March 2, 2010: We are currently experiencing periods of instability in BioPortal. We are working to resolve the issue. We apologize for the inconvenience and thank you for your patience. [close]
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.
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.
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:
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:
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:
Copy the code below and paste it to your HTML page
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/"
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
Number of classes:
24779
Number of individuals:
110
Number of properties:
478
Maximum depth of the class hierarchy:
23
Maximum number of siblings in the class hierarchy:
137
Average number of siblings in the class hierarchy:
10
Classes with a single subclass:
502 / 24779 (2.03%) of classes have only one subclass
Classes with large number of subclasses:
30 / 24779 (0.12%) of classes have more than 25 subclasses (details)
Classes with large number of subclasses
set of nerves (137 subclasses) inflammation (76 subclasses) brodmann area (52 subclasses) dental neoplasm (30 subclasses) nucleus of spinal cord (26 subclasses) cyst (41 subclasses) segment of Brodmann area (52 subclasses) position modifier (33 subclasses) chemical element (118 subclasses) medulla oblongata (37 subclasses) tract of brain (43 subclasses) morphologic characteristic (60 subclasses) nucleus of brain (114 subclasses) sub-part modifier (43 subclasses) RID6588 (42 subclasses) nucleus of medulla oblongata (28 subclasses) organ zone (51 subclasses) part of tooth (30 subclasses) gray matter of neuraxis (32 subclasses) route of administration (112 subclasses) gray matter of segment of cerebellum (27 subclasses) set of neuraxis fibers (62 subclasses) subdivision of nucleus of neuraxis (30 subclasses) RadLex attribute (137 subclasses) Caviness neocortex parcellation unit (47 subclasses) internal jugular vein (29 subclasses) radiopharmaceutical (48 subclasses) neoplasm (34 subclasses) suture of skull (32 subclasses) peripheral nerve (49 subclasses)
Classes with no author:
Classes with no definition:
No definition property specified or no values for the definition property
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