Added the LIGHT version of the OBO Relation ontology from IFOMIS/NCBO at http://www.ifomis.org/obo/ro/1.0/light. (BB: 2007-03-01). OBO-RO LIGHT version no longer available from IFOMIS/NCBO at http://www.ifomis.org/obo/ro/1.0/light. Switched to Chris M's OWL version of OBO-RO at http://www.berkeleybop.org/ontologies/obo-all/relationship/relationship.owl. Need to look at using Chris M's OBO-RO to BFO bridge as well (BB: 2007-05-07). Christine Fennema-Notestine Jessica Turner Bill Bug v1.3.2 (2007-10-08) - switched to importing BIRNLex_annoation_properties.owl so would have access to _birnlex_retired_class ID use: 1 - 25 en 2008-03-22 Jeff Grethe Added the is_bearer_of ObjectProperty - inverse of inheres_in property used to link PATO dependent_continuants to independent_continuants. is_bearer_of enables one to represent the link from independen_continuant to dependent_continuant. David Kennedy (BB:2008-03-22) - Added a molecule and biomolecule class. The former was added to classify entities that are ChEBI derived, but are not of biomaterial origin. The latter was for those that are of biomaterial origin. Also shifted macromolecule and macromolecular complex to be childre of biomolecule. v1.2.2 (2007-03-19): Since Protege-OWL automatically sets new class identifiers to rdf:ID, but SOME of the classes appear to have been setup using rdf:about, I'm changing these across the files, to help make it more deterministic when parsing the RDF/XML. Upper Biomedical Ontology (BIRN proposal) The BIRN project lexicon next ID: birnlex_25 Amarnath Gupta 2006-09-07 Carol Bean The BIRN Ontology Task Force Maryann Martone 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). 1.3.2 This is a proposed upper biomedial ontology derived by examples from the Biodynamic Ontology, the Simple Upper Bio Ontology, the Ontology of Biomedical Reality, and the Foundational Model of Anatomy. It is designed to be a very slim layer intervening between the Basic Formal Ontology (BFO) and the generic, domain, and application ontologies developed to formally represent entities relevant to biomedical research and clinical practice. The intension is for their to be a shared layer for all of these ontologies to use to declares a biological context from which they can all derive required classes thereby making the equivalent foundational entities 100% algorithmically commensurate across all of these ontological artifacts. At this date (2006-10-06), this is just a proposal meant for: review by the community of OBO Foundry-associated biomedical ontology developers; very sparse and preliminary with the bulk of the coverage in the domain of biomaterial and immaterial objects; immediate use by the BIRN Ontology Task Force with the expectation this normalized layer will expedite future integration/import of the upper level biomedical ontology eventually adopted and endorsed by the OBO Foundry participant ontology development community members. v1.3.0 (2007-08-03) - Changed many things, but primarily: (1) removed rdf:datatype xsd:string specs for all AnnotationProperties, since they are now all untyped and should assume STRING as a the default; (2) added the typing of AnnotationProperties using annotationType which should aid in algorithmically processing; (3) Removed all underscore characters from the prefLabel field, and since the rdfs:labels are regenerated in the cleanser from prefLabel, they too are now free of underscores; (4) Also updated the XSLT BIRNLex cleanser to clean up more Protege mangling and provide a fixed order for certain properties. This last tool is brittle, as it probably will require continued maintenance to handle more complex OWL constructs than we know have in the file - especially highly nested constructs using class axioms. This is likely to be replaced soon by some combination of BioTop (http://www.ifomis.uni-saarland.de/biotop/), the Simple Upper Bio Ontology (http://www.cs.man.ac.uk/~rector/ontologies/simple-top-bio/), OBO-UBO from NCBO, and the contents of this current file (BB: 2007-02-27). Arachnoid membrane Arachnoid mater FMAID: 9591 Arachnoid membrane Arachnoid http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#nlx_anat_090208 true February 24, 2009 One of two leptomeningeal membranes covering the brain and spinal cord. The arachnoid membrane lies under the dura mater and above the pial membrane. It closely hugs the outside surface of the brain in many places, but does not extend into sulci in gyrencephalic species. http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#nlx_anat_090204 February 24, 2009 Meninx Meninx true FMAID: 9589 Meninges One of three membranous coverings that surrounds the brain and spinal cord Meninges is not technally a synonym but the plural form; however, it is more commonly used than "meninx" http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#nlx_anat_090202 Nolte, J., The Human Brain 3rd edition true Endoneurium February 24, 2009 The loose connective tissue within the perineurium that continues into nerve fascicles and surrounds individual fibers. (Nolte, J. The Human Brain 3rd edition) Endoneurium Dura Mater February 24, 2009 Dura http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#nlx_anat_090206 true Pachymeninges Thick, fibrous meningeal covering surrounding the brain and spinal cord. It is the outermost of the three meningeal coverings. It consists of two layers: the periosteal dura linking the inner surface of the skull and the meningeal dura that lies above the arachnoid dural membrane. The meningeal layer draws away from the periosteal layer and certain locations to form the dural reflections. Dura Mater Bill Bug Organism Organismal_object This part of the graph will need to adjust as organism taxonomy is handled more consistently by the biomedical-ontology community _6 2006-10-09 insect macaque monkey 2006-09-07 Organism vascular plant procaryote A biomaterial object capable of reproduction and harvesting energy from some biomaterial source in order to sustain its existance. glutaraldehyde Bill Bug http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#birnlex_21 2008-03-21 Saponin true Molecule Molecule 2008-03-21 An object consisting of a set of bonded atoms that is not of organismal origin. Sample population http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#birnlex_13 A defined subset of a population whose spatio-temporal interactions or aggregate behavior is representative of the whole population. Bill Bug Sample population 2006-09-07 true 2006-10-09 Supracellular structure Bill Bug Node of Ranvier Anatomical structure consisting of an identifable arrangement of multiple cellular structures into a functional unit. true 2006-10-09 2006-09-07 neuropil Supracellular structure http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_3 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_11 peripheral nervous system arterial vasculature Regional part of body system Regional part of body system Bill Bug true 2006-09-07 2006-10-09 mitochondrion mouse Biomaterial object hemoglobin molecule 2006-09-07 heart The entity descriptions in this branch of the ontology are informed by previous efforts in biomedical ontology development, particularly the Foundational Model of Anatomy, Biodynamic ontology, and the Ontology of Biomedical Reality, though they do not necessary recapitulate the principles defined there verbatim. true Biomaterial object erythrocyte head 2006-10-09 An object constituting a biological organism either in whole or in part, or one derived from a biological organism. Bill Bug Bill Bug 2006-09-07 sulcal invaginations of the mammalian brain. anterior compartment of right arm apex of right lung http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_9 Bio physical immaterial entity true body space Physical entity of biological origin which is a three-dimensional space, surface, line or point associated with a biomaterial object. 2006-10-09 surface of heart Bio physical immaterial entity third ventricle of the mammalian brain. http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#birnlex_15 Macromolecule 2008-03-22 2006-09-07 _5.2_6 Bill Bug true Macromolecule A macromolecule consisting exclusively of a single covalently bound array of naturally occuring amino acids. Peptide http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBO-UBO.owl#birnlex_23 2008-03-22 somatostatin http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#nifext_5000 Peptide Bill Bug insulin 2008-03-22 true vasopressin Protein A macromolecule consisting primarily of a single covalently bound array of naturally occuring amino acids. http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBO-UBO.owl#birnlex_15 2008-03-22 Bill Bug Protein insulin This class hes been retired. 2008-03-22 true http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao26622963 Bill Bug 2006-09-07 Regional part of body antenna head true leg 2006-10-09 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_7 Regional part of body 2008-03-22 true February 18, 2009 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#birnlex_22 An object consisting of a set of bonded atoms that is of organismal origin. insulin Bill Bug voltage-gated Ca++ ion channel Biomolecule Biomolecule This class has been retired. February 24, 2009 Pia Pial membrane http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#nlx_anat_090209 true Pia mater The innermost layer of the leptomeninges, consisting of a delicate membrane closely covering the surface of the brain and spinal cord,and lying under the arachnoid membrane. The pia, unlike the arachnoid, extends into the sulci in gyrencephalic animals. Pial membrane February 24, 2009 Epineurium A loose connective tissue sheath surrounding each peripheral nerve. Composed mainly of colagen and fibroblasts, it forms a substantial covering over nerve trunks, then thins to an incomplete layer around smaller branches near their terminations. The epineurium is continuous centrally with the dura. Peripherally, it usually ends near the termination of a nerve fiber, but it may continue as the capsule of Meissner corpuscles and a few other encapsulated endings. Nolte, J. The Human Brain 3rd edition http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#nlx_anat_090203 Nolte, J., The Human Brain 3rd edition Epineurium true true neuronal nicotinic Acetylcholine receptor Macromolecular complex A large, multi-molecular biological aggregate held together by van der Waals, hydrophobic, and hydrophilic interactions. Such complexes have a myriad of interactions with other cellular constituents with help to situate them within the cell - e.g., with the periphery of the phospholipid bilayer, penetrating some or all of the bilayer, interactions with intra- or extracellular fibrous matrices, and finally with other macromolecular complexes. Conformational changes in one molecular constituent of a complex frequently caused by covalent modification will tend to high non-local effects on the over conformation and energy profile of all the constituents in the complex. 2006-09-07 Macromolecular complex 16S ribosomal complex http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Molecule.owl#birnlex_1 2008-03-22 Bill Bug axonal Na+-K+ ATPase transporter Nolte, J., The Human Brain 3rd edition true Perineurium February 24, 2009 Perineurium A layer of thin, concentrically arranged cells with interspersed collagen that lies within the epineurium. (Nolte, J., The Human Brain 3rd edition) http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#nlx_anat_090205 2006-10-09 true http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#birnlex_10 2006-09-07 Bill Bug http://ccdb.ucsd.edu/NIF/OBO_annotation_properties.owl#UMLS Constitutional part of cell cytoskeletal system post-synaptic density Constitutional part of cell http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#nlx_anat_090207 true Leptomeninges February 24, 2009 FMAID: 231515 Leptomeninx Leptomeninx Leptomeninges is technically not a synonym but a plural form. However, it is more commonly used that the singular form. Delicate meningeal covering of the brain and spinal cord, consisting of an outer arachnoid membrane that sits beneath the dura and an inner pial membrane that lies on the surface of the brain and spinal cord. 2007-10-18 2007-10-18 true Bodily fluid Bodily fluid Bill Bug http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_20 2006-10-09 Biomaterial object constituting the structural organization of a biological organism or an attribute of that organization. Bill Bug _5.2 Constitutional part of organismal object http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_6 voltage-dependent ion-channel head cell 2006-09-07 Constitutional part of organismal object glucose-6-phosphate heart A biomaterial object constituting a part of a complete organismal object. true anatomical_object This class has been retired insect tracheolar network http://ccdb.ucsd.edu/NIF/OBO_annotation_properties.owl#FMA 2006-09-07 true nervous system 2006-10-09 Bill Bug http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_14 Body system Body system liver Organ Manduca sexta prothoracic gland Organ tracheobronchial tree bicep skeletal muscle vertebrate femur http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_4 ovary http://ccdb.ucsd.edu/NIF/OBO_annotation_properties.owl#FMA heart 2006-09-07 Bill Bug true Anatomical structure, which consists of the maximal set of organ parts so connected to one another that together they constitute a unit of macroscopic anatomy, structurally distinct from other such units. skin 2006-10-09 coral snake venom sac true Tissue http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_19 2007-10-10 Tissue Bill Bug 2007-10-10 _1_3.3 stomatal guard cell Cell 2007-10-09 sao1813327414 Cell oocyte true 2006-09-07 hepatocyte http://ccdb.ucsd.edu/NIF/OBO_annotation_properties.owl#OBR Bill Bug Mauthner cell http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBO-UBO.owl#birnlex_6 true Body membrane http://ontology.neuinfo.org/NIF/Backend/BIRNLex-OBO-UBO.owl#birnlex_5 Body membrane February 24, 2009 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#nlx_anat_090201 Not sure this is the correct designation; FMA has "membranous organ" but that doesn't seem quite right either. Part of body that takes the form of a thin sheet of cells or fibrous material, e.g., the meningeal coverings of the brain. cardiac ventricle 2006-09-07 regional part of brain true 2006-10-09 Regional part of organ http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_16 ommatidium of insect eye Bill Bug Regional part of organ Protein complex Protein complex true A macromolecule consisting primarily of a multiple covalently bound arrays of naturally occuring amino acids where the individual proteins are typically bound together through ionic and hydrogen bond interactions. Bill Bug 2008-03-22 2008-03-22 This class has been retired. voltage-gated Na++ ion channel _5.2_1 http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-GrossAnatomy.owl#birnlex_18 Body 2007-10-08 Body 2007-10-08 true Bill Bug 2006-10-09 This class has been retired. Population Population http://ontology.neuinfo.org/NIF/BiomaterialEntities/NIF-Subcellular.owl#sao2254405550 2006-09-07 A collection of independent organismal entities engaged in some form of spatio-temporal interaction or aggregate behavior Bill Bug true Bill Bug Makes it possible for an independent_continuant to represent its relation to a dependent_continuant, such as a PATO quality, a bfo:disposition, or a bfo:function. 2007-10-02 2007-10-02 is_bearer_of is_bearer_of