Ontolog Forum
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/ |
| Download page | |
| 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) |