The LUMC Clinical Ontology (LCO) provides an ontology for integration of health observational data collected in the LUMC hospital for patient monitoring and research. 16-06-2021 16-06-2021 free to use,share,modify. modify with attribution [http://creativecommons.org/licenses/by/4.0/]. LUMC Clinical Ontology (LCO) 1.0 hasVersion A related resource that is a version, edition, or adaptation of the described resource. has version SIO_000001 A is related to B iff there is some relation between A and B. is related to hasScale has scale LABO_0000118 has minimal value LABO_0000119 has maximal value CMO_0001109 Any measurement of the degree to which the presentation of a disease state has caused pain or damage, established one or more lesions or infectious colonies, and/or taken over or interfered with the normal functioning of the body as a whole, or of one or more organs, tissues, cells or subcellular mechanisms of an organism. disease severity measurement NCIT_C164796 an identifier for a donor in a biobank. donor registry identifier NCIT_C25214 Systematic, objective appraisal of the significance, effectiveness, and impact of activities or condition according to specified objectives and criteria. evaluation NCIT_C25664 An ordered reference standard used to measure incremental changes. scale NCIT_C81265 A description of the technique for the appraisal of a subject or object. evaluation method OBI_1110087 a role which inheres in an organism or part thereof from which any part including cell, organ or tissue is removed with the intention that the donated part will be placed into another organism and/or cultured in vitro. donor role Standard a reference point against which other things can be evaluated or compared. standard SIO_000000 every thing is an entity. entity SIO_000015 information content entity is an object that requires some background knowledge or procedure to correctly interpret. information content entity SIO_000614 an attribute is a characteristic of some entity. attribute SIO:000653 A version label is a label for a particular form or variation of an earlier or original type. version label SIO_000883 a subject role is the role of an individual that is the target of the study. subject role SIO_001023 a medical screening is a medical test or series used to detect or predict the presence of disease in individuals at risk for disease within a defined group, such as a population, family, or workforce medical screening SIO_001331 a diagnosis is the result of a medical investigation to identify a disorder from its signs and symptoms. diagnosis has agent SIO_000642 is base for is a relation between a quality and the realizable entity that it is the basis for. is base for SIO_001024 A medical procedure is a procedure to identify, examine, alleviate or eliminate an undesirable biological disease or disorder. medical procedure a core relation that holds between a part and its whole. BFO_0000050 part of a measurement unit label is as a label that is part of a scalar measurement datum and denotes a unit of measure. IAO_0000003 measurement unit label a measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. measurement datum IAO_0000109 a primitive, instance-level, relation obtaining between an information content entity and some portion of reality. Denotation is what happens when someone creates an information content entity E in order to specifically refer to something. The only relation between E and the thing is that E can be used to 'pick out' the thing. This relation connects those two together. denotes IAO_0000219 NCIT_C21541 healthcare facility the buildings and organizations where healthcare services are provided, e.g. ward. NCIT_C25164 date the particular day, month and year an event has happened or will happen. order the act of requesting that a person, business, or organization do or supply something. NCIT_C48906 a planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. OBI_0000070 assay OBI_0000272 a plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. protocol OBI_0000968 a material entity that is designed to perform a function in a scientific investigation, but is not a reagent. device RO_0001025 located in a relation between two independent continuants, the target and the location, in which the target is entirely within the location. starts during is a relation between a process and an information content entity that states a point or period of time when the process has to start. X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y)), e.g. the patient sampling starts during what is stated in the order done by the medical doctor. RO_0002091 starts during an identifier for a patient participating in the Beat-COVID study. beat_covid_id beat-covid identifier clinical_id an identifier for a patient in the clinical database. clinical identifier an identifier for a sample or set of samples. sample identifier record_id an established standard to which the described resource conforms. conforms to conformsTo date a point or period of time associated with an event in the lifecycle of the resource. date an unambiguous reference to the resource within a given context. identifier identifier a material entity is a physical entity that is spatially extended, exists as a whole at any point in time and has mass. material entity SIO_000004 SIO_000005 quality a quality is an attribute that is intrinsically associated with its bearer (or its parts), but whose presence/absence and observed/measured value may vary. SIO_000006 process a process is an entity that is identifiable only through the unfolding of time, has temporal parts, and unless otherwise specified/predicted, cannot be identified from any instant of time in which it exists. SIO_000008 has attribute is a relation that associates a entity with an attribute where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type. has attribute SIO_000011 is attribute of is attribute of is a relation that associates an attribute with an entity where an attribute is an intrinsic characteristic such as a quality, capability, disposition, function, or is an externally derived attribute determined from some descriptor (e.g. a quantity, position, label/identifier) either directly or indirectly through generalization of entities of the same type. SIO_000016 a role is a realizable entity that describes behaviours, rights and obligations of an entity in some particular circumstance. role an identifier is a label that specifically refers to (identifies) an entity (instance/type). identifier SIO_000115 SIO_000132 has participant has participant is a relation that describes the participation of the object in the (processual) subject. has quality has quality is a relation between an entity and the quality that it bears. SIO_000217 has unit is a relation between a quantity and the unit it is a multiple of. has unit SIO_000221 has role SIO_000228 has role is a relation between an entity and a role that it bears. SIO_000229 has output is a relation between a process and an entity, where the entity is present at the end of the process. has output has input is a relation between a process and an entity, where the entity is present at the beginning of the process. SIO_000230 has input SIO_000291 has target is a relation between a process and an entity, where the entity is present at the beginning of the process and undergoes a change or transformation in the process. has target a relation between a informational entity and its actual value (numeric, date, text, etc). has value SIO_000300 realizable entity a realizable entity is an attribute that is exhibited under some condition and is realized in some process. SIO_000340 SIO_000356 the role of a patient is realized in medical examination. is realized in person SIO_000498 a person is an object that has certain capacities or attributes constituting personhood. refers to refers to is a relation between one entity and the entity that it makes reference to. SIO_000628 is identifier for SIO_000672 a relation between an identifier and an entity. institute is a society or organization having a object or common factor, and is normally applied to those with a scientific, educational, or social objective, e.g. Leiden University Medical Center (LUMC). SIO_000688 institute SIO_000715 patient role a patient role is the role of an individual that is the recepient of medical care. an object is an entity that is wholly identifiable at any instant of time during which it exists. object SIO_000776 measured at is a relation between a measurement value and the time measurement. measured at SIO_000793 real real is the quality of an entity that exists in real space and time. SIO_000960 unsupported SIO_000992 unsupported is an existence quality in which there is no evidence to support the existence of the entity in any world (real or hypothetical). age is the length of time that a person has lived or a thing has existed. SIO_001013 age sampling sampling is the act of obtaining a sample, whether through selection, collection or preparation. SIO_001049 sample a sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use. SIO_001050 positive SIO_001210 positive is an assertional qualifier that expresses the validity or truth of a basic assertion, e.g. in a medical examination the observation is the presence of a trait or phenotype. negative negative is an assertional qualifier that expresses the falsity or lack of truth of a basic assertion, e.g. in a medical examination the observation is the absence of a trait or phenotype. SIO_001211 never refers to in none of the occasions. SIO_001289 never always indicates that the event occurs at all times. SIO_001292 always SIO_001403 is associated with x is associated with y when x and y are logically or statistically related to one another. organ an organ is a collection of tissues joined in structural unit to serve a common function. SIO_010003 a gene is part of a nucleic acid that contains all the necessary elements to encode a functional transcript. gene SIO_010035 protein a protein is an organic polymer that is composed of one or more linear polymers of amino acids. SIO_010043 phenotype SIO_010056 a phenotype is an observable characteristic of an individual. is encoded by SIO_010079 a relation between two objects, in which the first object is produced from the information contained in the second object. has bioassay type is a relation that associates the output of a property evaluated in a bioassay and the category of bioassay based on the property or process that the assay is interrogating, e.g. ADMET, functional, etc. has bioassay type BAO_0002854 A human-readable name for the subject. label label was informed by wasInformedBy was informed by is a relation between two processes where one process communicates to another process. Communication is the exchange of an entity by two activities, one activity using the entity generated by the other.