Linked Life Data

19145492

Source:http://linkedlifedata.com/resource/pubmed/id/19145492

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2009-2-13
pubmed:abstractText
Brain atlases are widely used in experimental neuroscience as tools for locating and targeting specific brain structures. Delineated structures in a given atlas, however, are often difficult to interpret and to interface with database systems that supply additional information using hierarchically organized vocabularies (ontologies). Here we discuss the concept of volume-to-ontology mapping in the context of macroscopical brain structures. We present Java tools with which we have implemented this concept for retrieval of mapping and connectivity data on the macaque brain from the CoCoMac database in connection with an electronic version of "The Rhesus Monkey Brain in Stereotaxic Coordinates" authored by George Paxinos and colleagues. The software, including our manually drawn monkey brain template, can be downloaded freely under the GNU General Public License. It adds value to the printed atlas and has a wider (neuro-)informatics application since it can read appropriately annotated data from delineated sections of other species and organs, and turn them into 3D registered stacks. The tools provide additional features, including visualization and analysis of connectivity data, volume and centre-of-mass estimates, and graphical manipulation of entire structures, which are potentially useful for a range of research and teaching applications.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:status
MEDLINE
pubmed:issn
1559-0089
pubmed:author
pubmed:issnType
Electronic
pubmed:volume
7
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
7-22
pubmed:meshHeading
pubmed:year
2009
pubmed:articleTitle
Matching spatial with ontological brain regions using Java tools for visualization, database access, and integrated data analysis.
pubmed:affiliation
Donders Institute for Brain, Cognition and Behaviour, Department of Cognitive Neuroscience, Radboud University Nijmegen Medical Centre, The Netherlands.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't