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Add remaining nifstd classes #632

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cmungall opened this Issue Dec 21, 2014 · 5 comments

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cmungall commented Dec 21, 2014

Plan:

  1. add all remaining nifstd classes from nifga lacking equivalence axioms
  2. add logical defs for regional parts (trivial)
  3. gradually replace all uses of regional part with unfolded expression
  4. gradually obsolete all regional part classes classes
  5. obsolete anything derived from nifstd which has been deleted from neurolex

cc @twhetzel

@cmungall cmungall added the neuro label Dec 21, 2014

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cmungall commented Dec 21, 2014

Note: we will make a supplemental file to the bridge file

This will be all obsolete classes with links to 'equivalent' in external ontology

Thus eventually, when regional-part-of-X terms in uberon are obsolete, they will vanish from the bridge (we never record logical axioms for obsolete classes), but there will still be a mapping

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twhetzel commented Dec 22, 2014

Related to (5) "obsolete anything derived from nifstd which has been deleted from neurolex", have you checked with folks that manage Neurolex as there may be some things inadvertently deleted or broken redirects in Neurolex?

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cmungall commented Dec 22, 2014

As part of this task, we should standardize on using NIFSTD as the obo prefix for all NIFSTD/NIFGA vocabs

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cmungall commented Dec 22, 2014

I will obsolete the following classes. (1) they are no longer present in nlx, apparently (2) they are 'regional part of' type terms that convey no useful info.

Note that due to problems with nlx, it's possible that my query for (1) may have false positives. However, as the pages have been manually checked for whether they are potentially useful, there is no problem with obsoleting them.

UBERON:0002635 ! regional part of midbrain tegmentum == NIFSTD:birnlex_1227
UBERON:0002554 ! regional part of superior colliculus == NIFSTD:birnlex_1014
UBERON:0002574 ! regional part of inferior olivary complex == NIFSTD:birnlex_1052
UBERON:0002579 ! regional part of medullary reticular formation == NIFSTD:birnlex_1060
UBERON:0002584 ! regional part of vestibular nuclear complex == NIFSTD:birnlex_1080
UBERON:0002619 ! regional part of cerebral cortex == NIFSTD:birnlex_1173
UBERON:0002621 ! regional part of cochlear nuclear complex == NIFSTD:birnlex_1195
UBERON:0002677 ! regional part of medullary raphe nuclear complex == NIFSTD:birnlex_1349
UBERON:0002678 ! regional part of medulla oblongata == NIFSTD:birnlex_1355
UBERON:0002680 ! regional part of metencephalon == NIFSTD:birnlex_1361
UBERON:0002757 ! regional part of epithalamus == NIFSTD:birnlex_1607
UBERON:0002780 ! regional part of forebrain == NIFSTD:birnlex_1677
UBERON:0002784 ! regional part of diencephalon == NIFSTD:birnlex_1685
UBERON:0002785 ! regional part of lateral hypothalamic region == NIFSTD:birnlex_1687
UBERON:0002789 ! regional part of posterior hypothalamic region == NIFSTD:birnlex_1697
UBERON:0002791 ! regional part of telencephalon == NIFSTD:birnlex_1700
UBERON:0002917 ! regional part of inferior colliculus == NIFSTD:birnlex_4036
UBERON:0002950 ! regional part of midbrain == NIFSTD:birnlex_763
UBERON:0002951 ! regional part of intermediate hypothalamic region == NIFSTD:birnlex_767
UBERON:0002966 ! regional part of midbrain tectum == NIFSTD:birnlex_795
UBERON:0003047 ! regional part of pretectal region == NIFSTD:birnlex_993
UBERON:0003048 ! regional part of hypothalamus == NIFSTD:birnlex_995
UBERON:0022480 ! predominantly gray regional part of pretectal region == NIFSTD:birnlex_1003
UBERON:0022543 ! regional part of solitary nucleus == NIFSTD:birnlex_1068
UBERON:0022598 ! regional part of peripheral nervous system == NIFSTD:birnlex_1122
UBERON:0022647 ! predominantly gray regional part of epithalamus == NIFSTD:birnlex_1174
UBERON:0022650 ! regional part of parietal lobe == NIFSTD:birnlex_1177
UBERON:0022660 ! regional part of occipital lobe == NIFSTD:birnlex_1188
UBERON:0022665 ! predominantly gray regional part of lateral hypothalamic region == NIFSTD:birnlex_1193
UBERON:0022681 ! regional part of cerebral peduncle == NIFSTD:birnlex_1209
UBERON:0022701 ! predominantly gray regional part of posterior hypothalamic region == NIFSTD:birnlex_1229
UBERON:0022732 ! superficial feature part of midbrain tectum == NIFSTD:birnlex_1260
UBERON:0022741 ! regional part of central nervous system == NIFSTD:birnlex_1269
UBERON:0022761 ! superficial feature part of intermediate hypothalamic region == NIFSTD:birnlex_1289
UBERON:0022778 ! regional part of medial mammillary nucleus == NIFSTD:birnlex_1306
UBERON:0022822 ! superficial feature part of diencephalon == NIFSTD:birnlex_1351
UBERON:0022828 ! predominantly gray regional part of medullary raphe nuclear complex == NIFSTD:birnlex_1357
UBERON:0022877 ! regional part of oculomotor nuclear complex == NIFSTD:birnlex_1405
UBERON:0022890 ! regional part of red nucleus == NIFSTD:birnlex_1418
UBERON:0022895 ! regional part of habenula == NIFSTD:birnlex_1423
UBERON:0022937 ! predominantly gray regional part of midbrain tegmentum == NIFSTD:birnlex_1465
UBERON:0022944 ! predominantly white regional part of midbrain tegmentum == NIFSTD:birnlex_1472
UBERON:0022957 ! regional part of midbrain reticular formation == NIFSTD:birnlex_1485
UBERON:0022988 ! regional part of thalamus == NIFSTD:birnlex_1517
UBERON:0022997 ! superficial feature part of medulla oblongata == NIFSTD:birnlex_1526
UBERON:0023007 ! predominantly white regional part of posterior hypothalamic region == NIFSTD:birnlex_1536
UBERON:0023013 ! superficial feature part of posterior hypothalamic region == NIFSTD:birnlex_1542
UBERON:0023020 ! predominantly white regional part of septum pellucidum == NIFSTD:birnlex_1549
UBERON:0023044 ! regional part of cerebral white matter == NIFSTD:birnlex_1573
UBERON:0023047 ! regional part of hypophysis == NIFSTD:birnlex_1576
UBERON:0023092 ! predominantly white regional part of epithalamus == NIFSTD:birnlex_1620
UBERON:0023097 ! regional part of temporal lobe == NIFSTD:birnlex_1625
UBERON:0023102 ! predominantly gray regional part of intermediate hypothalamic region == NIFSTD:birnlex_1630
UBERON:0023127 ! predominantly gray regional part of hypothalamus == NIFSTD:birnlex_1656
UBERON:0023163 ! regional part of septum == NIFSTD:birnlex_1693
UBERON:0023294 ! cytoarchitectural part of cerebral cortex == NIFSTD:birnlex_2546
UBERON:0023317 ! regional part of ventral cochlear nucleus == NIFSTD:birnlex_2570
UBERON:0023362 ! predominantly gray part of medulla oblongata == NIFSTD:birnlex_2633
UBERON:0023547 ! regional part of stratum pyramidale hippocampi == NIFSTD:birnlex_4109
UBERON:0023552 ! regional part of stratum oriens == NIFSTD:birnlex_4114
UBERON:0023556 ! regional part of stratum radiatum == NIFSTD:birnlex_4118
UBERON:0023560 ! regional part of stratum lacunosum moleculare == NIFSTD:birnlex_4122
UBERON:0023572 ! regional part of basal nuclear complex == NIFSTD:birnlex_702
UBERON:0023587 ! predominantly gray regional part of inferior colliculus == NIFSTD:birnlex_718
UBERON:0023628 ! regional part of anterior hypothalamic region == NIFSTD:birnlex_761
UBERON:0023636 ! regional part of pons == NIFSTD:birnlex_771
UBERON:0023648 ! regional part of granular layer of cerebellar cortex == NIFSTD:birnlex_784
UBERON:0023649 ! predominantly white regional part of hypothalamus == NIFSTD:birnlex_785
UBERON:0023670 ! predominantly white regional part of tectum == NIFSTD:birnlex_808
UBERON:0023677 ! predominantly gray regional part of tectum == NIFSTD:birnlex_815
UBERON:0023687 ! regional part of septal nuclear complex == NIFSTD:birnlex_825
UBERON:0023695 ! superficial feature part of telencephalon == NIFSTD:birnlex_833
UBERON:0023703 ! regional part of fornix == NIFSTD:birnlex_842
UBERON:0023783 ! gross anatomical part of cerebral cortex == NIFSTD:birnlex_940
UBERON:0023789 ! regional part of limbic lobe == NIFSTD:birnlex_947
UBERON:0023791 ! regional part of hindbrain == NIFSTD:birnlex_949
UBERON:0023824 ! regional part of frontal lobe == NIFSTD:birnlex_984
UBERON:0023825 ! predominantly white regional part of inferior colliculus == NIFSTD:birnlex_985
UBERON:0023827 ! cytoarchitectural part of the cerebellum == NIFSTD:birnlex_987
UBERON:0023915 ! regional part of nose == NIFSTD:nlx_anat_100305
UBERON:0024065 ! regional part of spinal nerve == NIFSTD:nlx_anat_20090206
UBERON:0024073 ! regional part of nucleus accumbens == NIFSTD:nlx_anat_20090305
UBERON:0024081 ! regional part of stratum lucidum == NIFSTD:nlx_anat_20090401
UBERON:0024086 ! cytoarchitectural part of dorsal tegmental nucleus == NIFSTD:nlx_anat_20090406
UBERON:0024125 ! regional part of adenohypophysis == NIFSTD:birnlex_1004
UBERON:0024161 ! regional part of pontine tegmentum == NIFSTD:birnlex_1041
UBERON:0024173 ! regional part of inner ear == NIFSTD:birnlex_1053
UBERON:0024182 ! superficial feature part of cerebral cortex == NIFSTD:birnlex_1063
UBERON:0024211 ! predominantly white regional part of cerebellar cortex == NIFSTD:birnlex_1092
UBERON:0024234 ! regional part of deep cerebellar nuclear complex == NIFSTD:birnlex_1114
UBERON:0024254 ! regional part of autonomic nervous system == NIFSTD:birnlex_1134
UBERON:0024285 ! regional part of basal part of pons == NIFSTD:birnlex_1168
UBERON:0024326 ! predominantly gray regional part of anterior hypothalamic region == NIFSTD:birnlex_1210
UBERON:0024329 ! predominantly white regional part of cerebral peduncle == NIFSTD:birnlex_1213
UBERON:0024335 ! predominantly white regional part of anterior hypothalamic region == NIFSTD:birnlex_1219
UBERON:0024347 ! regional part of orbital gyri complex == NIFSTD:birnlex_1231
UBERON:0024381 ! regional part of transverse frontopolar gyri complex == NIFSTD:birnlex_1265
UBERON:0024394 ! regional part of Parahippocampal gyrus == NIFSTD:birnlex_1278
UBERON:0024397 ! regional part of tuberomammillary nucleus == NIFSTD:birnlex_1281
UBERON:0024437 ! predominantly gray regional part of medial mammillary nucleus == NIFSTD:birnlex_1322
UBERON:0024439 ! superficial feature part of frontal lobe == NIFSTD:birnlex_1324
UBERON:0024479 ! regional part of inferior parietal cortex == NIFSTD:birnlex_1364
UBERON:0024518 ! regional part of neuraxis cavity == NIFSTD:birnlex_1402
UBERON:0024524 ! predominantly gray regional part of midbrain reticular formation == NIFSTD:birnlex_1408
UBERON:0024528 ! predominantly gray regional part of oculomotor nuclear complex == NIFSTD:birnlex_1412
UBERON:0024541 ! predominantly gray regional part of red nucleus == NIFSTD:birnlex_1425
UBERON:0024550 ! predominantly white regional part of red nucleus == NIFSTD:birnlex_1434
UBERON:0024559 ! predominantly gray regional part of habenula == NIFSTD:birnlex_1443
UBERON:0024622 ! predominantly gray regional part of basal nuclear complex == NIFSTD:birnlex_1507
UBERON:0024653 ! superficial feature part of temporal lobe == NIFSTD:birnlex_1538
UBERON:0024708 ! superficial feature part of hypophysis == NIFSTD:birnlex_1593
UBERON:0024714 ! regional part of cingulate gyrus == NIFSTD:birnlex_1599
UBERON:0024721 ! regional part of outer ear == NIFSTD:birnlex_1605
UBERON:0024793 ! predominantly gray regional part of thalamus == NIFSTD:birnlex_1679
UBERON:0024800 ! predominantly white regional part of thalamus == NIFSTD:birnlex_1686
UBERON:0024826 ! regional part of middle ear == NIFSTD:birnlex_1713
UBERON:0024828 ! regional part of Preoptic area == NIFSTD:birnlex_1715
UBERON:0024962 ! predominantly gray part of ventral cochlear nucleus == NIFSTD:birnlex_2571
UBERON:0025033 ! predominantly gray part of solitary nucleus == NIFSTD:birnlex_2660
UBERON:0025067 ! regional part of corticomedial nuclear complex == NIFSTD:birnlex_2697
UBERON:0025078 ! regional part of olfactory cortex == NIFSTD:birnlex_2708
UBERON:0025128 ! regional part of longitudinal fissure == NIFSTD:birnlex_4046
UBERON:0025147 ! cytoarchitectural part of occipital lobe == NIFSTD:birnlex_4065
UBERON:0025148 ! cytoarchitectural part of frontal lobe == NIFSTD:birnlex_4066
UBERON:0025250 ! predominantly white regional part of fornix == NIFSTD:birnlex_738
UBERON:0025254 ! regional part of anterior commissure == NIFSTD:birnlex_742
UBERON:0025268 ! regional part of hippocampal formation == NIFSTD:birnlex_757
UBERON:0025284 ! regional part of substantia nigra == NIFSTD:birnlex_775
UBERON:0025327 ! regional part of inferior frontal gyrus == NIFSTD:birnlex_821
UBERON:0025338 ! predominantly gray regional part of septal nuclear complex == NIFSTD:birnlex_832
UBERON:0025409 ! regional part of neurohypophysis == NIFSTD:birnlex_921
UBERON:0025418 ! regional part of cingulate cortex == NIFSTD:birnlex_930
UBERON:0025744 ! regional part of dorsal cochlear nucleus == NIFSTD:nlx_anat_20090510
UBERON:0025764 ! predominantly gray regional part of adenohypophysis == NIFSTD:birnlex_1013
UBERON:0025778 ! predominantly white regional part of basal part of pons == NIFSTD:birnlex_1027
UBERON:0025811 ! predominantly gray regional part of pontine tegmentum == NIFSTD:birnlex_1061
UBERON:0025827 ! regional part of pontine reticular formation == NIFSTD:birnlex_1077
UBERON:0025828 ! regional part of superior olivary complex == NIFSTD:birnlex_1078
UBERON:0025848 ! regional part of anterior nucleus of hypothalamus == NIFSTD:birnlex_1098
UBERON:0025897 ! regional part of dentate gyrus == NIFSTD:birnlex_1147
UBERON:0025899 ! predominantly white regional part of hippocampal formation == NIFSTD:birnlex_1149
UBERON:0025927 ! regional part of enteric nervous system == NIFSTD:birnlex_1179
UBERON:0025928 ! predominantly gray regional part of basal part of pons == NIFSTD:birnlex_1180
UBERON:0025930 ! regional part of dentate nucleus == NIFSTD:birnlex_1182
UBERON:0025934 ! regional part of hippocampus proper == NIFSTD:birnlex_1186
UBERON:0025983 ! predominantly gray regional part of orbital gyri complex == NIFSTD:birnlex_1236
UBERON:0025993 ! predominantly gray medial regional part of thalamus == NIFSTD:birnlex_1246
UBERON:0026000 ! regional part of cerebral ventricular cavity == NIFSTD:birnlex_1253
UBERON:0026001 ! regional part of median eminence == NIFSTD:birnlex_1254
UBERON:0026020 ! predominantly gray regional part of transverse frontopolar gyri complex == NIFSTD:birnlex_1273
UBERON:0026032 ! predominantly gray regional part of Parahippocampal gyrus == NIFSTD:birnlex_1285
UBERON:0026040 ! predominantly gray dorsal regional part of thalamus == NIFSTD:birnlex_1293
UBERON:0026048 ! predominantly white dorsal regional part of thalamus == NIFSTD:birnlex_1301
UBERON:0026063 ! regional part of middle frontal gyrus == NIFSTD:birnlex_1317
UBERON:0026079 ! regional part of suprachiasmatic nucleus == NIFSTD:birnlex_1333
UBERON:0026106 ! superficial feature part of cerebral peduncle == NIFSTD:birnlex_1360
UBERON:0026113 ! regional part of neostriatum == NIFSTD:birnlex_1367
UBERON:0026117 ! predominantly Gray regional part of inferior parietal cortex == NIFSTD:birnlex_1371
UBERON:0026153 ! regional part of paraventricular nucleus of hypothalamus == NIFSTD:birnlex_1406
UBERON:0026270 ! predominantly gray anterior regional part of thalamus == NIFSTD:birnlex_1524
UBERON:0026296 ! predominantly gray regional part of cingulate gyrus == NIFSTD:birnlex_1550
UBERON:0026324 ! regional part of transverse temporal cortex == NIFSTD:birnlex_1578
UBERON:0026445 ! predominantly gray ventral regional part of thalamus == NIFSTD:birnlex_1701
UBERON:0026456 ! predominantly gray posterior regional part of thalamus == NIFSTD:birnlex_1712
UBERON:0026536 ! regional part of cochlea == NIFSTD:birnlex_1794
UBERON:0026588 ! regional part of cochlear duct == NIFSTD:birnlex_2565
UBERON:0026686 ! regional part of basolateral nuclear complex == NIFSTD:birnlex_2685
UBERON:0026700 ! predominantly gray part of corticomedial nuclear complex == NIFSTD:birnlex_2699
UBERON:0026720 ! regional part of posterior superior frontal sulcus == NIFSTD:birnlex_4007
UBERON:0026762 ! regional part of calcarine sulcus == NIFSTD:birnlex_4049
UBERON:0026845 ! predominantly gray regional part of Preoptic area == NIFSTD:birnlex_700
UBERON:0026921 ! predominantly gray regional part of substantia nigra == NIFSTD:birnlex_782
UBERON:0026966 ! predominantly gray regional part of inferior frontal gyrus == NIFSTD:birnlex_829
UBERON:0026975 ! predominantly white regional part of anterior commissure == NIFSTD:birnlex_839
UBERON:0026982 ! predominantly gray midline regional part of thalamus == NIFSTD:birnlex_849
UBERON:0026986 ! regional part of superior temporal sulcus == NIFSTD:birnlex_856
UBERON:0027052 ! predominantly gray regional part of neurohypophysis == NIFSTD:birnlex_933
UBERON:0027076 ! regional part of Anterior cingulate cortex == NIFSTD:birnlex_960
UBERON:0027078 ! predominantly gray intralaminal regional part of thalamus == NIFSTD:birnlex_962
UBERON:0027094 ! regional part of cerebellar peduncular complex == NIFSTD:birnlex_979
UBERON:0027103 ! predominantly gray lateral regional part of thalamus == NIFSTD:birnlex_988
UBERON:0027227 ! cytoarchitectural part of retina == NIFSTD:nlx_anat_1005029
UBERON:0027243 ! matrix part of body of caudate nucleus == NIFSTD:nlx_anat_1010003
UBERON:0027247 ! striosomal part of tail of caudate nucleus == NIFSTD:nlx_anat_1010007
UBERON:0027352 ! regional part of supraoptic nucleus == NIFSTD:nlx_anat_20090309
UBERON:0027376 ! cytoarchitectural part of dorsal cochlear nucleus == NIFSTD:nlx_anat_20090511
UBERON:0027417 ! predominantly gray regional part of dentate nucleus == NIFSTD:birnlex_1034
UBERON:0027453 ! predominantly gray regional part of pontine reticular formation == NIFSTD:birnlex_1071
UBERON:0027563 ! predominantly gray regional part of dentate gyrus == NIFSTD:birnlex_1183
UBERON:0027584 ! regional part of caudate nucleus == NIFSTD:birnlex_1205
UBERON:0027600 ! predominantly gray regional part of neostriatum == NIFSTD:birnlex_1221
UBERON:0027603 ! regional part of globus pallidus == NIFSTD:birnlex_1224
UBERON:0027604 ! predominantly gray regional part of ventral nuclear group == NIFSTD:birnlex_1225
UBERON:0027631 ! predominantly gray regional part of medial dorsal nucleus == NIFSTD:birnlex_1252
UBERON:0027649 ! regional part of lateral ventricle == NIFSTD:birnlex_1270
UBERON:0027651 ! predominantly gray regional part of median eminence == NIFSTD:birnlex_1272
UBERON:0027665 ! predominantly gray regional part of metathalamus == NIFSTD:birnlex_1286
UBERON:0027687 ! predominantly white dorsal regional part of metathalamus == NIFSTD:birnlex_1308
UBERON:0027728 ! predominantly gray regional part of anterior nuclear group == NIFSTD:birnlex_1350
UBERON:0027748 ! predominantly gray regional part of superior olivary complex == NIFSTD:birnlex_1370
UBERON:0027755 ! predominantly white regional part of superior olivary complex == NIFSTD:birnlex_1377
UBERON:0027758 ! regional part of paraventricular nucleus of hypothalamus magnocellular division == NIFSTD:birnlex_1380
UBERON:0027760 ! regional part of superior olive == NIFSTD:birnlex_1382
UBERON:0027814 ! regional part of paraventricular nucleus of hypothalamus descending division == NIFSTD:birnlex_1435
UBERON:0027828 ! predominantly gray regional part of hippocampal formation == NIFSTD:birnlex_1449
UBERON:0028192 ! regional part of spiral organ of Corti == NIFSTD:birnlex_2530
UBERON:0028314 ! predominantly gray regional part of amygdala == NIFSTD:birnlex_2681
UBERON:0028317 ! predominantly gray part of basolateral nuclear complex == NIFSTD:birnlex_2684
UBERON:0028326 ! regional part of basal amygdaloid nucleus == NIFSTD:birnlex_2693
UBERON:0028337 ! regional part of entorhinal cortex == NIFSTD:birnlex_2704
UBERON:0028544 ! predominantly gray part of posterior nuclear complex == NIFSTD:birnlex_772
UBERON:0028615 ! predominantly gray part of Intralaminar nuclear group == NIFSTD:birnlex_852
UBERON:0028616 ! predominantly gray regional part of midline nuclear group == NIFSTD:birnlex_854
UBERON:0028725 ! regional part of substantia nigra pars reticulata == NIFSTD:birnlex_978
UBERON:0028744 ! predominantly gray regional part of lateral nuclear group == NIFSTD:birnlex_997
UBERON:0029140 ! predominantly gray regional part of ventral lateral nucleus == NIFSTD:birnlex_1124
UBERON:0029215 ! predominantly white dorsal regional part of medial geniculate body == NIFSTD:birnlex_1203
UBERON:0029396 ! predominantly gray regional part of superior olive == NIFSTD:birnlex_1385
UBERON:0029415 ! regional part of paraventricular nucleus of hypothalamus magnocellular division - posterior magnocellular part == NIFSTD:birnlex_1403
UBERON:0029594 ! predominantly gray regional part of lateral geniculate body == NIFSTD:birnlex_1583
UBERON:0029603 ! predominantly gray regional part of medial geniculate body == NIFSTD:birnlex_1592
UBERON:0029629 ! predominantly white regional part of globus pallidus == NIFSTD:birnlex_1617
UBERON:0029681 ! predominantly gray regional part of ventral posterior nucleus == NIFSTD:birnlex_1671
UBERON:0029822 ! regional part of basilar membrane == NIFSTD:birnlex_2527
UBERON:0029861 ! regional part of trapezoid nuclear complex == NIFSTD:birnlex_2574
UBERON:0029954 ! regional part of lateral amygdaloid nucleus == NIFSTD:birnlex_2688
UBERON:0029960 ! predominantly gray part of basal amygdaloid nucleus == NIFSTD:birnlex_2694
UBERON:0030119 ! predominantly gray regional part of ventral anterior nucleus == NIFSTD:birnlex_709
UBERON:0030242 ! predominantly gray regional part of pulvinar == NIFSTD:birnlex_841
UBERON:0030330 ! predominantly gray part of rostral intralaminar nuclei == NIFSTD:birnlex_948
UBERON:0031196 ! predominantly gray regional part of globus pallidus == NIFSTD:birnlex_1545
UBERON:0031314 ! predominantly gray regional part of ventral posterolateral nucleus == NIFSTD:birnlex_1664
UBERON:0031948 ! predominantly gray regional part of ventral posteromedial nucleus == NIFSTD:birnlex_924

cmungall added a commit that referenced this issue Dec 22, 2014

Performed mass obsoletion on a subset of the regional-part-of-X terms
The majority of these never saw the light of day in an actual release,
but some have been in uberon a while.

The criteria for obsoletion were (1) the class was no longer
there in the rdf dump or neurolex and (2) the class was a non-informational
regional-part type class

See issue #632
@cmungall

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cmungall added a commit that referenced this issue Jan 2, 2015

This release encompasses multiple imrpovements in the representation
of the nervous system. Many wikipedia-sourced definitions have been
replaced with definitions from neurolex ([632](#632)). We have defined and
implemented a design pattern for cranial and spinal nerves, ganglia
and nuclei ([634](#634)). We made improvements to the mapping to Allen
ontologies. Additionally, we now use the numeric identifiers for all
Allen classes, rather than acronyms. Please note that the "ABA" prefix
has been superseded by "MBA" (mouse brain atlas), to be consistent
with the others (HBA, PBA, DMBA, DHBA). New terms were added from the
HarvardOxford Cortical atlas based on work by Russ Poldrack and Trish
Whetzel ([630](#630)).

This release also ensures that every class from NIF_GrossAnatomy (but
not its successor, neurolex) is represented in Uberon. Note that not
all classes will be in the bridge file. Many of the region-part-of-X
classes are present in Uberon as obsolete classes.
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