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Biomedical Resource Ontology Subscribe to updates

Metadata
Views (6)
Projects (4)
Reviews (1)
Metrics
Ontology Widgets

Ontology Name:	Biomedical Resource Ontology
Ontology Id:	1104
Format:	OWL
Categories:	Biomedical Resources
Groups:
Contact:	Daniel Rubin, Natasha Noy, dlrubin@stanford.edu
Home Page:
Publications Page:
Documentation Page:
Description:	An ontology of compuational biomedical resources.

Version Number	Release Date	Ontology File	Visualize	Download Diff File
3.0	03/09/2010	Download Ontology	Explore
2.7.1	09/29/2009	Download Ontology	Explore
2.7	05/14/2009	Download Ontology	Explore	Download Diff with previous version ( Txt \| RDF)
2.6	03/02/2009	Download Ontology	Explore	Download Diff with previous version ( Txt \| RDF)
2.5	12/09/2008	Download Ontology	Explore
2.3	11/03/2008	Download Ontology	Explore	Download Diff with previous version ( Txt \| RDF)
2.2	10/06/2008	Download Ontology	Explore	Download Diff with previous version ( Txt \| RDF)
2.1	09/17/2008	Download Ontology	Explore	Download Diff with previous version ( Txt \| RDF)
2.0	08/05/2008	Download Ontology	Explore	Download Diff with previous version ( Txt \| RDF)
1.1	06/05/2008	Download Ontology	Explore

Notes

Mappings

Biositemaps
The Biositemaps Working Group of the NIH Roadmap National Centers of Biomedical Computing (NCBC) (www.ncbcs.org) has developed technologies to address (i) locating, (ii) querying, (iii) composing or combining, and (iv) mining biomedical resources. Each site which intends to contribute to the inventory instantiates a file on its Internet site ‘'biositemap.rdf' which conforms to a defined RDF schema and uses concepts from the Biomedical Resource Ontology to describe the resources.
People:
Institution:
Homepage:	http://biositemaps.ncbcs.org/

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

CTSA Inventory Resource Web Presence (CIRWP)
The CTSA Inventory Resource Web Presence (CIRWP) is a federated, inter-institutional project to facilitate resource discovery. The CIRWP project contains informatics and translational resources from over 40 CTSA and NCBC organizations. The project utilizes the categories provided by the Biomedical Resource Ontology (BRO). Through the CIRWP framework, the BRO facilitates semantic search and discovery of biomedical resources, breaking down barriers to scientific discoveries that will improve human health.
People:
Institution:
Homepage:	http://biositemaps.ncbcs.org/cirwp/about.htm

Review This Ontology

Review By alanruttenberg
Usability Domain Coverage Correctness Quality Of Content Degree Of Formality Documentation And Support The ontology does not validate as OWL DL, for reasons that are easily fixed.

Adding NCBO Widgets for Biomedical Resource Ontology to Your Site

Step 1: Select a widget

Widget Description	Widget Demonstration
Type a term in Biomedical Resource Ontology 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 = "1104"; </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 Biomedical Resource Ontology 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-1104-uri" size="100"/> Example 2 (get the ID for a term) <br/> <input type="text" name="b" class="bp_form_complete-1104-shortid" size="100"/> Example 3 (get the preferred name for a term) <br/> <input type="text" name="c" class="bp_form_complete-1104-name" size="100"/> For more help visit NCBO Widget Wiki
Get RSS feed for changes in Biomedical Resource Ontology 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 = "1104" </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 Biomedical Resource Ontology 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=38672&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 Biomedical Resource Ontology 2.7.1 version.

Number of classes:	456
Number of individuals:	0
Number of properties:	63
Maximum depth of the class hierarchy:	9
Maximum number of siblings in the class hierarchy:	29
Average number of siblings in the class hierarchy:	9
Classes with a single subclass:	22 / 456 (4.82%) of classes have only one subclass (details) Classes with a single subclass 'Communication and Collaborative Work' 'Data Editor' 'Data Transform' 'Graph Alignment' 'Graph Viewer' 'Hyperbolic Graph' 'Interaction Modeling' 'Interaction Network' 'Network Model' 'Non Computational Service' 'Object Database' 'Provenance and Intellectual Property' 'Research Animals Facility' 'Symbolic and Analytic Model' 'Unstructured Data' Atlas Document Knowledgebase Matrix Portal Support core:Collection
Classes with large number of subclasses:	1 / 456 (0.22%) of classes have more than 25 subclasses (details) Classes with large number of subclasses Instrument (29 subclasses)
Classes with no author:	No author property specified or no values for the author property
Classes with no definition:	No definition property specified or no values for the definition property

Create New View

View Name:	Biomedical Resource Ontology - Activity View	Created By:	Csongor Nyulas
View Id:	2001	View Generation Engine:
View Definition:	This view was manually created by deleting all the classes from BRO except the activity:Activity and activity:Deprecated_Activity and their subclasses.	View Definition Language:	Manual
Description:	This view represent a subset of the BRO containing all the Activity classes that are relevant in the biomedical domain.

Versions

Version	Base Version	Created	Ontology File	Visualize
1.0	2.2	06/03/2009	Download View	Explore

View Name:	Biomedical Resource Ontology - Area of Research View	Created By:	Csongor Nyulas
View Id:	2002	View Generation Engine:
View Definition:	This view was manually created by deleting all the classes from BRO except the area:Area_of_Research and area:Deprecated_Area_of_Research and their subclasses.	View Definition Language:	Manual
Description:	This view represent a subset of the BRO containing all the Area of Research classes that are relevant in the biomedical domain.

Versions

Version	Base Version	Created	Ontology File	Visualize
1.0	2.2	06/03/2009	Download View	Explore

View Name:	Biositemap Information Model	Created By:	Csongor Nyulas, Trish Whetzel
View Id:	2003	View Generation Engine:
View Definition:	This view was manually created by deleting all the classes from BRO except the desc:Biositemaps_Information_Model and its subclasses.	View Definition Language:	Manual
Description:	This view represent a subset of the BRO containing the classes that define the biositemap information model (IM).

Versions

Version	Base Version	Created	Ontology File	Visualize
1.0	2.2	06/03/2009	Download View	Explore

View Name:	BRO Resource View	Created By:	Trish Whetzel
View Id:	2022	View Generation Engine:
View Definition:		View Definition Language:	Manual
Description:	Contains only the Resource subtree of BRO.

Versions

Version	Base Version	Created	Ontology File	Visualize
1.1	2.2	10/28/2009	Download View	Explore
2.7.1	2.2	10/28/2009	Download View	Explore

View Name:	Biomedical Resource Ontology with Simplified Chinese annotations.	Created By:	Lin Zhang
View Id:	2017	View Generation Engine:
View Definition:		View Definition Language:	Manual
Description:	This view contains the entire BRO with the addition of three DataType properties, i.e., preferredName, shortName and synonym; then for all the classes and properties, Simplified Chinese (and some English) annotations were inserted into the ontology.

Versions

Version	Base Version	Created	Ontology File	Visualize
2.5	2.2	02/24/2009	Download View	Explore

View Name:	Biomedical Resource Ontology - Resource View	Created By:	Csongor Nyulas
View Id:	2000	View Generation Engine:
View Definition:	This view was manually created by deleting all the classes from BRO except the BRO:Resource and BRO:Deprecated_Resource and their subclasses.	View Definition Language:	Manual
Description:	This view represent a subset of the BRO containing all the Resource types that are relevant for the biomedical domain.

Versions

Version	Base Version	Created	Ontology File	Visualize
3.0	2.2	03/09/2010	Download View	Explore
1.0	2.2	06/03/2009	Download View	Explore

Biomedical Resource Ontology Subscribe to updates

Notes

Mappings

Adding NCBO Widgets for Biomedical Resource Ontology to Your Site

Step 1: Select a widget

Type a term in Biomedical Resource Ontology ontology and jump to it in BioPortal

Step 2: Follow the Instructions

Fill in a field in your form with a term from Biomedical Resource Ontology ontology

Step 2: Follow the Instructions

Get RSS feed for changes in Biomedical Resource Ontology ontology

Step 2: Follow the Instructions

Referencing an ontology in your widgets

Visualize Biomedical Resource Ontology 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 Biomedical Resource Ontology 2.7.1 version.

Classes with a single subclass

Classes with large number of subclasses

Create New View

Versions

Versions

Versions

Versions

Versions

Versions