioPortal ontologies: `bp_form_complete-all-uri` You can use the following parameters to select which value will be placed into the user-visible input field: `uri`put the complete URI of the term (e.g., http://bioportal.bioontology.org/visualize/39478/Common_Neoplasm); `shortid`put the short id of the term, as used in BioPortal (e.g., "Common_Neoplasm"); `name`put the preferred name of the term (e.g., "Common Neoplasm"); In addition to the input element you defined, there are four hidden form elements that are created and then set when a user selects a term from the list. For example, if you create a field with this code: <input type="text" name="a" class="bp_form_complete-all-uri" size="100"/> The 'name' attribute is used to create the four following fields (note how the 'a' from the name attribute is appended to the id attribute): <input type="hidden" id="a_bioportal_preferred_name"> <input type="hidden" id="a_bioportal_concept_id"> <input type="hidden" id="a_bioportal_ontology_id"> <input type="hidden" id="a_bioportal_full_id"> Examples: Example 1 (start typing the term name to get its full URI) <br/> <input type="text" name="a" class="bp_form_complete-1032-uri" size="100"/> Example 2 (get the ID for a term) <br/> <input type="text" name="b" class="bp_form_complete-1032-shortid" size="100"/> Example 3 (get the preferred name for a term) <br/> <input type="text" name="c" class="bp_form_complete-1032-name" size="100"/> For more help visit NCBO Widget Wiki
Get RSS feed for changes in NCI Thesaurus ontology Get Code	Step 2: Follow the Instructions Copy the code below and paste it to your HTML page <script type="text/javascript"> var BP_ontology_id = "1032" </script> <script src="http://bioportal.bioontology.org/javascripts/widgets/feed_widget.js" type="text/javascript" charset="utf-8"> </script> Referencing an ontology in your widgets For more help visit NCBO Widget Wiki
Visualize NCI Thesaurus ontology Get Code	Step 2: Follow the Instructions Copy the code below and paste it to your HTML page <object classid="clsid:D27CDB6E-AE6D-11cf-96B8-444553540000" id="FlexoViz" width="100%" height="100%" codebase="http://fpdownload.macromedia.com/get/flashplayer/current/swflash.cab"> <param name="movie" value="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf?v=1.0.8" /><param name="quality" value="high" /><param name="bgcolor" value="#ffffff" /><param name="allowScriptAccess" value="always" /> <embed src="http://keg.cs.uvic.ca/ncbo/flexviz/FlexoViz.swf?v=1.0.8" bgcolor="#ffffff" width="100%" height="100%" name="FlexoViz" align="middle" play="true" loop="false" quality="high" allowScriptAccess="always" type="application/x-shockwave-flash" flashVars="widget=true&ontology=13578&server=http://rest.bioontology.org/bioportal/" pluginspage="http://www.adobe.com/go/getflashplayer"> </embed> </object> If you want the visualization to be focused on a particular term in the ontology, you can add the term id to the parameters above. For example, to have the widget focus on Melanoma in NCI Thesaurus, replace the following line in the snippet above: flashVars="widget=true&ontology=39478&server=http://rest.bioontology.org/bioportal/" with flashVars="widget=true&ontology=39478&nodeid=Melanoma&server=http://rest.bioontology.org/bioportal/" For more help visit NCBO Widget Wiki

BioPortal calculates the metrics on the salient properties of the ontology, including statistics and quality-control and quality-assurance metrics. Each ontology may have all, some, or no values filled in for its metrics and only metrics for the most recent version are reflected. See metrics descriptions

Metrics are not available for the most recent version of this ontology. The metrics displayed below are for the NCI Thesaurus 09.07 version.

Number of classes:	74646
Number of individuals:	0
Number of properties:	191
Maximum depth of the class hierarchy:	14
Maximum number of siblings in the class hierarchy:	3215
Average number of siblings in the class hierarchy:	139
Classes with a single subclass:	5153 / 74646 (6.90%) of classes have only one subclass
Classes with large number of subclasses:	22932 / 74646 (30.72%) of classes have more than 25 subclasses
Classes with no author:	No author property specified or no values for the author property
Classes with no definition:	37788 / 74646 (50.62%) of classes have no definition property specified or no values for the definition property

Create New View

View Name:	Activity-View	Created By:	Trish Whetzel
View Id:	2026	View Generation Engine:
View Definition:		View Definition Language:	Manual
Description:	Activity subtree of NCIt.

Versions

Version	Base Version	Created	Ontology File	Visualize
09.0	7.06D	11/18/2009	Download View	Explore

NCI Thesaurus Subscribe to updates

Notes

Mappings

Adding NCBO Widgets for NCI Thesaurus to Your Site

Step 1: Select a widget

Type a term in NCI Thesaurus ontology and jump to it in BioPortal

Step 2: Follow the Instructions

Fill in a field in your form with a term from NCI Thesaurus ontology

Step 2: Follow the Instructions

Get RSS feed for changes in NCI Thesaurus ontology

Step 2: Follow the Instructions

Referencing an ontology in your widgets

Visualize NCI Thesaurus ontology

Step 2: Follow the Instructions

Metrics are not available for the most recent version of this ontology. The metrics displayed below are for the NCI Thesaurus 09.07 version.

Create New View

Versions