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General

Full name of the tool NCBO BioPortal
Description of the tool Repository for Biomedical Ontologies
Link to the tool http://bioportal.bioontology.org/
Tool home page http://bioportal.bioontology.org/
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Author
Contact
Institutional sponsor Stanford University
Last version
License BSD
Mailing List

Exploration

Find ontologies with specific domain coverage No
-- comment Optional remarks
Compare domain coverage across ontologies No
-- comment Optional remarks
Assess or characterize breadth of domain coverage of an ontology No
-- comment Optional remarks
Assess or characterize depth or detail of domain coverage of an ontology No
-- comment Optional remarks
Assess or characterize use considerations of ontology including licensing, training, cost, updating, software requirements, and security Yes
-- comment We have description and license information about each ontology.
Assess complexity of concept definitions (necessary and sufficient properties) and use of axioms No
-- comment Optional remarks
Identify number and ratio of concepts, relations, and subclassing No
-- comment Optional remarks
Identify frequency of use of ontology language features in an ontology No
-- comment Optional remarks
Identify age and use statistics of an ontology and its versions No
-- comment Optional remarks
Assess the inferencing power of an ontology No
-- comment Optional remarks
Rate ontologies on their popularity or review feedback Yes
-- comment We display the more popular 5 ontologies on our home page.
Other ontology quality and fitness support for exploration phase (describe capability)

Management

Distinguish between conceptual and operational ontologies and objectives No
-- comment Optional remarks
Generate ontology application and performance requirements No
-- comment Optional remarks
Organize and track the life cycle requirements and progression of an ontology Yes
-- comment we allow users to specific "beta", "production" or "retired" ontologies
Organize and maintain a collection of related ontologies and ontology modules Yes
-- comment Optional remarks
Provide statistics on ontology versioning and use No
-- comment Optional remarks
Guide ontology development per a quality assurance methodology No
-- comment Optional remarks
Assess the reusability of a planned ontology No
-- comment Optional remarks
Other ontology quality and fitness support for management phase (describe capability)

Design

Does NCBO BioPortal guide formulation of ontology requirements?
Guide formulation of domain scope and detail requirements No
-- comment Optional remarks
Guide formulation of goodness of design requirements No
-- comment Optional remarks
Guide formulation of data and information requirements No
-- comment Optional remarks
Guide formulation of semantic and reasoning requirements No
-- comment Optional remarks
Guide formulation of interface requirements No
-- comment Optional remarks
Guide formulation of level of effort requirements No
-- comment Optional remarks
Facilitate framing a set of competency questions exemplifying ontology objectives No
-- comment Optional remarks
Choose metaphysical methodology No
-- comment Optional remarks
Does NCBO BioPortal allow one to choose an extant ontology for reuse?
Choose extant top ontology for reuse No
-- comment Optional remarks
Choose extant core ontologies for reuse No
-- comment Optional remarks
Apply a style of ontological analysis to design No
-- comment Optional remarks
Guide design to optimize normalization, factoring, and simplicity of ontology No
-- comment Optional remarks
Guide application of open world or closed world semantics No
-- comment Optional remarks
Guide ontology design to achieve inferencing requirements No
-- comment Optional remarks
Guide ontology design to achieve scalability requirements No
-- comment Optional remarks
Enable adjustable query and inference performance No
-- comment Optional remarks
Does NCBO BioPortal offer design patterns based on current ontology or design context?
Offer application patterns based on current ontology or design context No
-- comment Optional remarks
Offer ontology language patterns based on current ontology or design context No
-- comment Optional remarks
Offer methodology patterns based on current ontology or design context No
-- comment Optional remarks
Offer other patterns based on current ontology or design context No
-- comment Optional remarks
Integrate selected design patterns into an ontology design No
-- comment Optional remarks
Assess correctness or performance of an ontology design No
-- comment Optional remarks
Guide and facilitate modularization of ontology No
-- comment Optional remarks
Guide ontology design for visualization No
-- comment Optional remarks
Other ontology quality and fitness support for design phase (describe capability)

Build

General Development

Does NCBO BioPortal allow one to choose an ontology language?
Choose ontology language No
-- comment Optional remarks
Choose formal logic language No
-- comment Optional remarks
Choose RDF support No
-- comment Optional remarks
Mix ontology languages No
-- comment Optional remarks
Generate ontology code from requirements specification No
-- comment Optional remarks
Generate or enforce selected design patterns in ontology code No
-- comment Optional remarks
Feedback on consistency of granularity and regularity of domain ontology structure No
-- comment Optional remarks
Manage lexical naming and annotation of ontology elements No
-- comment Optional remarks
Ensure proper use and coding of RDF and Web resources No
-- comment Optional remarks
Enforce proper use and coding of URIs No
-- comment Optional remarks
Produce the current terminological inferences of an ontology No
-- comment Optional remarks
Optimize query and inference performance No
-- comment Optional remarks
Detect violations of domain, referential, or semantic integrity No
-- comment Optional remarks
Overall, detect and correct coding errors or inconsistencies No
-- comment Optional remarks
Other ontology quality and fitness support for build phase (describe capability)

Concept Development

Ensure proper separation and coding of concepts and facts No
-- comment Optional remarks
Ensure kind-of nature and consistency of subclassing No
-- comment Optional remarks
Guide subclass versus class individual determinations No
-- comment Optional remarks
Monitor depth of subclassing consistency across a domain ontology No
-- comment Optional remarks
Generate prototypical instances (individuals) to help verify class intent and class subsumption No
-- comment Optional remarks
Detect and guide use of multiple inheritance No
-- comment Optional remarks
Guide use of disjointness axioms No
-- comment Optional remarks
Guide use of necessary and sufficient properties in concept definitions No
-- comment Optional remarks
Guide use of existential versus universal quantification in class restrictions No
-- comment Optional remarks
Enforce proper use of conjunctions versus disjunctions No
-- comment Optional remarks

Relationship Development

Ensure proper use and coding of relations No
-- comment Optional remarks
Ensure proper use and coding of data types No
-- comment Optional remarks
Assess and enforce consistency and completeness of range and domain constraints No
-- comment Optional remarks
Assess and enforce consistency and completeness of inverse relations No
-- comment Optional remarks
Ensure proper use and coding of transitive relations No
-- comment Optional remarks

Validation

Verify that ontology requirements are met No
-- comment Optional remarks
Can NCBO BioPortal assess query performance?
Assess query precision and recall performance No
-- comment Optional remarks
Assess query time performance No
-- comment Optional remarks
Can NCBO BioPortal assess inference performance?
Assess inferencing time performance No
-- comment Optional remarks
Assess inferencing completeness performance No
-- comment Optional remarks
Generate characteristic queries and tests No
-- comment Optional remarks
Accept validation test sets or inputs No
-- comment Optional remarks
Can NCBO BioPortal assure computability of ontology?
Assure semantically adequate computability of ontology No
-- comment Optional remarks
Assure mathematically complete computability of ontology No
-- comment Optional remarks
Verify that two ontologies are interoperable No
-- comment Optional remarks
Validate the intended functionality of software using the ontology No
-- comment Optional remarks
Validate instance data conforming to an ontology No
-- comment Optional remarks
Assess accuracy, correctness, and completeness of ontology terminological content No
-- comment Optional remarks
Guide or adjust ontology in accord with validation results No
-- comment Optional remarks
Other ontology quality and fitness support for validation phase (describe capability)

Integration and Use

Export ontology in different languages No
-- comment Optional remarks
Integrate ontology with other ontologies No
-- comment Optional remarks
Integrate ontology with other information system resources No
-- comment Optional remarks
Assess or track user experience with ontology No
-- comment Optional remarks
Enable user to modify or extend ontology to address deficiencies No
-- comment Optional remarks
Create mappings from ontologies to and from data and data sources No
-- comment Optional remarks
Other ontology quality and fitness support for integration and use phase (describe capability)

Maintenance

Promote reuse of ontology No
-- comment Optional remarks
Capture ontology errors during use No
-- comment Optional remarks
Profile use of ontology elements during use No
-- comment Optional remarks
Compare and map between ontologies Yes
-- comment We create and store maps between ontology terms.
Track ontology changes and control versions Yes
-- comment We maintain old versions and diff's between version.
Other ontology quality and fitness support for maintenance phase (describe capability)