1.2 This is the factored (normalized) version of the biomaterial/bioimmaterial entity branches branch from the original BIRNLex OWL file. In that original file, BFO elements were either hard-coded into BIRNLex.owl or derived from the FuGO.owl file. The factoring process performed here now imports the IFOMIS BFO.owl file and derives its foundational classes directly from there. Christine Fennema-Notestine The BIRN Project lexicon will provide entities for data and database annotation for the BIRN project. This is the module containing definitions of all relevant biomaterial entities including organismal taxonomic entities and the neuroanatomical framework to be imported for use in the BIRNLex_main.owl. The neuroanatomical framework will eventually derive it's foundational layer from the Common Anatomy Reference Ontology (and the more specific Mouse Anatomy Reference Ontology), once these resources are available. This will also be submitted on it's own as a OBO Foundry candidate ontology. 2006-09-26 David Kennedy Added the LIGHT version of the OBO Relation ontology from IFOMIS/NCBO (BB: 2007-03-01). Duplicated all SKOS core:prefLabel Annotations as rdfs:label Annotations using a parsing script supplied by Trish Whetzel (UPenn/OBI community). This makes it possible to use rdfs:label as the DISPLAY_SLOT in Protege to match OBI and to use it to generate OWLDocs where both BIRNLex and OBI classes will use the same AnnotationProperty for their preferred display name (BB: 2007-02-27). 2007-03-02 Amarnath Gupta Jessica Turner Bill Bug 2006-10-08: Factored upper biomedical classes completely to the BIRN-OBO-OBU begun several weeks back. Maryann Martone Carol Bean The BIRN project lexicon. Jeff Grethe The BIRN Ontology Task Force BIRNLex Organism Anatomical Entity Lexicon limiting fissure 2006-10-05 C0228258 Circular_sulcus_of_insula 2006-10-05 circular sulcus (of Reil) circular fissure circuminsular sulcus marginal insular sulcus raw import ciruclar insular sulcus Circular_sulcus_of_insula Bill Bug NeuroNames C0228258 Transverse_pontine_fibers C0228446 NeuroNames raw import 2006-07-15 2006-10-07 615 Bill Bug C0228446 Transverse_pontine_fibers 68 Triangular_part_of_inferior_frontal_gyrus NeuroNames Bill Bug C0262350 Christine Fennema-Notestine 2006-10-08 Component of the inferior frontal gyrus.defined as the second gyrus from the precentral gyrus (Christine Fennema-Notestine). 2006-10-08 Triangular_part_of_inferior_frontal_gyrus graph position temporary C0262350 pars triangularis gyri frontalis inferioris Predominantly_white_regional_part_of_hippocampal_formation raw import NeuroNames Bill Bug Predominantly_white_regional_part_of_hippocampal_formation 2006-10-08 39 Frontal_operculum 2006-10-08 raw import NeuroNames Frontal_operculum Bill Bug C0149547 C0149547 NeuroNames ventral mediodorsal nucleus MDPL raw import mediodorsal thalamic nucleus, paralaminar part 2007-03-05 nucleus medialis dorsalis, pars paralaminaris paralaminar part of medial dorsal nucleus Paralaminar_part_of_medial_dorsal_nucleus C0228332 paralaminar part of dorsomedial nucleus nucleus medialis dorsalis thalami, pars multiformis 2007-03-05 Bill Bug Paralaminar_part_of_medial_dorsal_nucleus C0228332 296 nucleus medialis dorsalis, pars multiformis nucleus medialis dorsalis caudalis (Hassler) 2006-10-08 Posterior_spinocerebellar_tract raw import C0175560 2006-10-08 804 Posterior_spinocerebellar_tract C0175560 NeuroNames Bill Bug 2006-10-07 Collection of nerve cells in the medial forebrain lying generally in front of the anterior commissure (Maryann Martone). 2006-07-15 Allan MacKenzie-Graham pending final vetting Septal_nuclear_complex BFO includes a "snap:ObjectAggregate". That would probably be more appropriate for these sort of aggregate structures (BB). Maryann Martone C0036687 septal nuclei Septal_nuclear_complex C0036687 This is not the typical name used for this collection of septal nuclei. Typically the preferred term is simply "septal nuclei" but I'm trying to avoid plurals. This commonly used preferred term is included as a synonym. UMLS Commissure_of_superior_colliculus C0152366 Bill Bug 466 2006-07-15 NeuroNames 2006-10-07 Commissure_of_superior_colliculus raw import C0152366 Bill Bug Transgenic_mouse International Mouse Strain Resource Glossary Transgenic_mouse 2006-10-08 2006-10-08 "A mouse that contains stably inherited DNA which has been experimentally inserted at random into the genome. The inserted gene sequence (the transgene) may or may not be derived from mouse sequence." (http://www.informatics.jax.org/imsr/glossary.jsp) raw import 776 Bill Bug C0152394 2006-10-08 Juxtarestiform_body Juxtarestiform_body C0152394 NeuroNames 2006-10-08 raw import Bill Bug raw import nucleus septofibrialis Septofimbrial_nucleus 2006-10-04 Septofimbrial_nucleus scattered nucleus of the septum NeuroNames 2006-10-07 246 C0694603 C0694603 C0175256 raw import 2007-03-05 Subfascicular_nucleus SF NeuroNames Subfascicular_nucleus 2007-03-05 C0175256 Bill Bug 294 NeuroNames 2006-10-05 Bill Bug 262 Anterior_olfactory_nucleus C0175225 C0175225 2006-10-05 definition incomplete Anterior_olfactory_nucleus Predominantly_white_regional_part_of_superior_olivary_complex 2006-10-07 NeuroNames raw import Bill Bug 2006-07-15 Predominantly_white_regional_part_of_superior_olivary_complex Predominantly_gray_regional_part_of_midline_nuclear_group Predominantly_gray_regional_part_of_midline_nuclear_group Bill Bug 2007-03-03 raw import 2007-03-03 Bill Bug raw import 583 C0175445 NeuroNames 2006-07-15 2006-10-07 Lateral_parabrachial_nucleus C0175445 Lateral_parabrachial_nucleus Predominantly_gray_regional_part_of_transverse_frontopolar_gyri_complex Predominantly_gray_regional_part_of_transverse_frontopolar_gyri_complex 2006-10-08 human-only Bill Bug 2006-10-08 raw import NeuroNames C0025927 uncurated MeSH Bill Bug 2006-10-05 2006-10-05 Currently (2006-10-07), the children of this class have been made mutually disjoint. In reality, there may be some mixing amongst strains - e.g., some strains and substrains were derived from crosses of other inbred strains. Ultimately, the disjoint sets will need to be worked out very carefully, but this approximately is kept for now as it will likely do no harm and serve as a reminder that this issue may require more thorough review in the future. C0025927 Inbred_mouse_strain Inbred_mouse_strain Genetically identical individuals developed from brother and sister matings which have been carried out for twenty or more generations, or by parent x offspring matings carried out with certain restrictions. All animals within an inbred strain trace back to a common ancestor in the twentieth generation. BF_T0000097 Need to determine whether there might not be a more specific sub-region of the telencephalon where this entity might be more appropriately placed. If these cellular aggregates are telencephalic in toto, then it is appropriate they be listed as a Regional_part_of_telencephalon. Rostral_migratory_stream Bill Bug Unique telencephalic subventricular zones that extend from the lateral ventricles into the olfactory bulbs. Newly produced GABAergic interneurons migrate along the RMS and settle in the bulb. pending final vetting 2006-10-06 2006-07-15 Rob Williams Rostral_migratory_stream pending final vetting Regional_part_of_cerebral_white_matter Bill Bug Regional_part_of_cerebral_white_matter NeuroNames 2007-03-03 Habenulo-interpeduncular_tract_of_diencephalon Habenulo-interpeduncular_tract_of_diencephalon NeuroNames C0228391 C0228391 444 2007-03-03 Bill Bug raw import C3 raw import C0175384 Bill Bug 2006-10-07 Central_oculomotor_nucleus Central_oculomotor_nucleus NeuroNames 490 2006-07-15 C0175384 NeuroNames NeuroNames 2006-09-28 raw import 2006-07-15 Predominantly_white_regional_part_of_midbrain_tegmentum Predominantly_white_regional_part_of_midbrain_tegmentum BIRN OTF 2006-10-05 Bill Bug Maryann Martone Nucleus_accumbens made a region of the telencephalon based on NN (BB). 259 Nucleus_accumbens 2006-08-04 A region of the brain consisting of a collection of neurons located in the forebrain ventral to the caudate and putamen. (caudoputamen in rodent) and continuous with these structures. There is no distinct boundary between the nucleus accumbens and the caudate/putamen, but in rodents, it can be identified by its lack of traversing fiber bundles in comparison to the dorsal striatum. Its principle neuron is the medium spiny neuron. Together with the caudate and putamen, the nucleus accumbens forms the striatum. BF_T0000143 pending final vetting 2006-10-07 This class is not intended to present a normative, comprehensive, taxonomic hierarchy, but rather is provided as an approximate indication of the phylogenetic relatedness amongst the taxonomic groups nested under it (BB). raw import 9528 subfamily: Cercopithecinae C0085225 Cercopithecinae 2006-10-07 Bill Bug NCBI Taxonomy Cercopithecinae C0085225 nucleus habenulae lateralis Bill Bug lateral habenula NeuroNames 2007-03-03 278 LHb C0228390 339 NeuroNames Lateral_habenular_nucleus nucleus habenularis lateralis Lateral_habenular_nucleus 2007-03-03 C0228390 raw import nucleus habenularis lateralis epithalami Line Merriam-Websters Dictionary, online edition, 2006 Bill Bug Line 6 a (2) : a strain produced and maintained especially by selective breeding or biological culture 2006-10-05 2006-10-05 graph position temporary Habenula 2006-07-15 Bill Bug 2007-03-03 raw import Hb 277 C0152362 C0152362 habenular nucleus Habenula NeuroNames NeuroNames Predominantly_gray_regional_part_of_midbrain_tegmentum NeuroNames 2006-09-28 BIRN OTF 2006-07-15 Predominantly_gray_regional_part_of_midbrain_tegmentum raw import 572 C0228447 2006-07-15 raw import efferent cochlear bundle Olivocochlear_bundle Olivocochlear_bundle olivocochlear bundle of Rasmussen 2006-10-07 Bill Bug C0228447 raw import Cerebral_crus NeuroNames 530 2006-07-15 Cerebral_crus NeuroNames C0175414 2006-09-28 ccr Bill Bug C0175414 MeSH C0006121 brain stem 2006-10-07 pending final vetting Brainstem NeuroNames 218 The part of the brain that connects the cerebral hemispheres with the spinal cord. It consists of the Mesencephalon, Pons, and Medulla Oblongata (MeSH). C0006121 As this aggregate structure includes portions of the forebrain, the midbrain, and the hindbrain, it must be kept here at the base of the brain region hierarchy in order to avoid multiple inheritance (BB). The term brain stem refers to a composite substructure of the brain. It includes the midbrain, the pons and the medulla oblongata. Some authors include the cerebellum and/or parts of the diencephalon. A discussion of differences in the use of this term is presented in Anthoney-94 (NeuroNames). Brainstem 2006-07-15 Maryann Martone MeSH Bill Bug NeuroNames raw import 110 Transverse_temporal_sulcus C0228239 2006-10-05 C0228239 human-only 2006-10-08 Transverse_temporal_sulcus uncurated Regional_part_of_Parahippocampal_gyrus Bill Bug 2006-10-07 2006-10-07 Regional_part_of_Parahippocampal_gyrus 2006-10-05 2006-10-05 257 Basal_nucleus definition incomplete Bill Bug C0004788 Basal nucleus of Meynert (sensu human) NeuroNames Basal_nucleus Pontine_raphe_nucleus C0175423 2006-07-15 NeuroNames 584 Bill Bug Pontine_raphe_nucleus raw import C0175423 2006-10-07 nuclei laterales thalami lateral nuclear group Lateral_nuclear_group 2007-03-03 2007-03-05 308 nucleus lateralis thalami LNG Lateral_nuclear_group lateral nucleus of thalamus lateral group of the dorsal thalamus Maryann Martone NeuroNames Bill Bug lateral thalamic nucleus raw import Substrain Bill Bug graph position temporary 2006-10-05 2006-10-05 Substrain 2006-07-15 Predominantly_gray_regional_part_of_basal_part_of_pons 2006-10-07 raw import NeuroNames Predominantly_gray_regional_part_of_basal_part_of_pons BIRN OTF C0034910 496 Red_nucleus 2006-07-15 2006-10-07 BIRN OTF Red_nucleus C0034910 raw import NeuroNames NeuroNames R 598 raw import Dorsal_acoustic_stria C0175454 C0175454 2006-07-15 NeuroNames Dorsal_acoustic_stria 2006-10-07 486 C0175379 Medial_oculomotor_nucleus raw import M3 C0175379 Bill Bug NeuroNames 2006-07-15 NeuroNames Medial_oculomotor_nucleus 2006-10-07 2006-10-11 uncurated Regional_part_of_inferior_olivary_complex Regional_part_of_inferior_olivary_complex Bill Bug 2006-10-11 nucleus lateropolaris magnocellularis (Hassler) magnocellular ventral anterior nucleus C0228335 ventral anterior thalamic nucleus, magnocellular part 2007-03-04 ventral anterior nucleus, magnocellular part nucleus lateropolaris (magnocellularis) 319 2007-03-04 VAMC nucleus ventralis anterior, pars magnocellularis NeuroNames Magnocellular_part_of_ventral_anterior_nucleus C0228335 nucleus thalamicus ventral anterior, pars magnocellularis Magnocellular_part_of_ventral_anterior_nucleus nucleus rostralis lateralis situs perifascicularis ventroanterior thalamic nucleus, magnocellular part Bill Bug raw import 736 2006-10-07 Bill Bug 2006-10-07 C0175515 Nucleus_raphe_magnus NeuroNames raphe magnus nucleus raw import C0175515 Nucleus_raphe_magnus C0228271 raw import 592 2006-07-15 NeuroNames C0228271 Uncinate_fasciculus 2006-10-07 Uncinate_fasciculus 2006-10-04 raw import Bill Bug Regional_part_of_limbic_lobe NeuroNames Regional_part_of_limbic_lobe 2006-10-07 order: Primate 2006-10-05 Primate uncurated Primate 9443 This class is not intended to present a normative, comprehensive, taxonomic hierarchy, but rather is provided as an approximate indication of the phylogenetic relatedness amongst the taxonomic groups nested under it (BB). C0033147 Primate 2006-10-05 C0033147 order: Primata NCBI Taxonomy Bill Bug graph position temporary Regional_part_of_cingulate_cortex Bill Bug 2006-10-08 Regional_part_of_cingulate_cortex 2006-10-08 C0175431 raw import 2006-07-15 568 NeuroNames Preolivary_nucleus Bill Bug C0175431 Preolivary_nucleus 2006-10-07 Rob Williams Maryann Martone 000664 Bill Bug JAX-mouse-stock 2006-10-07 pending final vetting C57BL6J 2006-10-05 C57BL/6J The C57BL/6 substrain of laboratory mouse bred by the Jackson Laboratory. From Jackson: Inbr (J) 150. Origin: substrains 6 and 10 were separated prior to 1937. This substrain is now probably the most widely used of all inbred strains. Substrain 6 and 10 differ at the H9, Igh2 and Lv loci. Maint. by J,N, Ola. \par (http://www.informatics.jax.org/external/festing/mouse/docs/C57BL.shtml) C57BL/6J BF_T0000259 Regional_part_of_diencephalon 2006-07-15 Regional_part_of_diencephalon 2006-10-07 Bill Bug pending final vetting NeuroNames raw import NeuroNames 2006-10-07 Bill Bug Predominantly_white_regional_part_of_septum_pellucidum Predominantly_white_regional_part_of_septum_pellucidum 2006-10-05 2006-10-09 Inferior_cerebellar_peduncle Inferior_cerebellar_peduncle uncurated 2006-10-09 Bill Bug 2006-07-15 BIRN OTF Regional_part_of_peripheral_nervous_system uncurated Regional_part_of_peripheral_nervous_system 2006-09-28 Maryann Martone NeuroNames 1007150190 Regional part of superior cerebellar peduncle, located in the dorsal pons, consisting of a large bundle of fibers largely projecting from the deep cerebellar nuclei to the midbrain and thalamus (MM). Superior_cerebellar_peduncle_of_pons 2006-10-07 pending final vetting 2006-07-15 Bill Bug Superior_cerebellar_peduncle_of_pons Predominantly_gray_regional_part_of_lateral_geniculate_body Bill Bug Predominantly_gray_regional_part_of_lateral_geniculate_body 2007-03-05 2007-03-05 raw import NCBI Taxonomy Cercopithecidae family: Cercopithecidae C0007752 This class is not intended to present a normative, comprehensive, taxonomic hierarchy, but rather is provided as an approximate indication of the phylogenetic relatedness amongst the taxonomic groups nested under it (BB). Cercopithecidae raw import 2006-10-07 Bill Bug monkeys C0007752 monkey 2006-10-07 Old World monkeys (Genbank common name) 9527 The use of this term is not consistent between Morph and Mouse BIRN or with NeuroNames UMLS Hippocampus A part of the brain consisting of a three layered cortex located in the forebrain bordering the medial surface of the lateral ventricle. The term hippocampus is often used synonymously with hippocampal formation which consists of the hippocampus proper or Cornu Ammonis, the dentate gyrus and the subiculum. C0019564 2006-10-07 Hippocampus Maryann Martone definition incomplete C0019564 Made a Regional_part_of_hippocampal_formation. Not certain what to do to reconcile this class with Hippocampus_proper. Should hippocampus be a synonym of Hippocampus_proper? This doesn't seem like a good idea, since this won't always fit the use of the term. Many will use the term hippocampus when referring exclusively to hippocampus_proper or to some combination of the hippocampus_proper, dentate gyrus, and subiculum the latter combination being defined here as Hippocampal_formation. Need to determine whether definition of hippocampus should be contained under hippocampal formation; reconcile with UCLA's definition Maryann Martone 2006-07-15 2006-10-07 Bill Bug Glires Rodents and rabbits (Genbank common name) NCBI Taxonomy 314147 Glires 2006-10-07 This class is not intended to present a normative, comprehensive, taxonomic hierarchy, but rather is provided as an approximate indication of the phylogenetic relatedness amongst the taxonomic groups nested under it (BB). raw import NeuroNames 512 Ventral_tegmental_area 2006-10-07 NeuroNames VTA Bill Bug raw import 2006-07-15 C0175405 C0175405 Ventral_tegmental_area Inferior_olivary_complex 2006-10-07 C0228540 Bill Bug NeuroNames raw import Inferior_olivary_complex 2006-10-07 745 C0228540 DTg NeuroNames 2006-07-15 2006-10-07 C0175393 C0175393 Bill Bug NeuroNames raw import Dorsal_tegmental_nucleus Dorsal_tegmental_nucleus 508 Part of ventricular system of brain consisting of a narrow channel in the midbrain connecting the third and fourth ventricles. (Maryann Martone) uncurated Maryann Martone 2006-07-15 UMLS C0007769 aqueduct of Sylvius 2006-09-28 Cerebral_aqueduct Allan MacKenzie-Graham Cerebral_aqueduct An inbred strain that is kept in forced heterozygosity for one or more loci. For example, the SM/J strain segregates for an agouti allele and animals are either Aw/a (white bellied agouti) or a/a (black) in color. (http://www.informatics.jax.org/imsr/glossary.jsp) Segregating_inbred_strain International Mouse Strain Resource Glossary 2006-10-08 2006-10-08 Segregating_inbred_strain raw import Bill Bug Central_gray_substance_of_midbrain 2006-10-07 Bill Bug raw import NeuroNames periaqueductal gray Griseum centrale Central_gray_substance_of_midbrain C0228398 periaqueductal gray matter C0228398 NeuroNames 501 Substantia grisea centralis 2006-07-15 CGMB 2006-10-08 graph position temporary Posterior_cingulate_cortex Posterior_cingulate_cortex Component of the cingulate cortex. The rostral and caudal extent were the caudal anterior and the isthmus divisions of the cingulate cortex respectively. The medial and lateral boundaries were the corpus callosum and as the superior frontal gyrus and/or paracentral lobule respectively (Christine Fennema-Notestine). 2006-10-08 Christine Fennema-Notestine 2006-07-15 Central_gray_substance_of_pons 2006-09-28 Central_gray_substance_of_pons 2006-10-08 NeuroNames 2006-10-08 Predominantly_white_regional_part_of_diencephalon raw import Bill Bug Predominantly_white_regional_part_of_diencephalon Oral_pontine_reticular_nucleus 2006-07-15 2006-09-28 Oral_pontine_reticular_nucleus Fronto-orbital_sulcus NeuroNames raw import C0262240 2006-10-08 C0262240 Bill Bug 2006-10-08 Fronto-orbital_sulcus 59 raw import C0228427 NeuroNames 612 Basal_part_of_pons Basal_part_of_pons C0228427 2006-07-15 2006-10-07 Bill Bug Peripeduncular_nucleus Bill Bug NeuroNames raw import 511 Peripeduncular_nucleus NeuroNames C0152368 PPd C0152368 2006-07-15 2006-10-07 Inferior_frontal_gyrus C0152298 Bill Bug C0152298 Inferior_frontal_gyrus 67 2006-10-08 2006-10-08 NeuroNames graph position temporary Component of the frontal lobe, lateral aspect. The rostral boundary is the first appearance of the inferior frontal sulcus whereas the caudal boundary is the precentral gyrus. The medial and lateral boundaries are the lateral bank of the inferior frontal sulcus and the medial bank of the lateral orbital sulcus and/or the circular insular sulcus respectively (Christein Fennema-Notestine). Maryann Martone MeSH C0206428 One of the two photoreceptor cell types in the vertebrate retina. In cones the photopigment is in invaginations of the cell membrane of the outer segment. Cones are less sensitive to light than rods, but they provide vision with higher spatial and temporal acuity, and the combination of signals from cones with different pigments allows color vision. Cone_cell Cone_cell 2006-09-28 rod MeSH raw import 2006-07-15 2006-10-11 pending final vetting This class is required to create a consistent grouping of body system parts. Regional_part_of_nervous_system Bill Bug 2006-10-11 Regional_part_of_nervous_system 790 Glossopharyngeal_nerve_fiber_bundle NeuroNames central part of glossopharyngeal nerve 2006-10-08 C0175550 NeuroNames uses the preferred term "glossopharyngeal nerve fibers", but I'm trying to avoid plurals. NN preferred term included as a synonym. 2006-10-08 raw import C0175550 Bill Bug glossopharyngeal nerve fibers ninth cranial nerve fibers Glossopharyngeal_nerve_fiber_bundle NeuroNames 2006-10-07 C0175401 Bill Bug RPC Parvocellular_part_of_red_nucleus C0175401 2006-07-15 Parvocellular_part_of_red_nucleus 497 raw import NeuroNames 2006-07-15 2006-10-10 Regional_part_of_superior_olivary_complex BIRN OTF NeuroNames Regional_part_of_superior_olivary_complex uncurated NeuroNames 2006-10-08