Neuroscience terminology

Nomenclature for receptors and ion channels is found in [Alexander et al., 1999]. The Mai atlas [Mai et al., 1997] has a hierarchy for selected brain structures. A text mining system for neuroanatomical terms has been applied for thalamic nuclei [Srinivas et al., 2005].

Table 21 lists some fo the frameworks for description of neuroscience terms, particularly neuroanatomy. Other frameworks: GRAFIP [Hudelot et al., 2006] and the system of [Dameron et al., 2004,Golbreich et al., 2005] where they are able to link the terms to 3D data.

Table 21: Neuroscience terminology, taxonomies and ontologies.

Name	Description	Reference
BAMS	``The Brain Architecture Management System''. Brain structure hierarchy, connections and chemicals	[Bota et al., 2003,Bota and Arbib, 2004,Bota and Swanson, 2006,Bota and Swanson, 2007], http://brancusi.usc.edu/bkms/
BIRNLex	Ontology for, e.g., neuroanatomy, behavioral processes, diseases.	http://fireball.drexelmed.edu/birnlex/OWLdocs/
BrainInfo	Merging of NeuroNames and Template Atlas	[Bowden and Dubach, 2003], http://braininfo.rprc.washington.edu/
BrainMapTM	The BrainMapTM database includes, e.g., a taxonomy for ``behavioral domains''	http://brainmap.org
Brede Database	Small taxonomy for neuroanatomy (WOROI) and, e.g., brain functions, neuroreceptors, brain diseases (WOEXT). Used for classifying experiments and locations in the Brede Database.	[Nielsen, 2003,Nielsen, 2005], http://hendrix.imm.dtu.dk/services/jerne/brede/index_roi_alphabetic.html, http://hendrix.imm.dtu.dk/services/jerne/brede/index_ext_alphabetic.html
CoCoMac	Brain areas such as Brodmann areas. Mapping between them called ``objective relational transformation'' (ORT).	[Stephan et al., 2001,Stephan et al., 2000b,Stephan and Kötter, 1999], http://cocomac.org/
FMA	Foundational Model of Anatomy. A Web-based ontology for anatomy, including the brain. An item such as ``straight gyrus'' is defined with synonyms, latin name, part-of information, arterial supply and whether it has dimension, mass and boundary.	[Rosse and Mejino Jr., 2003], http://sig.biostr.washington.edu/projects/fm/.
(Jerne, ``Volumes of Interest'')	List of words and phrases used in the ``lobar anatomy'' field of BrainMapTM. Generation of volumes and determination of related volumes.	[Nielsen and Hansen, 2002a], http://hendrix.imm.dtu.dk/services/jerne/ninf/voi.html
MeSH	A hierarchy of medical terms used in conjunction with the PubMed web-service	http://www.nlm.nih.gov/mesh/
NeuroNames	A hierarchy and thesaurus of neuroanatomical names with an Internet service. See also BrainInfo	[Bowden and Martin, 1995,Bowden and Martin, 1997,Bowden and Dubach, 2003,Martin et al., 1990] http://rprcsgi.rprc.washington.edu/neuronames/
OpenGALEN	Ontology for clinical data which include, e.g., neuroanatomy	http://www.opengalen.org/, [Rector et al., 1998]
Petilla 2005	GABAergic interneurons	[Alonso-Nanclares et al., 2005] http://www.columbia.edu/cu/biology/faculty/yuste/petilla/, Background: [Yuste, 2005]
SBML	Systems Biology Markup Language	[Hucka et al., 2003], http://sbml.org/

Jörg Niggemann: Representation of Neuroanatomical Knowledge: The Description Language ADL. Terminology and Knowledge Engineering (Vol. 1) 1990: 200-209

Table 22: Functional and cytoarchitectonic areas. See also http://defiant.ssc.uwo.ca/Jody_web/fMRI4Dummies/functional_brain_areas.htm and [Heimer, 1994, pages 285-286].

Name	Description	Reference
cmc	Caudal cingulate motor area. Posterior cingulate motor areas. Human area corresponding to macaque 24d	[Zilles et al., 1995]
cmr	Rostral cingulate motor area. Human area corresponding to macaque 24c. Anterior cingulate motor areas	[Zilles et al., 1995]
DP	Dorsal prelunate area. An area in the macaque bordering V3A, V4, 7a, LIP, VIP according to Felleman and Van Essen. Seems to be mostly used by Van Essen.	[Andersen, 1985,Van Essen, 2003,Felleman and Van Essen, 1991]
F1	Designation used by Matelli for macaque primary motor cortex.	[Matelli et al., 1985,Matelli et al., 1991]
F2	Macaque area in Brodmann area 6	[Matelli et al., 1985,Matelli et al., 1991]
F3	Macaque area in Brodmann area 6	[Matelli et al., 1985,Matelli et al., 1991]
F4	Macaque area in Brodmann area 6	[Matelli et al., 1985,Matelli et al., 1991]
F5	Macaque area in Brodmann area 6. Reported to contain ``canonical'' and ``mirror'' neurons	[Matelli et al., 1985,Matelli et al., 1991,Picard and Strick, 2001]
F6	Macaque area in Brodmann area 6.	[Matelli et al., 1985,Matelli et al., 1991]
F7	Macaque area in Brodmann area 6	[Matelli et al., 1985,Matelli et al., 1991]
FA	Precentral area	[von Economo and Koskinas, 1925, pp. 218, 260+]
FB	Agranular frontal area	[von Economo and Koskinas, 1925, pp. 260+]
FBA
FC	Intermediate frontal area	[von Economo and Koskinas, 1925, pp. 260+, 315+]
FCBm
PCop
FD	Granular frontal area	[von Economo and Koskinas, 1925, pp. 260+, 336-364]
FD$\Delta$
FD$\Gamma$
FDC
FDE
FDL
FE	Frontopolar area	[von Economo and Koskinas, 1925, pp. 260+, 364-373]
FEF	Frontal eye field. Precentral cortex
FEL	Limbic frontopolar area	[von Economo and Koskinas, 1925, p. 371]
FF	Orbital area	[von Economo and Koskinas, 1925, pp. 260+, 373+]
FG	Rectus gyrus area	[von Economo and Koskinas, 1925, pp. 260+, 384+]
FH	Prefrontal area	[von Economo and Koskinas, 1925, pp. 391+]
FI	Area frontoinsularis	[von Economo and Koskinas, 1925, p. 219]
FK	Area piriformis frontalis	[von Economo and Koskinas, 1925, p. 219]
FL	Area parolfactoria	[von Economo and Koskinas, 1925, p. 219]
FM	Area geniculata	[von Economo and Koskinas, 1925, p. 219]
FN	Area praecommissuralis	[von Economo and Koskinas, 1925, p. 219]
FST	Fundus superior temporal. Floor of superior temporal area
hMT	Human correspondent to MT
IA	Insula	[Bonin and Bailey, 1947, p. 78]
IB	Insula	[Bonin and Bailey, 1947, p. 78]
KO	Kinetic occipital. A shape/contour (from motion?) selective area
LA	Anterior limbic area in macaque corresponding to Brodmann area 24. Heterotypic and agranular cortex	[Bonin and Bailey, 1947, pp. 26 and 78]
LC	``Posterior part of the cingulate gyrus and extends into the cingulate sulcus''. Corresponding to Brodmann area 23.	[Bonin and Bailey, 1947, p. 78]
LIP	Lateral intraparietal area
LO	``Lateral occipital''.
M1	Primary motor cortex.
MDP	Medial dorsal parietal area
MST	Medial superior temporal area
MST1	Lateral-anterior area of MST on the floor and the posterior bank of the STS	[Komatsu and Wurtz, 1988]
MSTd	Dorsal division of MST on the anterior bank of STS
MT	Middle temporal area. Visual motion area. Particular in monkey. Almost the same as V5.
MT+	Middle temporal area plus. Used for humans. Sometimes viewed as a complex comprising ``MT'' and MST. Visual motion.	[Huk et al., 2002]
MTf	Fovial region of MT	[Komatsu and Wurtz, 1988]
OA
OB
OC	Striate area in macaque	[Bonin and Bailey, 1947, p. 27]
PA
PB	``Posterior wall of the central sulcus'' in macaque. Part of koniocortex and heterotypical cortex. Corresponding to Brodmann area 3.	[Bonin and Bailey, 1947, pp. 28-29]
PC
PCop
PD
PE
PEm
PF
PFC
PG
PO	Parieto-occipital area. The same as V6
pre-SMA	rostral SMA.
SEF	Supplementary eye field.
SMA	Supplementary motor area. Probably consists of SMA-proper and pre-SMA	[Zilles et al., 1995]
SMA-proper	Caudal part of SMA	[Zilles et al., 1995]
SSA	Supplementary sensory area
TA	``Area temporalis superior'' according to Economo. An area in the temporal lobe. A subarea of BA22	[Bonin and Bailey, 1947, pp. 76-77]
TAa	Temporal area TAa. A subdivision of TA	[Seltzer and Pandya, 1978]
TB
TC	The temporal pole of the macaque	[Bonin and Bailey, 1947, p. 77]
TCB
TE	Inferotemporal area. ``Lateral surface of the temporal lobe below the superior temporal sulcus (except at the pole)'' in the macaque	[Bonin and Bailey, 1947, pp. 42 and 76]
TE1	Subdivision 1 of TE. Inferotemporal area in macaque.	[Seltzer and Pandya, 1978]
TE2	Subdivision 2 of TE. Inferotemporal area in macaque.	[Seltzer and Pandya, 1978]
TE3	Subdivision 3 of TE. Inferotemporal area in macaque.	[Seltzer and Pandya, 1978]
TEa	Subdivision a of TE. Inferotemporal area in macaque.	[Seltzer and Pandya, 1978]
TEc
TEm	Subdivision m of TE. Inferotemporal area in macaque.	[Seltzer and Pandya, 1978]
TEO
TEr
TF		[Bonin and Bailey, 1947, pp. 42-43]
TG		[Bonin and Bailey, 1947, pp. 38-39]
TH		[Bonin and Bailey, 1947, p. 78]
TS1	Area in the supratemporal plane (in macaque)
TS2	Area in the supratemporal plane (in macaque)
TS3	Area in the supratemporal plane (in macaque)
TSA	Transitional sensory area. Upper bank of cingulate sulcus (Macaca)	[Morecraft et al., 2004]
V1	Visual area one. Primary visual cortex. Striate cortex. Brodmann area 17.
V2	Visual area two. Extrastriate. Approximately(?) Brodmann area 18 (with V3).	[Roland and Zilles, 1998]
V2d	Visual area two, dorsal. Cuneus.
V2v	Visual area two, ventral. Lingual gyrus
V3 complex	Group of areas consisting of V3 and V3A (and V3B? ...). Orientation and form sensitive. Color insensitive.
V3	A visual area between V2 and V4. Sometimes V3 is used to designate only the dorsal part of V3, aka V3d. V3 is not a superarea of V3A	[Zeki, 1969,Van Essen, 2003]
V3A	A dorsal area next to V3
V3B	Visual area three, B. Possible the same area as KO. V3A are possibly two area: V3A and V3B according to human studies by Smith and Press, see Van Essen 2003	[Smith et al., 1998,Press et al., 2001a,Van Essen, 2003,Zeki et al., 2003]
V3d	Visual area three, dorsal. Lower visual field	[Van Essen, 2003]
V3v	Visual area three, ventral. Upper visual field. Situated between V2 (V2v) and V4 (V4v)	[Van Essen, 2003]
V4	Visual area four. Brodmann area 19. Color sensitive. The prelunate gyrus in macaque	[Zeki, 1973], [Zeki, 1977, figure 16]
V4d	Visual area four, dorsal.
V4t	Visual area four transitional. An area between V4 and MT.
V4v	Visual area four, ventral. Also VA
V5	Visual area five. Motion sensitive. Brodman area 19(?).	[Zeki et al., 1991]
V5+	Visual area. Used by some to denote human V5 in constrast to monkey V5
V5A
V6	Visual area six. Also PO. Eye position-related activity	[Galletti et al., 1995]
V6A	Corresponds to MDP (Van Essen, 2003)	[Van Essen, 2003]
V7	Visual area seven. Dorsal human visual area lying anterior to V3A	[Press et al., 2001a,Tootell and Hadjikhani, 2001,Van Essen, 2003]
V7A	Posterior parietal area.
V8	Visual area eight. Color vision. Disputed to be the same area as V4. It is defined in human, not (yet?) in macaque	[Hadjikhani et al., 1998,Zeki et al., 1998,Tootell and Hadjikhani, 1998,Tootell and Hadjikhani, 2001]
VA	Ventroanterior area.
VIP
vMST	The floor of superior temporal sulcus (in macaque)	[Vanduffel et al., 2001]
VP	Another name for V3v. Van Essen seems to use VP rather than V3v	[Van Essen, 2003]

Table 22 shows some of the functional areas, cytoarchitectonic area (excluding Brodmann areas) as well as some anatomical area with abbreviations. For visual areas see also http://cogsci.ucsd.edu/~sereno/brain.html. [Van Essen, 2003] describes the differences and similarities between human and macaque cortical areas. Human and macaque areas for speech perception are displayed in [Scott and Johnsrude, 2003, Figure 1], and [Petrides and Pandya, 1994] is a comparative study of human and macaque for the frontal cortex.

Common modifiers are: anterior/posterior, dorsal/ventral, superior/inferior, caudal/rostral, ipsilateral/contralateral, lateral/medial, and floor/fundus, bank and lip.

Cytoarchitectonic areas with respect to Brodmann's scheme are displayed in table 23. Classic cytology references are [Brodmann, 1909,Brodmann, 1994,von Economo and Koskinas, 1925,von Economo, 1929,Bonin and Bailey, 1947] and Braak. The nomenclature used for macaque by [Bonin and Bailey, 1947] is based on that from Economo-Koskinas for humans [von Economo and Koskinas, 1925]. A structured overview of Brodmann areas (and other areas) is also available from the CoCoMac database (http://cocomac.org). Furthermore, this database provides data on the relationship between brain areas (called ``mapping'' in the database), e.g., whether an area is a subarea of another, see also http://www.cocomac.org/regionalmap.pdf. Illustrations of the spatial organization and characteristics of Brodmann areas appear at http://spot.colorado.edu/~dubin/talks/brodmann/brodmann.html.

Table 23: Brodmann areas. BA and the Brodmann area numbers. EK refers to Economo-Koskinas identifiers [von Economo and Koskinas, 1925,Zilles and Palomero-Gallagher, 2001] and [Roland, 1992, figure 5.20].

BA	EK	Area	Description	Reference
1	PC	Intermediate postcentral area	Postcentral region	[Brodmann, 1994, p. 112], [Zilles and Palomero-Gallagher, 2001, table 1]
2	PD, PDE	(Caudal) postcentral gyrus		[Brodmann, 1994, p. 112], [Zilles and Palomero-Gallagher, 2001, table 1]
3		(Rostral) postcentral gyrus		[Brodmann, 1994, p. 112]
3a	PA1			[Zilles and Palomero-Gallagher, 2001]
3b	PB1, PB2		Primary somatosensory area	[Zilles and Palomero-Gallagher, 2001]
4		Giant pyramidal area	Precentral region, primary motor cortex	[Brodmann, 1994, p. 113]
4a		4 anterior	``slightly larger, more densely packed pyramidal cells in layer III than [...] 4p''	[Geyer et al., 1996], Jülich atlas
4p		4 posterior	Between 3a and 4a towards the bottom of the precentral gyrus.	[Geyer et al., 1996]
5		Preparietal area	Parietal region
6		Agranular frontal area		[Brodmann, 1994, p. 115]
7		Superior parietal area
8		Intermediate frontal area		[Brodmann, 1994, p. 116]
9		Granular frontal area
10		Frontopolar area
11
12
13			Does not appear in humans
14			Does not appear in humans
15			Does not appear in humans
16			Does not appear in humans
17		Striate area		[Brodmann, 1994, p. 119]
18		Occipital area		[Brodmann, 1994, p. 120]
19		Preoccipital area		[Brodmann, 1994, p. 120]
20		Inferior temporal area		[Brodmann, 1994, p. 124]
21		Middle temporal area		[Brodmann, 1994, p. 121]
22		Superior temporal area		[Brodmann, 1994, p. 121]
23	LC2	Ventral posterior cingulate	Isocortex	[Brodmann, 1994, p. 126-127]
23a			Isocortex, (Proisocortex?). Could be classified as 30 (Kobayashi)	[Vogt et al., 2001,Kobayashi and Amaral, 2000]
23b			Isocortex	[Vogt et al., 2001,Vogt et al., 1987,Vogt and Pandya, 1987]
pv23b		Posteroventral	Thalamic projections mainly from anterior nuclei	[Shibata and Yukie, 2003]
d23b		Dorsal		[Shibata and Yukie, 2003]
23c			Isocortex. Lower bank of the cingulate sulcus. Part of caudal cingulate motor area (M4)	[Morecraft et al., 2004]
23d			Curvature of the depth of the cingulate sulcus. Part of caudal cingulate motor area (M4)	[Morecraft et al., 2004]
23e		External	Dorsal 23. (Macaca fascicularis). Related to 23c	[Kobayashi and Amaral, 2000]
23i		Internal	Rostral and ventral compared to 23e. (Macaca fascicularis). Related to 23b.	[Kobayashi and Amaral, 2000]
23v		Ventral	The most inferior part of 23. (Macaca fascicularis)	[Kobayashi and Amaral, 2000]
24		Ventral anterior cingulate		[Brodmann, 1994, p. 127]
24a			Proisocortex
24b			Proisocortex
24c			Part of rostral cingulate motor area (M3)	[Morecraft et al., 2004]
24d			Part of rostral cingulate motor area (M3)	[Morecraft et al., 2004]
25		Subgenual		[Brodmann, 1994, p. 127]
26	LF	Ectosplenial	In the retrosplenial region. ``es'' of Braak	[Brodmann, 1994, p. 128], [Vogt et al., 2001, p. 358] [Braak, 1979]
27		Presubicular area, Parahippocampal		[Brodmann, 1994, p. 128]
28		Ectorhinal area		[Brodmann, 1994, p. 129]
29		Granular retrolimbic	Granular. In the retrosplenial region in the depth of the callosal sulcus	[Brodmann, 1994, p. 128], [Vogt et al., 2001]
29a			Periallocortex (Macaca mulatta)	[Morris et al., 1999]
29b			Periallocortex (Macaca mulatta)	[Morris et al., 1999]
29c			Transitional periallocortex/proisocortex (Macaca mulatta)	[Morris et al., 1999]
29d			Proisocortex. Most medial part of 29. (Macaca mulatta)	[Morris et al., 1999]
29l		Lateral 29		[Kobayashi and Amaral, 2000,Vogt et al., 2001]
29m		Medial 29		[Kobayashi and Amaral, 2000,Vogt et al., 2001]
30	LD	Agranular retrolimbic	Dysgranular. Proisocortex. In the retrosplenial region in the lib of the callosul sulcus. ``Variable thickness layer IV that is interrupted by large NFP-ir neurons in layers IIIc and Va''	[Brodmann, 1994, p. 128], [Vogt et al., 2001,Morris et al., 1999,Morecraft et al., 2004]
30v			Transition between 29 and visual association cortex	[Kobayashi and Amaral, 2000]
31	LC1	Dorsal posterior cingulate
32		Dorsal anterior cingulate		[Brodmann, 1994, p. 127]
33		Pregenual
34
35
36		Ectorhinal area, (Parahippocampal?)		[Brodmann, 1994, p. 122]
36'd				[Vogt et al., 2001]
36'v				[Vogt et al., 2001]
37
38		Temporopolar		[Brodmann, 1994, p. 124]
39	PG	Angular	``Corresponds broadly to the angular gyrus''. Myeloarchitectonic PG and PEG (Eidelberg-Galaburda)	[Brodmann, 1994, p. 119], [Eidelberg and Galaburda, 1984], [Zilles and Palomero-Gallagher, 2001, table 1]
40		Supramarginal
41		Medial (anterior transverse temporal area		[Brodmann, 1994, p. 125], Jülich atlas
42		Lateral (posterior) transverse temporal area		[Brodmann, 1994, p. 125]
43	PDF			[Zilles and Palomero-Gallagher, 2001, table 1]
44		Opercular area	Subfrontal region
45		Triangular area	Subfrontal region
46		Middle frontal area
46d		Dorsal area 46
46v		Ventral area 46 (also v46)
47		Orbital area	Subfrontal region
48
49
50
51
52		Parainsular		[Brodmann, 1994, p. 125]