UPenn. Center for Bioinformatics Computational Biology and Informatics Laboratory



  The following table shows the hierarchical controlled vocabulary of anatomy terms used in CBIL's databases. The controlled vocabulary is based on a table of anatomy terms taken from the Mouse Gene Expression Database at the Jackson Laboratory (specifically GXD mouse stage 28 - adult.) However, it has been extended to incorporate human anatomy and also revised in a number of areas, particularly the haematolymphoid system, based on the 37th edition of Gray's Anatomy, and the brain, thanks to the contributions of Dr. Jonathan Nissanov of Drexel University. Further value has been added to the vocabulary by mapping each anatomy term onto the relevant set of EST libraries in dbEST.

If you have questions or comments about this controlled vocabulary, please contact its maintainer Chris Stoeckert.


Key to the sources from which terms were drawn
GXDJackson Labs Mouse Gene Expression Database (mouse stage 28 - adult)
GRAYSGray's Anatomy, 37th edition
STEDMANStedman's Medical Dictionary, 24th edition
CBILComputational Biology and Informatics Laboratory
NISSANOVDr. Jonathan Nissanov, Drexel University

             
 1. connective tissue   GXD
   2. cartilage   GXD
   3. chondroblast   GXD
   4. chondrocyte   GXD
   5. fibroblast   GXD
   290. cell line   CBIL
   6. fibrocyte   GXD
   7. ligament   GXD
   240. synovium   GRAYS
   8. tendon   GXD
 224. embryo   CBIL
   314. cell line   CBIL
   312. stem cells   CBIL
   313. cell line (ES cells)   CBIL
 223. fetus   CBIL
 9. limb   GXD
   10. forelimb   GXD
   11. arm   GXD
   12. handplate (paw)   GXD
   13. hindlimb   GXD
   14. footplate (paw)   GXD
   15. leg   GXD
   16. lower leg   GXD
   17. skeleton (bone)   GXD
   18. fibula   GXD
   19. sesamoid bone of gastrocnemius   GXD
   20. tibia   GXD
   21. upper leg   GXD
   22. skeleton (bone)   GXD
   23. femur   GXD
 24. muscle   GXD
   25. cardiac muscle (myocardium,heart muscle)   GXD
   26. skeletal muscle   GXD
   280. cell line (rhabdomyosarcoma)   STEDMAN
   317. diaphragm   GRAYS
   27. smooth muscle   GXD
 28. organ system   GXD
   29. adipose tissue (fat)   GXD
   30. adipoblast   GXD
   31. adipocyte   GXD
   32. adipogenic reticular cell   GXD
   33. brown (brown fat,BAT)   GXD
   34. adipoblast   GXD
   35. adipocyte   GXD
   36. adipogenic reticular cell   GXD
   37. preadipocyte (pre-adipocyte)   GXD
   38. preadipocyte (pre-adipocyte)   GXD
   39. white (white fat,WAT)   GXD
   40. adipoblast   GXD
   41. adipocyte   GXD
   42. adipogenic reticular cell   GXD
   43. preadipocyte (pre-adipocyte)   GXD
   44. cardiovascular system   GXD
   45. arterial system   GXD
   46. arteriole   GXD
   47. artery   GXD
   292. aorta   GRAYS
   298. endothelium (endothelial cells)   GRAYS
   696. carotid artery   GRAYS
   697. endothelium (endothelium, carotid artery)   GRAYS
   48. capillary   GXD
   301. endothelium (endothelial cells)   GRAYS
   49. heart   GXD
   691. atrioventricular node   GRAYS
   217. myocardium   GRAYS
   218. valve   GRAYS
   50. lymphatic vessel   GXD
   51. venous system   GXD
   52. vein   GXD
   299. umbilical vein   GRAYS
   300. endothelium (endothelial cells)   GRAYS
   53. venule   GXD
   54. endocrine system   GXD
   55. adrenal gland   GXD
   221. adrenal cortex   GRAYS
   222. adrenal medulla   GRAYS
   56. pancreas   GXD
   58. acinar cell   GXD
   277. cell line   CBIL
   57. islet (islet of Langerhans)   GXD
   59. alpha cell   GXD
   60. beta cell   GXD
   321. cell line   CBIL
   61. parathyroid gland   GXD
   62. pineal gland   GXD
   63. pituitary gland   GXD
   64. adenohypophysis   GXD
   65. neurohypophysis (posterior lobe)   GXD
   66. thyroid gland   GXD
   324. cell line   CBIL
   67. haemolymphoid system   GXD
   68. blood   GXD
   285. cord blood   GRAYS
   75. erythrocyte (red blood cell)   GXD
   353. cell line   CBIL
   76. leukocyte (white blood cell)   GXD
   105. basophil (basophilic myelocyte)   GRAYS
   106. eosinophil (eosinophilic myelocyte)   GRAYS
   77. lymphoblast   GXD
   79. B-lymphoblast   GRAYS
   80. immature B-lymphocyte   GXD
   81. pre-B-lymphocyte   GXD
   322. cell line   CBIL
   82. pro-B-lymphocyte   GXD
   87. T-lymphoblast   GRAYS
   281. cell line   CBIL
   88. immature T-lymphocyte   GXD
   89. pre-T-lymphocyte   GXD
   90. pro-T-lymphocyte   GXD
   78. lymphocyte   GXD
   83. B-lymphocyte   GXD
   84. antibody secreting B-lymphocyte (large B-lymphocyte, plasma cell)   GXD
   308. cell line   CBIL
   275. cell line   CBIL
   85. memory B-lymphocyte   GXD
   86. plasma cell   GXD
   91. T-lymphocyte   GXD
   274. cell line   CBIL
   92. cytotoxic   GXD
   325. cell line   CBIL
   93. helper   GXD
   94. supressor   GXD
   95. natural killer cell   GXD
   97. mast cell   GXD
   102. monocyte   GXD
   286. dendritic cell   GRAYS
   96. macrophage   GRAYS
   311. cell line   CBIL
   107. neutrophil (neutrophilic myelocyte)   GRAYS
   108. polymorphonucleated neutrophil (PMN)   GRAYS
   211. bone marrow   GRAYS
   69. erythroblast   GRAYS
   70. basophilic erythroblast   GXD
   72. polychromatophilic erythroblast   GXD
   73. proerythroblast   GXD
   74. reticulocyte   GXD
   98. megakaryoblast   GRAYS
   99. megakaryocyte   GRAYS
   100. platelet (thrombocyte)   GXD
   109. myelocyte   GRAYS
   104. myeloblast   GRAYS
   282. promyelocyte   GRAYS
   283. cell line   CBIL
   71. normoblast   GRAYS
   103. premonocyte (promonocyte)   GRAYS
   351. cell line   CBIL
   101. monoblast   GRAYS
   110. stem cells   GRAYS
   111. hematopoietic stem cells (CD34,hemopoietic stem cells,haematopoietic stem cells,haemopoietic stem cell)   GXD
   288. lymphoid   GRAYS
   303. cell line   CBIL
   287. myeloid (CFU-GEMM)   GRAYS
   284. cell line   CBIL
   632. lineage-committed progenitor   CBIL
   628. mature blood cell   CBIL
   112. stromal cells   GXD
   316. cell line   CBIL
   113. lymph node   GXD
   114. spleen   GXD
   315. erythroblast   CBIL
   115. thymus   GXD
   297. tonsil   GRAYS
   116. integumental system   GXD
   117. gland   GXD
   118. mammary gland (breast)   GXD
   215. areola   GRAYS
   276. cell line   CBIL
   216. nipple   GRAYS
   119. skin gland   GXD
   120. apocrine gland   GXD
   121. mucous gland   GXD
   122. sebaceous gland   GXD
   123. sweat gland (eccrine sweat gland)   GXD
   124. skin   GXD
   125. dermis   GXD
   126. epidermis   GXD
   289. keratinocyte   GRAYS
   295. melanocyte   GRAYS
   354. cell line   CBIL
   127. hair and follicles   GXD
   128. nervous system   GXD
   129. central nervous system (CNS)   GXD
   130. brain (encephalon)   GXD
   131. prosencephalon (forebrain)   GXD
   132. diencephalon   GXD
   365. cavities   NISSANOV
   133. third ventricle   NISSANOV
   134. epithalamus   GXD
   401. habenular nuclei (LHb, MHb)   NISSANOV
   135. hypothalamus   GXD
   402. lateral zone   NISSANOV
   414. lateral hypothalamic area (LH)   NISSANOV
   413. lateral preoptic area (LPO)   NISSANOV
   404. medial zone   NISSANOV
   409. anterior region (AHA, RCh)   NISSANOV
   412. mammillary region (MM, LM, PM, SuM, VTA, PHA, TM)   NISSANOV
   410. preoptic region (MPA, MPO, AVPO, ADPO, PDPO)   NISSANOV
   411. tuberal region (TA, VMH, DMH, TU)   NISSANOV
   403. periventricular zone (Pe)   NISSANOV
   408. anterior region (PeA, SCh, Pa, SO)   NISSANOV
   405. mammillary region (PeP)   NISSANOV
   407. preoptic region (PePO, MnPO, AVPV, PSCh)   NISSANOV
   406. tuberal region (Pel, Arc)   NISSANOV
   250. subthalamus (ventral thalamus)   GRAYS
   251. subthalamic nucleus (STh)   NISSANOV
   136. thalamus   GXD
   400. anterior pole (AD, AV, AM, IAM, LD)   NISSANOV
   393. lateral geniculate body (LG)   NISSANOV
   398. medical and intralaminar nuclei (PT, PV, CM, Rh, Re)   NISSANOV
   394. medical geniculate body (MG)   NISSANOV
   399. middle section (MD, LD, VL, VP, VM, Po, CL, PC, PF)   NISSANOV
   395. posterior section (LG, MG, Po, LP, SG, Li, PIL, SPF)   NISSANOV
   396. reticular nucleus (Rt)   NISSANOV
   397. ventral nuclear complex (VA, VL)   NISSANOV
   137. telencephalon (cerebrum,cerebral hemisphere)   GXD
   356. basal ganglia   NISSANOV
   249. amygdala (amygdaloid body)   NISSANOV
   386. amygdalo-hippocampal area (AHi)   NISSANOV
   387. anterior amygdaloid area (AA)   NISSANOV
   392. basolateral complex (BL, BM, La)   NISSANOV
   390. bed nucleus of the stria terminalis (BST)   NISSANOV
   391. central nucleus (Ce)   NISSANOV
   389. corticomedial group (Me)   NISSANOV
   388. intercalated masses (I, IM)   NISSANOV
   385. nuclei of lateral and accessory olfactory tracts (LOT, BAOT)   NISSANOV
   357. pallidum   NISSANOV
   362. entopeduncular nucleus (EP)   NISSANOV
   359. globus pallidus (GP)   NISSANOV
   361. horizontal limb of the diagonal band of the Broca (HDB)   NISSANOV
   360. olfactory tubercle (Tu)   NISSANOV
   358. substantia innominata (SI)   NISSANOV
   139. striatum   NISSANOV
   252. caudate-putamen (CPu)   NISSANOV
   377. islands of calleja (ICj)   NISSANOV
   375. ventral striatum including the accumbens nucleus (Acb)   NISSANOV
   363. cavities   NISSANOV
   364. lateral ventricle   NISSANOV
   138. cerebral cortex (neopallium)   GXD
   255. frontal region (Fr1, Fr2, Fr3) (prefrontal cortex)   NISSANOV
   140. hippocampal region   NISSANOV
   376. entorhinal Cx (Ent)   NISSANOV
   378. hippocampus   NISSANOV
   588. CA-1   NISSANOV
   585. CA-2   NISSANOV
   587. CA-3   NISSANOV
   586. dentate   NISSANOV
   379. subiculum (S), presubiculum (PrS), parasubiculum (PaS)   NISSANOV
   257. occipital region (Oc1, Oc2MM, Oc2ML, Oc2L)   NISSANOV
   256. parietal region (Par1, Par2, FL, HL)   NISSANOV
   258. temporal region (Te1, Te2, Te3)   NISSANOV
   694. cingulate gyrus (cingulate cortex)   GRAYS
   141. olfactory bulb (OB)   NISSANOV
   253. white matter   NISSANOV
   254. corpus callosum   NISSANOV
   142. rhombencephalon (hindbrain)   NISSANOV
   148. mesencephalon (midbrain)   NISSANOV
   367. cavities   NISSANOV
   370. cerebral aqueduct (Aq)   NISSANOV
   368. crura cerebri   NISSANOV
   369. tectum   NISSANOV
   416. inferior colliculus (ECIC, CIC, DCIC)   NISSANOV
   415. superior colliculus (SC)   NISSANOV
   366. tegmentum   NISSANOV
   425. central gray (CGPN, CGA, CGB, CGG, PAG)   NISSANOV
   424. interpeduncular nucleus (IP, IPD, IPR)   NISSANOV
   417. nuclei related to the visual system   NISSANOV
   421. edinger-westphal nucleus (EW)   NISSANOV
   418. nucleus of darkschewitsch (Dk)   NISSANOV
   419. oculomoter nucleus (3)   NISSANOV
   422. parabigeminal nucleus (PBG)   NISSANOV
   420. trochlear nucleus (4)   NISSANOV
   427. raphe nuclei (RIP, RMg, Rob, RPa)   NISSANOV
   423. red nucleus (R, RMC, RPC)   NISSANOV
   426. substantia nigra and ventral tegmental area (SNC, SNR & VTA)   NISSANOV
   143. metencephalon   GXD
   371. cavities   NISSANOV
   372. fourth ventricle   NISSANOV
   144. cerebellum   GXD
   441. caudal group of cerebellar nuclei   NISSANOV
   444. medical (fastigial) cerebellar nucleus (Med)   NISSANOV
   443. posterior interposed nucleus (IntP, IntPPC)   NISSANOV
   442. rostral group of cerebellar nuclei   NISSANOV
   445. anterior interposed nucleus (IntA)   NISSANOV
   446. lateral cerebellar nucleus (Lat)   NISSANOV
   145. pons   GXD
   436. auditory relay nuclei   NISSANOV
   438. dorsal nucleus of the lateral lemniscus (DLL)   NISSANOV
   439. ventral nucleus of the lateral lemniscus (VLL)   NISSANOV
   435. gustatory relay nuclei   NISSANOV
   440. parabrachial nuclei (PB, PBW, PBP)   NISSANOV
   437. locus coeruleus (LC)   NISSANOV
   434. reticular formation and raphe pontis (Pn, PnR, PnC, PnO, PnV & RIP, RMg, Rob, RPa)   NISSANOV
   433. tegmental nuclei (DTg, DTgC, DTgP)   NISSANOV
   428. trigeminal complex   NISSANOV
   429. infratrigeminal nucleus   NISSANOV
   431. mesencephalic nucleus (Me5)   NISSANOV
   430. motor nucleus (Mo5)   NISSANOV
   432. principal sensory nucleus (Pr5, Pr5DM, Pr5VL)   NISSANOV
   146. myelencephalon   GXD
   147. medulla oblongata   GXD
   450. motor nuclei in the lower medulla   NISSANOV
   455. ambiguus nucleus (Amb)   NISSANOV
   457. dorsal motor nucleus of vagus (10)   NISSANOV
   456. hypoglossal nucleus (12)   NISSANOV
   449. motor nuclei in the upper medulla   NISSANOV
   454. abducens nucleus (6)   NISSANOV
   452. facial nucleus (7)   NISSANOV
   453. retrofacial nucleus   NISSANOV
   451. superior salivatory nucleus (SuS)   NISSANOV
   447. raphe complex and reticular formation   NISSANOV
   575. raphe complex:   NISSANOV
   578. raphe magnus nucleus (RMg)   NISSANOV
   577. raphe obscurus nucleus (Rob)   NISSANOV
   576. raphe pallidus nucleus (RPa)   NISSANOV
   579. reticular formation   NISSANOV
   589. gigantoreticular nucleus (Gi, GiA, GiV)   NISSANOV
   448. sensory relay nuclei   NISSANOV
   566. auditory complex:   NISSANOV
   567. cochlear nucleus (DC, VCA, VCP)   NISSANOV
   568. olive nuclei (IO, SPO)   NISSANOV
   569. trapezoid body (tz)   NISSANOV
   551. nucleus of the solitary tract (NTS)   NISSANOV
   548. somatosensory relay nuclei:   NISSANOV
   550. cuneate nucleus (Cu)   NISSANOV
   549. gracile nucleus (Gr)   NISSANOV
   523. trigeminal complex   NISSANOV
   525. intertrigeminal nucleus (I5)   NISSANOV
   590. mesencephalic nucleus (Me5)   NISSANOV
   528. paratrigeminal nucleus (Pa5)   NISSANOV
   524. principal sensory nucleus (Pr5)   NISSANOV
   527. spinal trigeminal nucleus (Sp5)   NISSANOV
   526. supratrigeminal nucleus (Su5)   NISSANOV
   529. trigeminal motor nucleus (Mo5)   NISSANOV
   559. vestibular complex:   NISSANOV
   564. inferior vestibular nucleus (InVe)   NISSANOV
   565. lateral vestibular nucleus (LVe)   NISSANOV
   560. medial vestibular nucleus (MVe)   NISSANOV
   562. prepositus hypoglossal nucleus (Pr)   NISSANOV
   561. superior vestibular nucleus (SuVe)   NISSANOV
   563. vestibulocerebellar nucleus (VeCb)   NISSANOV
   247. meninges   GRAYS
   248. dura mater   GRAYS
   260. neuroglia   GRAYS
   261. astrocytes   GRAYS
   350. cell line   CBIL
   268. ependymal cells (ependymocytes,neuroepithelium)   GRAYS
   263. glioblasts   GRAYS
   306. cell line   CBIL
   262. oligodendrocytes   GRAYS
   149. spinal cord   GXD
   373. cavities   NISSANOV
   374. central canal(CC)   NISSANOV
   236. nerve   GRAYS
   266. neuroblast   GRAYS
   267. cell line   CBIL
   265. neuron   GRAYS
   352. cell line   CBIL
   150. peripheral nervous system (PNS)   GXD
   264. Schwann cells (lemmocytes)   GRAYS
   695. ciliary ganglion   GRAYS
   319. dorsal root ganglion (spinal ganglia)   GRAYS
   151. sensory organ   GXD
   152. ear   GXD
   153. external ear   GXD
   154. inner ear   GXD
   155. middle ear (tympanic cavity)   GXD
   156. eye   GXD
   243. ciliary body (ocular ciliary body)   GRAYS
   246. cornea   GRAYS
   157. iris   GXD
   158. lens   GXD
   159. retina   GXD
   244. macula (macula lutea)   GRAYS
   245. fovea (fovea centralis,foveola)   GRAYS
   241. retinal pigment epithelium (RPE)   GRAYS
   242. cell line   CBIL
   160. nose   GXD
   302. olfactory epithelium   GRAYS
   161. visceral organ   GXD
   162. alimentary system   GXD
   163. intestine   GXD
   164. large intestine   GXD
   165. anal region (anus)   GXD
   166. caecum (cecum)   GXD
   167. apex of caecum (apex of cecum,appendix)   GXD
   168. colon   GXD
   169. ascending colon   GXD
   269. cell line   CBIL
   170. descending colon   GXD
   323. mucosa   GRAYS
   171. transverse colon   GXD
   172. rectum   GXD
   173. small intestine   GXD
   174. duodenum   GXD
   175. ileum   GXD
   176. jejunum   GXD
   177. oesophagus (esophagus)   GXD
   178. oral region (mouth)   GXD
   296. gingiva   GRAYS
   179. salivary gland   GXD
   272. cell line   CBIL
   220. parotid   GRAYS
   180. tooth   GXD
   181. incisor   GXD
   182. molar   GXD
   183. pharynx   GXD
   237. nasopharynx   GRAYS
   271. cell line   CBIL
   184. tongue   GXD
   698. tongue mucousa (tongue epidermis)   GRAYS
   185. stomach   GXD
   273. cell line   CBIL
   186. fundus   GXD
   187. pyloric antrum   GXD
   188. liver and biliary system   GXD
   219. bile duct   GRAYS
   189. gall bladder   GXD
   190. liver   GXD
   278. cell line (hepatoma)   CBIL
   657. hematopoietic stem cells (These cells are found in the fetal liver.)   CBIL
   318. hepatocyte   CBIL
   656. lineage-committed progenitor (These cells are found in the fetal liver.)   CBIL
   655. mature blood cell (These cells are found in the fetal liver.)   CBIL
   191. renal/urinary system   GXD
   192. bladder   GXD
   193. kidney   GXD
   225. ureter   GRAYS
   226. urethra   GRAYS
   194. reproductive system   GXD
   195. female   GXD
   196. ovary   GXD
   197. placenta   GXD
   198. decidua (decidua basalis,maternal placenta)   GXD
   693. umbilical cord   GRAYS
   199. unfertilized egg (oocyte,ovum,germ cell)   GXD
   227. uterine tube (fallopian tube)   GRAYS
   200. uterus   GXD
   201. cervix   GXD
   279. cell line (HeLa)   CBIL
   228. mucosa (endometrium)   GRAYS
   229. pregnant uterus   GRAYS
   230. vagina   GRAYS
   231. vulva   GRAYS
   304. germ cell   CBIL
   202. male   GXD
   203. epididymis   GXD
   232. penis   GRAYS
   291. foreskin (prepuce)   GRAYS
   233. prostate   GRAYS
   305. cell line   CBIL
   234. seminal vesicle   GRAYS
   235. sperm (germ cell)   GRAYS
   204. testis   GXD
   690. interstitial cell   GRAYS
   205. respiratory system   GXD
   206. larynx   GXD
   207. lung   GXD
   692. bronchial epithelial cell (epithelium of the intrapulmonary bronchi and bronchioles)   GRAYS
   270. cell line   CBIL
   307. fibroblast   CBIL
   309. cell line   CBIL
   239. pleura   GRAYS
   208. respiratory tract (bronchi)   GXD
   238. trachea   GRAYS
   310. fibroblast   CBIL
 293. peritoneum   GRAYS
   294. greater omentum   GRAYS
 209. skeleton (bone)   GXD
   210. bone   GXD
   212. osteoblast   GXD
   213. osteoclast   GXD
   214. osteocyte   GXD



Last updated: February 07, 2005.  
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