Representation of the NeuroNames Ontology in OWL
Filed under:
General neuroinformatics
Douglas Bowden (University of Washington - Seattle), Fahim Imam (Fahim Imam [smtifahim@gmail.com]), Maryann Martone (University of California at San Diego (UCSD))
The goal of this project is to make NeuroNames contents accessible and reusable via modern tools of Semantic Web technologies. It is an on-going project to convert the NeuroNames (NN) specification of relations between ~16000 structure names in eight languages, ~2800 neuroanatomical concepts and ~20 hierarchical models. NeuroNames, which supports the BrainInfo web portal (http://braininfo.org), is being translated into an ontology in W3C standard Web Ontology Language (OWL). Since the contents of NN in BrainInfo are under continuous development, this project will also develop a software tool that can automate the updating process of the corresponding OWL version on a regular basis. Major phases of the project include:
Development of Test Cases by which to demonstrate utility of the product, such as automated ways to generate human readable hierarchies from the ontology database; mediation of data exchange based on standardized metadata; exploitation of logical inference in responding to specific kinds of query
Identification of Existing Protocols developed for NIFSTD that can be applied to the conversion and outline protocols to incorporate the remaining knowledge base of NN
Use OWL API tools to develop a first draft of the ontology with simple constraints extracted from NN, augmenting more rigorous relations manually or semi-automatically and utilizing OBO-RO for object properties and IAO for annotation properties.
Integrate information on the presence or absence of structures in the four species most studied by neuroscientists: human, macaque, rat and mouse.
Integrate information from NN on brain structures that do not map to the boundaries of classical neuroanatomical structures but whose overlaps can be represented in OWL
The OWL document will be made available from a permanent URL and will be accessible through the INCF portal via the PONS and the NCBO Bioportal.
This work supported by grants from INCF, Office of the Director (ORIP), NIH and USPHS grant RR00166.
Development of Test Cases by which to demonstrate utility of the product, such as automated ways to generate human readable hierarchies from the ontology database; mediation of data exchange based on standardized metadata; exploitation of logical inference in responding to specific kinds of query
Identification of Existing Protocols developed for NIFSTD that can be applied to the conversion and outline protocols to incorporate the remaining knowledge base of NN
Use OWL API tools to develop a first draft of the ontology with simple constraints extracted from NN, augmenting more rigorous relations manually or semi-automatically and utilizing OBO-RO for object properties and IAO for annotation properties.
Integrate information on the presence or absence of structures in the four species most studied by neuroscientists: human, macaque, rat and mouse.
Integrate information from NN on brain structures that do not map to the boundaries of classical neuroanatomical structures but whose overlaps can be represented in OWL
The OWL document will be made available from a permanent URL and will be accessible through the INCF portal via the PONS and the NCBO Bioportal.
This work supported by grants from INCF, Office of the Director (ORIP), NIH and USPHS grant RR00166.
Preferred presentation format:
Poster
Topic:
General neuroinformatics
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