2011-09-20 Barry Smith Anand Kumar Albert Goldfain Bill Hogan Cornelius Rosse Richard Scheuermann The Ontology for General Medical Science (OGMS) is based on the papers Toward an Ontological Treatment of Disease and Diagnosis and On Carcinomas and Other Pathological Entities. The ontology attempts to address some of the issues raised at the Workshop on Ontology of Diseases (Dallas, TX). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology. The latest version of OGMS is always available at http://purl.obolibrary.org/obo/ogms.owl This is version 2011-09-20 aka '0.9' http://purl.obolibrary.org/obo/ogms/2011-09-20/ogms.owl The OGMS developer site is http://code.google.com/p/ogms/ The discussion group is http://groups.google.com/group/ogms-discuss If you are interested in participating in the development of OGMS, please send email to albertgoldfain@gmail.com. Be sure to include a google-account username with your request (this will be the username associated with a gmail address). This ontology is in early development. Expect it to change. Lindsay Cowell Werner Ceusters Alan Ruttenberg Sivaram Arabandi Daniel Merico definition editor note curator note definition source definition editor OBO:imported "http://purl.obolibrary.org/obo/iao.owl" 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. OBO:sourced "OBI:0000142" an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity obsolete_representation Albert Goldfain creation date: 2009-06-23T10:17:44Z clinical finding 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 history 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 picture creation date: 2010-07-19T10:20:20Z http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain A representation of the clinically significant bodily components and/or bodily processes of a human being that is inferred from the totality of relevant clinical findings. image finding http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain creation date: 2009-06-23T10:21:10Z A representation of an image that supports an inference to an assertion about some quality of a patient. laboratory finding creation date: 2009-06-23T10:21:58Z 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 preclinical finding Albert Goldfain A representation of a quality of a patient that is (1) recorded by a clinician because the quality is hypothesized to be of clinical significance and (2) refers to qualities obtaining in the patient prior to their becoming detectable in a clinical history taking or physical examination. creation date: 2009-06-23T10:22:44Z http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf symptom http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-11-18T11:02:10Z A quality of a patient that is observed by the patient or a processual entity experienced by the patient, either of which is hypothesized by the patient to be a realization of a disease. note: defined class obsolete_bodily feature of a patient Albert Goldfain creation date: 2009-06-23T11:09:37Z manifestation of a disease http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain creation date: 2009-06-23T11:12:33Z A quality of a patient that is (a) a deviation from clinical normality that exists in virtue of the realization of a disease and (b) is observable. phenotype creation date: 2010-07-19T11:13:49Z A (combination of) quality(ies) of an organism determined by the interaction of its genetic make-up and environment that differentiates specific instances of a species from other instances of the same species. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain sign Albert Goldfain note: defined class A quality of a patient, a material entity that is part of a patient, or a processual entity that a patient participates in, any one of which is observed in a physical examination and is deemed by the clinician to be of clinical significance. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2010-11-18T11:14:36Z clinical manifestation of a disease creation date: 2009-06-23T11:15:43Z A manifestation of a disease that is detectable in a clinical history taking or physical examination. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf preclinical manifestation of a disease http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf A manifestation of a disease that exists prior to the time at which it would be detected in a clinical history taking or physical examination, if the patient were to present to a clinician. A realization of a disease that exists prior to its becoming detectable in a clinical history taking or physical examination. Albert Goldfain creation date: 2009-06-23T11:16:50Z clinical phenotype http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain A clinically abnormal phenotype. creation date: 2009-06-23T11:18:05Z disease phenotype A clinically abnormal phenotype that is characteristic of a single disease. creation date: 2009-06-23T11:18:39Z http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain vital sign Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive. creation date: 2009-06-23T11:19:17Z predisposition to disease of type X A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X. creation date: 2009-06-23T11:20:25Z Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf disease Albert Goldfain creation date: 2009-06-23T11:21:20Z A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf homeostasis creation date: 2009-06-23T11:22:01Z Albert Goldfain genetic predisposition to disease of type X A predisposition to disease of type X whose physical basis is a constitutional abnormality in an organism's genome. This abnormality is the physical basis for the increased risk of acquiring the disease X. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain creation date: 2009-06-23T11:23:07Z acquired genetic disease A disease whose physical basis is an acquired genetic disorder. creation date: 2009-06-23T11:24:05Z http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain constitutional genetic disease http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:24:59Z A disease whose physical basis is a constitutional genetic disorder. Albert Goldfain obsolete_infectious disease A disease whose physical basis is an infectious disorder. creation date: 2009-06-23T11:25:51Z http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain abnormal homeostasis Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:26:44Z Albert Goldfain normal homeostasis http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain Homeostasis of a type that is not clinically abnormal. creation date: 2009-06-23T11:27:28Z configuration http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:36:24Z Albert Goldfain A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region. pathological physical configuration A configuration which deviates in some way from a canonical configuration for a particular organism. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain creation date: 2009-06-23T11:36:58Z disorder http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease. creation date: 2009-06-23T11:39:44Z epigenetic disorder Albert Goldfain creation date: 2009-06-23T11:40:27Z A disorder whose etiology involves (1) a modification to the patient's genomic DNA which leads to alterations in the normal expression pattern of the genome, but is (2) not a change in the nucleotide sequence. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf genetic disorder creation date: 2009-06-23T11:41:14Z Albert Goldfain A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf obsolete_infectious disorder creation date: 2009-06-23T11:41:45Z A disorder whose etiology includes the presence of a pathogenic organism within a host organism or an abnormal imbalance in the normal resident organismal flora. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf obsolete_secondary infection A disorder consisting in the presence of a pathogenic organism within a host organism that occurs due to the disposition established by a prior infection with a pathogenic organism of a different kind. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:42:20Z Albert Goldfain acquired genetic disorder http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder. Albert Goldfain creation date: 2009-06-23T11:43:09Z constitutional genetic disorder http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf A genetic disorder inherited during conception that is part of all cells in the organism. Albert Goldfain creation date: 2009-06-23T11:43:44Z obsolete_standardized clinical process A fiat process part which involves the execution of a standardized protocol for measuring qualities of a patient. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:47:06Z clinical history taking creation date: 2009-06-23T11:49:16Z Albert Goldfain An interview in which a clinician elicits a clinical history from a patient or from a third party who is reporting on behalf of the patient. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf laboratory test A measurement assay that has as input a patient-derived specimen, and as output a result that represents a quality of the specimen. creation date: 2009-06-23T11:49:49Z http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain physical examination creation date: 2010-07-19T11:50:18Z A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain etiological process http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T11:53:07Z Albert Goldfain A process in an organism that leads to a subsequent disorder. bodily process creation date: 2009-06-23T11:53:49Z Albert Goldfain pathological bodily process creation date: 2009-06-23T11:54:29Z A bodily process that is clinically abnormal. Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf disease course http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain creation date: 2009-06-23T11:55:44Z The totality of all processes through which a given disease instance is realized. chronic disease course http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range. creation date: 2009-06-23T11:56:26Z Albert Goldfain progressive disease course creation date: 2009-06-23T11:57:09Z http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, involve an increasing deviation from homeostasis. transient disease course http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf Albert Goldfain A disease course that terminates in a return to normal homeostasis. creation date: 2009-06-23T11:57:44Z _undefined primitive term Albert Goldfain creation date: 2009-06-23T11:58:22Z obsolete_bodily feature creation date: 2009-06-23T11:58:39Z Albert Goldfain clinically abnormal creation date: 2009-06-23T11:59:24Z Albert Goldfain physical basis Albert Goldfain creation date: 2009-06-23T12:00:09Z realization creation date: 2009-06-23T12:00:39Z Albert Goldfain diagnosis Albert Goldfain The representation of a conclusion of a diagnostic process. http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf creation date: 2009-06-23T12:42:23Z normal value A value for a quality reported in a lab report and asserted by the testing lab or the kit manufacturer to be normal based on a statistical treatment of values from a reference population. creation date: 2009-06-26T10:31:34Z Albert Goldfain http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf obsolete_infection Albert Goldfain creation date: 2009-07-08T12:20:49Z pathological formation Albert Goldfain TODO: Define, relate to disorder, and place in the OGMS hierarchy. http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf creation date: 2009-07-13T02:14:59Z pathological anatomical structure creation date: 2009-07-13T02:14:05Z Albert Goldfain An anatomical structure (FMA) is pathological whenever (1) it has come into being as a result of changes in some pre-existing canonical anatomical structure, (2) through processes other than the expression of the normal complement of genes of an organism of the given type, and (3) is predisposed to have health-related consequences for the organism in question manifested by symptoms and signs. http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf portion of pathological body substance http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf Albert Goldfain TODO: Define, relate to disorder, and place in the OGMS hierarchy. creation date: 2009-07-13T02:15:17Z pathological transformation creation date: 2009-07-13T02:17:07Z Albert Goldfain http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure. pathological derivation creation date: 2009-07-13T02:17:24Z http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier. Albert Goldfain pathological invasion Albert Goldfain creation date: 2009-07-13T02:17:47Z http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf TODO: Define. physical examination finding Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=26 TODO: Define. creation date: 2009-11-24T04:51:11Z organism population An aggregate of organisms of the same type. creation date: 2009-11-24T04:51:11Z http://code.google.com/p/ogms/issues/detail?id=33 Albert Goldfain pain TODO: Define. http://code.google.com/p/ogms/issues/detail?id=13 creation date: 2009-11-24T04:51:11Z Albert Goldfain syndrome http://code.google.com/p/ogms/issues/detail?id=32 A pattern of signs and symptoms that typically co-occur. creation date: 2009-11-24T04:51:11Z Albert Goldfain extended organism Albert Goldfain An object aggregate consisting of an organism and all material entities located within the organism, overlapping the organism, or occupying sites formed in part by the organism. http://code.google.com/p/ogms/issues/detail?id=3 creation date: 2010-01-25T04:51:11Z patient symptom report creation date: 2010-01-25T04:51:11Z Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=12 A communication from a patient about something they perceive as being abnormal about their body or life. congenital malformation http://code.google.com/p/ogms/issues/detail?id=28 A structurally anomalous part of an organism acquired during fetal development and present at birth (but not necessarily hereditary) which is hypothesized to be harmful for the organism. Albert Goldfain creation date: 2010-03-31T04:51:11Z treatment http://code.google.com/p/ogms/issues/detail?id=35 creation date: 2010-03-31T04:51:11Z Albert Goldfain A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder convalescence A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course. Albert Goldfain creation date: 2010-03-31T04:51:11Z http://code.google.com/p/ogms/issues/detail?id=35 life course creation date: 2010-03-31T04:51:11Z A processual entity which has as parts all the processes in which a given organism is participant. Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=38 prognosis A hypothesis about the course of a disease. creation date: 2010-03-31T12:42:23Z Albert Goldfain http://code.google.com/p/ogms/issues/detail?id=35 acute disease course creation date: 2010-07-19T11:57:44Z Albert Goldfain http://code.google.com/p/ogms/wiki/Meeting_notes_20100513 a disease course with a rapid onset but typical unfolding of signs and symptoms after this rapid onset. inflammation process http://code.google.com/p/ogms/wiki/Meeting_notes_20100513 A process which is a response by an organism's tissues that is generally identified by swelling or localized pain creation date: 2010-07-19T11:57:44Z Albert Goldfain health care process A social process that has at least one human participant and that includes as parts the treatment, diagnosis, or prevention of disease or injury--or the following of instructions of another human for treatment, diagnosis, or prevention--of a participant in the process Albert Goldfain creation date: 2011-02-21T09:57:44Z http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 health care encounter Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z A temporally-connected health care process that has as participants an organization or person realizing the health care provider role and a person realizing the patient role. The health care provider role and patient are realized during the health care encounter hospitalization http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 Albert Goldfain creation date: 2011-02-21T09:57:44Z TODO outpatient encounter creation date: 2011-02-21T09:57:44Z http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 Albert Goldfain TODO inpatient encounter http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 creation date: 2011-02-21T09:57:44Z Albert Goldfain TODO ED encounter Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6 TODO creation date: 2011-02-21T09:57:44Z injury Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 A part of an organism that has undergone a change in structural integrity and has a higher chance of dysfunction or causing dysfunction in another structure. At the scale of organism (as opposed to the cellular scale or the population scale), an injury is typically the result of a catastrophic event. Consider the implications of making 'injury' a subtype of 'disorder'. creation date: 2011-09-20T09:57:44Z prophylaxis Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/e42bde79218ee34e A planned process that has the objective to reduce the risk of acquiring one or more disorders. Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question. creation date: 2011-09-20T09:57:44Z diagnostic process Albert Goldfain http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e An interpretive process that has as input a clinical picture of a given patient and as output an assertion (diagnostic statement) to the effect that the patient has a disease of such and such a type. creation date: 2011-09-20T09:57:44Z 2009-08-07