The INCF Program on Ontologies for Neural Structures
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1
University of California, San Diego, United States
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2
George Mason University, United States
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3
Neurocommons, United States
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4
Washington University, United States
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5
INCF, International, Sweden
The goal of the program on Ontologies of Neural Structures (PONS) of the International Neuroinformatics Coordinating Facility (INCF) is to promote data exchange and integration in the neurosciences by developing terminology standards and formal ontologies for neural structures. PONS was established in recognition that a lack of a consistent or computable terminology for neuroanatomy across structural scales and species is an impediment to data integration in the neurosciences, with its diversity of model systems. PONS has two main subprograms: creation of a lexicon for neural structures and creation of a neuronal registry. These programs are organized into two task forces, comprising an international group of neuroscientists. These task forces are supported by the Representation and Deployment (R & D) Task Force, comprising experts in ontology construction and knowledge representation. The structural lexicon subprogram is creating a lexicon of neural structures in primate and rodent brain from the gross anatomical to the macromolecular scale, including defining criteria by which these structures can be recognized in experimental material. Work to date has established a proposed standard metadata scheme for defining criteria for brain structures that has been implemented within a semantic Wiki (http://neurolex.org). A second subproject is establishing a set of high level consensus structures for mammalian brain to serve as a framework for cross-species translations of major brain regions and for relating more granular parcellation schemes for these brain regions established by different atlas providers and research scientists. The goal is to translate high level concepts such as "cerebral cortex" to a standard set of parts within primates and rodents. This basic upper ontology is also being linked to the Waxholm mouse brain atlas to implement a set of standardized spatial and semantic representations of major brain structures across the INCF atlasing and PONS programs. The neuronal registry subprogram is determining a set of properties for defining neurons in order to create a knowledge base to facilitate comparison among existing and yet to be discovered neuronal types. With the R & D task force, it is reviewing different representations to derive a set of standard relationships that can be used to express properties of neurons in a computable and interoperable form, particularly in the area of connectivity among brain regions, cell populations and individual cells. The two subprograms are designed to work together, with the structural lexicon providing the building blocks to be used by the neuronal registry for building representations of neurons. The R & D Task Force is responsible for establishing a semantic framework for brain structures and neurons that can be used to compute relationships among structures across scales. Initial work has been understanding and aligning the different representations of brain structures and neurons proposed by a variety of groups working in these areas with the aim of harmonization and consolidation. One target is having all terms and relations at least have definitions in, and consonant with, OBO Foundry reference ontologies, and to lay the groundwork for being able to share knowledge on the semantic web. Members of the task force include representatives from several community ontology and database efforts so as to ensure that the results of the PONS program address known needs and are likely to be generally acceptable. As with other INCF programs, the PONS provides a community forum where basic standards, procedures and tools can be established to facilitate interoperability among these different and valuable efforts. All products of the PONS are meant to be evaluated and extended by the larger community. In this way, the neuroscientists can pool their efforts more effectively and add to the growing ecosystem of linked resources within the broader life sciences community.
Conference:
Neuroinformatics 2010 , Kobe, Japan, 30 Aug - 1 Sep, 2010.
Presentation Type:
Oral Presentation
Topic:
INCF Japan-Node Special Symposium
"How Neuroinformatics can revolutionize Neuroscience"
Citation:
Martone
M,
Ascoli
G,
Ruttenberg
A,
Van Essen
D and
Force Members
IP
(2010). The INCF Program on Ontologies for Neural Structures.
Front. Neurosci.
Conference Abstract:
Neuroinformatics 2010 .
doi: 10.3389/conf.fnins.2010.13.00067
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Received:
11 Jun 2010;
Published Online:
11 Jun 2010.
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Correspondence:
Maryann Martone, University of California, San Diego, San Diego, United States, mmartone@ucsd.edu