Sivaram Arabandi
Albert Goldfain
2009-08-07
Alan Ruttenberg
Werner Ceusters
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 2018-11-27 aka 'v2018'
The OGMS developer site is https://github.com/OGMS/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 baeverma@jcvi.org. Be sure to include a google-account username with your request (this will be the username associated with a gmail address).
Bill Hogan
Lindsay Cowell
Cornelius Rosse
Richard Scheuermann
This ontology is in early development. Expect it to change.
Anand Kumar
Daniel Merico
2018-11-27
Barry Smith
definition
editor note
definition editor
definition source
curator note
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
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.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2010-07-19T10:18:02Z
clinical finding
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
A representation of clinically significant bodily components, dispositions, and/or bodily processes of a human being that is inferred from relevant clinical findings.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2010-07-19T10:20:20Z
clinical picture
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
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
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.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T10:22:44Z
preclinical finding
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
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2010-11-18T11:02:10Z
symptom
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.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:12:33Z
manifestation of a disease
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.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2010-07-19T11:13:49Z
phenotype
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.
note: defined class
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2010-11-18T11:14:36Z
sign
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
creation date: 2009-06-23T11:15:43Z
clinical manifestation of a disease
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
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:16:50Z
preclinical manifestation of a disease
A clinically abnormal phenotype.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:18:05Z
clinical phenotype
A clinically abnormal phenotype that is characteristic of a single disease.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:18:39Z
disease phenotype
A physical sign in which a non-zero value is standardly considered to be an indication that the organism is alive.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:19:17Z
vital sign
A disposition in an organism that constitutes an increased risk of the organism's subsequently developing the disease X.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:20:25Z
predisposition to disease of type X
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:21:20Z
disease
Albert Goldfain
creation date: 2009-06-23T11:22:01Z
homeostasis
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.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:23:07Z
genetic predisposition to disease of type X
A disease whose physical basis is an acquired genetic disorder.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:24:05Z
acquired genetic disease
A disease whose physical basis is a constitutional genetic disorder.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:24:59Z
constitutional genetic disease
Homeostasis that is clinically abnormal for an organism of a given type and age in a given environment.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:26:44Z
abnormal homeostasis
Homeostasis of a type that is not clinically abnormal.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:27:28Z
normal homeostasis
A quality which is an spatial arrangement or distribution of a(n) independent continuant(s) across a Three Dimensional Region.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:36:24Z
configuration
A configuration which deviates in some way from a canonical configuration for a particular organism.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:36:58Z
pathological physical configuration
A material entity which is clinically abnormal and part of an extended organism. Disorders are the physical basis of disease.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:39:44Z
disorder
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.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:40:27Z
epigenetic disorder
A disorder whose etiology involves an abnormality in the nucleotide sequence of an organism's genome.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:41:14Z
genetic disorder
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
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:43:09Z
acquired genetic disorder
A genetic disorder inherited during conception that is part of all cells in the organism.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:43:44Z
constitutional genetic disorder
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.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:49:16Z
clinical history taking
A measurement assay that has as input a patient-derived specimen and as output a data itme that is about a quality of the specimen.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:49:49Z
laboratory test
A sequence of acts of observing and measuring qualities of a patient performed by a clinician; measurements may occur with and without elicitation.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2010-07-19T11:50:18Z
physical examination
A process in an organism that leads to a subsequent disorder.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:53:07Z
etiological process
Albert Goldfain
creation date: 2009-06-23T11:53:49Z
bodily process
A bodily process that is clinically abnormal.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:54:29Z
pathological bodily process
The totality of all processes through which a given disease instance is realized.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:55:44Z
disease course
A disease course that (a) does not terminate in a return to normal homeostasis and (b) would, absent intervention, fall within abnormal homeostatic range.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:56:26Z
chronic disease course
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.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:57:09Z
progressive disease course
A disease course that terminates in a return to normal homeostasis.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T11:57:44Z
transient disease course
Albert Goldfain
creation date: 2009-06-23T11:58:22Z
_undefined primitive term
Albert Goldfain
creation date: 2009-06-23T11:59:24Z
clinically abnormal
Albert Goldfain
creation date: 2009-06-23T12:00:09Z
physical basis
Albert Goldfain
creation date: 2009-06-23T12:00:39Z
realization
The representation of a conclusion of a diagnostic process.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-23T12:42:23Z
diagnosis
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.
Albert Goldfain
http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf
creation date: 2009-06-26T10:31:34Z
normal value
TODO: Define, relate to disorder, and place in the OGMS hierarchy.
Albert Goldfain
http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
creation date: 2009-07-13T02:14:59Z
pathological formation
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.
Albert Goldfain
http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
creation date: 2009-07-13T02:14:05Z
pathological anatomical structure
TODO: Define, relate to disorder, and place in the OGMS hierarchy.
Albert Goldfain
http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
creation date: 2009-07-13T02:15:17Z
portion of pathological body substance
A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure.
Albert Goldfain
http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
creation date: 2009-07-13T02:17:07Z
pathological transformation
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
http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
creation date: 2009-07-13T02:17:24Z
pathological derivation
TODO: Define.
Albert Goldfain
http://ontology.buffalo.edu/bio/ISMB/ISMB_Bio-ontologies.pdf
creation date: 2009-07-13T02:17:47Z
pathological invasion
TODO: Define.
Albert Goldfain
http://code.google.com/p/ogms/issues/detail?id=26
creation date: 2009-11-24T04:51:11Z
physical examination finding
An aggregate of organisms of the same type.
Albert Goldfain
http://code.google.com/p/ogms/issues/detail?id=33
creation date: 2009-11-24T04:51:11Z
organism population
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.
Albert Goldfain
http://www.referent-tracking.com/RTU/sendfile/?file=painTokyo1_27_2011.pdf
creation date: 2009-11-24T04:51:11Z
pain
A pattern of signs and symptoms that typically co-occur.
Albert Goldfain
http://code.google.com/p/ogms/issues/detail?id=32
creation date: 2009-11-24T04:51:11Z
syndrome
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.
Albert Goldfain
http://code.google.com/p/ogms/issues/detail?id=3
creation date: 2010-01-25T04:51:11Z
extended organism
A communication from a patient about something they perceive as being abnormal about their body or life.
Albert Goldfain
http://code.google.com/p/ogms/issues/detail?id=12
creation date: 2010-01-25T04:51:11Z
patient symptom report
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
http://code.google.com/p/ogms/issues/detail?id=28
creation date: 2010-03-31T04:51:11Z
congenital malformation
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
Albert Goldfain
http://code.google.com/p/ogms/issues/detail?id=35
creation date: 2010-03-31T04:51:11Z
treatment
A processual entity during which a patient participating in a disease course gradually returns to participating in a canonical life course.
Albert Goldfain
http://code.google.com/p/ogms/issues/detail?id=35
creation date: 2010-03-31T04:51:11Z
convalescence
A process which has as parts all the processes in which a given organism is participant.
Albert Goldfain
Richard Scheuermann
Sagar Jain
http://code.google.com/p/ogms/issues/detail?id=38
creation date: 2010-03-31T04:51:11Z
EDIT: 10 NOV 2015
life course
A hypothesis about some future part of a disease course.
Albert Goldfain
http://code.google.com/p/ogms/issues/detail?id=35
creation date: 2010-03-31T12:42:23Z
prognosis
a disease course with an acute onset
Albert Goldfain
http://code.google.com/p/ogms/wiki/Meeting_notes_20100513
creation date: 2010-07-19T11:57:44Z
acute disease course
A bodily process caused by some disorder that results in recruitment of leukocytes into a localized tissue site, typically causing localized pain and swelling.
Albert Goldfain
Richard Scheuermann
Sagar Jain
http://code.google.com/p/ogms/wiki/Meeting_notes_20100513
creation date: 2010-07-19T11:57:44Z
Updated: 10 NOV 2015
inflammatory process
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
Albert Goldfain
Sagar Jain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
editor date: 2017-04-18
health care 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
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
health care encounter
TODO
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
hospitalization
TODO
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
outpatient encounter
TODO
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
inpatient encounter
TODO
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/a2dbc2ed1dff99d6
creation date: 2011-02-21T09:57:44Z
ED encounter
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.
Albert Goldfain
Sagar Jain
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
injury
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.
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/e42bde79218ee34e
creation date: 2011-09-20T09:57:44Z
disease prophylaxis
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).
Albert Goldfain
http://groups.google.com/group/ogms-discuss/browse_thread/thread/2a7008f311fac766/e7de486c94dfd82e
creation date: 2011-09-20T09:57:44Z
diagnostic process
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.
Albert Goldfain
Richard Scheuermann
Sagar Jain
http://code.google.com/p/ogms/issues/detail?id=73
10 NOV 2015
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.
Albert Goldfain
Richard Scheuermann
Sagar Jain
http://code.google.com/p/ogms/issues/detail?id=73
10 NOV 2015
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.
2017-04-18
Sagar Jain
ancillary health care process
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.
creation: 16MAY2017
Sagar Jain
health care process assay
A health care process which results in physical changes in a specified input material
creation: 16MAY2017
Sagar Jain
health care process biomaterial transformation
A health care process that produces output from input data
creation: 16MAY2017
Sagar Jain
health care process data transformation
A treatment whose completion is hypothesized by a health care provider to prevent the signs and symptoms of a disorder or pathological process.
Creation date: 2018-11-27
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.
Creation data: 2018-11-27
therapeutic procedure
A therapeutic procedure that uses synthetic or naturally-occurring chemicals
creation date: 2018-11-27
chemotherapy procedure
A therapeutic procedure that uses immune system derived entities.
creation date: 2018-11-27
immunotherapy procedure
a therapeutic procedure that uses physical conditioning
creation date: 2018-11-27
physical therapy procedure
A therapeutic procedure that uses radiation.
creation date: 2018-11-27
radiation therapy procedure
a disease stage characterized by the lack of symptoms associated with a given disease
creation date: 2018-11-27
asymptomatic
a disease stage that marks the beginning of a disease
creation date 2018-11-27
onset
a disease stage with a rapid unfolding of signs and symptoms
creation date 2018-11-27
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
creation date: 2018-11-27
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
creation date: 2018-11-27
clinical data item
A part of a disease course
This class should be imported from OBI. https://github.com/OGMS/ogms/issues/105
disease stage