Cell Ontology

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OBO FOUNDRY A FAMILY OF REFERENCE
ONTOLOGIES Fabian Neuhaus, Barry Smith
University at Buffalo
INTRODUCTION The National Center for Biomedical
Ontology (http//bioontology.org) is a consortium
that comprises leading informaticians,
biologists, clinicians, and ontologists funded by
the NIH Roadmap to develop innovative technology
and methods that allow scientists to record,
manage, and disseminate biomedical information
and knowledge in machine-processable form. One
goal of the center is to propagate best practices
and quality control methods that will improve the
utility increase the lasting value of biomedical
ontologies that are developed, and allow for
greater interoperability between them.
OBJECTIVE The OBO Foundry is a collaborative
experiment to overcome the Babel problem. It
involves a group of leading ontology developers
who have agreed in advance to the adoption of a
growing set of principles specifying best
practices in ontology development. These
principles are designed to foster
interoperability of ontologies within the broader
OBO framework, 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. In
particular, these principles ensure that the
ontologies which are part of the Foundry are not
tailored to a specific problem, but can be used
as a reference ontology for the community.
Further, the ontologies do not overlap, their
terms are well defined, and the semantic
relations are used consistently across the
ontologies. The objective is to establish a
family of interoperable, high-quality reference
ontologies to be used in the annotation of
biomedical data.
OBO FOUNDRY MEMBERS
THE BABEL PROBLEM The value of scientific data is
greatly enhanced when it exists in a form which
allows it to be integrated with other data. One
route to integration is through the annotation of
data using common controlled vocabularies or
ontologies. A variety of terminology resources
have been assembled, often these are homegrown
solutions that are tied to the specific needs of
the designers who developed them. These has lead
to the following situation 1. Many controlled
vocabularies have grown in an ad hoc way
without clear boundaries and design principles.
2. The existing ontologies are of uneven
quality. 3. The reusability of many controlled
vocabularies is limited. 4. The ontologies
dont cover the biomedical domain in a
systematic way. 5. The semantic relations
(e.g. is_a, part_of) are used inconsistently
within the same ontologies as well as across
different ontologies. 6. Ontologies overlap
and use inconsistent terminology. Consequently,
a Babylonian problem arises there are many
ontologies each of which assigns semantic content
to its terms in its own idiosyncratic way. This
problem thwart not only the integration of data
but also the exploitation of ontologies for
purposes of reasoning.
Cell Ontology cell types from prokaryotes to
mammals
Chemical Entities of Biological
Interest Molecular entities which are used to
intervene in the process of living organisms
OBO FOUNDRY PRINCIPLES Availability and Community
Collaboration 1. The ontology is open and
available to be used by all without any
constraint other than (a) its origin must be
acknowledged and (b) it is not to be altered and
subsequently redistributed except under a new
name and with different identifiers. 2. The
ontology is developed in a collaborative effort.
3. The ontology has a plurality of independent
users. Formal Structure and Scope 4. The
ontology has a clearly specified and clearly
delineated subject-matter. 5. The ontology
uses relations which are unambiguously defined
following the pattern of definitions laid down in
the OBO Relation Ontology. 6. The ontology is
in, or can be expressed in, a common formal
language. Documentation and Maintenance 7. The
ontology has documentation that is clearly
written for non-experts in ontologies. 8. The
ontology includes textual definitions for all
terms. 9. The ontology provider has procedures
for identifying distinct successive versions.
10. The ontology possesses a unique identifier
space within OBO.
Relation Ontology Relations between
universals and instances in biomedical ontologies
Sequence Ontology features and properties of
nucleic sequences
Protein Ontology protein types and modifications
classified on the basis of evolutionary principles

RNA Ontology three-dimensional RNA structures and
homologous sequence alignments and
associated attributes and processes
Foundational Model of Anatomy structure of the
human body
Functional Genomics Investigation Ontology
design, protocol, instrumentation, data, and
analysis applied in functional genomics
investigations
Gene Ontology cellular components,
molecular functions, biological processes in all
organisms