relationship cjm This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi <p>This ontology contains logical relations to be shared across the different OBO ontologies. Each OBO ontology is free to extend this set with relations specific to the biology within that ontology</p><div class="notes"><p>In the definitions, variables c, d, ..., p, q, ... range over instances of continuants and processes respectively. C, D, ..., P, Q, ... range over the corresponding classes</p><p> For a discussion of instance-level relations and also of additional axioms needed to infer transitivity and other properties of the relations listed above see <a href="http://genomebiology.com/2005/6/5/R46">http://genomebiology.com/2005/6/5/R46</a> or the OBO relations page hosted at <a href="http://obo.sourceforge.net/relationship">http://obo.sourceforge.net/relationship</a></div> cvs version $Revision: 1.5 $ release version 1.01 relationship editor preferred term The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> editor preferred term example A phrase describing how a class name should be used. May also include other kinds of examples that facilitate immediate understanding of a class semantics, such as widely known prototypical subclasses or instances of the class. Although essential for high level terms, examples for low level terms (e.g., Affymetrix HU133 array) are not PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> example of usage OBI_0000281 has curation status definition The official OBI definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions. PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition definition editor note An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology. PERSON:Daniel Schober GROUP:OBI:<http://purl.obfoundry.org/obo/obi> editor note definition editor Name of editor entering the definition in the file. The definition editor is a point of contact for information regarding the term. The definition editor may be, but is not always, the author of the definition, which may have been worked upon by several people PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition editor definition editor alternative term An alternative name for a class or property which means the same thing as the preferred name (semantically equivalent) PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> alternative term definition source formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007 PERSON:Daniel Schober GROUP:OBI:<http://purl.obolibrary.org/obo/obi> definition source definition source curator note imported from For external terms/classes, the ontology from which the term was imported GROUP:OBI:<http://purl.obolibrary.org/obo/obi> imported from ObsoleteProperty ObsoleteProperties ObsoletePropertied adjacent_to adjacents_to adjacented_to OBO_REL:0000012 relationship Note that adjacent_to as thus defined is not a symmetric relation, in contrast to its instance-level counterpart. For it can be the case that Cs are in general such as to be adjacent to instances of C1 while no analogous statement holds for C1s in general in relation to instances of C. Examples are: nuclear membrane adjacent_to cytoplasm; seminal vesicle adjacent_to urinary bladder; ovary adjacent_to parietal pelvic peritoneum adjacent_to agent_in agents_in agented_in OBO_REL:0000022 relationship agent_in contained_in containeds_in containeded_in OBO_REL:0000010 relationship Containment obtains in each case between material and immaterial continuants, for instance: lung contained_in thoracic cavity; bladder contained_in pelvic cavity. Hence containment is not a transitive relation. If c part_of c1 at t then we have also, by our definition and by the axioms of mereology applied to spatial regions, c located_in c1 at t. Thus, many examples of instance-level location relations for continuants are in fact cases of instance-level parthood. For material continuants location and parthood coincide. Containment is location not involving parthood, and arises only where some immaterial continuant is involved. To understand this relation, we first define overlap for continuants as follows: c1 overlap c2 at t =def for some c, c part_of c1 at t and c part_of c2 at t. The containment relation on the instance level can then be defined (see definition): contained_in contains containses containsed OBO_REL:0000011 relationship contains derived_into deriveds_into deriveded_into OBO_REL:0000016 relationship derived_into derives_from deriveses_from derivesed_from OBO_REL:0000015 relationship Derivation as a relation between instances. The temporal relation of derivation is more complex. Transformation, on the instance level, is just the relation of identity: each adult is identical to some child existing at some earlier time. Derivation on the instance-level is a relation holding between non-identicals. More precisely, it holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. Thus we will have axioms to the effect that from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t. We will also be able to infer that the spatial region occupied by c as it begins to exist at t overlaps with the spatial region occupied by c1 as it ceases to exist in the same instant. derives_from has_agent has_agents has_agented OBO_REL:0000021 relationship has_agent has_improper_part has_improper_parts has_improper_parted OBO_REL:0000024 relationship See reasons for obsoletion of improper_part_of has_improper_part has_integral_part has_integral_parts has_integral_parted OBO_REL:0000005 relationship has_integral_part has_part has_parts has_parted OBO_REL:0000003 relationship has_part has_participant has_participants has_participanted OBO_REL:0000019 relationship Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant has_proper_part has_proper_parts has_proper_parted OBO_REL:0000007 relationship has_proper_part improper_part_of improper_part_ofs improper_part_ofed OBO_REL:0000025 relationship OBSOLETE. The definition is "As for part_of, with the additional constraint that subject and object may be identical". However, part_of is already reflexive, therefore improper_part_of is identical to part_of. If read differently, as "improper_part_of is part_of but not proper_part_of",improper_part_of becomes identity. So, improper_part_of is either identical to part_of or to identity, and not an intuitive synonym for either of them. [Robert Hoehndorf] improper_part_of inheres_in inhereses_in inheresed_in integral_part_of integral_part_ofs integral_part_ofed OBO_REL:0000004 relationship integral_part_of located_in locateds_in locateded_in OBO_REL:0000008 relationship Location as a relation between instances: The primitive instance-level relation c located_in r at t reflects the fact that each continuant is at any given time associated with exactly one spatial region, namely its exact location. Following we can use this relation to define a further instance-level location relation - not between a continuant and the region which it exactly occupies, but rather between one continuant and another. c is located in c1, in this sense, whenever the spatial region occupied by c is part_of the spatial region occupied by c1. Note that this relation comprehends both the relation of exact location between one continuant and another which obtains when r and r1 are identical (for example, when a portion of fluid exactly fills a cavity), as well as those sorts of inexact location relations which obtain, for example, between brain and head or between ovum and uterus located_in location_of location_ofs location_ofed OBO_REL:0000009 relationship location_of part_of part_ofs part_ofed There is controversy about this relation intended to represent the relation between some arbitrary physical thing that is used as a represention/proxy/pointer to something else OBO_REL:0000002 relationship Parthood as a relation between instances: The primitive instance-level relation p part_of p1 is illustrated in assertions such as: this instance of rhodopsin mediated phototransduction part_of this instance of visual perception. This relation satisfies at least the following standard axioms of mereology: reflexivity (for all p, p part_of p); anti-symmetry (for all p, p1, if p part_of p1 and p1 part_of p then p and p1 are identical); and transitivity (for all p, p1, p2, if p part_of p1 and p1 part_of p2, then p part_of p2). Analogous axioms hold also for parthood as a relation between spatial regions. For parthood as a relation between continuants, these axioms need to be modified to take account of the incorporation of a temporal argument. Thus for example the axiom of transitivity for continuants will assert that if c part_of c1 at t and c1 part_of c2 at t, then also c part_of c2 at t. Parthood as a relation between classes: To define part_of as a relation between classes we again need to distinguish the two cases of continuants and processes, even though the explicit reference to instants of time now falls away. For continuants, we have C part_of C1 if and only if any instance of C at any time is an instance-level part of some instance of C1 at that time, as for example in: cell nucleus part_ of cell. part_of participates_in participateses_in participatesed_in OBO_REL:0000020 relationship participates_in proper_part_of proper_part_ofs proper_part_ofed OBO_REL:0000006 relationship proper_part_of relationship relationships relationshiped relationship this relation was superfluous, so it has been obsoleted relationship transformation_of transformation_ofs transformation_ofed OBO_REL:0000013 relationship When an embryonic oenocyte (a type of insect cell) is transformed into a larval oenocyte, one and the same continuant entity preserves its identity while instantiating distinct classes at distinct times. The class-level relation transformation_of obtains between continuant classes C and C1 wherever each instance of the class C is such as to have existed at some earlier time as an instance of the distinct class C1 (see Figure 2 in paper). This relation is illustrated first of all at the molecular level of granularity by the relation between mature RNA and the pre-RNA from which it is processed, or between (UV-induced) thymine-dimer and thymine dinucleotide. At coarser levels of granularity it is illustrated by the transformations involved in the creation of red blood cells, for example, from reticulocyte to erythrocyte, and by processes of development, for example, from larva to pupa, or from (post-gastrular) embryo to fetus or from child to adult. It is also manifest in pathological transformations, for example, of normal colon into carcinomatous colon. In each such case, one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes. transformation_of transformed_into transformeds_into transformeded_into OBO_REL:0000014 relationship Obsoleted transformed_into Anterior-Lateral_Extensions Anterior-Lateral_Extension anterior-lateral extension Anterior_Extensions Anterior_Extension anterior extension Inferior-Laterals Inferior-Lateral inferior-lateral extension Inferior-Medial_Extensions Inferior-Medial_Extension inferior-medial extension Inferior_Extensions Inferior_Extension inferior extension Lateral_Extensions Lateral_Extension lateral extension Medial_Extensions Medial_Extension medial extension Posterior-Inferior_Extensions Posterior-Inferior_Extension posterior-inferior extension Posterior-Medial_Extensions Posterior-Medial_Extension posterior-medial extension Posterior_Extensions Posterior_Extension posterior extension Superior-Lateral_Extensions Superior-Lateral_Extension superior-lateral extension Superior-Medial-Alveolars Superior-Medial-Alveolar superior-medial-alveolar extension Superior_Extensions Superior_Extension superior extension alcohols alcohol alcohol alveolar_resections alveolar_resection alveolar resection anterolateral_tigh_flaps anterolateral_tigh_flap anterolateral tigh flap arterial_anastomosis_flaps arterial_anastomosis_flap arterial anastomosis flap auricle_resections auricle_resection auricle resection cervicofacial_flaps cervicofacial_flap cervicofacial flap cervicoperctoral_flaps cervicoperctoral_flap cervicopectoral flap cheek_resections cheek_resection cheek resection chemotherapies chemotherapy chemotherapy clinical_reoccurrence_predictions clinical_reoccurrence_prediction clinical reoccurrence prediction cordectomies cordectomy cordectomy corticotomies corticotomy corticotomy deglutition_evaluations deglutition_evaluation deglutition evaluation dental_cuspses dental_cusps dental cusps diet_deficits diet_deficit diet deficit distant_pedicled_flaps distant_pedicled_flap distant pedicled flap eating_habitses eating_habits eating habits external_carotid_artery_flaps external_carotid_artery_flap external carotid artery flap external_lugular_vein_flaps external_lugular_vein_flap external lugular vein flap external_vestibular_corticotomies external_vestibular_corticotomy external vestibular corticotomy facial_artery_flaps facial_artery_flap facial artery flap facial_bone_resections facial_bone_resection facial bone resection facial_nerve_flaps facial_nerve_flap facial nerve flap facial_nerve_resections facial_nerve_resection facial nerve resection family_malignance_histories family_malignance_history family malignance history fibula_flaps fibula_flap fibula flap forearm_flaps forearm_flap forearm flap free_flaps free_flap free flap full_thickness_resections full_thickness_resection full thickness resection galvanic_currents galvanic_current galvanic current 1 gene_ontology_terms gene_ontology_term A term from the Gene Ontology gene ontology term 1 List of the genes associated to a gene ontology term, as result of enrichment analysis. gene ontology term gene list gene_ontology_term_lists gene_ontology_term_list A list of terms from the Gene Ontology, as result from the enrichment analysis. gene ontology term list genomic_reoccurrence_predictions genomic_reoccurrence_prediction genomic reoccurrence prediction glossectomies glossectomy glossectomy Gene list used to feed the Gorilla enrichment tool. gorilla input gene list hard_palate_resections hard_palate_resection hard palate resection hemiglossectomies hemiglossectomy hemiglossectomy hemimandibulectomies hemimandibulectomy hemimandibulectomy hemimaxilectomies hemimaxilectomy hemimaxilectomy horizontal_supracricoid_laryngectomies horizontal_supracricoid_laryngectomy horizontal supracricoid laryngectomy horizontal_supraglottic_laryngectomies horizontal_supraglottic_laryngectomy horizontal supraglottic laryingectomy hypogloss_flaps hypogloss_flap hypogloss flap illiac_crest_flaps illiac_crest_flap illiac flap imaging_reoccurrence_predictions imaging_reoccurrence_prediction imaging reoccurrence prediction immunosupressor_tratments immunosupressor_tratment immunosupressor treatment immunotherapies immunotherapy immunotherapy infections infection infection internal_lingual_corticotomies internal_lingual_corticotomy internal lingual corticotomy internal_lugular_vein_flaps internal_lugular_vein_flap internal lugular vein flap ionizing_radiations ionizing_radiation ionizing radiation laryngeal_nerve_resections laryngeal_nerve_resection laryngeal nerve resection laryngectomies laryngectomy laryngectomy latissimus_dorsii_flaps latissimus_dorsii_flap latissimus dorsii flap lingual_artery_flaps lingual_artery_flap lingual artery flap lingual_nerve_flaps lingual_nerve_flap lingual nerve flap lip_resections lip_resection lip resection local_flaps local_flap local flap locoregional_flaps locoregional_flap locoregional flap lymph_node_bilateral_stations lymph_node_bilateral_station lymph_node_bone_infiltrations lymph_node_bone_infiltration lymph_node_carotid_infiltrations lymph_node_carotid_infiltration lymph_node_clinical_datas lymph_node_clinical_data lymph node clinical data lymph_node_clusters lymph_node_cluster lymph_node_consistences lymph_node_consistence lymph_node_contralateral_stations lymph_node_contralateral_station lymph_node_contrast_take_up_rates lymph_node_contrast_take_up_rate lymph_node_cutaneous_invasions lymph_node_cutaneous_invasion lymph_node_depths lymph_node_depth lymph_node_dimensions lymph_node_dimension lymph_node_extra_capsular_spreadings lymph_node_extra_capsular_spreading lymph_node_extra_spreadings lymph_node_extra_spreading 1 lymph_node_findings lymph_node_finding lymph node finding lymph_node_forms lymph_node_form lymph_node_growing_rates lymph_node_growing_rate lymph_node_homolateral_stations lymph_node_homolateral_station lymph_node_imaging_datas lymph_node_imaging_data lymph node imaging data lymph_node_infiltrations lymph_node_infiltration lymph_node_invasions lymph_node_invasion lymph_node_minor_axes lymph_node_minor_axis lymph_node_necroses lymph_node_necrosis lymph_node_quantities lymph_node_quantity lymph_node_shape_deviations lymph_node_shape_deviation lymph_node_sides lymph_node_side lymph_node_side_near_tumors lymph_node_side_near_tumor lymph_node_sites lymph_node_site lymph_node_skin_mobilities lymph_node_skin_mobility lymph_node_stations lymph_node_station lymph_node_surgical_procedures lymph_node_surgical_procedure lymph node surgical procedure lymph_node_textures lymph_node_texture lymph_node_water_contents lymph_node_water_content mandibulectomies mandibulectomy mandibulectomy marginal_mandibulectomies marginal_mandibulectomy marginal mandibulectomy masseter_flaps masseter_flap masseter flap maxilectomies maxilectomy maxilectomy mechanical_traumas mechanical_trauma mechanical trauma microarray_datas microarray_data microarray data 1 List of genes used to feed the microarray. microarray input gene list 1 List of the differently expressed genes analysed in the microarray. microarray output gene list mobile_protheses mobile_prothesis mobile prothesis mucosa_resections mucosa_resection mucosa resection nerve_anastomosis_flaps nerve_anastomosis_flap nerve anastomosis flap nerve_resections nerve_resection nerve resection non_surgical_treatments non_surgical_treatment non surgical treatment nose_resections nose_resection nose resection oral_hygiene_habitses oral_hygiene_habits oral hygiene habits other_arterial_flaps other_arterial_flap other arterial flap other_distant_pedicled_flaps other_distant_pedicled_flap other distant pedicled flap other_locoregional_flaps other_locoregional_flap other locoregional flap other_nerve_flaps other_nerve_flap other nerve flap paliative_treatments paliative_treatment paliative treatment palpebral_resections palpebral_resection palpebral resection parathyroidectomies parathyroidectomy parathyroidectomy partial_glossectomies partial_glossectomy partial glossectomy partial_pharyngectomies partial_pharyngectomy partial pharyngectomy patient_quality_of_life_evaluations patient_quality_of_life_evaluation patient quality of life evaluation patient_risk_factors patient_risk_factor patient risk factor pectoralis_major_flaps pectoralis_major_flap pectoralis major flap pelvectomies pelvectomy pelvectomy pharyngectomies pharyngectomy pharyngectomy physical_agents physical_agent physical agent post_treatments post_treatment post treatment precancerous_lesions precancerous_lesion precancerous lesion qPCR_datas qPCR_data qPCR data Gene set used to feed the qPCR. qPCR input gene list radiotherapies radiotherapy radiotherapy rectus_abdominis_flaps rectus_abdominis_flap rectus abdominis flap reoccurrence_predictions reoccurrence_prediction reoccurrence prediction resections resection resection respiration_evaluations respiration_evaluation respiration evaluation segmental_left_mandibulectomies segmental_left_mandibulectomy segmental left mandibulectomy segmental_left_maxilectomies segmental_left_maxilectomy segmental left maxilectomy segmental_mandibulectomies segmental_mandibulectomy segmental mandibulectomy segmental_maxilectomies segmental_maxilectomy segmental maxilectomy segmental_right_mandibulectomies segmental_right_mandibulectomy segmental right mandibulectomy segmental_right_maxilectomies segmental_right_maxilectomy segmental right maxilectomy sialoadenectomies sialoadenectomy sialoadenectomy skin_resections skin_resection skin resection social_rehabilitations social_rehabilitation social rehabilitation soft_palate_resections soft_palate_resection soft palate resection speech_evaluations speech_evaluation speech evaluation submental_flaps submental_flap submental flap substances substance substance subtotal_glossectomies subtotal_glossectomy subtotal glossectomy surgical_procedures surgical_procedure surgical procedure surgical_reconstructions surgical_reconstruction surgical reconstruction surgical_treatments surgical_treatment surgical treatment temporalis_flaps temporalis_flap temporalis flap thyreolingual_trunk_flaps thyreolingual_trunk_flap thyreolingual trunk flap thyroid_artery_flaps thyroid_artery_flap thyroid artery flap thyroidectomies thyroidectomy thyroidectomy tobaccos tobacco tobacco tonsilla_resections tonsilla_resection tonsilla resection total_extended_to_pharynx_laryngectomies total_extended_to_pharynx_laryngectomy total extended to pharynx laryngectomy total_glossectomies total_glossectomy total glossectomy total_laryngectomies total_laryngectomy total laryngectomy total_mandibulectomies total_mandibulectomy total mandibulectomy total_maxilectomies total_maxilectomy total maxilectomy total_pharyngectomies total_pharyngectomy total pharyngectomy transverse_cervical_artery_flaps transverse_cervical_artery_flap transverse cervical artery flap trapezious_flaps trapezious_flap trapezious flap tumor_Anneroths-Mod_scores tumor_Anneroths-Mod_score tumor_D2-40_stains tumor_D2-40_stain tumor_EGFR_stains tumor_EGFR_stain tumor_HPV_DNAs tumor_HPV_DNA tumor_HPV_Types tumor_HPV_Type tumor_Ki-67_stains tumor_Ki-67_stain tumor_Martinez-Gimeno_scores tumor_Martinez-Gimeno_score tumor_P16Ink4a_stains tumor_P16Ink4a_stain tumor_TNM_stagings tumor_TNM_staging tumor_basaloid_featureses tumor_basaloid_features tumor_bone_infiltrations tumor_bone_infiltration tumor_buccal_face_invasions tumor_buccal_face_invasion tumor_clinical_datas tumor_clinical_data tumor clinical data tumor_consistences tumor_consistence tumor_contrast_take_up_rates tumor_contrast_take_up_rate tumor_cuataneous_invasions tumor_cuataneous_invasion tumor_degree_of_cells_keratinisations tumor_degree_of_cells_keratinisation tumor_depth_of_invasions tumor_depth_of_invasion tumor_extension_site_C0s tumor_extension_site_C0 tumor_extension_site_C1s tumor_extension_site_C1 tumor_extra_spreadings tumor_extra_spreading 1 tumor_findings tumor_finding tumor finding tumor_floor_of_the_mouth_invasions tumor_floor_of_the_mouth_invasion tumor_grade_of_differentiations tumor_grade_of_differentiation tumor_haemorrages tumor_haemorrage tumor_imaging_datas tumor_imaging_data tumor imaging data tumor_infiltrations tumor_infiltration tumor_internal_carotid_invasions tumor_internal_carotid_invasion tumor_invasions tumor_invasion tumor_level_of_invasions tumor_level_of_invasion tumor_localization_datas tumor_localization_data tumor localization data tumor_lymphoplasmacytic_reactions tumor_lymphoplasmacytic_reaction tumor_lymphovascular_invasions tumor_lymphovascular_invasion tumor_macroscopic_views tumor_macroscopic_view tumor_masticator_space_invasions tumor_masticator_space_invasion tumor_max_diameters tumor_max_diameter tumor_maxilary_sinus_invasions tumor_maxilary_sinus_invasion tumor_metastasis_sites tumor_metastasis_site tumor_necroses tumor_necrosis tumor_nuclear_pleomorphisms tumor_nuclear_pleomorphism tumor_number_of_metastatic_lymphnodes_per_levels tumor_number_of_metastatic_lymphnodes_per_level tumor_number_of_mitoses_per_10_HPFs tumor_number_of_mitoses_per_10_HPF tumor_p53_stains tumor_p53_stain tumor_parapharingeal_space_invasions tumor_parapharingeal_space_invasion tumor_pathological_datas tumor_pathological_data tumor pathological data tumor_pathological_invasions tumor_pathological_invasion tumor_pattern_of_invasions tumor_pattern_of_invasion tumor_perineural_infiltrations tumor_perineural_infiltration tumor_perineural_invasions tumor_perineural_invasion tumor_periosteal_infiltrations tumor_periosteal_infiltration tumor_previous_pathological_samples tumor_previous_pathological_sample tumor_principal_sites tumor_principal_site tumor_pterigo_palatine_invasions tumor_pterigo_palatine_invasion tumor_related_muscle_atrophies tumor_related_muscle_atrophy tumor_sides tumor_side tumor_sites tumor_site tumor_sizes tumor_size tumor_skull_base_invasions tumor_skull_base_invasion tumor_spread_across_midlines tumor_spread_across_midline tumor_stage_groupings tumor_stage_grouping tumor_stains tumor_stain tumor_sublingual_space_invasions tumor_sublingual_space_invasion tumor_surgical_marginses tumor_surgical_margins tumor_surgical_procedures tumor_surgical_procedure tumor surgical procedure tumor_thicknesses tumor_thickness tumor_total_number_of_lymphnodes_per_levels tumor_total_number_of_lymphnodes_per_level tumor_ulcerations tumor_ulceration tumor_water_contents tumor_water_content venous_anastomosis_flaps venous_anastomosis_flap venous anastomosis flap IAO_0000027s IAO_0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data OBO:imported "http://purl.obolibrary.org/obo/iao.owl" data item IAO_0000030s IAO_0000030 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity PERSON: Chris Stoeckert OBI_0000142 OBO:sourced "OBI:0000142" information content entity IAO_0000100s IAO_0000100 data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set 1 1 OBI_0000093s OBI_0000093 patient role a hospitalized person; a person with controlled diabetes; the patient's role http://www.fertilityjourney.com/testingAndDiagnosis/theRightDoctor/thePatientsRole/index.asp?C=55245395146924652778 a role which inheres in a person and is realized by the process of being under the care of a physician or health care provider GROUP:Role Branch patient OBI, CDISC patient role OBI_0000118s OBI_0000118 gene list Gene lists may arise from analysis to determine differentially expressed genes, may be collected from the literature for involvement in a particular process or pathway (e.g., inflammation), or may be the input for gene set enrichment analysis. A gene list is a report of the names or identifiers of genes that are the outcome of an analysis or have been put together for the purpose of an analysis. person:Chris Stoeckert group:OBI gene list OBI_0100015s OBI_0100015 anatomical entity Tissue, organ, system, sperm, blood or body location (arm). An anatomical entity is a material entity that is part of a multicellular organism, and which is large enough so that it forms an identifiable structure in the organism. Specifically, it excludes granular parts of the organism, such as atoms, molecules, cells, which can be removed from the organism without affecting it. It is defined as the union of 'multi-tissue structure', 'body substance' and 'portion of tissue' 10/20/09: This class and all subclasses are currently problematic. They should all be imported from other OBO foundry ontologies. (FMA / CARO / UBERON). Currently two problems exist: There is no cross species anatomy that covers all the entities we need. Secondly: there is not good boundary between anatomical entities and smaller parts in FMA. Currently we will use anatomical entities as if they are valid across species. not super happy about liquids (blood, sperm), as they seem to be 'granular' somewhat, and not form a structure. Bjoern Peters Philippe Rocca-Serra Tina Boussard MO anatomical entity OBI_1110055s OBI_1110055 disease placeholder to be imported from disease ontology IEDB IEDB disease 1 OGMS_0000014s OGMS_0000014 A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:02Z clinical finding OGMS_0000015s OGMS_0000015 A series of statements representing health-relevant qualities of a patient and of a patient's family. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-07-19T10:18:59Z clinical history OGMS_0000017s OGMS_0000017 A representation of an image that supports an inference to an assertion about some quality of a patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:10Z image finding OGMS_0000018s OGMS_0000018 A representation of a quality of a specimen that is the output of a laboratory test and that can support an inference to an assertion about some quality of the patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T10:21:58Z laboratory finding OGMS_0000083s OGMS_0000083 TODO: Define. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=26 creation date: 2009-11-24T04:51:11Z physical examination finding 1 OGMS_0000090s OGMS_0000090 A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z treatment 1 OGMS_0000093s OGMS_0000093 A hypothesis about the course of a disease. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T12:42:23Z prognosis DOID_14566s DOID_14566 DOID:0000818 disease_ontology disease of cellular proliferation DOID_162s DOID_162 disease_ontology cancer 1 DOID_3680s DOID_3680 DOID:8722 DOID:8862 DOID:8894 DOID:8952 disease_ontology malignant neoplasm of lip, oral cavity and pharynx DOID_449s DOID_449 disease_ontology head neoplasm DOID_462s DOID_462 DOID:8996 disease_ontology cancer by anatomical entity DOID_8533s DOID_8533 DOID:12202 DOID:8532 disease_ontology malignant neoplasm of hypopharynx DOID_8556s DOID_8556 disease_ontology malignant neoplasm of vallecula DOID_8557s DOID_8557 DOID:8851 disease_ontology malignant neoplasm of oropharynx DOID_8564s DOID_8564 DOID:8563 DOID:8605 DOID:9031 disease_ontology malignant neoplasm of lip DOID_8578s DOID_8578 disease_ontology malignant neoplasm of soft palate DOID_8601s DOID_8601 disease_ontology malignant neoplasm of upper gum DOID_8602s DOID_8602 DOID:8734 disease_ontology malignant neoplasm of gum DOID_8617s DOID_8617 disease_ontology malignant neoplasm of lateral portion of floor of mouth DOID_8618s DOID_8618 DOID:9049 disease_ontology malignant neoplasm of floor of mouth DOID_8630s DOID_8630 disease_ontology malignant neoplasm of upper lip, inner aspect DOID_8635s DOID_8635 disease_ontology malignant neoplasm of uvula DOID_8649s DOID_8649 DOID:8648 DOID:9196 disease_ontology malignant neoplasm of tongue DOID_8660s DOID_8660 disease_ontology malignant neoplasm of postcricoid region of hypopharynx DOID_8663s DOID_8663 disease_ontology malignant neoplasm of aryepiglottic fold, hypopharyngeal aspect DOID_8684s DOID_8684 disease_ontology malignant neoplasm of junctional region of oropharynx DOID_8688s DOID_8688 disease_ontology malignant neoplasm of tonsillar pillars (anterior) (posterior) DOID_8702s DOID_8702 disease_ontology malignant neoplasm of cheek mucosa DOID_8779s DOID_8779 disease_ontology malignant neoplasm of dorsal surface of tongue DOID_8814s DOID_8814 DOID:8813 disease_ontology malignant neoplasm of nasopharynx DOID_8849s DOID_8849 disease_ontology malignant neoplasm of sublingual gland DOID_8850s DOID_8850 DOID:8873 DOID:9148 disease_ontology malignant neoplasm of major salivary glands DOID_8858s DOID_8858 disease_ontology malignant neoplasm of tonsil DOID_8883s DOID_8883 disease_ontology vermilion border malignant neoplasm of lower lip DOID_8896s DOID_8896 disease_ontology malignant neoplasm of anterior aspect of epiglottis DOID_8900s DOID_8900 disease_ontology malignant neoplasm of tip and lateral border of tongue DOID_8930s DOID_8930 disease_ontology malignant neoplasm of retromolar area DOID_8937s DOID_8937 disease_ontology malignant neoplasm of waldeyer's ring DOID_8940s DOID_8940 disease_ontology malignant neoplasm of lingual tonsil DOID_8949s DOID_8949 disease_ontology malignant neoplasm of lateral wall of oropharynx DOID_8969s DOID_8969 disease_ontology malignant neoplasm of tonsillar fossa DOID_8975s DOID_8975 disease_ontology malignant neoplasm of commissure of lip DOID_8984s DOID_8984 disease_ontology malignant neoplasm of upper lip, vermilion border DOID_8999s DOID_8999 disease_ontology malignant neoplasm of junctional zone of tongue DOID_9036s DOID_9036 disease_ontology malignant neoplasm of parotid gland DOID_9055s DOID_9055 disease_ontology malignant neoplasm of anterior portion of floor of mouth DOID_9057s DOID_9057 disease_ontology malignant neoplasm of posterior wall of nasopharynx DOID_9058s DOID_9058 disease_ontology malignant neoplasm of base of tongue DOID_9068s DOID_9068 disease_ontology malignant neoplasm of ventral surface of tongue DOID_9125s DOID_9125 disease_ontology malignant neoplasm of lower gum DOID_9135s DOID_9135 disease_ontology malignant neoplasm of other sites of lip DOID_9144s DOID_9144 disease_ontology malignant neoplasm of anterior wall of nasopharynx DOID_9149s DOID_9149 disease_ontology malignant neoplasm of hard palate DOID_9160s DOID_9160 disease_ontology malignant neoplasm of posterior hypopharyngeal wall DOID_9168s DOID_9168 disease_ontology malignant neoplasm of posterior wall of oropharynx DOID_9173s DOID_9173 disease_ontology malignant neoplasm of submandibular gland DOID_9188s DOID_9188 disease_ontology malignant neoplasm of vestibule of mouth DOID_9197s DOID_9197 disease_ontology malignant neoplasm of superior wall of nasopharynx DOID_9229s DOID_9229 disease_ontology malignant neoplasm of lateral wall of nasopharynx DOID_9235s DOID_9235 disease_ontology malignant neoplasm of pyriform sinus 1 FMA_5034s FMA_5034 Lymph node Lymph node Entities Entity entity Continuants Continuant Definition: An entity [bfo:Entity] that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. Examples: a heart, a person, the color of a tomato, the mass of a cloud, a symphony orchestra, the disposition of blood to coagulate, the lawn and atmosphere in front of our building Synonyms: endurant continuant DependentContinuants DependentContinuant Definition: A continuant [snap:Continuant] that is either dependent on one or other independent continuant [snap:IndependentContinuant] bearers or inheres in or is borne by other entities. dependent_continuant Dispositions Disposition Definition: A realizable entity [snap:RealizableEntity] that essentially causes a specific process or transformation in the object [snap:Object] in which it inheres, under specific circumstances and in conjunction with the laws of nature. A general formula for dispositions is: X (object [snap:Object] has the disposition D to (transform, initiate a process) R under conditions C. Examples: the disposition of vegetables to decay when not refrigerated, the disposition of a vase to brake if dropped, the disposition of blood to coagulate, the disposition of a patient with a weakened immune system to contract disease, the disposition of metal to conduct electricity. disposition GenericallyDependentContinuants GenericallyDependentContinuant Definition: A continuant [snap:Continuant] that is dependent on one or other independent continuant [snap:IndependentContinuant] bearers. For every instance of A requires some instance of (an independent continuant [snap:IndependentContinuant] type) B but which instance of B serves can change from time to time. Examples: a certain PDF file that exists in different and in several hard drives generically_dependent_continuant IndependentContinuants IndependentContinuant Definition: A continuant [snap:Continuant] that is a bearer of quality [snap:Quality] and realizable entity [snap:RealizableEntity] entities, in which other entities inhere and which itself cannot inhere in anything. Examples: an organism, a heart, a leg, a person, a symphony orchestra, a chair, the bottom right portion of a human torso, the lawn and atmosphere in front of our building Synonyms: substantial entity independent_continuant MaterialEntities MaterialEntity Definition: An independent continuant [snap:IndependentContinuant] that is spatially extended whose identity is independent of that of other entities and can be maintained through time. Note: Material entity [snap:MaterialEntity] subsumes object [snap:Object], fiat object part [snap:FiatObjectPart], and object aggregate [snap:ObjectAggregate], which assume a three level theory of granularity, which is inadequate for some domains, such as biology. Examples: collection of random bacteria, a chair, dorsal surface of the body material_entity RealizableEntities RealizableEntity Comment: If a realizable entity [snap:RealizableEntity] inheres in a continuant [snap:Continuant], this does not imply that it is actually realized. Definition: A specifically dependent continuant [snap:SpecificallyDependentContinuant] that inheres in continuant [snap:Continuant] entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. Examples: the role of being a doctor, the function of the reproductive organs, the disposition of blood to coagulate, the disposition of metal to conduct electricity realizable_entity Roles Role Definition: A realizable entity [snap:RealizableEntity] the manifestation of which brings about some result or end that is not essential to a continuant [snap:Continuant] in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant [snap:Continuant] in some kinds of natural, social or institutional contexts. Examples: the role of a person as a surgeon, the role of a chemical compound in an experiment, the role of a patient relative as defined by a hospital administrative form, the role of a woman as a legal mother in the context of system of laws, the role of a biological grandfather as legal guardian in the context of a system of laws, the role of ingested matter in digestion, the role of a student in a university role SpecificallyDependentContinuants SpecificallyDependentContinuant Definition: A continuant [snap:Continuant] that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. Examples: the mass of a cloud, the smell of mozzarella, the liquidity of blood, the color of a tomato, the disposition of fish to decay, the role of being a doctor, the function of the heart in the body: to pump blood, to receive de-oxygenated and oxygenated blood, etc. Synonyms: property, trope, mode specifically_dependent_continuant Occurrents Occurrent Definition: An entity [bfo:Entity] that has temporal parts and that happens, unfolds or develops through time. Sometimes also called perdurants. Examples: the life of an organism, a surgical operation as processual context for a nosocomical infection, the spatiotemporal context occupied by a process of cellular meiosis, the most interesting part of Van Gogh's life, the spatiotemporal region occupied by the development of a cancer tumor Synonyms: perdurant occurrent ProcessualEntities ProcessualEntity Definition: An occurrent [span:Occurrent] that exists in time by occurring or happening, has temporal parts and always involves and depends on some entity. Examples: the life of an organism, the process of meiosis, the course of a disease, the flight of a bird processual_entity Thing relationship cjm This is an OWL translation of an ontology whose native representational form is .obo. The translation was performed using the oboInOwl xslt library. For details, see http://www.berkeleybop.org/obo-conv.cgi <p>This ontology contains logical relations to be shared across the different OBO ontologies. Each OBO ontology is free to extend this set with relations specific to the biology within that ontology</p><div class="notes"><p>In the definitions, variables c, d, ..., p, q, ... range over instances of continuants and processes respectively. C, D, ..., P, Q, ... range over the corresponding classes</p><p> For a discussion of instance-level relations and also of additional axioms needed to infer transitivity and other properties of the relations listed above see <a href="http://genomebiology.com/2005/6/5/R46">http://genomebiology.com/2005/6/5/R46</a> or the OBO relations page hosted at <a href="http://obo.sourceforge.net/relationship">http://obo.sourceforge.net/relationship</a></div> cvs version $Revision: 1.5 $ release version 1.01 relationship malignant neoplasm of palate NOS (disorder) malignant neoplasm of mouth, unspecified malignant neoplasm of mouth NOS (disorder) malignant neoplasm of other specified mouth parts (disorder) malignant neoplasm of pharynx unspecified (disorder) malignant tumour of mouth malignant Pharyngeal tumor malignant neoplasm of oral cavity NOS oral cancer malignant neoplasm of pharynx, unspecified malignant tumor of palate (disorder) malignant tumor of oral cavity (disorder) malignant neoplasm of other specified parts of mouth malignant neoplasm of roof of mouth malignant Oral cavity neoplasm malignant neoplasm of pharynx A neoplastic disease that is malignant and characterized by uncontrolled cellular proliferation, local cell invasion and metastasis. neoplasm of the head head neoplasm neoplasm of head (disorder) A cancer that affects an anatomical entity. malignant neoplasm of aortic body and other paraganglia (disorder) malignant neoplasm of mouth malignant neoplasm of aortic body and other paraganglia A disease that is characterized by abnormally rapid cell division. cell process disease malignant tumor of pharynx (disorder) malignant tumor of the Palate malignant Oral neoplasm malignant neoplasm of palate, unspecified malignant neoplasm of palate unspecified (disorder) malignant neoplasm of pharynx, NOS For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) malignant tumor of vallecula (disorder) malignant neoplasm of palatine tonsil (disorder) malignant tumor of junctional zone of tongue (disorder) malignant tumor of posterior wall of nasopharynx malignant tumor of posterior wall of nasopharynx (disorder) malignant neoplasm of posterior wall of nasopharynx NOS (disorder) malignant neoplasm of border of tongue malignant neoplasm of tip and/or lateral border of tongue malignant neoplasm of tip and/or lateral border of tongue malignant neoplasm of tongue, tip and lateral border (disorder) malignant neoplasm of lip, inner aspect malignant tumor of lip (disorder) malignant neoplasm tonsil NOS (disorder) malignant neoplasm of lip unspecified, inner aspect (disorder) malignant tumor of lower labial mucosa (disorder) malignant neoplasm of lower lip, inner aspect NOS (disorder) malignant tumour of lip malignant neoplasm of lower lip, oral aspect malignant tumor of the Lip malignant neoplasm of vermilion border of lip unspecified (disorder) malignant neoplasm of lower lip, mucosa (disorder) malignant neoplasm of lip, vermilion border NOS (disorder) malignant neoplasm of lip, unspecified, inner aspect malignant neoplasm of tonsil, faucial malignant neoplasm of oral aspect of lip, not specified whether upper or lower malignant tumor of labial mucosa (disorder) malignant neoplasm of lower lip, buccal aspect (disorder) malignant neoplasm of vermilion border of lip malignant neoplasm of lip, unspecified malignant neoplasm of external Lip, not specified as upper or lower malignant neoplasm of lip, unspecified, vermilion border malignant neoplasm of lip, unspecified (disorder) malignant neoplasm of lip, unspecified, external (disorder) malignant neoplasm of lip, inner aspect NOS (disorder) malignant neoplasm of faucial tonsil (disorder) malignant tumor of soft palate (disorder) malignant tumor of the soft Palate malignant tumor of tonsillar fossa malignant tumor of tonsillar fossa (disorder) malignant neoplasm of tonsillar fossa NOS (disorder) malignant neoplasm of labial commissure of lip malignant tumor of commissure of lip malignant tumor of commissure of lip (disorder) malignant tumour of labial commissure malignant neoplasm of anterior epiglottis NOS (disorder) malignant neoplasm tonsil malignant neoplasm of anterior surface of epiglottis malignant neoplasm of anterior epiglottis (disorder) malignant tumor of posterior wall of oropharynx (disorder) malignant neoplasm of dorsal tongue NOS malignant neoplasm of dorsum of tongue NOS (disorder) malignant neoplasm of posterior wall of hypopharynx malignant tumor of posterior wall of hypopharynx (disorder) malignant neoplasm of roof of nasopharynx malignant tumor of roof of nasopharynx (disorder) malignant neoplasm of fixed part of tongue NOS (disorder) malignant tumor of tonsil (disorder) malignant tumor of base of tongue (disorder) malignant neoplasm of fixed part of tongue NOS malignant tumor of Posterior Tongue malignant neoplasm of upper lip, external (disorder) malignant neoplasm of upper lip, vermilion border NOS (disorder) malignant tumour of lipstick area of upper lip malignant tumor of vermilion border of upper lip malignant neoplasm of upper lip, external malignant neoplasm of upper lip, lipstick area (disorder) malignant tumor of vermilion border of upper lip (disorder) malignant Tonsillar tumor malignant tumor of tongue (disorder) malignant neoplasm of other sites of tongue malignant neoplasm of tongue malignant tumor of anterior two-thirds of tongue (disorder) malignant neoplasm of other sites of tongue (disorder) malignant neoplasm of mobile part of tongue NOS Tongue neoplasm malignant stage Unspecified malignant neoplasm of tongue NOS (disorder) malignant neoplasm of anterior 2/3 of tongue unspecified (disorder) malignant neoplasm of anterior two-thirds of tongue, part unspecified malignant tumor of hard palate (disorder) malignant neoplasm of tongue malignant neoplasm of tongue, NOS malignant neoplasm of tongue NOS malignant tumor of mobile part of tongue malignant tumor aryepiglottic fold - hypopharyngeal aspect (disorder) malignant neoplasm of hypopharyngeal aspect of aryepiglottic fold primary malignant neoplasm of anterior wall of nasopharynx malignant tumor of anterior wall of nasopharynx malignant tumor of anterior wall of nasopharynx (disorder) malignant neoplasm of anterior wall of nasopharynx NOS (disorder) malignant neoplasm of hard palate malignant neoplasm of gum NOS (disorder) malignant neoplasm of other sites of gum malignant tumour of gingiva malignant neoplasm of gum malignant Gingival tumor malignant tumor of gum (disorder) malignant neoplasm of other sites of gum (disorder) malignant neoplasm of ventral tongue surface NOS (disorder) malignant Uvular tumor malignant tumor of uvula (disorder) Hard Palate malignant neoplasm of major salivary gland, NOS malignant neoplasm of salivary gland NOS malignant neoplasm of other major salivary glands (disorder) malignant neoplasm of salivary gland duct malignant tumor of salivary gland (disorder) malignant tumor of the Salivary gland malignant neoplasm of salivary gland, unspecified malignant neoplasm of major salivary gland malignant neoplasm of other major salivary glands malignant tumor of major salivary gland (disorder) malignant neoplasm of floor of mouth NOS (disorder) malignant tumor of the Hard Palate malignant neoplasm of major salivary gland NOS (disorder) malignant neoplasm of major salivary gland NOS malignant tumor of the Major Salivary gland malignant neoplasm of salivary gland malignant neoplasm of submaxillary gland malignant neoplasm of submaxillary gland malignant tumor of submandibular gland (disorder) malignant tumor of the Submandibular gland malignant tumor of retromolar area (disorder) malignant tumor of lateral wall of nasopharynx (disorder) malignant tumour of hard palate malignant neoplasm of lateral wall of nasopharynx NOS (disorder) malignant tumor of lateral wall of nasopharynx malignant tumor of the Sublingual gland malignant tumor of sublingual gland (disorder) malignant tumor of lingual tonsil malignant tumor of lingual tonsil (disorder) malignant tumor of pyriform fossa (disorder) malignant neoplasm of pyriform fossa malignant neoplasm of the Pyriform Fossa malignant neoplasm of vestibule of mouth NOS (disorder) malignant tumour of lipstick area of lower lip malignant tumor of vestibule of mouth malignant tumor of vestibule of mouth (disorder) malignant tumor of buccal mucosa (disorder) malignant neoplasm of buccal mucosa malignant neoplasm of cheek, inner aspect malignant neoplasm of the Buccal Mucosa malignant tumour of upper labial mucosa malignant neoplasm of upper lip, buccal aspect (disorder) malignant neoplasm of upper lip, oral aspect malignant neoplasm of inner aspect of upper lip malignant tumour of vermilion border of lower lip malignant tumour of upper labial mucosa malignant tumor of upper labial mucosa (disorder) malignant neoplasm of upper lip, inner aspect NOS (disorder) malignant tumor of lower gingiva (disorder) malignant tumour of lower gum malignant neoplasm of lateral wall of oropharynx primary malignant neoplasm of lateral wall of oropharynx malignant neoplasm of other sites of lip (disorder) malignant tumor of anterior floor of mouth (disorder) malignant tumor of upper gingiva malignant tumor of vermilion border of lower lip malignant tumor of upper gingiva (disorder) malignant tumour of upper gum malignant neoplasm of lower lip, vermilion border NOS (disorder) malignant neoplasm of lower lip, lipstick area malignant tumor of vermilion border of lower lip (disorder) malignant neoplasm of oral cavity NOS malignant neoplasm of palate, unspecified malignant neoplasm of floor of mouth malignant neoplasm of pharynx malignant neoplasm of other specified parts of mouth malignant tumor of palate (disorder) malignant neoplasm of mouth, unspecified malignant tumour of mouth malignant tumor of the Palate malignant neoplasm of palate NOS (disorder) malignant neoplasm of pharynx unspecified (disorder) malignant tumor of pharynx (disorder) malignant neoplasm of mouth malignant neoplasm of floor of mouth, NOS malignant Pharyngeal tumor malignant neoplasm of other specified mouth parts (disorder) malignant Oral neoplasm oral cancer malignant neoplasm of pharynx, NOS malignant neoplasm of palate unspecified (disorder) malignant tumor of oral cavity (disorder) malignant Oral cavity neoplasm malignant neoplasm of pharynx, unspecified malignant neoplasm of mouth NOS (disorder) malignant tumor of the Floor of the Mouth malignant neoplasm of roof of mouth malignant neoplasm of other specified hypopharyngeal site (disorder) malignant neoplasm of hypopharynx malignant neoplasm of ill-defined sites within the lip and oral cavity malignant tumour of hypopharynx malignant neoplasm of other specified sites of hypopharynx malignant neoplasm of hypopharynx, NOS Hypopharyngeal cancer malignant neoplasm of hypopharynx NOS malignant neoplasm of hypopharynx NOS (disorder) malignant neoplasm of other sites of floor of mouth (disorder) malignant Hypopharyngeal tumor malignant tumor of hypopharynx (disorder) malignant neoplasm of oropharynx, other specified sites (disorder) malignant Oropharyngeal tumor malignant tumour of mesopharynx (disorder) malignant neoplasm of other specified sites of oropharynx malignant neoplasm of oropharynx malignant neoplasm of oropharynx NOS (disorder) malignant neoplasm of oropharynx, NOS malignant neoplasm of other specified site of oropharynx NOS (disorder) malignant tumor of floor of mouth (disorder) malignant neoplasm of oropharynx malignant tumor of oropharynx (disorder) Oropharyngeal carcinoma oropharyngeal cancer cancer of parotid gland malignant neoplasm of the Parotid malignant tumor of parotid gland (disorder) malignant neoplasm of nasopharynx malignant neoplasm of nasopharyngeal wall (disorder) malignant Nasopharyngeal tumor malignant neoplasm of floor of mouth malignant tumor of nasopharynx (disorder) malignant neoplasm of nasopharyngeal wall NOS malignant neoplasm of other specified site of nasopharynx (disorder) malignant neoplasm of nasopharynx NOS (disorder) malignant neoplasm of other specified sites of nasopharynx malignant neoplasm of nasopharynx malignant neoplasm of nasopharynx (disorder) [Ambiguous] malignant tumor of lateral floor of mouth (disorder) malignant neoplasm of lateral floor of mouth malignant tumor of tonsillar pillar (disorder) malignant neoplasm of other sites of floor of mouth malignant tumour of tonsillar pillar malignant tumour of tonsillar pillar malignant neoplasm of tonsillar pillar malignant neoplasm of tonsillar pillars, posterior malignant tumor of pharyngoesophageal junction malignant neoplasm of postcricoid region malignant Postcricoid tumor malignant neoplasm of postcricoid region malignant tumor of Waldeyer's ring (disorder) malignant neoplasm of Waldeyer's ring example to be eventually removed Class has all its metadata, but is either not guaranteed to be in its final location in the asserted IS_A hierarchy or refers to another class that is not complete. metadata complete This isn't a class that OBI will keep - it's a placeholder for edits that are underway. The class name should start with an underscore PERSON:Alan Ruttenberg placeholder Class has undergone final review, is ready for use, and will be included in the next OBI release. Any class lacking "ready_for_release" should be considered likely to change place in hierarchy, have its definition refined, or be obsoleted in the next release. Those classes deemed "ready_for_release" will also derived from a chain of ancestor classes that are also "ready_for_release." ready for release Class is being worked on; however, the metadata (including definition) are not complete or sufficiently clear to the branch editors. metadata incomplete Nothing done yet beyond assigning a unique class ID and proposing a preferred term. uncurated All definitions, placement in the asserted IS_A hierarchy and required minimal metadata are complete. The class is awaiting a final review by someone other than the definition editor. pending final vetting IAO_0000136 IAO_0000136s IAO_0000136ed This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about For continuants: C part_of C' if and only if: given any c that instantiates C at a time t, there is some c' such that c' instantiates C' at time t, and c *part_of* c' at t. For processes: P part_of P' if and only if: given any p that instantiates P at a time t, there is some p' such that p' instantiates P' at time t, and p *part_of* p' at t. (Here *part_of* is the instance-level part-relation.) http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 C adjacent to C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c and c' are in spatial proximity http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation. Formally: C transformation_of C' if and only if given any c and any t, if c instantiates C at time t, then for some t', c instantiates C' at t' and t' earlier t, and there is no t2 such that c instantiates C at t2 and c instantiates C' at t2. http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later. We say that one class C derives_from class C' if instances of C are connected to instances of C' via some chain of instance-level derivation relations. Example: osteocyte derives_from osteoblast. Formally: C derives_immediately_from C' if and only if: given any c and any t, if c instantiates C at time t, then there is some c' and some t', such that c' instantiates C' at t' and t' earlier-than t and c *derives_from* c'. C derives_from C' if and only if: there is an chain of immediate derivation relations connecting C to C'. http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 derived_from P preceded_by P' if and only if: given any process p that instantiates P at a time t, there is some process p' such that p' instantiates P' at time t', and t' is earlier than t. http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 P has_participant C if and only if: given any process p that instantiates P there is some continuant c, and some time t, such that: c instantiates C at t and c participates in p at t http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 As for has_participant, but with the additional condition that the component instance is causally active in the relevant process http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 As for part_of, with the additional constraint that subject and object may be identical http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 A relationship between two classes (terms). Relationships between classes are expressed in terms of relations on underlying instances. http://purl.org/obo/owl/GOC#GOC_cjm GOC:cjm C integral_part_of C' if and only if: C part_of C' AND C' has_part C http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 As for part_of, with the additional constraint that subject and object are distinct http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 C located_in C' if and only if: given any c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c *located_in* c'. (Here *located_in* is the instance-level location relation.) http://purl.org/obo/owl/PMID#PMID_15892874 PMID:15892874 C contained_in C' if and only if: given any instance c that instantiates C at a time t, there is some c' such that: c' instantiates C' at time t and c located_in c' at t, and it is not the case that c *overlaps* c' at t. (c' is a conduit or cavity.) preceded_by preceded_bies preceded_bied OBO_REL:0000017 relationship An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other. preceded_by precedes precedeses precedesed OBO_REL:0000018 relationship precedes