Neuroinformatics Databases about the Brain: Different Species

 

Species

Source Name

Purposes/Features/Methods

Contents

Applications

URL

References

Mouse 3D digital atlas database of the mouse brain Lower spatial resolution images were utilized to enhance time efficiency for morphological phenotyping

The in vivo data were compared to available in vitro C57BL/6J mouse brain atlases from literatures

The morphological differences were described

Analyzed unexpected geometrical differences between the in vivo and in vitro brain groups

From magnetic resonance microscopy (MRM)

About C57BL/6J adult mouse brains

Used sufficient signal-to-noise (SNR) and contrast-to-noise ratio (CNR)

Multiple atlases were built

Average geometrical deformation maps

A probabilistic atlas

In vivo atlases provide a better geometric match than in vitro datasets

In vivo atlases are needed for longitudinal analysis and for functional brain activation analyses

 

http://brainatlas.mbi.ufl.edu

 

Ma et al., 2008
Avian The Avian Brain Circuitry Database (ABCD) To support avian connectivity studies

To support the nomenclature

To support brain network research

For collecting, querying, and referencing neuroscience information

Focuses on the connectivity of the avian brain

The terminology of the areas

The hierarchy of the vocabularies

Collection of data on connections between brain areas

A functional keyword platform with associations to brain areas and connections

Data were gathered from the literature and textbooks

An online submission platform available for data collection from researchers

http://www.behav.org/abcd

 

Schrott & Kabai, 2008
Drosophila BrainTrap To analyze the 3D-expression patterns of the proteins and protein complexes of the Drosophila melanogaster brain Reporter gene expression

Protein localization

Full size images of the entire brain

Interactive visualization

Annotations that can be queried

Connected to the FlyBase Drosophila anatomy ontology

Anatomical searches have features of automatic completion

A hierarchical browser for the ontology

Annotations are kept

The annotator locations are highlighted

http://fruitfly.inf.ed.ac.uk/braintrap Knowles-Barley et al., 2010
Flybrain Neuron Database (Flybrain NDB) To track the known neurons in a specific nervous system Projection patterns of the neurons were documented with text-based descriptions, images, and videos

Information of the labeling patterns to visualize neurons

The possible olfactory sensory map in the lateral horn

 

 

A visualization tool for interactive analysis of 3D reconstruction of the confocal serial section images

Search functions enable the analyses of the associations between various brain regions

The links among optic lobe layers

http://flybrain-ndb.iam.u-tokyo.ac.jp

 

Shinomiya et al., 2011
MidExDB (Drosophila CNS Midline Gene Expression Database) The Drosophila CNS midline cells as a model system

For analyzing neuronal and glial development

Datasets of midline gene expression patterns from in situ hybridization experiments

Images and data about midline gene expression from in situ hybridization experiments

Information about each midline cell type and the development

Integration of large-scale gene expression data with the identification of individual cell types

Search tools for data visualization and comparison

Analyses of CNS midline cell neuronal and glial development and functions

 

http://midline.bio.unc.edu/MDB_Home.aspx Wheeler et al., 2009
Platygyra carnosus PcarnBase To sequence the transcriptome

To organize the sequence data

For the brain coral Platygyra carnosus (a species in southern China)

Healthy and tumorous coral tissues

A cDNA library

De novo assembly of the sequence to generate Unigenes

The transcriptome dataset for a species with genome sequences

BLASTx searches

Unigenes with protein annotations, GO annotations, and KEGG pathways

Functional genomic analyses of P. carnosus

Biomarker findings

Genetic basis of stress resistance

http://www.comp.hkbu.edu.hk/~db/PcarnBase

 

Sun et al., 2012

 

References

 

Ma, Y., Smith, D., Hof, P. R., Foerster, B., Hamilton, S., Blackband, S. J., … Benveniste, H. (2008). In Vivo 3D Digital Atlas Database of the Adult C57BL/6J Mouse Brain by Magnetic Resonance Microscopy. Frontiers in neuroanatomy, 2, 1. doi:10.3389/neuro.05.001.2008

Schrott, A., & Kabai, P. (2008). ABCD: a functional database for the avian brain. Journal of neuroscience methods, 167(2), 393–395. doi:10.1016/j.jneumeth.2007.08.007

Knowles-Barley, S., Longair, M., & Armstrong, J. D. (2010). BrainTrap: a database of 3D protein expression patterns in the Drosophila brain. Database: the journal of biological databases and curation, 2010, baq005. doi:10.1093/database/baq005

Shinomiya, K., Matsuda, K., Oishi, T., Otsuna, H., & Ito, K. (2011). Flybrain neuron database: a comprehensive database system of the Drosophila brain neurons. The Journal of comparative neurology, 519(5), 807–833. doi:10.1002/cne.22540

Wheeler, S. R., Stagg, S. B., & Crews, S. T. (2009). MidExDB: a database of Drosophila CNS midline cell gene expression. BMC developmental biology, 9, 56. doi:10.1186/1471-213X-9-56

Sun, J., Chen, Q., Lun, J. C. Y., Xu, J., & Qiu, J.-W. (2012). PcarnBase: Development of a Transcriptomic Database for the Brain Coral Platygyra carnosus. Marine biotechnology (New York, N.Y.). doi:10.1007/s10126-012-9482-z

 

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