The Ontology for General Medical Science (OGMS) is an ontology of entities involved in a clinical encounter. OGMS includes very general terms that are used across medical disciplines, including: 'disease', 'disorder', 'disease course', 'diagnosis', 'patient', and 'healthcare provider'. OGMS uses the Basic Formal Ontology (BFO) as an upper-level ontology. The scope of OGMS is restricted to humans, but many terms can be applied to a variety of organisms. OGMS provides a formal theory of disease that can be further elaborated by specific disease ontologies. This theory is implemented using OWL-DL and OBO Relation Ontology relations and is available in OWL and OBO formats. 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) and the Signs, Symptoms, and Findings Workshop(Milan, Italy). OGMS was formerly called the clinical phenotype ontology. Terms from OGMS hang from the Basic Formal Ontology.
url: http://creativecommons.org/licenses/by/4.0/
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 2020-07-06 aka 'v2020' The OGMS developer site is https://github.com/OGMS/ogms If you are interested in participating in the development of OGMS, please send email to baeverma
An information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity
An information content entity whose concretizations indicate to their bearer how to realize them in a process.
directive information content entity
An infection that is clinically abnormal.
A processual entity that realizes a plan which is the concretization of a plan specification.
planned process
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 process experienced by the patient, which can only be experienced by the patient, that is hypothesized to be clinically relevant.
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.
The class sign has been replaced by three seperate classes which reflect the different types of signs possible.
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.
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.
genetic predisposition to disease of type 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.
A health care process in which a clinician elicits a description of previous sign and symptoms of disease 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 data item that is about 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 planned process whose completion is hypothesized by a health care provider to eliminate, prevent, or alleviate the signs and symptoms of a disorder or pathological process
A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course.
A process which has as parts all the processes in which a given organism is participant.
Albert Goldfain Richard Scheuermann Sagar Jain
A hypothesis about some future part of a disease course.
A disease course with an acute onset
A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling.
A planned process with the objective to improve the health status of a patient that directly involves the treatment, diagnosis, or prevention of disease or injury of a patient
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
A health care encounter in which care is provided for undifferentiated and unscheduled patients with illnesses or injuries requiring immediate medical attention.
A disorder that involves some structural damage that is immediately caused by a catastrophic external force.
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'. Note: Adopted subtype of disorder, and injury can occur at the scale of organism down to cellular level.
http://groups.google.com/group/ogms-discuss/browse_thread/thread/ca0ad373f27774c5 OGMS call adoption- 16 SEPT 2015 https://docs.google.com/document/d/1iiV1-fTS7BUUSzDw3N_Afx42698YWf54-FOTY2NkAxo/edit
creation date: 2011-09-20T09:57:44Z edited date: 30 SEPT 2015
A planned process whose completion is hypothesized by a health care provider to reduce the risk of developing a disorder or the signs and symptoms of a disorder.
Whether or not 'prophylaxis' and 'treatment' classes are disjoint is an open question.
A health care process that involves the interpretation of a clinical picture from a given patient (input) and the assertion to the effect that the patient has a disease, disorder, or syndrome of a certain type, or none of these (output).
A disease stage which is preceded by a remission and characterized by the return of a manifestation of a disease.
A pathological bodily process which is part of a disease couse that occurs after an incomplete remission and that is similar to earlier parts of the disease course.
relapse
A disease stage which is characterized by the lack of a manifestation of a disease
A part of a disease course in which the extent or rate of change of the signs and symptoms of a disorder has decreased.
remission
A planned process that has the objective to support the objective of a health care process without directly involving the treatment, diagnosis, or prevention of disease or injury of a patient.
A health care process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies.
A health care process which results in physical changes in a specified input material
health care process biomaterial transformation
A health care process that produces output from input data
A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process.
prophylactic treatment
A treatment whose completion is hypothesized by a health care provider to eliminate a disorder or to alleviate the signs and symptoms of a disorder or pathological process.
therapeutic procedure
A therapeutic procedure that uses synthetic or naturally-occurring chemicals
chemotherapy procedure
A therapeutic procedure that uses immune system derived entities.
immunotherapy procedure
A therapeutic procedure that uses physical conditioning
physical therapy procedure
A therapeutic procedure that uses radiation.
radiation therapy procedure
A disease stage characterized by the lack of symptoms associated with a given disease
asymptomatic
A disease stage that marks the beginning of a disease
onset
A disease stage with a rapid unfolding of signs and symptoms
acute onset
A remission which is characterized by a prolonged lack of all manifestations of a disease
complete remission
A remission which is characterized by a prolonged lack of some manifestations of a disease
partial remission
A quality in which complete clearance of the disorder is attained; however, physiological 'memory' may persist
recovered from disease
A data item that is about a patient and is the specified output of a health care process assay or diagnostic process
clinical data item
An abnormal material entity that is part of a patient and hypothesized to be clinically relevant.
Example: an abnormal growth, an inflammatory infiltrate, swollen tissue, distension
The process in which an allergic disease unfolds.
The process in which an autoimmune disease unfolds.
A cancer progression stage characterized by abnormal cellular growth contained within normal tissue boundaries (e.g. carcinoma in situ).
A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass.
A cancer progression stage characterized by abnormal cellular growth that extends well beyond normal local tissue boundaries as a contiguous mass.
A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to one or more regional draining lymph nodes.
A cancer progression stage characterized by abnormal cellular growth that extends through normal local tissue boundaries as a contiguous mass and includes metastasis to other distant tissues besides lymph nodes.
The process in which an infectious disease unfolds
An abnormal processual entity occuring in a patient that is hypothesized to be clinically relevant.
An abnormal observable quality of a part of a patient that is hypothesized to be clinically relevant.
Example: the color of a rash; the shape of a melanoma
A therapeutic procedure in which a body part is transferred into a organism
A transplantation in which the body part is a non-fluid tissue
A transplantation in which the body part is a bodily fluid
A disorder of some macroscopic part of a tissue
A tissue disorder that has resulted from a dysregulation of cell proliferation leading to a net increase in mass
This class should be imported from OBI. https://github.com/OGMS/ogms/issues/105
disease stage