Data sources

**Table 2:** Specific data sources. A star ``*'' indicates that the data source has public data easily available, e.g., through the Internet. The second column refer to Shepherd's levels listed in table 1. See also the *The SfN Neuroscience Database Gateway* at http://big.sfn.org/ndg/site/ [Gardner and Shepherd, 2004], Neuroguide web-page on databases: http://www.neuroguide.com/neuroresac_4.html.
Name		Description	Reference

Allen Brain Atlas *	AH	Mouse brain atlas of gene transcriptions. In situ hybridization stained 3D images	http://www.brain-map.org/, http://www.brainatlas.org/, [Dong, 2006,Lein et al., 2007,Markram, 2007]
(Old) BrainMap^TM *	AB	Neuroimaging location data. Contains Bibliographic information, experimental descriptors and 3D Talairach coordinates. This ``old'' and closed database is continued as ``BrainMap DBJ'' (which now is referred to as ``BrainMap'')	[Fox and Lancaster, 1994,Fox et al., 1994,Fox et al., 1995,Lancaster et al., 1994,Lancaster et al., 1997a,Fox and Lancaster, 2002]
(New) BrainMap^TM / BrainMap DBJ $\textregistered$ *	AB	Neuroimaging location data. Continuation of (original) BrainMap. As of 2005 referred to as ``BrainMap''	[Fox et al., 2002,Fox and Lancaster, 2002,Fox et al., 2005a,Laird et al., 2005b], http://www.brainmap.org
Brede Database *	AB	Neuroimaging location data, brain region taxonomy, brain function taxonomy.	[Nielsen, 2003], http://hendrix.imm.dtu.dk/services/jerne/brede/, http://hendrix.imm.dtu.dk/software/brede/
fMRIDC *	(A)B	fMRI scanning data, summary images	[Van Horn et al., 2001a,Van Horn and Gazzaniga, 2002,Grethe et al., 2001,Van Horn et al., 2003,Van Horn, 2003] http://www.fmridc.org
NeuroGenerator	AB	Database for human brain imaging.	[Roland et al., 2001,Svensson and Forsberg, 2002,Halldorsson and Fredriksson, 2002,Svensson et al., 2003,Forsberg, 2003,Forsberg, 2004] http://www.neurogenerator.org
BrainWeb *	B	Simulated MRIs of the human brain	[Cocosco et al., 1997,Kwan et al., 1996,Kwan et al., 1999,Collins et al., 1998] http://www.bic.mni.mcgill.ca/brainweb/
IBSR *	B	MGH CMA Internet Brain Segmentation Repository (IBSR). Repository with raw and segmented (GM/WM/CSF) MRI volumes	http://neuro-www.mgh.harvard.edu/cma/ibsr/
IBVD *	B	MGH CMA Internet Brain Volume Database (IBVD). ``Neuroanatomic volumetric observations'', e.g., from MRI morphological studies.	[Kennedy et al., 2003,Haselgrove and Kennedy, 2003], http://www.cma.mgh.harvard.edu/ibvd/
CoCoMac *	B	Neural connectivity database for the Macaque brain	[Stephan et al., 2001,Stephan et al., 2000b,Stephan and Kötter, 1999,Kötter and Wanke, 2005] http://cocomac.org/
``Cat connectivity'' *	B	Cortico-cortical, thalamo-cortical, and cortico-thalamic connectivity of the cat. Distributed as ASCII and Excel files.	[Scannell et al., 1995] http://www.ncl.ac.uk/biol/research/psychology/nsg/neuroinformatics.htm
MC-ET *	B	Simulation data sets for emission tomography	http://www.ibfm.cnr.it/mcet/index.html
NeSys *	B	Database of pontine projections to SI cortex in rat	[Bjaalie, 2002], http://www.nesys.uio.no/Database/
OASIS	B	Open Access Series of Imaging Studies. Structural MR from 416 subjects.	http://www.oasis-brains.org
Thalamic Connectivity Atlas *	B	Probabilistic mapping of thalamo-cortical connections based on probabilistic diffusion tractography	[Behrens et al., 2003a,Behrens et al., 2003b], http://www.fmrib.ox.ac.uk/connect/
XANAT	B	Neural connectivity	[Press et al., 2001b,Olshausen and Press, 1994], http://redwood.ucdavis.edu/xanat/
SumsDB	B	``Surface Management Systems DataBase''	[Van Essen et al., 2001,Van Essen, 2002,Van Essen et al., 2005,Dickson et al., 2001], http://sumsdb.wustl.edu:8081/sums/index.jsp
CoCoDat	C	Database ``Collation of Cortical Data'' -- for ``organization of single cell and microcircuitry data''	[Dyhrfjeld-Johnsen et al., 2001]
WormAtlas	CD	Complete neuronal connectivity for the small worm C. elegans	[Chen et al., 2006], http://www.wormatlas.org
L-NEURON	CD	Database with dendritic trees. L-Neuron and ArborVitae are programs.	[Ascoli et al., 2001], http://www.krasnow.gmu.edu/L-Neuro/
Duke-Southampton archive of neuronal morphology	D	Database with rat hippocampal neurons.	[Cannon et al., 1998] http://www.cns.soton.ac.uk/~jchad/cellArchive/index/topindex.html
Neurodatabase.org *	D	Neurophysiology database with time-series and histogram data. Java program as entrance and with the data structure used termed ``common data model'' (CDM). Previously called ``Cortical Neuron Net Database''. Associated with BrainML	[Gardner et al., 2001b,Gardner et al., 2001a], http://neurodatabase.org/, http://brainml.org/
Neocortical microcircuit database *	DE(H)	Neuron type (anatomical, electrophysiological), neuron connections	http://microcircuit.epfl.ch/
WebQTL *	H		[Wang et al., 2003,Chesler et al., 2004], http://www.webqtl.org/
SenseLab *	DG	Organization of neurons, neurotransmitters, receptors, cellular ionic currents, computation neuroscientific models (GENESIS, NEURON). Separate database for olfactory receptors.	[Mirsky et al., 1998,Marenco et al., 1999,Skoufos et al., 1990,Skoufos et al., 2000,Crasto et al., 2003,Marenco et al., 2003,Crasto et al., 2007], http://senselab.med.yale.edu/senselab/
GPCRDB *	G	A database of G protein-coupled receptors. Ligand dissociation constants, 3D models	[Horn et al., 1998,Horn et al., 2001], http://www.gpcr.org/
LGICdb *	G	``The Ligand Gated Ion Channel Database''.	[Le Novère and Changeux, 1999,Le Novère and Changeux, 2001,Le Novère and Changeux, 2001], http://www.pasteur.fr/recherche/banques/LGIC/
HPMR *	G	``Human Plasma Membrane Receptome''. A database of plasma membrane receptors	[Ben-Shlomo et al., 2003], http://receptome.stanford.edu/HPMR/
WormBase	GH	Gene expression in Caenorhabditis elegans and other worms	[Harris et al., 2004,Bieri et al., 2007], http://www.wormbase.org/
PubMed *	--	Bibliographic data within biomedical sciences	http://www.ncbi.nlm.nih.gov/entrez/ [Wilbur and Yang, 1996]
CiteSeer *	--	Also called ResearchIndex. Index of research articles in PostScript on the Internet	[Lawrence et al., 1999] http://citeseer.ist.psu.edu/
Publisher's website *	--		E.g., http://www.sciencedirect.com/, http://www.interscience.wiley.com/
Bibliographic databases *	--	Special subject databases, e.g., MuSICA (previously ``Music & Brain Information Database'' -- MBI) and ``Copenhagen Neuropsychology Database''	E.g., http://www.musica.uci.edu/, http://www.open-rehab.com/ris/risweb.isa

Researchers in functional neuroimaging typically both acquired (from original experiments) and analyze the data. However, a number of Internet services store data (raw or analyzed), enabling other researchers to reanalyze, meta-analyze: Table 2 lists Internet databases with available neuroscientific data.

Neuroscientific data can be voluminous, e.g., A fMRI study can have a size of a gigabyte and a few minutes of a single EEG multi-electrode recordings can generate hundreds of megabyte. Table 3 is an overview of the different types and sizes of data from experimental measurements and associated sources that are collected in neuroscientific databases.

Brain images

Table 4 shows some to the web-sites with brain images and programs. These are usually not in any reference (stereotaxic) space. The images are often more applicable for educational purposes rather than research purposes.

A dead link is ``David'' (Online Atlas of Human Anatomy for Clinical Imaging Diagnosis developed by J.-C. Oberson. CT and MRI (T1, T2, PD) labeled sections) http://www.cid.ch/DAVID/head.html

**Table 4:** Brain images -- either on the web, as program or digitized. More brain images listed in [Toga, 2002a, table 1] and at http://www.msu.edu/~brains/atlases/.
Name	Description	Reference

BrainInfo	`The Template Atlas' 62 drawings from the longtailed macaque (Macaca fascicularis), nissl, myelin, photographs (unstained), MRI of Macaca fascicularis. Integrated with NeuroNames	http://www.elsevier.com/homepage/sah/pbm/, http://rprcsgi.rprc.washington.edu/~atlas/, http://braininfo.rprc.washington.edu/; [Martin and Bowden, 1996,Rauschning, 1983]
GENSAT	Gene expression atlas of the mouse brain	[Heintz, 2004], http://www.gensat.org
Brain stem (MSU)	``Atlas of the Human Brain Stem'' with axial images	http://www.msu.edu/~brains/brains/human/brainstem/
Brain stem (Swenson)	``Atlas of the Brain Stem'' with axial images	http://www.dartmouth.edu/~rswenson/Atlas/
The Whole Brain Atlas	Extensive site with human brain transversal sections images (and movies) of normal as well as pathological brains in multiple modalities (T1, T2, PD, PET, CT). Navigation and often labeled images	http://www.med.harvard.edu/AANLIB/, [Johnson and Becker, 1999].
SPL/NSL Anatomy Browser	3D views of segmented human brain	[Golland et al., 1998,Anderson et al., 1998,Umans et al., 1997,Kikinis et al., 1996,Shenton et al., 1995] http://splweb.bwh.harvard.edu:8000/pages/papers/AnatomyBrowser/current/index.html
Atlas of the Sheep Brain	Cell and fiber stained sections with optional labeling. Labeled external surface images.	http://www.msu.edu/user/brains/sheepatlas/
Columbia Brain Atlas	MRI and In vivo (PET) and in vitro (autoradiography) molecular neuroimages	http://cba.cpmc.columbia.edu/
Flybrain	Images and illustration of Drosophila	[Armstrong et al., 1995], http://www.flybrain.org/
Digital Anatomist	Human brain image in sections, surface and 3D views with interactive labels from Seattle	[Brinkley and Rosse, 1997], http://www9.biostr.washington.edu/da.html
Neur@nat	Human brain images with interactive labels	http://www.chups.jussieu.fr/ext/neuranat/
MBL C57BL/6J Atlas	Mouse brain pictures in coronal and horizontal sections with/out grid. C57BL/6J is a specific strain. DBA/2J atlas is also available.	http://www.mbl.org/atlas232/atlas232_frame.html, http://www.mbl.org/atlas170/atlas170_frame.html
PET Brain Atlas (PBA)	PET images of the normal and diseased human brain. Labeled and unlabel illustrations.	http://oracle.crump.ucla.edu:8001/pet/pba/. http://laxmi.nuc.ucla.edu:8000/PBA/HTML/
Neuroanatomy	Neuroanatomy, A Photografic Study of the Central Nervous System	http://www.neuroanatomy.hpg.ig.com.br/
The NPAC Visible Human Viewer	Java applet for viewing the Visible Human data set in coronal, transversal and sagittal sections	[Chang et al., 1998] http://www.npac.syr.edu/projects/vishuman/VisibleHuman.html
Comparative Mammalian Brain Collections	Photographs of external surfaces of 175 mammalian species, some (stained?) section images	http://brainmuseum.org/
The Human Brain. Dissection of the Real Brain	Photographs and labeled drawings of the human brain from the Virtual Hospital	http://www.vh.org/Providers/Textbooks/BrainAnatomy/BrainAnatomy.html
Brain stem of Rhesus	Label sections in stereotaxic coordinates with links to BrainInfo	[Smith et al., 1972] http://braininfo.rprc.washington.edu/otheratlas/Brainstem/index.html

The HCIL Visible Human Explorer	Not a web application but a SUN computer program to display images from the visible human data set	[North and Korn, 1996,North et al., 1996] http://www.cs.umd.edu/hcil/visible-human/
	(Items below do not seem (or has not seemed) to work on a Linux system)
LONI Human atlas	Cryosection images from two normal female cadavers. Possible the termed ``Human cryotome data'' and ``LADY'' before.	[Toga et al., 1994] (?), http://www.loni.ucla.edu/Research/Atlases/HumanAtlas.html
LONI Monkey Atlas	Sections and images of 3D models	[Cannestra et al., 1997] (?), http://www.loni.ucla.edu/Research/Atlases/MonkeyAtlas.html
LONI Rat Atlas	Labeled Coronal, sagittal and transversal cryosections with coordinates	[Toga et al., 1995] (?) http://www.loni.ucla.edu/Research/Atlases/RatAtlas.html
DTI Atlas	Labeled images of analyzed diffusion tensor images	http://www.DTIatlas.org

Genetics

**Table 5:** Genetics association databases
Name	Description	Reference

AlzGene	Limited to Alzeimer's disease. Numerical results from published studies are entered and results of meta-analysis are displayed in tables and plots	http://www.alzforum.org/res/com/gen/alzgene/ [Bertram et al., 2007]
CGEMS	Cancer Genetic Markers of Susceptibility	http://cgems.cancer.gov/
dbGaP	Genome-wide association studies	http://www.ncbi.nlm.nih.gov/gap
GAD	Genetics Association Database from NIH	http://geneticassociationdb.nih.gov/, [Becker et al., 2004]
HuGE Pub Lit	Human Genome Epidemiology (HuGE) Published Literature database	http://hugenavigator.net/, [Lin et al., 2006]
OMIM	The text-oriented web-site Online Mendelian Inheritance in Man links gene and genetic disorders	http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM, [McKusick, 1998]
PADB	Published Association Database automatically extracts text from published association study abstracts. For the studies were this is possible the database can sort them according to risk measure.	http://www.medclue.com/padb [Rhee and Lee, 2007]
PDGene	Limited to Parkinson's disease.	http://www.pdgene.org/
PharmGKB	The Pharmacogenetics and Pharmacogenomics Knowledge Base	http://www.pharmgkb.org/
SzGene	Limited to schizophrenia	[Allen et al., 2008]
T1DBase	Limited to type 1 diabetes	http://www.t1dbase.org/

Name	Description	Reference

Data source	Data size	Neuroinformatics topic
Neuroimaging scanning data	Gigabytes / study	Reanalyses
		Meta-analyses

Neuroimaging summary images	Megabyte / study	Meta-analyses
		Volume searches

Neuroimaging location data	Kilobytes / study	Meta-analyses
		volumes searches

Neural connectivity	Kilobytes / study	Neural network analysis


Literature	11 million	Bibliographic searches