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Vaccine Ontology Subscribe to updates

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Projects (3)
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Metrics
Ontology Widgets

Ontology Name:	Vaccine Ontology
Ontology Id:	1172
Format:	OWL
Categories:	Health
Groups:
Contact:	, yongqunh@med.umich.edu
Home Page:	http://www.hegroup.org/
Publications Page:
Documentation Page:	http://www.violinet.org/vaccineontology/
Description:	Vaccines play a central role in preventing infectious diseases and improving public health. To standardize vaccine annotation, integrate varied vaccine types for comprehensive data analysis, and support automated reasoning, the community-based Vaccine Ontology (VO) has been developed. VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. Currently VO covers varied vaccine related aspects with an emphasis on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines.

Version Number	Release Date	Ontology File	Visualize
296	03/08/2010	Download Ontology	Explore
294	02/23/2010	Download Ontology	Explore
290	02/19/2010	Download Ontology	Archived, not available to explore
289	02/18/2010	Download Ontology	Archived, not available to explore
286	02/09/2010	Download Ontology	Explore
273	01/28/2010	Download Ontology	Archived, not available to explore
264	01/26/2010	Download Ontology	Archived, not available to explore
261	01/21/2010	Download Ontology	Archived, not available to explore
255	01/16/2010	Download Ontology	Archived, not available to explore
254	01/15/2010	Download Ontology	Archived, not available to explore
250	01/14/2010	Download Ontology	Archived, not available to explore
249	01/13/2010	Download Ontology	Archived, not available to explore
244	01/12/2010	Download Ontology	Archived, not available to explore
240	01/05/2010	Download Ontology	Archived, not available to explore
237	12/15/2009	Download Ontology	Archived, not available to explore
236	12/15/2009	Download Ontology	Archived, not available to explore
231	12/10/2009	Download Ontology	Archived, not available to explore
1.0.205	11/30/2009	Download Ontology	Archived, not available to explore
1.0.125	09/10/2009	Download Ontology	Explore
1.0.63	07/13/2009	Download Ontology	Explore
1.0.45	06/09/2009	Download Ontology	Parsing Error
0.71	03/04/2009	Download Ontology	Explore
0.6	02/17/2009	Download Ontology	Archived, not available to explore

Notes

obo2:OBI_0000011

Mappings

Influenza Ontology
The Influenza Ontology is an application ontology covering the numerous aspects if influenza virus basic research, and surveillance. The influenza ontology extends the Infectious Disease Ontology (IDO).
People:	Burke Squires, Lynn Schriml, Joanne Luciano
Institution:	UT Southwestern, Univ of Maryland, MITRE
Homepage:	http://influenzaontologywiki.igs.umaryland.edu/wiki/index.php/Main_Page

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

Review This Ontology

Adding NCBO Widgets for Vaccine Ontology to Your Site

Step 1: Select a widget

Widget Description	Widget Demonstration
Type a term in Vaccine 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 = "1172"; </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 Vaccine 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-1172-uri" size="100"/> Example 2 (get the ID for a term) <br/> <input type="text" name="b" class="bp_form_complete-1172-shortid" size="100"/> Example 3 (get the preferred name for a term) <br/> <input type="text" name="c" class="bp_form_complete-1172-name" size="100"/> For more help visit NCBO Widget Wiki
Get RSS feed for changes in Vaccine 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 = "1172" </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 Vaccine 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=39424&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 Vaccine Ontology 237 version.

Number of classes:	1347
Number of individuals:	0
Number of properties:	32
Maximum depth of the class hierarchy:	9
Maximum number of siblings in the class hierarchy:	49
Average number of siblings in the class hierarchy:	15
Classes with a single subclass:	121 / 1347 (8.98%) of classes have only one subclass (details) Classes with a single subclass 'AE: abscess' 'AE: acute brain syndrome' 'AE: gastrointestinal disorder' 'AE: headache' 'AE: infect viral' 'AE: purpura' 'AE: speech disorder' 'AE: twitching' 'Aeromonas salmonicida vaccine' 'BCG vaccine' 'BHV-1 vaccine' 'Babesia bigemina vaccine' 'Babesia bovis vaccine' 'Bordetella avium vaccine' 'Brucella gene' 'CFU reduction assay' 'Canine coronavirus vaccine' 'Canine parvovirus-1 vaccine' 'Chlamydophila abortus vaccine' 'Clostridium tetani vaccine' 'Clostridium vaccine' 'Dhori virus vaccine' 'Diphtheria-Tetanus-Pertussis-Poliovirus-Haemophilus b-Hepatitis B vaccine' 'Diphtheria-Tetanus-Pertussis-Poliovirus-Hepatitis B vaccine' 'Diphtheria-Tetanus-Poliovirus vaccine' 'Eimeria maxima vaccine' 'Eimeria tenella vaccine' 'Feline leukemia virus vaccine' 'Giardia duodenalis vaccine' 'H. influenzae gene' 'Haemophilus b and Hepatitis B vaccine' 'Infectious hematopoietic necrosis virus vaccine' 'Japanese encephalitis virus vaccine' 'Lawsonia intracellularis vaccine' 'Leishmania donovani vaccine' 'Measles virus vaccine' 'Measles-Mumps vaccine' 'Measles-Rubella vaccine' 'Mumps virus vaccine' 'Mycoplasma gallisepticum vaccine' 'Mycoplasma synoviae vaccine' 'Neospora caninum vaccine' 'Papillomavirus vaccine' 'Plasmodium gene' 'Plasmodium vivax vaccine' 'Porphyromonas gulae vaccine' 'Pseudorabies virus vaccine' 'Rubella virus vaccine' 'Salmonella typhi-Hepatitis A vaccine' 'Sarcocystis neurona vaccine' 'Shigella sonnei vaccine' 'Streptococcal vaccine' 'Streptococcus equi vaccine' 'Theileria annulata vaccine' 'Theileria parva vaccine' 'Toxoplasma gondii vaccine' 'Vibrio anguillarum vaccine' 'Vibrio cholerae vaccine' 'Vibro-E.coli vaccine' 'Yellow fever virus vaccine' 'Yersinia ruckeri vaccine' 'animal model of vaccine research' 'cancer vaccine' 'cattle gene' 'disorder prevention' 'human gene' 'human papillomavirus vaccine' 'hypersensitivity to chicken product' 'inactivated vaccine preparation' 'inactivated vaccine' 'injection-site AE' 'licensed cattle vaccine role' 'licensed cattle vaccine' 'life-threatening reaction to previous vaccination' 'lipopolysaccharide of pathogen organism as vaccine component' 'live attenuated vaccine preparation' 'live vaccine' 'mouse gene' 'oral route' 'organ or tissue specific immune response to vaccine' 'poxvirus vaccine vector' 'preventive vaccine function' 'reaction to previous vaccination' 'subunit vaccine preparation' 'vaccination target group' 'vaccine approval process' 'vaccine protection assay' 'vaccine-induced leukocyte activation' 'vaccine-induced lymphocyte activation' DOID:DOID_4 NCBITaxon:NCBITaxon_10090 NCBITaxon:NCBITaxon_836 PATO:PATO_0000165 PATO:PATO_0001237 dizziness obo:IAO_0000001 obo:IAO_0000005 obo:IAO_0000032 obo:OBI_0000245 obo:OBI_0000272 obo:OBI_0000426 obo:OBI_0000444 obo:OBI_0000450 obo:OBI_0302893 obo:OBI_0600007 obo:VO_0000130 obo:VO_0000257 obo:VO_0000967 obo:VO_0000976 obo:VO_0000980 obo:VO_0000991 obo:VO_0001025 obo:VO_0001030 obo:VO_0001051 obo:VO_0001067 oboInOwl:ObsoleteClass paresthesia snap:Disposition snap:FiatObjectPart snap:Function snap:Quality
Classes with large number of subclasses:	4 / 1347 (0.30%) of classes have more than 25 subclasses (details) Classes with large number of subclasses company (49 subclasses) 'adverse event' (29 subclasses) 'bacterial vaccine' (30 subclasses) 'viral vaccine' (33 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

Vaccine Ontology Subscribe to updates

Notes

Mappings

Adding NCBO Widgets for Vaccine Ontology to Your Site

Step 1: Select a widget

Type a term in Vaccine Ontology ontology and jump to it in BioPortal

Step 2: Follow the Instructions

Fill in a field in your form with a term from Vaccine Ontology ontology

Step 2: Follow the Instructions

Get RSS feed for changes in Vaccine Ontology ontology

Step 2: Follow the Instructions

Referencing an ontology in your widgets

Visualize Vaccine 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 Vaccine Ontology 237 version.

Classes with a single subclass

Classes with large number of subclasses

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