This ontology is in early development. Expect it to change.
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 2014-06-20 aka '0.11' http://purl.obolibrary.org/obo/ogms/2014-06-20/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).
An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
directive information content entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
planned process
A processual entity that realizes a plan which is the concretization of a plan specification.
A representation that is either the output of a clinical history taking or a physical examination or an image finding, or some combination thereof.
A series of statements representing health-relevant qualities of a patient and of a patient's family.
A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings.
A representation of an image that supports an inference to an assertion about some quality of a patient.
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.
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.
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.
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.
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.
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.
A manifestation of a disease that is detectable in a clinical history taking or physical examination.
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.
A clinically abnormal phenotype.
A clinically abnormal phenotype that is characteristic of a single disease.
A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive.
A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X.
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
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.
A disease whose physical basis is an acquired genetic disorder.
A disease whose physical basis is a constitutional genetic disorder.
Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment.
Homeostasis of a type that is not clinically abnormal.
A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region.
A configuration which deviates in some way from a canonical configuration for a particular organism.
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
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.
A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome.
A genetic disorder acquired by a single cell in an organism that leads to a population of cells within the organism bearing the disorder.
A genetic disorder inherited during conception that is part of all cells in the organism.
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.
A measurement assay that has as input a patient-derived specimen, and as output a result that represents a quality of the specimen.
A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation.
A process in an organism that leads to a subsequent disorder.
A bodily process that is clinically abnormal.
The totality of all processes through which a given disease instance is realized.
A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range.
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.
A disease course that terminates in a return to normal homeostasis.
The representation of a conclusion of a diagnostic process.
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.
TODO: Define, relate to disorder, and place in the OGMS hierarchy.
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.
A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure.
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.
TODO: Define.
An aggregate of organisms of the same type.
A bodily process in an organism S involving two integrated levels: (a) activation of the nociceptive system and associated emotion generating brain components of S, and (b) a simultaneous aversive sensory and emotional experience on the part of S, where (b) is phenomenologically similar to the sort of aversive experience involved in pain with concordant tissue damage.
A pattern of signs and symptoms that typically co-occur.
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.
A communication from a patient about something they perceive as being abnormal about their body or life.
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.
A processual entity whose completion is hypothesized (by a healthcare provider) to alleviate the signs and symptoms associated with a disorder
A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course.
A processual entity which has as parts all the processes in which a given organism is participant.
A hypothesis about some future part of a disease course.
a disease course with a rapid onset but typical unfolding of signs and symptoms after this rapid onset.
A process which is a response by an organism's tissues that is generally identified by swelling or localized pain
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
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
TODO
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'.
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.
Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question.
A planned process that has the objective to reduce the risk of acquiring one or more disorders.
An interpretive process that has as input a clinical picture of a given patient and as output an assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these.
relapse
A part of a disease course that occurs after an incomplete remission and that is similar to earlier parts of the disease course.
remission
A part of a disease course that includes a temporary convalescense.