]> hasCountryOfOrigin the relationship between a fraction and the number above the line Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB has numerator the relationship between a fraction and the number below the line (or divisor) Alejandra Gonzalez-Beltran Orlaith Burke Philippe Rocca-Serra AGB has denominator A generically dependent continuant which derives its existence and its entire endowment from an intending experience of consciousness (an "act") that is laden with determinate, uniformily structured content. MB: Right now we represent 'purely intentional entities' as siblings to 'information content entities'. Given their nature I am not entirly sure that this is correct. It seems that both 'information content entity' and 'simulation' are subclass to 'purely intentional entity'. purely intentional entity A duration of the parts of an infection during which the host bears an infectious disposition in a population of hosts. Mathias Brochhausen MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs. infectious period duration A duration of the time interval between the host acquiring an infection and the host bearing a contagiousness disposition during the same disease course within a population of hosts. Mathias Brochhausen MB: In order to get the temporal occupation relations I added properties that I renamed with BFO2 URIs The duration of the period between when an organism becomes infected and when it becomes infectious. latent period duration Mathias Brochhausen count of simulated exposed population Mathias Brochhausen count of simulated contagious population Mathias Brochhausen count of simulated resistant population The count of (simulated organisms) in a simulated population. Mathias Brochhausen MW: I know this causes problems with our set-theoretic definition. Unfortunately the compartmental models produce fractional counts at each of their time steps, including the final step. Any ideas? I’ve considered and rejected allowing individual organisms to be fractional. Perhaps if we just replace the term “cardinality” in the definition with ‘computed size’ count of simulated population A simulation of a population or populations of organisms of a particular biological taxon that simulates a particular type of event or types of event that occur in a specified time interval. Mathias Brochhausen simulated population simulation of population A measurement datum that is the output of counting. Mathias Brochhausen count The planned process of finding the number of elements in a finite set of objects. Mathias Brochhausen http://en.wikipedia.org/wiki/Counting counting Mathias Brochhausen Motivating use case is to cover Synthia data, and possibly configuration/output of the MRSA simulator in the MIDAS community (CA-MRSA Repast). hospital patient population census A purely intentional entity that simulates an entity and its properties. simulation The count of individuals in a contagious population (empirical or virtual). count of contagious population The count of individuals in a resistant population (empirical or virtual). count of resistant population A census that is the outcome of a population survey. population census Motivating use case is Synthia synthetic population data. nursery school student population census Motivating use case is Synthia synthetic population data. primary school student population census Motivating use case is Synthia synthetic population data. secondary school student population census A data set of a specific entity in a specified region at a specified time. Mathias Brochhausen census Mathias Brochhausen Motivating use case is Synthia synthetic population data. school student population census The probability of the occurence of an infection acquisition from one infected organism to another when in contact. transmission probability asymptomatic host An organism of a particular biological taxon that is the site of reproduction of an organism of a different taxon. host A information content entity that specifies the date of a census. Mathias Brochhausen census reference date A measurement datum that quantifies a temporal region that is occupied by a processual entity. Mathias Brochhausen duration The duration between the appearance of symptoms of a disease and the start of a treatment. Mathias Brochhausen delay from symptoms to treatment An infection acquisition whereby a susceptible host acquires an infection from an infectious host. William R. Hogan infection acquisition from infectious host The duration from the time an organism satisfies a case definition until a process or system detects the organism as satisfying that case definition Mathias Brochhausen time delay to case detection A duration that measures the temporal interval occupied by a treatment course. Mathias Brochhausen duration of treatment course The count of the number of doses that are part of a treatment course. Mathias Brochhausen number of doses in a treatment course The duration from the time an individual receives a treatment until the time a system designed to detect that the treatment occurred detects it in a population William R. Hogan time delay of treatment detection A data item that is about a proposition and has a numeric value between 0 and 1, inclusive, that is the output of some process of inference, such that 1) logical falsehoods and logical truths are assigned a value of 0 and 1, respectively, while contingent propositions are assigned some intermediate value; and 2) the process of inference conforms with rules for the calculation of probabilities, and that any interpretation of probability must specify the extent to which probabilities might be used to constrain the degrees of belief of rational agents. Matthew Diller William R. Hogan The first criterion is derived from Kolmogorov's Probability Calculus, while the second is derived from Salmon's Admissibility and Applicability Criteria of Adequacy. Salmon's ascertainability criterion is subsumed by the definition for 'data item'. probability A count of individuals in a population who meet the criteria of some case definition during some time interval. Matthew Diller William R. Hogan count of disease cases A count of disease cases in an infected population that meet the case definition criteria within a particular epidemic interval. Matthew Diller William R. Hogan count of cases in an epidemic A population census about the organisms specific to that population that were the host in some colonization acquisition. Matthew Diller William R. Hogan population colonization census An infection acquistion from infectious host that is causally downstream of some potentially infectious sexual contacting Matthew Diller Note that infections that are acquired in this manner do not fall within the class of sexually transmitted infections (STI's), ipso facto. This type of transmission can also occur with non-STI pathogens--such as meningitis and Zika. infection acquisition through sexual activity with infectious host Qualitative description of a microbial response to antimicrobial agents and the expected clinical outcome. Bacteria may be susceptible or resistant to a broad range of antibiotic drugs or drug classes, with several intermediate states or phases. antimicrobial phenotype Intermediate sensitivity of a bacterial strain to a given antibiotic occurs when it is inhibited by a concentration of the drug that is associated with uncertain therapeutic effect. The elimination of intermediate phenotype bacteria may depend on the site of infection and/or the concentration of the administered drug. intermediate antimicrobial phenotype A bacterial strain is said to be resistant to a given antibiotic when it is inhibited in vitro by a concentration of this drug that is associated with a high likelihood of therapeutic failure. resistant antimicrobial phenotype A bacterial strain is said to be susceptible to a given antibiotic when it is inhibited in vitro by a concentration of a drug that is associated with a high likelihood of therapeutic success susceptible antimicrobial phenotype A bacterial strain is said to be nonsusceptible to a given antibiotic drug if it demonstrates either an intermediate or resistant phenotype when exposed to a concentration of a drug that is associated with a high likelihood of therapeutic failure, i.e. if the bacterial strain is not susceptible to the antibiotic drug but not necessarily totally resistant under all conditions. nonsensitive antimicrobial phenotype nonsusceptible antimicrobial phenotype A bacterial strain is said to be susceptible-dose dependent (SDD) to a given antibiotic when growth is inhibited with a high likelihood of therapeutic success, but when multiple approved dosing options exist. When a higher or more frequent dose is used, the predicted therapeutic result is the same as for susceptible individuals. SDD Sensitive dose dependent antimicrobial phenotype susceptible dose dependent antimicrobial phenotype Multidrug-resistant organisms are defined as bacterial strains that have become resistant to multiple classes of antibacterial drugs or other agents. The phenotype of these organisms is defined by the spectrum of antibiotic drug classes to which that organism is resistant. Often, these organisms are susceptible to a narrow range of available drugs, making treatment difficult and urgent. MDRO multidrug resistance antimicrobial phenotype Uses breakpoints to create standards for interpreting the clinical outcome of an MIC value for a particular microbial species and antimicrobial agent antimicrobial resistance testing reference standard BSAC is a British inter-professional organisation involved in antibiotic education, research and leadership. Baquero F. found that the BSAC system recommends lower breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG). British Society for Antimicrobial Chemotherapy (BSAC) The Clinical and Laboratory Standards Institute develops and implements clinical laboratory testing standards. Clinical and Laboratory Standards Institute (CLSI) DIN is recognized by the Federal Government of Germany as the competent standards organization for Germany and as the national standards body representing Germany in non-governmental international standards organizations. Baquero F. found that the DIN system recommends lower breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG). Deutsches Institut für Normung (DIN) EUCAST is a standing committee jointly organized by ESCMID, ECDC and European national breakpoint committees; it deals with breakpoints and technical aspects of phenotypic in-vitro antimicrobial susceptibility testing. European Committee on Antimicrobial Susceptibility Testing (EUCAST) The French Society of Microbiology (SFM) is a non-profit association which aims to bring together microbiologists from French-speaking countries, working in the domains of bacteria, viruses, Fungi and parasites, and related medical, industrial and environmental microbiology, physiology, genetics, taxonomy, hygiene, and antimicrobial agents. Baquero F. found that the SFM system recommends higher breakpoints than the consensus standard of all systems for antimicrobial susceptibility testing used in Europe (BSAC, DIN, SFM, SIR, NCCLS and WRG). Société Française de Microbiologie (SFM) The measured or quantified MIC MIC value mg/L MIC unit An experimental test conducted outside of a living organism, usually in a tube or plate. in-vitro microbial susceptibility test System of analysis for determining antimicrobial susceptibility. antimicrobial resistance test platform Microbial species are inoculated in a growth medium onto which antimicrobial agents are transferred by diffusion. diffusion method Components of complex mixtures such as plant extracts are separated across a TLC plate and tested for anti-microbial activity. thin-layer chromatography (TLC)-bioautography Allows for time-dependent or concentration-dependent analysis of antimicrobial effects. Several tubes of broth culture medium containing a suspension of the test microbe are treated with varying concentrations of the antimicrobial agent and the percentage of dead cells determined at various time points. time kill curve time-kill test Relies on the indirect measurement of microbe populations by quantifying microbial ATP production. ATP bioluminescence assay Microbes exposed to antimicrobial agents are then stained with the intercalating agent propidium iodide. Damaged cells emit a positive signal that is detected by flow cytometry analysis. Flow cytometry can also be used to discriminate between dead, damaged and live cells. flow cytofluorometric method Test that directly detect the presence of a particular resistance mechanism. mechanism-specific test The microbial species are inoculated in liquid growth medium containing incremental dilutions (usually 2-fold) of the antimicrobial agent. broth dilution method Automated system of analysis for determining antimicrobial susceptibility. automated testing platform Non-automated system of analysis for determining antimicrobial susceptibility. noncommercial testing platform manual testing platform Specific automated system of analysis for determining antimicrobial susceptibility developed by Omron. MicroScan Specific automated system of analysis for determining antimicrobial susceptibility developed by Becton Dickinson. Phoenix Specific automated system of analysis for determining antimicrobial susceptibility developed by Trek, Thermo Fisher Scientific. Sensitire Specific automated system of analysis for determining antimicrobial susceptibility developed by bioMérieux. Vitek System Vendor of automated system of analysis for determining antimicrobial susceptibility. automated testing platform vendor Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in New Jersey, USA. Becton Dickinson is the developer of the Phoenix automated testing platform. Becton Dickinson Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in France. bioMérieux is the developer of the Vitek automated testing platform. bioMérieux Specific vendor of automated system of analysis for determining antimicrobial susceptibility headquartered in Berlin and Munich. Siemens Specific vendor of automated system of analysis for determining antimicrobial susceptibility based in Japan. Omron is the developer of the MicroScan automated testing platform. Omron Specific vendor of automated system of analysis for determining antimicrobial susceptibility that was acquired by Thermo Fisher Scientific Inc. Thermo Fisher Scienfiic Inc. is headquartered in Massachusetts, USA. Trek is the developer of the Sensitire automated testing platform. Thermo Fisher Scientific Trek Broth dilution conducted on 96-well microtiter plates (≤200 µL per well). micro broth dilution method This test is a common method of evaluating the antimicrobial activity of plants or microbial extracts. In this method, bacteria are inoculated onto agar plates and the antimicrobial agent is injected into the plate and allowed to diffuse. agar well diffusion method This method is commonly used to study the antagonism between microorganisms. The first bacterial strain is inoculated onto agar plates in tight streaks. The bacteria will secrete molecules that diffuse in the agar medium; this medium is cut and placed on another agar plate inoculated with another microorganism. agar plug diffusion method This method is commonly used to study the antagonism between microorganisms. The microbial strain of interest is seeded by a single streak in the center of the agar plate. After incubation, the plate is seeded with the second microorganism by single streak perpendicular to the central streak. cross streak method The antimicrobial agent is transferred from a chromatogram to an agar plate previously inoculated with the test microorganism. agar diffusion bioautography A developed TLC plate is dipped into or sprayed with a microbial suspension and then incubated. Live microbial cells are visualized using tetrazolium salts. direct bioautography The TLC plate is covered with a molten agar medium seeded with the test microbe and the antimicrobial compounds are allowed to diffuse onto the agar medium. Tetrazolium dye staining allows for visualization. agar overlay bioassay agar overlay bioautography Assay for beta lactamase detection chromogenic cephalosporinase test Commercial colorimetric assay for detection of chloramphenicol modifying enzyme chloramphenicol acetyltransferase. chloramphenicol acetyltransferase assay (CAT) The tissue type used to select breakpoints from a particular standard, for the interpretation of MIC results. antimicrobial resistance tissue specificity Qualitative description of a microbial response to antimicrobial agents as described by EUCAST using breakpoints determined through in-vitro testing. These breakpoints are determined irrespective of tissue specificity of infection. EUCAST antimicrobial phenotype A microbe whose susceptibility to antibiotics is comparable to that of a reference susceptible microbe, meaning that the microbe is sensitive to the particular antibiotic. wild-type A microbe whose susceptibility to antibiotics differs from that of a reference susceptible microbe, meaning that the microbe is resistant to the particular antibiotic. non wild-type Qualitative description of a microbial response to antimicrobial agents as described by CLSI using breakpoints that take into consideration tissue specificity of infection. CLSI antimicrobial phenotype A method to determine microbial susceptibility to antibiotics in which test bacteria is inoculated onto an agar plate that contains a concentration gradient of antibiotic. The minimum inhibitory concentration of antibiotic is assessed. gradient plate method entity 实体 entity entity 实体 continuant 常体 An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. 一个在任何时候都存在的实体，它持续存在，在维持其特性的同时且没有暂时的部分。 continuant continuant 常体 occurrent An entity that has temporal parts and that happens, unfolds or develops through time. occurrent independent continuant 独立常体(Independent Continuant) A continuant that is a bearer of quality and realizable entity entities, in which other entities inhere and which itself cannot inhere in anything. b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) b是一个独立常体= Def. b是一个常体，使得在t时刻不存在c，也不存在t，从而在t时刻b s-依赖_于c。 （BFO2公理标签参考：[017-002]） 常体是质量和可实现实体的载体，其中其他实体在其中并且本身不能在任何地方存在。 independent continuant 独立常体 process An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) process process disposition A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. realizable entity quality A dependent entity that inheres in a bearer by virtue of how the bearer is related to other entities. A quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. 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. https://en.wikipedia.org/wiki/Quality_(philosophy) https://www.wikidata.org/wiki/Q1207505 The etymology of "quality" is fairly well elucidated coming from Middle English, from Old French qualité, from Latin qualitatem, accusative of qualitas, from qualis (“of what kind”), from Proto-Indo-European *kʷo- (“who, how”). Cicero coined qualitas as a calque to translate the Ancient Greek word ποιότης (poiótēs, “quality”), coined by Plato from ποῖος (poîos, “of what nature, of what kind”). quality quality specifically dependent continuant A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. A continuant that inheres in or is borne by other entities. Every instance of A requires some specific instance of B which must always be the same. b is a relational specifically dependent continuant = Def. b is a specifically dependent continuant and there are n > 1 independent continuants c1, … cn which are not spatial regions are such that for all 1 i < j n, ci and cj share no common parts, are such that for each 1 i n, b s-depends_on ci at every time t during the course of b’s existence (axiom label in BFO2 Reference: [131-004]) b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) specifically dependent continuant A realizable entity the manifestation of which brings about some result or end that is not essential to a continuant in virtue of the kind of thing that it is but that can be served or participated in by that kind of continuant in some kinds of natural, social or institutional contexts. role ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. object aggregate A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) generically dependent continuant material entity 物质实体 A material entity is an entity that exists in full during the length of time of its existence, persists through this time while maintaining its identity and has no temporal parts. For example a heart, a human, a fly, a microarray. An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time. 一个独立常体，是空间扩展的，其性质独立于其他实体，可以通过时间来维持。 James Malone http://www.ifomis.org/bfo/1.1/snap#MaterialEntity material type material entity material entity 物质实体 intestinal cell line kidney cell line adenocarcinoma cell line colonic cell line Human colon adenocarcinoma cell line, established from the primary colon tumor (adenocarcinoma) of a 72-year-old Caucasian man in 1974. CACO-2 cell carcinoma cell line lung cell line Hepatoma is a cancer originating in the liver, in liver cells. More often called hepatocarcinoma or hepatocellular carcinoma. hepatoma cell line A glioma is a type of tumor that starts in the glial cells of the brain or the spine. Gliomas comprise about 30 per cent of all brain tumors and central nervous system tumors, and 80 per cent of all malignant brain tumors. glioma cell line lung cancer cell line colonic cancer cell line The MDBK cell line was derived from a kidney of an apparently normal adult steer, February 18, 1957, by S.H. Madin and N.B. Darby. MDBK cell epithelial cell line The Vero cell line was initiated from the kidney of a normal adult African green monkey on March 27, 1962, by Y. Yasumura and Y. Kawakita at the Chiba University in Chiba, Japan. Vero cell Pig kidney cell line. Original line: PK-2a; contains type C viruses. Morphology: epithelial-like. PK-15 cell lung adenocarcinoma cell line colonic adenocarcinoma cell line Human hepatoma cell line. HuH-7 cell bronchial epithelial cell line Human glioma cell line. Morphology: glial; Species: human; Tumor: glioma. U-251MG cell A highly transformed human renal epithelial line expressing two viral oncogenes, adenovirus E1a and SV40 large T antigen. HEK-293T cell respiratory epithelium cell line Human lung adenocarcinoma cell line; established from a 25-year-old caucasian male. Calu-3 cell renal epithelium cell line Rabbit renal epithelium cell line. RK-13 cell Normal human bronchial epithelial cell line. NHBE cell This line is a clone of VERO 76. VERO C1008 cell anatomical structure 解剖结构 material anatomical entity 物质解剖实体 Any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer etc., identifiable as a separately distinguishable entity. molecular entity An independent material continuant that is self-connected and retains its identity over time. portion of material A method that results in the separation of two or more components according to some property. FIX:0000002 partition separation method A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium, across which an electric field is applied. FIX:0000097 sep:00140 cataphoresis electrophoretic analysis electrophoresis A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium consisting of gel, across which an electric field is applied. sep:00150 gel electrophoresis An electrophoresis method where the separation medium contains a reticulated system, for example an entangled polymer network, that further separates the analytes according to their size and shape. sieving electrophoresis A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium, across which a pulsed electric field is applied (a field in which the voltage changes direction). pulsed-field electrophoresis A separation method where colloidal particles move at different speeds according to their electrophoretic mobilities in a separation medium consisting of gel, across which a pulsed electric field is applied (one in which the voltage direction is periodically switched among three directions; one that runs through the central axis of the gel and two that run at an angle of 120° either side). PFGE pulsed field gel electrophoresis pulsed-field gel electrophoresis Those components of a sample that are not measured by an experiment. matrix cell line cell cell line cell 细胞系细胞 A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture A cultured cell that is part of a cell line - a stable and homogeneous population of cells with a common biological origin and propagation history in culture 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 一个培养细胞，它是一个细胞株（一个稳定的，同质的细胞群，具有共同的生物学起源和增殖史）的一部分 Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters Yongqun He, Matthew Brush, Sirarat Sarntivijai, Alexander Diehl, Jie Zheng, Yu Lin, Bjoern Peters A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures. A 'cell line cell' is a part of a cell line established through the passaging/selection of a primary cultured cells or the experimental modification of an existing cell line. New types of cell line cells are established after sufficient passaging of a primary culture to establish a stable and homogenous population that qualifies as a line (typically 1-20 passages), or following some spontaneous or experimental modification that confers novel characteristics to an existing line. A cell line cell typically has mutations of five or more genes compared to the original cell that derives the cell line cell. Some gene mutations may turn on some oncogenes. Cell line cells can be in active culture, stored in a quiescent state for future use (e.g. frozen in liquid nitrogen), or applied in experimental procedures. “细胞系细胞”是通过原代培养细胞的传代/选择或现有细胞系的实验性修饰而建立的细胞系的一部分。新类型的细胞系细胞的建立过程是原代培养物充分传代后以建立符合条件（典型地1-20代）的稳定且同质的群体，或者在某些自发或实验性修饰之后赋予现有细胞系新的特征。与产生细胞系细胞的原始细胞相比，细胞系细胞通常具有5个或更多个基因的突变。 一些基因突变可能会开启一些致癌基因。 细胞系细胞可处于活性培养物中，以静止状态储存以供将来使用（例如在液氮中冷冻），或者在实验程序使用。 cell line cell cell line cell 细胞系细胞 immortal cell line cell immortal cell line cell 永生细胞系细胞 A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. A cell line cell that is expected to be capable of an unlimited number of divisions, and is thus able to support indefinite propagation in vitro as part of an immortal cell line. 预期能够进行无限次分裂的细胞系细胞，作为永生细胞系一部分，能够支持体外无限增殖。 Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak Yongqun He, Matthew Brush, Allen Xiang, Asiyah Yu Lin, Sirarat Sarntivijai, James Malone, Jie Zheng, Tomasz Adamusiak continuous cell line cell continuous cell line cell permanent cell line cell permanent cell line cell 永久细胞系细胞 连续细胞系细胞 immortal cell line cell immortal cell line cell 永生细胞系细胞 cell line 细胞系 A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). A cultured cell population that represents a genetically stable and homogenous population of cultured cells that shares a common propagation history (i.e. has been successively passaged together in culture). 一个培养细胞群体，其代表具有共同增殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 培养的细胞群体代表具有共同繁殖历史（即已经在培养中一起连续传代）的遗传稳定且同质的培养细胞群体。 MB, SS, JZ, MAH, BP, CS, YH MB, SS, JZ, MAH, BP, CS, YH The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history.  As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use. The term 'line' is used when a culture has undergone an intentional experimental process to establish a more uniform and stable population of cells (see 'establishing cell line'). This will require one or more passages, but may involve additional selection processes. Through such passaging and/or selection processes, the resulting 'line' attains some level of genetic stability and compositional homogeneity which is typically absent in primary cultures. Because of their relative homogeneity, ‘lines’ are capable of being characterized and stably propagated over a period of time. A new *type* of cell line can be established not only through the passaging/selection of a primary culture, but also through experimental modifications of existing lines (e.g. immortalization, stable genetic modifications, drug selection for a resistant subset, etc.). The definition provided here establishes the 'scale' of cell populations that qualify as cell lines - specifically those with a shared propagation history in culture. In this way, the 'cell line' class demarcates populations that represent what researchers actually use in the practice of science - e.g. as inputs to culturing, experimentation, and sharing. The definition is such that cell lines will exhibit important attributes. For example, they will have a relatively homogenous cell type composition as they have experienced similar selective pressures due to their continuous co-propagation. In addition, these populations can also be characterized by a passage number, again owing to their common passaging history.  As defined here, 'cell line' can refer to a population of cells in active culture, applied experimentally, or stored in a quiescent state for future use. 当培养物经过有意的实验过程以建立更均匀和稳定的细胞群时（参见“建立细胞系”），使用术语“系”。这将需要一个或多次传代，但可能涉及额外的选择过程。通过这样的传代和/或选择过程，产生的'细胞系'达到一定水平的遗传稳定性和组成均一性，这在原代培养物中通常是不存在的。由于它们的相对同质性，“细胞系”能够在一段时间内被表征和稳定地增殖。一种新*型*细胞系不仅可以通过原代培养物的传代/选择建立，而且可以通过对现有系列的实验性修饰（例如永生化，稳定的遗传修饰，用于抗性子集的药物选择等）来建立。 这里提供的定义确立了符合细胞系特征的细胞群的“范围” - 特别是那些在培养中具有共同繁殖历史的细胞群。通过这种方式，“细胞系”类划分代表研究人员在科学实践中实际使用的细胞群 - 例如作为培养、实验和分享的投入。定义是这样的，细胞系将显示重要的属性。例如，它们将具有相对均匀的细胞类型组成，因为它们的连续共增殖而经历了类似的选择压力。此外，这些细胞群还可以通过传代数来表征，这也是由于它们共同的传代史。如此处所定义的，“细胞系”可以指活性培养物中，实验性应用的或以静止状态存储以备将来使用的细胞群。 cell line 细胞系 An immortal cell line cell that derives from kidney. An immortal cell line cell that derives from kidney. 源自肾的永生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal kidney-derived cell line cell immortal kidney-derived cell line cell 永生化的肾衍生细胞系细胞 An immortal kidney-derived cell line cell that derives from rhesus macaque. An immortal kidney-derived cell line cell that derives from rhesus macaque. 源自恒河猴的永生肾衍生细胞系细胞。 Yue Liu, Yongqun He Yue Liu, Yongqun He immortal rhesus macaque kidney-derived cell line cell immortal rhesus macaque kidney-derived cell line cell 永生的恒河猴肾衍生细胞系细胞 LLC-MK subscript(2) LLC-MK subscript(2) LLC-MK subscript(2) cell LLC-MK subscript(2) cell LLC-MK subscript(2) 细胞 cell cell 细胞 A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. A material entity of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane. 解剖学起源（生物体的一部分或来源于生物体）的物质实体，其组成部分是一个被浆膜包围的最大连接的细胞室 CALOHA:TS-2035 CALOHA:TS-2035 FMA:68646 FMA:68646 GO:0005623 GO:0005623 KUPO:0000002 KUPO:0000002 VHOG:0001533 VHOG:0001533 WBbt:0004017 WBbt:0004017 XAO:0003012 XAO:0003012 The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). 细胞的定义是为了表示所有的细胞，因此细胞被定义为一个物质实体，而不是一个解剖结构，这意味着它是一个生物体的一部分（或一个整体）。 cell cell cell type cell type 细胞 细胞类型 cultured cell cultured cell 培养细胞 A cell in vitro that is or has been maintained or propagated as part of a cell culture. A cell in vitro that is or has been maintained or propagated as part of a cell culture. 一种体外细胞，其作为或已被维持或增殖为细胞培养物的一部分。 Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. Note that this class was re-labeled to 'cultured cell' instead of 'cell line cell', as it intent was clarified to cover any cultured cells of multicellular and unicellular organisms. This includes cells actively being cultured, or cells that have been cultured but are stored in a quiescent state for future use. In having been cultured, cells must establish homeostasis and often replicate in a foreign environment. Accomodation of this stress initiates a selection of cells fit for such challenges, wherein necessary adaptive biochemical and.or genetic changes can occur. These changes can set them apart from the in vivo cells from which they derive, and such changes will typically accumulate and change over increasing time in culture. 注意到这一类被重新标记为“培养细胞”而不是“细胞系细胞”，因为其目的被澄清以涵盖多细胞和单细胞生物体的任何培养细胞。这包括活化培养的细胞，或已经培养但以静止状态储存以供将来使用的细胞。在培养过程中，细胞必须建立稳态，并经常在外部环境中复制。这种压力适应启动了适应这种挑战的细胞选择，其中可能发生必要的适应性生化和/或遗传改变。这些变化可以使它们与其来源的体内细胞分开，这种变化通常会随着培养时间的增加而积累和改变。 cultured cell cultured cell 培养细胞 experimentally modified cell in vitro experimentally modified cell in vitro 体外实验修饰细胞 A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. A cell in vitro that has undergone physical changes as a consequence of a deliberate and specific experimental procedure. 经过一个深思熟虑和特定的实验过程而发生物理变化的细胞。 This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 This class has been re-labeled to imply reference only to in vitro experimentally modified cells, similarly, the definition has been slightly updated to reflect this. 'experimentally modified cell' refers only to cells in vitro, and not modified in vivo/in environment cells. There is currently no class representing unmodified in vitro cells (other than the parent 'cell in vitro'), or a class representing modified native cells. More granular subclassing of experimentally modified cell can be found in ReO. MHB 1.12.12 这个类已经被重新标记为仅仅涉及体外实验修饰的细胞，类似地，这个定义已经稍微更新以反映这一点。 “实验修饰的细胞”仅指体外细胞，而不是体内/环境细胞中的修饰。目前没有代表未经修饰的体外细胞的类别（除了亲代“体外细胞”）或代表修饰的天然细胞的类别。在ReO中可以找到更细化的实验修饰细胞亚类。 MHB 1.12.12 experimentally modified cell in vitro experimentally modified cell in vitro 体外实验修饰细胞 A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. A cell that is maintained or propagated in a controlled artificial environment for use in an investigation. 在受控人造环境中维持或繁殖的细胞，其用于调查。 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. 'In vitro', translating literally to 'in glass', typically refers to a controlled, often sterile, laboratory setting where cells or other specimens are placed by some agent for the purpose of studying or manipulating them as part of some research investigation. 'In vitro' is intended to contrast with 'native',which refers to cells or other biological entities that are found in a natural setting. It describes unicellular organisms removed from a natural environement and multicellular organism cells removed from an organism, or cells derived in culture from such displaced cells. 在字面上翻译成“类中”的“体外”通常指的是受控的，通常是无菌的实验室环境，其中细胞或其他样本被某些机构放置以用于研究或操纵它们作为一些研究调查的一部分。 “体外”旨在与“天然”形成对比，“天然”是指在自然环境中发现的细胞或其他生物实体。它描述了从天然环境中除去的单细胞生物体和从生物体中除去的多细胞生物体细胞，或从这种置换的细胞培养中得到的细胞。 cell in vitro cell in vitro 体外细胞 A exposure event involving the interaction of an exposure receptor to environmental material. environmental material exposure exposure to environmental material A exposure event involving the interaction of an exposure receptor to environmental system. environmental system exposure exposure to environmental system A exposure event involving the interaction of an exposure receptor to construction. construction exposure exposure to construction A exposure event involving the interaction of an exposure receptor to abattoir. abattoir exposure exposure to abattoir A exposure event involving the interaction of an exposure receptor to farm. farm exposure exposure to farm A exposure event involving the interaction of an exposure receptor to hospital. hospital exposure exposure to hospital A exposure event involving the interaction of an exposure receptor to laboratory facility. laboratory facility exposure exposure to laboratory A exposure event involving the interaction of an exposure receptor to office. office exposure exposure to office A exposure event involving the interaction of an exposure receptor to restaurant. restaurant exposure exposure to restaurant A exposure event involving the interaction of an exposure receptor to shop. shop exposure exposure to retail shop A history of exposure to root. root exposure exposure to organism A history of exposure to Homo sapiens. Homo sapiens exposure exposure to humans A exposure event involving the interaction of an exposure receptor to geographic feature. geographic feature exposure exposure to geographic feature A exposure event involving the interaction of an exposure receptor to petting zoo. petting zoo exposure exposure to petting zoo A exposure event involving the interaction of an exposure receptor to campground. campground exposure exposure to campground An exposure event involving behavior behavior exposure exposure to behavior An exposure event involving physical aggression behavior physical aggression behavior exposure exposure to violence An exposure event involving hunting behavior hunting behavior exposure exposure to hunting A system which has the disposition to environ one or more material entities. EcoLexicon:environment environment In ENVO's alignment with the Basic Formal Ontology, this class is being considered as a subclass of a proposed BFO class "system". The relation "environed_by" is also under development. Roughly, a system which includes a material entity (at least partially) within its site and causally influences that entity may be considered to environ it. Following the completion of this alignment, this class' definition and the definitions of its subclasses will be revised. environmental system A DNA sequencing by synthesis technique used to increase the sensitivity of the DNA sequencing process and permits the use of very small amounts of DNA starting material. This is accomplished by using a temperature cycling process similar to that employed in the polymerase chain reaction. PERSON: Nicole Vasilevsky http://www.answers.com/topic/cycle-sequencing cycle sequencing An assay that generates data about the presence, abundance, structure, function, or activity of biological molecules, or a process that occurs at a molecular level of granularity. PERSON: Nicole Vasilevsky PERSON: Matthew Brush molecular assay A DNA sequencing technique that became commercially available in 2004 and is used by specific commercial platforms that embody a complex interplay of enzymology, chemistry, high-resolution optics, hardware, and software engineering. These instruments allow highly streamlined sample preparation steps prior to DNA sequencing, which provides a significant time savings and a minimal requirement for associated equipment in comparison to the highly automated, multistep pipelines necessary for clone-based high-throughput sequencing. Each technology amplifies single strands of a fragment library and perform sequencing reactions on the amplified strands. The fragment libraries are obtained by annealing platform-specific linkers to blunt-ended fragments generated directly from a genome or DNA source of interest. Because the presence of adapter sequences means that the molecules then can be selectively amplified by PCR, and no bacterial cloning step is required to amplify the genomic fragment in a bacterial intermediate as is done in traditional sequencing approaches. PERSON: Nicole Vasilevsky Genome sequencing High throughput DNA sequencing High throughput nucleotide sequencing NGS Next gen Next gen sequencing Next generation sequencing of target genes Nucleotide sequencing, high-throughput Second generation sequencing Sequencing, high-throughput nucleotide Mardis (2008) Annu. Rev. Genomics Hum. Genet. 9:387-402 next generation DNA sequencing A DNA sequencing by ligation technique that involves a bead-based method that uses a complex approach of adapter ligation followed by adapter decoding, reading the sequence in increments of four nucleotides; this method made it susceptible to sequence-specific bias or loss of specific sequences. PERSON: Nicole Vasilevsky Lynx Therapeutics' Massively Parallel Signature Sequencing MPSS Massively Parallel Sequencing Massively-Parallel Sequencing Sequencing, Massively-Parallel Sequencings, Massively-Parallel http://en.wikipedia.org/wiki/DNA_sequencing#High-throughput_sequencing massively parallel signature sequencing A molecular assay that generates data about the presence, abundance, structure, function, or activity of nucleic acids. PERSON: Nicole Vasilevsky PERSON: Matthew Brush nucleic acid assay A next generation sequencing that monitors the incorporation of a nucleotide into a strand of DNA by sensing pH change from the release of a hydrogen ion corresponding to a bonding event. PERSON: Scott Hoffmann Ion torrent NGS NGS http://uagc.arl.arizona.edu/index.php/next-gen-sequencing-services/ion-torrent.html ion torrent next generation sequencing An interaction between an exposure stressor and an exposure_receptor. exposure event A process in which an organism or part of an organism participates towards the generation of offspring. James Malone NCIt:C21173 SNOMEDCT:272515006 reproductive process cellular_component cellular_component 细胞组分 cell cell 细胞 The actions or reactions of an object or organism, usually in relation to the environment or surrounding world of stimuli. E.g. Fixed action pattern courtship behaviour in Drosophila. Forager behaviour in honey bees. The internally coordinated responses (actions or inactions) of animals (individuals or groups) to internal or external stimuli, via a mechanism that involves nervous system activity. The observable response a person makes to any situation. James Malone Tomasz Adamusiak GO:0023032 GO:0044708 GO:0044709 GO:0007610 MeSH:D001519 NCIt:C16326 Wikipedia:Behavior Acceptance Process Acceptance Processes Behaviors Process, Acceptance Processes, Acceptance behavioral response to stimulus behaviour behavioural response to stimulus 1. Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation reviews. 2. While a broader definition of behavior encompassing plants and single cell organisms would be justified on the basis of some usage (see PMID:20160973 for discussion), GO uses a tight definition that limits behavior to animals and to responses involving the nervous system, excluding plant responses that GO classifies under development, and responses of unicellular organisms that has general classifications for covering the responses of cells in multicellular organisms (e.g. cell chemotaxis). I am trying to determine the difference between a process and a behaviour. Is behaviour dancing any different from the process dancing? behavior biological_process A biological process represents a specific objective that the organism is genetically programmed to achieve. Biological processes are often described by their outcome or ending state, e.g., the biological process of cell division results in the creation of two daughter cells (a divided cell) from a single parent cell. A biological process is accomplished by a particular set of molecular functions carried out by specific gene products (or macromolecular complexes), often in a highly regulated manner and in a particular temporal sequence. Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. Any process specifically pertinent to the functioning of integrated living units: cells, tissues, organs, and organisms. A process is a collection of molecular events with a defined beginning and end. The activities of living organisms that support life in single- or multi-cellular organisms from their origin through the progression of life. GO:0000004 GO:0007582 GO:0044699 GO:0008150 MeSH:D055705 NCIt:C17828 Wikipedia:Biological_process Physiological Processes biological process biological_process physiological process biological process unknown Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. Note that when this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code ND, no data, is used to indicate this. Note that, in addition to forming the root of the biological process ontology, this term is recommended for use for the annotation of gene products whose biological process is unknown. When this term is used for annotation, it indicates that no information was available about the biological process of the gene product annotated as of the date the annotation was made; the evidence code 'no data' (ND), is used to indicate this. biological process biological process biological_process Behavior directed towards society, or taking place between members of the same species. Occurs predominantly, or only, in individuals that are part of a group. Wikipedia:Social_behavior social behaviour Behavior such as predation which involves members of different species is not social. Communication between members of different species is also not social behavior. social behavior Penetration by an organism into the body, tissues, or cells of the host organism. The host is defined as the larger of the organisms involved in a symbiotic interaction. entry into host Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism. GO:0051869 physiological response to stimulus Note that this term is in the subset of terms that should not be used for direct gene product annotation. Instead, select a child term or, if no appropriate child term exists, please request a new term. Direct annotations to this term may be amended during annotation QC. response to stimulus Any process in which an organism has an effect on an organism of the same species. intraspecies interaction between organisms intraspecies interaction with other organisms biological process involved in intraspecies interaction between organisms An umbrella term often used in medical literature to include transgender persons and gender nonconforming people who may or may not be transgender. transgender and gender nonconforming An umbrella term often used in research to covered genderqueer and gender nonbinary identities, as well as gender nonconforming persons. genderqueer, gender non-conforming, and gender nonbinary genderqueer, gender nonconforming and gender nonbinary genderqueer, gender nonconforming, and gender nonbinary Either, a specific gender identity which is not male or female; or, more broadly, an umbrella term for gender identities not considered male or female. https://en.wikipedia.org/wiki/Category:Non-binary_gender gender non-binary "Non-binary" (with the hyphen) is more common in the United Kingdom, whereas "nonbinary" (as one word) is more common in the United States. Note that "nonbinary" as itself is preferable if the context in relationship to gender is known. Most therefore "nonbinary persons" not "gender nonbinary persons" can be used. gender nonbinary Equitable representation of persons of different genders. https://en.wikipedia.org/wiki/Gender_diversity https://www.wikidata.org/wiki/Q1501335 gender diversity Having a feminine gender (identity) which is different from the sex one was assigned at birth. https://en.wikipedia.org/wiki/Transfeminine https://www.wikidata.org/wiki/Q27679684 trans feminine transfeminine Having a masculine gender (identity) which is different from the sex one was assigned at birth. https://www.wikidata.org/wiki/Q27679766 trans masculine transmasculine Population category defined using ancestry informative markers (AIMs) based on genetic/genomic data ancestral group ancestry category Includes individuals who either self-report or have been described by authors as European, Caucasian, White or one of the sub-populations from this region (e.g Dutch). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CEU, FIN, GBR, IBS and TSI populations. Caucasian white European Includes individuals who either self-report or have been described by authors as South Asian or one of the sub-populations from this region (e.g Asian Indian). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap BEB, GIH, ITU, PJL and STU populations. South Asian Includes individuals who either self-report or have been described by authors as South East Asian or one of the sub-populations from this region (e.g Vietnamese). This category also includes includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes KHV population. We note that East Asian and South East Asian populations are often conflated. However, recent studies indicate a unique genetic background for South East Asian populations. South East Asian Includes individuals that either self-report or have been described as Asian but there was not sufficient information to allow classification as East Asian, Central Asian, South Asian or South-East Asian. Asian unspecified Asian Includes individuals who either self-report or have been described by authors as East Asian or one of the sub-populations from this region (e.g Chinese). This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CDX, CHB, CHS and JPT populations. East Asian Includes individuals that either self-report or have been described as African, but there was not sufficient information to allow classification as African American, AfroCaribbean or Sub-Saharan African. African unspecified African Includes individuals who either self-report or have been described by authors as SubSaharan African or one of the subpopulations from this region (e.g. Yoruban). This category also includes individuals who genetically cluster with reference populations from this region for example 1000 Genomes and/or HapMap ESN, LWK, GWD, MSL, MKK and YRI populations. Sub-Saharan African Includes indigenous individuals of North, Central and South America, descended from the original human migration into the Americas from Siberia. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. American Indian Native American Includes individuals who either self-report or are described by authors as Hispanic, Latino, Latin American or one of the sub-populations from this region. This category includes individuals with known admixture of primarily European, African and Native American ancestries, though some may have also a degree of Asian (e.g. Peru). We also note that the levels of admixture vary depending on the country, with Caribbean countries carrying higher levels of African admixture when compared to South American countries, for example. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap CLM, MXL, PEL and PUR populations Jackie MacArthur Joannella Morales Hispanic or Latin American Includes individuals who self-report or were described by authors as Middle Eastern, North African, Persian or one of the subpopulations from this region (e.g. Saudi Arabian). We note there is heterogeneity in this category with different degrees of admixture as well as levels of genetic isolation. We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. Middle Eastern/North African Greater Middle Eastern (Middle Eastern, North African or Persian) Includes individuals who either self-report or have been described by authors as African American or Afro-Caribbean. This category also includes individuals who genetically cluster with reference populations from this region, for example 1000 Genomes and/or HapMap ACB or ASW populations. We note that there is likely to be significant admixture with European ancestry populations. African American or Afro-Caribbean Includes individuals that either self-report or have been described by authors as Oceanian or one of the sub-populations from this region (e.g. Native Hawaiian). We note that there does not appear to be a suitable reference population for this category and efforts are required to fill this gap. Oceanian A population for which specific ancestry information is known but that does not fall into any of the defined ancestry categories uncategorised population Japanese non-aboriginal Taiwanese Taiwanese Chinese Korean Mongolian Macanese Singaporean Chinese Hong Kong Chinese Han Chinese Includes individuals who either self-report or have been described by authors as Central Asian. We note that there does not appear to be a suitable reference population for this population and efforts are required to fill this gap. Central Asian A population with increased genetic homogeneity and reduced genetic variation due to cultural or geographic isolation founder population population isolate genetically isolated population Italian Sardinian Val Borbera Friuli Venezia Giulia Carlantino Old Order Amish Sorbian Hutterite Amish Erasmus Rucphen Orcadian Korculan Dutch Finnish Finnish founder Dutch founder Ashkenazi Jew Sudanese Sahrawi Anguillan Antiguan or Barbudan Barbadian Haitian Jamaican Tajikistani Turkmen Uzbekistani Afghan Kazakhstani Kyrgyzstani Albanian Andorran Australian Austrian Belarusian Belgian Bermudian Bosnian or Herzegovinian Brazilian Bulgarian Canadian Channel Islander Chilean Croatian Czech Danish Estonian Faroese Falkland Islander French German Gibraltarian Greek Greenlander Hungrian Icelandic Manx Latvian Liechtensteiner Lithuanian Luxembourgish Maltese Monegasque Montenegrin New Zealandish Norfolk Islander Norwegian Polish Portugese Irish Moldovan Romanian Russian Saint-Pierrais or Miquelonnais Sammarinese Serb Slovak Slovene Spanish Swedish Swiss Macedonian Ukrainian Argentine Bahamian Belizean Bolivian British Virgin Islander Caymanian Colombian Costa Rican Cuban Dominican Ecuadorian Salvadoran French Guianese Grenadian Guatemalan Guyanese Honduran Martinican Mexican Montserratian Nicaraguan Panamanian Paraguayan Peruvian Puerto Rican Kittitian or Nevisian Saint Lucian Saint Vincentian Surinamer Surinamese Trinidadian or Tobagonian Turks and Caicos Islander Virgin Islander Uruguayan Venezuelan Algerian Armenian Azerbaijani Bahraini Cypriote Egyptian Georgian Iranian Iraqi Israeli Jordanian Kuwaiti Lebanese Libyan Moroccan Palestinian Omani Qatari Saudi Arab Saudi Tunisian Turkish Emirati Yemeni Aruban Christmas Islander Cocos Islander Curacaoan Kosovar Northern Mariana Islander South Sudanese Syrian British American American Samoan Cook Islander Fijian French Polynesian Guamanian I-Kiribati Marshallese Micronesian Nauruan New Caledonian Niuean Palauan Papua New Guinean Pitcairn Islander Samoan Solomon Islander Tokelauan Tongan Tuvaluan Ni-Vanuato Wallis and Futuna Islander Bangladeshi Bhutanese Asian Indian Indian Asian Indian Maldivian Nepalese Pakistani Sri Lankan Bruneian Cambodian Indonesian Lao Malaysian Burmese Filipino Thai Timorese Vietnamese Cameroonian Cape Verdean Chadian Ethiopian Kenyan Liberian Malagasy Mauritanian Mauritian Mahoran Namibian Sao Tomean Senegalese Seychellois Sierra Leonean Somali South African St. Helenian Ugandan Angolan Beninese Motswana Burkinabe Burundian Central African Comoran Congolese Ivoirian Djiboutian Equatorial Guinean Eritrean Gabonese Gambian Ghanaian Guinean Bissau-Guinean Mosotho Malawian Malian Mozambican Nigerien Nigerian Rwandan Swazi Togolese Tanzanian Zambian Zimbabweian Irish founder genetically homogenous Irish Includes individuals who either self-report or have been described by authors as Australian Aboriginal. These are expected to be descendents of early human migration into Australia from Eastern Asia and can be distinguished from other Asian populations by mtDNA and Y chromosome variation. Aboriginal Australian Silk Road founder Israeli Arab Arab Israeli founder Cilento Costa Rican founder French Canadian founder Italian founder Northern Finnish founder Romanian founder South Tyrolean Vis founder Split founder Population for which insufficient information is available to allocate it to a specific ancestral group or which contain individuals from a range of known ancestry categories, eg American undefined ancestry population African Caribbean Afro-Caribbean African American Talana Pima Indian Plains American Indian Kosraen Native Hawaiian Pacific Islander Yoruban West African Dai Chinese Hui Chinese Jingpo Chinese Malaysian Chinese Uigur Chinese Uygur Chinese Tibetan Han Taiwanese Taiwanese Han Sri Lankan Sinhalese Tatar Bashkir Martu Australian Aboriginal Jewish Israeli Punjabi Sikh American of European ancestry European American The Esan people are one of the major ethnic groups in Edo State, Nigeria who speak the Esan language. (PMID:10146569) Samples from this population were studied as part of the full 1000 Genomes project (https://www.coriell.org/1/NHGRI/Collections/1000-Genomes-Collections/Esan-in-Nigeria-ESN) Esan The Luhya are the second-largest ethnic group in Kenya and are comprised of subgroups that speak a common Bantu language. (PMID: 27813082) The Luhya ancestry group was assembled as part of phase III of the HapMap project and used in a number of rare variant density studies (PMID:22373165, PMID:26673965) Luhya The Maasai are an indigenous African ethnic group of semi-nomadic people located in northern Tanzania and Kenya. (PMID:29868928) The Maasai ancestry group was assembled as part of phase III of the HapMap project and used as reference in a range of population genetic studies (PMID:28049708). Maasai The Mende people are one of the largest ethnic groups in Sierra Leone who speak a language of the Mande branch of the Niger-Congo family. (PMID:15761855) Samples from this population were studied as part of the full 1000 Genomes project (https://www.coriell.org/1/NHGRI/Collections/1000-Genomes-Collections/Mende-in-Sierra-Leone-MSL) Mende Native people residing in the Arctic of Alaska, northern Canada, Greenland, or eastern Siberia PMID:25884279 PMID:29220501 Eskimo Includes individuals with ethnic origins in the Semitic people populating the Arabian Peninsula and other countries in the Middle East and Northern Africa PMID:27393651 PMID:28106113 Arab UMLS:C0444868 Root of all terms in the Human Phenotype Ontology. All The pattern in which a particular genetic trait or disorder is passed from one generation to the next. HP:0001453 HP:0001461 UMLS:C1708511 Inheritance Mode of inheritance An abnormality of the kidney. MSH:D007674 SNOMEDCT_US:44513007 SNOMEDCT_US:90708001 UMLS:C0022658 UMLS:C0266292 Abnormal kidney Abnormality of the kidney Renal anomalies Renal anomaly The kidney is a paired organ whose primary function is the production of urine. Abnormality of the kidney An abnormality of the urinary system. UMLS:C4021821 Urinary tract abnormalities Urinary tract abnormality Urinary tract anomalies Abnormality of the urinary system A reduction in the level of performance of the kidneys in areas of function comprising the concentration of urine, removal of wastes, the maintenance of electrolyte balance, homeostasis of blood pressure, and calcium metabolism. HP:0000084 HP:0004723 MSH:D051437 SNOMEDCT_US:236423003 SNOMEDCT_US:42399005 UMLS:C0035078 UMLS:C1565489 UMLS:C1839604 Renal failure Renal failure in adulthood Renal insufficiency A phenotypic abnormality. UMLS:C4021819 Organ abnormality This is the root of the phenotypic abnormality subontology of the HPO. Phenotypic abnormality The presence of any abnormality of the genitourinary system. HP:0008658 HP:0008688 HP:0008704 HP:0008713 MSH:D014564 SNOMEDCT_US:287085006 SNOMEDCT_US:42030000 UMLS:C0042063 UMLS:C0080276 UMLS:C4020895 Abnormality of the GU system Genitourinary abnormality Genitourinary tract anomalies Genitourinary tract malformation Urogenital abnormalities Urogenital anomalies Abnormality of the genitourinary system An abnormality of head and neck. UMLS:C4021817 Abnormality of head or neck Head and neck abnormality Abnormality of head or neck An abnormality of the mouth. MSH:D009056 SNOMEDCT_US:128334002 UMLS:C0026633 Abnormal mouth Abnormality of the mouth Abnormality of the mouth Any abnormality of the tongue. UMLS:C0878638 Abnormal tongue Abnormality of the tongue Glossal abnormality Lingual abnormality Tongue abnormality Abnormality of the tongue Abnormality of the oral cavity, i.e., the opening or hollow part of the mouth. UMLS:C4025887 Abnormality of the oral cavity Abnormal oral cavity morphology Inflammation of the tongue. MSH:D005928 SNOMEDCT_US:45534005 UMLS:C0017675 Inflammation of the tongue Lingual inflammation Smooth swollen tongue Glossitis Dryness of the mouth due to salivary gland dysfunction. HP:0002709 HP:0100756 Decreased salivary flow MSH:D014987 SNOMEDCT_US:300268000 SNOMEDCT_US:56893005 SNOMEDCT_US:87715008 UMLS:C0043352 Dry mouth Dry mouth syndrome Reduced salivation Xerostomia UMLS:C4025879 Abnormality of taste sensation Abnormality of taste sensation A decreased ability to perceive flavor. MSH:D000370 SNOMEDCT_US:697990000 UMLS:C0151934 Decreased taste Decreased taste sensation Hypogeusia An abnormality of the head. UMLS:C4021812 Abnormal head Abnormality of the head Head abnormality Abnormality of the head An abnormality of the face. Abnormality of the countenance Abnormality of the physiognomy Abnormality of the visage Disorder of face SNOMEDCT_US:118930001 SNOMEDCT_US:32003007 SNOMEDCT_US:398206004 SNOMEDCT_US:398302004 UMLS:C0266617 UMLS:C1290857 UMLS:C4025871 Abnormal face Abnormality of the face Facial abnormality Disorder of the face Abnormality of the face HP:0000284 UMLS:C4025863 Abnormality of the eye region Abnormality of the region around the eyes Anomaly of the orbital region of the face Deformity of the orbital region of the face Malformation of the orbital region of the face Abnormality of the orbital region An abnormality of the nose. SNOMEDCT_US:128274005 SNOMEDCT_US:72089000 UMLS:C0240547 UMLS:C0265736 UMLS:C2235909 Abnormality of the nose Anomaly of the nose Nasal abnormality Nasal anomaly Deformity of the nose Malformation of the nose Nasal deformity Nasal malformation Abnormality of the nose Epistaxis, or nosebleed, refers to a hemorrhage localized in the nose. COHD:318556 EFO:0003895 ICD10:R04.0 ICD9:784.7 MSH:D004844 NCIT:C26766 SNOMEDCT_US:12441001 SNOMEDCT_US:249366005 UMLS:C0014591 Bloody nose Frequent nosebleeds Nasal haemorrhage Nasal hemorrhage Nose bleed Nose bleeding Nosebleed Epistaxis An inability to perceive odors. This is a general term describing inability to smell arising in any part of the process of smelling from absorption of odorants into the nasal mucous overlying the olfactory epithelium, diffusion to the cilia, binding to olfactory receptor sites, generation of action potentials in olfactory neurons, and perception of a smell. MSH:D000857 SNOMEDCT_US:44169009 UMLS:C0003126 Loss of smell Lost smell Anosmia An abnormality of the neck. SNOMEDCT_US:298390003 SNOMEDCT_US:40052002 UMLS:C0266623 UMLS:C0575167 UMLS:C4280628 Abnormality of the neck Anomaly of the neck Deformity of the neck Malformation of the neck Abnormality of the neck Any abnormality of the eye, including location, spacing, and intraocular abnormalities. MSH:D005124 MSH:D005128 SNOMEDCT_US:19416009 SNOMEDCT_US:371405004 SNOMEDCT_US:371409005 UMLS:C0015393 UMLS:C0015397 Abnormal eye Abnormality of the eye Abnormality of the eye An abnormality of the eyelids. HP:0000285 UMLS:C4021803 Abnormality of the eyelid Abnormality of the eyelids Abnormal eyelid morphology An abnormality of the conjunctiva. UMLS:C4025847 The conjunctiva is a thin, sparsely vascularized transparent membrane that covers and protects the sclera (the bulbar conjunctiva), and forms the inner lining of the eyelids (the tarsal conjunctiva). Abnormal conjunctiva morphology Abnormality of eyesight (visual perception). UMLS:C4025846 Abnormality of sight Abnormality of vision Vision issue Abnormality of vision The upper eyelid margin is positioned 3 mm or more lower than usual and covers the superior portion of the iris (objective); or, the upper lid margin obscures at least part of the pupil (subjective). MSH:D001763 SNOMEDCT_US:11934000 UMLS:C0005745 Blepharoptosis Drooping upper eyelid Eyelid ptosis Ptosis Inflammation of the conjunctiva. MSH:D003231 SNOMEDCT_US:9826008 UMLS:C0009763 UMLS:C1864156 Pink eye Conjunctivitis An abnormality of the ear. SNOMEDCT_US:275259005 UMLS:C0266589 Abnormality of the ear Ear anomaly Either a morphological abnormality or hearing deficit. This should be split more cleanly in the future. Abnormality of the ear An anomaly of the pharynx, i.e., of the tubular structure extending from the base of the skull superiorly to the esophageal inlet inferiorly. UMLS:C4025838 The pharynx is tubular structure extending from base of skull superiorly to esophageal inlet inferiorly, and is composed of three distinct areas: the nasopharynx, the oropharynx, and the hypopharynx, with the pharyngeal walls being composed of the superior, middle, and inferior pharyngeal constrictor muscles. It is part of the digestive system and of the conducting zone of the respiratory system. Abnormality of the pharynx Lack of sharpness of vision resulting in the inability to see fine detail. HP:0007723 SNOMEDCT_US:111516008 SNOMEDCT_US:246636008 UMLS:C0344232 Blurred vision This is a very nonspecific term and it is preferable to describe the correlates of blurred vision with the corresponding terms if possible. Blurred vision An abnormality of the nervous system. HP:0001333 HP:0006987 Brain and/or spinal cord issue MSH:D009421 SNOMEDCT_US:88425004 UMLS:C0497552 Abnormality of the nervous system Neurologic abnormalities Neurological abnormality The nervous system comprises the neuraxis (brain, spinal cord, and ventricles), the autonomic nervous system, the enteric nervous system, and the peripheral nervous system. Abnormality of the nervous system An abnormality of mental functioning including various affective, behavioural, cognitive and perceptual abnormalities. HP:0000715 HP:0002368 HP:0002456 MSH:D000066553 MSH:D001526 SNOMEDCT_US:25786006 SNOMEDCT_US:277843001 UMLS:C0004941 UMLS:C0233514 Behavioral abnormality Behavioral changes Behavioral disorders Behavioral disturbances Behavioral problems Behavioral/psychiatric abnormalities Behavioural abnormality Behavioural changes Behavioural disorders Behavioural disturbances Behavioural problems Behavioural/Psychiatric abnormality Psychiatric disorders Psychiatric disturbances Behavioral abnormality A proneness to anger, i.e., a condition of being easily bothered or annoyed. UMLS:C2700617 Irritability Irritable Irritability The presence of blood in the urine. Hematuria may be gross hematuria (visible to the naked eye) or microscopic hematuria (detected by dipstick or microscopic examination of the urine). High urine occult blood MSH:D006417 SNOMEDCT_US:34436003 SNOMEDCT_US:53298000 UMLS:C0018965 Blood in urine Hematuria An abnormality of the endocrine system. MSH:D004700 SNOMEDCT_US:362969004 UMLS:C0014130 UMLS:C4025823 The endocrine system is composed of glands that secrete hormones directly into the bloodstream and includes the following glands: thyroid, parathyroids, adrenals, pancreas, gonads (testicles and ovaries), and pituitary. Many other organs, such as the kidney, liver, and heart, have secondary endocrine functions. Abnormality of the endocrine system A group of abnormalities characterized by hyperglycemia and glucose intolerance. HP:0004908 HP:0008217 HP:0008234 HP:0008260 MSH:D003920 SNOMEDCT_US:73211009 UMLS:C0011849 Diabetes mellitus The presence of chronic increased pressure in the systemic arterial system. HP:0004949 HP:0005126 MSH:D006973 SNOMEDCT_US:24184005 SNOMEDCT_US:38341003 UMLS:C0020538 UMLS:C0497247 Arterial hypertension Systemic hypertension Hypertension is sustained elevation of resting systolic BP (140 mm Hg or higher), diastolic BP (90 mm Hg or higher), or both. Hypertension An abnormality of the skeletal system. UMLS:C4021790 Abnormality of the skeletal system Skeletal abnormalities Skeletal anomalies Abnormality of the skeletal system An abnormality of the skin. HP:0001478 HP:0001479 HP:0005591 HP:0006736 HP:0007415 HP:0007580 MSH:D012868 MSH:D012871 SNOMEDCT_US:199879009 SNOMEDCT_US:95320005 UMLS:C0037268 UMLS:C0037274 Abnormality of the skin dermatopathy dermopathy Abnormality of the skin Bluish discoloration of the skin and mucosa due to poor circulation or inadequate oxygenation of arterial or capillary blood. MSH:D003490 SNOMEDCT_US:119419001 SNOMEDCT_US:3415004 UMLS:C0010520 Blue discoloration of the skin Cyanosis Eczema is a form of dermatitis. The term eczema is broadly applied to a range of persistent skin conditions and can be related to a number of underlying conditions. Manifestations of eczema can include dryness and recurring skin rashes with redness, skin edema, itching and dryness, crusting, flaking, blistering, cracking, oozing, or bleeding. HP:0001481 MSH:D004485 SNOMEDCT_US:281104002 SNOMEDCT_US:43116000 UMLS:C0013595 Eczema Eczema has several forms including atopic dermatitis, contact dermatitis, dyshidrotic eczema, nummular eczema, seborrheic dermatitis, and stasis dermatitis. Eczema An abnormal accumulation of fluid beneath the skin, or in one or more cavities of the body. HP:0000990 MSH:D004487 SNOMEDCT_US:20741006 SNOMEDCT_US:267038008 SNOMEDCT_US:423666004 SNOMEDCT_US:79654002 UMLS:C0013604 Dropsy Fluid retention Hydrops Oedema Water retention Edema may be related to one or more of the following factors: 1) increased capillary hydrostatic pressure, 2) decreased osmotic pressure of plasma, 3) decreased tissue tension and lymphatic drainage, 4) increased osmotic pressure of tissue fluids, and 5) increased capillary permeability. Edema A red eruption of the skin. Rash MEDDRA:10037844 MSH:D005076 SNOMEDCT_US:112625008 SNOMEDCT_US:271807003 UMLS:C0015230 Skin rash Skin rash UMLS:C4025812 Dermatological manifestations of systemic disorders Bluish discoloration of the skin of the hands or feet. SNOMEDCT_US:25003006 UMLS:C0221347 Persistent blue color of hands or feet Persistent blue colour of hands or feet Cyanosis is caused by increased levels of deoxygenated hemoglobin. Acrocyanosis Hard, pebble-like deposits that form within the gallbladder. MSH:D002769 SNOMEDCT_US:266474003 UMLS:C0008350 Gallstones Gallstones range in size from as small as a grain of sand to as large as a golf ball. Cholesterol gallstones are the most common type of gallstone. Gallstones resulting from too much bilirubin in the bile are referred to as pigment stones. Cholelithiasis An abnormality of the fetus or the birth of the fetus, excluding structural abnormalities. UMLS:C4025797 Abnormality of prenatal development or birth Because of the close link between prenatal developmental abnormalities and abnormalities of the birth process, a single term is chosen to subsume both classes of abnormality. Abnormality of prenatal development or birth A seizure is an intermittent abnormality of nervous system physiology characterised by a transient occurrence of signs and/or symptoms due to abnormal excessive or synchronous neuronal activity in the brain. HP:0001275 HP:0001303 HP:0002125 HP:0002182 HP:0002279 HP:0002306 HP:0002348 HP:0002391 HP:0002417 HP:0002430 HP:0002431 HP:0002432 HP:0002434 HP:0002437 HP:0002466 HP:0002479 HP:0002794 HP:0006997 HP:0010520 MSH:D004827 MSH:D012640 SNOMEDCT_US:128613002 SNOMEDCT_US:246545002 SNOMEDCT_US:313307000 SNOMEDCT_US:84757009 SNOMEDCT_US:91175000 UMLS:C0014544 UMLS:C0036572 Epileptic seizure Seizures A type of electrographic seizure has been proposed in neonates which does not have a clinical correlate, it is electrographic only. The term epilepsy is not used to describe recurrent febrile seizures. Epilepsy presumably reflects an abnormally reduced seizure threshold. Seizure Complete absence of wakefulness and content of conscience, which manifests itself as a lack of response to any kind of external stimuli. ICD-10:R40.2 MSH:D003128 SNOMEDCT_US:371632003 UMLS:C0009421 Coma Coma is generally a result of diffuse or extensive involvement of both hemispheres of the brain or lesions in the brainstem. Coma Inflammation of the meninges. MSH:D008581 SNOMEDCT_US:7180009 UMLS:C0025289 Meningitis Lack of clarity and coherence of thought, perception, understanding, or action. HP:0000731 MSH:D003221 SNOMEDCT_US:286933003 UMLS:C0009676 Confusion Disorientation Easily confused Mental disorientation Confusion Sudden impairment of blood flow to a part of the brain due to occlusion or rupture of an artery to the brain. HP:0002452 MSH:D020521 SNOMEDCT_US:230690007 UMLS:C0038454 Cerebral vascular events Cerebrovascular accident Stroke Stroke Encephalopathy is a term that means brain disease, damage, or malfunction. In general, encephalopathy is manifested by an altered mental state. MSH:D001927 SNOMEDCT_US:81308009 UMLS:C0085584 This term and its children are general and bundled terms that are kept for convenience. For new annotations, it is recommended that the specific phenotypic abnormalities be noted. Encephalopathy Reduced strength of muscles. HP:0002309 HP:0008979 HP:0009012 HP:0009061 MSH:D018908 SNOMEDCT_US:26544005 UMLS:C0151786 Muscle weakness Muscular weakness It is important clinical to distinguish between muscle weakness, fatigue, and asthenia. Fatigue describes the inability to continue performing a task after multiple repetitions; in contrast, a patient with primary weakness is unable to perform the first repetition of the task. Asthenia is a sense of weariness or exhaustion in the absence of muscle weakness. Conditions that result in intrinsic muscle weakness can be divided into several main categories: infectious, neurologic, endocrine, inflammatory, rheumatologic, genetic, metabolic, electrolyte-induced, or drug-induced. Muscle weakness Abnormal coordination of muscles involved in speech. SNOMEDCT_US:289195008 UMLS:C0234518 Slurred speech Slurred speech An abnormal structure or form of the joints, i.e., one or more of the articulations where two bones join. MSH:D007592 SNOMEDCT_US:399269003 UMLS:C0022408 UMLS:C0240083 Abnormal shape of joints Abnormality of the joints Anomaly of the joints Abnormal joint morphology A reduction in the freedom of movement of one or more joints. HP:0003101 UMLS:C1857108 Decreased joint mobility Decreased mobility of joints Limitation of joint mobility Limited joint mobility Limited joint motion Limitation of joint mobility SNOMEDCT_US:271771009 UMLS:C0152031 Joint swelling Joint swelling Joint stiffness is a perceived sensation of tightness in a joint or joints when attempting to move them after a period of inactivity. Joint stiffness typically subsides over time. HP:0002775 HP:0003033 SNOMEDCT_US:84445001 UMLS:C0162298 Joint stiffness Stiff joint Stiff joints Joint stiffness An abnormality of the liver. MSH:D008107 SNOMEDCT_US:235856003 UMLS:C0023895 UMLS:C4021780 Abnormal liver Abnormality of the liver Liver abnormality Abnormality of the liver Steatosis is a term used to denote lipid accumulation within hepatocytes. HP:0002252 HP:0200121 MSH:D005234 SNOMEDCT_US:197321007 SNOMEDCT_US:442191002 UMLS:C2711227 Fatty infiltration of liver Fatty liver Liver steatosis Steatosis Although steatosis is the hallmark of the fatty liver disease, it is not a specific feature because it can be seen as part of other disease processes, such as drug injury, Wilson disease, or hepatitis C virus infection (especially genotype-3). Involvement of less than 5% of the hepatocytes by steatosis is considered clinically insignificant and within reference range. Based on the morphologic appearance and the size of the lipid droplets within the cytoplasm of the hepatocytes, steatosis is characterized as macrovesicular or microvesicular. Macrovesicular steatosis is characterized by large lipid droplets occupying the cytoplasm, displacing the nucleus to the periphery (large droplet macrovesicular steatosis) or multiple small lipid droplets of variable size occupying the cytoplasm with the nucleus maintaining its central location (small droplet macrovesicular steatosis). Microvesicular steatosis is characterized by innumerable tiny, relatively uniform lipid vacuoles that result in a bubbly appearance of the hepatocytes. Hepatic steatosis Reduced ability of the liver to perform its functions. HP:0004393 HP:0005228 HP:0006570 MSH:D008107 SNOMEDCT_US:75183008 SNOMEDCT_US:77981007 UMLS:C0086565 UMLS:C0232744 UMLS:C3279149 Decreased liver function Liver dysfunction Decreased liver function HP:0008904 UMLS:C0262361 Abnormal growth Growth abnormality Growth issue Growth abnormality Accumulation of substantial excess body fat. MSH:D009765 SNOMEDCT_US:414915002 SNOMEDCT_US:414916001 UMLS:C0028754 Having too much body fat Obesity Obesity A thrusting or bulging out of the abdomen. UMLS:C1854928 Abdominal protuberance Belly sticks out Extended belly Protuberant abdomen An abnormality of the integument, which consists of the skin and the superficial fascia. UMLS:C4025761 Abnormality of skin, hair, or nails. Abnormality of the integument UMLS:C4021776 Abnormality of the voice Voice abnormality This term describes any abnormality of the voice, i.e., of the sounds produced by humans by the passage of air through the larynx and over the vocal cords, and then modified by the resonance organs, the nasopharynx, and the mouth. Abnormality of the voice SNOMEDCT_US:2120003 UMLS:C0234860 Weak cry Any abnormality of the cardiovascular system. MSH:D002318 MSH:D018376 SNOMEDCT_US:49601007 UMLS:C0007222 UMLS:C0243050 Abnormality of the cardiovascular system Cardiovascular abnormality The cardiovascular system consists of the heart, vasculature, and the lymphatic system. Abnormality of the cardiovascular system Any structural anomaly of the heart. HP:3000001 MSH:D006330 SNOMEDCT_US:13213009 UMLS:C0018798 UMLS:C0152021 Abnormality of cardiac morphology Abnormality of the heart Abnormally shaped heart Cardiac abnormality Cardiac anomalies Cardiac anomaly Congenital heart defect Congenital heart defects Heart defect Abnormal heart morphology The presence of an abnormality of cardiac function that is responsible for the failure of the heart to pump blood at a rate that is commensurate with the needs of the tissues or a state in which abnormally elevated filling pressures are required for the heart to do so. Heart failure is frequently related to a defect in myocardial contraction. HP:0006686 MSH:D006333 SNOMEDCT_US:42343007 SNOMEDCT_US:84114007 UMLS:C0018801 UMLS:C0018802 CHF Cardiac failure Cardiac failures Cardiac insufficiency Chronic heart failure Heart failure Congestive heart failure A structural anomaly of the muscle layer of the heart wall. UMLS:C4025758 Abnormality of the myocardium Abnormal myocardium morphology A myocardial disorder in which the heart muscle is structurally and functionally abnormal, in the absence of coronary artery disease, hypertension, valvular disease and congenital heart disease sufficient to cause the observed myocardial abnormality. Fyler:1840 MSH:D009202 SNOMEDCT_US:57809008 SNOMEDCT_US:85898001 UMLS:C0878544 Disease of the heart muscle Cardiomyopathy A rapid heartrate that exceeds the range of the normal resting heartrate for age. HP:0001673 HP:0001720 MSH:D013610 SNOMEDCT_US:3424008 SNOMEDCT_US:86651002 UMLS:C0039231 UMLS:C4020868 Fast heart rate Heart racing Racing heart Tachycardia An abrupt loss of heart function. MSH:D006323 SNOMEDCT_US:397829000 SNOMEDCT_US:410429000 UMLS:C0018790 Heart stops beating Cardiac arrest Irreversible damage to heart tissue (myocardium) due to lack of oxygen after a heart attack (myocardial infarction). SNOMEDCT_US:251061000 UMLS:C1442837 Myocardial necrosis Reduced ability to pass air through the nasal cavity often leading to mouth breathing. MSH:D015508 SNOMEDCT_US:232209000 SNOMEDCT_US:267100006 SNOMEDCT_US:68235000 UMLS:C0027424 UMLS:C0027429 Blockage of nose Nasal blockage Nasal obstruction Obstruction of nose Stuffy nose Congestion of nose Nasal congestion An abnormality of the functioning of the vestibular apparatus. HP:0006917 HP:0007921 UMLS:C1843865 Impaired vestibular function Interictal vestibular dysfunction Vestibular function defect The vestibular apparatus is the nonauditory portion of the inner ear that mediates the subjective sensation of motion and spatial orientation of the head, adjusts muscular activity and body position to maintain posture, and stabilizes in space the fixation point of the eyes when the head moves, in order to provide a stable image upon the retina. The functioning of the vestibular system is often checked clinically by means of the caloric test, in which the head is tilted backward by about 60 degrees and either warm or cold water is introduced into the external auditory meatus on one side. The immediate results are usually vertigo, nausea, nystagmus, and twisting of the head and body. Vestibular dysfunction An abnormality of the birth process. SNOMEDCT_US:274127000 UMLS:C0549629 Abnormal delivery Delivery complication Abnormal delivery Reduction of total body weight. MSH:D015431 SNOMEDCT_US:161832001 SNOMEDCT_US:262285001 SNOMEDCT_US:89362005 UMLS:C1262477 Loss of weight Weight loss An abnormality of the hematopoietic system. HP:0003135 MSH:D006402 SNOMEDCT_US:191124002 SNOMEDCT_US:34093004 UMLS:C0018939 UMLS:C0850715 UMLS:C4020864 Abnormality of blood and blood-forming tissues Abnormality of the haematopoietic system Abnormality of the hematopoietic system Haematological abnormality Hematological abnormality The hematopoietic system comprises the organs that are involved in the production of blood, primarily the bone marrow, spleen, tonsils, and lymph nodes. Abnormality of blood and blood-forming tissues Any structural abnormality of erythrocytes (red-blood cells). HP:0010973 SNOMEDCT_US:12222001 UMLS:C0391870 UMLS:C4020862 Abnormality of erythrocytes Abnormality of red blood cells Abnormal erythrocyte morphology An abnormal susceptibility to bleeding, often referred to as a bleeding diathesis. A bleeding diathesis may be related to vascular, platelet and coagulation defects. HP:0004830 HP:0004834 HP:0004849 HP:0004862 HP:0004865 HP:0008183 SNOMEDCT_US:248250000 SNOMEDCT_US:64779008 UMLS:C1458140 Bleeding diathesis Bleeding tendency Hemorrhagic diathesis This term is kept for historical reasons. If possible, a more exact description of the phenotype (i.e., whether there is a vascular, platelet and coagulation defect) should be attempted. Abnormal bleeding A reduction in erythrocytes volume or hemoglobin concentration. HP:0001926 HP:0003136 HP:0005509 MSH:D000740 SNOMEDCT_US:165397008 SNOMEDCT_US:271737000 UMLS:C0002871 UMLS:C0162119 Anaemia Low number of red blood cells or haemoglobin Low number of red blood cells or hemoglobin Anemia is not a specific entity but can result from many underlying pathologic processes. The three main causes of anemia are blood loss, decreased or faulty red blood cell production, and increased destruction of red blood cells. Various classifications are in clinical use including a classification according to the mean corpuscular volume (MCV) of the erythrocytes: microcytic, macrocytic, or normocytic. Anemias can also be classified according to variations in cell size and shape, as reflected by the red-cell distribution width (RDW). Additionally, anemias can be classified into those of inadequate production and hemolytic anemias. Anemia Sudden loss of renal function, as manifested by decreased urine production, and a rise in serum creatinine or blood urea nitrogen concentration (azotemia). MSH:D058186 SNOMEDCT_US:14350001000004108 SNOMEDCT_US:14669001 UMLS:C0022660 UMLS:C2609414 Acute kidney failure Acute renal failure Acute renal failure is usually classified into prerenal (response to severe volume depletion), intrinsic (response to acute cytotoxic, ischemic, or inflammatory insults) and postrenal (response to obstruction of the passage of urine) etiologies. Acute kidney injury HP:0002146 HP:0004355 HP:0004367 UMLS:C4021768 Laboratory abnormality Metabolism abnormality Abnormality of metabolism/homeostasis MSH:D003681 SNOMEDCT_US:34095006 UMLS:C0011175 Dehydration Exsiccosis Dehydration Body temperature elevated above the normal range. MSH:D005334 SNOMEDCT_US:386661006 SNOMEDCT_US:50177009 UMLS:C0015967 Fever Hyperthermia Pyrexia Fever has been defined as a state of elevated core temperature, which is often, but not necessarily, part of the defensive responses of multicellular organisms (host) to the invasion of live (microorganisms) or inanimate matter recognized as pathogenic or alien by the host. The febrile response (of which fever is a component) is a complex physiologic reaction to disease, involving a cytokine-mediated rise in core temperature, generation of acute phase reactants, and activation of numerous physiologic, endocrinologic, and immunologic systems. The rise in temperature during fever is to be distinguished from that occurring during episodes of hyperthermia. Unlike fever, hyperthermia involves an unregulated rise in body temperature in which pyrogenic cytokines are not directly involved and against which standard antipyretics are ineffective. It represents a failure of thermoregulatory homeostasis, in which there is uncontrolled heat production, inadequate heat dissipation, or defective hypothalamic thermoregulation. Fever Glucose intolerance (GI) can be defined as dysglycemia that comprises both prediabetes and diabetes. It includes the conditions of impaired fasting glucose (IFG) and impaired glucose tolerance (IGT) and diabetes mellitus (DM). HP:0000833 Abnormal glucose tolerance UMLS:C0235401 Glucose intolerance Glucose intolerance Venous or arterial thrombosis (formation of blood clots) of spontaneous nature and which cannot be fully explained by acquired risk (e.g. atherosclerosis). UMLS:C4025731 Abnormal blood clot Abnormal blood clotting Abnormal thrombosis A structural abnormality of the central nervous system. HP:0002405 HP:0002413 HP:0002481 HP:0007319 MSH:D002493 SNOMEDCT_US:23853001 UMLS:C0007682 UMLS:C4021765 Abnormality of the central nervous system Morphological abnormality of the CNS Morphological abnormality of the central nervous system Morphological central nervous system abnormality An abnormality of the viscera of the abdomen. UMLS:C4021764 Abnormality of the abdominal organs Gastrointestinal tract defects The abdominal organs comprise the stomach, small and large intestines, liver, pancreas, bile tract, and spleen. Abnormality of the abdominal organs Forceful ejection of the contents of the stomach through the mouth by means of a series of involuntary spasmic contractions. MEDDRA:10047700 MSH:D014839 SNOMEDCT_US:249497008 SNOMEDCT_US:300359004 SNOMEDCT_US:422400008 UMLS:C0042963 Emesis Throwing up Vomiting Vomiting Abnormally increased frequency of loose or watery bowel movements. MSH:D003967 SNOMEDCT_US:267060006 SNOMEDCT_US:62315008 UMLS:C0011991 Diarrhea Diarrhoea Watery stool Diarrhea Difficulty in swallowing. HP:0002569 MEDDRA:10013950 MSH:D003680 SNOMEDCT_US:288939007 SNOMEDCT_US:40739000 UMLS:C0011168 Difficulty swallowing Poor swallowing Swallowing difficulties Swallowing difficulty Dysphagia Nausea is a commonly encountered symptom that has been defined as an unpleasant painless subjective feeling that one will imminently vomit. Vomiting has been defined as the forceful expulsion of the contents of the stomach, duodenum, or jejunum through the oral cavity. While nausea and vomiting are often thought to exist on a temporal continuum, this is not always the case. There are situations when severe nausea may be present without emesis and less frequently, when emesis may be present without preceding nausea. SNOMEDCT_US:16932000 UMLS:C0027498 Nausea and vomiting Nausea and vomiting A sensation of unease in the stomach together with an urge to vomit. MEDDRA:10028813 MSH:D009325 SNOMEDCT_US:422587007 UMLS:C0027497 Nausea Nausea Infrequent or difficult evacuation of feces. HP:0002241 HP:0003786 MSH:D003248 SNOMEDCT_US:14760008 SNOMEDCT_US:225595004 UMLS:C0009806 UMLS:C0237326 Constipation Costiveness Dyschezia Constipation An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) and perceived to originate in the abdomen. Gastro pain Gastrointestinal pain MEDDRA:10000081 MSH:D015746 SNOMEDCT_US:21522001 UMLS:C0000737 Abdominal pain Pain in stomach Stomach pain Abdominal pain can be crampy, achy, dull, intermittent or sharp. The terms stomach ache and stomach cramps are nonmedical terms often used to describe pain in the mid- or upper abdominal area, even though it is not the case that the (smooth) muscles of the stomach or the abdomen have cramps. Stomach pain is another layperson term commonly used to refer to abdominal pain. Abdominal pain The presence of chronic diarrhea, which is usually taken to mean diarrhea that has persisted for over 4 weeks. SNOMEDCT_US:236071009 UMLS:C0401151 Chronic diarrhea Chronic diarrhoea Chronic diarrhea An inadequate sucking reflex, resulting in the difficult of newborns to be breast-fed. UMLS:C1837142 Poor suck Poor sucking Sucking weakness Poor suck Inflammation, or an inflammatory state in the large intestine. MSH:D015212 SNOMEDCT_US:24526004 SNOMEDCT_US:302168000 UMLS:C0021390 UMLS:C0578878 Inflammation of the large intestine Inflammation of the large intestine UMLS:C1839531 Protein avoidance A lack or loss of appetite for food (as a medical condition). MSH:D000855 SNOMEDCT_US:79890006 UMLS:C0003123 Anorexia Note that this term does not refer to the condition anorexia nervosa (A disorder characterized by an obsessive desire to lose weight by refusing to eat). Anorexia UMLS:C0743178 Intractable diarrhoea Intractable diarrhea Migraine is a chronic neurological disorder characterized by episodic attacks of headache and associated symptoms. HP:0007194 MSH:D008881 SNOMEDCT_US:37796009 UMLS:C0149931 UMLS:C0744641 Intermittent migraine headaches Migraine Migraine headache Migraine headaches Migraine An abnormality of the respiratory system, which include the airways, lungs, and the respiratory muscles. UMLS:C4018871 Respiratory abnormality Abnormality of the respiratory system An abnormality of the upper respiratory tract. UMLS:C4025727 Abnormality of the upper respiratory tract Upper respiratory tract issues Abnormality of the upper respiratory tract Any structural anomaly of the lung. MSH:D008171 SNOMEDCT_US:19829001 UMLS:C0024115 UMLS:C4021760 Abnormality of lung structure Abnormality of the lungs Abnormally shaped lung Unusal lung shape Abnormal lung morphology Inflammation of any part of the lung parenchyma. MSH:D011014 SNOMEDCT_US:233604007 UMLS:C0032285 Pneumonia Pneumonia HP:0004893 HP:0005937 HP:0006542 MSH:D012131 SNOMEDCT_US:409623005 UMLS:C0035229 UMLS:C4020855 Respiratory impairment progressive respiratory failure Respiratory insufficiency Difficult or labored breathing. Dyspnea is a subjective feeling only the patient can rate, e.g., on a Borg scale. MSH:D004417 SNOMEDCT_US:230145002 SNOMEDCT_US:267036007 UMLS:C0013404 Abnormal breathing Breathing difficulty Difficult to breathe Difficulty breathing Dyspnoea Shortness of breath Trouble breathing Dyspnea HP:0006534 MSH:D011656 SNOMEDCT_US:87433001 UMLS:C0034067 Pulmonary emphysema Emphysema Asthma is characterized by increased responsiveness of the tracheobronchial tree to multiple stimuli, leading to narrowing of the air passages with resultant dyspnea, cough, and wheezing. HP:0002112 MSH:D001249 SNOMEDCT_US:195967001 SNOMEDCT_US:991000119106 UMLS:C0004096 UMLS:C3714497 Asthma Bronchial asthma Asthma An abnormality of the pulmonary pleura, the thin, transparent membrane which covers the lungs and lines the inside of the chest walls. UMLS:C4025726 Abnormality of the pleura Abnormal pleura morphology Coughing up (expectoration) of blood or blood-streaked sputum from the larynx, trachea, bronchi, or lungs. MSH:D006469 SNOMEDCT_US:66857006 SNOMEDCT_US:6686005 UMLS:C0019079 Coughing up blood Haemoptysis Hemoptysis Accumulation of air in the pleural cavity leading to a partially or completely collapsed lung. MSH:D011030 SNOMEDCT_US:36118008 UMLS:C0032326 Collapsed lung Pneumothorax Pneumothorax occurring without traumatic injury to the chest or lung. MSH:D011030 SNOMEDCT_US:80423007 UMLS:C0149781 Spontaneous collapsed lung Spontaneous pneumothorax Acute ischemic stroke (AIS) is defined by the sudden loss of blood flow to an area of the brain with the resulting loss of neurologic function. It is caused by thrombosis or embolism that occludes a cerebral vessel supplying a specific area of the brain. During a vessel occlusion, there is a core area where damage to the brain is irreversible and an area of penumbra where the brain has lost function owing to decreased blood flow but is not irreversibly injured. SNOMEDCT_US:422504002 UMLS:C0948008 Ischaemic stroke Ischemic stroke MSH:D013064 UMLS:C0037822 Speech disorder Speech impairment Speech impediment Neurological speech impairment The presence of an excessive amount of fluid in the pleural cavity. MSH:D010996 SNOMEDCT_US:60046008 UMLS:C0032227 Fluid around lungs Pleural effusion An embolus (that is, an abnormal particle circulating in the blood) located in the pulmonary artery and thereby blocking blood circulation to the lung. Usually the embolus is a blood clot that has developed in an extremity (for instance, a deep venous thrombosis), detached, and traveled through the circulation before becoming trapped in the pulmonary artery. MSH:D011655 SNOMEDCT_US:59282003 UMLS:C0034065 Blood clot in artery of lung Pulmonary embolism Replacement of normal lung tissues by fibroblasts and collagen. HP:0006523 MSH:D011658 SNOMEDCT_US:51615001 UMLS:C0034069 Pulmonary fibrosis leads to an irreversible impairment of alveolar oxygen transfer. Pulmonary fibrosis Hemorrhage affecting the gastrointestinal tract. MSH:D006471 SNOMEDCT_US:74474003 UMLS:C0017181 GI haemorrhage GI hemorrhage Gastrointestinal bleeding Gastrointestinal haemorrhage Gastrointestinal hemorrhage An abnormality of the intestine. The closely related term enteropathy is used to refer to any disease of the intestine. HP:0002628 MSH:D007410 SNOMEDCT_US:85919009 UMLS:C0021831 Abnormality of the intestine Enteropathy Abnormal intestine morphology The passage of blackish, tarry feces associated with gastrointestinal hemorrhage. Melena occurs if the blood remains in the colon long enough for it to be broken down by colonic bacteria. One degradation product, hematin, imbues the stool with a blackish color. Thus, melena generally occurs with bleeding from the upper gastrointestinal tract (e.g., stomach ulcers or duodenal ulcers), since the blood usually remains in the gut for a longer period of time than with lower gastrointestinal bleeding. MSH:D008551 SNOMEDCT_US:249627005 SNOMEDCT_US:267055007 SNOMEDCT_US:269899009 SNOMEDCT_US:2901004 SNOMEDCT_US:35064005 UMLS:C0025222 UMLS:C0474585 Black faeces Black feces Melena Any abnormality of the large intestine. UMLS:C4025715 Abnormality of the large intestine The large intestine comprises the cecum and colon. Abnormal large intestine morphology Repeated episodes of diarrhea separated by periods without diarrhea. UMLS:C0239181 Episodic diarrhea Episodic diarrhoea Intermittent diarrhoea Intermittent diarrhea Cephalgia, or pain sensed in various parts of the head, not confined to the area of distribution of any nerve. HP:0000266 HP:0001354 MSH:D006261 SNOMEDCT_US:25064002 UMLS:C0018681 Headache Headaches Headache is one of the most common types of recurrent pain as well as one of the most frequent symptoms in neurology. In addition to occasional headaches, there are well-defined headache disorders that vary in incidence, prevalence and duration and can be divided into two broad categories. In secondary headache disorders, headaches are attributed to another condition, such as brain tumour or head injury; for the primary disorders the headache is not due to another condition. Headache An abnormal sensation of spinning while the body is actually stationary. MSH:D004244 MSH:D014717 SNOMEDCT_US:271789005 SNOMEDCT_US:399090003 SNOMEDCT_US:399153001 SNOMEDCT_US:404640003 UMLS:C0012833 UMLS:C0042571 Dizzy spell Vertigo UMLS:C0542223 Loss of speech Loss of speech A disorder of the brain caused by an infectious agent that presents with fever, headache, and an altered level of consciousness. There may also be focal or multifocal neurologic deficits, and focal or generalized seizure activity. MSH:D004660 SNOMEDCT_US:45170000 UMLS:C0014038 Brain inflammation Infectious encephalitis Paroxysmal, recurrent episodes of vomiting. UMLS:C1838993 UMLS:C1857202 Episodic vomiting Episodic vomiting The passage of fresh (red) blood per anus, usually in or with stools. Most rectal bleeding comes from the colon, rectum, or anus. HP:0002255 HP:0002609 MSH:D006471 SNOMEDCT_US:236068001 SNOMEDCT_US:405729008 UMLS:C0018932 Rectal bleeding Bright red blood in stool, most frequentoly caused by hemorrhoids or diverticulosis. Hematochezia An intermittent form of abdominal pain. UMLS:C0262527 UMLS:C3808022 Episodic abdominal pain Colitis refers to an inflammation of the colon and is often used to describe an inflammation of the large intestine (colon, cecum and rectum). Colitides may be acute and self-limited or chronic, and broadly fit into the category of digestive diseases. MSH:D003092 SNOMEDCT_US:64226004 UMLS:C0009319 Colitis Vomiting that ejects the gastric contents with great force. SNOMEDCT_US:8579004 UMLS:C0221151 Projectile vomiting Projectile vomiting An abnormality of the vasculature. UMLS:C0241657 Abnormality of blood vessels Abnormality of the vasculature Vascular abnormalities Abnormality of the vasculature Low Blood Pressure, vascular hypotension. HP:0005127 HP:0006701 MSH:D007022 SNOMEDCT_US:45007003 UMLS:C0020649 Arterial hypotension Low blood pressure Hypotension Formation of a blot clot in a deep vein. The clot often blocks blood flow, causing swelling and pain. The deep veins of the leg are most often affected. MSH:D020246 SNOMEDCT_US:128053003 UMLS:C0149871 Blood clot in a deep vein Deep vein thrombosis Multiple deep venous thrombosis Deep venous thrombosis Inflammation of blood vessel. MSH:D014657 SNOMEDCT_US:31996006 UMLS:C0042384 Angiitis Inflammation of blood vessel Vasculitis MSH:D002545 SNOMEDCT_US:287731003 SNOMEDCT_US:389100007 UMLS:C0007786 UMLS:C0917798 Brain ischemia Cerebrovascular ischemia Disruption of blood oxygen supply to brain Cerebral ischemia An abnormality of the immune system. HP:0003257 HP:0003346 HP:0010986 UMLS:C4021753 Abnormality of the immune system Immunological abnormality The immune system is composed of organs and interdependent cell types that collectively protect the body from infections and from the growth of tumor cells. The organs of the immune system comprise the bone marrow, the spleen, the thymus,the lymph nodes, and the cell types comprise B cells, T cells, natural killer cells, granulocytes,dendritic cells, and macrophages. Abnormality of the immune system Enlargment (swelling) of a lymph node. HP:0002735 MSH:D000072281 SNOMEDCT_US:30746006 UMLS:C0497156 Lymph node hyperplasia Swollen lymph nodes Lymphadenopathy A lymph node abnormality. HP:0008149 UMLS:C0149727 Abnormal lymph node histology Abnormality of the lymph nodes Abnormality of the lymph nodes Very rapid breathing. HP:0002874 HP:0004346 MSH:D059246 SNOMEDCT_US:271823003 UMLS:C0231835 Increased respiratory rate or depth of breathing Polypnea In adults, a beathing rate of between 12-20 breaths per minute is normal and tachypnea is present with a ventilatory rate greater than 20 breaths per minute. Tachypnea An anomaly of the rhythm or depth of breathing. UMLS:C1837388 Abnormal pattern of respiration Abnormal respiratory patterns Unusual breathing patterns Abnormal pattern of respiration Fyler:4200 UMLS:C4025677 Abnormal respiration Functional respiratory abnormality Abnormal respiratory system physiology Joint pain. MSH:D018771 SNOMEDCT_US:57676002 UMLS:C0003862 Arthralgias Joint pain Arthralgia is distinct from Arthritis, which is not a symptom but a diagnosis with articular inflammation or signs of osteoarthritis. Arthralgia A severe form of respiratory insufficiency characterized by inadequate gas exchange such that the levels of oxygen or carbon dioxide cannot be maintained within normal limits. HP:0004877 MSH:D012131 SNOMEDCT_US:409622000 UMLS:C1145670 Respiratory failure Respiratory failure is classified as type 1 with hypoxemia (arterial partial pressure of oxygen less than 60 mmHg) without hypercapnea, and type 2 with hypoxemia in the present of hypercapnea (partial pressure of carbon dioxide over 50 mmHg). Respiratory failure An abnormally decreased potassium concentration in the blood. MSH:D007008 SNOMEDCT_US:166690008 SNOMEDCT_US:43339004 UMLS:C0020621 Low blood potassium levels Hypokalemia An abnormally decreased calcium concentration in the blood. MSH:D006996 SNOMEDCT_US:5291005 UMLS:C0020598 Hypocalcaemia Low blood calcium levels Hypocalcemia An abnormally decreased magnesium concentration in the blood. HP:0003284 SNOMEDCT_US:190855004 UMLS:C0151723 Low blood Mg levels Low blood magnesium levels Hypomagnesemia Abnormality originating in one or more muscles, i.e., of the set of muscles of body. HP:0003197 HP:0003708 HP:0040290 UMLS:C4021745 Muscular abnormality Abnormality of the musculature An abnormality of the composition of urine or the levels of its components. HP:0011865 HP:0011866 UMLS:C4025655 Pee issues Urine issues Abnormality of urine homeostasis Abnormality of the homeostasis (concentration) of a monoatomic ion. HP:0003253 SNOMEDCT_US:237840007 UMLS:C1704431 UMLS:C4025654 Abnormality of ion homeostasis Electrolyte disorders Electrolyte disturbance Abnormal blood ion concentration Breakdown of muscle fibers that leads to the release of muscle fiber contents (myoglobin) into the bloodstream. MSH:D012206 SNOMEDCT_US:240131006 SNOMEDCT_US:89010004 UMLS:C0035410 Breakdown of skeletal muscle Rhabdomyolysis Distention of the abdomen. HP:0001542 HP:0003364 SNOMEDCT_US:41931001 SNOMEDCT_US:60728008 UMLS:C0000731 Abdominal bloating Abdominal distension Abdominal swelling Belly bloating Bloating Distended abdomen Abdominal distention can be a secondary feature associated with a number of conditions such as bowel obstruction. Abdominal distention Pain in muscle. HP:0003718 MSH:D063806 SNOMEDCT_US:68962001 UMLS:C0231528 Muscle ache Muscle pain Myalgia Paralysis of voluntary muscles means loss of contraction due to interruption of one or more motor pathways from the brain to the muscle fibers. Although the word paralysis is often used interchangeably to mean either complete or partial loss of muscle strength, it is preferable to use paralysis or plegia for complete or severe loss of muscle strength, and paresis for partial or slight loss. Motor paralysis results from deficits of the upper motor neurons (corticospinal, corticobulbar, or subcorticospinal). Motor paralysis is often accompanied by an impairment in the facility of movement. MSH:D010243 SNOMEDCT_US:44695005 UMLS:C0522224 Inability to move Paralysis Paralysis The age group in which disease manifestations appear. HP:0003588 HP:0003590 HP:0003597 HP:0003602 HP:0003603 HP:0003618 HP:0003626 HP:0003628 HP:0003630 HP:0003663 HP:0003664 HP:0003668 HP:0011007 MSH:D017668 MeSH:D017668 UMLS:C0206132 Age of onset Age symptoms begin Adolescent is defined by WHO as a person between 10-19 years of age. Onset Cases of the disease in question occur without a previous family history, i.e., as isolated cases without being transmitted from a parent and without other siblings being affected. HP:0001420 HP:0003747 HP:0003769 UMLS:C1853237 Isolated cases No previous family history Sporadic An abnormal, increased fatiguability of the musculature. MSH:D018763 SNOMEDCT_US:80449002 UMLS:C0242979 UMLS:C4025573 Increased muscle fatiguability Death of the fetus in utero after at least 20 weeks of gestation. HP:0001624 HP:0001625 MSH:D005313 MSH:D050497 SNOMEDCT_US:237364002 SNOMEDCT_US:276507005 UMLS:C0015927 UMLS:C0595939 Stillbirth Stillborn Stillbirth An abnormality of the biliary system. UMLS:C0940767 Abnormality of the biliary system SNOMEDCT_US:44103008 UMLS:C0085612 Ventricular arrhythmias Ventricular arrhythmia An abnormal increase or decrease of weight or an abnormal distribution of mass in the body. HP:0010718 UMLS:C0878621 UMLS:C4025357 Abnormality of body weight Abnormality of body weight Abnormally increased body weight. HP:0045083 MSH:D015430 SNOMEDCT_US:161831008 SNOMEDCT_US:262286000 SNOMEDCT_US:8943002 UMLS:C0043094 Increased body weight Increased body weight Abnormally low body weight. HP:0001823 HP:0001826 MSH:D013851 MSH:D015431 SNOMEDCT_US:161832001 SNOMEDCT_US:248342006 SNOMEDCT_US:262285001 SNOMEDCT_US:89362005 UMLS:C0041667 UMLS:C1262477 UMLS:C1844806 Decreased body weight Decreased weight Low body weight Low weight Weight less than 3rd percentile Decreased body weight Any deviation from the normal concentration of calcium in the blood circulation. HP:0040077 Abnormal blood calcium concentration Abnormal blood calcium levels Abnormal circulating Ca concentration Abnormal circulating Ca2+ concentration Abnormal circulating calcium concentration An abnormality of temperature homeostasis. MSH:D001832 UMLS:C0005904 UMLS:C1832160 Abnormality of temperature regulation Poor temperature regulation Abnormality of temperature regulation SNOMEDCT_US:3006004 UMLS:C0234428 Disturbances of consciousness Lowered consciousness Reduced consciousness/confusion Reduced consciousness/confusion SNOMEDCT_US:236077008 UMLS:C0473133 Protracted diarrhoea Protracted diarrhea Inflammation of the alimentary part of the gastrointestinal system. UMLS:C1535950 GI inflammation Gastrointestinal inflammation Gastrointestinal inflammation A deficiency in the intake of energy and nutrients. MSH:D044342 SNOMEDCT_US:248325000 SNOMEDCT_US:2492009 SNOMEDCT_US:47563007 SNOMEDCT_US:65404009 SNOMEDCT_US:70241007 UMLS:C0162429 Malnutrition Malnutrition A reduced desire to eat. SNOMEDCT_US:64379006 UMLS:C0232462 Decreased appetite Loss of appetite Poor appetite Poor appetite An anomaly in the ability to perceive and distinguish scents (odors). HP:0004410 UMLS:C4021655 Abnormal sense of smell Abnormality of olfaction Abnormality of the sense of smell Smell defect Abnormality of the sense of smell A decreased sensitivity to odorants (that is, a decreased ability to perceive odors). SNOMEDCT_US:83156004 UMLS:C2364082 Decreased smell sensation Sense of smell impaired Hyposmia The formation of a blood clot inside an artery. SNOMEDCT_US:65198009 UMLS:C0151942 Blood clot in artery Arterial thrombosis Chronic inflammation of the bronchi. MSH:D029481 SNOMEDCT_US:63480004 UMLS:C0008677 Chronic bronchitis A tachycardia originating in the ventricles characterized by rapid heart rate (over 100 beats per minute) and broad QRS complexes (over 120 ms). Fyler:7160 MSH:D017180 SNOMEDCT_US:25569003 UMLS:C0042514 Ventricular tachycardia (VT) is a potentially life-threatening ventricular arrhythmia that presents as a wide QRS complex tachycardia, and is defined as three or more consecutive QRS complexes with a duration longer than 120 milliseconds (ms) and a rate of 100 beats per minute or more, whereby the complexes have a ventricular origin. VT can be subdivided as follows: (i) sustained VT persists for 30 seconds or more; (ii) non-sustained VT lasts less than 30 seconds; (iii) monomorphic VT displays a uniform QRS morphology; and (iv) polymorphic VT displays QRS morphologies that variy from beat to beat. VT is observed most commonly in individuals with structural heart disease or acute myocardial infarction (MI). VT may also be observed in in the setting of drug toxicity or electrolyte abnormalities or in individuals with Mendelian disease. Ventricular tachycardia A state of respiratory distress that requires a life saving intervention in the form of gaining airway access and instituting positive pressure ventilation. HP:0004883 UMLS:C4025279 Respiratory distress necessitating mechanical ventilation Respiratory distress requiring endotracheal intubation Respiratory distress requiring mechanical ventilation Respiratory failure requiring assisted ventilation An abnormality of magnesium ion homeostasis. HP:0008274 UMLS:C4020826 UMLS:C4025274 Abnormal Mg concentration Abnormality of magnesium homeostasis Abnormal magnesium concentration Formation of a blood clot (thrombus) inside a vein, causing the obstruction of blood flow. MSH:D020246 SNOMEDCT_US:111293003 UMLS:C0042487 Blood clot in vein Venous thrombosis Watery voluminous diarrhea resulting from an imbalance between ion and water secretion and absorption. SNOMEDCT_US:15699003 UMLS:C0267557 Secretory diarrhoea Secretory diarrhea An abnormality of the gallbladder. SNOMEDCT_US:253803008 SNOMEDCT_US:49714001 UMLS:C0266249 Abnormality of the gallbladder Anomaly of the gallbladder Abnormality of the gallbladder A pregnancy that ends at a stage in which the fetus is incapable of surviving on its own, defined as the spontaneous loss of a fetus before the 20th week of pregnancy. MSH:D000022 SNOMEDCT_US:17369002 UMLS:C0000786 Miscarriage Spontaneous abortion A type of diabetes mellitus initially characterized by insulin resistance and hyperinsulinemia and subsequently by glucose interolerance and hyperglycemia. HP:0005965 HP:0100652 MSH:D003924 SNOMEDCT_US:44054006 UMLS:C0011860 Diabetes mellitus Type II Diabetes mellitus, noninsulin-dependent NIDDM NIDDM diabetes mellitus Non-insulin dependent diabetes Noninsulin dependent diabetes mellitus Noninsulin-dependent diabetes Type 2 diabetes Type II diabetes Persons with type II diabetes mellitus rarely develop ketoacidosis. Type II diabetes mellitus Limited neck mobility MSH:D009127 SNOMEDCT_US:161882006 SNOMEDCT_US:405947006 UMLS:C0151315 UMLS:C1320474 UMLS:C1847392 Limitation of neck motion Restricted neck movement Limitation of neck motion An anomaly that is characterized progressive airflow obstruction that is only partly reversible, inflammation in the airways, and systemic effects or comorbities. HP:0006541 MSH:D029424 SNOMEDCT_US:13645005 UMLS:C0024117 COPD Chronic obstructive pulmonary disease COPD is usually conceptualized as a disease entity. It is heterogeneous histologically and pathogenically, and conventionally includes emphysema and chronic bronchitis, It is included as a phenotype term as COPD is often annotated as a feature of other diseases. Chronic pulmonary obstruction According to the definitions of the American and British Thoracic Societies, including pulmonary functional tests, X-rays, and CT scans for items such as fibrosis, bronchiectasis, bullae, emphysema, nodular or lymphomatous abnormalities. SNOMEDCT_US:413839001 UMLS:C0746102 Chronic lung disease Chronic lung disease Abnormality of the lung parenchyma extending to the pulmonary interstitium and leading to diffuse pulmonary fibrosis. HP:0006513 HP:0006547 MSH:D017563 SNOMEDCT_US:233703007 UMLS:C0206062 Abnormal lung parenchyma morphology Abnormality in area between air sacs in lung Interstitial lung disease Interstitial pulmonary disease Abnormal pulmonary interstitial morphology Obstruction of conducting airways of the lung. HP:0006512 MSH:D008173 UMLS:C0600260 Obstructive lung disease Pulmonary obstruction Airway obstruction UMLS:C1837257 Lipid accumulation in hepatocytes UMLS:C4024752 Abnormality of eye blood vessels Abnormality of the vasculature of the eye Impaired feeding performance of an infant as manifested by difficulties such as weak and ineffective sucking, brief bursts of sucking, and falling asleep during sucking. There may be difficulties with chewing or maintaining attention. HP:0002016 HP:0002022 HP:0002568 UMLS:C2674608 Feeding difficulties in infancy Loss of elasticity of the upper and lower eyelids causing the skin to sag and bulge. SNOMEDCT_US:246815009 UMLS:C0423124 UMLS:C2674149 Baggy eyes Droopy eyelid skin Extra eyelid skin Eyelid dermatochalasia Redundant eyelid skin Dermatochalasis An abnormality of divalent inorganic cation homeostasis. UMLS:C4023648 Abnormality of divalent inorganic cation homeostasis Abnormal blood inorganic cation concentration An abnormality of cation homeostasis. UMLS:C4023646 Abnormality of cation homeostasis Abnormal blood cation concentration An abnormality of monovalent inorganic cation homeostasis. UMLS:C4023645 Abnormality of monovalent inorganic cation homeostasis Abnormal blood monovalent inorganic cation concentration An abnormality of the upper urinary tract. UMLS:C4023641 Abnormality of the upper urinary tract The upper urinary tract is a subdivision of urinary system which consists of the kidney and the ureters. Abnormality of the upper urinary tract A functional abnormality of the immune system. UMLS:C4023616 Abnormality of immune system physiology Abnormality of glucose homeostasis. UMLS:C4023598 An abnormality of any process involved in the maintenance of an internal steady state of glucose within an organism or cell. Abnormal glucose homeostasis An abnormality of the gastrointestinal tract. MSH:D004066 MSH:D005767 SNOMEDCT_US:119292006 SNOMEDCT_US:25374005 SNOMEDCT_US:53619000 UMLS:C0012242 UMLS:C0017178 UMLS:C4023588 Abnormality of the GI tract Abnormality of the gastrointestinal tract Abnormality of the gastrointestinal tract Abnormal functionality of the cardiovascular system. UMLS:C4023587 Abnormality of cardiovascular system physiology Abnormal cardiovascular system physiology An abnormality of blood circulation. UMLS:C4020760 UMLS:C4023585 Abnormality of blood circulation The presence of hemorrhage within the body. UMLS:C1390214 Internal bleeding Internal haemorrhage Internal hemorrhage An abnormality of the regulation of body fluids. SNOMEDCT_US:1860003 SNOMEDCT_US:190902006 UMLS:C2364164 Abnormality of fluid regulation Fluid imbalance Abnormality of fluid regulation An abnormal concentration of potassium. UMLS:C4023575 Abnormal blood K concentration Abnormality of potassium homeostasis Abnormal blood potassium concentration A sudden flexion, extension, or mixed extension-flexion of predominantly proximal and truncal muscles that is usually more sustained than a myoclonic movement but not as sustained as a tonic seizure. Limited forms may occur: Grimacing, head nodding, or subtle eye movements. Epileptic spasms frequently occur in clusters. Infantile spasms are the best known form, but spasms can occur at all ages MSH:D013036 SNOMEDCT_US:28055006 UMLS:C0037769 UMLS:C1527366 Epileptic spasms Salaam convulsion Salaam convulsions Salaam seizure Salaam seizures The maximum age of onset is between 3 and 12 months, the peak being at 6 months. However, spasms may start from birth, or appear long after the age of 12 months, including into adulthood. Infantile spasms represent a specific type of seizure seen in an epilepsy syndrome of infancy and childhood known as West Syndrome. West Syndrome is characterized by infantile spasms, developmental regression, and hypsarrhythmia (as demonstrated by electroencephalography). Epileptic spasm Any morphological abnormality of the skin. Fyler:4133 UMLS:C4023528 Abnormal skin morphology Abnormal skin structure Abnormality of skin morphology Any abnormality of the physiological function of the skin. UMLS:C4023527 Abnormality of skin physiology Abnormality of skin physiology The presence of inflammation of the skin. That is, an abnormality of the skin resulting from the local accumulation of fluid, plasma proteins, and leukocytes. HP:0002727 HP:0007423 MP:0004947 MSH:D003872 SNOMEDCT_US:703938007 UMLS:C0011603 UMLS:C3875321 Abnormal tendency to infections of the skin Inflammatory abnormality of the skin Skin inflammation Inflammatory abnormality of the skin UMLS:C4023437 Abnormality of the urinary system physiology An abnormality of the skin that is not localized to any one particular region. UMLS:C4021157 Generalised abnormality of skin Generalized abnormality of skin Generalized abnormality of skin An abnormality of the function of the inner ear. UMLS:C4023382 Functional abnormality of the inner ear The inner ear comprises the cochlea, three semicircular canals and the vestibule (labyrinth), and is directly responsible for hearing. Additionally, the vestibule and semicircular canals function to maintain balance or equilibrium. Functional abnormality of the inner ear Delivery of a fetus through surgical incisions made through the abdominal wall (laparotomy) and the uterine wall (hysterotomy). SNOMEDCT_US:200144004 UMLS:C1384674 Caesarian section Caesarian section An anomaly of the control or production of movement in the central nervous system. UMLS:C4023354 Abnormality of central motor function Abnormal central motor function UMLS:C4023353 Abnormality of coordination Coordination issue Abnormality of coordination Cognitive, psychiatric or memory anomaly. UMLS:C4023352 Abnormality of higher mental function A type of infection of the central nervous system that can be regarded as a sign of a pathological susceptibility to infection. MSH:D002494 SNOMEDCT_US:128117002 UMLS:C0007684 Central nervous system infection Unusual CNS infection A subjective manifestation of disease localized to the abdomen. UMLS:C0740651 Abdominal symptom Regurgitation of milk through the nose. SNOMEDCT_US:85023004 UMLS:C0232608 Nasal regurgitation Feeding problem necessitating nasogastric tube feeding. UMLS:C4023343 This is a severe form of feeding problems in infancy. Nasogastric tube feeding in infancy Feeding problem necessitating gastrostomy tube feeding. UMLS:C4020748 UMLS:C4023342 This is an extremely severe form of feeding problems in infancy. Gastrostomy tube feeding in infancy Any cardiac rhythm other than the normal sinus rhythm. Such a rhythm may be either of sinus or ectopic origin and either regular or irregular. An arrhythmia may be due to a disturbance in impulse formation or conduction or both. HP:0001656 HP:0001661 HP:0001665 HP:0001666 HP:0001675 HP:0001687 HP:0001721 HP:0004351 HP:0005158 MSH:C562490 MSH:D001145 SNOMEDCT_US:102594003 SNOMEDCT_US:44808001 SNOMEDCT_US:698247007 UMLS:C0003811 UMLS:C0264886 UMLS:C0522055 UMLS:C0855329 UMLS:C1832603 UMLS:C1842820 Abnormal heart rate Arrhythmias Cardiac arrhythmia Cardiac arrhythmias Cardiac rhythm disturbances Heart rhythm disorders Irregular heart beat Irregular heartbeat Arrhythmia An abnormality in the range and ease of motion of joints across their normal range. UMLS:C4023216 Abnormality of joint mobility A functional abnormality of a skeletal muscle. UMLS:C4023182 Abnormality of muscle physiology Issue with muscle function Abnormal muscle physiology A structural abnormality of a skeletal muscle. HP:0003735 UMLS:C4023181 Abnormal muscle morphology Abnormality of muscle morphology Abnormally shaped muscle Issue with muscle structure Abnormal skeletal muscle morphology An abnormality of the form, structure, or size of the skeletal system. UMLS:C4023165 Abnormally shaped skeletal Abnormality of skeletal morphology An abnormality of the function of the skeletal system. UMLS:C4023164 Abnormality of musculoskeletal physiology A type of abdominal pain that comes and goes in waves, most often starting and ending suddenly and being of severe intensity. MSH:D003085 SNOMEDCT_US:9991008 UMLS:C0232488 Colicky abdominal pain can be caused by kidney stones and gallstones, among other etiologies. This type of pain is thought to be caused by spasm, obstruction, or distension of any of the hollow viscera of the gastrointestinal system. Abdominal colic An infection of the upper or lower respiratory tract. MSH:D012141 SNOMEDCT_US:275498002 UMLS:C0035243 Respiratory infection Respiratory tract infection Respiratory tract infection Impaired ability to eat related to problems gathering food and getting ready to suck, chew, or swallow it. SNOMEDCT_US:78164000 UMLS:C0232466 Feeding difficulties Feeding problems Poor feeding Feeding difficulties An abnormal functionality of the kidney. HP:0000082 HP:0000087 HP:0005566 HP:0008646 SNOMEDCT_US:39539005 UMLS:C0151746 Abnormal kidney function Abnormal renal function Abnormality of renal physiology Kidney function issue Renal functional abnormality Abnormal renal physiology A structural anomaly of the respiratory system. Fyler:4235 UMLS:C4022992 Abnormal respiratory system morphology An anomaly in the processes involved in the maintenance of an internal equilibrium. MP:0001764 UMLS:C4022950 Abnormal homeostasis A structural anomaly of the globe of the eye, or bulbus oculi. HP:0000489 HP:0012374 Fyler:4863 UMLS:C4022925 Abnormal eye structure Abnormality of the globe Abnormally shaped eye previously: Abnormal globe morphology Abnormal eye morphology A functional anomaly of the eye. UMLS:C4022924 Abnormal eye physiology Abnormal eye physiology A subjective feeling of tiredness characterized by a lack of energy and motivation. MSH:D005221 SNOMEDCT_US:248274002 SNOMEDCT_US:84229001 UMLS:C0015672 Fatigue Tired Tiredness Fatigue is distinct from muscle weakness. Fatigue A delay in the development of skills required to feed oneself in the toddler period (between one and three years of age). UMLS:C4022920 Delayed self-feeding during toddler years Inflammation of the large airways in the lung including any part of the bronchi from the primary bronchi to the tertiary bronchi. MSH:D001991 SNOMEDCT_US:32398004 UMLS:C0006277 Bronchitis An abnormality of the partial pressure of oxygen or carbon dioxide in the arterial blood. SNOMEDCT_US:312391003 UMLS:C0476337 Abnormal blood gas level Abnormal blood gas level Abnormally reduced blood carbon dioxide (CO2) level. MSH:D016857 SNOMEDCT_US:61031008 UMLS:C0085383 Hypocarbia Reduced carbon dioxide in the blood Hypocapnia An abnormally low level of blood oxygen. MSH:D000860 SNOMEDCT_US:389087006 UMLS:C0700292 Low blood oxygen level Note that hypoxemia is defined as a condition where arterial oxygen tension is below normal (80-100mmHg). Hypoxia is defined as the failure of oxygenation at the tissue level. Hypoxia is not measured directly by a standard laboratory value. Hypoxemia A structural anomaly of the gallbladder. UMLS:C4022904 Abnormal gallbladder structure Abnormal shape of gallbladder Abnormal gallbladder morphology A structural abnormality of the brain, which has as its parts the forebrain, midbrain, and hindbrain. UMLS:C4021085 Abnormal shape of brain Abnormality of the brain Abnormality of brain morphology Constipation for longer than three months with fewer than 3 bowel movements per week, straining, lumpy or hard stools, and a sensation of anorectal obstruction or incomplete defecation. SNOMEDCT_US:236069009 UMLS:C0401149 Chronic constipation Infrequent bowel movements Chronic constipation Constipation of sudden onset and lasting for less than three months. SNOMEDCT_US:197119006 UMLS:C0401148 Acute constipation An unpleasant sensory and emotional experience associated with actual or potential tissue damage, or described in terms of such damage. MSH:D010146 SNOMEDCT_US:22253000 UMLS:C0030193 Pain Pain An anomalous finding in the examination of the urine for cells. SNOMEDCT_US:310439007 UMLS:C0587955 Abnormal urine cytology Functional anomaly of the kidney persisting for at least three months. HP:0000106 HP:0001918 HP:0008671 MSH:D051436 SNOMEDCT_US:709044004 UMLS:C0748318 UMLS:C1561643 Chronic kidney disease Chronic kidney disease A functional anomaly of the nervous system. UMLS:C4022811 Abnormality of nervous system physiology Abnormal nervous system physiology A structural anomaly of the nervous system. Fyler:4135 Fyler:4300 UMLS:C4022810 Abnormal nervous system morphology Abnormal shape of nervous system Abnormality of nervous system morphology Abnormal nervous system morphology Any anomaly of the inflammatory response, a response to injury or infection characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages. UMLS:C4022805 Abnormal inflammatory response Abnormal inflammatory response A abnormal increase in the inflammatory response to injury or infection. UMLS:C4022803 Increased inflammatory response Abnormal structure of the gastrointestinal tract. UMLS:C4021073 Abnormal shape of the digestive system Morphological abnormality of the GI tract Morphological anomaly of the digestive system Morphological abnormality of the gastrointestinal tract Abnormal functionality of the gastrointestinal tract. UMLS:C4022755 Functional abnormality of the GI tract GI dysfunction Functional abnormality of the gastrointestinal tract A sudden, audible expulsion of air from the lungs through a partially closed glottis, preceded by inhalation. MSH:D003371 SNOMEDCT_US:263731006 SNOMEDCT_US:272039006 SNOMEDCT_US:49727002 UMLS:C0010200 Cough Coughing The European Respiratory Society Task Force recommended two possible definitions of cough: (1) A three-phase expulsive motor act characterized by an inspiratory effort (inspiratory phase) followed by a forced expiratory effort against a closed glottis (compressive phase) and then by opening of the glottis and rapid expiratory airflow (expulsive phase);and (2) A forced expiratory manoeuvre, usually against a closed glottis and associated with a characteristic sound. The term Cough or any of its more specific descendents can be modified by the terms Acute (HP:0011009), Subacute (HP:0011011), and Chronic (HP:0011010). In adults, an acute cough lasts less than 3 weeks, a subacute cough from 3 to 8 weeks, and a chronic cough longer than 8 weeks. In children aged less than 15 years a chronic cough is defined as a daily cough lasting for over 4 weeks. Cough This subontology is designed to provide terms to characterize and specify the phenotypic abnormalities defined in the Phenotypic abnormality subontology, with respect to severity, laterality, age of onset, and other aspects. HP:0000004 UMLS:C4021064 Phenotypic modifier Note that some of the terms, such as Intellectual disability, have children terms such as Severe intellectual disability that represent precomposed combinations of modifiers and phenotypic abnormality terms. This done where the medical community commonly uses these terms with a fixed meaning (for instance, the Intellectual disability terms are used with specific IQ ranges). For computational reasoning, the semantics are intended to be the same as if there was a combination of the phenotype term and the clinical modifier term. Clinical modifier A motor seizure is a type of seizure that is characterized at onset by involvement of the skeletal musculature. The motor event could consist of an increase (positive) or decrease (negative) in muscle contraction to produce a movement. This term describes the initial semiology of the seizure without specifying whether the onset is focal or generalized. Motor seizure Abnormal vascular morphology Any anomaly of the digestive system, a collection of organs that is made up of the gastrointestinal tract and the liver, pancreas, and gallbladder. The gastrointestinal tract is a series of hollow organs joined in a long, twisting tube from the mouth to the anus, including the mouth, esophagus, stomach, small intestine, large intestine and anus. Abnormality of the digestive system A functional anomaly of the digestive system. Abnormality of digestive system physiology A structural anomaly of the digestive system. Abnormality of digestive system morphology The anterior abdominal wall is sunken and presents a concave rather than a convex contour. Scaphoid abdomen can be observed in diseases such as congenital diaphragmatic hernia (since the abdominal contents can be in the thorax). Scaphoid abdomen Passage of many stools containing blood. Blood in stool Bloody stool Bloody bowel movement Bloody diarrhea Bloody diarrhoea Diarrhea that contains bright red or maroon-colored blood may be referred to as hematochezia, while melena is used to describe black, tarry, and smelly diarrhea. Bloody diarrhea Passage of many stools containing blood and mucus. Bloody mucoid diarrhoea Bloody mucoid diarrhea Vomiting of material that is of fecal origin. Faecal vomiting Fecal vomiting Stercoraceous vomiting Vomiting faecal matter Vomiting fecal matter Feculent vomiting is usually due to mechanical intestinal obstruction but it can be due to paralytic obstruction (adynamic ileus). Feculent vomiting A sudden violent, spasmodic, audible expiration of breath through the nose and mouth. Sneeze A symptom or manifestation indicating a systemic or general effect of a disease and that may affect the general well-being or status of an individual. Note that we use the preferred term label constitutional symptom because this reflects common usage, but we do not restrict the term or its descendents to the narrow meaning of symptom, i.e., a complaint related by a patient to a physician. There is no generally accepted classification of what defines a constitutional symptom, but examples include weight loss, fatigue, general weakness, night sweats, shaking, chills, fever, and vomiting. Constitutional symptom A sudden sensation of feeling cold. Chills The word chills can also refer to an episode of shivering, accompanied by paleness and feeling cold. Chills Involuntary contraction or twitching of the muscles. Shivering Shuddering Shivering is a physiologic method of heat production in man and other mammals. Shivering is a bodily function in response to fever, early hypothermia or feeling cold. Shivering Severe chills with violent shivering. A rigor is an episode of shaking or exaggerated shivering which can occur with a high fever. Rigours A sudden attack of severe shivering accompanied by chills (a feeling of coldness) is called a rigor and may be associated with a marked rise in body temperature. Patients often describe rigors as an attack of uncontrollable shaking. Rigors are often a sign of infection, particularly bacterial infection. Rigors A functional anomaly of the hepatobiliary system Abnormality of hepatobiliary system physiology Any physiological abnormality of the esophagus. Abnormality of esophagus physiology Abnormality of oesophagus physiology Functional abnormality of the esophagus Functional abnormality of the oesophagus Abnormal esophagus physiology An anomaly of arterial function. Abnormal arterial physiology A reddish appearance over the white part (sclera) of the eye ranging from a few enlarged blood vessels appearing as wiggly lines over the sclera to a bright red color completely covering to sclera. Red eye Red eyes Red eye A state characterized by a feeling of weakness and loss of strength leading to a generalized weakness of the body. Lack of energy and strength Weakness Asthenia is to be distinguished from fatigue, because asthenia refers to a sensation of exhaustion which occurs before any effort. Asthenia is to be distinguished from myasthenia, which means a specific weakness of one or more muscles. Asthenia and fatigue can coexist. Asthenia Any anomaly of the vocalizing of an infant's crying, i.e.,the typically loud voice production that is accompanied by tears and agitation. Abnormal cry Inflammation (due to infection or irritation) of the pharynx. Pharyngitis Abscess An anomaly of the amount or nature of abdominal sounds. Abdominal sounds (bowel sounds) are made by the movement of the intestines as they promote passage of abdominal contents by peristalsis. SNOMEDCT_US:60612008 UMLS:C0159060 Abnormal bowel sounds Abnormal bowel sounds Abnormally increased gurgling/rumbling sounds made by the movement of fluid and gas in the intestines. SNOMEDCT_US:18101008 UMLS:C0232694 Borborygmi Increased bowel sounds Hyperactive bowel sounds An decreased amount of bowel sounds. SNOMEDCT_US:15280003 UMLS:C0232695 Decreased bowel sounds Hypoactive bowel sounds Complete lack of abdominal sounds as assayed by examination of the abdomen with a stethoscope. UMLS:C4022606 Lack of bowel sounds This feature reflects lack of intestinal activity. Lack of bowel sounds Severely decreased cardiac output with evidence of inadequate end-organ perfusion (i.e., tissue hypoxia) in the presence of adequate intravascular volume. MSH:D012770 SNOMEDCT_US:89138009 UMLS:C0036980 Cardiovascular shock Cardiogenic shock can result from a number of different of cardiac insults, the most common of which is acute myocardial infarction. Cardiogenic shock Abnormality of vascular function. UMLS:C4022603 Abnormal vascular physiology A structural anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. UMLS:C4073120 Abnormal ocular adnexa morphology Any structural anomaly of the heart and great vessels. HP:0001632 HP:0002564 HP:0002565 UMLS:C4049796 Cardiovascular malformations Abnormality of cardiovascular system morphology Any structural anomaly of the tongue. UMLS:C4280755 Abnormal tongue morphology Any functional anomaly of the tongue. UMLS:C4280754 Abnormal tongue physiology An anomalous (adventitious) sound produced by the breathing process. SNOMEDCT_US:301273002 UMLS:C0231856 Abnormal lung auscultation finding Abnormal breath sound A functional anomaly of that portion of the cardiosvascular system that carries deoxygenated blood from the heart to the lungs and returns oxygenated blood back to the heart. UMLS:C4280730 Abnormal pulmonary circulation Abnormality of respiratory circulation Abnormality of pulmonary circulation Feeding problem necessitating gastrojejunal tube feeding. UMLS:C4280681 Gastro-jejunal tube feeding in infancy The rationale for gastrojejunal tube feeding is that placing the tip of the tube beyond the ligament of Treitz prevented duodenogastric reflux or gastro-esophageal reflux. Gastrojejunal feeding tubes have since been used in children who are deemed too unfit for antireflux surgery or where fundoplication has failed. Gastrojejunal tube feeding in infancy Dilatation of the blood vessels of the conjunctiva leading to a red appearance of the sclera. Conjunctival hyperaemia Conjunctival injection Conjunctival vascular congestion Conjunctival hyperemia An anomaly of the electrical conduction physiology of the heart. Abnormality of cardiovascular system electrophysiology A chronic deviation from normal pressure in the systemic arterial system. Abnormal systemic BP Abnormal systemic blood pressure Hepatocytes (liver parenchymal cells) exhibit a bloated appearance because of expansion of the cytoplasm by accumulated material. Storage in hepatocytes Resistance of the extensor muscles of the neck to being bent forwards (i.e., impaired neck flexion) as a result of muscle spasm of the extensor muscles of the neck. Nuchal rigidity is not a fixed rigidity. Nuchal rigidity has been used as a bedside test for meningism, although its sensitivity for this purpose has been debated. Meningism is resistance to neck flexion due to painful spasm of extensor muscles resulting from meningeal irritation. The diagnosis of meningism is made in someone whose symptoms simulate meningitis, but in which no actual inflammation of these membranes is present. Nuchal rigidity can thus be observed in individuals with meningitis or with meningism. Nuchal rigidity A cough that produces phlegm or mucus. Cough with mucus production Wet cough Productive cough A cough that does not produce phlegm or mucus. Dry cough Dry coughing Nonproductive cough A distortion of the sense of taste, often characterized by the sensation of a metallic taste. Altered sense of taste Dysgeusia Metallic taste Metallic taste in mouth Parageusia A state of sudden and severe confusion. Delirium The state in which profound and widespread reduction of effective tissue perfusion leads first to reversible, and then if prolonged, to irreversible cellular injury. Shock A circumscribed area of pus or necrotic debris in the skin. Skin abscess Cutaneous abscess An unpleasant sensation of tightness or pressure in the chest. Tightness in chest Tightness of chest Chest tightness Any deviation from the normal quantity of secretion of nasal mucus, a thick viscous liquid produced by the mucous membranes of the nose. Abnormal nasal mucus secretion Increased discharge of mucus from the nose. Nasal Discharge Runny Nose Rhinorrhea A type of ventricular tachycardia that is characterized by variable QRS complexes within each lead (i.e., QRS complexes may be different from beat to beat). Polymorphic ventricular tachycardia Any functional anomaly of the ear. Abnormal ear physiology The course a disease typically takes from its onset, progression in time, and eventual resolution or death of the affected individual. Clinical course A functional anomaly of the mouth (which is also known as the oral cavity). The physiological functions of the mouth include salivary gland secretory function, mastication (chewing) and preparation of food for swallowing. Abnormal oral physiology Any structural anomaly of the mouth, which is also known as the oral cavity. Abnormal oral morphology Abnormal appearance of material expectorated (coughed up) from the respiratory system and that is composed of mucus but may contain other substances such as pus, blood, microorganisms, and fibrin. Abnormal sputum morphology Abnormal sputum An anomaly of the adjacent structures (i.e., adnexa) of the eye, defined as the lacrimal apparatus, the extraocular muscles and the eyelids, eyelashes, eyebrows and the conjunctiva. Abnormality of the ocular adnexa A type of infection that is regarded as a sign of a pathological susceptibility to infection. There are five general subtypes. (i) Opportunistic infection, meaning infection by a pathogen that is not normally able to cause infection in a healthy host (e.g., pneumonia by Pneumocystis jirovecii or CMV); (ii) Unusual location (focus) of an infection (e.g., an aspergillus brain abscess); (iii) a protracted course or lack of adequate response to treatment (e.g., chronic rhinosinusitis); (iv) Unusual severity or intensity of an infection; and (v) unusual recurrence of infections. Unusual infection Intermittent pain, i.e., pain that occurs occasionally and at irregular intervals. Episodic pain A type of abdominal pain characterized by a feeling of contractions and typically fluctuating in intensity. Abdominal cramps An unusual infection classified by the affected body part. Unusual infection by anatomical site An abnormal level of an analyte measured in the blood. Abnormal circulating metabolite concentration Abnormal immune system morphology Abnormal increase in blood pressure. An individual measurement of increased blood pressure does not necessarily imply hypertension. In practical terms, multiple measurements are recommended to diagnose the presence of hypertension. Increased BP Increased blood pressure Involuntary tightening of the abdominal musculature that occurs in response to touching the abdomen to avoid pain. Rigidity can occur in the presence of abdominal inflammation and usually involves only the inflamed area. Rigid abdomen Abdominal rigidity A voluntary contraction of the abdominal wall musculature to avoid pain. Abdominal guarding tends to be generalized over the entire abdomen. In contrast to abdominal rigidity, guarding can often be overcome by having the patient purposely relax the muscles; rigidity cannot be. Abdominal guarding Persistent blue color of the skin that surrounds the mouth. Bluish around mouth Circumoral cyanosis may be a sign of peripheral or of central cyanosis. Circumoral cyanosis A cutaneous wound is a defined as a disruption of normal anatomic structure and function of the skin that occured owing to an injury of the skin. Wound healing is a dynamic, interactive processinvolving soluble mediators, blood cells, extracellularmatrix, and parenchymal cells. Wound healing has three phases: inflammation, tissue formation, and tissue remodeling, that overlap in time. Skin wound Cutaneous wound A cutaneous wound that is proceeding through an orderly and timely reparative process that results in sustained restoration of the anatomic and functional integrity of the skin. Wound healing accors in multiple overlapping stages, with re=-eipthelialization normally beginning on day one or two. In most clinical settings, closure of acute and chronic wounds is considered the wound healing end point, but wounds can continue to undergo remodeling or tissue maturation for several months or even years. Acute cutaneous wound A cutaneous wound that has failed to proceed through the orderly and timely process to produce an atomic and functional integrity, or proceeded through the repair process without establishing a sustained anatomic and functional result. Chronic nonhealing cutaneous wound Chronic cutaneous wound An anomaly of the musculoskeletal system, which consists of the bones of the skeleton, muscles, cartilage, tendons, ligaments, joints, and other connective tissue. The musculoskeletal system supports the weight of the body, maintains body position and produces movements of the body or of parts of the body. Abnormality of the musculoskeletal system A structural anomaly of the pharynx. Abnormal pharynx morphology Osmotic diarrhea results from the presence of osmotically active, poorly absorbed solutes in the bowel lumen that inhibit normal water and electrolyte absorption. Osmotic diarrhea involves an unabsorbed substance that draws water from the plasma into the intestinal lumen along osmotic gradients. Secretory diarrhea results from disordered electrolyte transport and, despite the term, is more commonly caused by decreased absorption rather than net secretion. Inflammatory diseases cause diarrhea with exudative, secretory, or osmotic components. Osmotic diarrhea Passage of an increased number of stools containing mucus, a thick fluid substance secreted by mucous membranes. Mucous diarrhea Mucous diarrhoea Mucoid diarrhea Any structural anomaly of a blood vessel (artery, arteriole, capillary, venule, or vein). Abnormal blood vessel morphology A sudden onset of abdominal pain with associated nausea or vomiting. The acute abdomen may be caused by an infection, inflammation, vascular occlusion, or obstruction. Acute abdominal pain Acute abdomen Ischemia is defined as a restriction of arterial blood supply to a tissue associated with insufficient oxygenation to support the metabolis requirements of the tissue. Depending on the involved tissues, clinical manifestations may include pain, pallor, lack of pulse, coldness, paresthesia, and paralysis. Additional associated manifestations include hemodynamic parameters (reduced blood pressure distal to the site of restricted arterial supply) and angiographic evidence of arterial occclusion. Tissue ischemia Feeding problem necessitating food and nutrient delivery via a tube. Tube feeding Passage of excessive amounts of gas and the feeling of abdominal fullness and bloating. Flatulence Intermittent abdominal pain with diarrhea and/or constipation. Bowel irritability Acute respiratory distress syndrome (ARDS) is defined as an acute disorder that starts within seven days of the inciting event and is characterized by bilateral lung infiltrates and severe progressive hypoxemia in the absence of any evidence of cardiogenic pulmonary edema. ARDS is defined by the patient's oxygen in arterial blood (PaO2) to the fraction of the oxygen in the inspired air (FiO2). These patients have a PaO2/FiO2 ratio of less than 300. ARDS Acute respiratory distress syndrome (ARDS) is a life-threatening condition of seriously ill patients, characterized by poor oxygenation, pulmonary infiltrates, and acuity of onset. On a microscopic level, the disorder is associated with capillary endothelial injury and diffuse alveolar damage. Once ARDS develops, patients usually have varying degrees of pulmonary artery vasoconstriction and may subsequently develop pulmonary hypertension. ARDS carries a high mortality, and few effective therapeutic modalities exist to combat this condition. ARDS can be observed as a complication of many diseases including pulmonary infection or aspiration, sepsis, trauma, massive transfusion, drowning, drug overdose, fat embolism, inhalation of toxic fumes, and pancreatitis. Acute respiratory distress syndrome Acral areas of erythema with vesicles or pustules. The lesions resemble chilblains and have purpuric areas, affecting hands and feet. Chilblain-like lesion This condition is termed pseudo-chilblain because of the similar appearance of these lesions to chilblains. Pseudochilblains may be observed in persons with COVID-19 without documented exposure to cold or other risk factors for chilblains. Pseudo-chilblain An increase in the amount of airway mucus. This feature may be characterized by frequent or excessive throat clearing (exhalation through tightly constricted laryngopharyngeal tissues accompanied by vibration of the palatoglossal arch and the vocal folds serving to clear mucus from the airway). Increased phlegm If excessive sputum production is manifested by frequent and often involuntary coughing, the HPO term Productive cough should be used. Increased sputum production Pleuritic chest pain is characterized by sudden and intense sharp, stabbing, or burning pain in the chest when inhaling and exhaling. Pleuritic chest pain A feeling of general discomfort, weakness, or lack of health. Malaise The condition of being unable to eat a full meal because of a feeling of fullness (satiety), or or feeling very full after eating only a small amount of food. Feeling full quickly when eating Not able to finish a normal-sized meal Early satiety Feeling excessively full after meals. Postprandial fullness Inability to ingest sufficient quantities of nutrition by mouth or by tube-feeding with the corresponding requirement for intravenous administration of nutrition. Dependency on parenteral nutrition Bluish discoloration of one or more regions of the face. Bluish face Cyanotic face Facial cyanosis Bluish discoloration of the distal extremities (hands, fingertips, toes), and can sometimes involve circumoral and periorbital areas. Mucous membranes are generally not involved. Peripheral cyanosis UMLS:C4073150 Abnormal consumption behaviour Abnormal consumption behavior The condition of inability to eat normally treated by placement of a thin tube through the nose into the stomach that is then used to carry food. Nasogastric tube feeding A rare condition that is characterized by a complete loss of taste function of the tongue. Absent sense of taste Impaired taste sensation Lost taste Ageusia A chronic inflammatory bowel disease that includes characteristic ulcers, or open sores, in the colon. The main symptom of active disease is usually constant diarrhea mixed with blood, of gradual onset and intermittent periods of exacerbated symptoms contrasting with periods that are relatively symptom-free. In contrast to Crohn's disease this special form of colitis begins in the distal parts of the rectum, spreads continually upwards and affects only mucose and submucose tissue of the colon. MSH:D003093 SNOMEDCT_US:64766004 UMLS:C0009324 Colitis ulcerosa Ulcerative colitis A chronic granulomatous inflammatory disease of the intestines that may affect any part of the gastrointestinal tract from mouth to anus, causing a wide variety of symptoms. It primarily causes abdominal pain, diarrhea which may be bloody, vomiting, or weight loss, but may also cause complications outside of the gastrointestinal tract such as skin rashes, arthritis, inflammation of the eye, tiredness, and lack of concentration. Crohn's disease is thought to be an autoimmune disease, in which the body's immune system attacks the gastrointestinal tract, causing inflammation. MSH:D003424 SNOMEDCT_US:34000006 UMLS:C0010346 Granulomatous enteritis and colitis Morbus Crohn Crohn's disease A chronic inflammatory disease of the large intestine (colon, cecum and rectum). SNOMEDCT_US:54597004 UMLS:C0267375 Chronic colitis Immunological states where the immune system produces harmful responses upon reexposure to sensitising antigens. UMLS:C0237653 Immunologic hypersensitivity Inflammation of the eye, parts of the eye or the periorbital region. HP:0007891 UMLS:C4020969 Inflammatory abnormality of the eye Ocular inflammation Inflammatory abnormality of the eye Abnormal cognition with deficits in thinking, reasoning, or remembering. HP:0002128 HP:0002129 HP:0002302 HP:0002337 HP:0002441 HP:0006972 HP:0006998 HP:0007211 MSH:D060825 SNOMEDCT_US:386806002 UMLS:C0338656 UMLS:C0683322 Abnormality of cognition Cognitive abnormality Cognitive defects Cognitive deficits Cognitive impairment Intellectual impairment An individual with cognitive impairment may have trouble remembering, learning new things, concentrating, or making decisions. Cognitive impairment Death between the age of 16 and 40 years. UMLS:C4022012 Death in early adulthood Death in early adulthood A chronic condition in which the pancreas produces little or no insulin. Type I diabetes mellitus is manifested by the sudden onset of severe hyperglycemia with rapid progression to diabetic ketoacidosis unless treated with insulin. MSH:D003922 SNOMEDCT_US:46635009 UMLS:C0011854 Diabetes mellitus Type I Juvenile diabetes mellitus Type 1 diabetes Type I diabetes The onset of type 1 diabetes is typically during adolescence, but it can develop at any age. Type I diabetes mellitus An anomaly of the cerebral blood vessels. UMLS:C4022001 Abnormality of the cerebral blood vessels Abnormality of the cerebral vasculature Abnormal cerebral vascular morphology Abnormal eating habit with excessive or insufficient consumption of food or any other abnormal pattern of food consumption. UMLS:C4021982 Abnormal eating behavior Abnormal eating behaviour Note that this HPO term refers to an abnormal eating habit but does not directly refer to an eating disorder, which is a psychological disorder that is characterized by one or more abnormal eating behaviors. Abnormal eating behavior An unpleasant sensation characterized by physical discomfort (such as pricking, throbbing, or aching) localized to the chest. MSH:D002637 SNOMEDCT_US:29857009 UMLS:C0008031 Chest pain Thoracic pain Chest pain UMLS:C4021978 Abnormal spit Abnormality of salivation Abnormality of salivation An anomaly of the lymphatic system, a network of lymphatic vessels that carry a clear fluid called lymph unidirectionally towards either the right lymphatic duct or the thoracic duct, which in turn drain into the right and left subclavian veins respectively. HP:0003012 MSH:D008206 SNOMEDCT_US:111590001 SNOMEDCT_US:234087005 SNOMEDCT_US:3305006 SNOMEDCT_US:362971004 UMLS:C0024228 UMLS:C4021976 Abnormality of the lymphatic system Systemic inflammatory response to infection. MSH:D018805 UMLS:C0036690 Infection in blood stream Sepsis An abnormality of emotional behaviour. UMLS:C4020949 Abnormal emotion/affect behaviour Abnormal emotion/affect behavior Any structural anomaly of the bile-secreting organ that is important for detoxification, for fat, carbohydrate, and protein metabolism, and for glycogen storage. Fyler:4447 Abnormal liver morphology A heterogeneous group of symptoms that are localized in the epigastric region. Typical dyspeptic symptoms include postprandial fullness, early satiation, epigastric pain and epigastric burning, but other upper gastrointestinal symptoms such as nausea, belching or abdominal bloating often occur. Indigestion Dyspepsia An abnormality of carbon dioxide (CO2) in the arterial blood. Abnormal CO2 levels in blood Abnormal blood carbon dioxide level Abnormal blood carbon dioxide level An abnormality of the partial pressure of oxygen in the arterial blood. Abnormal blood O2 level Abnormal blood oxygen levels Abnromal O2 blood concentration Abnormal blood oxygen level data item data item 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. PERSON: Alan Ruttenberg PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Chris Stoeckert PERSON: Jonathan Rees PERSON: Jonathan Rees data data item information content entity A generically dependent continuant that is about some thing. An information entity is an entity that represents information about some other entity. For example, a measurement, a clustered data set. an information content entity is an entity that is generically dependent on some artifact and stands in relation of aboutness to some entity James Malone PERSON: Chris Stoeckert PERSON: Chris Stoeckert OBI_0000142 OBI_0000142 information content entity information content entity information entity a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum An information content entity whose concretizations indicate to their bearer how to realize them in a process. PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity data set A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. person:Allyson Lister person:Chris Stoeckert OBI_0000042 OBI_0000042 group:OBI data set measurement datum A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. person:Chris Stoeckert OBI_0000305 group:OBI measurement datum A scalar measurement datum that is the result of measuring a temporal interval Person:Alan Ruttenberg time measurement datum A pathogen host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell By this definition, vectors and other organisms that may not be infected are bearers of the infectious agent host role. infectious agent host role A host role borne by an organism in virtue of the fact that its extended organism contains a pathogen. Albert Goldfain Alexander Diehl Lindsay Cowell Bearing the infectious agent host role implies bearing the pathogen host role, but the reverse is not true. See comment for infectious agent host role. pathogen host role An infectious agent host role borne by an organism in virtue of the fact that its extended organism contains an infectious agent, the infectious agent has the infectious disposition towards the host, and the host has no symptoms of the infectious disease caused by the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent carrier role A disposition that inheres in a material entity in virtue of the fact that the entity has a part (e.g. a gene product), which itself has a disposition to mitigate damage to the entity. Albert Goldfain Alexander Diehl Lindsay Cowell Examples include the following: CCR5 mutations protect T cells from HIV invasion. A tumor cell's resistance to chemotherapy protects the cell from damage by the drug (although this harms the patient). An insect's resistance to insecticide protects it from the insecticide. The disposition is realized in a process that mitigates damage to the bearer and has the part as a participant. protective resistance A protective resistance that mitigates the damaging effects of a drug. Albert Goldfain Alexander Diehl Lindsay Cowell drug resistance resistance to drug A disposition borne by an infectious agent that is the disposition to penetrate the epithelial barriers of an organism of another Species. Albert Goldfain Alexander Diehl Lindsay Cowell invasive disposition An infectious disease course that begins soon after infection is established and progresses rapidly to severe stages. Albert Goldfain Alexander Diehl Lindsay Cowell acute infectious disease course A disease course that is the realization of an infectious disease. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease course A chronic infectious disease course that does not progress to severe stages for a long period of time. Albert Goldfain Alexander Diehl Lindsay Cowell long-term non-progressing infectious disease course A process of infectious disease realizations and for which there is a statistically significant increase in the infectious disease incidence of a population. Albert Goldfain Alexander Diehl Lindsay Cowell infectious disease outbreak infectious disease epidemic An aggregate of organisms of the same Species. Albert Goldfain Alexander Diehl Lindsay Cowell The organism population may be delineated by spatio-temporal proximity or by demographic criteria such as age. organism population An organism population whose members have an infection. Albert Goldfain Alexander Diehl Lindsay Cowell infected population An organism population in whose members an infectious disease is being realized. Albert Goldfain Alexander Diehl Lindsay Cowell diseased population An organism population whose members each have an infectious disposition. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent population An organism population whose members are not infected with an infectious agent and who lack immunity to the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell at-risk population susceptible population An organism population whose members are participating in non-parasitic symbiosis with a particular host. Albert Goldfain Alexander Diehl Lindsay Cowell normal resident microflora population normal resident microbiota population An organism bearing a host role. Albert Goldfain Alexander Diehl Lindsay Cowell host An organism bearing an infectious agent host role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent host An organism bearing a pathogen host role. Albert Goldfain Alexander Diehl Lindsay Cowell pathogen host An organism bearing an infectious agent vector role. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent vector A material entity bearing an infectious agent vehicle role. Albert Goldfain Alexander Diehl Lindsay Cowell vehicle of infectious agent A biological macromolecule produced by a pathogen and that has a virulence factor disposition. Albert Goldfain Alexander Diehl Lindsay Cowell virulence factor An organism that is host to an infectious agent and has no symptoms of the infectious disease associated with the infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell asymptomatic host of infectious agent An organism who is host to an infectious agent and has symptoms of the infectious disease associated with the infectious agent Albert Goldfain Alexander Diehl Lindsay Cowell symptomatic host of infectious agent A resistance to drug that mitigates the damaging effects of an antibiotic. Albert Goldfain Alexander Diehl Lindsay Cowell antibiotic resistance An infectious disease course that unfolds over a long period of time. Albert Goldfain Alexander Diehl Lindsay Cowell persistent infectious disease course chronic infectious disease course An organism population whose members have acquired immunity to an infectious agent. Albert Goldfain Alexander Diehl Lindsay Cowell immune population An organism population persisting in a site it has colonized. Albert Goldfain Alexander Diehl Lindsay Cowell colony A colony whose members are infectious agents. Albert Goldfain Alexander Diehl Lindsay Cowell infectious agent colony A role borne by an organism in virtue of the fact that it's extended organism contains a material entity other than the organism. Albert Goldfain Alexander Diehl Lindsay Cowell host role An organism that is not infected with an infectious agent and lacks protective immunity to the infectious agent. Alex Diehl Lindsay Cowell susceptible organism domestic animal that bears a food production role. YL Livestock refers to one or more domesticated animals raised in an agricultural setting to produce commodities such as food, fiber and labor. The term "livestock" as used in this article does not include poultry or farmed fish; however the inclusion of these, especially poultry, within the meaning of "livestock" is common. (http://en.wikipedia.org/wiki/Livestock) livestock The manner, procedure or technique by which a morphological or physiological state or property in a single individual or sample or a group of individuals or samples is assessed and a quantitative or qualitative value assigned. measurement method A postmortem examination of a body to determine the cause of death or the character and extent of changes produced by disease. autopsy A postmortem examination of the body of an animal to determine the cause of death or the character and extent of changes produced by disease. necropsy A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. DOID:4 EFO:0000408 ICD9:799.9 MESH:D004194 NCIT:C2991 OGMS:0000031 Orphanet:377788 SCTID:64572001 UMLS:C0012634 condition disease disease or disorder disease or disorder, non-neoplastic diseases diseases and disorders disorder disorders medical condition other disease disease or disorder A disease involving the lower respiratory tract. DOID:0050161 ICD9:478.1 ICD9:478.19 SCTID:128272009 UMLS:C1290325 disease of lower respiratory tract disease or disorder of lower respiratory tract disorder of lower respiratory tract lower respiratory tract disease lower respiratory tract disease or disorder lower respiratory tract disease DOID:0050338 primary bacterial infectious disease A malignant neoplasm involving the respiratory system DOID:0050615 ICD9:165.8 ICD9:165.9 SCTID:449096009 UMLS:C3164456 cancer of respiratory system malignant neoplasm of respiratory system malignant respiratory system neoplasm respiratory system cancer respiratory system cancer A monogenic disease that is has material basis in a mutation in a single gene on one of the non-sex chromosomes. DOID:0050739 ICD9:758.5 SCTID:1899006 UMLS:C0265384 autosomal hereditary disorder autosomal inherited disease autosomal inherited disorder autosomal genetic disease A hypersensitivity reaction type II disease that involves the peripheral nervous system. DOID:0060033 peripheral nervous system autoimmune disease peripheral nervous system hypersensitivity reaction type II disease autoimmune disease of peripheral nervous system An immune system disease that has basis in dysregulation of the hypersensitivity reaction, an inflammatory response to an exogenous environmental antigen or an endogenous antigen initiated by the adaptive immune system. sensitive sensitivity DOID:0060056 EFO:1002003 NCIT:C3114 SCTID:473010000 allergic reaction hypersensitive hypersensitivity hypersensitivity reaction hypersensitivity reaction disease A non-neoplastic or neoplastic disorder that affects the thorax and/or the organs of the thoracic cavity. Representative examples include pleural infection, mediastinitis, thymoma, mediastinal lymphoma, and pleural mesothelioma. DOID:0060118 MESH:D013896 NCIT:C35742 SCTID:118946009 SCTID:609622007 UMLS:C0039978 UMLS:C3661979 disease of thoracic segment of trunk disease or disorder of thoracic segment of trunk disorder of thoracic segment of trunk disorder of thorax thoracic disease thoracic disorder thoracic segment of trunk disease thoracic segment of trunk disease or disorder thoracic disease Life-threatening respiratory failure that develops rapidly. Causes include injury, sepsis, drug overdose, and pancreatitis. It manifests with dyspnea and cyanosis and may lead to cardiovascular shock. ICD9:518.81 NCIT:C27043 SCTID:65710008 UMLS:C0264490 acute respiratory failure respiratory failure, acute acute respiratory failure A disorder characterized by behavioral and/or psychological abnormalities, often accompanied by physical symptoms. The symptoms may cause clinically significant distress or impairment in social and occupational areas of functioning. Representative examples include anxiety disorders, cognitive disorders, mood disorders and schizophrenia. DOID:150 ICD10:F99 ICD10:F99-F99 MESH:D001523 MFOMD:0000004 NCIT:C2893 Psychiatric disease Psychiatric disorder disease of mental health mental disorder mental dysfunction mental illness psychiatric disorder A non-neoplastic or neoplastic disorder that affects the pleura. Representative examples include pleural infection, pleural mesothelioma, and pleural solitary fibrous tumor. DOID:1532 ICD9:518.89 MESH:D010995 NCIT:C26859 SCTID:88075009 UMLS:C0032226 disease of pleura disease or disorder of pleura disorder of pleura non-neoplastic pleural disease pleura disease pleura disease or disorder pleural disorder pleural disorders pleural disease The use of alcoholic beverages to excess, either on individual occasions ("binge drinking") or as a regular practice. DOID:1574 ICD10:F10.1 ICD9:305.0 ICD9:305.00 MESH:D000437 MESH:D019973 NCIT:C20701 SCTID:15167005 alcohol abuse ethanol abuse alcohol abuse Acute or chronic inflammation of one or more lymph nodes. It is usually caused by an infectious process. DOID:1602 HP:0002840 ICD10:I88.1 ICD10:I88.9 ICD10:L04 ICD10:L04.9 ICD9:289.1 ICD9:683 MESH:D008199 NCIT:C26821 SCTID:41174002 UMLS:C0024205 UMLS:C0154304 UMLS:C0157705 Inflammation of lymph node acute adenitis acute lymphadenitis adenitis chronic adenitis chronic lymphadenitis inflammation of lymph node lymph node inflammation lymph nodeitis lymphadenitis lymphadenitis (disease) lymphadenitis DOID:1672 ICD10:J93.0 ICD9:512.0 SCTID:196102003 UMLS:C0155907 spontaneous tension pneumothorax Abnormal presence of air in the pleural cavity. DOID:1673 HP:0002107 ICD10:J93.1 ICD9:512.8 MESH:D011030 NCIT:C38006 SCTID:36118008 pneumothorax pneumothorax (disease) pneumothorax A disease involving the musculoskeletal system. DOID:17 ICD9:729.99 MESH:D009140 NCIT:C107377 SCTID:928000 UMLS:C0026857 disease of musculoskeletal system disease or disorder of musculoskeletal system disorder of musculoskeletal system musculoskeletal disease musculoskeletal system disease musculoskeletal system disease or disorder musculoskeletal system disorder musculoskeletal system disease A disease involving the renal system. DOID:18 ICD9:V47.4 MESH:D014570 NCIT:C3430 SCTID:128606002 UMLS:C1335051 disease of renal system disease or disorder of renal system disorder of renal system disorder of the urinary system disorder of urinary system non-neoplastic urinary tract disease renal system disease renal system disease or disorder urinary system disease urinary tract disease urinary tract disorder urologic disorder urological disorders urinary system disease A disorder characterized by decreased function of the gonads. Clinical manifestations in both males and females include poor libido, infertility, and osteoporosis. Additional signs in males include erectile dysfunction, muscle atrophy, gynecomastia and increased abdominal fat. In females, additional signs include shrinking of the breasts and loss of, or failure to develop menstruation. DOID:1924 ICD9:253.4 MESH:D007006 NCIT:C9227 OMIM:241100 OMIM:307300 SCTID:48130008 UMLS:C0020619 gonadotropin deficiency hypogonadotropism hypogonadism A group of signs, symptoms, and clinicopathological characteristics that may or may not have a genetic basis and collectively define an abnormal condition. DOID:225 MESH:D013577 NCIT:C28193 OGMS:0000086 SCTID:64572001 UMLS:C0039082 cluster, symptom clusters, symptom symptom cluster symptom clusters syndrome syndrome associated with disease or disorder syndromes syndromic disease syndromic disease or disorder syndromic disease A non-neoplastic or neoplastic disorder that affects the testis or the ovary. DOID:2277 MESH:D006058 NCIT:C26786 UMLS:C0018050 disease of gonad disease or disorder of gonad disorder of gonad disorder of gonads gonad disease gonad disease or disorder gonadal disorder gonadal disorders gonadal disease A disease involving the female reproductive system. DOID:229 ICD9:629.9 MESH:D005831 NCIT:C27020 SCTID:310789003 disease of female reproductive system disease or disorder of female reproductive system disorder of female genital system disorder of female reproductive system female reproductive disease female reproductive system disease female reproductive system disease or disorder female reproductive system disorder female reproductive system disease A reduction in the number of red blood cells, the amount of hemoglobin, and/or the volume of packed red blood cells. Clinically, anemia represents a reduction in the oxygen-transporting capacity of a designated volume of blood, resulting from an imbalance between blood loss (through hemorrhage or hemolysis) and blood production. Signs and symptoms of anemia may include pallor of the skin and mucous membranes, shortness of breath, palpitations of the heart, soft systolic murmurs, lethargy, and fatigability. DOID:2355 EFO:0004272 HP:0001903 ICD10:D64.9 ICD9:285.8 ICD9:285.9 MESH:D000740 NCIT:C2869 SCTID:271737000 anaemia anemia anemia (disease) anemia The use of a drug for a reason other than which it was intended or in a manner or in quantities other than directed. DOID:302 ICD9:305.90 MESH:D019966 NCIT:C16522 SCTID:66214007 substance abuse A category of psychiatric disorders which include disorders related to the taking of a drug of abuse (including alcohol, prescribed medications and recreational drugs). DOID:303 MESH:D019966 NCIT:C92203 substance-related disorder substance-related disorder A non-neoplastic or neoplastic disorder that affects the liver, bile ducts, and gallbladder. Representative examples of non-neoplastic disorders include hepatitis, cirrhosis, cholangitis, and cholecystitis. Representative examples of neoplastic disorders include hepatocellular adenoma, hepatocellular carcinoma, and cholangiocarcinoma. DOID:3118 NCIT:C3959 UMLS:C0267792 disease of hepatobiliary system disease or disorder of hepatobiliary system disorder of hepatobiliary system hepatobiliary disorder hepatobiliary system disease hepatobiliary system disease or disorder liver and biliary disease liver and biliary disorder liver and biliary system disorder liver and biliary tract disease hepatobiliary disease A primary or metastatic malignant neoplasm involving any part of the digestive system. DOID:3119 ICD10:C15.C26 ICD10:C26.9 ICD9:239.0 MESH:D005770 NCIT:C3052 NCIT:C4890 GI tumor cancer of digestive system digestive system cancer gastrointestinal system cancer gastrointestinal tract cancer malignant digestive system neoplasm malignant gastrointestinal neoplasm malignant gastrointestinal system neoplasm malignant neoplasm of digestive system digestive system cancer A disease involving the central nervous system. DOID:331 ICD10:G96.9 MESH:D002493 NCIT:C2934 SCTID:23853001 UMLS:C0007682 central nervous disease central nervous system disease central nervous system disease or disorder central nervous system disorder disease of central nervous system disease of the central nervous system disease or disorder of central nervous system disorder of central nervous system central nervous system disease A disease involving the breast. DOID:3463 ICD10:N60-N65 ICD10:N64.9 ICD9:610-612.99 ICD9:611.8 ICD9:611.9 MESH:D001941 NCIT:C26709 SCTID:79604008 UMLS:C0006145 breast disease breast disease or disorder breast diseases breast disorder disease of breast disease or disorder of breast disorder of breast breast disease A disorder characterized by the degeneration of the nervous system due to autoimmunity. Representative examples include multiple sclerosis, Guillain-Barre syndrome, and myasthenia gravis. DOID:438 MESH:D020274 NCIT:C99383 UMLS:C0751871 UMLS:C0751872 autoimmune disease of nervous system autoimmune disease, neurologic autoimmune diseases, nervous system autoimmune diseases, neurologic autoimmune disorders of the nervous system autoimmune disorders, nervous system autoimmune nervous system diseases autoimmune nervous system disorder disease, neurologic autoimmune diseases, neurologic autoimmune immune diseases, nervous system immune disorders, nervous system nervous system autoimmune disease nervous system autoimmune diseases nervous system hypersensitivity reaction type II disease nervous system immune diseases nervous system immune disorders neurologic autoimmune disease neurologic autoimmune diseases autoimmune disease of the nervous system A disease involving the male reproductive system. DOID:48 ICD10:N40.N51 ICD10:N50.9 ICD9:600-608.99 ICD9:608.9 MESH:D005832 NCIT:C27019 SCTID:363194005 Male reproductive system disease Male reproductive system disorder disease of male reproductive system disease or disorder of male reproductive system disorder of Male reproductive system disorder of male reproductive system male reproductive disease male reproductive system disease male reproductive system disease or disorder male reproductive system disease A primary or metastatic malignant neoplasm affecting the tissues of the thorax. thorax neoplasm tumor of thorax DOID:5093 ICD10:C76.1 ICD9:195.1 NCIT:C3406 NCIT:C3576 SCTID:188361007 SCTID:255058005 UMLS:C0039981 UMLS:C0153661 cancer of thoracic segment of trunk malignant neoplasm of the thorax malignant neoplasm of thoracic segment of trunk malignant neoplasm of thorax malignant thoracic neoplasm malignant thoracic segment of trunk neoplasm malignant thoracic tumor malignant tumor of the thorax malignant tumor of thorax thoracic segment of trunk cancer thoracic tumor thorax cancer thoracic cancer Vasculitis affecting the blood vessels of the brain and/or spinal cord. DOID:525 MESH:D020293 NCIT:C84622 UMLS:C0751878 central nervous system vasculitis vasculitis of central nervous system central nervous system vasculitis A disease involving the peripheral nervous system. DOID:574 ICD10:G64 ICD9:350-359.99 ICD9:356.9 MESH:D010523 NCIT:C119734 NCIT:C27580 SCTID:42658009 PNS (peripheral nervous system) diseases PNS disease PNS diseases disease of peripheral nervous system disease or disorder of peripheral nervous system disorder of peripheral nervous system disorder of the peripheral nervous system peripheral nervous system disease peripheral nervous system disease or disorder peripheral nervous system disorder peripheral nervous system disorders nerve disease, peripheral nerve diseases, peripheral neuropathy, peripheral peripheral Neuropathies peripheral nerve disease peripheral nerve diseases peripheral neuropathy peripheral nervous system disease A broad classification of disorders that affect the cell-mediated aspect of the immune response. Circulating numbers of T lymphocytes are decreased or ineffective. DOID:613 NCIT:C27145 SCTID:402792003 UMLS:C1274233 T-cell immunodeficiency T-lymphocyte deficiency (finding) T-lymphocyte immunodeficiency T-cell immunodeficiency A disease that is caused by genetic modifications where those modifications are inherited from a parent's genome. genetic condition genetic disease genetic disorder DOID:630 EFO:0000508 ICD9:799.89 MESH:D030342 NCIT:C3101 SCTID:32895009 UMLS:C0019247 hereditary disease hereditary disease or disorder hereditary diseases inherited disease inherited genetic disease molecular disease Usage note: this is intended only for diseases with an inherited genetic etiology. Somatic genetic mutations are excluded. Some ontologies use the term 'genetic disease' in the sense of inherited disorders only, we are here careful to distinguish. Mendelian disease A disease involving the connective tissue. DOID:65 MESH:D003240 NCIT:C26729 SCTID:105969002 UMLS:C0009782 connective tissue disease connective tissue disease or disorder connective tissue diseases connective tissue disorder connective tissue disorders disease of connective tissue disease or disorder of connective tissue disease, connective tissue disorder of connective tissue primary disorder of connective tissue tissue disease, connective Following clinical usage of the term 'connective tissue disorder' this grouping excludes some diseases affecting tissues classically considered to be connective tissue, such as bone. connective tissue disease An imbalanced nutritional status resulting from excessive intake of nutrients. Generally, overnutrition generates an energy imbalance between food consumption and energy expenditure leading to disorders such as obesity. DOID:654 ICD9:278.8 MESH:D044343 SCTID:302872003 UMLS:C1257763 overnutrition A disease or disorder that involves the digestive system. DOID:77 EFO:0000405 ICD10:K92.9 ICD9:520-579.99 ICD9:V47.3 MESH:D005767 NCIT:C2990 SCTID:53619000 alimentary system disease digestive disease digestive system disease digestive system disease or disorder digestive system disorder disease of digestive system disease or disorder of digestive system disorder of digestive system gastroenterological system disease gastroenterological system disorder gastroenteropathy gastrointestinal disease gastrointestinal disorder gastrointestinal system disease gastrointestinal system disorder git disease stomach or intestinal disorder digestive system disease An autoimmune, connective tissue chronic inflammatory disorder affecting the skin, joints, kidneys, lungs, heart, and the peripheral blood cells. It is more commonly seen in women than men. Variants include discoid and systemic lupus erythematosus. DOID:8857 ICD10:L93 ICD10:L93.0 ICD9:695.4 NCIT:C27153 SCTID:200936003 UMLS:C0409974 lupus lupus erythematosus lupus erythematosus Necrosis of the myocardium, as a result of interruption of the blood supply to the area. It is characterized by a severe and rapid onset of symptoms that may include chest pain, often radiating to the left arm and left side of the neck, dyspnea, sweating, and palpitations. DOID:9408 EFO:0008583 ICD10:I21.3 ICD10:I21.9 ICD9:410 ICD9:410.80 ICD9:410.81 ICD9:410.82 ICD9:410.9 ICD9:410.90 ICD9:410.91 ICD9:410.92 NCIT:C35204 SCTID:57054005 UMLS:C0155626 acute myocardial infarction (disease) myocardial infarction (disease), acute acute myocardial infarction Any disorder of the lymph nodes. DOID:9942 NCIT:C35346 SCTID:76616003 UMLS:C0272394 disease of lymph node disease or disorder of lymph node disorder of lymph node lymph node disease lymph node disease or disorder lymph node disorder lymph node disease A tumor composed of atypical neoplastic, often pleomorphic cells that invade other tissues. Malignant neoplasms often metastasize to distant anatomic sites and may recur after excision. The most common malignant neoplasms are carcinomas (adenocarcinomas or squamous cell carcinomas), Hodgkin and non-Hodgkin lymphomas, leukemias, melanomas, and sarcomas. DOID:0050686 DOID:0050687 DOID:162 EFO:0000311 GARD:0011960 ICD10:C80 ICD10:C80.1 ICD9:195.8 ICD9:199 ICD9:199.1 ICDO:8000/3 MESH:D009369 NCIT:C9305 NIFSTD:birnlex_406 ONCOTREE:MT SCTID:363346000 UMLS:C0006826 CA cancer cell type cancer malignancy malignant Growth malignant neoplasm malignant neoplasm (disease) malignant neoplastic disease malignant tumor neoplasm (disease), malignant neoplasm, malignant organ system cancer primary cancer cancer A disease involving the cardiovascular system. DOID:1287 EFO:0000319 ICD10:I00.I99 ICD9:390-459.99 ICD9:420-429.99 ICD9:423 ICD9:423.8 ICD9:424 ICD9:429 ICD9:429.2 ICD9:429.7 ICD9:429.8 ICD9:429.81 ICD9:429.89 ICD9:459.89 ICD9:459.9 MESH:D002318 NCIT:C2931 SCTID:49601007 UMLS:C0007222 cardiovascular disease cardiovascular disease (CVD) cardiovascular disorder cardiovascular system disease cardiovascular system disease or disorder disease of cardiovascular system disease of subdivision of hemolymphoid system disease or disorder of cardiovascular system disorder of cardiovascular system cardiovascular disease A non-neoplastic or neoplastic disorder that affects the small or large intestine. DOID:5295 ICD10:K63.9 ICD9:520-579.99 ICD9:560-569.99 ICD9:564 ICD9:564.4 ICD9:569 ICD9:569.4 ICD9:569.49 ICD9:569.89 ICD9:569.9 ICD9:570-579.99 ICD9:575 MESH:D005767 MESH:D007410 NCIT:C26801 SCTID:53619000 SCTID:85919009 disease of intestine disease or disorder of intestine disorder of intestine intestinal disease intestinal disorder intestine disease intestine disease or disorder intestinal disease A brain disorder characterized by episodes of abnormally increased neuronal discharge resulting in transient episodes of sensory or motor neurological dysfunction, or psychic dysfunction. These episodes may or may not be associated with loss of consciousness or convulsions. DOID:1826 EFO:0000474 ICD10:G40 ICD10:G40.9 ICD10:G40.909 ICD9:345 ICD9:345.8 ICD9:345.80 ICD9:345.9 ICD9:345.90 ICD9:345.91 MESH:D004827 NCIT:C3020 NIFSTD:birnlex_12718 SCTID:84757009 epilepsy seizure disorder epilepsy A disease involving the reproductive system. DOID:15 EFO:0000512 NCIT:C4875 SCTID:362968007 UMLS:C0178829 Wikipedia:Reproductive_system_disease disease of reproductive system disease or disorder of reproductive system disorder of reproductive system genital disorders genital system disease reproductive disease reproductive system disease reproductive system disease or disorder reproductive system disorder reproductive system disease A disorder resulting from an abnormality in the immune system. DOID:2914 EFO:0000540 ICD10:D89.9 ICD9:279 ICD9:279.1 ICD9:279.10 ICD9:279.19 ICD9:279.4 ICD9:279.49 ICD9:279.8 ICD9:279.9 MESH:D001327 MESH:D007154 NCIT:C3507 OMIM:109100 SCTID:414029004 disease of immune system disease or disorder of immune system disorder of immune system immune disease immune disorder immune dysfunction immune system disease or disorder immune system disorder immune system disease Inability to conceive for at least one year after trying and having unprotected sex. Causes of female infertility include endometriosis, fallopian tubes obstruction, and polycystic ovary syndrome. Causes of male infertility include abnormal sperm production or function, blockage of the epididymis, blockage of the ejaculatory ducts, hypospadias, exposure to pesticides, and health related issues. DOID:5223 EFO:0000545 MESH:D007246 NCIT:C3836 Sterile fertility disorders infertile sterile sterility Editor note: dubious as to whether this is a disease as defined, check with clingen before obsoleting infertility disorder Bleeding within the cranium. EFO:0000551 ICD9:432.9 MESH:D020300 NCIT:C50438 UMLS:CN236663 Editor note: consider obsoleting https://github.com/EBISPOT/OLS/issues/207 intracranial hemorrhage Gross necrosis of the myocardium, as a result of interruption of the blood supply to the area, as in coronary thrombosis. DOID:5844 EFO:0000612 HP:0001658 ICD10:I21 ICD10:I22 MESH:D009203 NCIT:C27996 OMIM:608446 OMIM:608557 SCTID:22298006 UMLS:C0027051 MI MI, myocardial infarction heart attack infarction (MI), myocardial myocardial infarct myocardial infarction myocardial infarction (disease) myocardial infarction, (MI) myocardial infarction A benign or malignant tissue growth resulting from uncontrolled cell proliferation. Benign neoplastic cells resemble normal cells without exhibiting significant cytologic atypia, while malignant cells exhibit overt signs such as dysplastic features, atypical mitotic figures, necrosis, nuclear pleomorphism, and anaplasia. Representative examples of benign neoplasms include papillomas, cystadenomas, and lipomas; malignant neoplasms include carcinomas, sarcomas, lymphomas, and leukemias. cell process disease DOID:14566 EFO:0000616 HP:0002664 ICD10:C00.D48 ICD9:140-239.99 ICD9:239.8 ICD9:239.9 MESH:D009369 NCIT:C3262 ONCOTREE:OTHER SCTID:55342001 UMLS:CN236628 disease of cellular proliferation neoplasia neoplasm neoplasm (disease) neoplastic disease neoplastic growth tumor tumor disease other neoplasm neoplasm A non-neoplastic or neoplastic disorder that affects the brain, spinal cord, or peripheral nerves. DOID:863 EFO:0000618 ICD10:G00-G99 ICD10:G00.G99 ICD10:G98 ICD10:G98.8 ICD9:349.89 ICD9:349.9 MESH:D009422 NCIT:C26835 NCIT:C2934 SCTID:118940003 UMLS:C0027765 Wikipedia:Nervous_system_disease disease of nervous system disease or disorder of nervous system disorder of nervous system nervous system disease nervous system disease or disorder nervous system disorder neurologic disease neurologic disorder neurological disease neurological disorder nervous system disorder A non-neoplastic or neoplastic disorder that affects the respiratory system. Representative examples include pneumonia, chronic obstructive pulmonary disease, pulmonary failure, lung adenoma, lung carcinoma, and tracheal carcinoma. DOID:1579 EFO:0000684 ICD10:J96-J99 ICD10:J98 ICD9:460-519.99 ICD9:500-508.99 ICD9:503 ICD9:508 ICD9:508.1 ICD9:508.8 ICD9:508.9 ICD9:510-519.99 ICD9:516 ICD9:516.8 ICD9:516.9 ICD9:517 ICD9:517.8 ICD9:519 ICD9:519.1 ICD9:519.3 ICD9:519.8 ICD9:519.9 ICD9:V12.60 ICD9:V47.2 MESH:D012140 NCIT:C26871 SCTID:50043002 disease of respiratory system disease or disorder of respiratory system disorder of respiratory system respiratory disease respiratory disorder respiratory system disease respiratory system disease or disorder respiratory system disorder respiratory system disease Any disease caused by a virus. DOID:934 EFO:0000763 ICD10:A94 ICD10:B34 ICD10:B34.9 ICD9:060-066.99 ICD9:066.9 ICD9:078.89 ICD9:079.99 MESH:D014777 NCIT:C3439 SCTID:34014006 Viruses caused disease or disorder Viruses disease or disorder Viruses infection Viruses infectious disease infection, viral viral disease viral disorder viral infection virus infection viral infectious disease An infection caused by the human immunodeficiency virus. DOID:526 EFO:0000764 ICD10:B20 ICD10:B20-B20 ICD10:B20.B24 ICD9:042 ICD9:042-042.99 MESH:D015658 NCIT:C3108 SCTID:86406008 UMLS:C0019693 HIV infection Human immunodeficiency virus caused disease or disorder Human immunodeficiency virus disease or disorder Human immunodeficiency virus infectious disease HIV infectious disease An acute infectious disorder that is caused by gram positive or gram negative bacteria; representative examples include pneumococcal, streptococcal, salmonella, and meningeal infections. DOID:104 EFO:0000771 ICD10:A49 ICD10:A49.9 ICD9:040.89 ICD9:041.89 ICD9:041.9 MESH:D001424 MESH:D016905 MESH:D016908 NCIT:C2890 SCTID:87628006 UMLS:C0004623 Bacteria caused disease or disorder Bacteria disease or disorder Bacteria infectious disease bacterial disease bacterial disorder bacterial infection bacterial infectious disease infection, bacterial bacterial infectious disease Any condition related to a disturbance between proper intake and utilization of nourishment. DOID:374 EFO:0001069 ICD9:783.9 MESH:D009748 NCIT:C26836 SCTID:2492009 UMLS:C3714509 nutritional disorder nutritional disorder An excess of body weight, normally defined as an individual with a body mass index greater than 35 or a body weight greater than one hundred percent of ideal body weight. DOID:11981 EFO:0001074 ICD9:278.01 MESH:D009767 NCIT:C34858 NIFSTD:nlx_dys_20090303 SCTID:83911000119104 UMLS:C0028756 severe obesity morbid obesity A disease involving the endocrine system. DOID:28 EFO:0001379 ICD10:E34.9 ICD9:259.8 ICD9:259.9 MESH:D004700 NCIT:C3009 SCTID:362969004 UMLS:C0014130 disease of endocrine system disease or disorder of endocrine system disorder of endocrine system endocrine disease endocrine disorder endocrine system disease endocrine system disease or disorder endocrine system disorder endocrinopathy thyroid or other glandular disorders endocrine system disease A disease involving the liver. DOID:409 EFO:0001421 ICD10:K70-K77 ICD10:K76.9 ICD9:573.8 ICD9:573.9 MESH:D008107 NCIT:C3196 NCIT:C50634 SCTID:235856003 UMLS:C0023895 disease of liver disease or disorder of liver disorder of liver hepatic disease hepatic disorder liver and intrahepatic bile duct disorder liver disease liver disease or disorder liver disorder liver disease A disease involving the skeletal system. EFO:0002461 SCTID:88230002 UMLS:C0263661 disease of skeletal system disease or disorder of skeletal system disorder of skeletal system skeletal system disease skeletal system disease or disorder skeletal system disease Acquired, familial, and congenital disorders of skeletal muscle and smooth muscle. DOID:0080000 EFO:0002970 MESH:D009135 disease of muscle organ disease or disorder of muscle organ disorder of muscle organ muscle organ disease muscle organ disease or disorder Editor note: consider merging with child muscular disease A disease involving the kidney. DOID:557 EFO:0003086 ICD10:N08 ICD10:N28.9 ICD9:583.81 MESH:D007674 NCIT:C3149 SCTID:90708001 UMLS:C0022658 disease of kidney disease or disorder of kidney disorder of kidney kidney disease kidney disease or disorder kidney disorder nephropathy renal disease renal disorder kidney disease A spectrum of small and large bowel inflammatory diseases of unknown etiology. It includes Crohn's disease, ulcerative colitis, and colitis of indeterminate type. DOID:0050589 EFO:0003767 ICD9:558.9 KEGG:05321 MESH:D015212 NCIT:C3138 OMIM:608448 OMIM:611081 OMIM:612244 OMIM:612245 OMIM:612261 OMIM:612278 OMIMPS:266600 SCTID:24526004 UMLS:C0021390 IBD autoimmune bowel disorder inflammatory bowel disease inflammatory bowel disease A disease involving the heart and/or pericardium. DOID:114 EFO:0003777 ICD10:I51.9 ICD9:429.89 ICD9:429.9 ICD9:V47.2 MESH:D006331 NCIT:C3079 SCTID:56265001 UMLS:C0018799 UMLS:CN236661 UMLS:CN239852 cardiac disease disease of heart disease or disorder of heart disorder of heart disorder of heart/pericardium heart disease heart disease or disorder heart disorder heart trouble heart/pericardial disease heart/pericardial disease or disorder heart/pericardial disorder heart/pericardial trouble heart disease A disease involving the lung. DOID:850 EFO:0003818 ICD10:J98.4 ICD9:518.89 MESH:D008171 NCIT:C3198 SCTID:19829001 disease of lung disease or disorder of lung disorder of lung lung disease lung disease or disorder lung disorders pulmonary diseases pulmonary disorder pulmonary disorders lung disease A benign or malignant neoplasm that affects the colon or rectum. Representative examples of benign neoplasms include lipoma and leiomyoma. Representative examples of malignant neoplasms include carcinoma, lymphoma, and sarcoma. Colorectal adenomas always exhibit epithelial dysplasia and are considered premalignant neoplasms. MONDO:0021236 EFO:0004142 MESH:D015179 NCIT:C2956 OMIM:114500 colorectal neoplasm colorectal tumor colorectum neoplasm colorectum neoplasm (disease) colorectum tumor large bowel neoplasm large bowel tumor large intestinal neoplasm large intestine neoplasm large intestine tumor neoplasm of colorectum neoplasm of large bowel neoplasm of the large bowel tumor of colorectum tumor of large bowel tumor of the large bowel colorectal neoplasm The inability of the male to effect fertilization of an ovum after a specified period of unprotected intercourse. Male sterility is permanent infertility. DOID:12336 EFO:0004248 ICD10:N46 ICD10:N46.9 ICD9:606 ICD9:606.9 MESH:D007248 SCTID:2904007 UMLS:C0021364 infertility disorder of male reproductive system male reproductive system infertility male reproductive system infertility disorder male infertility A none disease characterized by death of bone tissue due to a lack of blood supply. DOID:0080008 DOID:10159 EFO:0004259 GARD:0012057 ICD10:M87 ICD10:M87.0 ICD10:M87.1 ICD10:M87.2 ICD10:M87.3 ICD10:M87.8 ICD10:M87.9 ICD9:732.3 ICD9:733.4 ICD9:733.41 ICD9:733.42 ICD9:733.43 ICD9:733.44 ICD9:733.49 MESH:D010020 NCIT:C34841 NCIT:C34880 NCIT:C35476 Orphanet:399158 SCTID:240196003 SCTID:397758007 aseptic necrosis bone necrosis ischemic bone disease osteonecrosis osteonecrosis Diseases of bones. DOID:0080001 EFO:0004260 ICD10:M89.9 ICD9:731.8 ICD9:733.99 MESH:D001847 Orphanet:364803 SCTID:76069003 UMLS:C0005940 UMLS:CN204768 bone element disease bone element disease or disorder disease of bone element disease or disorder of bone element disorder of bone element bone disease A general term used to describe any disease affecting blood vessels]. It includes vascular abnormalities caused by degenerative, metabolic and inflammatory conditions, embolic diseases, coagulative disorders, and functional disorders such as posteri or reversible encephalopathy syndrome. DOID:178 EFO:0004264 ICD10:I72.9 ICD9:442.9 MESH:D014652 NCIT:C26693 NCIT:C35117 SCTID:27550009 UMLS:C0042373 disease of vasculature disease or disorder of vasculature disorder of vasculature vascular disorder vascular tissue disease vasculature disease vasculature disease or disorder The etiology of vasculopathy is generally unknown and the condition is frequently not pathologically proven. Vasculitis, on the other hand, is a more specific term and is defined as inflammation of the wall of a blood vessel. However, the term vasculopathy is also used for “vasculitis” that has not been pathologically established. vascular disease A medical condition characterized by long-term fatigue and other symptoms that limit a person's ability to carry out ordinary daily activities. DOID:8544 EFO:0004540 ICD10:G93.3 ICD10:R53.82 ICD9:780.71 ICD9:780.79 MESH:D015673 NCIT:C3037 SCTID:51771007 UMLS:C0015674 CFS Postviral fatigue syndrome chronic fatigue syndrome myalgic encephalitis myalgic encephalomyelitis systemic exertion intolerance disease myalgic encephalomeyelitis/chronic fatigue syndrome A disorder directly resulting from the presence and activity of a microbial, viral, or parasitic agent. It can be transmitted by direct or indirect contact. DOID:0050117 EFO:0005741 ICD10:A00.B99 ICD9:079.0 ICD9:136.8 ICD9:136.9 IDO:0000436 MESH:D003141 NCIT:C26726 SCTID:40733004 clinical infection communicable disease infection infectious infectious disease infectious diseases and manifestations infectious disorder transmissible disease Replaces 'infection' in disease hierarchy. OBI imported term infection is moved to pathologic process. This class is a container class for infectious diseases, not the process of infection itself. infectious disease Inflammatory and degenerative diseases of connective tissue structures, such as arthritis. DOID:1575 EFO:0005755 ICD9:729.0 MESH:D012216 NCIT:C27204 SCTID:396332003 UMLS:C0035435 Wikipedia:Rheumatism rheumatic disease rheumatologic disorder This is an umbrella term encompassing conditions causing chronic, often intermittent pain affecting the joints and/or connective tissue rheumatic disorder A disease affecting the brain or part of the brain. DOID:936 EFO:0005774 ICD10:G93.40 ICD10:G93.9 ICD9:348.3 ICD9:348.30 ICD9:348.8 ICD9:348.9 MESH:D001927 NCIT:C96413 SCTID:81308009 UMLS:C0006111 UMLS:C0085584 brain disease brain disease or disorder disease of brain disease or disorder of brain disorder of brain encephalopathy Editor note: NCIT has different classes for brain disease and encephalopathy brain disease A disease involving the hematopoietic system. DOID:74 EFO:0005803 GTR:AN1320635 ICD10:D75.9 ICD9:280-289.99 ICD9:289.8 ICD9:289.9 MESH:D006402 NCIT:C26323 Orphanet:97992 SCTID:414022008 UMLS:C0018939 UMLS:CN206939 UMLS:CN882913 blood disease blood disorder blood dyscrasia disease of hematopoietic system disease of the blood and blood-forming organs disease or disorder of hematopoietic system disorder of hematopoietic system hematologic and lymphocytic disorder hematologic disorder hematological disease hematological disorder hematological system disease hematopoietic disease hematopoietic system disease hematopoietic system disease or disorder rare hematologic disease placeholder for lymphoid disease hematologic disease A primary or metastatic malignant neoplasm that affects the colon or rectum. Representative examples include carcinoma, lymphoma, and sarcoma. MONDO:0003576 MONDO:0021307 DOID:5672 DOID:9256 EFO:0005842 ICD10:C18.9 KEGG:05210 MESH:D015179 NCIT:C2955 NCIT:C4978 NCIT:C5105 OMIM:114500 OMIM:608812 OMIM:611469 OMIM:612229 OMIM:612230 OMIM:612231 OMIM:612232 OMIM:612589 OMIM:612590 OMIM:612591 OMIM:612592 OMIM:615083 SCTID:363510005 SCTID:408645001 UMLS:C0699790 UMLS:C1319315 UMLS:C1527249 cancer of colorectum cancer of large bowel cancer of large intestine cancer of the large bowel colorectal cancer colorectum cancer malignant colorectal neoplasm malignant colorectal tumor malignant colorectum neoplasm malignant large bowel neoplasm malignant large bowel tumor malignant large intestine neoplasm malignant large intestine tumor malignant neoplasm of colorectum malignant neoplasm of large bowel malignant neoplasm of large intestine malignant neoplasm of the large bowel malignant neoplasm of the large intestine malignant tumor of large bowel malignant tumor of large intestine malignant tumor of the large bowel malignant tumor of the large intestine Editor note: some sources make distinct classes for colorectal vs large intestine. We follow NCIT and make these equivalent colorectal cancer Virus diseases caused by coronaviridae. EFO:0007223 UMLS:C0010078 Coronaviridae infectious disease A malignant neoplasm involving the intestine DOID:10155 EFO:0007330 ICD10:C26.0 ICD9:159.0 MESH:D007414 NCIT:C4572 SCTID:363508008 UMLS:C0346627 bowel cancer cancer of intestine cancer of the intestine intestinal cancer intestinal neoplasms, malignant intestinal tumors, malignant intestine cancer malignant intestinal neoplasm malignant intestinal neoplasms malignant intestinal tumor malignant intestinal tumors malignant intestine neoplasm malignant intestine tumor malignant neoplasm of intestine malignant neoplasm of the intestine malignant tumor of intestine malignant tumor of the intestine intestinal cancer A disease involving the lymphatic part of lymphoid system. DOID:75 EFO:0007352 MESH:D008206 NCIT:C50764 SCTID:362971004 UMLS:C0024228 disease of lymphatic part of lymphoid system disease or disorder of lymphatic part of lymphoid system disorder of lymph node and lymphatics disorder of lymphatic part of lymphoid system disorder of lymphatic system glands, swollen lymphatic disease lymphatic disorder lymphatic part of lymphoid system disease lymphatic part of lymphoid system disease or disorder swollen gland swollen glands lymphadenopathy lymphangiopathy Editor note: check alignment to anatomy, consider lymphoid system disease lymphatic system disease Infections with viruses of the order nidovirales. The concept includes arterivirus infections and coronaviridae infections. EFO:0007396 MESH:D030341 UMLS:C0969753 Nidovirales caused disease or disorder Nidovirales disease or disorder Nidovirales infectious disease Autosomal recessive form of disease. DOID:0050737 EFO:1000017 ICD9:758.5 SCTID:85995004 UMLS:C0265388 autosomal recessive disease or disorder autosomal recessive hereditary disease autosomal recessive hereditary disorder autosomal recessive inherited disease autosomal recessive inherited disorder disease or disorder, autosomal recessive disease, autosomal recessive autosomal recessive disease Progressive and life-threatening pulmonary distress in the absence of an underlying pulmonary condition, usually following major trauma or surgery. Cases of neonatal respiratory distress syndrome are not included in this definition. EFO:1000637 GARD:0005698 ICD10:J80 MedDRA:10001052 NCIT:C3353 ARDS acute respiratory distress syndrome shock lung This disease can present as a mild ARDS (PaO2/FiO2 of 201–300 mmHg) moderate ARDS (PaO2/FiO2 of 101–200 mmHg) and severe ARDS (PaO2/FiO2 ≤100 mmHg). [PMID:30872586] acute respiratory distress syndrome A disorder resulting from loss of function or tissue destruction of an organ or multiple organs, arising from humoral or cellular immune responses of the individual to their own tissue constituents. It may be systemic (e.g., systemic lupus erythematosus), or organ specific, (e.g., thyroiditis). DOID:417 EFO:0005140 ICD9:279.4 ICD9:279.49 ICD9:720 MESH:D001327 NCIT:C2889 OBI:1110054 OMIM:109100 OMIM:613551 OMIM:615952 SCTID:85828009 UMLS:C0004364 autoimmune disease autoimmune disease or disorder autoimmune disorder disease, autoimmune Editor note: check OMIM autoimmune disease A primary or metastatic malignant neoplasm involving the breast. The vast majority of cases are carcinomas arising from the breast parenchyma or the nipple. Malignant breast neoplasms occur more frequently in females than in males. breast tumor mammary tumor DOID:1612 ICD10:C50 ICD10:C50-C50 ICD9:174.8 MESH:D001943 NCIT:C9335 OMIM:600048 OMIM:605365 SCTID:126926005 SCTID:254837009 breast cancer cancer of breast malignant breast neoplasm malignant breast tumor malignant neoplasm of breast malignant neoplasm of the breast malignant tumor of breast malignant tumor of the breast mammary cancer primary breast cancer breast cancer A malignant neoplasm involving the lung. DOID:1324 ICD10:C34.1 ICD10:C34.2 ICD10:C34.3 ICD9:162.3 ICD9:162.4 ICD9:162.5 ICD9:162.8 ICD9:162.9 NCIT:C7377 OMIM:211980 OMIM:608935 OMIM:612571 OMIM:612593 OMIM:614210 SCTID:363358000 UMLS:C0007131 UMLS:C0152013 UMLS:C0684249 cancer of lung lung cancer malignant lung neoplasm malignant lung tumor malignant neoplasm of lung malignant neoplasm of the lung malignant tumor of lung malignant tumor of the lung lung cancer Cystic fibrosis (CF) is a genetic disorder characterized by the production of sweat with a high salt content and mucus secretions with an abnormal viscosity. DOID:1485 GARD:0006233 ICD10:E84 ICD10:E84.0 ICD10:E84.1 ICD10:E84.8 ICD10:E84.9 ICD9:277.0 MESH:D003550 MedDRA:10011762 NCIT:C2975 OMIM:219700 Orphanet:586 SCTID:190905008 UMLS:C0010674 CF cystic fibrosis mucoviscidosis cystic fibrosis Infant acute respiratory distress syndrome is a lung disorder that affects premature infants caused by developmental insufficiency of surfactant production and structural immaturity of the lungs. The symptoms usually appear shortly after birth and may include tachypnea, tachycardia, chest wall retractions (recession), expiratory grunting, nasal flaring and cyanosis during breathing efforts. RDS respiratory distress syndrome DOID:12716 EFO:1000644 GARD:0000112 ICD10:P22.0 ICD9:769 NCIT:C27560 OMIM:267450 Orphanet:70587 SCTID:46775006 UMLS:C0020192 UMLS:C0035220 UMLS:C1968593 HMD - hyaline membrane disease RDS Of newborns RDS, respiratory distress syndrome Of newborns hyaline membrane disease infant ARDS infant acute respiratory distress syndrome infant respiratory distress syndrome neonatal respiratory distress neonatal respiratory distress syndrome newborns (RDS), respiratory distress syndrome Of pulmonary hyaline membrane disease pulmonary hypoperfusion syndrome of newborn respiratory distress syndrome Of newborns respiratory distress syndrome Of newborns (RDS) respiratory distress syndrome in the newborn respiratory distress syndrome of newborn syndrome Of newborns (RDS), respiratory distress newborn respiratory distress syndrome A disorder resulting from inadequate blood flow in the vessels that supply the brain. Representative examples include cerebrovascular ischemia, cerebral embolism, and cerebral infarction. DOID:6713 EFO:0000712 EFO:0003763 ICD10:I60-I69 ICD10:I60.I69 ICD10:I63.9 ICD10:I67.9 ICD9:430-438.99 ICD9:434.91 ICD9:437.8 ICD9:437.9 MESH:D002561 MESH:D020521 NCIT:C2938 NCIT:C3390 OMIM:601367 SCTID:230690007 SCTID:62914000 UMLS:C0007820 cerebrovascular disease cerebrovascular disorder CVA CVA (cerebral vascular accident) cerebral infarction cerebrovascular accident stroke cerebrovascular disorder A disorder involving an excessive amount of body fat. DOID:9970 EFO:0001073 HP:0001513 ICD10:E66.9 ICD9:278.0 ICD9:278.00 NCIT:C3283 NIFSTD:nlx_dys_20090302 Orphanet:71529 SCTID:414916001 UMLS:C0028754 obesity obesity disease Obesity is a complex disease that may involve multiple environmental and genetic causes. See the subclass monogenic disease for genetic subtypes obesity disorder Sickle cell anemias are chronic hemolytic diseases that may induce three types of acute accidents: severe anemia, severe bacterial infections, and ischemic vasoocclusive accidents (VOA) caused by sickle-shaped red blood cells obstructing small blood vessels and capillaries. Many diverse complications can occur. DOID:10923 EFO:1001797 GARD:0008614 ICD10:D57 ICD10:D57.0 ICD10:D57.1 ICD10:D57.2 ICD10:D57.20 ICD9:282.6 ICD9:282.60 ICD9:282.63 MESH:D000755 MedDRA:10040641 NCIT:C34383 OMIM:603903 Orphanet:232 UMLS:C0002895 Hb SC disease Hb-S/Hb-C disease Hb-SS disease without crisis Hemoglobin S disease without crisis drepanocytosis hemoglobin SC disease sickle cell anemia sickle cell disease sickle-cell/Hb-C disease without crisis sickling disorder due to Hemoglobin S sickle cell anemia A syndrome resulting from the acquired deficiency of cellular immunity caused by the human immunodeficiency virus (HIV). It is characterized by the reduction of the Helper T-lymphocytes in the peripheral blood and the lymph nodes. Symptoms include generalized lymphadenopathy, fever, weight loss, and chronic diarrhea. Patients with AIDS are especially susceptible to opportunistic infections (usually pneumocystis carinii pneumonia, cytomegalovirus (CMV) infections, tuberculosis, candida infections, and cryptococcosis), and the development of malignant neoplasms (usually non-Hodgkin lymphoma and Kaposi sarcoma). The human immunodeficiency virus is transmitted through sexual contact, sharing of contaminated needles, or transfusion of contaminated blood. DOID:635 EFO:0000765 ICD10:B20 MESH:D000163 NCIT:C2851 SCTID:62479008 AIDS AIDS, acquired immunodeficiency syndrome acquired immune deficiency acquired immunodeficiency disease acquired immunodeficiency syndrome, AIDS AIDS Kawasaki disease (KD) is a febrile, systemic, self-limiting vasculitis affecting children and characterized by inflammation in the medium sized vessels associated with coronary arterial aneurysms (CAA) that may be life threatening when untreated. KD is the most common cause of acquired heart disease in children in developed countries and is a risk factor for ischemic heart disease in adulthood. DOID:13378 EFO:0004246 GARD:0006816 ICD10:M30.3 ICD9:446.1 MESH:D009080 MedDRA:10023320 NCIT:C34825 OMIM:611775 Orphanet:2331 SCTID:75053002 UMLS:C0026691 Kawasaki's disease MLNS acute febrile MCLS acute febrile mucocutaneous lymph node syndrome acute febrile mucocutaneous lymph node syndrome [MCLS] infantile polyarteritis nodosa mucocutaneous lymph node syndrome mucocutaneous lymph node syndrome Bleeding into one or both cerebral hemispheres including the basal ganglia and the cerebral cortex. It is often associated with hypertension and craniocerebral trauma. EFO:0005669 ICD9:431 MESH:D002543 OMIM:614519 SCTID:274100004 Editor note: consider separate subclass for OMIM ID intracerebral hemorrhage ICD10:E23.0 Orphanet:101957 Editor note: in ORDO, Orphanet:101957 is classified as genetic, yet has acquired subtypes pituitary deficiency Orphanet:156143 predominantly medium-vessel vasculitis MESH:D006130 Orphanet:156643 UMLS:CN237424 growth disorder genetic endocrine growth disease Congenital hypogonadotropic hypogonadism (CHH) is a rare disorder of sexual maturation characterized by gonadotropin (Gn) deficiency with low sex steroid levels associated with low levels of follicle stimulating hormone (FSH) and luteinizing hormone (LH). ICD10:E23.0 NCIT:C120162 Orphanet:174590 SCTID:722944006 UMLS:C3899503 congenital hypogonadotropic hypogonadism A condition of lung damage that is characterized by bilateral pulmonary infiltrates (pulmonary edema) rich in neutrophils, and in the absence of clinical heart failure. This can represent a spectrum of pulmonary lesions, endothelial and epithelial, due to numerous factors (physical, chemical, or biological). EFO:0004610 MESH:D055371 MedDRA:10069351 NCIT:C155766 Orphanet:178320 SCTID:315345002 acute lung injury Orphanet:180208 anomaly of puberty or/and menstrual cycle A diverse group of lung diseases that affect the lung parenchyma. They are characterized by an initial inflammation of pulmonary alveoli that extends to the interstitium and beyond leading to diffuse pulmonary fibrosis. Interstitial lung diseases are classified by their etiology (known or unknown causes), and radiological-pathological features. DOID:3082 EFO:0004244 GARD:0013336 ICD10:J84.9 MESH:D017563 MedDRA:10022611 OMIM:616414 Orphanet:182095 SCTID:233703007 UMLS:C0206062 ILD interstitial lung disease interstitial lung disease An instance of anomaly of puberty or/and menstrual cycle that is caused by a modification of the individual's genome. Orphanet:202940 genetic anomaly of puberty or/and menstrual cycle anomaly of puberty or/and menstrual cycle of genetic origin A spectrum of rare post-infectious neuropathies that usually occur in otherwise healthy patients. GBS is clinically heterogeneous and encompasses acute inflammatory demyelinating polyradiculoneuropathy (AIDP), acute motor axonal neuropathy (AMAN) and acute motor-sensory axonal neuropathy (AMSAN), Miller-Fisher syndrome (MFS) and some other regional variants. DOID:12842 EFO:0007292 GARD:0006554 ICD10:G61.0 MESH:D020275 MedDRA:10018767 NCIT:C116345 Orphanet:2103 SCTID:40956001 UMLS:C0018378 GBS Guillain Barre syndrome Guillain Barré syndrome Guillain-Barre-Strohl syndrome Guillain-Barré syndrome Guillain-Barré-Strohl syndrome acute postinfectious polyneuropathy post-infectious polyneuritis post-infective polyneuritis postinfectious polyneuritis Guillain-Barre syndrome A interstitial lung disease that occurs during childhood. Orphanet:264656 SCTID:328661000119108 UMLS:CN202324 ILD specific to childhood childhood interstitial lung disease interstitial lung disease of childhood pediatric interstitial lung disease interstitial lung disease specific to childhood GARD:0010559 Orphanet:264665 UMLS:CN202326 primary ILD specific to childhood primary interstitial lung disease specific to childhood primary interstitial lung disease specific to childhood Orphanet:264670 UMLS:CN202327 primary ILD specific to childhood due to alveolar structure disorder Reason: out of scope. This is an Orphanet grouping class that is considered out of scope for Mondo.Term to consider: interstitial lung disease' primary interstitial lung disease specific to childhood due to alveolar structure disorder Orphanet:264735 UMLS:CN202338 ILD specific to adulthood interstitial lung disease specific to adulthood Orphanet:264740 UMLS:CN202339 primary ILD specific to adulthood primary interstitial lung disease specific to adulthood Genetic infertility. Orphanet:275742 genetic infertility hereditary infertility disorder genetic infertility ICD10:D57.0 ICD10:D57.1 ICD10:D57.2 ICD10:D57.3 ICD10:D57.8 Orphanet:275752 UMLS:CN202572 sickle cell disease and related diseases A chronic, recurrent infection caused by the bacterium Mycobacterium tuberculosis. Tuberculosis (TB) may affect almost any tissue or organ of the body with the lungs being the most common site of infection. The clinical stages of TB are primary or initial infection, latent or dormant infection, and recrudescent or adult-type TB. Ninety to 95% of primary TB infections may go unrecognized. Histopathologically, tissue lesions consist of granulomas which usually undergo central caseation necrosis. Local symptoms of TB vary according to the part affected; acute symptoms include hectic fever, sweats, and emaciation; serious complications include granulomatous erosion of pulmonary bronchi associated with hemoptysis. If untreated, progressive TB may be associated with a high degree of mortality. This infection is frequently observed in immunocompromised individuals with AIDS or a history of illicit IV drug use. DOID:399 GARD:0007827 ICD10:A15.A19 ICD9:017.90 ICD9:017.92 ICD9:017.94 ICD9:017.96 MESH:D014376 MedDRA:10044755 NCIT:C3423 OMIM:607948 Orphanet:3389 SCTID:56717001 UMLS:C0041296 UMLS:C0151332 active tuberculosis tuberculosis disease tuberculosis Necrotic changes in the bone tissue due to interruption of blood supply. Most often affecting the epiphysis of the long bones, the necrotic changes result in the collapse and the destruction of the bone structure. ICD10:M87.0 ICD10:M87.1 ICD10:M87.2 ICD10:M87.3 ICD10:M87.8 ICD10:M87.9 NCIT:C34841 Orphanet:399164 SCTID:397758007 AVN avascular necrosis of bone avascular necrosis ICD10:M87.1 ICD10:M87.2 ICD10:M87.3 Orphanet:399169 secondary AVN secondary avascular necrosis An instance of osteonecrosis that is caused by a modification of the individual's genome. ICD10:M93.9 Orphanet:399380 bone necrosis of genetic origin genetic osteonecrosis osteonecrosis of genetic origin An instance of avascular necrosis that is caused by a modification of the individual's genome. ICD10:M93.9 Orphanet:399388 genetic avascular necrosis avascular necrosis of genetic origin Abnormal ovarian or testicular function due to insufficient hormonal stimulation from the hypothalamic-pituitary axis. DOID:0090070 DOID:7455 HP:0000044 ICD10:E23.0 ICD9:253.4 NCIT:C113347 OMIM:146110 OMIM:147950 OMIM:244200 OMIM:308700 OMIM:610628 OMIM:612370 OMIM:612702 OMIM:614837 OMIM:614838 OMIM:614839 OMIM:614840 OMIM:614841 OMIM:614842 OMIM:614858 OMIM:614880 OMIM:615266 OMIM:615269 OMIM:615270 OMIMPS:147950 Orphanet:432 Orphanet:478 SCTID:33927004 UMLS:CN235466 Normosmic idiopathic hypogonadotropic hypogonadism central hypogonadism gonadotropic deficiency hypogonadism, hypogonadotropic hypogonadotropic hypogonadism hypogonadotropic hypogonadism with or without anosmia hypogonadotropism low gonadotropins (secondary hypogonadism) nIHH normosmic congenital hypogonadotropic hypogonadism secondary hypogonadism congenital idiopathic hypogonadotropic hypogonadism isolated congenital gonadotropin deficiency hypogonadotropic hypogonadism Vasculitis represents a clinically heterogenous group of diseases of multifactorial etiology characterized by inflammation of either large-sized vessels (large-vessel vasculitis, e.g. Giant-cell arteritis and Takayasu arteritis), medium-sized vessels (medium-vessel vasculitis e.g. polyarteritis nodosa and Kawasaki disease), or small-sized vessels (small-vessel vasculitis, e.g. granulomatosis with polyangiitis, microscopic polyangiitis, immunoglobulin A vasculitis, and cutaneous leukocytoclastic angiitis). Vasculitis occurs at any age, may be acute or chronic, and manifests with general symptoms such as fever, weight loss and fatigue, as well as more specific clinical signs depending on the type of vessels and organs affected. The degree of severity is variable, ranging from life or sight threatening disease (e.g. BehC'et disease) to relatively minor skin disease. DOID:865 EFO:0006803 GARD:0009565 MESH:D014657 MedDRA:10036023 MedDRA:10047115 NCIT:C26912 OMIM:615688 Orphanet:52759 SCTID:31996006 UMLS:C0042384 Wikipedia:Vasculitis systemic vasculitis vasculitis An inherited disorder characterized by structural alterations of a globin chain within the hemoglobin molecule. DOID:2860 GARD:0012455 ICD10:D56.0 ICD10:D56.1 ICD10:D56.2 ICD10:D56.3 ICD10:D56.4 ICD10:D56.8 ICD10:D56.9 ICD10:D57.0 ICD10:D57.1 ICD10:D57.2 ICD10:D57.3 ICD10:D57.8 ICD10:D58.0 ICD10:D58.1 ICD10:D58.2 ICD10:D58.8 ICD10:D58.9 ICD9:282.7 MESH:D006453 MedDRA:10060892 NCIT:C3092 Orphanet:68364 SCTID:427306008 SCTID:80141007 UMLS:C0019045 UMLS:C1960031 Hemoglobinopathies / iron metabolism hemoglobinopathies hereditary hemoglobinopathy inherited hemoglobinopathy Any disease that impairs the functioning of the muscles, either directly, being pathologies of the voluntary muscle, or indirectly, being pathologies of nerves or neuromuscular junctions DOID:440 EFO:1001902 ICD10:G70.9 ICD9:358 ICD9:358.9 MESH:D009468 MedDRA:10029323 Orphanet:68381 UMLS:C0027868 nerve and muscle disorder neuromuscular disease neuromuscular disease An instance of nervous system disease that is caused by a modification of the individual's genome. Orphanet:71859 UMLS:CN205639 genetic nervous system disorder genetic neurological disorder rare genetic neurological disorder genetic nervous system disorder Orphanet:93614 UMLS:CN227684 Reason: out of scope. This is an Orphanet grouping class that is considered out of scope for Mondo.Term to consider: hematologic disease' hematological disorder with renal involvement ICD10:E23.0 Orphanet:95488 Editor note: consider merging with familial hypopituitarism non-acquired pituitary hormone deficiency A infectious disease that involves the nervous system. ICD9:349.89 NCIT:C27590 Orphanet:98010 SCTID:128116006 UMLS:C0597039 nervous system infectious disease nervous system infectious disorder infectious disease of the nervous system Infection due to organisms from the genus Mycobacteria. MESH:D009164 NCIT:C26831 SCTID:88415009 UMLS:C0026918 mycobacterial infection mycobacteriosis mycobacterium infection mycobacterial infectious disease A benign or malignant, primary or metastatic neoplasm involving the respiratory tract. EFO:0003853 MESH:D012142 NCIT:C3355 SCTID:126667002 neoplasm of respiratory tract neoplasm of the respiratory tract neoplasm, respiratory tract neoplasms, respiratory tract respiratory system neoplasm respiratory tract neoplasm respiratory tract tumor tract neoplasm, respiratory tract neoplasms, respiratory tumor of respiratory tract tumor of the respiratory tract respiratory tract neoplasm central nervous system or retinal vascular disease retina/CNS vascular disease Editor note: even though retinal diseases may be located outside the CNS, they are often indicators of CNS disease disease of central nervous system or retinal vasculature Disease having a short and relatively severe course. ICD9:799.89 MESH:D000208 SCTID:2704003 UMLS:C0001314 acute disease acute diseases disease, acute acute disease Infectious disease causes by viruses in the subfamily Orthocoronavirinae (coronaviruses). In humans, coronaviruses cause respiratory tract infections that can be mild, such as some cases of the common cold (among other possible causes, predominantly rhinoviruses), and others that can be lethal, such as SARS, MERS, and COVID-19. DOID:0080599 coronavirus infectious disease Orthocoronavirinae infectious disease Disease in which there is a deficiency or defect in the mechanisms of immunity, either cellular or humoral. ICD9:279.3 NCIT:C3131 OMIMPS:300755 SCTID:234532001 UMLS:C0021051 immuno-deficiency immunodeficiency immunodeficiency disorder immunodeficiency disease A benign or malignant neoplasm of the breast parenchyma. It can originate from the ducts, lobules or the breast adipose tissue. Breast neoplasms are much more common in females than males. EFO:0003869 ICD9:239.3 MESH:D001943 NCIT:C2910 ONCOTREE:BREAST SCTID:126926005 UMLS:CN236627 breast neoplasm breast neoplasm (disease) breast tumor neoplasm of breast neoplasm of the breast neoplasm, breast tumor of breast tumor of the breast breast neoplasm The significant impairment of gas exchange within the lungs resulting in hypoxia, hypercarbia, or both, to the extent that organ tissue perfusion is severely compromised. Causes include chronic obstructive pulmonary disease, asthma, emphysema, acute respiratory distress syndrome, pneumonia, pulmonary edema, pneumothorax, and congestive heart failure. Treatment requires intubation and mechanical ventilation until the time the lungs recover sufficient function. DOID:11162 ICD10:J96.0 ICD9:518.81 ICD9:518.83 MESH:D012131 NCIT:C26872 NCIT:C27043 SCTID:39871006 SCTID:65710008 UMLS:C0264490 UMLS:C1145670 failure, respiratory respiratory failure respiratory insufficiency/failure acute respiratory failure chronic respiratory failure respiratory failure A benign or malignant, primary or metastatic neoplasm involving the lungs. Representative examples of benign neoplasms include adenoma, papilloma, chondroma, and endobronchial lipoma. Representative examples of malignant neoplasms include carcinoma, carcinoid tumor, sarcoma, and lymphoma. MESH:D008175 NCIT:C3200 ONCOTREE:LUNG lung neoplasm lung neoplasm (disease) lung neoplasms lung tumor neoplasm of lung neoplasm of the lung tumor of lung tumor of the lung lung neoplasm A benign or malignant neoplasm involving the small or large intestine. DOID:4610 MESH:D007414 NCIT:C3141 ONCOTREE:BOWEL SCTID:126769007 intestinal neoplasm intestinal neoplasms intestinal tumor intestinal tumors intestine growth intestine neoplasm intestine neoplasm (disease) intestine tumor neoplasm of intestinal tract neoplasm of intestine neoplasm of intestines neoplasm of the intestines tumor of intestine tumor of intestines tumor of the intestines intestinal neoplasm Diminished or absent ability of a female to achieve conception. EFO:0008560 ICD10:N97 ICD9:628.8 ICD9:628.9 MESH:D007247 SCTID:6738008 UMLS:C0341869 female infertility female reproductive system infertility female reproductive system infertility disorder infertility disorder of female reproductive system female infertility A disease that involves the genitourinary system. ICD10:N00.N99 SCTID:42030000 UMLS:C0080276 disease of genitourinary system disease or disorder of genitourinary system disorder of genitourinary system disorder of the genitourinary system genitourinary system disease genitourinary system disease or disorder disease of genitourinary system A disease involving a pathogenic inflammatory response in the anatomical structure. ICD9:799.89 NCIT:C93210 SCTID:128139000 UMLS:C1290884 anatomical structure inflammation inflammation of anatomical structure inflammatory disease inflammatory disorder inflammatory disease Damage inflicted on the body as the direct or indirect result of an external force, with or without disruption of structural continuity. EFO:0000546 ICD10:S00.T98 MESH:D014947 NCIT:C3671 injury trauma traumatic injury wound injury A neoplasm (disease) that involves the digestive system. EFO:0008549 MESH:D005770 NCIT:C3052 GI neoplasm GI system neoplasm GI system tumor GI tumor digestive neoplasm digestive system neoplasm (disease) digestive system tumor digestive tumor gastrointestinal neoplasm gastrointestinal system neoplasm gastrointestinal system tumor gastrointestinal tumor neoplasm of GI system neoplasm of digestive system neoplasm of gastrointestinal system neoplasm of the GI system neoplasm of the digestive system neoplasm of the gastrointestinal system tumor of GI system tumor of digestive system tumor of gastrointestinal system tumor of the GI system tumor of the digestive system tumor of the gastrointestinal system digestive system neoplasm A neoplasm (disease) that involves the thoracic segment of trunk. ICD9:239.89 NCIT:C3406 SCTID:255058005 UMLS:C0039981 neoplasm of the thorax neoplasm of thoracic segment of trunk thoracic neoplasm thoracic segment of trunk neoplasm thoracic segment of trunk neoplasm (disease) thoracic segment of trunk tumor thoracic tumor tumor of the thorax tumor of thoracic segment of trunk tumor of thorax neoplasm of thorax A disorder that follows infection but is distinct from the infection itself and its usual manifestations. ICD9:139.8 SCTID:123976001 sequela of infectious disorder post-infectious disorder A post-infectious disorder that follows viral infection but is distinct from the viral infection itself and its usual manifestations. ICD9:139.8 SCTID:123948009 sequela of viral disease post-viral disorder A Disease due to or propagated by sexual contact. ICD10:A50.A64 ICD9:099.8 ICD9:099.9 MESH:D012749 NCIT:C3365 SCTID:8098009 UMLS:C0036916 STD VD VD, venereal disease disease (VD), venereal sexually Transmitted disorder sexually transmitted disease venereal disease (VD) sexually transmitted disease Viral diseases which are potentially transmitted or propagated by sexual conduct. MESH:D015229 UMLS:C0036918 viral sexually transmitted disease viral sexually transmitted disease Disorders related to or resulting from abuse or mis-use of alcohol. MESH:D019973 SCTID:29212009 alcohol-related disorders Virus diseases caused by the Lentivirus genus. They are multi-organ diseases characterized by long incubation periods and persistent infection. EFO:1001357 MESH:D016180 UMLS:C0079680 lentivirus infection Either an isolated neoplasm or a syndrome with neoplasm as a major feature. neoplastic disease or syndrome An infectious process that affects the brain and/or spinal cord. Representative examples include encephalitis, poliomyelitis, arachnoiditis, and meningitis. EFO:1001456 ICD9:349.89 MESH:D002494 NCIT:C27582 SCTID:128117002 UMLS:C0007684 central nervous system infectious disease central nervous system infectious disorder infectious disease of central nervous system central nervous system infectious disorder A disease that involves the large intestine. SCTID:119523007 UMLS:C0341321 disease of large intestine disease or disorder of large intestine disorder of large intestine large intestine disease or disorder large intestine disease A disorder that affects the muscle tissue of the heart. Representative examples include myocardial infarction, myocarditis, and cardiomyopathy. NCIT:C35544 SCTID:57809008 disease of myocardium disease or disorder of myocardium disorder of myocardium myocardial disease myocardial disorder myocardium disease myocardium disease or disorder myocardial disorder A malignant tumor that has spread from its original (primary) site of growth to another site close to or distant from the primary site. NCIT:C36263 malignant metastatic neoplasm metastatic cancer metastatic malignant neoplasm metastatic neoplasm, malignant Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. metastatic malignant neoplasm A malignant neoplasm that arises from a pre-existing lower grade lesion, or as a result of a primary lesion that has spread to secondary sites, or due to a complication of a cancer treatment. ICD9:198.89 ICD9:199.1 NCIT:C4968 SCTID:128462008 secondary cancer secondary malignancy secondary malignant neoplasm Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. secondary malignant neoplasm A neoplasm that arises from a pre-existing lower grade lesion, or as a result of a primary lesion that has spread to secondary sites, or due to a complication of a cancer treatment. NCIT:C36255 secondary neoplasm secondary tumor Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. secondary neoplasm A tumor that has spread from its original (primary) site of growth to another site, close to or distant from the primary site. Metastasis is characteristic of advanced malignancies, but in rare instances can be seen in neoplasms lacking malignant morphology. ICDO:8000/6 NCIT:C3261 metastatic disease metastatic neoplasm metastatic tumor Note that we currently treat secondary neoplasms as being neoplastic diseases that are derived from neoplasm; classes such as 'neoplasm', 'carcinoma' are implicitly primary. This may change in future. metastatic neoplasm ICD10:U10.9 Orphanet:598363 MIS-C/A multisystem inflammatory syndrome in children and adults A very serious type of heart attack during which one of the heart’s major arteries (one of the arteries that supplies oxygen and nutrient-rich blood to the heart muscle) is blocked. ST-segment elevation is an abnormality detected on the 12-lead ECG. EFO:0008585 SCTID:401303003 ST segment elevation myocardial infarction STEMI acute-ST segment elevation myocardial infarction ST-elevation myocardial infarction A disorder of the nervous system related to a vascular etiology. NCIT:C117007 UMLS:C3898144 disease of nervous system vasculature nervous system disorder of vasculature neurovascular disorder vasculature nervous system disorder neurovascular disease A disease or disorder that involves the erythrocyte. ICD9:289.9 SCTID:38292009 UMLS:C0221016 disease of erythrocyte disease or disorder of erythrocyte disorder of erythrocyte erythrocyte disease erythrocyte disease or disorder red blood cell disease red blood cell disorder erythrocyte disease ICD9:282.7 SCTID:80141007 hemoglobinopathy hemoglobinopathy A disease or disorder that involves the abdominal segment of trunk. SCTID:609618002 UMLS:C3661988 abdominal segment of trunk disease abdominal segment of trunk disease or disorder disease of abdominal segment of trunk disease or disorder of abdominal segment of trunk disorder of abdominal segment of trunk abdominal and pelvic region disorder A disease or disorder that involves the lymphoid system. SCTID:111590001 disease of lymphoid system disease or disorder of lymphoid system disorder of lymphoid system lymphoid system disease lymphoid system disease or disorder lymphoid system disease Any disorder that features disrupted cell proliferation. Includes hyperplasia, neoplastic syndrome and isolated neoplasm diseases as well as precancerous conditions. cell proliferation disorder neoplasm cancer or benign tumor A disease caused by infection with severe acute respiratory syndrome coronavirus 2. DOID:0080600 ICD10:U07.1 ICD10:U07.2 ICD11:RA01.0 ICD11:RA01.2 MESH:C000657245 MESH:D000086382 SCTID:840539006 2019 novel coronavirus infection 2019-nCoV infection coronavirus disease 2019 severe acute respiratory syndrome coronavirus 2 infectious disease COVID-19 Acute respiratory distress syndromet that occurs in pediatric patients and includes findings of new infiltrates (unilateral or bilateral) consistent with acute parenchymal disease, edema not fully explained by fluid overload or cardiac failure, and may present as new acute lung disease in setting of chronic lung disease and/or heart disease, and perinatal lung disease is excluded. PARDS pediatric acute respiratory distress syndrome A inflammatory syndrome in children infected by the SARS-CoV-2 with similarities to Kawasaki disease. Clinical manifestations range from fever and inflammation to myocardial injury, shock, and development of coronary artery aneurysms. DOID:0080711 NCIT:C172127 COVID-19 -related pediatric inflammatory multisystem syndrome COVID-19 Kawasaki-like syndrome COVID-19 associated multisystem inflammatory syndrome in children MIS-C PIMS PIMS-TS PMIS SARS-CoV-2 Kawasaki-like syndrome multisystem inflammatory syndrome in children multisystem inflammatory syndrome in children associated with COVID-19 multisystem inflammatory syndrome in children associated with coronavirus disease 2019 paediatric inflammatory multisystem syndrome: temporally associated with SARS-CoV-2 pediatric inflammatory multisystem syndrome pediatric inflammatory multisystem syndrome temporally associated with SARS-CoV-2 pediatric multi-system inflammatory syndrome potentially associated with COVID-19 pediatric multisystem inflammatory syndrome The clinical presentation of MIS-C includes fever, severe illness, and the involvement of two or more organ systems, in combination with laboratory evidence of inflammation and laboratory or epidemiologic evidence of SARS-CoV-2 infection. Some features of MIS-C resemble Kawasaki Disease, toxic shock syndrome, and secondary hemophagocytic lymphohistiocytosis/macrophage activation syndrome. COVID-19–associated multisystem inflammatory syndrome in children A liver disease characterized by the liver losing or has lost all of its function. NCIT:C26922 hepatic failure liver failure A chronic disease triggered by acute COVID-19 infection that is characterized by persistent symptoms following the acute phase of the SARS-CoV-2 infection, which may include fatigue, coughing, dyspnea, clouding of mentation, sleep disturbances, exercise intolerance and autonomic symptoms including tachycardia upon mild exercise or standing, night sweats, temperature dysregulation, gastroparesis, constipation or loose stools, and peripheral vasoconstriction. PASC long haul COVID-19 long-haul COVID-19 post-acute sequelae of COVID-19 post-acute sequelae of SARS-CoV-2 infection sequelae of COVID-19 long COVID-19 A viral disease or post-viral disorder caused by infection with severe acute respiratory syndrome coronavirus 2 or the associated aftereffects of the disease. COVID-19-related disease SARS-CoV-2-related disease A SARS-CoV-2-related disease that is caused by infection by SARS-CoV-2, and manifests after the original primary infection. post-COVID-19 disorder A viral infectious disease that result from the presence and activity of a viral agent, or a disorder that follows infection with an viral agent but is distinct from the usual manifestations of the infection itself. viral infectious disease or sequela viral disease or post-viral disorder The initial viral infectious disase that causes illness. primary viral infectious disease A disease or disorder that result from the presence and activity of a microbial, viral, fungal or parasitic agent, or a disorder that follows infection with an infectious agent but is distinct from the usual manifestations of the infection itself. infectious disease or sequela infectious disease or post-infectious disorder A syndrome that occurs after therapeutic infusion of antibodies into the blood and is characterized by nausea, headache, tachycardia, hypotension, rash, and shortness of breath. It is caused by the release of cytokines from the cells that are targeted by the antibodies. Most patients experience a mild to moderate reaction; however, the reaction may be severe and life-threatening. NCIT:C78251 CRS cytokine storm cytokine-associated toxicity cytokine release syndrome Pathological structure or process pathological entity Phenotypic observation of the presence or absence of a pathological entity. pathological phenotype observation Lesions leading to or consequent on failure of, or atypical movement of, blood throughout the body. circulatory disorder A syndrome consequent to uncontrolled activation of blood clotting factors leading to disseminated platelet lysis, and fibrin deposition, ultimately leading to bleeding and necrosis as a consequence of inhibition of fibrin polymerisation by degradation products. Diagnosed by microthrombi in many organs. disseminated intravascular coagulation Anatomically located instance of pathological response or entity. pathological anatomical entity the observable morphological, physiological, behavioral and other characteristics of mammalian organisms that are manifested through development and lifespan mammalian phenotype any anomaly in the cessation of function at the cellular level MP:0001647 abnormal cell viability abnormal cellular death abnormal cell death pathologic death of cells, usually from irreversible damage cellular necrosis deviation from the normal function of the immune system MP:0001789 GO:0006955 immune system/response abnormalities immune system: response/ function abnormalities abnormal immune system physiology aberrant reaction of the microcirculation characterized by movement of fluid and leukocytes from the blood into extravascular tissues inflammation inflammatory response abnormal inflammatory response greater than expected response to injury, infection, or insult increased inflammatory response local accumulation of fluid, plasma proteins, and leukocytes in the proximal portion of the respiratory passages nasal inflammation inflammation of the mucous membrane of the nose MP:0001113 nasal catarrh rhinitis any functional anomaly of the pulmonary system; inability or reduced ability to intake and exchange oxygen and carbon dioxide with the environment MGI:2173593 respiratory system dysfunction respiratory system physiology abnormalities respiratory system: respiratory distress/failure/functional anomalies abnormal respiratory system physiology local accumulation of fluid, plasma proteins, and leukocytes in the respiratory system respiratory system inflammation the observable morphological and physiological characteristics of the basic structural and functional unit of all mammalian organisms that are manifested through development and lifespan cell phenotype cellular phenotype the observable morphological and physiological characteristics of the mammalian system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies that are manifested through development and lifespan immune system phenotype the observable morphological and physiological characteristics of the mammalian system responsible for the exchange of oxygen and carbon dioxide with the environment that are manifested through development and lifespan respiratory system phenotype any functional anomaly of the vital processes of the cell abnormal cell physiology necrosis or death of soft tissue due to lack of blood flow resulting from injury, infection or other conditions that affect blood circulation gangrenous necrosis gangrene a form of coagulative necrosis that develops in ischemic tissue, where the blood supply is inadequate to keep tissue viable, in the absence of superimposed microbial infection; can be due to peripheral artery disease or acute limb ischemia; the affected body part is dry, shrunken, and dark reddish-black and can fall off (autoamputate) if not removed surgically The term dry is used only when referring to a limb or to the gut; in other locations, this same type of necrosis is called an infarction, such as myocardial infarction dry gangrene "The action, reaction, or performance of an organism in response to external or internal stimuli." [GO:GO\:0007610] NBO:0000000 behavior behaviour behavior process "Behavior related to the intake of substances." [NBOC:GVG] ingest consumption behavior Consumption behavior that involves inhaling a material (such as finely ground tobacco leaves) through the nose. smoking behavior A method to determine microbial susceptibility to antibiotics wherein bacteria are inoculated onto agar plates and the antimicrobial agent diffused onto the agar plate from a filter paper disk. An approximate, but not exact, MIC is determined by the diameter of growth inhibition zones. This method has been found to have good correlation between in-vivo data and in-vitro data. Kirby-Bauer disk assay disk-diffusion method A method to determine microbial susceptibility to antibiotics in which a plastic strip impregnated with the antibiotic of interest is placed on an agar plate that has been inoculated with bacteria. The antibiotic diffuses from the strip producing a concentration gradient of drug on the agar. The point at which the elliptical shaped area of growth inhibition meets the strip is the minimum inhibitory concentration of the drug of interest. antimicrobial gradient method (E-test) A method to determine the minimum inhibitory concentration (MIC) of antibiotics in which growth media is pipetted into a multi-well plate. Each well contains a known concentration of drug which is inoculated with a known quantity of bacteria. The plate is incubated for a specified period of time and each well is assessed for bacterial cell growth. The drug concentration in the first well showing no growth is known as the MIC for that antibiotic. Minimum 2 mL total broth dilution volume. macro broth dilution method A person that is associated with another person in some manner or action. Partner Partner An individual who provides support to a pregnant individual. PREGNANCY PARTNER Pregnancy Partner Pregnancy Partner A person with whom one has had sexual relations. SEXUAL PARTNER Sexual Partner Sexual Partner A statement that defines conventions, guidelines, characteristics or methods for consistent data handling to facilitate exchange or processing of the data. This set of criteria are reviewed by and agreed upon by the user community or a governing body before they are released and adopted for use. Data Standard data standards Data Standard A vial used to store specimens in a cryopreservative at very low temperatures. Cryovial Cryovial The RNA component of the small (30S) subunit of prokaryotic ribosomes. 16S Ribosomal RNA 16S rRNA Bacterial 16S RNA Bacterial 16S Ribosomal RNA Bacterial 16S rRNA Bacterial 16S RNA The fluid which runs through a dialysis machine and captures, for discard or analysis, the excess water and waste from the blood stream through diffusion and ultrafiltration. DIALYSIS FLUID Dialysate Dialysis Fluid Dialysis Fluid An indicator as to whether the female subject is pregnant during the study period. PREGST Pregnant During the Study Pregnant During the Study An unexpected death without warning. Sudden Death Sudden Death, NOS Sudden Death Indicates that no answer was given. Not Answered Not answered Not Answered Unexpected death of an infant less than one year of age, whose cause of death is not immediately obvious prior to investigation. SUID Sudden Unexplained Infant Death Sudden Unexplained Infant Death Unexpected death of a child over one year of age, which remains unexplained when all known and possible causes of death have been ruled out. Sudden Unexplained Death in Childhood Sudden Unexplained Death in Childhood A test tube, capillary tube, or other tube designed for the collection of blood. BCT Blood Collection Tube Blood Collection Tube A blood collection tube that contains a vacuum, allowing it to draw blood through a needle to fill the tube. Evacuated Blood Specimen Collection Tube Evacuated Blood Specimen Collection Tube A person who shares a house with another person. Housemate Housemate Hepatic necrosis, inflammation, or scarring due to any cause that persists for more than 6 months. Manifestations may include signs and symptoms of cholestasis, portal hypertension, and/or abnormal liver function tests. Chronic Liver Disease Chronic_Liver_Disease Chronic Liver Disease An identifying designation assigned to an individual that corresponds with their function. Person Role Person Role Title Role Title Title title Person Role Title A title that describes the function of a designated group, governing body, or institution. Organization Role Organization Role A fetus of 16-20 weeks gestational age that shows signs of life at birth but dies after delivery. Post-Natal Death at 16-20 Weeks Gestation Post-Natal Death at 16-20 Weeks Gestation An age group comprised of infants delivered after full 37 weeks gestation whose 5 minute Apgar score was above 7, has no major congenital anomalies and was discharged home with mother without any additional diagnoses except for physiologic hyperbilirubinemia. Healthy Term Newborn Healthy Term Newborn An age group comprised of healthy newborns whose only diagnoses are those related to prematurity. Healthy Preterm Newborn Healthy Preterm Newborn An age group comprised of infants greater than or equal to 34 weeks, 0 days and less than 37 weeks, 0 days gestational age. Late Preterm Infant Near Term Infant Late Preterm Infant An age group comprised of infants less than 28 weeks, 0 days gestational age. Extreme Immaturity Extremely Preterm Infant Extremely Preterm Infant An age group comprised of infants greater than or equal to 42 weeks, 0 days gestational age. Post Dates Postmature Postterm Infant Postterm Infant Having no significant health-related issues. Healthy Healthy A laboratory test to determine the concentration of a substance that will inhibit a biological or biochemical function, such as microorganism growth or enzymatic activity. Inhibitory Concentration Test Inhibitory Concentration Test Irreversible absence of cortical and brain stem functioning. Brain Death Brain Death Interventions or procedures not otherwise categorized. Other Intervention or Procedure Other Intervention or Procedure Death of a live newborn during the first 7 days of life. Early Neonatal Death Early Neonatal Mortality Early Neonatal Death Death of live newborn between 7and 27 days after birth. Late Neonatal Death Late Neonatal Mortality Late Neonatal Death Symptoms, physical examination results, and/or laboratory test results related to the female reproductive system. Female Reproductive System Finding Female Reproductive System Finding An age group comprised of infants greater than 28 weeks, 0 days and less than 34 weeks, 0 days. Very Preterm Infant Very Preterm Infant Death of a live newborn during the first 24 hours of life Very Early Neonatal Death Very Early Neonatal Death Death between 28 days and 1 year of life. Post Neonatal Death Post Neonatal Death A response indicating that a person has lost their ability for fine movement: cannot button, write, eat, etc., or minor loss of sensitivity. Loss of Fine Movements Loss of fine movements Loss of Fine Movements A human biological structure, fluid or other substance; excludes single molecular entities. Anatomic Structure, System, or Substance Anatomic Structures and Systems Anatomic Structure, System, or Substance A bacterial toxin produced by Shigella dysenteriae and by some strains of E. coli that inhibits protein synthesis by blocking the interaction of ribosomal RNA with peptide elongation factors. The non-catalytic beta subunit of Shiga toxin may be useful as a fusion vector for induction of antigen-specific cytotoxic T lymphocyte responses. Shiga Toxin Shiga Toxin Observed to be or have been pregnant. PREGNANT Pregnant Pregnant A death of the embryo occurring inside the uterus. EARLY INTRAUTERINE DEATH Early IUD Early Intrauterine Death Early Intrauterine Death A death of the fetus occurring inside the uterus. LATE INTRAUTERINE DEATH Late IUD Late Intrauterine Death Late Intrauterine Death A general term comprising tissue that is not hardened or calcified; including muscle, fat, blood vessels, nerves, tendons, ligaments and fascia. SOFT TISSUE Soft Tissue soft tissue Soft Tissue The absence of disease or pathology. NON-PATHOLOGICAL Non-Pathological Non-Pathological Any individual with whom the subject attends or attended the same school. SCHOOLMATE Schoolmate Schoolmate An anatomical structure consisting of similarly specialized cells and intercellular matrix, aggregated according to genetically determined spatial relationships, performing a specific function. Normal Normal Tissue TISSUE Tissue Tissue, NOS Tissues tissue Tissue An age group comprised of infants born alive with a gestational age between 32 to less than 37 weeks. Moderate to Late Preterm Infant Moderate to Late Preterm Infant A laboratory test to determine the lowest concentration of a substance that will inhibit a biological or biochemical function, such as microorganism growth or enzymatic activity. MIC Minimum Inhibitory Concentration Minimum Inhibitory Concentration Test Minimum Inhibitory Concentration Test The supporting connective tissue of an organ. Connective and Soft Tissue Connective and Soft Tissue An individual who is receiving a transplant of a solid organ. Solid Organ Transplant Recipient Solid Organ Transplantation Recipient Solid Organ Transplant Recipient An individual receiving a bone marrow transplant. Bone Marrow Transplant Recipient Bone Marrow Transplantation Recipient Bone Marrow Transplant Recipient A body part, organ or organ component that is formed during the embryonic stage of life of an organism. Embryologic Structure Embryonic Structure Embryonic Structure An unborn or unhatched vertebrate in the later stages of development showing the main recognizable features of the mature being. FETUS Fetal Fetus fetus Fetus A female who is married to a spouse with children whom are not biologically related to her. MOTHER, STEP Step Mother Stepmother Stepmother Pertaining to, affecting, or associated with the liver. Hepatic hepatic Hepatic Fluid withdrawn from a body cavity, organ, cyst, or tumor. ASPIRATE Aspirate aspirate Aspirate An adjectival term used to specify a region of the body or other concepts associated with the body. Anatomy Qualifier Anatomy Qualifiers Anatomy Qualifier Named locations of or within the body. Anatomic Location Anatomic Site Anatomic Sites Anatomical Location Anatomical_Location CDISC Location Site Topographic (Anatomic) Site Topographic Site Anatomic Site An indication that death occurred on or within 90 days of a patient's initial admission to a hospital. Death During, or within 90 Days of, Index Hospital Admission Death Less than 90 Days or During Index Hospital Admission Death During, or within 90 Days of, Index Hospital Admission A loss of any arm of immune functions, resulting in potential or actual increase in infections. This state may be reached secondary to specific genetic lesions, syndromes with unidentified or polygenic causes, acquired deficits from other disease states, or as result of therapy for other diseases or conditions. Immunocompromised Immunocompromised Host Immunocompromised Patient Immunosuppressed Immunosuppressed Host Immunosuppressed Patient immunocompromised immunocompromised host immunocompromised patient immunosuppressed host immunosuppressed patient Immunocompromised A living organism that has membranous cell walls, requires oxygen and organic foods, and is capable of voluntary movement, as distinguished from a plant or mineral. ANIMAL Animal Animalia Animals Animal A large order of insects having a single pair of wings and sucking or piercing mouths; includes true flies and mosquitoes and gnats and crane flies. Diptera Flies Diptera A taxonomic class of arthropods that includes praying mantises, dragonflies, grasshoppers, true bugs, flies, bees, wasps, ants, butterflies, moths, and beetles. Insect Insecta Invertebrates, Insects Insect A living entity. BiologicEntity Organism Organismal Organisms Taxon organism Organism A non-taxonomic grouping of organisms based on a shared characteristic. Other Organism Groupings Other Organism Groupings A population or type of organisms that is genetically different from others of the same species and possessing a set of defined characteristics. Organism Strain STRAIN Strain Strain Number strain Organism Strain Any agent that can alter hormone levels or modulate hormone effects. Hormonal Therapy Agent Hormone Therapy Hormone Therapy Agent Hormone Therapy Agent A plan of action intended to accomplish a specific goal. Strategy Strategy A heterogeneous and variable aggregate of body fluids, tissues, cells, microorganisms, and other materials that are collected from a swab biospecimen collection procedure. SWABBED MATERIAL Swabbed Material Swabbed Material The removal of tissue specimens or fluid from the living body for microscopic examination, performed to establish a diagnosis. BIOPSY BIOPSY_TYPE Biopsy Bx biopsy Biopsy A procedure to remove toxic substances from the blood that is used in patients with end-stage chronic kidney disease or acute kidney failure. This includes hemodialysis and peritoneal dialysis. Dialysis Dialysis Procedure Dialysis Therapy dialysis Dialysis