FAQ

General

Known Issues

The following are known issues with BioPortal -

1. When browsing ontologies in category view, clicking the download ontology icon and then using the browser back button can cause the view by links to behave inconsistently. To workaround this issue, click on the Browse tab.
2. Due to parsing difficulties the FMA ontology has approximately 390 nodes which have incorrect entries and will appear as Unknown during visualization.
3. The RadLex ontology has both is_A and hasSubtype resolved for each concept resulting in incorrect graphs and resolution.
4. OWL ontologies do not parse correctly and, therefore, are not available for searching and visualization.

What browsers does BioPortal support?

BioPortal supports most modern browsers. For visualization, BioPortal utilizes the Yahoo! UI Library which has Graded Browser Support.

Does BioPortal have web services?

For information about BioPortal's web services see Web Services.

Ontology Browse

What do the icons mean?

- Download ontology

- Search ontology content and search ontology metadata

- Either Search ontology content or search ontology metadata disabled

- Search ontology content and search ontology metadata disabled

- Search ontology content and search ontology metadata disabled due to error

- Visualize ontology

- Visualize ontology disabled

- Visualize ontology disabled due to error

An image tooltip gives details of each disabled status.

Why can't I visualize a specific ontology? Why is the visualize icon grayed out?

• Ontologies whose content location is Remote cannot be visualized in the BioPortal.
• Ontologies which contain no classes/types cannot be visualized in the BioPortal.
• Ontologies which are currently being parsed and indexed or generated a parsing or indexing error cannot be visualized in the BioPortal.
• Ontologies which do not resolve in any top nodes cannot be visualized in the BioPortal.

Why can't I search a specific ontology? Why is the search icon grayed out?

• The content of ontologies whose content location is Remote cannot be searched in the BioPortal. Only the metadata or project information of remote ontologies is searchable.
• Ontologies which are currently being parsed and indexed or generated a parsing or indexing error cannot be searched in the BioPortal.

What are pending submissions?

When an ontology is submitted to BioPortal it becomes a pending submission. The ontology submission is reviewed by the Open Biomedical Ontology (OBO) Librarian for inclusion in the library (e.g., whether the ontology is biomedical - either biological and/or medical).

Pending submissions cannot be searched or visualized. The ontology metadata or project details of the ontology is only viewable by the ontology submitter and the OBO Librarian.

What are remote ontologies? What does Content Location pertain to?

When an ontology is submitted to BioPortal the submitter has the choice of submitting the ontology file to BioPortal (the actual ontology content) or providing an URL to the ontology location. If the submitter submits the ontology file, the BioPortal indexes and parses the file making the ontology content available for search and visualization. However, the if the submitter provides an URL to the ontology location (perhaps due to licensing issues) only the ontology metadata or project information is searchable.

• NCBO Library - the ontology content has been submitted to BioPortal. If the content is successfully indexed and parsed, visualization and search of the ontology content is possible.
• Remote - the ontology content has not been submitted to BioPortal. Please see the remote site for the ontology. Only search of the ontology metadata or project information is possible.

Ontology Details

What is Foundry Inclusion and Foundry?

The Open Biomedical Ontology Foundry is a collaborative experiment, involving a group of ontology developers who have agreed to the adoption of a growing set of principles specifying best practices in ontology development. These principles are designed to foster interoperability of ontologies and also to ensure a gradual improvement of quality and formal rigor in ontologies, in ways designed to meet the increasing needs of data and information integration in the biomedical domain.

By joining the Foundry, the authors of an ontology commit to its maintenance and to soliciting community feedback for its improvement. They also give an assurance that they will work with other groups to ensure that, for any particular domain, there is community convergence on a single reference ontology, which will incorporate multiple perspectives wherever necessary. Application ontologies developed for specific purposes will then be referred back to this reference ontology. For more information, please see OBO Foundry.

• Foundry Inclusion - When an ontology is submitted to the BioPortal the submitter can select to Opt-In or Opt-Out of inclusion in the Foundry
• Foundry - If the ontology is considered for inclusion in the Foundry, does it qualify as a Foundry ontology

Why is the 'Visualize' button disabled?

See Why can't I visualize a specific ontology? Why is the visualize icon grayed out?

Why is the 'Search' button disabled?

See Why can't I search a specific ontology? Why is the search icon grayed out?.

Who can modify the ontology metadata or project details?

The ontology submitter is the owner of the ontology and can modify the ontology metadata or project details.

If you believe that certain information is inaccurate please contact .

Why is one ontology version indicated as current?

BioPortal allows an ontology owner to submit multiple versions of an ontology. However, one and only one version of the ontology must be marked as current (indicated by ). The ontology marked as current is the one that BioPortal parses and indexes which allows that version to be searched and visualized.

Ontology Search

Why does a specific ontology not appear in the Ontology list on the Search page?

See Why can't I search a specific ontology? Why is the search icon grayed out?.

What is the difference between Search Ontology Content and Search Ontology Metadata?

Search Ontology Content searches the actual textual content of the ontology file. Search Ontology Metadata searches the metadata or project information that describes the ontology.