BioPortal provides access to commonly used biomedical ontologies and to tools for working with them. BioPortal allows you to
All information available through the BioPortal website is also available through the BioPortal REST API. Please see REST API documentation for more information.
Explore our library of biomedical ontologies or submit your own. The ontology browse page provides summary information about each ontology. For more detailed information, visit the ontology’s dedicated page by clicking its name.
To quickly find a specific ontology, type its name or abbreviation into the search field at the top-center of the page, labeled “Search…”. You can further narrow your results using the faceted browsing elements on the left-hand side of the page. These facets allow you to filter ontologies by attributes such as category (domain), group, format, or other criteria.
Ontologies on this page are ordered by popularity, determined by the number of Google Analytics page views they received in the previous month. Ontologies with more views appear higher in the list, helping you quickly locate the most widely accessed resources.
To submit an ontology, click the “Submit New Ontology” button. Note that you must be logged in to BioPortal to upload an ontology.
Submitters control who can browse the terms in their ontology by selecting one of three visibility designations when uploading:
These designations allow submitters to control the visibility and accessibility of their ontologies based on their sharing preferences and requirements.
To access ontologies programmatically, see our Resources REST API documentation (then look under Available Media Types).
Enter text and find terms across multiple terminologies that contain this text. The names, ids, synonyms, properties for a term are searched for matches to the entered text, and the best match (only) from each ontology is displayed.
To find a term in any ontology enter the name of the term in the search box and simply hit the Search button. The system looks for matches in the term name, synonyms, term ids, and in property values. You can filter the returned values by ontology or by the type of match by selecting one of the filter links in the output table. If you want to search only in a subset of ontologies you can specify the desired ontologies in the Ontologies box. (Note that it is no faster to search a subset than to search all ontologies.) Simply type the ontology name or acronym to chose the desired ontology. You can also select a set of ontologies from a list of all ontologies using the “select from list” link.
Note that, for performance reasons, only the top 100 matches (that is, matched ontologies) are returned. If one or more ontologies are specified in the Ontologies box, all matches are returned.
To search programmatically see our Search REST API documentation.
Mappings are associations between two or more terms in different ontologies. This association typically, but not always, represents a degree of similarity between the terms. The author of the mapping defines the semantics of a particular mapping. It is also usual for a mapping to be bi-directional, but again, this is not required. The mapping author defines directionality (for details, please see our Mapping Documentation).
To browse mappings for an ontology, select the ontology from the drop-down list. You will then see a table showing all ontologies for which at least one mapping exists between that ontology and the ontology you selected. Select an ontology from this table to browse the mappings between the two ontologies.
To access mappings programmatically, please see our Mappings REST API documentation.
The Recommender takes as input a text or a list of keywords and suggests appropriate ontologies for it.
The ontology ranking algorithm used by the Recommender evaluates the adequacy of each ontology to the input using a combination of four evaluation criteria:
For each of these four criteria, a score is computed. Then, the scores obtained are weighted and aggregated into a final score for the ontology. The default weights used to aggregate the scores can be changed at the advanced options section.
Note that besides the ontologies output, which returns a ranked list of ontologies, the Recommender also has an ontology sets output, which allows to find those ontology sets that improve the coverage provided by individual ontologies.
To retrieve ontology recommendations programmatically, please see our Ontology Recommender REST API documentation.
To cite the NCBO Ontology Recommender, please use:
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).
To generate annotations for text, simply enter text in the box and press the submit button. The system matches words in the text to terms in ontologies by doing an exact string comparison (a “direct” match) between the text and ontology term names, synonyms, and ids.
In addition to the direct matches, the user may expand the set of matches by including matches from mapped terms and from hierarchical expansion. For most ontologies (OWL and UMLS RRF) the system performs the hierarchical expansion on the superclass (“is-a”) relationship. For OBO ontologies the hierarchical expansion also includes the part-of relationship. You use the “number of levels” field to control the number of levels up the hierarchy for which the system will return terms for a given match.
To generate annotations programmatically see the REST API documentation.
Further information about the workings of the Annotator is available at Shah et al BMC Bioinformatics. 2009 Sep 17;10 Suppl 9:S14
This page shows selected projects which make use of BioPortal technology. To add your project to this list press the "Create new project" button. Note that you must be logged in to BioPortal to create a project.
You need to create an account on BioPortal if you don’t already have one:
http://bioportal.bioontology.org/accounts/new
This will allow you to manage submissions and updates to your ontology.
BioPortal supports several standard formats for ontologies. Ensure that your ontology is in one of the following formats:
For SKOS vocabularies, please note that BioPortal requires particular SKOS constructs to be present. Read more on our SKOS Support page.
The ontology file should not be excessively large (though there are no strict file size limits, smaller files are easier to process).
As part of the submission process, you’ll need to provide certain metadata attributes. Some of the key metadata fields include:
Once you have an account and are logged in, navigate to the Browse page:
http://bioportal.bioontology.org/ontologies
… and click the "Submit New Ontology" button.
In the resulting form, you’ll be asked to fill out some metadata about your ontology. If you do not want the public to see your ontology, you can specify it as private, then indicate what accounts should have access to it.
Once you’ve filled out the form, click the "Create ontology" button. This will create the ontology summary page for your ontology. Note that so far you are only describing the ontology in general terms, not submitting a specific file.
Finally on the summary page, you can click the "Add submission” link. This new submission form is where you’ll be able to specify your ontology file, as well as things like the description of this update, the version number, and so on.
Once you have created the ontology submission, usually right away you can access its basic information and possibly its classes, if there are not too many of them. More detailed indexing takes place asynchronously, often scheduled at night. All of that should be finished by the next day (Pacific Time); if not, send an email to the support list.
If your ontology already is in BioPortal and you have a new version, it can be updated in one of two ways if you are logged in as a manager of the ontology.
If the original submission was set to automatically update from a source URL, you can learn the source URL using the Submissions edit icon (pencil icon to the right of the Submissions header on the Summary page). BioPortal examines the content at this URL nightly, and re-submits the content if it has changed in any way (determined by the checksum). If the updated submission does not parse, the ontology manager(s) should be notified via email.
If the original submission was not set to automatically update, or if you want to update the ontology immediately, you can upload the ontology directly from your computer. This will begin the upload process immediately, and schedule the ontology to be parsed shortly thereafter. (After the successful submission, don't forget to re-enter the URL and setting for the automatic update process, if you want that to be enabled.) Usually ontology parsing is complete within a a few minutes to an hour, except for large ontologies; ontology indexing and automatic mappings occur overnight (Pacific Time).
To begin this process, click on the plus sign to the right of the Submissions header on the Summary page. This gives you a chance to update the metadata for the submission, and change the way it is uploaded to BioPortal (manually from a local file, or automatically from a URL).
If you just want to change the metadata for your ontology's latest submission, use the Submissions edit (pencil) icon to the right of the Submissions header on the Summary page. Although the UI implies the new ontology will be downloaded, this should not occur if you do not change the download settings; only your metadata changes will be saved.
To change the settings for the ontology—this includes things like name, administrators, viewing restrictions, categories, and whether the ontology is a View of another ontology—click on the edit (pencil) icon to the far right of the ontology name (at the top of the page).
Note that you can not change the ontology acronym, because BioPortal uses this as a primary key and identifier for the ontology. If you want your ontology to have another acronym, you would need to resubmit it as a new ontology, using the new acronym, and then ask us to delete or deprecate the previous ontology.
BioPortal offers the ability for users to request changes or extensions to an ontology when the ontology source file is maintained in GitHub. For more details, please refer to our Ontology Change Requests page.
To view all mappings for an ontology, chose the ontology from the Browse page and then select "Mappings" from the drop-down list.
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Mappings" tab in the right-hand panel.
To view all notes for an ontology, chose the ontology from the Browse page and then select "Notes" from the drop-down list.
To view the notes for a particular term, navigate to the ontology and term (using the "Browse" tab and select the terms item from the dropdown) and then select the "Notes" tab in the right-hand panel.
Navigate to the ontology summary page by selecting the ontology name from the Browse tab. Create a review by pressing the "Create Review" button near the top of the page.
With the BioPortal user interface, you can visualize ontology concepts and their mappings with other ontologies.
Documentation about how to use the BioPortal REST API to access information is available here:
http://data.bioontology.org/documentation
Use of the BioPortal REST API requires an API key.
To retrieve your API key, log into your account on the BioPortal website. If you don't have an account, you'll need to create one.
Your API key will be listed in plain text on your account page.
Many specific questions are addressed at our FAQ for the BioPortal system.
Musen MA, Noy NF, Shah NH, Whetzel PL, Chute CG, Story MA, Smith B; NCBO team. The National Center for Biomedical Ontology. J Am Med Inform Assoc. 2012 Mar-Apr;19(2):190-5. Epub 2011 Nov 10.
Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 (https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0128-y).
Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications. Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. Epub 2011 Jun 14.
Salvadores M, Horridge M, Alexander PR, Fergerson RW, Musen MA, and Noy NF. Using SPARQL to Query BioPortal Ontologies and Metadata. International Semantic Web Conference. Boston US. LNCS 7650, pp. 180195, 2012.