ICDO: International Classification of Diseases Ontology
Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification.
Really of interest to developers only
BFO OWL specification label
Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2
BFO CLIF specification label
editor preferred term
The concise, meaningful, and human-friendly name for a class or property preferred by the ontology developers. (US-English)
PERSON:Daniel Schober
example of usage
has curation status
PERSON:Alan Ruttenberg
PERSON:Bill Bug
PERSON:Melanie Courtot
definition
The official definition, explaining the meaning of a class or property. Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions.
2012-04-05: Barry Smith The official OBI definition, explaining the meaning of a class or property: 'Shall be Aristotelian, formalized and normalized. Can be augmented with colloquial definitions' is terrible. Can you fix to something like: A statement of necessary and sufficient conditions explaining the meaning of an expression referring to a class or property. Alan Ruttenberg Your proposed definition is a reasonable candidate, except that it is very common that necessary and sufficient conditions are not given. Mostly they are necessary, occasionally they are necessary and sufficient or just sufficient. Often they use terms that are not themselves defined and so they effectively can't be evaluated by those criteria. On the specifics of the proposed definition: We don't have definitions of 'meaning' or 'expression' or 'property'. For 'reference' in the intended sense I think we use the term 'denotation'. For 'expression', I think we you mean symbol, or identifier. For 'meaning' it differs for class and property. For class we want documentation that let's the intended reader determine whether an entity is instance of the class, or not. For property we want documentation that let's the intended reader determine, given a pair of potential relata, whether the assertion that the relation holds is true. The 'intended reader' part suggests that we also specify who, we expect, would be able to understand the definition, and also generalizes over human and computer reader to include textual and logical definition. Personally, I am more comfortable weakening definition to documentation, with instructions as to what is desirable. We also have the outstanding issue of how to aim different definitions to different audiences. A clinical audience reading chebi wants a different sort of definition documentation/definition from a chemistry trained audience, and similarly there is a need for a definition that is adequate for an ontologist to work with.
editor note
An administrative note intended for its editor. It may not be included in the publication version of the ontology, so it should contain nothing necessary for end users to understand the ontology.
term editor
Name of editor entering the term in the file. The term editor is a point of contact for information regarding the term. The term editor may be, but is not always, the author of the definition, which may have been worked upon by several people
20110707, MC: label update to term editor and definition modified accordingly. See https://github.com/information-artifact-ontology/IAO/issues/115.
alternative term
definition source
formal citation, e.g. identifier in external database to indicate / attribute source(s) for the definition. Free text indicate / attribute source(s) for the definition. EXAMPLE: Author Name, URI, MeSH Term C04, PUBMED ID, Wiki uri on 31.01.2007
Discussion on obo-discuss mailing-list, see http://bit.ly/hgm99w
curator note
An administrative note of use for a curator but of no use for a user
imported from
expand expression to
OBO foundry unique label
elucidation
has associated axiom(nl)
has associated axiom(fol)
has gbt_14396 code
has icd11 code
has_alternative_id in icd10
has icd10 code
has icd9 code
An annotation property that indicates whether the code is specific enough to be used as a billable medical code.
The following 72,186 ICD-10-CM codes are billable/specific and can be used to indicate a diagnosis for reimbursement purposes as there are no codes with a greater level of specificity under each code. Reference: https://www.icd10data.com/ICD10CM/Codes/Rules/Billable_Specific_Codes
code billability
An assertion that holds between an OWL Object Property and a temporal interpretation that elucidates how OWL Class Axioms that use this property are to be interpreted in a temporal context.
temporal interpretation
S dubious_for_taxon T if it is probably the case that no instances of S can be found in any instance of T.
this relation lacks a strong logical interpretation, but can be used in place of never_in_taxon where it is desirable to state that the definition of the class is too strict for the taxon under consideration, but placing a never_in_taxon link would result in a chain of inconsistencies that will take time to resolve. Example: metencephalon in teleost
S present_in_taxon T if some instance of T has some S. This does not means that all instances of T have an S - it may only be certain life stages or sexes that have S
An assertion that involves at least one OWL object that is intended to be expanded into one or more logical axioms. The logical expansion can yield axioms expressed using any formal logical system, including, but not limited to OWL2-DL.
logical macro assertion
A logical macro assertion whose domain is an IRI for a property
logical macro assertion on a property
Used to annotate object properties to describe a logical meta-property or characteristic of the object property.
logical macro assertion on an object property
logical macro assertion on an annotation property
relation p is the direct form of relation q iff p is a subPropertyOf q, p does not have the Transitive characteristic, q does have the Transitive characteristic, and for all x, y: x q y -> exists z1, z2, ..., zn such that x p z1 ... z2n y
The general property hierarchy is: "directly P" SubPropertyOf "P" Transitive(P) Where we have an annotation assertion "directly P" "is direct form of" "P"
If we have the annotation P is-direct-form-of Q, and we have inverses P' and Q', then it follows that P' is-direct-form-of Q'
relation p is the indirect form of relation q iff p is a subPropertyOf q, and there exists some p' such that p' is the direct form of q, p' o p' -> p, and forall x,y : x q y -> either (1) x p y or (2) x p' y
Used to annotate object properties representing a causal relationship where the value indicates a direction. Should be "+", "-" or "0"
part-of is homeomorphic for independent continuants.
R is homemorphic for C iff (1) there exists some x,y such that x R y, and x and y instantiate C and (2) for all x, if x is an instance of C, and there exists some y some such that x R y, then it follows that y is an instance of C.
R homeomorphic-for C expands to: C SubClassOf R only C. Additionally, for any class D that is disjoint with C, we can also expand to C DisjointWith R some D, D DisjointWith R some C.
An alternate textual definition for a class taken unmodified from an external source. This definition may have been used to derive a generalized definition for the new class.
This annotation property may be replaced with an annotation property from an external ontology such as IAO
A textual description of an axiom loss in this ontology compared to an external ontology.
Notes on the homology status of this class.
Used to connect a class to an adjectival form of its label. For example, a class with label 'intestine' may have a relational adjective 'intestinal'.
Notes on the how instances of this class vary across species.
Notes on the evolved function of instances of this class.
Notes on the structure, composition or histology of instances of this class.
Notes on the ontogenic development of instances of this class.
Notes on how similar or equivalent classes are represented in other ontologies.
Notes on how lexical conventions regarding this class, in particular any issues that may arise due to homonyny or synonymy.
FMA has terms like 'set of X'. In general we do not include set-of terms in uberon, but provide a mapping between the singular form and the FMA set term
anatomical location
has ICD10 name
is part of
my brain is part of my body (continuant parthood, two material entities)
my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity)
this day is part of this year (occurrent parthood)
a core relation that holds between a part and its whole
Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other.
Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime
Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'.
part_of
part of
has part
my body has part my brain (continuant parthood, two material entities)
my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity)
this year has part this day (occurrent parthood)
a core relation that holds between a whole and its part
Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part.
Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'.
has_part
realized in
this disease is realized in this disease course
this fragility is realized in this shattering
this investigator role is realized in this investigation
is realized by
realized_in
[copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
realizes
this disease course realizes this disease
this investigation realizes this investigator role
this shattering realizes this fragility
to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003])
Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process
preceded by
x is preceded by y if and only if the time point at which y ends is before or equivalent to the time point at which x starts. Formally: x preceded by y iff ω(y) <= α(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
An example is: translation preceded_by transcription; aging preceded_by development (not however death preceded_by aging). Where derives_from links classes of continuants, preceded_by links classes of processes. Clearly, however, these two relations are not independent of each other. Thus if cells of type C1 derive_from cells of type C, then any cell division involving an instance of C1 in a given lineage is preceded_by cellular processes involving an instance of C. The assertion P preceded_by P1 tells us something about Ps in general: that is, it tells us something about what happened earlier, given what we know about what happened later. Thus it does not provide information pointing in the opposite direction, concerning instances of P1 in general; that is, that each is such as to be succeeded by some instance of P. Note that an assertion to the effect that P preceded_by P1 is rather weak; it tells us little about the relations between the underlying instances in virtue of which the preceded_by relation obtains. Typically we will be interested in stronger relations, for example in the relation immediately_preceded_by, or in relations which combine preceded_by with a condition to the effect that the corresponding instances of P and P1 share participants, or that their participants are connected by relations of derivation, or (as a first step along the road to a treatment of causality) that the one process in some way affects (for example, initiates or regulates) the other.
is preceded by
preceded_by
precedes
x precedes y if and only if the time point at which x ends is before or equivalent to the time point at which y starts. Formally: x precedes y iff ω(x) <= α(y), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
occurs in
b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
occurs_in
unfolds in
unfolds_in
Paraphrase of definition: a relation between a process and an independent continuant, in which the process takes place entirely within the independent continuant
site of
[copied from inverse property 'occurs in'] b occurs_in c =def b is a process and c is a material entity or immaterial entity& there exists a spatiotemporal region r and b occupies_spatiotemporal_region r.& forall(t) if b exists_at t then c exists_at t & there exist spatial regions s and s’ where & b spatially_projects_onto s at t& c is occupies_spatial_region s’ at t& s is a proper_continuant_part_of s’ at t
Paraphrase of definition: a relation between an independent continuant and a process, in which the process takes place entirely within the independent continuant
contains process
A disease process may occurs in the left side of ear. In this case, the domain is the disease process, and the range is the left side.
An object property that represents a relation between a disease process (i.e., DP) and the lateral side of an anatomical entity where the disease process occurs.
DP occurs in anatomical lateral side
has syndrome
has DP material quality
caused by
An object property that represents a relation between a disease process and a material entity where the disease process has the material entity as a typically abnormal material output.
has DP output
An object property that represents a relation between a process and a process profile where the process has the process profile.
has process profile
inheres in
this fragility inheres in this vase
this red color inheres in this apple
a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence
A dependent inheres in its bearer at all times for which the dependent exists.
inheres_in
bearer of
this apple is bearer of this red color
this vase is bearer of this fragility
a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence
A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist.
bearer_of
is bearer of
participates in
this blood clot participates in this blood coagulation
this input material (or this output material) participates in this process
this investigator participates in this investigation
a relation between a continuant and a process, in which the continuant is somehow involved in the process
participates_in
has participant
this blood coagulation has participant this blood clot
this investigation has participant this investigator
this process has participant this input material (or this output material)
a relation between a process and a continuant, in which the continuant is somehow involved in the process
Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time.
has_participant
this enzyme has function this catalysis function (more colloquially: this enzyme has this catalysis function)
a relation between an independent continuant (the bearer) and a function, in which the function specifically depends on the bearer for its existence
A bearer can have many functions, and its functions can exist for different periods of time, but none of its functions can exist when the bearer does not exist. A function need not be realized at all the times that the function exists.
has_function
has function
this apple has quality this red color
a relation between an independent continuant (the bearer) and a quality, in which the quality specifically depends on the bearer for its existence
A bearer can have many qualities, and its qualities can exist for different periods of time, but none of its qualities can exist when the bearer does not exist.
has_quality
has quality
this person has role this investigator role (more colloquially: this person has this role of investigator)
a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence
A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists.
has_role
has role
a relation between an independent continuant (the bearer) and a disposition, in which the disposition specifically depends on the bearer for its existence
has disposition
disposition of
penicillin (CHEBI:17334) is allergic trigger for penicillin allergy (DOID:0060520)
A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
is allergic trigger for
A relation between a material entity and a condition (a phenotype or disease) of a host, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
is autoimmune trigger for
penicillin allergy (DOID:0060520) has allergic trigger penicillin (CHEBI:17334)
A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is not part of the host, and is considered harmless to non-allergic hosts, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has allergic trigger
A relation between a condition (a phenotype or disease) of a host and a material entity, in which the material entity is part of the host itself, and the condition results in pathological processes that include an abnormally strong immune response against the material entity.
has autoimmune trigger
x 'regulates in other organism' y if and only if: (x is the realization of a function to exert an effect on the frequency, rate or extent of y) AND (the agents of x are produced by organism o1 and the agents of y are produced by organism o2).
A part of relation that applies only between occurents.
A 'has regulatory component activity' B if A and B are GO molecular functions (GO_0003674), A has_component B and A is regulated by B.
A relationship that holds between a GO molecular function and a component of that molecular function that negatively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is negatively regulated by B.
By convention GO molecular functions are classified by their effector function. Internal regulatory functions are treated as components. For example, NMDA glutmate receptor activity is a cation channel activity with positive regulatory component 'glutamate binding' and negative regulatory components including 'zinc binding' and 'magnesium binding'.
has negative regulatory component activity
A relationship that holds between a GO molecular function and a component of that molecular function that positively regulates the activity of the whole. More formally, A 'has regulatory component activity' B iff :A and B are GO molecular functions (GO_0003674), A has_component B and A is positively regulated by B.
By convention GO molecular functions are classified by their effector function and internal regulatory functions are treated as components. So, for example calmodulin has a protein binding activity that has positive regulatory component activity calcium binding activity. Receptor tyrosine kinase activity is a tyrosine kinase activity that has positive regulatory component 'ligand binding'.
has positive regulatory component activity
A has necessary component activity B if A and B are GO molecular functions (GO_0003674), A has_component B and B is necessary for A. For example, ATPase coupled transporter activity has necessary component ATPase activity; transcript factor activity has necessary component DNA binding activity.
A 'has component activity' B if A is A and B are molecular functions (GO_0003674) and A has_component B.
w 'has process component' p if p and w are processes, w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
A relationship that holds between between a receptor and an chemical entity, typically a small molecule or peptide, that carries information between cells or compartments of a cell and which binds the receptor and regulates its effector function.
Holds between p and c when p is a transport process or transporter activity and the outcome of this p is to move c from one location to another.
Process(P2) is directly regulated by process(P1) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
Process(P2) is directly negatively regulated by process(P1) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P2 directly negatively regulated by P1.
Process(P2) is directly postively regulated by process(P1) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P2 is directly postively regulated by P1.
A 'has effector activity' B if A and B are GO molecular functions (GO_0003674), A 'has component activity' B and B is the effector (output function) of B. Each compound function has only one effector activity.
This relation is designed for constructing compound molecular functions, typically in combination with one or more regulatory component activity relations.
X ends_after Y iff: end(Y) before_or_simultaneous_with end(X)
ends after
X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y)
immediately preceded by
X immediately_precedes_Y iff: end(X) simultaneous_with start(Y)
immediately precedes
X starts_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (start(X) before_or_simultaneous_with end(Y))
starts during
X happens_during Y iff: (start(Y) before_or_simultaneous_with start(X)) AND (end(X) before_or_simultaneous_with end(Y))
happens during
X ends_during Y iff: ((start(Y) before_or_simultaneous_with end(X)) AND end(X) before_or_simultaneous_with end(Y).
ends during
x overlaps y if and only if there exists some z such that x has part z and z part of y
http://purl.obolibrary.org/obo/BFO_0000051 some (http://purl.obolibrary.org/obo/BFO_0000050 some ?Y)
overlaps
a 'toe distal phalanx bone' that is connected to a 'toe medial phalanx bone' (an interphalangeal joint *connects* these two bones).
a is connected to b if and only if a and b are discrete structure, and there exists some connecting structure c, such that c connects a and b
connected to
c connects a if and only if there exist some b such that a and b are similar parts of the same system, and c connects b, specifically, c connects a with b. When one structure connects two others it unites some aspect of the function or role they play within the system.
connects
Relation between an collecting structure and another structure, where the collecting structure acts as a conduit channeling fluid, substance or energy away from the other structure.
Individual ontologies should provide their own constraints on this abstract relation. For example, in the realm of anatomy this should hold between a vein and an anatomical structure
drains
w 'has component' p if w 'has part' p and w is such that it can be directly disassembled into into n parts p, p2, p3, ..., pn, where these parts are of similar type.
The definition of 'has component' is still under discussion. The challenge is in providing a definition that does not imply transitivity.
For use in recording has_part with a cardinality constraint, because OWL does not permit cardinality constraints to be used in combination with transitive object properties. In situations where you would want to say something like 'has part exactly 5 digit, you would instead use has_component exactly 5 digit.
has component
A relationship that holds between a biological entity and a phenotype. Here a phenotype is construed broadly as any kind of quality of an organism part, a collection of these qualities, or a change in quality or qualities (e.g. abnormally increased temperature). The subject of this relationship can be an organism (where the organism has the phenotype, i.e. the qualities inhere in parts of this organism), a genomic entity such as a gene or genotype (if modifications of the gene or the genotype causes the phenotype), or a condition such as a disease (such that if the condition inheres in an organism, then the organism has the phenotype).
Chris Mungall
has phenotype
phenotype of
process(P1) regulates process(P2) iff: P1 results in the initiation or termination of P2 OR affects the frequency of its initiation or termination OR affects the magnitude or rate of output of P2.
We use 'regulates' here to specifically imply control. However, many colloquial usages of the term correctly correspond to the weaker relation of 'causally upstream of or within' (aka influences). Consider relabeling to make things more explicit
Regulation precludes parthood; the regulatory process may not be within the regulated process.
regulates
Process(P1) negatively regulates process(P2) iff: P1 terminates P2, or P1 descreases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
negatively regulates (process to process)
negatively regulates
Process(P1) postively regulates process(P2) iff: P1 initiates P2, or P1 increases the the frequency of initiation of P2 or the magnitude or rate of output of P2.
positively regulates (process to process)
positively regulates
'human p53 protein' SubClassOf some ('has prototype' some ('participates in' some 'DNA repair'))
heart SubClassOf 'has prototype' some ('participates in' some 'blood circulation')
x has prototype y if and only if x is an instance of C and y is a prototypical instance of C. For example, every instance of heart, both normal and abnormal is related by the has prototype relation to some instance of a "canonical" heart, which participates in blood circulation.
Experimental. In future there may be a formalization in which this relation is treated as a shortcut to some modal logic axiom. We may decide to obsolete this and adopt a more specific evolutionary relationship (e.g. evolved from)
This property can be used to make weaker forms of certain relations by chaining an additional property. For example, we may say: retina SubClassOf has_prototype some 'detection of light'. i.e. every retina is related to a prototypical retina instance which is detecting some light. Note that this is very similar to 'capable of', but this relation affords a wider flexibility. E.g. we can make a relation between continuants.
has prototype
mechanosensory neuron capable of detection of mechanical stimulus involved in sensory perception (GO:0050974)
osteoclast SubClassOf 'capable of' some 'bone resorption'
A relation between a material entity (such as a cell) and a process, in which the material entity has the ability to carry out the process.
For compatibility with BFO, this relation has a shortcut definition in which the expression "capable of some P" expands to "bearer_of (some realized_by only P)".
capable of
c stands in this relationship to p if and only if there exists some p' such that c is capable_of p', and p' is part_of p.
capable of part of
'heart development' has active participant some Shh protein
x has participant y if and only if x realizes some active role that inheres in y
This may be obsoleted and replaced by the original 'has agent' relation
Do not use this relation directly. It is ended as a grouping for relations between occurrents involving the relative timing of their starts and ends.
A relation that holds between two occurrents. This is a grouping relation that collects together all the Allen relations.
temporally related to
Every insulin receptor signaling pathway starts with the binding of a ligand to the insulin receptor
x starts with y if and only if x has part y and the time point at which x starts is equivalent to the time point at which y starts. Formally: α(y) = α(x) ∧ ω(y) < ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
starts with
x ends with y if and only if x has part y and the time point at which x ends is equivalent to the time point at which y ends. Formally: α(y) > α(x) ∧ ω(y) = ω(x), where α is a function that maps a process to a start point, and ω is a function that maps a process to an end point.
ends with
p has input c iff: p is a process, c is a material entity, c is a participant in p, c is present at the start of p, and the state of c is modified during p.
has input
p has output c iff c is a participant in p, c is present at the end of p, and c is not present at the beginning of p.
has output
A broad relationship between an exposure event or process and any entity (e.g., an organism, organism population, or an organism part) that interacts with an exposure stimulus during the exposure event.
A broad relationship between an exposure event or process and any agent, stimulus, activity, or event that causes stress or tension on an organism and interacts with an exposure receptor during an exposure event.
A broad relationship between an exposure event or process and a process by which the exposure stressor comes into contact with the exposure receptor
A broad relationship between an exposure event or process and the course takes from the source to the target.
Any relationship between an exposure event or process and any other entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving exposure events or processes.
c has-biological-role r iff c has-role r and r is a biological role (CHEBI:24432)
c has-application-role r iff c has-role r and r is an application role (CHEBI:33232)
c has-chemical-role r iff c has-role r and r is a chemical role (CHEBI:51086)
A faulty traffic light (material entity) whose malfunctioning (a process) is causally upstream of a traffic collision (a process): the traffic light acts upstream of the collision.
c acts upstream of p if and only if c enables some f that is involved in p' and p' occurs chronologically before p, is not part of p, and affects the execution of p. c is a material entity and f, p, p' are processes.
A gene product that has some activity, where that activity may be a part of a pathway or upstream of the pathway.
c acts upstream of or within p if c is enables f, and f is causally upstream of or within p. c is a material entity and p is an process.
p results in the developmental progression of s iff p is a developmental process and s is an anatomical structure and p causes s to undergo a change in state at some point along its natural developmental cycle (this cycle starts with its formation, through the mature structure, and ends with its loss).
This property and its subproperties are being used primarily for the definition of GO developmental processes. The property hierarchy mirrors the core GO hierarchy. In future we may be able to make do with a more minimal set of properties, but due to the way GO is currently structured we require highly specific relations to avoid incorrect entailments. To avoid this, the corresponding genus terms in GO should be declared mutually disjoint.
results in developmental progression of
every flower development (GO:0009908) results in development of some flower (PO:0009046)
p 'results in development of' c if and only if p is a developmental process and p results in the state of c changing from its initial state as a primordium or anlage through its mature state and to its final state.
results in development of
an annotation of gene X to anatomical structure formation with results_in_formation_of UBERON:0000007 (pituitary gland) means that at the beginning of the process a pituitary gland does not exist and at the end of the process a pituitary gland exists.
every "endocardial cushion formation" (GO:0003272) results_in_formation_of some "endocardial cushion" (UBERON:0002062)
results in formation of
an annotation of gene X to cell morphogenesis with results_in_morphogenesis_of CL:0000540 (neuron) means that at the end of the process an input neuron has attained its shape.
tongue morphogenesis (GO:0043587) results in morphogenesis of tongue (UBERON:0001723)
The relationship that links an entity with the process that results in the formation and shaping of that entity over time from an immature to a mature state.
results in morphogenesis of
an annotation of gene X to cell maturation with results_in_maturation_of CL:0000057 (fibroblast) means that the fibroblast is mature at the end of the process
bone maturation (GO:0070977) results_in_maturation_of bone (UBERON:0001474)
The relationship that links an entity with a process that results in the progression of the entity over time that is independent of changes in it's shape and results in an end point state of that entity.
results in maturation of
foramen ovale closure SubClassOf results in disappearance of foramen ovale
results in disappearance of
every mullerian duct regression (GO:0001880) results in regression of some mullerian duct (UBERON:0003890)
results in developmental regression of
holds between x and y if and only if x is causally upstream of y and the progression of x increases the frequency, rate or extent of y
holds between x and y if and only if x is causally upstream of y and the progression of x decreases the frequency, rate or extent of y
A relationship between an exposure event or process and any agent, stimulus, activity, or event that causally effects an organism and interacts with an exposure receptor during an exposure event.
Holds between p and c when p is a localization process (localization covers maintenance of localization as well as its establishment) and the outcome of this process is to regulate the localization of c.
transports or maintains localization of
q inheres in part of w if and only if there exists some p such that q inheres in p and p part of w.
Because part_of is transitive, inheres in is a sub-relation of inheres in part of
inheres in part of
an annotation of gene X to cell differentiation with results_in_maturation_of CL:0000057 (fibroblast) means that at the end of the process the input cell that did not have features of a fibroblast, now has the features of a fibroblast.
The relationship that links a specified entity with the process that results in an unspecified entity acquiring the features and characteristics of the specified entity
results in acquisition of features of
A mereological relationship or a topological relationship
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving parthood or connectivity relationships
mereotopologically related to
A relationship that holds between entities participating in some developmental process (GO:0032502)
Do not use this relation directly. It is ended as a grouping for a diverse set of relations, all involving organismal development
developmentally related to
ATP citrate lyase (ACL) in Arabidopsis: it is a heterooctamer, composed of two types of subunits, ACLA and ACLB in a A(4)B(4) stoichiometry. Neither of the subunits expressed alone give ACL activity, but co-expression results in ACL activity. Both subunits contribute_to the ATP citrate lyase activity.
Subunits of nuclear RNA polymerases: none of the individual subunits have RNA polymerase activity, yet all of these subunits contribute_to DNA-dependent RNA polymerase activity.
eIF2: has three subunits (alpha, beta, gamma); one binds GTP; one binds RNA; the whole complex binds the ribosome (all three subunits are required for ribosome binding). So one subunit is annotated to GTP binding and one to RNA binding without qualifiers, and all three stand in the contributes_to relationship to "ribosome binding". And all three are part_of an eIF2 complex
We would like to say if and only if exists c', p' c part_of c' and c' capable_of p and c capable_of p' and p' part_of p then c contributes_to p However, this is not possible in OWL. We instead make this relation a sub-relation of the two chains, which gives us the inference in the one direction.
In the context of the Gene Ontology, contributes_to may be used only with classes from the molecular function ontology.
contributes to
a particular instances of akt-2 enables some instance of protein kinase activity
This relation differs from the parent relation 'capable of' in that the parent is weaker and only expresses a capability that may not be actually realized, whereas this relation is always realized.
This relation is currently used experimentally by the Gene Ontology Consortium. It may not be stable and may be obsoleted at some future time.
enables
A grouping relationship for any relationship directly involving a function, or that holds because of a function of one of the related entities.
This is a grouping relation that collects relations used for the purpose of connecting structure and function
functionally related to
this relation holds between c and p when c is part of some c', and c' is capable of p.
part of structure that is capable of
c involved_in p if and only if c enables some process p', and p' is part of p
involved in
enabled by
regulated by
negatively regulated by
positively regulated by
A relationship that holds via some process of localization
Do not use this relation directly. It is a grouping relation.
related via localization to
Holds between p and c when p is a transportation or localization process and the outcome of this process is to move c to a destination that is part of some s, where the start location of c is part of the region that surrounds s.
imports
'pollen tube growth' results_in growth_of some 'pollen tube'
results in growth of
exports
input of
output of
formed as result of
A relationship between a process and an anatomical entity such that the process contributes to the act of creating the structural organization of the anatomical entity.
results in structural organization of
'protein catabolic process' SubClassOf has_direct_input some protein
p has direct input c iff c is a participant in p, c is present at the start of p, and the state of c is modified during p.
This is likely to be obsoleted. A candidate replacement would be a new relation 'has bound input' or 'has substrate'
has direct input
translation SubClassOf has_direct_output some protein
p has direct input c iff c is a participanti n p, c is present at the end of p, and c is not present at the beginning of c.
causally downstream of
immediately causally downstream of
p directly activates q if and only if p is immediately upstream of q and p is the realization of a function to increase the rate or activity of q
directly activates
p indirectly activates q if and only if p is upstream of q and there is a chain of directly activates relationships connecting p and q, where the chain is of length greater than one.
indirectly activates
directly inhibits
indirectly inhibits
This relation groups causal relations between material entities and causal relations between processes
This branch of the ontology deals with causal relations between entities. It is divided into two branches: causal relations between occurrents/processes, and causal relations between material entities. We take an 'activity flow-centric approach', with the former as primary, and define causal relations between material entities in terms of causal relations between occurrents. To define causal relations in an activity-flow type network, we make use of 3 primitives: * Temporal: how do the intervals of the two occurrents relate? * Is the causal relation regulatory? * Is the influence positive or negative The first of these can be formalized in terms of the Allen Interval Algebra. Informally, the 3 bins we care about are 'direct', 'indirect' or overlapping. Note that all causal relations should be classified under a RO temporal relation (see the branch under 'temporally related to'). Note that all causal relations are temporal, but not all temporal relations are causal. Two occurrents can be related in time without being causally connected. We take causal influence to be primitive, elucidated as being such that has the upstream changed, some qualities of the donwstream would necessarily be modified. For the second, we consider a relationship to be regulatory if the system in which the activities occur is capable of altering the relationship to achieve some objective. This could include changing the rate of production of a molecule. For the third, we consider the effect of the upstream process on the output(s) of the downstream process. If the level of output is increased, or the rate of production of the output is increased, then the direction is increased. Direction can be positive, negative or neutral or capable of either direction. Two positives in succession yield a positive, two negatives in succession yield a positive, otherwise the default assumption is that the net effect is canceled and the influence is neutral. Each of these 3 primitives can be composed to yield a cross-product of different relation types.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all involving cause and effect.
causally related to
p is causally upstream of q if and only if p precedes q and p and q are linked in a causal chain
causally upstream of
p is immediately causally upstream of q iff both (a) p immediately precedes q and (b) p is causally upstream of q. In addition, the output of p must be an input of q.
immediately causally upstream of
p1 directly provides input for p2 iff there exists some c such that p1 has_output c and p2 has_input c
This is currently called 'directly provides input for' to be consistent with our terminology where we use 'direct' whenever two occurrents succeed one another directly. We may relabel this simply 'provides input for', as directness is implicit
directly provides input for (process to process)
directly provides input for
transitive form of directly_provides_input_for
This is a grouping relation that should probably not be used in annotation. Consider instead the child relation 'directly provides input for' (which may later be relabeled simply to 'provides input for')
transitively provides input for (process to process)
transitively provides input for
p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q.
We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2
inverse of causally upstream of or within
c involved in regulation of p if c is involved in some p' and p' regulates some p
c involved in regulation of p if c is involved in some p' and p' positively regulates some p
c involved in regulation of p if c is involved in some p' and p' negatively regulates some p
c involved in or regulates p if and only if either (i) c is involved in p or (ii) c is involved in regulation of p
OWL does not allow defining object properties via a Union
involved in or involved in regulation of
A relationship that holds between two entities in which the processes executed by the two entities are causally connected.
This relation and all sub-relations can be applied to either (1) pairs of entities that are interacting at any moment of time (2) populations or species of entity whose members have the disposition to interact (3) classes whose members have the disposition to interact.
Note that this relationship type, and sub-relationship types may be redundant with process terms from other ontologies. For example, the symbiotic relationship hierarchy parallels GO. The relations are provided as a convenient shortcut. Consider using the more expressive processual form to capture your data. In the future, these relations will be linked to their cognate processes through rules.
An interaction relationship in which the two partners are molecular entities that directly physically interact with each other for example via a stable binding interaction or a brief interaction during which one modifies the other.
The entity A, immediately upstream of the entity B, has an activity that regulates an activity performed by B. For example, A and B may be gene products and binding of B by A regulates the kinase activity of B. A and B can be physically interacting but not necessarily. Immediately upstream means there are no intermediate entity between A and B.
The entity A, immediately upstream of the entity B, has an activity that negatively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A negatively regulates the kinase activity of B.
directly negatively regulates activity of
The entity A, immediately upstream of the entity B, has an activity that positively regulates an activity performed by B. For example, A and B may be gene products and binding of B by A positively regulates the kinase activity of B.
directly positively regulates activity of
Experimental: relation used for defining interaction relations. An interaction relation holds when there is an interaction event with two partners. In a directional interaction, one partner is deemed the subject, the other the target
Experimental: relation used for defining interaction relations; the meaning of s 'subject participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the subject is the predator. We can imagine a reciprocal prey-predatory process with subject and object reversed.
Experimental: relation used for defining interaction relations; the meaning of s 'target participant in' p is determined by the type of p, where p must be a directional interaction process. For example, in a predator-prey interaction process the target is the prey. We can imagine a reciprocal prey-predatory process with subject and object reversed.
A relationship between a material entity and a process where the material entity has some causal role that influences the process
p is causally related to q if and only if p or any part of p and q or any part of q are linked by a chain of events where each event pair is one of direct activation or direct inhibition. p may be upstream, downstream, part of or a container of q.
'lysine biosynthetic process via diaminopimelate' SubClassOf has_intermediate some diaminopimelate
p has intermediate c if and only if p has parts p1, p2 and p1 has output c, and p2 has input c
The intent is that the process branch of the causal property hierarchy is primary (causal relations hold between occurrents/processes), and that the material branch is defined in terms of the process branch
A coral reef environment is determined by a particular coral reef
s determined by f if and only if s is a type of system, and f is a material entity that is part of s, such that f exerts a strong causal influence on the functioning of s, and the removal of f would cause the collapse of s.
The label for this relation is probably too general for its restricted use, where the domain is a system. It may be relabeled in future
determined by (system to material entity)
s 'determined by part of' w if and only if there exists some f such that (1) s 'determined by' f and (2) f part_of w, or f=w.
p results in the end of s if p results in a change of state in s whereby s either ceases to exist, or s becomes functionally impaired or s has its fate committed such that it is put on a path to be degraded.
Holds between p and c when p is locomotion process and the outcome of this process is the change of location of c
The entity or characteristic A is causally upstream of the entity or characteristic B, A having an effect on B. An entity corresponds to any biological type of entity as long as a mass is measurable. A characteristic corresponds to a particular specificity of an entity (e.g., phenotype, shape, size).
Process(P1) directly regulates process(P2) iff: P1 regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding regulates the kinase activity (P2) of protein B then P1 directly regulates P2.
gland SubClassOf 'has part structure that is capable of' some 'secretion by cell'
s 'has part structure that is capable of' p if and only if there exists some part x such that s 'has part' x and x 'capable of' p
p 'results in closure of' c if and only if p is a developmental process and p results in a state of c changing from open to closed.
p results in breakdown of c if and only if the execution of p leads to c no longer being present at the end of p
p results in catabolism of c if and only if p is a catabolic process, and the execution of p results in c being broken into smaller parts with energy being released.
p results in organization of c iff p results in the assembly, arrangement of constituent parts, or disassembly of c
A relationship that holds between a material entity and a process in which causality is involved, with either the material entity or some part of the material entity exerting some influence over the process, or the process influencing some aspect of the material entity.
causal relation between material entity and a process
Holds between c and p if and only if c is capable of some activity a, and a regulates p.
Holds between c and p if and only if c is capable of some activity a, and a negatively regulates p.
renin -> arteriolar smooth muscle contraction
Holds between c and p if and only if c is capable of some activity a, and a positively regulates p.
Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a inhibits p.
The entity c may be a molecular entity with a drug role, or it could be some other entity used in a therapeutic context, such as a hyperbaric chamber.
capable of inhibiting or preventing pathological process
Holds between a material entity c and a pathological process p if and only if c is capable of some activity a, where a negatively regulates p.
capable of upregulating or causing pathological process
c is a substance that treats d if c is a material entity (such as a small molecule or compound) and d is a pathological process, phenotype or disease, and c is capable of some activity that negative regulates or decreases the magnitude of d.
Process(P1) directly postively regulates process(P2) iff: P1 positively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding positively regulates the kinase activity (P2) of protein B then P1 directly positively regulates P2.
directly positively regulates (process to process)
Process(P1) directly negatively regulates process(P2) iff: P1 negatively regulates P2 via direct physical interaction between an agent executing P1 (or some part of P1) and an agent executing P2 (or some part of P2). For example, if protein A has protein binding activity(P1) that targets protein B and this binding negatively regulates the kinase activity (P2) of protein B then P1 directly negatively regulates P2.
directly negatively regulates (process to process)
Holds between entity A (a transcription factor) and a nucleic acid B if and only if A down-regulates the expression of B. The nucleic acid can be a gene or an mRNA.
Holds between entity A (a transcription factor) and nucleic acid B if and only if A up-regulates the expression of B. The nucleic acid can be a gene or mRNA.
The genetic variant 'NM_007294.3(BRCA1):c.110C>A (p.Thr37Lys)' casues or contributes to the disease 'familial breast-ovarian cancer'. An environment of exposure to arsenic causes or contributes to the phenotype of patchy skin hyperpigmentation, and the disease 'skin cancer'.
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal or contributing role that influences the condition.
Note that relationships of phenotypes to organisms/strains that bear them, or diseases they are manifest in, should continue to use RO:0002200 ! 'has phenotype' and RO:0002201 ! 'phenotype of'.
Genetic variations can span any level of granularity from a full genome or genotype to an individual gene or sequence alteration. These variations can be represented at the physical level (DNA/RNA macromolecules or their parts, as in the ChEBI ontology and Molecular Sequence Ontology) or at the abstract level (generically dependent continuant sequence features that are carried by these macromolecules, as in the Sequence Ontology and Genotype Ontology). The causal relations in this hierarchy can be used in linking either physical or abstract genetic variations to phenotypes or diseases they cause or contribute to. Environmental exposures include those imposed by natural environments, experimentally applied conditions, or clinical interventions.
causes or contributes to condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some causal role for the condition.
causes condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity has some contributing role that influences the condition.
contributes to condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the severity with which a condition manifests in an individual.
contributes to expressivity of condition
contributes to severity of condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the entity influences the frequency of the condition in a population.
contributes to frequency of condition
A relationship between an entity (e.g. a genotype, genetic variation, chemical, or environmental exposure) and a condition (a phenotype or disease), where the presence of the entity reduces or eliminates some or all aspects of the condition.
ameliorates condition
A relationship between an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) and a condition (a phenotype or disease), where the presence of the entity worsens some or all aspects of the condition.
exacerbates condition
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are reduced or eliminated by the presence of the entity.
condition ameliorated by
A relationship between a condition (a phenotype or disease) and an entity (e.g. a chemical, environmental exposure, or some form of genetic variation) where some or all aspects of the condition are worsened by the presence of the entity.
condition exacerbated by
Do not use this relation directly. It is intended as a grouping for a more specific relations
has material basis in gain of function germline mutation in
has material basis in loss of function germline mutation in
has material basis in germline mutation in
has material basis in somatic mutation in
has partial material basis in germline mutation in
p 'has primary input ot output' c iff either (a) p 'has primary input' c or (b) p 'has primary output' c.
p has primary output c if (a) p has output c and (b) the goal of process is to modify, produce, or transform c.
p has primary input c if (a) p has input c and (b) the goal of process is to modify, consume, or transform c.
Relates a gene to condition, such that a mutation in this gene in a germ cell provides a new function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
is causal gain of function germline mutation of in
Relates a gene to condition, such that a mutation in this gene in a germ cell impairs the function of the corresponding product and that is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
is causal loss of function germline mutation of in
Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition and that can be passed on to offspring[modified from orphanet].
Relates a gene to condition, such that a mutation in this gene is sufficient to produce the condition but that cannot be passed on to offspring[modified from orphanet].
Relates a gene to condition, such that a mutation in this gene predisposes to the development of a condition and that is necessary but not sufficient to develop the condition[modified from orphanet].
Relates a gene to condition, such that a mutation in this gene partially contributes to the presentation of this condition[modified from orphanet].
is causal germline mutation partially giving rise to
A relation that holds between the disease and a material entity where the physical basis of the disease is a disorder of that material entity that affects its function.
disease has basis in dysfunction of (disease to anatomical structure)
A relation that holds between the disease and a process where the physical basis of the disease disrupts execution of a key biological process.
disease has basis in disruption of (disease to process)
A relation that holds between the disease and a feature (a phenotype or other disease) where the physical basis of the disease is the feature.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, all of which have a disease as the subject.
causal relationship with disease as subject
A relationship between a disease and a process where the disease process disrupts the execution of the process.
disease causes disruption of (disease to process)
disease causes dysfunction of (disease to anatomical entity)
A relationship between a realizable entity R (e.g. function or disposition) and a material entity M where R is realized in response to a process that has an input stimulus of M.
A relationship between a disease and an anatomical structure where the material basis of the disease is some pathological change in the structure.
acts upstream of or within, positive effect
acts upstream of or within, negative effect
c 'acts upstream of, positive effect' p if c is enables f, and f is causally upstream of p, and the direction of f is positive
c 'acts upstream of, negative effect' p if c is enables f, and f is causally upstream of p, and the direction of f is negative
causally upstream of or within, negative effect
causally upstream of or within, positive effect
A drought sensitivity trait that inheres in a whole plant is realized in a systemic response process in response to exposure to drought conditions.
An inflammatory disease that is realized in response to an inflammatory process occurring in the gut (which is itself the realization of a process realized in response to harmful stimuli in the mucosal lining of th gut)
Environmental polymorphism in butterflies: These butterflies have a 'responsivity to day length trait' that is realized in response to the duration of the day, and is realized in developmental processes that lead to increased or decreased pigmentation in the adult morph.
r 'realized in response to' s iff, r is a realizable (e.g. a plant trait such as responsivity to drought), s is an environmental stimulus (a process), and s directly causes the realization of r.
realized in response to
The entity A has an activity that regulates an activity of the entity B. For example, A and B are gene products where the catalytic activity of A regulates the kinase activity of B.
The entity A has an activity that regulates the quantity or abundance or concentration of the entity B.
The entity A is not immediately upstream of the entity B but A has an activity that regulates an activity performed by B.
indirectly regulates activity of
The entity A has an activity that down-regulates by repression the quantity of B. The down-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly decreases by repression the quantity of protein B (gene product) if and only if A negatively regulates the process of transcription or translation of a nucleic acid element that produces B.
The entity A has an activity that up-regulates by expression the quantity of B. The up-regulation is due to A having an effect on an intermediate entity (typically a DNA or mRNA element) which can produce B. For example, protein A (transcription factor) indirectly increases by expression the quantity of protein B (gene product) if and only if A positively regulates the process of transcription or translation of a nucleic acid element that produces B.
The entity A has an activity that directly positively regulates the quantity of B.
directly positively regulates quantity of
The entity A has an activity that directly negatively regulates the quantity of B.
directly negatively regulates quantity of
The entity A is not immediately upstream of the entity B and has an activity that up-regulates an activity performed by B.
indirectly positively regulates activity of
AKT1 destabilizes quantity of FOXO (interaction from Signor database: SIGNOR-252844)
An entity A directly interacts with B and A has an activity that decreases the amount of an entity B by degradating it.
AKT1 stabilizes quantity of XIAP (interaction from Signor database: SIGNOR-119488)
An entity A physically interacts with B and A has an activity that increases the amount of an entity B by stabilizing it.
The entity A is not immediately upstream of the entity B and has an activity that down-regulates an activity performed by B.
indirectly negatively regulates activity of
The entity A, immediately upstream of B, has an activity that directly regulates the quantity of B.
The entity A is not immediately upstream of the entity B, but A has an activity that regulates the quantity or abundance or concentration of B.
The entity A does not physically interact with the entity B, and A has an activity that down-regulates the quantity or abundance or concentration of B.
indirectly negatively regulates quantity of
The entity A does not physically interact with the entity B, and A has an activity that up-regulates the quantity or abundance or concentration of B.
indirectly positively regulates quantity of
This relation groups relations between diseases and any other kind of entity.
Do not use this relation directly. It is intended as a grouping for a diverse set of relations, in which the subject or object is a disease.
p has anatomical participant c iff p has participant c, and c is an anatomical entity
Relation between biological objects that resemble or are related to each other sufficiently to warrant a comparison.
Julius Caesar
Verdi’s Requiem
the Second World War
your body mass index
BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81
Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf
An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001])
entity
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.
BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240
Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants
A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002])
if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001])
if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002])
if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002])
(forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002]
(forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001]
(forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002]
(forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002]
continuant
An entity that has temporal parts and that happens, unfolds or develops through time.
BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region
BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players.
Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process.
Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame.
An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002])
Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001])
b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001])
(forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001]
(forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001]
occurrent
a chair
a heart
a leg
a molecule
a spatial region
an atom
an orchestra.
an organism
the bottom right portion of a human torso
the interior of your mouth
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])
For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001])
For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002])
(forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001]
(forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002]
(iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002]
independent continuant
BFO 2 Reference: Spatial regions do not participate in processes.
Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional.
A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001])
All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001])
(forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001]
(forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001]
spatial region
Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional
A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001])
All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001])
Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002])
(forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002]
(forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001]
(forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001]
temporal region
an infinitely thin plane in space.
the surface of a sphere-shaped part of space
A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001])
(forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001]
two-dimensional spatial region
the spatiotemporal region occupied by a human life
the spatiotemporal region occupied by a process of cellular meiosis.
the spatiotemporal region occupied by the development of a cancer tumor
A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001])
All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001])
Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001])
Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001])
Every spatiotemporal region occupies_spatiotemporal_region itself.
Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002])
(forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002]
(forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001]
(forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001]
(forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001]
(forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001]
spatiotemporal region
a process of cell-division, \ a beating of the heart
a process of meiosis
a process of sleeping
the course of a disease
the flight of a bird
the life of an organism
your process of aging.
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])
BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war)
(iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003]
process
an atom of element X has the disposition to decay to an atom of element Y
certain people have a predisposition to colon cancer
children are innately disposed to categorize objects in certain ways.
the cell wall is disposed to filter chemicals in endocytosis and exocytosis
BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type.
b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002])
If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002])
(forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002]
(forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002]
disposition
the disposition of this piece of metal to conduct electricity.
the disposition of your blood to coagulate
the function of your reproductive organs
the role of being a doctor
the role of this boundary to delineate where Utah and Colorado meet
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.
To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002])
All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002])
(forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002]
(forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002]
realizable entity
A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001])
(forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001]
zero-dimensional spatial region
the ambient temperature of this portion of air
the color of a tomato
the length of the circumference of your waist
the mass of this piece of gold.
the shape of your nose
the shape of your nostril
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. (axiom label in BFO2 Reference: [055-001])
If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001])
(forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001]
(forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001]
quality
Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key
of one-sided specifically dependent continuants: the mass of this tomato
of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates.
the disposition of this fish to decay
the function of this heart: to pump blood
the mutual dependence of proton donors and acceptors in chemical reactions [79
the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction
the pink color of a medium rare piece of grilled filet mignon at its center
the shape of this hole.
the smell of this portion of mozzarella
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 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 doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc.
(iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003]
specifically dependent continuant
John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married.
the priest role
the role of a boundary to demarcate two neighboring administrative territories
the role of a building in serving as a military target
the role of a stone in marking a property boundary
the role of subject in a clinical trial
the student role
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.
BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives.
b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001])
(forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001]
role
or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29
the FMA:regional parts of an intact human body.
the Western hemisphere of the Earth
the division of the brain into regions
the division of the planet into hemispheres
the dorsal and ventral surfaces of the body
the upper and lower lobes of the left lung
BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions
b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004])
(forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004]
fiat object part
an edge of a cube-shaped portion of space.
A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001])
(forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001]
one-dimensional spatial region
a cube-shaped region of space
a sphere-shaped region of space,
A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001])
(forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001]
three-dimensional spatial region
Manhattan Canyon)
a hole in the interior of a portion of cheese
a rabbit hole
an air traffic control region defined in the airspace above an airport
the Grand Canyon
the Piazza San Marco
the cockpit of an aircraft
the hold of a ship
the interior of a kangaroo pouch
the interior of the trunk of your car
the interior of your bedroom
the interior of your office
the interior of your refrigerator
the lumen of your gut
your left nostril (a fiat part – the opening – of your left nasal cavity)
b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002])
(forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002]
site
The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity.
the pdf file on your laptop, the pdf file that is a copy thereof on my laptop
the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule.
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])
(iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001]
generically dependent continuant
the function of a hammer to drive in nails
the function of a heart pacemaker to regulate the beating of a heart through electricity
the function of amylase in saliva to break down starch into sugar
BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc.
A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001])
(forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001]
function
the temporal region during which a process occurs.
BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks).
A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001])
(forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001]
one-dimensional temporal region
a flame
a forest fire
a human being
a hurricane
a photon
a puff of smoke
a sea wave
a tornado
an aggregate of human beings.
an energy wave
an epidemic
the undetached arm of a human being
An independent continuant that is spatially extended whose identity is independent of that of other entities and can be maintained through time.
BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60
BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity.
BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here.
A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002])
Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002])
every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002])
(forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002]
(forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002]
material entity
b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001])
BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions.
BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29
Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions.
Every continuant fiat boundary is located at some spatial region at every time at which it exists
(iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001]
continuant fiat boundary
BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10
immaterial entity
The Equator
all geopolitical boundaries
all lines of latitude and longitude
the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin.
the median sulcus of your tongue
a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001])
(iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001]
one-dimensional continuant fiat boundary
On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels
One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance.
The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on.
b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002])
b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005])
(forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005]
(iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002]
process profile
a marriage bond, an instance of requited love, an obligation between one person and another.
b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001])
(iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001]
relational quality
a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001])
(iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001]
two-dimensional continuant fiat boundary
the geographic North Pole
the point of origin of some spatial coordinate system.
the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet
zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona.
a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001])
(iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001]
zero-dimensional continuant fiat boundary
a temporal region that is occupied by a process boundary
right now
the moment at which a child is born
the moment at which a finger is detached in an industrial accident
the moment of death.
temporal instant.
A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001])
(forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001]
zero-dimensional temporal region
A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001])
history
anatomical entity
connected anatomical structure
material anatomical entity
Disease process is the progression disease in an individual over time. The process begins with the appropriate exposure to or accumulation of factors sufficient for the disease process to begin in a susceptible host. For an infectious disease, the exposure is a microorganism. For cancer, the exposure may be a factor that initiates the process, such as asbestos fibers or components in tobacco smoke (for lung cancer), or one that promotes the process, such as estrogen (for endometrial cancer).
disorder
disease process
病程
ear or mastoid disease process
耳或乳突疾病
atresia DP
闭锁
infectious DP of external ear
外耳感染性疾病
external ear DP
外耳疾病病程
ossification DP
骨化
cellulitis DP
蜂窝织炎病程
otitis externa DP
外耳炎
infectious
感染性
is a major abnormality in the shape of a body part or organ compared to the normal shape of that part.
deformity DP
畸形
cholesteatoma DP
胆脂瘤
pinna fistula DP
耳郭瘘
noninfectious inflammation of external ear DP
外耳非感染性炎症病程
pathological anatomical entity DP
A disease process that has the outcome of the formation of a cyst
cyst DP
囊肿
inflammatory anatomical entity that is located in ear
otitis anatomical entity
耳炎体
fistula DP
granuloma DP
肉芽肿病程
noninflammatory DP
非炎症性疾病病程
tumor DP
肿物
scar DP
瘢痕病程
noninflammatory disorders of the external ear
noninflammatory DP of the external ear
非炎症性外耳疾患
A hernia occurs when an organ pushes through an opening in the muscle or tissue that holds it in place. For example, the intestines may break through a weakened area in the abdominal wall. Hernias are most common in the abdomen, but they can also appear in the upper thigh, belly button, and groin areas. Most hernias aren’t immediately life-threatening, but they don’t go away on their own. Sometimes they can require surgery to prevent potentially dangerous complications.
hernia DP
obstructive
阻塞性
otitis DP
耳炎病程
stenosis DP
狭窄
pseudocyst DP
假性囊肿
感染
infectious DP
感染性疾病过程
immune system DP
免疫系统疾病过程
developed after birth : not congenital or hereditary
获得性
acquired
后天性
other
其他的
specified
特指的
unspecified
非特指的
diseases claasified elsewhere
可分类于他处的疾病
necrotic otitis externa LHPM
坏死性外耳炎 LHPM
syndrome DP
an immune system disease process that undergoes an inflammation process and has output of an inflammatory anatomical entity.
inflammation DP
炎症病程
Aspergillus
曲霉菌
Candida
念珠菌
chemical
化学性
necrosis DP
坏死
severe necrosis DP
严重坏死
diffuse
弥漫性
hemorrhagic
出血性
water
fungus
真菌
Perichondritis is inflammation of the perichondrium, a layer of connective tissue which surrounds cartilage
perichondritis DP
软骨膜炎
chondrodermatitis DP
软骨皮炎
nodularis
结节性
noninfectious
非感染性
skin DP
皮肤疾病
abscess DP
脓肿病程
seborrhoeic
脂溢性
noninflammatory
非炎症性
cauliflower like
菜花样的
environment entity
环境因素
keloid DP
瘢痕瘤病程
exostosis DP
外生骨疣
disease (process) of the circulatory system
hypertensive disease process
hematoma
血肿
角化症
keratosis DP
角化病程
is a closed sac, having a distinct membrane and division compared with the nearby tissue. Hence, it is a cluster of cells that has grouped together to form a sac (not unlike the manner in which water molecules group together, forming a bubble); however, the distinguishing aspect of a cyst is that the cells forming the "shell" of such a sac are distinctly abnormal (in both appearance and behaviour) when compared with all surrounding cells for that given location. It may contain air, fluids, or semi-solid material. A collection of pus is called an abscess, not a cyst. Once formed, sometimes a cyst may resolve on its own. When a cyst fails to resolve, it may need to be removed surgically, but that would depend upon its type and location.
cyst
actinic
光化性
impacted
栓塞性的
chemical entity
化学物质
infectious via bacterium
细菌性
parasitic
寄生性
viral
病毒性
I15.9 is a billable ICD code used to specify a diagnosis of secondary hypertension, unspecified. A 'billable code' is detailed enough to be used to specify a medical diagnosis.
unspecified secondary hypertension DP
A hypertensive disease that shows up with persistently elevated high blood pressure in the arteries, and has no identifiable cause. It does not include those hypertensive diseases complicating pregnancy, childbirth and the puerperium. Note that the essential hypertension affects 95% of hypertensive patients.
essential primary hypertension DP
eczematoid
湿疹样
is a pathological anatomical structures transformed from pathological continuant entities.
On carcinomas and other pathological entities ,Comp Funct Genomics. 2005;6(7-8):379-87. doi: 10.1002/cfg.497.. https://www.ncbi.nlm.nih.gov/pubmed/18629199
pathological anatomical entity
erysipelas DP
丹毒病程
is the abnormal exit of tissue or an organ, such as the bowel, through the wall of the cavity in which it normally resides.[1] Hernias come in a number of different types.[6] Most commonly they involve the abdomen, specifically the groin.[6] Groin hernias are most common of the inguinal type but may also be femoral.[1] Other hernias include hiatus, incisional, and umbilical hernias.[6] Symptoms are present in about 66% of people with groin hernias.[1] This may include pain or discomfort especially with coughing, exercise, or going to the bathroom.[1] Often it gets worse throughout the day and improves when lying down.[1] A bulging area may occur that becomes larger when bearing down.[1] Groin hernias occur more often on the right than left side.[1] The main concern is strangulation, where the blood supply to part of the bowel is blocked.[1] This usually produces severe pain and tenderness of the area.[1] Hiatus or hiatal hernias often result in heartburn but may also cause chest pain or pain with eating.[
hernia
is a form of cell injury which results in the premature death of cells in living tissue by autolysis.
necrotic
坏死性
pinna defect after burn PKPM
烧伤后耳廓缺损 PKPM
is an irreversible condition that occurs when the external portion of the ear is hit and develops a blood clot or other collection of fluid under the perichondrium. This separates the cartilage from the overlying perichondrium that supplies its nutrients, causing it to die and resulting in the formation of fibrous tissue in the overlying skin. As a result, the outer ear becomes permanently swollen and deformed, resembling a cauliflower.
cauliflower ear
菜花耳
abnormality in the shape of a body part or organ
defect
缺损
deformity entity
畸形体
Obsolete class
noninfectious inflammation DP
非感染性炎症病程
sunlight
日光
阳光
mycotic
真菌性
dermatitis DP
皮炎病程
枪伤
acquired from gun shoot
枪伤后
is a destructive and expanding growth consisting of keratinizing squamous epithelium in the middle ear and/or mastoid process. Cholesteatomas are not cancerous as the name may suggest, but can cause significant problems because of their erosive and expansile properties. This can result in the destruction of the bones of the middle ear (ossicles), as well as growth through the base of the skull into the brain. They often become infected and can result in chronically draining ears. Treatment almost always consists of surgical removal.
cholesteatoma entity
胆脂瘤体
is an area of fibrous tissue that replaces normal skin after an injury. Scars result from the biological process of wound repair in the skin, as well as in other organs and tissues of the body. Thus, scarring is a natural part of the healing process. With the exception of very minor lesions, every wound (e.g., after accident, disease, or surgery) results in some degree of scarring. An exception to this are animals with complete regeneration, which regrow tissue without scar formation.
scar entity
瘢痕体
Keloid, also known as keloid disorder and keloidal scar,[1] is the formation of a type of scar which, depending on its maturity, is composed mainly of either type III (early) or type I (late) collagen. It is a result of an overgrowth of granulation tissue (collagen type 3) at the site of a healed skin injury which is then slowly replaced by collagen type 1. Keloids are firm, rubbery lesions or shiny, fibrous nodules, and can vary from pink to the color of the person's skin or red to dark brown in color. A keloid scar is benign and not contagious, but sometimes accompanied by severe itchiness, pain,[2] and changes in texture. In severe cases, it can affect movement of skin. Keloid scars are seen 15 times more frequently in people of sub-Saharan African descent than in people of European descent.
keloid entity
瘢痕瘤体
is a structure formed during inflammation that is found in many diseases. It is a collection of immune cells known as macrophages.[1] Granulomas form when the immune system attempts to wall off substances it perceives as foreign but is unable to eliminate. Such substances include infectious organisms including bacteria and fungi, as well as other materials such as keratin and suture fragments.
granuloma
肉芽肿体
TEST: cellulitis of external ear
外耳蜂窝织炎 TSEM
This term exists in ICD-9 but not ICD-10
malignant essential hypertension DP
is an abnormal connection between two hollow spaces (technically, two epithelialized surfaces), such as blood vessels, intestines, or other hollow organs. Fistulas are usually caused by injury or surgery, but they can also result from an infection or inflammation.[3] Fistulas are generally a disease condition, but they may be surgically created for therapeutic reasons.
fistula
Pseudocysts are like cysts, but lack epithelial or endothelial cells. Initial management consists of general supportive care. Symptoms and complications caused by pseudocysts require surgery. Computed tomography (CT) scans are used for initial imaging of cysts, and endoscopic ultrasounds are used in differentiating between cysts and pseudocysts. Endoscopic drainage is a popular and effective method of treating pseudocysts. This is not to be confused with the so-called "pseudocystic appearance", mainly radiographically, of other lesions, such as Stafne static bone cyst and aneurysmal bone cyst[1] of the jaws.
pseudocyst
is a type of abnormal and excessive growth, called neoplasia, of tissue. The growth of a neoplasm is uncoordinated with that of the normal surrounding tissue, and it persists growing abnormally, even if the original trigger is removed.[1][2][3] This abnormal growth usually (but not always) forms a mass.[4] When it forms a mass, it may be called a tumor.
neoplasm
tumor
inflammatory
炎症性
is a growth of keratin on the skin or on mucous membranes stemming from keratinocytes, the prominent cell type in the epidermis.
角质化体
keratosis entity
角化体
is a condition in which an orifice or passage in the body is (usually abnormally) closed or absent. Examples of atresia include: Biliary atresia, a condition in newborns in which the common bile duct between the liver and the small intestine is blocked or absent.
atresia entity
闭锁体
An exostosis, also known as bone spur, is the formation of new bone on the surface of a bone.[1] Exostoses can cause chronic pain ranging from mild to debilitatingly severe, depending on the shape, size, and location of the lesion. It is most commonly found in places like the ribs, where small bone growths form, but sometimes larger growths can grow on places like the ankles, knees, shoulders, elbows and hips. Very rarely are they on the skull.
exostosis
benign essential hypertension DP
inflammatory anatomical entity that is located in a cellulite
cellulitis anatomical entity
蜂窝织炎体
stenosis
狭窄体
is an acute infection typically with a skin rash, usually on any of the legs and toes, face, arms, and fingers.[1] It is an infection of the upper dermis and superficial lymphatics, usually caused by beta-hemolytic group A Streptococcus bacteria on scratches or otherwise infected areas.[2] Erysipelas is more superficial than cellulitis, and is typically more raised and demarcated.[1] The term is from Greek ἐρυσίπελας, meaning "red skin".
erysipelas
丹毒
abscess of external ear DP
外耳脓肿病程
ossification entity
骨化体
a physical pathological anatomic entity that is a result of an inflammation process
炎症体
inflammatory anatomical entity
发炎体
is a collection of pus that has built up within the tissue of the body.[1] Signs and symptoms of abscesses include redness, pain, warmth, and swelling.[1] The swelling may feel fluid-filled when pressed.[1] The area of redness often extends beyond the swelling.[6] Carbuncles and boils are types of abscess that often involve hair follicles, with carbuncles being larger.
abscess
脓肿
is a cluster of boils caused by bacterial infection, most commonly with Staphylococcus aureus or Streptococcus pyogenes.[1] The presence of a carbuncle is a sign that the immune system is active and fighting the infection.[2] The infection is contagious and may spread to other areas of the body, or other people; those living in the same residence may develop carbuncles at the same time.[3] In the early 21st century, infection involving methicillin-resistant staphylococcus aureus (MRSA) has become more common.
carbuncle
is a deep folliculitis, infection of the hair follicle. It is most commonly caused by infection by the bacterium Staphylococcus aureus, resulting in a painful swollen area on the skin caused by an accumulation of pus and dead tissue.[1] Boils which are expanded are basically pus-filled nodules.[2][verification needed] Individual boils clustered together are called carbuncles.[3] Most human infections are caused by coagulase-positive S. aureus strains, notable for the bacteria's ability to produce coagulase, an enzyme that can clot blood. Almost any organ system can be infected by S. aureus.
boil
furuncle
mycosis DP
真菌病
a necrotic object
necrosis entity
坏死体
external acoustic meatus atresia after burn JYPM
烧伤后外耳道闭锁 JYPM
TEST: cholesteatoma of external auditory canal
外耳道胆脂瘤
inflammatory anatomical entity that is located in the skin of a cartilage tissue
chondrodermatitis anatomical entity
软骨皮炎体
inflammatiory anatomical entity in the membrane of cartilage tissue
perichondritis anatomical entity
软骨膜炎体
acquired from injury
因外伤导致的
after burn
烧伤后
acquired from burn
烧伤所致
砍伤后
acquired from knife
刀伤后
infectious disorder in pinna PKDM
耳廓感染 PKDM
dermis and subcutaneous tissues
皮及皮下组织
external ear furuncle PKPM
外耳道疖 PKPM
inflammatory anatomical entity that is located in skin
dermatitis anatomical entity
皮炎体
granuloma in pinna PKPM
耳廓肉芽肿 PKPM
external ear carbuncle DP
外耳痈病程
external ear furuncle DP
外耳疖病程
infectious via virus
malignant disease profile
belign disease profile
A hypertensive disease that is caused by an identifiable underlying primary cause
secondary hypertension DP
disease (process) in the respiratory system
pneumonia due to pathogen
Inflammation of the lung that is caused by viral infection; causes air sacs in lungs to fill up with fluid.
viral pneumonia
influenza pneumonia
an infection of your lungs caused by certain bacteria.
Bacterial pneumonia, not elsewhere classified
bacterial pneumonia
an infection that inflames the air sacs in one or both lungs. Caused by Streptococcus pneumoniae bacteria
Pneumonia due to Streptococcus pneumoniae
COVID-19 pneumonia
a mild to severe respiratory illness that is caused by a coronavirus
COVID-19, virus not identified
clinically-epidemiologically diagnosied COVID-19
high blood pressure after a surgical procedure
postprocedural hypertension DP
disease primary
A disease profile that does not have a known secondary cause
primary disease profile
A disease profile that is caused by another medical condition
secondary disease profile
disease profile
acute disease profile
chronic disease profile
a common sickness combined with a lung infection caused by an unspecified pathogen.
Influenza due to unidentified influenza virus with pneumonia
pneumonia attacks the respiratory system caused by SARS-CoV-2
Pneumonia due to SARS-associated coronavirus
Heart conditions caused by high blood pressure
Hypertensive heart disease without heart failure
hypertensive heart disease process without heart failure
pneumonia attacks the respiratory system. Contagious and hard to treat.
other viral pneumonia
influenza due to pathogen
Also called coronary artery disease, describes heart problems caused by narrowed arteries that supply blood to the heart.
ischemic heart DP
a highly contagious viral infection of the respiratory passages causing fever and severe aching, often occuring in epidemics.
Influenza due to other identified influenza virus with pneumonia
influenza due other identified influenza virus with pneumonia
acute or chronic inflammation of the renal tubules and interstitium. Acute interstitial nephritis is commonly caused by allergic reactions to drugs, but infection or systemic disease may also precipitate the disease.
renal tubulo-interstitial disease processes
A common viral infection that can be deadly, especially in high-risk groups.
Influenza due to unidentified influenza virus with other respiratory manisfestations
Influenza due to unidentified influenza virus with other manisfestations
heart problems caused by narrowed heart arteries. When arteries are narrowed, less blood and oxygen reaches the heart muscle. This is also called coronary artery disease and coronary heart disease. This can ultimately lead to heart attack.
chronic ischemic heart DP
Atherosclerotic heart disease of native coronary artery
atherosclerotic heart DP of native coronary artery
ischemic disease profile
A highly contagious, common viral infection of the respiratory passages causing fever and severe aching
lung inflammation caused by bacterial infection, in which air sacs fill with pus
pneumonia due to staphylococcus
atherosclerotic disease profile
An inflammatory attack of the pharynx and nassal cavities. Minor and is a common contagious throat disease.
acute nasopharyngitis (common cold)
Inflammation of the pharynx, which is in the back of the throat. Commonly referred to as "sore throat"
acute pharyngitis, unspecified
upper respiratory system is infected and parts will become inflamed or damaged.
Acute upper respiratory infection, unspecified
Pneumonia due to other aerobic Gram-negative bacteria
Pneumonia due to other specified bacteria
inflammation of the lung that is caused by bacterial infections
unspecified bacterial pneumonia
bacterial
pneumonia caused by other viral diseases
pneumonia in viral diseases classified elsewhere
pneumonia in other diseases classified elsewhere
Thickening and loss of elasticity of the coronary arteries, leading to progressive arterial insufficiency (coronary disease).
Atherosclerotic heart disease of native coronary artery without angina pectoris
a lung infection that inflames and infects the aveoli
bronchopneumonia
Documented history of previous myocardial infarction, a sudden and sometimes fatal occurrence of coronary thrombosis, typically resulting in the death of part of a heart muscle. Also known as heart attack.
old myocardial infarction DP
a form of pneumonia characterized by inflammatory exudate within the intra-alveolar space
lobar pneumonia
A lung infection caused by an unspecified pathogen
other pneumonia
pneumonia, unspecified organism
lower respiratoy tract infection that causes reversible bronchia inflammation
acute bronchitis
contagious infection of upper respiratory tract
acute upper respiratory infections
contagious infection of lower respiratory tract
Other acute lower respiratory infections
acute infection that affects the lower respiratory tract.
unspecified acute lower respiratory infection
unspecified acute lower respiratory tract infection
chronic infection of lower respiratory tract
chronic lower respiratory diseases
a chronic pulmonary disease that obstructs bloodlflow
centrilobular emphysema
a chronic inflammatory lung disease that causes obstructed airflow from the lungs
Other chronic obstructive pulmonsry disease
other chronic obstructive pulmonary disease
Chronic obstructive pulmonary disease with (acute) lower respiratory infection
chronic obstructive pulmonary disease with acute lower respiratory infection
a chronic inflammatory lung disease that causes airway inflammation and reduced air flow from exacerbations
chronic obstructive pulmonary disease with acute exacerbation
other specified chronic obstructive pulmonary disease
a chronic inflammatory lung disease that causes permanent damage to the lungs, making it hard to breathe
chronic obstructive pulmonary disease, unspecified
myocardial disease profile
a chronic disease in which the bronchial airways in the lungs become narrowed and swollen, making it difficult to breathe
asthma
Bronchial airways in the lungs become narrowed and swollen, making it hard to breathe
uncomplicated asthma
a condition where the bronchial tubes of the lungs are permanently damaged, widened, and thickened
bronchiectasis
conditions of the lng caused by outside agents
lung disease processes due to external agents
Inflammation of the lung tissue; noninfectious causes of lung inflammation
Pneumonitis due to inhalation of food and vomit
respiratory diseases affecting the interstitum, a fluid-filled space between a structural barrier (ie cell wall, skin) and internal structures (ie organs, muscles).
Other respiratory diseases principally affecting the interstitum
other respiratory diseases affecting the interstitum
fluids fill up the lung's air sacs, causing the lung to not function properly
acute respiratory distress syndrome
extravascular accumulation of fluid in the pulmonary tissue and air sacs
pulmonary edema
Other interstitial pulmonary diseases with fibrosis
Interstitial pulmonary disease, unspecified
diseases affecting the pleura, a membrane that lines the thorax
other diseases of the pleura
increased amounts of fluid in pleural cavity
Pleural effusion, not elsewhere classified
increased amounts of fluid between the thin layers of tissue lining the lung and wall of the chest cavity
pleural effusion in conditions classified elsewhere
the heart's ability to pump blood is decreased because the left ventricle is weak. This is caused by a lack of blood supply to the heart muscle caused by coronary artery disease and heart attacks.
ischemic cardiomyopathy DP
diseases affecting the respiratory system
Other diseases of the respiratory system
occurs when fluid builds up in air sacs of lungs
acute respiratory failure
acute respiratory failure, unsure if it is hypoxemic (not enough oxygen, normal CO2 levels) or hypercapnic (too much CO2, oxygen normal or too low)
acute respiratory failure, unspecified whether with hypoxia or hypercapnia
acute respiratory failure where a portion of the body is hypoxemic (not enough oxygen, normal CO2 levels)
acute respiratory failure with hypoxia
respiratory system is unable to function properly; is long-term (chronic)
chronic respiratory failure
respiratory system is unable to function properly; is long-term (chronic) or short-term (acute)
acute and chronic respiratory failure
respiratory system is unable to function properly; is long-term (chronic) or short-term (acute); can be with hypoxia (too little oxygen) or hypercapnia (too much CO2, normal/low oxygen)
acute and chronic respiratory failure, unspecified whether with hypoxia or hypercapnia
respiratory system has been attacked, used to specify symptoms
respiratory failure, unspecified
respiratory system has been damaged, unspecified whether there is too much CO2 (hypercapnia) or too little oxygen (hypoxmia) in the body
Respiratory failure, unspecified whether with hypoxia or hypercapnia
respiratory failure, unspecified whether with hypoxmia or hypercapnia
when the alveoli (helps exchange oxygen in air for CO2), don't fill with air
atelectasis
disorders affecting the lungs, ie asthma, COPD, influenza, etc.
other disorders of the lung
conditions affecting the respiratory system
other sepcified respiratory disorders
when the blood vessels that carry oxygen and nutrients from your heart to the rest of your body (arteries) become thick and stiff — sometimes restricting blood flow to your organs and tissues.
coronary atherosclerosis DP due to lipid rich plaque
Ischemic heart disease is the term given to heart problems caused by narrowed heart (coronary) arteries that supply blood to the heart muscle. It's most often it is caused by buildup of plaque, called atherosclerosis.
Chronic ischemic heart disease, unspecified
chronic ischemic heart DP, unspecified
the enlargement and failure of the right ventricle of the heart as a response to increased vascular resistance or high blood pressure in the lungs.
Pulmonary heart disease and diseases of pulmonary circulation
pulmonary heart DP and disease processes of pulmonary circulation
A blockage of an artery in the lungs by a foreign substance
pulmonary embolism without acute cor pulmonale
pulmonary embolism DP without acute cor pulmonale
A disorder characterized by cessation of the pumping function of the heart.
cardiac arrest DP
cardiac arrest, cause unspecified
abnormally fast heartbeat. It's a broad term that includes many forms of heart rhythm problems
supraventricular tachycardia
In atrial fibrillation, the atria beat irregularly. In atrial flutter, the atria beat regularly, but faster than usual and more often than the ventricles
atrial fibrillation and flutter DP
atrial disease profile
supraventricular disease profile
a rapid, erratic heart rate begins suddenly and then stops on its own within 7 days
paroxysmal atrial fibrillation DP
refers to AF that occurs for longer than 7 days and ends spontaneously or with treatment
persistent atrial fibrillation DP
a type of heart arrhythmia that causes the top chambers of your heart, the atria, to quiver and beat irregularly. Lasts over a week.
chronic atrial fibrillation DP
A problem with the rate or rhythm of your heartbeat. It means that your heart beats too quickly, too slowly, or with an irregular pattern
cardiac arrhythmia DP, unspecified
very fast electrical discharge patterns that make the atria contract very rapidly, causing them to contract faster and less efficiently than normal.
Unspecified atrial fibrillation and atrial flutter
unspecified atrial fibrillation and atrial flutter DP
a common electrocardiographic (ECG) abnormality seen in patients whose normal cardiac conduction down both anterior and posterior left fascicles of the His-Purkinje system is compromised.
left bundle-branch block DP, unspecified
Electrical impulses that cause your heart to beat originate in the upper right chamber of the heart and travel to the lower chambers. In bundle branch block, the pathway that these impulses travel on is delayed or blocked.
Atrioventricular and left bundle-branch block
atrioventricular and left bundle-branch block DP
A disorder characterized by the inability of the heart to pump blood at an adequate volume to meet tissue metabolic requirements, or, the ability to do so only at an elevation in the filling pressure.
heart failure DP
atrioventricular disease profile
heart failure, unspecified
An episode of acute neurological dysfunction presumed to be caused by ischemia or hemorrhage, persisting ≥24 hours or until death
Stroke, not specified as haemorrhage or infarction
stroke DP, not specified as haemorrhage or infarction
residual effects or conditions produced after the acute phase of a stroke
Sequelae of stroke, not specified as haemorrhage or infarction
sequelae DP of stroke, not specified as haemorrhage or infarction
When plaque (fatty deposits) clogs your arteries
Atherosclerosis of native arteries of extremities with gangrene
atherosclerosis DP of native arteries of extremities with gangrene
A thickening and loss of elasticity of the walls of arteries that occurs with formation of atherosclerotic plaques within the arterial intima.
atherosclerosis DP
Diseases of the lymphatic system, a network of tissues and organs.
Diseases of veins, lymphatic vessels and lymph nodes, not elsewhere classified
disease processes of veins, lymphatic vessels and lymph nodes
a condition that occurs when the venous wall and/or valves in the leg veins are not working effectively, making it difficult for blood to return to the heart from the legs.
Venous insufficiency (chronic) (peripheral)
venous insufficiency DP
A disorder characterized by a blood pressure that is below the normal expected for an individual in a given environment.
hypotension DP
A significant drop in blood pressure after assuming a standing position
orthostatic hypotension DP
A decrease in systemic blood pressure below accepted low values (pressures less than 90/60 are recognized as hypotensive)
other hypotension DP
hypotension DP, unspecified
any cardiac complications occurring in the postanesthetic care unit (PACU)
Other postprocedural complications and disorders of the circulatory system, not elsewhere classified
Other postprocedural complications and disorders of the circulatory system
enzymes that confer resistance to most beta-lactam antibiotics, including penicillins, cephalosporins, and the monobactam aztreonam
Extended spectrum betalactamase (ESBL) resistance
antibiotic resistance
bacterial disease (process)
a type of common virus that infects humans, typically leading to an upper respiratory infection
coronavirus infection DP, unspecified
Genitourinary disease involves disorders of the genital and urinary organs. These organs are involved in reproduction and urination
disease (process) of the genitourinary system
Erysipelas is a relatively common bacterial infection of the superficial layer of the skin (upper dermis), extending to the superficial lymphatic vessels within the skin, characterized by a raised, well-defined, tender, bright red rash, typically on the face or legs, but which can occur anywhere on the skin. It is a form of cellulitis and is potentially serious. Erysipelas is usually caused by the bacteria Streptococcus pyogenes.
Erysipelas
a bacterial infection causing inflammation of the kidneys and is one of the most common diseases of the kidney.
acute pyelonephritis DP
A disorder characterized by the acute loss of renal function
acute kidney failure DP
Acute kidney failure and chronic kidney disease
acute kidney failure or chronic kidney DP
Acute kidney failure resulting from destruction of epithelial cells of the kidney tubules.
Acute kidney failure with tubular necrosis
acute kidney failure with tubular necrosis DP
kidney is no longer able to filter blood.
N17.8 is a billable code used to specify a medical diagnosis of other acute kidney failure. The code is valid for the year 2020 for the submission of HIPAA-covered transactions. The ICD-10-CM code N17.8 might also be used to specify conditions or terms like acute renal failure due to ischemia or ischemic nephropathy or post-renal renal failure.
other acute kidney failure DP
kidney(s)'s functions are compromised. This will be a short term problem
acute kidney failure DP, unspecified
A disorder characterized by gradual and usually permanent loss of kidney function resulting in renal failure.
chronic kidney disease DP
A disease that causes moderate kidney damage. A person is more likely to develop complications of kidney disease such as high blood pressure, anemia, and/or early bone disease.
Chronic kidney disease, stage 3 (moderate)
chronic kidney DP, stage 3
kidneys are moderately or severely damaged and are not working as they should. Stage 4 kidney disease should be taken very seriously – it is the last stage before kidney failure.
Chronic kidney disease, stage 4 (severe)
chronic kidney DP, stage 4
chronic kidney DP, stage 5
end stage renal DP
chronic kidney DP unspecified
A clinical syndrome associated with the retention of renal waste products or uremic toxins in the blood. It is usually the result of renal insufficiency.
unspecified kidney failure DP
the unirary tract is infected and cannot function properly
urinary tract infection, site not specified
urinary tract infection DP
A benign (noncancerous) condition in which an overgrowth of prostate tissue pushes against the urethra and the bladder, blocking the flow of urine.
benign prostatic hyperplasia DP
when your prostate gland becomes suddenly inflamed
acute prostatitis DP
Diseases that affect the male reproductive and genital organs
DP of male genital organs
Anemia caused by low iron intake, inefficient iron absorption in the gastrointestinal tract, or chronic blood loss.
iron deficiency anemia DP
caused by a shortage of iron in your body.
other iron deficiency anemia DP
Iron deficiency anemia is a common type of anemia — a condition in which blood lacks adequate healthy red blood cells.
iron deficiency anemia, unspecified
It occurs when you inherit copies of the hemoglobin S gene from both parents
Hb-SS DP with crisis
a condition in which a person quickly loses a large volume of circulating hemoglobin.
acute posthemorrhagic anemia DP
failure of the bone marrow to produce blood
Aplastic and other anemias and other bone marrow failure syndromes
other anemias and bone marrow failure syndromes
a condition marked by a deficiency of red blood cells or of hemoglobin in the blood
Anemia in other chronic diseases classified elsewhere
anemia DP in other chronic diseases classified elsewhere
decrease in the amount of red blood cells in the patient's blood stream
other specified anemia DP
patient lacks enough red blood cells to carry oxygen to the body's tissues
anemia DP, unspecified
a bleeding disorder caused by circulating anticoagulants (autoantibodies that neutralize specific clotting)
Hemorrhagic disorder due to circulating anticoagulants
hemorrhagic disorder DP due to circulating anticoagulants
Hemorrhagic diseases are caused by bleeding, or they result in bleeding
Coagulation defects, purpura and other hemorrhagic conditions
abnormally low levels of thrombocytes, also known as platelets, in the blood.
secondary thrombocytopenia DP
Thrombocytopenia is a condition characterized by abnormally low levels of thrombocytes, also known as platelets, in the blood.
thrombocytopenia DP, unspecified
People with neutropenia have an unusually low number of cells called neutrophils. Neutrophils are cells in your immune system that attack bacteria and other organisms when they invade your body
neutropenia DP
white blood cell disorders effect the functionallity of the body's immune response
Other specified disorders of white blood cells
low level of lymphocytes, which are white blood cells
lymphocytopenia
A disorder resulting from an abnormality in the immune system
Disorder involving the immune mechanism, unspecified
a small class of medical conditions affecting the nervous system.
disease (process) of the nervous system
Deficiency of a coagulation factor (proteins in the blood that help control bleeding) that is not caused by genetic alterations. Causes include vitamin k deficiency, amyloidosis, and severe liver disease.
acquired coagulation factor deficiency
a brain disorder that leads to shaking, stiffness, and difficulty with walking, balance, and coordination.
parkinson's disease process
A degenerative disease of the brain characterized by the insidious onset of dementia. Impairment of memory, judgment, attention span, and problem solving skills are followed by severe apraxias and a global loss of cognitive abilities.
alzheimer's disease process
characterized by clinical symptoms and signs of AD that become apparent after the age of 60.
alzheimer's DP with late onset
alzheimer's DP, unspecified
a neurological disorder marked by sudden recurrent episodes of sensory disturbance, loss of consciousness, or convulsions, associated with abnormal electrical activity in the brain.
epilepsy, unspecified
A disorder characterized by cessation of breathing for short periods during sleep.
sleep apnea DP
A disorder characterized by recurrent apneas during sleep despite persistent respiratory efforts. It is due to upper airway obstruction.
Obstructive sleep apnea (adult) (pediatric)
obstructive sleep apnea DP
a neurological disorder that results in diabetes
diabetic polyneuropathy DP
any health problem that occurs in the digestive tract.
disease (process) of the digestive system
A chronic disorder characterized by reflux of the gastric and/or duodenal contents into the distal esophagus. It is usually caused by incompetence of the lower esophageal sphincter.
Gastro-esophageal reflux disease without esophagitis
gastro-esophageal reflux disease process without esophagitis
An inflammatory disorder that affects the upper and lower gastrointestinal tract; a disorder characterized by inflammation of the colon.
Noninfective gastroenteritis and colitis, unspecified
noninfective gastroenteritis and colitis DP, unspecified
A condition in which stool becomes hard, dry, and difficult to pass, and bowel movements don't happen very often.
constipation DP
A complication of type 2 diabetes, involving extremely high blood sugar (glucose) level without the presence of ketones.
HHS (Hyperglycemic hyperosmolar syndrome)
type 2 diabetes mellitus with hyperosmolarity
infrequent bowel movements or difficult passage of stools that persists for several weeks or longer.
other constipation DP
a problem with how your stomach and bowels function or work
functional intestinal disorders
loose stool consistency and chronicity and absence of coexisting irritable bowel syndrome
functional diarrhea
bleeding in the rectum caused by various things such as infections, proctitis, etc.
hemorrhage of anus and rectum DP
liver is damaged which makes it hard to digest food.
toxic liver disease with cholestasis DP
acute and subacute hepatic failure DP
Abnormally dark tarry feces containing blood (usually from gastrointestinal bleeding)
melena DP
disorders caused by organisms — such as bacteria, viruses, fungi or parasites.
infectious and parasitic disease processes
Certain infectious and parasitic diseases
infectious and parasitic disease (process)
A viral or bacterial infectious process affecting the large intestine.
Infectious gastroenteritis and colitis, unspecified
infectious gastroenteritis and colitis DP, unspecified
the presence of bacteria or their toxins in the blood or tissues.
sepsis DP, unspecified organism
A general term for diseases produced by viruses.
viral infection DP of unspecified site
viral infection DP, unspecified
E. coli are usually harmless bacteria that help with digestion, but they can be strained and cause diarreha or worse
Escherichia coli [E. coli ] as the cause of diseases classified elsewhere.
E. coli as the cause of diseases classified elsewhere
bacteria that infect the body cause diseases
Other specified bacterial agents as the cause of diseases classified elsewhere
other bacterial agents as the cause of diseases classified elsewhere
viruses that infect the body cause diseases
Viral agents as the cause of diseases classified elsewhere
viral agents as the cause of diseases
Coronavirus as the cause of diseases classified elsewhere
coronavirus as the cause of diseases
Other coronavirus as the cause of diseases classified elsewhere
other coronavirus as the cause of diseases
Other viral agents as the cause of diseases classified elsewhere
other viral agents as the cause of diseases
Infectious diseases are disorders caused by organisms — such as bacteria, viruses, fungi or parasites.
Other and unspecified infectious diseases
An abnormal mass of tissue that results when cells divide more than they should or do not die when they should.
neoplasm DP
a malignant lung tumor characterized by uncontrolled cell growth in tissues of the lung.
Malignant neoplasm of unspecified part of bronchus or lung
malignant neoplasm DP of bronchus or lung
A primary or metastatic malignant neoplasm involving the breast.
malignant neoplasm DP of breast
A primary or metastatic malignant tumor involving the prostate gland.
malignant neoplasm DP of prostate
Cancer that has spread from the original (primary) tumor to the liver.
Secondary malignant neoplasm of liver and intrahepatic bile duct
secondary malignant neoplasm of liver and intrahepatic bile duct DP
Cancer that has spread from the original (primary) tumor to the bone.
Secondary malignant neoplasm of bone and bone marrow
secondary malignant neoplasm of bone and bone marrow DP
A malignancy of mature plasma cells engaging in monoclonal immunoglobulin production.
multiple myeloma DP
Diseases and conditions affecting the eyes
disease (process) of the eye and adnexa
a common eye disorder among people over 50. It causes blurred or reduced central vision, due to thinning of the macula
Degeneration of macula and posterior pole
Retinal disorders in diseases classified elsewhere
A disorder characterized by an increase in pressure in the eyeball due to obstruction of the aqueous humor outflow.
unspecified glaucoma
Diseases and conditions affecting the skin and subcutaneous tissue
Other disorders of the skin and subcutaneous tissue
disorders of the skin and subcutaneous tissue
are injuries to skin and underlying tissue resulting from prolonged pressure on the skinv
pressure ulcer of back
a defect in the skin below the level of knee persisting for more than six weeks and shows no tendency to heal after three or more months.
non-pressure chronic ulcer of lower limb, not elsewhere classified
Diseases and conditions affecting the muskoskeletal system and connective tissue
Diseases of the musculoskeletal system and connective tissue
disease (process) of the musculoskeletal system and connective tissue
Acute or chronic pain in the lumbar or sacral regions
low back pain DP
Muscle disorders that cause weakness, pain or even paralysis
other specified disorders of muscle
A chronic disorder of unknown etiology characterized by pain, stiffness, and tenderness in the muscles
myalgia DP
muscle aches and pain, which can involve ligaments, tendons and fascia, the soft tissues that connect muscles, bones and organs
myalgia, unspecified site DP
Osteoporosis is the most common bone disease and is caused by the thinning of the bones
Age-related osteoporosis with current pathological fracture
a viral respiratory illness caused by a coronavirus called SARS-associated coronavirus (SARS-CoV).
Severe acute respiratory syndrome, unspecified
when you have symptoms of both asthma and chronic obstructive pulmonary disease
mixed asthma DP
injury/other consequences caused by external sources
Injury, poisoning and certain other consequences of external causes
A violent jar or shock, or the condition which results from such an injury.
concussion DP
Fractures of the short, constricted portion of the thigh bone between the femur head and the trochanters.
fracture of head and neck of femur DP
there is a need for specific instruction for the patient
Complications of procedures, not elsewhere classified
complications of procedures
an event which results in a person coming to rest inadvertently on the ground or floor or other lower level
slipping, tripping, stumbling and falls
unspecified fall
alcoholic cirrhosis DP of liver
An ulceration caused by prolonged pressure on the skin and tissues when one stays in one position for a long period of time, such as lying in bed.
pressure ulcer
A type of permanent damage to muscles and nerves that results from prolonged lack blood flow to those tissues. It is characterized by shortening and stiffening of the muscles.
traumatic ischemia DP of muscle
tuberculous infection caused by resistance to at least isoniazid and rifampin, the two most potent TB drugs.
Primary multidrug resistant tuberculosis
to descend freely by the force of gravity
fall from one level to another
symptoms, signs, abnormal results of clinical or other investigative procedures, and ill-defined conditions regarding which no diagnosis classifiable elsewhere is recorded.
Symptoms, signs and abnormal clinical and laboratory findings, not elsewhere classified
symptoms, signs and abnormal clinical and laboratory findings
A disorder characterized by laboratory test results that indicate blood in the urine.
hematuria DP
anosmia DP
Sepsis associated with organ dysfunction distant from the site of infection.
severe sepsis DP without septic shock
Persons encountering health services for examinations, Genetic carrier and genetic susceptibility to disease, Resistance to antimicrobial drugs, etc
Factors influencing health status and contact with health services
Encounter for general adult medical examination
a procedure in which blood is collected, part of the blood such as platelets or white blood cells is taken out, and the rest of the blood is returned to the donor.
Encounter for therapeutic drug level monitoring
Problem related to social environment, unspecified
problem related to social environment
long term (current) use of aspirin
when immune system reacts to a foreign substance or food that doesn't cause a reaction in most people
Allergy status to other antibiotic agents status
inflammation of the glomeruli, which are structures in your kidneys that are made up of tiny blood vessels. These knots of vessels help filter your blood and remove excess fluids. If your glomeruli are damaged, your kidneys will stop working properly, and you can go into kidney failure
glomerular disorders in diseases classified elsewhere
glomerular disorders
middle ear or mastoid DP
inner ear DP
Intraoperative and postprocedural complications and disorders of ear and mastoid process, not elsewhere classified
Conductive and sensorineural hearing loss
hearing loss
Unspecified hearing loss, unspecified ear
interoperative and postprocedural ear and mastoid disease process
Loss of memory, language, problem-solving and other thinking abilities in an Alzheimer's patient
dementia in Alzheimer’s disease, atypical or mixed type
Chondritis and perichondritis of external ear
chondritis or perichondritis of external ear
Nonsuppurative otitis media DP
Hypertension (Elevated blood pressure) in patients with stage 5 kidney disease or end stage renal disease
hypertensive chronic kidney disease with stage 5 chronic kidney disease or end stage renal disease
Presence of a blockage in one of the pulmonary arteries in the lungs in patients with acute cor pulmonale (acute right heart failure)
pulmonary embolism with acute cor pulmonale
Backflow of blood from the left ventricle into the left atrium due to imperfect closure of the mitral valve
nonrheumatic mitral (valve) insufficiency
upper respiratory system is infected in multiple sites and parts will become inflamed or damaged.
acute upper respiratory infections of multiple sites
Pneumonia (infection that inflames the air sacs in the lungs) caused by Klebsiella pneumoniae bacteria
pneumonia due to Klebsiella pneumoniae
Pneumonia (infection that inflames the air sacs in the lungs) caused by Pseudomonas bacteria
pneumonia due to Pseudomonas
A condition of the lung characterized by increase beyond normal in the size of air spaces distal to the terminal bronchioles, either from dilatation of the alveoli or from destruction of their walls.
emphysema, unspecified
Injury to elbow skin and underlying tissue resulting from prolonged pressure on skin around elbow
pressure ulcer of elbow
The existence of type 2 diabetes mellitus in pregnant patients or patients who had a child within the last 6 weeks
pre-existing type 2 diabetes mellitus, in pregnancy, childbirth and the puerperium
Lymph nodes in one particular area of the body swell up
localized enlarged lymph nodes
A disorder characterized by bleeding from the nose
epistaxis
Abnormal buildup of fluid in the abdomen
ascites
Death in circumstances where the body of the deceased was found and no cause could be discovered
unattended death
Infection in the body found after a procedure
infection following a procedure
Presence of implant into the urethra to help control urine leakage (foley catheter, ureteral stent, pessary, etc).
presence of urogenital implants
presence of other bone and tendon implants
Inflammation of the liver caused by hepatitis c virus lasting six months or more
chronic viral hepatitis C
Infection of the mucous membranes of the mouth by a fungus of the genus candida
candidal stomatitis
Cancer that has spread from the original tumor to the lung
secondary malignant neoplasm of lung
Iron deficiency anemia (a condition in which blood lacks adequate healthy blood cells) caused by chronic blood loss
iron deficiency anemia secondary to blood loss (chronic)
The prescense of diabetic ketoacidosis (body produces high levels of ketones and not enough insulin) in type 1 diabetic patients
type 1 diabetes mellitus with ketoacidosis
Overweight and obesity caused by miscellaneous disorders
other obesity
Delirium of mixed origin, postoperative delirium
other dilirum
An abrupt change in the brain that causes mental confusion and emotional disruption with unspecified cause
delirium, unspecified
Personality/behavioral disorders caused by physiological disorder
other personality and behavioral disorders due to known physiological condition
A mental disorder in which a person has trouble telling the difference between real and unreal experiences, thinking logically, and behaving normally in social situations.
schizophrenia, unspecified
A disorder of the nervous system marked by weakness, numbness, a loss of muscle coordination, and problems with vision, speech, and bladder control
multiple sclerosis
Paralysis of one side of the body with unspecified cause
hemiplegia, unspecified
An infection that inflames the air sacs in one or both lungs caused by Escherichia coli bacteria
pneumonia due to Escherichia coli
Nonallergic asthma (a condition in which your airways narrow and swell)
nonallergic asthma
Asthma symptoms (airway swelling) occuring fewer than three times a week
mild intermittent asthma, uncomplicated
Unspecified late stage scarring of the liver
other and unspecified cirrhosis of liver
A chronic inflammation of the tear and salivary glands, often accompanied by rheumatoid arthritis and the presence of autoantibodies in the blood
sicca syndrome [Sjögren]
muscle wasting and atrophy, not elsewhere classified, unspecified site
other congenital malformations of tongue
other chest pain
Unspecified fracture of the proximal femur between the cervical region and the shaft
unspecified trochanteric fracture of femur
encounter for prophylactic immunotherapy
inadequate family support
Continous supervision needed, problems related to care provider dependency
need for continuous supervision
Personal history of exposure to radiation
personal history of irradiation
presence of prosthetic heart valve
Patient was exposed to SARS-associated coronavirus
exposure to SARS-associated coronavirus
Diseases in body caused by Staphylococcus aureus bacteria
Staphylococcus aureus as the cause of diseases classified elsewhere
Secondary abnormal growth of cells in the pleural space (the cavity between the lungs and chest wall that contains pleural fluid)
secondary malignant neoplasm of pleura
A disease characterized by the growth of tiny collections of inflammatory cells (granulomas) in any part of your body
sarcoidosis of other sites
An unspecified condition in which the adrenal glands do not produce adequate amounts of steroid hormones (cortisol)
other and unspecified adrenocortical insufficiency
A condition caused by not getting enough calories or the right amount of key nutrients, such as vitamins and minerals, that are needed for health.
unspecified protein-calorie malnutrition
A nutritional condition produced by a deficiency of B group vitamins (folic acid, B-12) in the diet
deficiency of other specified B group vitamins
Disorders in the processing, absorption, transport, storage, and utilization of phosphorus in the body
disorders of phosphorus metabolism and phosphatases
Unspecified loss of memory, language,and other thinking abilities in a patient with Alzheimer's
dementia in Alzheimer disease, unspecified
Single major depressive disorder episode (a depressed mood for two weeks or more)
major depressive disorder, single episode, moderate
Recurrent major depressive disorder episodes (a depressed mood for two weeks or more)
major depressive disorder, recurrent, unspecified
A brief stroke (from a few minutes to an hour) of cerebral dysfunction when the blood supply to this part of the brain is blocked
transient cerebral ischemic attack, unspecified
A neuromuscular condition of spasticity that results in the muscles on one side of the body to be in a constant state of contraction
spastic hemiplegia
Failure of adequate output by the left ventricle
left ventricular failure, unspecified
The result of thickening and hardening of the walls of the arteries in the brain
cerebral atherosclerosis
An infection that inflames the air sacs in one or both lungs caused by Parainfluenza virus
parainfluenza virus pneumonia
Respiratory tract infections not specified as acute, chronic, lower, or upper
respiratory infection, not elsewhere classified
Injury to hip skin and underlying tissue resulting from prolonged pressure on skin around hip
pressure ulcer of hip
When water content of the body cartilage increases and the protein makeup of cartilage degenerates
polyosteoarthritis, unspecified
irritability and anger
Anarthria is a severe form of dysarthria. Dysarthria is a motor speech disorder that occurs when someone can't coordinate or control the muscles used for speaking.
dysarthria and anarthria
Uncommon severe weight loss for an unspecified cause
abnormal weight loss
This describes the circumstance causing an injury, not the nature of the injury. The injury in this case is caused by the lack of administration of surgical or medical care.
nonadministration of surgical and medical care
Anemia (a condition in which you lack enough healthy red blood cells to carry adequate oxygen to your body's tissues) in patients with neoplasm (tumors)
anemia in neoplastic disease
Patient had a viral disease screening done
encounter for screening for other viral diseases
Patient had specificed bacterial disease / infectious disease
carrier of other specified bacterial diseases
Patient had implanted devices managed and adjusted
encounter for adjustment and management of other implanted devices
Patient did not undergo treatment due to patients decision
procedure and treatment not carried out because of patient's decision for other and unspecified reasons
Inflammation of the liver in humans caused by hepatitis b virus lasting six months or more.
chronic viral hepatitis B without delta-agent
The aftereffect of respiratory disease and tuberculosis
sequelae of respiratory and unspecified tuberculosis
Diseases in the body caused by enterococcus genus
Enterococcus as the cause of diseases classified elsewhere
Diseases in the body caused by Klebsiella pneumoniae bacteria
Klebsiella pneumoniae [K. pneumoniae] as the cause of diseases classified elsewhere
malignant neoplasm of colon, unspecified
Carcinoma (cancerous tumor) of the liver
liver cell carcinoma
other viral enteritis
Sepsis (when the body's response to an infection is out of balance) caused by a staph infection. Could lead to organ damage or failure
sepsis due to Staphylococcus aureus
Hepatitis (not hepatitis A or hepatitis B); inflammation of the liver
other specified acute viral hepatitis
Tumor of the connective tissues of the bile ducts
intrahepatic bile duct carcionoma
Cancerous tumor of a respiratory organ (upper lobe, bronchus, or lung)
malignant neoplasm of upper lobe, bronchus or lung
malignant neoplasm of endometrium
A lung disease characterized by the growth of inflammatory cells (granulomas) in the lungs
sarcoidosis of lung
A disease characterized by the growth of inflammatory cells (granulomas) in a specific part of your body (most commonly liver, lungs, skin, and lymph nodes)
sarcoidosis, unspecified
An uncommon condition characterized by elevated levels of immunoglobulins in your blood
polyclonal hypergammaglobulinemia
A common form of hyperthyroidism affecting the entire thyroid gland and causing the gland to become enlarged
thyrotoxicosis with diffuse goiter
The prescense of diabetic ketoacidosis (body produces high levels of ketones and not enough insulin) in type 1 diabetic patients, resulting in a coma
type 1 diabetes mellitus with ketoacidosis with coma
Type 1 diabetes (body cannot break down sugars very easily) with unspecified complications
type 1 diabetes mellitus with unspecified complications
Type 2 diabetes with diabetic macular edema (when blood vessels in the eye retina leak fluid, causing swelling in the macula)
type 2 diabetes mellitus with unspecified diabetic retinopathy with macular edema
Type 2 diabetes with diabetic retinopathy (vision loss and blindness) without macular edema (swelling in the macula cause by fluid leaking from the retina)
type 2 diabetes mellitus with unspecified diabetic retinopathy without macular edema
Cataracts (cloudy area in the lens of your eye) caused by type 2 diabetes
type 2 diabetes mellitus with diabetic cataract
Other eye diseases caused by type 2 diabetes
type 2 diabetes mellitus with other diabetic ophthalmic complication
The coexistences of 2 or more primary acid-base disorders in the same patient
mixed disorder of acid-base balance
Development of hypothyroidism (when the thyroid gland doesn't produce enough of crucial hormones) following surgery
postprocedural hypothyroidism
Dementia that is gradual in onset, following a number of transient ischaemic episodes which produce an accumulation of infarcts in the cerebral parenchyma
multi-infarct dementia
Other vascular dementia (problems with reasoning, planning, judgement, memory, and other thought processes caused by brain damage from impaired blood blow to your brain)
other vascular dementia
Unspecified vascular dementia (problems with reasoning, planning, judgement, memory, and other thought processes caused by brain damage from impaired blood blow to your brain)
vascular dementia, unspecified
A disorder characterized by the development either of a single delusion or of a set of related delusions that are usually persistent and sometimes lifelong.
delusional disorder
A condition that affects the way your brain processes information and causes you to lose touch with reality. In this case, not caused by substance abuse or a known physiological condition
unspecified psychosis not due to a substance or known physiological condition
Single episode of major depressive disorder (persistent feeling of sadness and loss of interest)
major depressive disorder, single episode, mild
A class of traumatic stress disorders with symptoms that last more than one month. There are various forms of post-traumatic stress disorder, depending on the time of onset and the duration of these stress symptoms. In the acute form, the duration of the symptoms is between 1 to 3 months. In the chronic form, symptoms last more than 3 months. With delayed onset, symptoms develop more than 6 months after the traumatic event.
post-traumatic stress disorder
Other form of Alzheimer's disease (diseases where dementia symptoms gradually worsen over time)
other Alzheimer's disease
Epilepsy with simple partial seizures and focal EEG abnoralities
localization-related (focal) (partial) symptomatic epilepsy and epileptic syndromes with simple partial seizures
Epilepsy with complex partial seizures and focal EEG abnoralities
localization-related (focal) (partial) symptomatic epilepsy and epileptic syndromes with complex partial seizures
A chronic autoimmune neuromuscular disorder characterized by skeletal muscle weakness
myasthenia gravis
Cataracts (cloudy area in the lens of your eye) in the center of the eye lens due to age
age-related nuclear cataract
Cataracts (cloudy area in the lens of your eye) caused by unspecified reason
unspecified cataract
A localized defect in the visual field bordered by an area of normal vision. This occurs with a variety of eye diseases (e.g., retinal diseases and glaucoma); optic nerve diseases, and other conditions.
visual field defects
blindness, one eye
A heart attack in the absence of observable q wave abnormalities in the ecg.
non-ST elevation (NSTEMI) myocardial infarction
A condition in which arteries become narrower and slow down the flow of blood accompanied with chest pain
atherosclerotic heart disease of native coronary artery with angina pectoris
bleeding into the space between the surface of the brain, or pia mater, and the arachnoid, one of three coverings of the brain
nontraumatic subarachnoid hemorrhage
Bleeding into one or both cerebral hemispheres including the basal ganglia and the cerebral cortex. It is often associated with hypertension and craniocerebral trauma.
nontraumatic intracerebral hemorrhage, unspecified
A balloon-like buldge like causes a dissection (a tear in the lining of the aorta)
aortic aneurysm and dissection
A contagious respiratory illness that can cause mild to severe illness (fever, chills, aches)
influenza due to certain identified influenza viruses
infection that inflames the air sacs in one or both lungs. The air sacs may fill with fluid or pus (purulent material), causing cough with phlegm or pus, fever, chills, and difficulty breathing.
pneumonia due to other specified infectious organisms
contagious viral infection caused by rhinovirus that causes inflammation of the bronchial tubes
acute bronchitis due to rhinovirus
unspecified chronic gastritis
Diverticular disease consists of three conditions that involve the development of small sacs or pockets in the wall of the colon, including diverticulosis, diverticular bleeding, and diverticulitis.
diverticular disease of large intestine without perforation or abscess
other diseases of anus and rectum
A disorder characterized by the inability of the liver to metabolize chemicals in the body.
hepatic failure, unspecified
Disease resulting in the inflammation of the liver
Other specified inflammatory liver diseases
Gallstones without inflammation of the gallbladder wall
calculus of gallbladder without cholecystitis
a blockage in the tubes that carry bile from the liver to the gallbladder and small intestine.
obstruction of bile duct
gastrointestinal hemorrhage, unspecified
A chronic disease of the skin marked by red patches covered with white scales.
Psoriasis, unspecified
a condition in which calcium pyrophosphate crystals build up in the knee
other chondrocalcinosis, knee
degeneration of the tissues of the hip joint, including hyaline cartilage, fibrocartilage, bone, and synovium
bilateral primary osteoarthritis of hip
A condition characterized by pain radiating from the back into the buttock and posterior/lateral aspects of the leg
Sciatica
a painful condition that occurs when pressure within the muscles builds to dangerous levels. This pressure can decrease blood flow, which prevents nourishment and oxygen from reaching nerve and muscle cells
Nontraumatic compartment syndrome
An acute or chronic inflammatory process affecting the kidney.
Tubulo-interstitial nephritis, not specified as acute or chronic
Gestational diabetes is diabetes that happens for the first time when a woman is pregnant. Gestational diabetes goes away when you have your baby, but it does increase your risk for having diabetes later.
Gestational diabetes mellitus
irregular uterine contractions before the 37th week of pregnancy that mimick real labor
False labor before 37 completed weeks of gestation
preexisting anemia in a pregnant woman that complicates pregnancy and childbirth
Anemia complicating pregnancy, childbirth and the puerperium
A disorder characterized by an unpleasant sensation of irregular and/or forceful beating of the heart.
Palpitations
an acute bleeding from the lung, from the upper respiratory tract and the trachea, and the alveoli
Hemorrhage from respiratory passages
a decrease in your normal sensations in the skin such as touch or temperature
Hypoesthesia of skin
A disorder characterized by lack of coordination of muscle movements
ataxia, unspecified
visual hallucinations
fluid accumulation that affects the whole body rather than particular organs or body areas.
Generalized edema
fracture or break in the upper end of the humerus
unspecified fracture of upper end of humerus
fracture in the anatomical portions of the femur which serve as the attachment sites for several muscles.
fracture of greater trochanter of femur
other complications of procedures, not elsewhere classified
infection and/or inflammation resulting from the implanation of an internal device, implant, or graft
Infection and inflammatory reaction due to other internal prosthetic devices, implants and grafts
application of an analog drug of cortisol that is used for its anti-inflammatory, immunosuppressive & antiproliferative effects
glucocorticoids and synthetic analogues
an occurance that requires attention to a tracheostomy procedure
encounter for attention to tracheostomy
an occurance that requires attention to a gastrostomy procedure
encounter for attention to gastrostomy
disease (process) of the liver
Malignant neoplasm of liver and intrahepatic bile ducts
disease (process) of gallbladder, biliary tract and pancreas
disease (process) of esophagus, stomach and duodenum
other disease (process) of the intestines
low income
financial problems related to housing or general economic standing
problem related to housing and economic circumstances, unspecified
problems related to dependency on health care providers
problems related to care provider dependency
other problems related to medical facilities and other health care
history of cancerous tumors of the digestive organs
personal history of malignant neoplasm of digestive organs
history of cancerous tumors of the lymphoid, hematopoietic and related tissues
personal history of other malignant neoplasms of lymphoid, hematopoietic and related tissues
patient refuses to follow medical treatment/regimen
patient's noncompliance with medical treatment and regimen
an infection in the bloodstream that may travel to different body organs.
streptococcal sepsis
An acute infectious disorder of an unspecified site caused by gram positive or gram negative bacteria.
bacterial infection of unspecified site
An unspecified acute infectious disorder caused by gram positive or gram negative bacteria.
bacterial infection, unspecified
A condition in which candida albicans, a type of yeast, grows out of control in moist skin areas of the body
candidiasis
Lung infections with the invasive forms of aspergillus
invasive pulmonary aspergillosis
diseases with bacteria (Streptococcus, Staphylococcus, and Enterococcus ) as the cause
Streptococcus, Staphylococcus, and Enterococcus as the cause of diseases classified elsewhere
malignant neoplasm of brain
secondary cancerous tumor of the brain and cerebral meninges
secondary malignant neoplasm of brain and cerebral meninges
An aggressive (fast-growing) type of leukemia (blood cancer) in which too many lymphoblasts (immature white blood cells) are found in the blood and bone marrow; no remission
acute lymphoblastic leukemia not having achieved remission
a brain tumor that is currently benign but has characteristics that make it possible for the tumor to become malignant (cancerous)
neoplasm of unspecified behavior of brain
A disease where the blood clots throughout the body and increases the risk of bleeding
disseminated intravascular coagulation [defibrination syndrome]
an elevated uric acid level in the blood without symptoms of inflammatory arthritis and tophaceous disease
hyperuricemia without signs of inflammatory arthritis and tophaceous disease
Abnormal increase in the volume of circulating fluid (plasma) in the body.
fluid overload
nicotine dependence
a potentially serious sleep disorder in which the brain makes no effort to breathe for short periods of time
primary central sleep apnea
sleep disorders
stopping breathing for a period of time (apnea) due to high altitude
high altitude periodic breathing
other disorders of brain
A disease of the heart muscle or myocardium proper. Cardiomyopathies may be classified as either primary or secondary, on the basis of etiology, or on the pathophysiology of the lesion: hypertrophic, dilated, or restrictive.
cardiomyopathy
nontraumatic intracerebral hemorrhage
diseases of the blood vessels in the brain
other specified cerebrovascular diseases
cerebrovascular disease (process)
rare conditions that result in obstruction of one or more arteries that supply blood to the brain
acute cerebrovascular insufficiency
A disorder characterized by a decrease or absence of blood supply to the brain
cerebral ischemia
when a blood clot develops in a blood vessel of the lower extremities and becomes stuck, obstructing blood flow
embolism and thrombosis of superficial veins of lower extremities
an acute inflammatory injury of the bronchioles that is usually caused by a viral infection
acute bronchiolitis, unspecified
complications/disorders of the respiratory system that occur during or after a procedure/operation
intraoperative and postprocedural complications and disorders of respiratory system, not elsewhere classified
diseases of bronchus, not elsewhere classified
respiratory disorder as a result of another disorder found elsewhere in the body
respiratory disorders in other diseases classified elsewhere
any disturbance of liver function that causes illness.
liver disease, unspecified
A disorder characterized by marked pain in the back region.
dorsalgia
a heart defect in which there are holes between the chambers of the right and left sides of the heart, and the valves that control the flow of blood between these chambers may not be formed correctly.
atrioventricular septal defect
congenital malformations, deformations and chromosomal abnormalities
pain occuring in the throat and chest of the patient
pain in throat and chest
aphagia
symptoms that have to do with food/fluid intake
symptoms and signs concerning food and fluid intake
feeding difficulties
open wound of head
fracture or break on ribs, sternum and thoracic spine
fracture of rib(s), sternum and thoracic spine
fracture or break on shoulder or upper arm
fracture of shoulder and upper arm
infection or inflammation due to the implementation of cardiac/vascular devices, implants, and grafts
infection and inflammatory reaction due to other cardiac and vascular devices, implants and grafts
other complications due to implementation of cardiac/vascular devices, implaces, grafts
other specified complications of cardiac and vascular prosthetic devices, implants and grafts
observation by doctors of suspected myocardial infarction (heart attack)
observation for suspected myocardial infarction
normal doctors appointment to ensure healthy supervised pregnancy
encounter for supervision of normal pregnancy
healthy person (family, friend) staying with a sick patient
healthy person accompanying sick person
other specified health condition/status not coded for
other specified health status
history of infectious or parasitic diseases
personal history of infectious and parasitic diseases
acquired absence of organs, not elsewhere classified
presence of other vascular implants and grafts
breast implant status
other and unspecified malignant neoplasm of skin of lip
A disorder affecting the cranial nerves or the peripheral nervous system.
polyneuropathy, unspecified
cognitive decline following cerebrovascular disease (disease of blood vessels in the brain)
cognitive deficits following unspecified cerebrovascular disease
A nonspecific hypersensitivity reaction caused by trauma causing pericardial effusion; high titers of anti-heart antibodies; low-grade fever; lethargy; loss of appetite; or abdominal pain.
postcardiotomy syndrome
heart muscle's pump function is reduced following heart surgery
postprocedural cardiac insufficiency following cardiac surgery
postprocedural heart failure following cardiac surgery
general cardiac funciton abnormalities following heart surgery
other postprocedural cardiac functional disturbances following cardiac surgery
a condition that results in the inability to effectively exchange carbon dioxide and oxygen, and induces chronically low oxygen levels or chronically high carbon dioxide levels, unspecified which
chronic respiratory failure, unspecified whether with hypoxia or hypercapnia
a skin condition that causes a dark discoloration in body folds and creases. It typically affects the armpits, groin and neck.
acanthosis nigricans
injuries to skin on back and underlying tissue resulting from prolonged pressure on the skin.
pressure ulcer of unspecified part of back
disease of the joints found in other diseases, multiple locations
arthropathies in other specified diseases classified elsewhere, multiple sites
supervision of a pregnancy in a woman who has delivered 5 or more infants who has achieved a gestational age of 24+ weeks
supervision of pregnancy with grand multiparity
complication in mechanical design.function of internal and external prosthetic devices, implants and grafts
mechanical complication of other specified internal and external prosthetic devices, implants and grafts
malignant neoplasm of eye
cancerous tumors within parts of the nervous system
malignant neoplasm of other and unspecified parts of nervous system
a sample of tissue taken from the external ear in order to examine it more closely.
external ear biopsy (Biopsy of external ear)
a chronic metabolic disease characterized by structural and functional alterations and interstitial fibrosis without coronary artery disease or hypertension
nutritional and metabolic cardiomyopathy
Mucositis is painful inflammation or ulceration of the mucous membranes anywhere along the gastrointestinal tract. Stomatitis (oral mucositis) refers to inflammation and ulceration that occur in the mouth.
stomatitis and mucositis (ulcerative)
chronic obstructive pulmonary disease (NEW)
respiratory failure (NEW)
respiratory infections (NEW)
influeza and pneumonia (NEW)
diseases of oral cavity and salivary glands
diseases of oral cavity and salivary glands (NEW)
diseases of appendix (NEW)
hernia (NEW)
noninfective enteritis and colitis (NEW)
diseases of peritoneum and retroperitoneum
diseases of peritoneum and retroperitoneum (NEW)
other diseases of the digestive system (NEW)
disorders of eyelid, lacrimal system and orbit
disorders of eyelid, lacrimal system and orbit (NEW)
disorders of conjunctiva (NEW)
disorders of sclera, cornea, iris and ciliary body
disorders of sclera, cornea, iris and ciliary body (NEW)
disorders of lens (NEW)
disorders of choroid and retina (NEW)
glaucoma (NEW)
disorders of vitreous body and globe (NEW)
disorders of optic nerve and visual pathways
disorders of optic nerve and visual pathways (NEW)
Disorders of ocular muscles, binocular movement, accommodation and refraction
disorders of ocular muscles, binocular movement, accommodation and refraction (NEW)
visual disturbances and blindness (NEW)
other disorders of eye and adnexa (NEW)
intraoperative and postprocedural complications and disorders of eye and adnexa, not elsewhere classified
intraoperative and postprocedural complications and disorders of eye and adnexa, not elsewhere classified (NEW)
acute rheumatic fever (NEW)
chronic rheumatic heart diseases (NEW)
hypertensive diseases (NEW)
congential malformations of the nervous system
congenital malformations of the nervous system (NEW)
congenital malformations of eye, ear, face and neck
congenital malformations of eye, ear, face and neck (NEW)
congenital malformations of the circulatory system
congenital malformations of the circulatory system (NEW)
congenital malformations of the respiratory system
congenital malformations of the respiratory system (NEW)
cleft lip and cleft palate (NEW)
other congenital malformations of the digestive system
other congenital malformations of the digestive system (NEW)
congenital malformations of genital organs
congenital malformations of genital organs (NEW)
congenital malformations of the urinary system
congenital malformations of the urinary system (NEW)
congenital malformations and deformations of the musculoskeletal system
congenital malformations and deformations of the musculoskeletal system (NEW)
other congenital malformations (NEW)
chromosomal abnormalities, not elsewhere classified
chromosomal abnormalities, not elsewhere classified (NEW)
infections of the skin and subcutaneous tissue
infections of the skin and subcutaneous tissue (NEW)
bullous disorders (NEW)
dermatitis and eczema (NEW)
papulosquamous disorders (NEW)
urticaria and erythema (NEW)
radiation-related disorders of the skin and subcutaneous tissue
radiation-related disorders of the skin and subcutaneous tissue (NEW)
disorders of skin appendages (NEW)
intraoperative and postprocedural complications of skin and subcutaneous tissue
intraoperative and postprocedural complications of skin and subcutaneous tissue (NEW)
other disorders of the skin and subcutaneous tissue (NEW)
endocrine, nutritional and metabolic diseases (NEW)
disorders of thyroid gland (NEW)
diabetes mellitus (NEW)
other disorders of glucose regulation and pancreatic internal secretion
other disorders of glucose regulation and pancreatic internal secretion (NEW)
disorders of other endocrine glands (NEW)
Intraoperative complications of endocrine system
intraoperative complications of endocrine system (NEW)
malnutrition (NEW)
other nutritional deficiencies (NEW)
Overweight, obesity and other hyperalimentation
overweight, obesity and other hyperalimentation (NEW)
metabolic disorders (NEW)
Postprocedural endocrine and metabolic complications and disorders, not elsewhere classified
postprocedural endocrine and metabolic complications and disorders, not elsewhere classified (NEW)
other infective otitis externa DP
感染性外耳炎，其他的
cholesteatoma of external ear DP
外耳胆脂瘤
noninfective DP of pinna
耳郭非感染性疾患病程
other specified disorders of external ear DP
外耳其他特指的疾患
disorders of external ear in diseases classified elsewhere DP
分类于他处的的外耳疾患
otitis externa in bacterial diseases classified elsewhere DP
Otitis externa in herpesviral [herpes simplex] infection
otitis externa in viral diseases classified elsewhere DP
otitis externa in mycoses DP
真菌性外耳炎
otitis externa in other infectious and parasitic diseases classified elsewhere DP
otitis externa in other diseases classified elsewhere DP
other disorders of external ear in diseases classified elsewhere DP
erysipelas of external ear DP
外耳丹毒
aspergillus otomycosis DP
曲霉菌真菌病
candida otomycosis DP
念珠菌属真菌病
cellulitis of external ear DP
外耳蜂窝织炎病程
malignant otitis externa DP
恶性外耳炎
otomycosis DP
耳真菌病
perichondritis of external ear DP
外耳软骨膜炎
other specified infectious diseases of external ear DP
其他特指的外耳感染
Infectious diseases of external ear, unspecified
Infectious DP of external ear, unspecified
耳廓感染，未特指的
seborrhoeic otitis externa DP
外耳脂溢性皮炎
acute otitis externa, noninfective DP
acute noninfectious otitis externa DP
急性非感染性耳炎
chondrodermatitis nodularis DP
结节性软骨皮炎病程
chronic otitis externa DP
慢性外耳炎
other specified noninfectious inflammation of external ear DP
其他特指的非感染性外耳炎症
Noninfectious inflammation of external ear, unspecified
Noninfectious inflammation of external ear, unspecified DP
外耳非感染性炎症，未特指的
otitis externa, unspecified DP
外耳炎，未特指的
acquired deformity of external auditory canal
acquired deformity of external auditory canal DP
获得性外耳道畸形
exostosis of external canal DP
外耳道外生骨疣
acquired stenosis of external auditory canal
acquired stenosis of external auditory canal DP
后天性外耳道狭窄
cholesteatoma of external auditory canal
cholesteatoma of external auditory canal DP
other specified acquired deformity of external auditory canal DP
其他特指的获得性外耳道畸形
后天性耳廓畸形
acquired deformity of pinna DP
获得性耳廓畸形
cauliflower ear DP
other specified acquired deformity of pinna DP
其他特指的获得性耳廓畸形
impacted cerumen DP
耵聍栓塞
other specified noninflammatory disorders of the external ear DP
其他特指的外耳非感染性疾患
noninflammatory disorders of the external ear, unspecified
noninflammatory DP of the external ear, unspecified
外耳非感染性疾患，未特指的
external ear, unspecified DP
耳廓疾病病程，未特指的
ear-lobe keloid DP
耳垂瘢痕瘤病程
contact dermatitis of external ear DP
外耳接触性皮炎
granuloma of external ear DP
外耳肉芽肿
obstructive keratosis of external ear DP
外耳阻塞性角化病程
external ear canal cyst DP
外耳道囊肿
hemorrhagic otitis externa DP
出血性外耳炎
diffuse otitis externa DP
弥漫性外耳炎
swimmer's ear DP
游泳者耳病
granuloma of external ear canal DP
外耳道肉芽肿
acute eczematoid otitis externa DP
外耳湿疹
acute actinic otitis externa DP
急性光化性外耳炎
acute chemical otitis externa DP
急性化学性外耳炎
chondrodermatitis nodularis chronica helicis
chondrodermatitis nodularis chronica helicis DP
慢性结节性耳轮软骨皮炎
pinna scar DP
耳郭瘢痕病程
acquired deformity of external ear DP
后天性外耳畸形
pinna pseudocyst DP
耳郭假性囊肿
hematoma ossification behind ear DP
耳后血肿骨化
pinna tumor DP
耳郭肿物
temporomandibular joint external ear canal hernia
temporomandibular joint external ear canal hernia DP
颞下颌关节外耳道疝
external ear fistula DP
外耳瘘
external ear canal keratosis DP
外耳道角化症病程
external ear canal necrosis DP
外耳道坏死
external ear canal tumor DP
外耳道肿物
acquired external ear canal atresia DP
后天性外耳道闭锁
A disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism.
A bodily process that is clinically abnormal.
A pathological bodily process in which a canonical anatomical structure becomes a pathological anatomical structure.
A pathological bodily process in which matter is reorganized in such a way as to give rise to new pathological formations which take the place of entities existing earlier.
TODO: Define.
A quality of a single physical entity inhering in the bearer by virtue of the bearer's size or shape or structure.
morphology
形态学的
A morphology quality inhering in a bearer by virtue of the bearer's relative position, shape, arrangements and connectivity of an organism's various parts; the pattern underlying its form.
structure
结构性
A quality of a process inhering in a bearer by virtue of the bearer's having a sudden onset, sharp rise, and short course.
acute
急性
See comments of relational quality of a physical entity.
A quality which inheres in a continuant.
multiply inhering quality of a physical entity
Relational qualities are qualities that hold between multiple entities. Normal (monadic) qualities such as the shape of a eyeball exist purely as a quality of that eyeball. A relational quality such as sensitivity to light is a quality of that eyeball (and connecting nervous system) as it relates to incoming light waves/particles.
A process quality inhering in a bearer by virtue of the bearer's magnitude of the temporal extent between the starting and ending point.
A structural quality inhering in a bearer by virtue of the bearer's being drawn together, compressed or squeezed physically.
constricted
狭窄的
A duration quality of a process inhering in a bearer by virtue of the bearer's having slow progressive course of indefinite duration.
chronic
慢性
A structural quality inhering in a bearer by virtue of the bearer's touching another entity.
contact
接触性
A structural quality which is held by a bearer when the latter's disposition the presence of abnormally proliferating masses of cells.
neoplastic
肿瘤性
A disposition inhering in a tumour by virtue of the bearer's disposition to progress, invade surrounding tissues or metastasize.
恶性
neoplastic, malignant
肿瘤性的，恶性
An exposure event in which a human is exposed to particulate matter in the air. Here the exposure stimulus/stress is the particulate matter, the receptor is the airways and lungs of the human,
A process occurring within or in the vicinity of an organism that exerts some causal influence on the organism via the interaction between an exposure stimulus and an exposure receptor. The exposure stimulus may be a process, material entity or condition (for example, lack of nutrients). The exposure receptor can be an organism, organism population or a part of an organism.
This class is intended as a grouping for various domain and species-specific exposure classes. The ExO class http://purl.obolibrary.org/obo/ExO_0000002 'exposure event' assumes that all exposures involve stressors, which limits the applicability of this class to 'positive' exposures, e.g. exposing a plant to beneficial growing conditions.
A material entity consisting of multiple components that are causally integrated.
May be replaced by a BFO class, as discussed in http://www.jbiomedsem.com/content/4/1/43
The olfactory organ of vertebrates, consisting of nares, olfactory epithelia and the structures and skeletal framework of the nasal cavity.
Organ that is the specialized structure of the face that contains olfactory neurons. The peripheral olfactory organ is paired[ZFA:0000047].
a protuberance in vertebrates that houses the nostrils, or nares, which admit and expel air for respiration in conjunction with the mouth. Behind the nose are the olfactory mucosa and the sinuses. Behind the nasal cavity, air next passes through the pharynx, shared with the digestive system, and then into the rest of the respiratory system. In humans, the nose is located centrally on the face; on most other mammals, it is on the upper tip of the snout[WP]. GO: The nose is the specialized structure of the face that serves as the organ of the sense of smell and as part of the respiratory system. Includes the nasi externus (external nose) and cavitas nasi (nasal cavity)[Wikipedia:Nose].
the organ that is specialized for smell and is part of the respiratory system
the structure of the nose varies across vertebrates. In tetrapods the nose is part of the respiratory system.[PMID:25312359]
Any portion of the organ that covers that body and consists of a layer of epidermis and a layer of dermis.
Note the distinction between the entire skin of the body, of which there is only 1 in an organism, and zones of skin, of which there can be many. Examples: skin of knee
(...) it is well-established that neural crest cells contribute to both the dermal skeleton (craniofacial bone, teeth, and the caudal fin rays of teleosts) and the integument, including craniofacial dermis and all pigment cells outside the retina (...).[well established][VHOG]
we assume that mouse, HOG and GAID all mean zone of skin when they say skin. We also choose skin as an exact synonym, as it is more intuitive
zong of skin
皮肤
An organ that is capable of transducing sensory stimulus to the nervous system.
Any hollow cylindrical anatomical structure containing a lumen through which substances are transported.
not every anatomical conduit is a tube - for example, a bone foramen is an opening in the bone, and there is no distinct separate tube structure. Tubes may transport large mixed objects (for example, a bolus of food in the digestive tube) or they may transport the secretions of a single gland (for example, gland ducts)
The head is the anterior-most division of the body [GO].
Organism subdivision that is the part of the body consisting of the cranial and pharyngeal regions.[AAO]
Organism subdivision which is the part of the body which consists of the cranial and pharygeal regions.[TAO]
Vertebrate evolution has been characterized by a fresh and vast array of cranial structures that collectively form the head.[well established][VHOG]
multi-tissue structure that is comprised of a secretory epithelial layer (mesothelium) and a connective tissue layer.
A multi-tissue structure that is comprised of a secretory epithelial layer and a connective tissue layer.[TAO]
a smooth membrane consisting of a thin layer of cells which excrete serous fluid. Serous membranes line and enclose several body cavities, known as serous cavities, where they secrete a lubricating fluid which reduces friction from muscle movement. Serosa is not to be confused with adventitia, a connective tissue layer which binds together structures rather than reducing friction between them. Each serous membrane is composed of a secretory epithelial layer and a connective tissue layer underneath. The epithelial layer, known as mesothelium, consists of a single layer of avascular flat nucleated cells (cuboidal epithelium) which produce the lubricating serous fluid. This fluid has a consistency similar to thin mucus. These cells are bound tightly to the underlying connective tissue. The connective tissue layer provides the blood vessels and nerves for the overlying secretory cells, and also serves as the binding layer which allows the whole serous membrane to adhere to organs and other structures.[WP]
in FMA, SM = mesothelium + connective tissue. It excludes the cavity. Serous sac = SM + cavity. Note that the SM is a subtype of wall in FMA.
A tubular structure that contains, conveys body fluid, such as blood or lymph.
A tubular structure that transports secreted or excreted substances.
A tube shaped portion of tissue lined with epithelial cells that collects secretions and routes them to their destination[ZFA:0005171].
Most ducts, but not all, are exocrine gland ducts. Some ontologies classify structures such as the oviduct here.
Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome.
Anatomical structure that performs a specific function or group of functions [WP].
Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4
A part of an organ that constitutes a distinct modular sub-unit. In some cases, the organ may also contain other sub-units of identical or similar types, in other cases this may be a distinct entity.
FMA distinguishes segment from zone by whether the fiat boundaries are fixed/anchored (segments) or floating (zone). It's not completely clear how to apply this distinction
Organ region with one or more anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyeball.
Organ region with one or more fixed or anchored fiat boundaries. Examples: artery, trunk of nerve, cervical part of esophagus, pelvic part of vagina, horn of thyroid cartilage, anterior segment of eyebal.
A multicellular structure that is a part of an organ.
currently defined in a very broad sense, may be replaced by more specific classes in the future
Anatomical structure that is part of the respiratory system. In mammals consists of upper and lower tracts
MA:0000434 has subclasses upper and lower, so it corresponds to a segment of the tract, rather than the tract as a whole
proximo-distal subdivision of respiratory tract
Anatomical cluster consisting of the skeletal elements and articular elements that are part of an individual subdivision of the organism.
An anatomical structure that develops from the endoderm and the mesoderm.
Grouping term for query purposes. Notes that the developmental relationships are being refined such that most structures should develop in whole from at most one layer, but may have contributions from multiple
mixed endoderm/mesoderm-derived structure
A fasciculated bundle of neuron projections (GO:0043005), largely or completely lacking synapses.
Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine.
Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO]
The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type.
The pair of anatomical structures comprised of a left lung and right lung.
Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms.
A fluid that is composed of blood plasma and erythrocytes.
This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid.
A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO]
Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO]
relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO]
Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG]
Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs.
The upper ventral region of the torso of an organism.
The breasts of a female primate's body contain the mammary glands, which secrete milk used to feed infants. Both men and women develop breasts from the same embryological tissues. However, at puberty female sex hormones, mainly estrogens, promote breast development, which does not happen with men. As a result women's breasts become more prominent than men's.
In anatomy, the throat is the anterior part of the neck, in front of the vertebral column. It consists of the pharynx and larynx. An important feature of the throat is the epiglottis, a flap which separates the esophagus from the trachea and prevents inhalation of food or drink. The throat contains various blood vessels, various pharyngeal muscles, the trachea (windpipe) and the esophagus. The hyoid bone and the clavicle are the only bones located in the throat of mammals. It is sometimes considered a synonym for fauces. [WP,unvetted].
The hyoid bone and the clavicle are the only bones located in the throat of mammals.
A portion of organism substance that is produced by exocrine glands.
BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions
Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body.
Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function.
Anatomical structure that is an individual member of a species and consists of more than one cell.
TODO - split body and mc organism? body continues after death stage
Anatomical structure which is a subdivision of a whole organism, consisting of components of multiple anatomical systems, largely surrounded by a contiguous region of integument.
Reflects CARO2. todo - check the inclusion of FMA 'cardinal body part here', and check child terms for consistency
Anatomical group that has its parts adjacent to one another.
Will be obsoleted in CARO v2 [https://github.com/obophenotype/caro/issues/3]
Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation.
changed label and definition to reflect CARO2
Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types.
Compound organ that contains one or more macroscopic anatomical spaces.
this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future
An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium.
Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO]
It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG]
We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa
A myogenic muscular circulatory organ found in the vertebrate cardiovascular system composed of chambers of cardiac muscle. It is the primary circulatory organ.
Blood pumping organ composed of four chambers: sinus venosus, atrium, cardiac ventricle and bulbus arteriosus.[TAO]
Part of the circulatory system responsible for pumping blood; composed of three chambers--two atria and one ventricle.[AAO]
relationship type change: differentiates_from lateral plate mesoderm (AAO:0010574) CHANGED TO: develops_from lateral plate mesoderm (UBERON:0003081)[AAO]
As noted, the hearts of birds and mammals have four chambers that arises from the two chambers (atrium and ventricle) of the fish heart.[well established][VHOG]
Taxon notes:" the ascidian tube-like heart lacks chambers....The ascidian heart is formed after metamorphosis as a simple tube-like structure with a single-layered myoepithelium that is continuous with a single-layered pericar- dial wall. It lacks chambers and endocardium.... The innovation of the chambered heart was a key event in vertebrate evolution, because the chambered heart generates one-way blood flow with high pressure, a critical requirement for the efficient blood supply of large-body vertebrates... all extant vertebrates have hearts with two or more chambers (Moorman and Christoffels 2003)" DOI:10.1101/gad.1485706
The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP].
requires review for applicability to invertebrate structures, e.g. synganglion
Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO]
Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO]
The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO)
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG]
This class encompasses a variety of light-detecting structures from different phyla with no implication of homology, from the compound insect eye to the vertebrate camera-type eye (distinct classes are provided for each)
Note that whilst this is classified as an organ, it is in fact more of a unit composed of different structures: in Drosophila, it includes the interommatidial bristle as a part; we consider here the vertebrate eye to include the eyeball/eye proper as a part, with the eye having as parts (when present): eyelids, conjuctiva,
The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
The serous membrane that covers the lungs and lines the pleural cavity. [Kaufman_MH_and_Bard_JBL, The_anatomical_basis_of_mouse_development_(1999)_San_Diego:_Academic_Press, p.264][VHOG]
In MA, is_a cavity lining (which we equate to parietal). In FMA, is_a (viscous) serous membrane (which includes mesothelium plus connective tissue). Note the MA structure should probably be associated with the mesothelium of pleura in FMA. JB/EHDAA2 argues the term 'pleura' is best used for the mesothelial lining (thus excluding connective tissue). See https://github.com/obophenotype/uberon/issues/86
The portion of the hindlimb that contains both the stylopod and zeugopod.
Most anatomists now agree that the three proximal bones of the tetrapod limbs are homologous to the two or three proximal elements of the paired fin skeleton of other sarcopterygians, that is the humerus-femur, radius-tibia, and ulna-fibula.[well established][VHOG]
The term leg can mean: [1] an appendage on which an animal walks [2] the entire hindlimb of a tetrapod [3] the segment of a human leg between knee and ankle (cf FMA) [4] the region of a hindlimb include the stylopod and zeugopod, but excluding the autopod. We define this class as [4], and thus 'leg' is compltely analagous to 'arm'. For [1], see the class 'locomotive weight-bearing appendage'. For [2] we use 'hindlimb'. For
we use the less open to misinterpretation 'hindlimb zeugopod'. Editor note: currently declared as overlapping foot, as AOs disagree over whether some ankle parts are in the leg or foot
Anatomical cluster that consists of two or more adjacent skeletal structures, which may be interconnected by various types of tissue[VSAO].
Anatomical cluster that consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[VSAO]
Anatomical cluster which consists of two or more adjacent bones or cartilages, which may be interconnected by various types of tissue.[TAO]
the female muscular organ of gestation in which the developing embryo or fetus is nourished until birth
The hollow muscular organ in female mammals in which the blastocyst normally becomes embedded and in which the developing embryo and fetus is nourished. Its cavity opens into the vagina below and into a uterine tube on either side. [TFD][VHOG]
An infundibulum, uterine tube, uterus, and vagina also differentiate along the oviducts of eutherian mammals.[well established][VHOG]
Most animals that lay eggs, such as birds and reptiles, have an oviduct instead of a uterus. In monotremes, mammals which lay eggs and include the platypus, either the term uterus or oviduct is used to describe the same organ, but the egg does not develop a placenta within the mother and thus does not receive further nourishment after formation and fertilization. Marsupials have two uteruses, each of which connect to a lateral vagina and which both use a third, middle 'vagina' which functions as the birth canal. Marsupial embryos form a choriovitelline 'placenta' (which can be thought of as something between a monotreme egg and a 'true' placenta), in which the egg's yolk sac supplies a large part of the embryo's nutrition but also attaches to the uterine wall and takes nutrients from the mother's bloodstream.
Two uteruses usually form initially in a female fetus, and in placental mammals they may partially or completely fuse into a single uterus depending on the species. In many species with two uteruses, only one is functional. Humans and other higher primates such as chimpanzees, along with horses, usually have a single completely fused uterus, although in some individuals the uteruses may not have completely fused [Wikipedia:Uterus]
Functional system which consists of structures involved in respiration.
The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO]
There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG]
An airway through which respiratory air passes in organisms.
This class generically groups trachea and analagous structures throughout metazoa. Consider renaming, as the term could be taken to mean lumen of tracheal system (e.g. in SNOMED). As a grouping class this is quite vague, as it is not clear where the airway begins and ends
Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes.
An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO]
many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class
organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP].
the cardiovascular system and the lymphatic system are parts of the circulatory system
Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO]
We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG]
The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO].
A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO]
Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO]
Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG]
A group of axons linking two or more neuropils and having a common origin, termination[FBbt].
White matter structure of CNS that contains axons that arise predominantly in one central nervous system part and terminate in another. Tracts are generally named by their region or origin followed by their region of primary termination, e.g., mammillothalamic tract contains axons that arise from neurons in the mammillary bodies and terminate in the thalamus. (CUMBO)
WP says this is the analog of peripheral nerves in CNS.
Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993).
Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO]
The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG]
esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995)
Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species.
A zone of skin that is part of a head [Automatically generated definition].
TODO - distinguish between entire skin of region and arbitrary zone of skin on region
Muscle tissue which is unstriated, composed primarily of smooth muscle fibers surrounded by a reticulum of collagen and elastic fibers. Smooth muscle differs from striated muscle in the much higher actin/myosin ratio, the absence of conspicuous sarcomeres and the ability to contract to a much smaller fraction of its resting length[GO].
A non-striated muscle that is composed of spindle-shaped cells. Smooth muscle usually is organized into sheets that line cavitated organs.[TAO]
Involuntary muscle tissue consisting of uninucleate spindle-shaped fibers.[AAO]
(...) the first bilateral animals possessed only smooth muscles with the molecular repertoire necessary to build a striated muscle. (...) it is more parsimonious to regard striated muscle cells as a sister cell type to the smooth muscle cells. In this scenario, striated and smooth muscles would have arisen in the stem lineage that led to the Nephrozoa (i.e. all Bilateria exclusive the acoelomorphs) (Hejnol et al., 2009), from an 'acoel-like' smooth muscle, by segregation and divergence of functions and through differential recruitment of additional genes[well established][VHOG]
GO uses visceral and smooth interchangeably. However visceral can also be used in the sense of the viscera. Many fly annotations to smooth muscle terms. If we want to be inclusive of insects have to have a general definition of tissue that includes cells.
textus muscularis levis; textus muscularis nonstriatus
A major subdivision of an organism that is the entire part of the organism dorsal to a horizontal plane and bounded on one side by the same transverse plane. In vertebrares this includes the vertebral column..
In humans, called the back, a large posterior area of the human body, rising from the top of the buttocks to the back of the neck and the shoulders. It is the surface opposite to the chest, its height being defined by the vertebral column (commonly referred to as the spine or backbone) and its breadth being supported by the ribcage and shoulders. The spinal canal runs through the spine and provides nerves to the rest of the body
distensible musculomembranous organ situated in the anterior part of the pelvic cavity in which urine collects before excretion[MP].
A saccular organ in which urine accumulates before discharge from the body. [Bemis_WE, Functional_Anatomy_of_the_Vertebrates:_An_Evolutionary_Perspective, Glossary_G-29, Grande_L, Liem_KF, Third_Edition_(2001)_Orlando_Fla.:_Harcourt_College_Publishers, Walker_WF][VHOG]
Anatomical structure which consists of a membranous sac used to temporarily store urine until it is excreted from the body.[AAO]
In tetrapods, the urinary bladder arises as an outpocketing of the cloaca. (...) The tetrapod urinary bladder appears first among amphibians and is present in Sphenodon, turtles, most lizards, ostriches among birds, and all mammals.[well established][VHOG]
The urinary bladder evolved in tetrapods. Birds to not possess a true urinary bladder, although Palaeognathae have an undifferentiated cloacal outpocketing that serves a similar function[https://github.com/obophenotype/uberon/issues/454]
An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO].
Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO]
In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG]
As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52)
The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm
The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans
the elongated structure connected to the posterior surface of the testis that transports, stores, and matures spermatozoa between testis and vas deferens
A similar, but probably non-homologous, structure is found in cartilaginous fishes
Typically divided into three main regions. In reptiles, there is an additional canal between the testis and the head of the epididymis, which receives the various efferent ducts. This is, however, absent in all birds and mammals. The epididymis is covered by a two layered pseudostratified epithelium. The epithelium is separated by a basement membrane from the connective tissue wall which has smooth muscle cells.
A tube running from the outer ear to the middle ear. The human ear canal extends from the pinna to the eardrum and is about 26 mm in length and 7 mm in diameter.
consider revisiting superclass after refinement of CARO/EAO, conduit may not be quite correct.
tympanic ring, which serves as support for the tympanic membrane, directs invagination of the first pharingeal cleft ectoderm to form the external acoustic meatus (EAM), which provides the outer layer of the membrane[PMID 11237469]
external acoustic meatus
外耳道
Subdivision of trunk proper, which is demarcated from the neck by the plane of the superior thoracic aperture and from the abdomen internally by the inferior surface of the diaphragm and externally by the costal margin and associated with the thoracic vertebral column and ribcage and from the back of the thorax by the external surface of the posterolateral part of the rib cage, the anterior surface of the thoracic vertebral column and the posterior axillary lines; together with the abdomen and the perineum, it constitutes the trunk proper[FMA].
FMA:24216 present in FMA1, but gone in subsequent versions
A zone of skin that is part of a external ear [Automatically generated definition].
zone of skin of auricular region of head
skin of external ear
外耳皮肤
Skeletal element that is composed of bone tissue.
Also called osseous tissue, (Latin: os). Is a type of hard endoskeletal connective tissue found in many vertebrate animals. Bone is the main tissue of body organs that support body structures, protect internal organs, (in conjunction with muscles) facilitate movement; and are involved with cell formation, calcium metabolism, and mineral storage.[AAO]
Portion of tissue which is calcified connective tissue making up the structural elements of the skeletal system.[TAO]
Skeletal element that is composed of bone tissue.[VSAO]
The 'new animal phylogeny' reveals that many of the groups known to biomineralize sit among close relatives that do not, and it favours an interpretation of convergent or parallel evolution for biomineralization in animals. (...) Whether this 'biomineralization toolkit'of genes reflects a parallel co-option of a common suite of genes or the inheritance of a skeletogenic gene regulatory network from a biomineralizing common ancestor remains an open debate.[debated][VHOG]
The segment of the respiratory tract that starts proximally with the trachea and includes all distal structures including the lungs[WP,modified]
An epithelial tube or tree of tibes that transports blood away from the heart[modified from AEO definition].
Note that in FMA an artery is a tree, whereas AEO/JB defines it as a tube; FMA includes a separate class for what it calls the trunk. Classification in this ontology may currently (Jan 2012) represent a mix of both schemes, although we are gradually revising in the direction of the AEO scheme.
Part of the circulatory system composed of blood vessels which carry oxygenated blood away from the heart to the rest of the body.[AAO]
The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG]
Sense organ in vertebrates that is specialized for the detection of sound, and the maintenance of balance. Includes the outer ear and middle ear, which collect and transmit sound waves; and the inner ear, which contains the organs of balance and (except in fish) hearing. Also includes the pinna, the visible part of the outer ear, present in some mammals.
The organ of hearing and of equilibrium. [TFD][VHOG]
Both vertebrate and invertebrate auditory organs are thought to have evolved from primitive mechanosensors, but the nature of the ancestral structure and the evolutionary trajectories followed in distinct animal lineages remain unknown. In particular, we do not know how many types of mechanosensor existed in the protostome-deuterostome ancestor from which insects and vertebrates evolved or whether the PDA had an auditory organ.[well established][VHOG]
ear
Part of the ear external to the tympanum (eardrum). It typically consists of a tube (the external auditory meatus) that directs sound waves on to the tympanum, and may also include the external pinna, which extends beyond the skull[GO].
The external part of the organ, which consists of an outer portion (external auditory meatus) which leads to the tympanum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Some species, like Amolops tormotus (Feng et al. 2006), have a cavity in front of the tympanic membrane which is considered to be an ear canal and thus an outer ear. (...) The ancestral lineage of amphibians separated from the mammalian lineage, approximately 350 million years ago, in the paleozoic era. Many of the important developments in the auditory systems emerged after the ancestral paths separated (Manley and Clack 2003). This implies that shared features, like the tympanic middle ear, developed independently in different vertebrate lineages.[uncertain][VHOG]
in XAO this includes and is only the tympanum
external ear
外耳
The part of the ear that projects from the head, connecting to the external acoustic meatus.
The external expanded part of the ear characterized by a funnel-shaped structure through which the sound vibrations are received. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
Mammals have a third type of tympanic ear. An external flap, the auricle or pinna, helps funnel sound waves down the external acoustic meatus to the tympanic membrane.[well established][VHOG]
In various species, the pinna can also signal mood and radiate heat
The purpose of the pinna is to collect sound. It does so by acting as a funnel, amplifying the sound and directing it to the ear canal. While reflecting from the pinna, sound also goes through a filtering process which adds directional information to the sound (see sound localization, head-related transfer function, pinna notch).
耳郭
pinna
耳廓
The soft lower part of the external ear, projecting below the antitragus.
The earlobe is composed of tough areolar and adipose (fatty) connective tissues, lacking the firmness and elasticity of the rest of the pinna. Since the earlobe does not contain cartilage the earlobe has a large blood supply and may help to warm the ears and maintain balance but generally earlobes are not considered to have any major biological function.
lobule of pinna
耳垂
A vessel through which blood circulates in the body.
consider adopting the EMAPA superclass 'vascular element', which includes microvasculature (e.g. capillaries), vascular plexus
Any of the vessels through which blood circulates in the body. [XAO:0001011_][VHOG]
Any of the vessels through which blood circulates in the body.[AAO]
annelids have blood vessels, but this class is not applicable to annelids.
FMA:63183 Blood vessel is categorized as 'general anatomical term'. Suggestion to map to region of vascular tree from Terry H at JAX
A two-lobed endocrine gland found in all vertebrates, located in front of and on either side of the trachea in humans, and producing various hormones, such as triiodothyronine and calcitonin[BTO].
Either of paired structures located in the throat which develop from the ventral wall of the pharynx and excretes hormones involved in the morphological and functional changes during metamorphosis as well as influencing other tissues.[AAO]
(...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (2) a groove in the pharyngeal floor known as the endostyle, or a thyroid gland derived from part of the endostyle (...).[well established][VHOG]
In fish, it is usually located below the gills and is not always divided into distinct lobes. However, in some teleosts, patches of thyroid tissue are found elsewhere in the body, associated with the kidneys, spleen, heart, or eyes
In larval lampreys, the thyroid originates as an exocrine gland, secreting its hormones into the gut, and associated with the larva's filter-feeding apparatus. In the adult lamprey, the gland separates from the gut, and becomes endocrine, but this path of development may reflect the evolutionary origin of the thyroid. For instance, the closest living relatives of vertebrates, the tunicates and Amphioxus, have a structure very similar to that of larval lampreys, and this also secretes iodine-containing compounds (albeit not thyroxine)
In tetrapods, the thyroid is always found somewhere in the neck region. In most tetrapod species, there are two paired thyroid glands - that is, the right and left lobes are not joined together. However, there is only ever a single thyroid gland in most mammals, and the shape found in humans is common to many other species
Respiration organ that develops as an outpocketing of the esophagus.
Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO]
Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG]
respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi
Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP]
An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen.
An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO]
general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs.
Cardiac chamber in which blood enters the heart.
One of two chambers of the heart which receive blood from the veins and forces it by muscular contration to the ventricle.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...).[well established][VHOG]
Cardiac chamber through which blood leaves the heart.
A chamber of the heart that receives blood from one or more atria and pumps it by muscular contraction into the arteries.[AAO]
In the primitive vertebrate heart the four chambers are: 1. Sinus venosus (...) 2. Atrium (...) 3. Ventricle (...) 4. Conus arteriosus (...)[well established][VHOG]
A cardiac ventricle that is in the left side of the heart.
Thick-walled muscular chamber constituting the left border and apex of the heart. It receives oxygenated blood from the left atrium through the mitral orifice and send it off into the aorta. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG]
The vertebrate heart initially forms as a tube from a population of precursor cells termed the first heart field (FHF). Cells from the adjacent second heart field (SHF) are then progressively added to the developing heart. In avian and mammalian hearts, the FHF contributes mainly to the left ventricle, whereas the SHF gives rise to the outflow tract and large portions of the right ventricle and atria. Both fields arise from common mesodermal progenitors, although the detailed lineage relationships between FHF and SHF remain uncertain.[well established][VHOG]
An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Organ which secretes bile and participates in formation of certain blood proteins.[AAO]
relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO]
All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG]
An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003).
The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates.
secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO].
Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function.
Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong].
The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO]
Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG]
A paired organ of the urinary tract which has the production of urine as its primary function.
One of either of a pair of structures lying on either side of the dorsal aorta in which fluid balance is regulated and waste is excreted out in the form of urine.[AAO]
Anatomical system that consists of the muscular and skeletal systems.
Anatomical system that provides locomotion and physical support to the organism.[AAO]
There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG]
Joint in which the articulating bones or cartilages are connected by an articular capsule which encloses a synovial membrane and a synovial cavity. Examples: Temporomandibular joint, knee joint.[FMA]
Is a joint that is located at the point of contact of articulating bones allowing movement. The joint has a capsule containing synovial fluid surrounding the articulating bone surfaces.[TAO]
An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ.
An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint
The yellow or brown waxy secretions produced by vestigial apocrine sweat glands in the external ear canal[MESH].
Cerumen keeps the eardrum pliable, lubricates and cleans the external auditory canal, waterproofs the canal, kills bacteria, and serves as a barrier to trap foreign particles (dust, fungal spores, etc.) by coating the guard hairs of the ear, making them sticky.
耵聍
A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas
Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses
The prostate gland is a partly muscular, partly glandular body that is situated near the base of the mammalian male urethra and secretes an alkaline viscid fluid which is a major constituent of the ejaculatory fluid.
TODO - FMA treats the gland as part of the prostate - see also FMA:74119.
Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified].
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.
One of the four types of tissue in traditional classifications. It is largely a category of exclusion rather than one with a precise definition, but there are certain characteristics shared by all or most tissues in this category, such as involvement in structure and support, derived from mesoderm, and characterized largely by the traits of non-living tissue.[AAO]
Portion of tissue that consists of mesodermally derived cells and intercellular matrix comprised of protein fibers and carbohydrates, which supports, ensheathes and binds together other tissues.[TAO]
Tissue with cells that deposit non-polarized extracellular matrix including connective tissue fibers and ground substance.[VSAO]
Muscle tissue is a contractile tissue made up of actin and myosin fibers[GO].
One of the four types of tissue in traditional classifications. Tissue that contains cells with contractile filaments that move past each other and change the size of the cell. Muscle tissue also is separated into three distinct categories.[AAO]
Vertebrate muscle is categorized into three major muscle types defined by their structural and functional properties: skeletal, cardiac and smooth. In Dmel the counterparts are somatic, heart/cardiac and visceral. Here we take a cell type based approach.
Anatomical 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.
The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.
A type of dense connective tissue. It is composed of cells called chondrocytes which are dispersed in a firm gel-like ground substance, called the matrix. Cartilage is avascular (contains no blood vessels) and nutrients are diffused through the matrix. Cartilage is found in the joints, the rib cage, the ear, the nose, in the throat and between intervertebral disks. It makes up virtually the entire skeleton in chondrichthyes.[AAO]
Portion of tissue which is connective tissue composed of collagen and/or elastin fibers and chondrocytes. Cartilage is avascular and provides both skeletal functions and a framework upon which bone is deposited.[TAO]
Skeletal tissue that is avascular, rich in glycosaminoglycans (GAGs) and typically includes chondrocytes within isolated lacunae. Cartilage tissue is deposited by chondroblasts.[VSAO]
Phylogenetic analysis suggests that cartilage arose independently in cnidarians, hemichordates, vertebrates, arthropods, annelids, brachiopods, and molluscs - or a common ancestor of brachiopods and molluscs (...). Analyses of cartilage as a tissue and of the development of invertebrate cartilages are consistent with homology between invertebrate and vertebrate cartilage. From the discussion above, it will be clear that understanding genetic changes underlying cartilage evolution is key to determining whether the multiple origins of cartilage represent parallel evolution.[well established][VHOG]
Previous: "A portion of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate[GO]. Regular connective tissue, which consists of chondrocytes and related cells, the intercellular matrix of which is chondrified. Examples: hyaline cartilage, fibrocartilage, elastic cartilage[FMA]. an avascular supporting and articular skeletal tissue. It also functions as the primary endoskeletal support in vertebrate embryos. Cartilage is deposited by and is composed of chondroblasts and chondrocytes separated by an extracellular matrix, which may or may not mineralize depending on cartilage type, age, or taxon[Hall and Witten]." See also FMA:71500 Set of cartilages, FMA:55107 Cartilage organ, FMA:12264 Articular cartilage. // elements made from cartilage, cartilage-like, or chondroid tissues evolved in invertebrates[H&W]
cartilage tissue
软骨组织
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.
see https://github.com/obophenotype/uberon/issues/27
Skeletal tissue with a collagen-rich extracellular matrix vascularized, mineralized with hydroxyapatite and typically including osteocytes located in lacunae that communicate with one another by cell processes (in canaliculi). Bone is deposited by osteoblasts.[VSAO]
The helix is the prominent rim of the pinna.
helix of outer ear
耳轮
A major subdivision of a mature or developing limb, including both skeletal elements (or the mesenchyme that gives rise to the skeletal elements) and associated tissues, such as muscle, connective tissue, integument. Examples: autopod region, zeugopod region, stylopod region, metapodial region, arm region. Excludes the limb girdles.
TODO - align this with the CARO2 class 'appendage segment'; note the FMA class does not appear to require repetition
FMA has both limb segment and free limb segment, the former includes the girdles. Note that MA uses the term more generally and includes A,S,Z,S+Z(arm/leg), whereas FMA is just A,S,Z
an organ that functions as a secretory or excretory organ
Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types.
this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs
Anatomical structure that is part of the head consisting entirely of cranium and mandible[WP].
in FMA the skull is divided into orbit, neurocranium (8 parts), viscerocranium (26 parts). Here we have a separate overlapping division into cranium and mandible.
in many ontologies, the structure called the cranium is inclusive of the mandible/lower jaw skeleton
A skull that is missing a mandible is only a cranium; this is the source of a very commonly made error in terminology. Those animals having skulls are called craniates
A blood vessel that is part of a heart [Automatically generated definition].
A blood vessel that is part of the arterial system. Includes artery, arteriole and aorta.
only in MA - supertype of artery, arteriole, aorta.
A blood vessel that is part of a trunk [Automatically generated definition].
A synovial joint of the jaw that connects the mandible to the temporal bone.
There are two TMJs, one on either side, working in unison. The unique feature of the TMJs is the articular disc. The disc is composed of fibrocartilagenous tissue (like the firm and flexible elastic cartilage of the ear) which is positioned between the two bones that form the joint. The TMJs are one of the only synovial joints in the human body with an articular disc, another being the sternoclavicular joint. The disc divides each joint into two. The lower joint compartment formed by the mandible and the articular disc is involved in rotational movement -- this is the initial movement of the jaw when the mouth opens. The upper joint compartment formed by the articular disk and the temporal bone is involved in translational movement -- this is the secondary gliding motion of the jaw as it is opened widely. The part of the mandible which mates to the under-surface of the disc is the condyle and the part of the temporal bone which mates to the upper surface of the disk is the glenoid (or mandibular) fossa[WP].
temporomandibular joint
颞下颌关节
A blood vessel that is part of a thorax [Automatically generated definition].
Any of the organized aggregations of cells that function as secretory or excretory organs and are associated with reproduction.
Any tube, opening or passage that connects two distinct anatomical spaces.
FMA has both conduit and conduit space. In EHDAA2 this is a surface feature
An anatomical structure that develops (entirely or partially) from the endoderm.
An anatomical structure that develops (entirely or partially) from the mesoderm.
An anatomical structure that develops (entirely or partially) from the ectoderm.
A cardiac chamber surrounds an enclosed cavity within the heart
generic enough to cover FBbt:00003156 heart chamber but this is a cavity. GO defines it as the cavity. TODO - move subclasses. Note this also includes sinus venosus
smooth muscle found within, and composing the majority of the wall of blood vessels.
Vascular smooth muscle contracts or relaxes to both change the volume of blood vessels and the local blood pressure, a mechanism that is responsible for the redistribution of the blood within the body to areas where it is needed (i.e. areas with temporarily enhanced oxygen consumption). Thus the main function of vascular smooth muscle tonus is to regulate the caliber of the blood vessels in the body. Excessive vasoconstriction leads to hypertension, while excessive vasodilation as in shock leads to hypotension.
The part of the cardiovascular system consisting of all arteries.
An artery of the systemic circulation, which is the part of the cardiovascular system which carries oxygenated blood away from the heart, to the body, and returns deoxygenated blood back to the heart.
A specialized form of connective tissue in which the extracellular matrix is firm, providing the tissue with resilience, and/or mineralized and that functions in mechanical and structural support.[VSAO]
Four classes of mineralized tissues are found in vertebrates: bone, cartilage, dentine, and enamel. We think of cartilage and bone as skeletal tissues and of enamel and dentine as dental tissues, but enamel and dentine arose evolutionarily together with bone as skeletal tissues in the dermal skeleton (exoskeleton) of early vertebrates. Scales and teeth of sharks are examples of dermal skeletal elements that are still composed of the three ancient components-enamel, dentine, and bone. Cartilage, on the other hand, provided the basis for the second vertebrate skeletal system, the endoskeleton (Smith and Hall, 1990; Hall, 1998a,b). some invertebrate skeletal tissues have surprisingly bone-like features. Examples include chondrocytes interconnected by cell processes in cephalopod cartilages (Cole and Hall, 2004a,b), and the calcium phosphate layer in the shells of brachiopods (Rodland et al., 2003). However, neither bone nor mineralized cartilage have been found in invertebrates. Editors notes: TODO - develops_from
Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles.
Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO]
Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO]
Anatomical cluster that connects two or more adjacent skeletal elements or hardened body parts.
A proximal-distal subdivision of the digestive tract.
intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct.
An organ part that is part of a long bone [Automatically generated definition].
Muscle structures are contractile cells, tissues or organs that are found in multicellular organisms[GO].
in some organisms such as drosophila, muscles can be single cells. This class groups together all discrete muscle elements, from multicellular muscle organs in vertebrates, to individual single-cell muscles in drisophila
Any anatomical structure that is part of the reproductive system.
A structure consisting of multiple cell components but which is not itself a cell and does not have (complete) cells as a part.
we go with the FMA classification rather than the CARO one. FMA def: 'Anatomical cluster which has as direct parts cell parts from two or more cells.'
An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland.
An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region.
An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions.
An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli.
An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions.
A sex gland that is part of a male reproductive system.
The part of the digestive system that excludes the hepatobiliary system.
the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system
The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System].
All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG]
that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla.
alimentary part of gastrointestinal system
Any of the ducts that are part of a male reproductive system.
this class groups the individual ducts in a variety of species
Any of the arteries or veins that supply blood to the heart or return blood from the heart muscles to the circulation
A collection of two or more connected limb segments. Examples: arm (comprising stylopod and zeugopod regions).
Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not.
Any gland that is part of the digestive system.
A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified].
note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis
The femur neck or neck of the femur is a flattened pyramidal process of bone, connecting the femoral head with the femoral shaft, and forming with the latter a wide angle opening medialward.
the NIFSTD class 'nerve tract' is classified under 'regional part of brain', so it may seem like it belongs here, but actually includes spinal cord tracts
Anatomical system that consists of all blood and lymph vessels.
The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System].
in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system
A limb segment that is part of a hindlimb.
An anatomical structure that has more than one cell as a part.
An organ of the digestive tract that is capable of retaining and storing food
This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates
Any gland, other than the gonad, associated with the genital tract, such as the ampulla of the ductus deferens and the bulbourethral, prostate and vesicular glands of the male.
An anatomical structure that has some part that develops from the neural crest.
structure with developmental contribution from neural crest
An appendage segment that is part of a limb/fin.
A major subdivision of an organism that divides an organism along an axis perpedicular to the main body anterior-posterior axis. In vertebrates, this is typically a fin or limb segment. In insects, this includes segments of appendages such as antennae, as well as segments of the insect leg.
subdivision of organism along appendicular axis
Synovial joint that articulates bones of upper and lower jaw.
Some synapsids retained two pairs of jaw joints - quadrate-articular and tempero-mandibular, but this unusual paired condition did not last long
A multi cell part structure that is part of a central nervous system.
central nervous system cell part cluster
A major subdivision of an organism that divides an organism along its main body axis (typically anterio-posterior axis). In vertebrates, this is based on the vertebral column.
Ideally this would be disjoint with analagous class for appendicular axes, but currently 'appendages' like antennae, horns cause a problem
subdivision of organism along main body axis
A zone of skin that is part of a craniocervical region.
A section through the tube or network of tubes that connects the ovaries to the outside of the body.
FMA class may only represent the uterine portion
The region of the organism associated with the visceral organs.
Cardinal body part, which consists of a maximal set of diverse subclasses of organ and organ part spatially associated with the vertebral column and ribcage. Examples: There is only one body proper[FMA:231424].
Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements.
Any structure that is placed on one side of the left-right axis of a bilaterian.
This class is primarily to implement taxon constraints. It may be removed in the future.
A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile.
A membranous sac in animals that serves as the receptacle of a liquid or contains gas.
An multicellular anatomical structure that has subparts of multiple organs as a part.
A collection of anatomical structures that are alike in terms of their morphology or developmental origin.
resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected
A region or zone on the surface of an organism that encompasses skin and any adnexa, down through muscles and bounded by underlying skeletal support structures.
organ region with floating fiat boundary
Any chamber of the left side of the heart
phenotype
Actions done to prevent a disease or to relieve a symptom i.e.: Surgery to remove blood clots
encounter for prophylactic measures, unspecified
having problems or an inability adapting to a new environment or culture
no symptoms, but HIV was found in patient's bloodstream
asymptomatic human immunodeficiency virus [HIV] infection status
code that can be used to indicate a diagnosis for reimbursement purposes. code that can be used to indicate a diagnosis for reimbursement purposes.
blood transfusion without reported diagnosis
Care involving use of other rehabilitation procedures
the treatment of disease, injury, or deformity by physical methods rather than by drugs or surgery.
Patient is thought to have been exposed to the virus in question
code is used to show that patient has probably been infected because they have been exposed to the infection
contact with and (suspected) exposure to other communicable diseases
contact with and (suspected) exposure to other viral communicable diseases
patient kept under observation for suspected disease/condition
observation for suspected disease or condition, unspecified
the provision of assistance and guidance in resolving personal, social, or psychological problems and difficulties, especially by a professional.
help with diet means the person is not eating healthy.
a medical diagnosis of other specified counseling
Encounter for antineoplastic chemotherapy and immunotherapy
the treatment of disease by the use of chemical substances, especially the treatment of cancer by cytotoxic and other drugs.
patient under observation for other suspected diseases and conditions
encounter for observation for other suspected diseases and conditions ruled out
encounter for observation due to suspected exposure to biological agents
encounter for observation for suspected exposure to other biological agents ruled out
Encounter for fitting and adjustment of extracorporeal dialysis catheter
encounter for fitting and adjustment of urinary device
improves the quality of life of patients and their families facing the problem associated with life-threatening illness
Follow-up examination after other treatment for other conditions
screening is done to prevent a disease or to help identify the disease.
encounter for screening for respiratory disorder NEC
Persons lacking permanent or reliable shelter, variously due to poverty, lack of affordable housing, mental illness, substance abuse, juvenile alienation, or other factors.
used to specify what condition the patient is under
Patient awaiting admission to adequate facility elsewhere
person awaiting admission to adequate facility elsewhere
patient needs assisstance with personal care
the patient needs help living everyday life at home.
need for assistance at home and no other household member able to render care
person is disabled physically or mentally, so they are in need of medical services
persons encountering health services in other specified circumstances
used to specify that the patient has used insulin. This can help identify diseases
Therapeutic drug induced immunosuppression, long term use
a procedure used to widen blocked or narrowed coronary arteries
presence of coronary angioplasty implant and graft
a surgical procedure that redirects blood flow from one area of the body to another by reconnecting the blood vessels
presence of other cardiac and vascular implants and grafts
someone that lives alone is more keen to become stressed, bored, or other mental states
signs such as jaw pain or chills that help identify the disease
a medical diagnosis of person with feared health complaint in whom no diagnosis is made.
person with feared health complaint in whom no diagnosis is made
describes the circumstance causing an injury
Abnormal findings on diagnostic imaging of lung
nonspecific abnormal finding of lung field
other nonspecific abnormal finding of lung field
this abnormal level indicates damage to the liver
tests on the patients liver have given results that are abnormal
abnormal results of liver function studies
Oliguria is defined as a urine output that is less than 400 mL/24 h or less than 17 mL/h in adults. Anuria is defined as urine output that is less than 100 mL/24 h or 0 mL/12 h.
Excessive slowness in the action of the heart
elevated blood-pressure reading, without diagnosis of hypertension
nonspecific elevation of levels of transaminase and lactic acid dehydrogenase
other abnormalities of gait and mobility
blood tests have found abnormalities of protiens in the blood which can indicate clues for a potential ilness
other specified abnormalities of plasma proteins
A condition characterized by alterations of the sense of taste which may range from mild to severe, including gross distortions of taste quality.
Prediabetes is when your blood sugar level is higher than it should be but not high enough for your doctor to diagnose diabetes
Abnormally rapid heartbeat, usually with a heart rate above 100 beats per minute for adults.
a person urinates when they do not want to
A profound state of unconsciousness associated with depressed cerebral activity from which the individual cannot be aroused.
main symptom of dyspnea is labored breathing. It's definition as a word is "labored breathing"
Body temprature is raised to fight pathogens
when your temperature rises above its normal range
Coughing or spitting up blood from the respiratory tract.
a symptom that makes one feel weakness, discomfort, or illness
A disorder characterized by a feeling of general discomfort or uneasiness, an out-of-sorts feeling.
A disorder characterized by a queasy sensation and/or the urge to vomit
symptoms of dizziness and vomiting that can help find the disease the patient is under
symptoms that can help find the disease the patient is under
patient is traumatized to a point that they cannot send commands to body parts
Shock resulting from primary failure of the heart in its pumping function
when a patient has lost more than 20% of their blood and he or she enter shock
severe and potentially fatal condition that occurs when sepsis leads to life-threatening low blood pressure.
A category of mental health disorders that primarily affect cognitive abilities including learning, memory, perception, and problem solving.
other symptoms and signs involving cognitive functions and awareness
physical suffering or discomfort caused by illness or injury
pain that lasts from 3-6 months related to soft tissue
pain in the chest not caused by heart disease or heart attack
Usually a symptom of a disease or caused by physical damage
a disorder characterized by a sensation of marked discomfort in the head
a type of pain that can't be controlled with standard medical care
A sudden movement downward (fall), usually resulting in injury.
this is a symptom of many diseases that attack the respiratory system
Examples: fever >38 degrees c or hypothermia <36 degrees c; tachycardia >90 beat/minute; tachypnea >24 breaths/minute; (4) leukocytosis >12,000 cells/cubic mm or 10% immature forms.
Symptoms and signs specifically associated with systemic inflammation and infection.
symptoms specifically associated with systemic inflammation and infection
is inflammation (swelling and irritation) of the epididymis, a tube at the back of the testicle that carries sperm
A disorder characterized by swelling due to excessive fluid accumulation at a specific anatomic site
a serious condition related to systemic inflammation, organ dysfunction, and organ failure.
systemic inflammatory response syndrome of non-infectious origin
decrease of strength in one or more muscles
Death occurring less than 24 hours from onset symptoms, not otherwise
A condition in which the blood is too acidic.
blood sugar (glucose) levels are abnormally high because the body does not produce enough insulin to meet its needs.
combined defect of insulin serection and insulin resistance
non-insulin-dependent diabetes mellitus with multiple complications
disorders of lipoprotein metabolism that lead to atherosclerosis. These abnormalities arise from genetic and secondary factors and are caused by excessive entry of lipoproteins into the bloodstream or an impairment in their removal, or both.
disorder of lipoprotein metabolism, unspecified
occur when the body has too little or too much calcium.
Conditions with excess lipids in the blood.
A condition characterized by a dry, waxy type of swelling (edema) with abnormal deposits of mucopolysaccharides in the skin and other tissues. It is caused by a deficiency of thyroid hormones.
A disorder characterized by laboratory test results that indicate a low concentration of potassium in the blood.
A disorder of lipoprotein metabolism characterized by high levels of cholesterol and triglycerides in the blood. It is caused by elevation of low density and very low density lipoproteins.
an energy deficit due to chronic deficiency of all macronutrients
having more weight than the average human
an abnormally high, unhealthy amount of body fat
morbid (severe) obesity due to excess calories
a condition marked by an abnormally high, unhealthy amount of body fat.
blood glucose, or blood sugar, levels are too high. With type 2 diabetes, the more common type, your body does not make or use insulin well.
type 2 diabetes mellitus with circulatory complications
a chronic medical condition in which sugar, or glucose, levels build up in your bloodstream. In type 2 diabetes, your body's cells aren't able to respond to insulin as well as they should.
type 2 diabetes mellitus with diabetic chronic kidney disease
A chronic condition that affects the way the body processes blood sugar (glucose)
type 2 diabetes mellitus with hyperglycemia
poorly controlled diabetes can lead to problems within the kidneys
type 2 diabetes mellitus with kidney complications
type 2 diabetes mellitus without complications
unspecified severe protein-calorie malnutrition
A nutritional condition produced by a deficiency of vitamin d in the diet, insufficient production of vitamin d in the skin, inadequate absorption of vitamin d from the diet, or abnormal conversion of vitamin d to its bioactive metabolites.
Abnormally decreased volume of circulating fluid (plasma) in body.
symptoms during pregnancy and the puerperium (after the pregnancy)
other specified diseases and conditions complicating pregnancy, childbirth and the puerperium
symptoms that are related to being pregnant, pregnancy is in the first trimester
other specified pregnancy related conditions, first trimester
a rare, itchy skin eruption that usually happens in the second or third trimester of pregnancy. It often begins with the appearance of very itchy red bumps or blisters on your abdomen and trunk, though it can show up on other parts of your body
when a mother gains weight during pregnancy
low weight gain in pregnancy, first trimester
when a mother becomes exhausted or fatigued during pregnancy
pregnancy related exhaustion and fatigue, first trimester
symptoms that are related to being pregnant, pregnancy is in the second trimester
other specified pregnancy related conditions, second trimester
low weight gain in pregnancy, second trimester
Fatigue caused from being pregnant, pregnancy is in the second trimester
pregnancy related exhaustion and fatigue, second trimester
symptoms that are related to being pregnant, pregnancy is in the third trimester
other specified pregnancy related conditions, third trimester
low weight gain in pregnancy, third trimester
Fatigue caused from being pregnant, pregnancy is in the third trimester
pregnancy related exhaustion and fatigue, third trimester
general changes in brain function, such as confusion, amnesia (memory loss), loss of alertness, disorientation (not cognizant of self, time, or place), defects in judgment or thought, unusual or strange behavior, poor regulation of emotions, and disruptions in perception
emotional disorder that makes the patient try to lose weight
Aphasia is the term for full loss of language and dysphasia is the term for partial loss of language.
effects a persons mental health and emotional state
mood disorder due to known physiological condition
someone has drank alcohol so much, that they depend on it to function
feelings of stress or fear that the patient cannot understand
A category of psychiatric disorders which are characterized by anxious feelings or fear often accompanied by physical symptoms associated with anxiety.
feelings of severe despondency and dejection, a feeling of worry, nervousness, or unease, typically about an imminent event or something with an uncertain outcome
A disorder characterized by melancholic feelings of grief or unhappiness.
major depressive disorder, single episode, unspecified
nicotine gives temprorary pleasure effects in your brain
A condition in which a person loses the ability to think, remember, learn, make decisions, and solve problems. Symptoms may also include personality changes and emotional problems.
majority of diagnosed are above the age of 65, this disease is not treatable.
dementia in alzheimer's disease with late onset
a damaging immune response by the body to a substance, especially pollen, fur, a particular food, or dust, to which it has become hypersensitive.
allergy status to other drugs, medicaments and biological substances status
code is used to show the patient cannot be given penicillin
patient is depending on renal dialysis which is a procedure that is a substitute for many of the normal functions of the kidneys
inability to breathe independently leading to dependence on respirator
dependence on respirator [ventilator] status
used to specify conditions like chronic kidey disease
Interruptions, blockage, or diseases that affect how your heart or blood vessels pump blood can cause complications such as heart disease or stroke.
personal history of diseases of the circulatory system
Treatment that lowers the activity of the body's immune system.
personal history of immunosupression therapy
personal history of long-term (current) use of anticoagulants
malignant, aggressive tumor that forms in the breast
personal history of malignant neoplasm of breast
tumors appear in the digestive system and stops functions
patient has had a history with nicotine. This information can be used to help pin down the exact disease
A cough that lasts for at least eight weeks. Usually just a minor annoyance
A condition due to lack of oxygen in respired air due to inhaling too much carbon monoxide
A condition in which there is not enough oxygen in the blood.
A condition of frequent and watery bowel movements. Causes of diarrhea include bacteria, viruses or parasites, certain medicines, food intolerances and diseases that affect the stomach, small intestine or colon.
A disorder characterized by a lack of clear and orderly thought and behavior.
A disorder characterized by elevation of the body's temperature above the upper limit of normal
fever and other physiologic disturbances of temperature regulation
Uremia resulting not from primary renal disease but from disturbances in circulation, fluid balance, or metabolism arising in other parts of the body.
chemistry tests are used to diagnose many conditions and diseases
other specified abnormal findings of blood chemistry
diabetes is usually an inherited disease that makes people obese and have problems with daily life
type 2 diabetes mellitus with unspecified complications
when a patient uses or loses more fluid than they take in
genetic anomaly that causes high cholesterol levels
careful watch of patient who has a high chance of being pregnant
supervision of other high-risk pregnancies
used to just note the patient's status with their pregnancy
high blood sugar because body cannot break down the sugar being taken in
type 2 diabetes mellitus with other specified complications
patient is unable to walk due to an unspecified reason
difficulty in walking, not elsewhere classified
Abnormally high blood glucose level, could be a sign of diabetes
type 2 diabetes mellitus with ketoacidosis
personal history of major surgery, not elsewhere classified
a serious condition resulting from the presence of harmful microorganisms in the blood or other tissues and the body’s response to their presence, potentially leading to the malfunctioning of various organs, shock, and death.
A disorder characterized by insufficiently healthy hematapoietic cell production by the bone marrow.
A blood disorder characterized by the appearance of sickle-shaped red blood cells and anemia.
body does not have enough nutrition to sustain itself
iron deficiecy is due to insufficient iron
this code must be sequenced as the second code, since it specifies that the disease has dementia in other diseases
https://acdis.org/articles/qa-%E2%80%98code-first%E2%80%99-versus-%E2%80%98-diseases-classified-elsewhere%E2%80%99 https://www.icd10data.com/ICD10CM/Codes/F01-F99/F01-F09/F02-/F02.8
dementia in other diseases classified elsewhere
An acutely disturbed state of mind that occurs in fever, intoxication, and other disorders and is characterized by restlessness, illusions, and incoherence of thought and speech
delirium due to known physiological condition
patients falls into depression, one episode
major depressive disorder, single episode, severe without psychotic features
A disorder characterized by difficulty in falling asleep and/or remaining asleep.
a sudden blockage in a lung artery. The cause is usually a blood clot in the leg called a deep vein thrombosis that breaks loose and travels through the bloodstream to the lung
other pulmonary embolism without acute cor pulmonale
A pathological constriction that can occur above (supravalvular stenosis), below (subvalvular stenosis), or at the aortic valve. It is characterized by restricted outflow from the left ventricle into the aorta.
Cessation of heart beat or myocardial contraction. If it is treated within a few minutes, heart arrest can be reversed in most cases to normal cardiac rhythm and effective circulation
A disease is a particular abnormal condition that negatively affects the structure or function of all or part of an organism, and that is not due to any immediate external injury.
New: disease
An anotomical entity that refers to the side of the body affected
laterality of anatomical entity
external ear canal eczema JYPM
外耳道湿疹 JYPM
eczema entity
湿疹体
chronic external ear canal otitis JYPM
慢性外耳道炎 JYPM
external ear canal abscess PKPM
外耳道脓肿 PKPM
granuloma behind ear PKPM
耳后肉芽肿 PKPM
behind ear
耳后
pinna perichondritis PKPM
耳廓软骨膜炎 PKPM
right side of anatomical entity
left side of anatomical entity
bilateral side of anatomical entity
unspecified unilateral side of anatomical entity
unspecified laterality of anatomical entity
swimmer's ear LHEM
游泳者耳病 LHEM
A benign condition in which there is a higher-than-normal level of a protein called m protein in the blood.
monoclonal gammopathy
the etiology entity is the reason or origination of disease process
Etiology Entity
Genetic Entity
遗传因素
Inflammation of bone caused by infection, generally in the legs, arm, or spine.
New: Other osteomyelitis
Coronary artery disease (CAD) is a group of diseases that includes: stable angina, unstable angina, myocardial infarction, and sudden coronary death.
Other forms of chronic ischemic heart disease
a broken bone that's caused by a disease, rather than an injury.
Pathological fracture, unspecified femur, sequela
other unspecified acquired perforation of ear DP
When fluid remains in the middle ear, the condition is called chronic serous otitis media. Sometimes a middle ear infection causes a hole (perforation) in the eardrum. A hole that does not heal within six weeks
Chronic serous otitis media
Chronic serous otitis media, unspecified ear
Pain in the inner or outer ear that may interfere with ability to hear, often caused by excess fluid and infection.
Otalgia, unspecified ear
Acute lymphoblastic leukemia is an acute form of leukemia, or cancer of the white blood cells, characterized by the overproduction and accumulation of cancerous, immature white blood cells, known as lymphoblasts.
Acute lymphoblastic leukemia, in relapse
Acute myeloid leukemia (AML), also known as acute myelogenous leukemia or acute nonlymphocytic leukemia (ANLL), is a cancer of the myeloid line of blood cells, characterized by the rapid growth of abnormal white blood cells that accumulate in the bone marrow and interfere with the production of normal blood cells.
Acute myeloblastic leukemia, minimal differentiation
Acute myeloblastic leukemia
Acute promyelocytic leukemia (APML, APL) is the M3 subtype of acute myelogenous leukemia (AML), a cancer of the white blood cells.
Acute promyelocytic leukemia
Pathological fracture, hip, unspecified, sequela
An acute myeloid leukemia (aml) in which abnormal promyelocytes predominate. It is characterized by the t(15;17)(q22;q12) translocation. There are two variants: the typical and microgranular variant. This aml is particularly sensitive to treatment with all trans-retinoic acid and has a favorable prognosis.
Acute promyelocytic leukemia, not having achieved remission
Acute myeloblastic leukemia, not having achieved remission
Subacute bacterial endocarditis is a type of endocarditis (more specifically, infective endocarditis). Subacute bacterial endocarditis can be considered a form of type III hypersensitivity.
Acute and subacute infective endocarditis
Infective endocarditis is a form of endocarditis. It is an inflammation of the inner tissues of the heart, the endocardium (such as its valves)
Acute and subacute endocarditis, unspecified
omental infarction, or omental torsion, is an acute vascular disorder which compromises tissue of the greater omentum – the largest peritoneal fold in the abdomen.
Acute vascular disorders of intestine
an irreversible injury to the intestine resulting from insufficient blood flow.
Acute infarction of intestine, part unspecified
Rheumatic disease profile
Rheumatic aortic stenosis
Rheumatic tricuspid valve diseases
Rheumatic tricuspid stenosis
Rheumatic tricuspid insufficiency
Rheumatic tricuspid stenosis and insufficiency
Other rheumatic tricuspid valve diseases
Rheumatic tricuspid valve disease, unspecified
Other nonrheumatic mitral valve disorders
Pathological fracture, unspecified tibia and fibula, sequela
Pathological fracture in other disease, left foot, subsequent encounter for fracture with routine healing
Remove mechanical kidney
Chronic kidney disease (CKD), also known as chronic renal disease, is progressive loss in kidney function over a period of months or years.
New: Chronic kidney disease, stage 1
Abortion is the ending of pregnancy by removing a fetus or embryo before it can survive outside the uterus. An abortion may be caused purposely and is then called an induced abortion, or less frequently, "induced miscarriage".
Complete abortion complicated by renal failure
Renal failure following (induced) termination of pregnancy
The biopsy findings were consistent with the renal lesions of toxemia of pregnancy, although other renal diseases such as Henoch Schonlein nephritis or lupus proliferative glomerulonephritis cannot be excluded
Kidney failure (acute) following ectopic and molar pregnancy
Renal failure following ectopic and molar pregnancy
Osteonecrosis occurs when your bones lose their blood supply. The bones die and eventually collapse, leading to pain and arthritis. You can have osteonecrosis in one or several bones. It is most common in the upper leg.
Osteonecrosis, unspecified
Bronchopneumonia, bronchial pneumonia or bronchogenic pneumonia (not to be confused with lobar pneumonia) is the acute inflammation of the walls of the bronchioles.
Pneumonia, unspecified organism
Respiratory disease is a medical term that encompasses pathological conditions affecting the organs and tissues that make gas exchange possible in higher organisms, and includes conditions of the upper respiratory tract, trachea, bronchi, bronchioles, alveoli, pleura and pleural cavity, and the nerves and muscles of breathing.
Influenza due to influenza a virus subtype h1n1
Influenza due to other identified influenza virus with other respiratory manifestations
Influenza, commonly known as "the flu", is an infectious disease caused by an influenza virus.
Influenza due to unidentified influenza virus with gastrointestinal manifestations
Gastroenteritis, also known as infectious diarrhea, is inflammation of the gastrointestinal tract that involves the stomach and small intestine.
Influenza due to unidentified influenza virus with encephalopathy
Influenza due to unidentified influenza virus with other manifestations
Other specified interstitial pulmonary diseases
Chronic obstructive pulmonary disease (COPD) is a type of obstructive lung disease characterized by chronically poor airflow.
Bronchitis, not specified as acute or chronic
Simple chronic bronchitis
Asthma is a common chronic inflammatory disease of the airways characterized by variable and recurring symptoms, reversible airflow obstruction and bronchospasm.
Unspecified asthma with (acute) exacerbation
the collapse or closure of a lung resulting in reduced or absent gas exchange.
Pulmonary collapse
Osteolysis is an active resorption of bone matrix by osteoclasts during the natural formation of healthy bones
Osteolysis, left ankle and foot
Coronary artery disease (CAD), also known as ischemic heart disease (IHD), is a group of diseases that includes: stable angina, unstable angina, myocardial infarction, and sudden coronary death. It is within the group of cardiovascular diseases of which it is the most common type.
Angina pectoris, unspecified
Unstable angina (UA) is a type of angina pectoris that is irregular.
ST elevation (STEMI) myocardial infarction of anterior wall
First-degree atrioventricular block (AV block), or PR prolongation, is a disease of the electrical conduction system of the heart in which the PR interval is lengthened beyond 0.20 seconds.
Atrioventricular block, first degree
Pulmonary hypertension (PH) is an increase of blood pressure in the pulmonary artery, pulmonary vein, or pulmonary capillaries, together known as the lung vasculature, leading to shortness of breath, dizziness, fainting, leg swelling and other symptoms.
Other secondary pulmonary hypertension
Enteritis (entero- + -itis) is inflammation of the small intestine.
Crohn's disease, unspecified
An enterolith is a mineral concretion or calculus formed anywhere in the gastrointestinal system.
Other impaction of intestine
A congenital or acquired weakness or opening in the diaphragm which allows abdominal contents to protrude into the chest cavity; congenital diaphragmatic hernias are caused when the embryonic diaphragm fails to fuse.
Diaphragmatic hernia without obstruction or gangrene
A mouth ulcer (also termed an oral ulcer, or a mucosal ulcer) is an ulcer that occurs on the mucous membrane of the oral cavity.
Oral mucositis (ulcerative), unspecified
A disorder characterized by acute inflammation to the vermiform appendix caused by a pathogenic agent.
Unspecified acute appendicitis
Acute inflammation of the appendix. Acute appendicitis is classified as simple, gangrenous, or perforated.
Unspecified appendicitis
A hernia is caused by the protrusion of a viscus (in the case of groin hernias, an intraabdominal organ) through a weakness in the containing wall.
Femoral hernia, unilateral with obstruction
Unilateral femoral hernia, with obstruction, without gangrene, not specified as recurrent
a hernia is the exit of an organ, such as the bowel, through the wall of the cavity in which it normally resides.
Unspecified abdominal hernia with obstruction, without gangrene
Enterocolitis or coloenteritis is an inflammation of the digestive tract, involving enteritis of the small intestine and colitis of the colon.
New: Ulcerative (chronic) pancolitis
A chronic, inflammatory bowel disease that causes inflammation in the digestive tract.
New: Other ulcerative colitis without complications
A biliary obstruction is a blockage of the bile ducts.
Obstruction of gallbladder
an eye disorder that involves a layer of blood vessels called the choroid.
New: Hereditary choroidal dystrophy
New: Hereditary choroidal dystrophy, unspecified
affect this vital tissue. They can affect your vision, and some can be serious enough to cause blindness.
Other retinal disorders
a decreased ability to see to a degree that causes problems not fixable by usual means, such as glasses.
Disorders of visual cortex
progressive loss in kidney function over a period of months or years.
New: Chronic kidney disease, stage 2 (mild)
Reflux nephropathy is kidney damage (nephropathy) due to urine flowing backward (reflux) from the bladder toward the kidneys; the latter is called vesicoureteral reflux (VUR).
Nonobstructive reflux-associated chronic pyelonephritis
Acute proliferative glomerulonephritis is a disorder of the glomeruli (glomerulonephritis), or small blood vessels in the kidneys.
Acute nephritic syndrome with other morphologic changes
a kidney disorder that causes your body to pass too much protein in your urine
Unspecified nephritic syndrome with unspecified morphologic changes
Ureteral stones are kidney stones that have become stuck in one or both ureters (the tubes that carry urine from the kidneys to the bladder)
New: Calculus of ureter
A genetic or acquired polyuric disorder characterized by persistent hypotonic urine and hypokalemia. ~ an inability to concentrate urine due to impaired renal tubule response to vasopressin (ADH), which leads to excretion of large amounts of dilute urine.
Nephrogenic diabetes insipidus
New: Acute cystitis
a sudden inflammation of the urinary bladder
New: Acute cystitis without hematuria
sudden onset of hematuria combined with bladder pain and irritative bladder symptoms. Hematuria is blood in the urine.
New: Acute cystitis with hematuria
Age-associated prostate gland enlargement that can cause urination difficulty.
Benign prostatic hyperplasia without lower urinary tract symptoms
Osteoarthritis (OA) is a type of joint disease that results from breakdown of joint cartilage and underlying bone.
Osteoarthritis of knee, unspecified
Spondyloarthropathy or spondyloarthrosis refers to any joint disease of the vertebral column.
New: Ankylosing spondylitis
Childhood arthritis is any form of arthritis or arthritis-related conditions which affects individuals under the age of 16.
New: Juvenile rheumatoid polyarthritis (seronegative)
New: Juvenile arthritis, unspecified, unspecified site
Toxic oil syndrome is a musculoskeletal disease most famous for a 1981 outbreak in Spain which killed over 600 people and was likely caused by contaminated colza oil.
Other specified systemic involvement of connective tissue
A disorder characterized by an infectious process involving the skeletal muscles.
New: Infective myositis
bacterial infection of the skeletal muscles which results in a pus-filled abscess.
New: Infective myositis, unspecified site
A chronic condition in which both the breakdown and regrowth of bone are increased.
Osteitis deformans in neoplastic diseases, unspecified site
a fatigue-induced fracture of the bone caused by repeated stress over time.
New: Stress fracture, unspecified tibia and fibula, sequela
New: Stress fracture, unspecified foot, sequela
infection and inflammation of the bone or bone marrow
New: Other chronic osteomyelitis
Flaccid paralysis is a clinical manifestation characterized by weakness or paralysis and reduced muscle tone without other obvious cause (e.g., trauma).
Flaccid hemiplegia
If you have epilepsy, you may have seizures repeatedly. A seizure that lasts longer than 5 minutes, or having more than 1 seizure within a 5 minutes period, without returning to a normal level of consciousness between episodes
Epilepsy, unspecified, not intractable, without status epilepticus
A slight paralysis or weakness of both legs.
New: araplegia
New: Paraplegia, unspecified
symmetric, ascending weakness that progresses over days and is associated with normal sensation, with often preserved tendon reflexes, and with an increased cerebrospinal fluid protein concentration.
Paralytic syndrome, unspecified
New: Communicating hydrocephalus
a rare medical condition in which there is an abnormal accumulation of cerebrospinal fluid (CSF) in the brain.
New: Hydrocephalus, unspecified
large number of infections of the bowels including: cholera, typhoid fever, paratyphoid fever, other types of salmonella infections, shigellosis, botulism, gastroenteritis, and amoebiasis among others.
Contact with and (suspected) exposure to intestinal infectious diseases
Encounter for care and examination of lactating mother
Encounter for attention to dressings, sutures and drains
Aftercare visit codes cover situations occurring when the initial treatment of a disease has been performed and the patient requires continued care during the healing or recovery phase, or care for the long-term consequences of the disease
Encounter for other specified postprocedural aftercare
Other problems related to social environment
Problem related to primary support group, unspecified
New: Acquired absence of lung [part of]
a person or other organism that has become infected with a pathogen, but that displays no signs or symptoms. Although unaffected by the pathogen, carriers can transmit it to others or develop symptoms in later stages of the disease.
Carrier of other infectious diseases
complication inserting a temporary long, flexible, y-shaped tube that is inserted through one of the central veins found in your neck, chest or groin to allow access to the bloodstream
Encounter for fitting and adjustment of non-vascular catheter
places one among the people considered obese, but also fall in the higher end of this category, meaning that gaining even more weight would put one in the danger of classifying as extremely obese
Body mass index [BMI] 38.0-38.9, adult
Personal history of malignant neoplasm of stomach
adenocarcinoma, primary gastric lymphoma, gastrointestinal stromal tumor (GIST), and neuroendocrine (carcinoid) tumors in the stomach
Personal history of other malignant neoplasm of stomach
Personal history of antineoplastic chemotherapy
a medical procedure — either temporary or permanent — that involves creating an opening in the neck in order to place a tube into a person's windpipe.
Tracheostomy status
a medical procedure performed to replace bone marrow that has been damaged or destroyed by disease, infection, or chemotherapy
Growth hormone deficiency after bone marrow transplant
New: Bone marrow transplant status
a condition or factor that serves as a reason to withhold a certain medical treatment due to the harm that it would cause the patient.
Procedure and treatment not carried out because of contraindication
Needs assistance with community resources
Other problems related to care provider dependency
New: Other transplanted organ and tissue status
Presence of other specified devices
Abdominal pain, also known as stomach pain or stomachache, is a common symptom associated with both temporary, non-serious disorders and more serious conditions.
Pain localized to upper abdomen
voluntary or involuntary fecal soiling in children who have usually already been toilet trained.
New: Fecal incontinence
Anterograde amnesia is a loss of the ability to create new memories after the event that caused the amnesia, leading to a partial or complete inability to recall the recent past, while long-term memories from before the event remain intact.
New: Anterograde amnesia
Very low level of personal hygiene
A general state of ill health involving marked weight loss and muscle loss.
Cachexia
Respiratory arrest is the cessation of normal breathing due to failure of the lungs to function effectively.
Respiratory arrest
a life-threatening lung injury that allows fluid to leak into the lungs. Breathing becomes difficult and oxygen cannot get into the body.
New: Acute respiratory distress
A disorder characterized by the reflexive act of ejecting the contents of the stomach through the mouth.
Vomiting, unspecified
An inability to experience pleasure from activities usually found enjoyable.
Anhedonia
colitis (inflammation of the large intestine) resulting from infection with Clostridium difficile, a spore-forming bacterium.
Enterocolitis due to Clostridium difficile
Sepsis is a whole-body inflammatory response to an infection.
Other specified sepsis
Other intestinal Escherichia coli infections
The viral hemorrhagic (or haemorrhagic) fevers (VHFs) are a diverse group of animal and human illnesses in which fever and hemorrhage are caused by a viral infection.
Sylvatic yellow fever
Urban yellow fever
A cervical fracture, commonly called a broken neck, is a catastrophic fracture of any of the seven cervical vertebrae in the neck
Fracture of neck, unspecified, initial encounter
occur when the bony block or vertebral body in the spine collapses, which can lead to severe pain, deformity and loss of height.
Unspecified fracture of unspecified thoracic vertebra, initial encounter for closed fracture
A break in the bone connecting the breastbone and shoulder.
Fracture of clavicle
an injury involving an external or internal break in body tissue, usually involving the skin
Unspecified open wound of unspecified forearm, initial encounter
A network of ligaments holds them in place and allows them to move. A tear in any of these ligaments can result in two or more of your carpal bones being pushed out of their usual position
Subluxation and dislocation of wrist and hand joints
A hip fracture is a serious femoral fracture that occurs in the proximal end of the femur (the long bone running through the thigh), near the hip.
Fracture of unspecified part of neck of unspecified femur, sequela
the proximal femur between the cervical region and the shaft. Subtrochanteric fracture, with a fracture line running from an area within 5 cm distal to the lesser trochanter
Unspecified trochanteric fracture of unspecified femur, initial encounter for closed fracture
disruptions in the cartilaginous physis of long bones that may or may not involve epiphyseal or metaphyseal bone.
Unspecified physeal fracture of upper end of unspecified femur, sequela
is a break in the patella, or kneecap, the small bone that sits at the front of your knee
Unspecified fracture of unspecified patella, sequela
a break or crack in one of the bones in your leg.
Unspecified fracture of unspecified lower leg, sequela
a complete or incomplete break in one of the five metatarsal bones in each foot.
New: Fracture of unspecified metatarsal bone(s), left foot, subsequent encounter for fracture with routine healing
a bone break that happens in the bones of your foot, heel, toes, or ankle. There are different types of foot fractures, but the most common is a hairline fracture.
New: Unspecified fracture of unspecified foot, sequela
Wound healing is a critical outcome in surgery, and postoperative wound disruption or separation of the layers of a surgical wound with disruption of the fascia is a serious complication
New: Unspecified fracture of unspecified toe(s), sequela
Pathologic process consisting of a partial or complete disruption of the layers of a surgical wound.
Disruption of external operation (surgical) wound, not elsewhere classified
Disruption of external operation (surgical) wound, not elsewhere classified, initial encounter
Complications of gaining I.V. may include infiltration, hematoma, an air embolism, phlebitis, extravascular drug administration, and intraarterial injection. Intraarterial injection is more rare, but as threatening.
Other mechanical complication of infusion catheter, initial encounter
used to specify a diagnosis of secondary and unspecified malignant neoplasm of intrathoracic lymph nodes.
Secondary and unspecified malignant neoplasm of intrathoracic lymph nodes
A rare condition in which chronic lymphocytic leukemia (cll) changes into a fast-growing type of lymphoma. Symptoms of richter syndrome include fever, loss of weight and muscle mass, and other health problems.
New: Chronic lymphocytic leukemia of B-cell type
B-cell chronic lymphocytic leukemia (B-CLL), also known as chronic lymphoid leukemia (CLL), is the most common type of leukemia (a type of cancer of the white blood cells) in adults.
New: Chronic lymphocytic leukemia of B-cell type not having achieved remission
A state of bone marrow suppression and failure that is caused by a cytotoxic or adverse immunologic response to a drug treatment, leading to a failure of production of red blood cells, white cells and platelets.
New: Drug-induced aplastic anemia
Renal cell carcinoma is a kidney cancer that originates in the lining of the proximal convoluted tubule, a part of the very small tubes in the kidney that transport waste molecules from the blood to the urine.
Malignant neoplasm of kidney, except renal pelvis
Bladder cancer is any of several types of cancer arising from the epithelial lining of the urinary bladder.
Malignant neoplasm of bladder, unspecified
Pseudomyxoma peritonei (PMP) is a clinical condition caused by cancerous cells (mucinous adenocarcinoma) that produce abundant mucin or gelatinous ascites.
Secondary malignant neoplasm of retroperitoneum and peritoneum
Evans syndrome is an autoimmune disease in which an individual's antibodies attack their own red blood cells and platelets.
Immune thrombocytopenic purpura
An immune disorder is a dysfunction of the immune system.
Other specified immunodeficiencies
A neoplasm without malignant characteristics arising from the lip.
Benign neoplasm of lip
New: Respiratory arrest
A condition in which the cavities around the nasal passages become inflamed.
*acute sinusitis
Parainfluenza virus pneumonia
a disease that attacks one or both lungs, virus is unspecified
Other viral pneumonia
Pneumonia due to Klebsiella pneumoniae
Pneumonia due to Pseudomonas
Pneumonia due to Escherichia coli
Pharyngitis, or acute pharyngitis, is an inflammation of the back of the throat, otherwise known as the pharynx. The condition generally causes pain and a sensation of scratchiness in the region of the throat, as well as difficulty swallowing. The condition is typically referred to as a sore throat.
*Acute pharyngitis
An inflammation of the two oval-shaped pads of tissue at the back of the throat.
*Acute tonsillitis
Laryngitis may cause sore throat and hoarse voice but can also be associated with tracheitis and even bronchiolitis as the pathogen, infection, and host responses move further down the respiratory tree.
*Acute laryngitis and tracheitis
Epiglottitis, acute laryngitis, and croup are infections of the upper airway, affecting the epiglottis, larynx, and larynx and trachea, respectively. Croup may also involve the bronchi.
Acute obstructive laryngitis [croup] and epiglottitis
*Acute obstructive laryngitis [croup] and epiglottitis
(bron-kye-tis) inflammation (swelling and reddening) of the bronchi.
*Bronchitis, not specified as acute or chronic
Mucoid sputum production characterizes simple chronic bronchitis. Persistent or recurrent purulent sputum production in the absence of localized suppurative disease, such as bronchiectasis, characterizes chronic mucopurulent bronchitis
Simple and mucopurulent chronic bronchitis
*Simple and mucopurulent chronic bronchitis
A subcategory of chronic obstructive pulmonary disease. The disease is characterized by hypersecretion of mucus accompanied by a chronic (more than 3 months in 2 consecutive years) productive cough. Infectious agents are a major cause of chronic bronchitis.
*Unspecified chronic bronchitis
*Emphysema
Acute bronchitis due to rhinovirus
A chronic disease in which the bronchial airways in the lungs become narrowed and swollen, making it difficult to breathe. Symptoms include wheezing, coughing, tightness in the chest, shortness of breath, and rapid breathing. An attack may be brought on by pet hair, dust, smoke, pollen, mold, exercise, cold air, or stress.
*Asthma
Influenza is a viral infection that attacks your respiratory system — your nose, throat and lungs.
*Influenza due to certain identified influenza viruses
Influenza, commonly known as "the flu", is an infectious disease caused by an influenza virus. Symptoms can be mild to severe.
Influenza due to other identified influenza virus
*Influenza due to other identified influenza virus
Influenza due to unidentified influenza virus with other respiratory manifestations
Influenza due to unidentified influenza virus
*Influenza due to unidentified influenza virus
Viral pneumonia is an infection of your lungs caused by a virus.
Viral pneumonia, not elsewhere classified
*Viral pneumonia, not elsewhere classified
Pneumococcal disease is caused by common bacteria (Streptococcus pneumoniae) that can attack different parts of the body. When these bacteria invade the lungs, they can cause pneumonia; when they invade the bloodstream, they can cause sepsis; and when they invade the covering of the brain, they can cause meningitis.
*Pneumonia due to Streptococcus pneumoniae
An acute URI is a contagious infection of your upper respiratory tract. Your upper respiratory tract includes the nose, throat, pharynx, larynx, and bronchi.
Acute upper respiratory infections of multiple and unspecified sites
*Acute upper respiratory infections of multiple and unspecified sites
H. influenzae most often cause pneumonia, but can also cause severe illnesses like meningitis and bloodstream infections
*Pneumonia due to Hemophilus influenzae
Inflammation of the lung parenchyma that is caused by bacterial infections.
*Bacterial pneumonia, not elsewhere classified
Pneumonia is an infection of one or both of the lungs caused by bacteria, viruses, or fungi.
Pneumonia due to other infectious organisms, not elsewhere classified
*Pneumonia due to other infectious organisms, not elsewhere classified
Infection that inflames air sacs in one or both lungs, which may fill with fluid.
Pneumonia in diseases classified elsewhere
*Pneumonia in diseases classified elsewhere
A type of disease that affects the lungs and other parts of the respiratory system
Respiratory conditions due to other external agents
*Respiratory conditions due to other external agents
Pneumonitis (noo-moe-NIE-tis) is a general term that refers to inflammation of lung tissue
*Pneumonitis due to solids and liquids
Respiratory conditions due to inhalation of chemicals, gases, fumes and vapors
*Respiratory conditions due to inhalation of chemicals, gases, fumes and vapors
allergic alveolitis and pneumonitis due to inhaled organic dust and particles of fungal, actinomycetic or other origin
Hypersensitivity pneumonitis due to organic dust
*Hypersensitivity pneumonitis due to organic dust
Pneumoconiosis is one of a group of interstitial lung disease caused by breathing in certain kinds of dust particles that damage your lungs.
Airway disease due to specific organic dust
*Airway disease due to specific organic dust
Pneumoconiosis associated with tuberculosis
*Pneumoconiosis associated with tuberculosis
A diffuse parenchymal lung disease caused by inhalation of dust and by tissue reaction to their presence. These inorganic, organic, particulate, or vaporized matters usually are inhaled by workers in their occupational environment, leading to the various forms (asbestosis; byssinosis; and others). Similar air pollution can also have deleterious effects on the general population.
*Unspecified pneumoconiosis
Pneumoconiosis literally means “dust in the lung,” and the term has come to refer to disease of the lung related to the inhalation of dusts.
Pneumoconiosis due to other inorganic dusts
*Pneumoconiosis due to other inorganic dusts
A form of pneumoconiosis resulting from inhalation of dust containing crystalline form of silicon dioxide, usually in the form of quartz. Amorphous silica is relatively nontoxic.
Pneumoconiosis due to dust containing silica
*Pneumoconiosis due to dust containing silica
A form of pneumoconiosis caused by inhalation of asbestos fibers which elicit potent inflammatory responses in the parenchyma of the lung. The disease is characterized by interstitial fibrosis of the lung, varying from scattered sites to extensive scarring of the alveolar interstitium.
Pneumoconiosis due to asbestos and other mineral fibers
*Pneumoconiosis due to asbestos and other mineral fibers
A chronic lung disorder characterized by deposition of coal dust in the lung parenchyma leading to the formation of black nodules and emphysema. It occurs in coal miners.
*Coalworker's pneumoconiosis
Bronchitis is an inflammation of the bronchial tubes, the airways that carry air to your lungs. It causes a cough that often brings up mucus, as well as shortness of breath, wheezing, and chest tightness.
*Acute bronchitis
Bronchiolitis is an acute inflammatory injury of the bronchioles that is usually caused by a viral infection (most commonly respiratory syncytial virus)
*Acute bronchiolitis
Pleural plaques are deposits of hyalinized collagen fibers in the parietal pleura.
*Pleural plaque
The most frequent air leak, called a pneumothorax, is when the air collects between the lung and the chest wall.
*Pneumothorax and air leak
There are three types of pleural disorders—pleurisy, pleural effusion, and pneumothorax—and they have varying causes.
*Other pleural conditions
Respiratory disorders, or lung diseases, are disorders such as asthma, cystic fibrosis, emphysema, lung cancer, mesothelioma, pulmonary hypertension, and tuberculosis.
Respiratory disorders in diseases classified elsewhere
*Respiratory disorders in diseases classified elsewhere
*Other respiratory disorders
When a person has acute respiratory failure, the usual exchange between oxygen and carbon dioxide in the lungs does not occur.
Respiratory failure, not elsewhere classified
*Respiratory failure, not elsewhere classified
Simple pulmonary eosinophilia (SPE), also known as Loeffler syndrome, is a rare, temporary (transient) respiratory disorder characterized by the accumulation of eosinophils in the lungs (pulmonary eosinophilia). Eosinophils are a type of white blood cell and are part of the immune system.
Pulmonary eosinophilia, not elsewhere classified
*Pulmonary eosinophilia, not elsewhere classified
Interstitial pneumonia, Idiopathic pulmonary fibrosis, Nonspecific interstitial pneumonitis
*Other interstitial pulmonary diseases
Acute bronchiolitis, unspecified
Emphysema, unspecified
Nonallergic asthma
Mild intermittent asthma, uncomplicated
facial pain, localized to the cheek, but also in the frontal area or the teeth, that is made worse by stooping down or straining. The pain can be unilateral or bilateral, and tenderness may overlie the sinus.
Acute maxillary sinusitis
Acute sinusitis causes the spaces inside your nose (sinuses) to become inflamed and swollen.
Acute maxillary sinusitis, unspecified
Acute frontal sinusitis (AFrS) is defined as an acute bacterial infection of the frontal sinus cavity.
Acute frontal sinusitis, unspecified
Other acute sinusitis
Acute sinusitis is most often caused by the common cold. Signs and symptoms may include a blocked and stuffy (congested) nose, which may block your sinuses and prevent drainage of mucus.
Acute sinusitis, unspecified
Strep throat is caused by infection with a bacterium known as Streptococcus pyogenes, also called group A streptococcus
Streptococcal pharyngitis
Acute pharyngitis is characterized by the rapid onset of sore throat and pharyngeal inflammation (with or without exudate)
Acute pharyngitis due to other specified organisms
An acute inflammation of the tonsils caused by viruses or bacteria. Signs and symptoms include fever, enlargement of the tonsils, difficulty swallowing, and enlargement of the regional lymph nodes.
Acute tonsillitis, unspecified
Acute laryngitis is characterized by inflammation and congestion of the larynx in the early stages
Acute laryngitis
Influenza is a common cause of pneumonia, especially among younger children, the elderly, pregnant women, or those with certain chronic health conditions or who live in a nursing home
Influenza due to other identified influenza virus with other specified pneumonia
Influenza due to other identified influenza virus with other manifestations
Flu (influenza) is an infection of the nose, throat and lungs, which are part of the respiratory system. Influenza is commonly called the flu, but it's not the same as stomach "flu" viruses that cause diarrhea and vomiting
Influenza due to unidentified influenza virus with unspecified type of pneumonia
Adenovirus pneumonia occasionally occurs in immunocompromised hosts and is characterized by rapid clinical deterioration compared to other viral pneumonias with a reported fatality rate of 50%.
Adenoviral pneumonia
RSV is the most common cause of bronchiolitis (inflammation of the small airways in the lung) and pneumonia (infection of the lungs) in children younger than 1 year of age in the United States.
Respiratory syncytial virus pneumonia
Human metapneumovirus is a negative-sense single-stranded RNA virus of the family Pneumoviridae and is closely related to the Avian metapneumovirus subgroup C.
Human metapneumovirus pneumonia
MSSA, or methicillin-susceptible Staphylococcus aureus, is an infection caused by a type of bacteria commonly found on the skin.
Pneumonia due to Methicillin susceptible Staphylococcus aureus
Group B (i.e.,Streptococcus agalactiae) streptococci are a major cause of neonatal sepsis and pneumonia. In adults, pneumonia accounts for approximately 15% of adult infections by group B streptococci. Most adults with group B streptococcal pneumonia are debilitated and develop pneumonia as a consequence of aspiration.
Pneumonia due to streptococcus, group B
Streptococcus pneumoniae is a gram-positive, lancet-shaped bacterium and a cause of community-acquired pneumonia.
Pneumonia due to other streptococci
Pneumonia is inflamed or swollen lung tissue due to infection with a germ. Mycoplasma pneumonia is caused by the bacteria Mycoplasma pneumoniae (M pneumoniae). This type of pneumonia is also called atypical pneumonia because the symptoms are different from those of pneumonia due to other common bacteria.
Pneumonia due to Mycoplasma pneumoniae
Allergic contact dermatitis of external ear
Allergic contact dermatitis of external ear DP
外耳过敏性接触性皮炎
其他特指的外耳炎性疾患
Other specified inflammatory disorder of external ear
Other specified inflammatory DP of external ear
Irritant contact dermatitis of external ear
Irritant contact dermatitis of external ear DP
刺激物接触性外耳皮炎
Acute serous otitis media, unspecified ear
Acute serous otitis media DP
急性浆液性中耳炎
other acute nonsuppurative otitis media DP
急性非化脓性中耳炎，其他的
blue drum syndrome DP
蓝鼓膜综合征
serous
浆液性
middle ear
nonsuppurative
非化脓性
ready for release
pending final vetting
requires discussion
## Elucidation This is used when the statement/axiom is assumed to hold true 'eternally' ## How to interpret (informal) First the "atemporal" FOL is derived from the OWL using the standard interpretation. This axiom is temporalized by embedding the axiom within a for-all-times quantified sentence. The t argument is added to all instantiation predicates and predicates that use this relation. ## Example Class: nucleus SubClassOf: part_of some cell forall t : forall n : instance_of(n,Nucleus,t) implies exists c : instance_of(c,Cell,t) part_of(n,c,t) ## Notes This interpretation is *not* the same as an at-all-times relation
axiom holds for all times
Please see the project site https://github.com/BFO-ontology/BFO, the bfo2 owl discussion group http://groups.google.com/group/bfo-owl-devel , the bfo2 discussion group http://groups.google.com/group/bfo-devel, the tracking google doc http://goo.gl/IlrEE, and the current version of the bfo2 reference http://purl.obolibrary.org/obo/bfo/dev/bfo2-reference.docx . This ontology is generated from a specification at https://github.com/BFO-ontology/BFO/tree/master/src/ontology/owl-group/specification/ and with the code that generates the OWL version in https://github.com/BFO-ontology/BFO/tree/master/src/tools/. A very early version of BFO version 2 in CLIF is at http://purl.obolibrary.org/obo/bfo/dev/bfo.clif
The BSD license on the BFO project site refers to code used to build BFO.
This BFO 2.0 version represents a major update to BFO and is not strictly backwards compatible with BFO 1.1. The previous OWL version of BFO, version 1.1.1 will remain available at http://ifomis.org/bfo/1.1 and will no longer be updated. The BFO 2.0 OWL is a classes-only specification. The incorporation of core relations has been held over for a later version.
BFO 2 Reference: For both terms and relational expressions in BFO, we distinguish between primitive and defined. ‘Entity’ is an example of a primitive term. Primitive terms in a highest-level ontology such as BFO are terms that are so basic to our understanding of reality that there is no way of defining them in a non-circular fashion. For these, therefore, we can provide only elucidations, supplemented by examples and by axioms.
BFO 2 Reference: BFO does not claim to provide complete coverage of entities of all types. It seeks only to provide coverage of those entities studied by empirical science together with those entities which affect or are involved in human activities such as data processing and planning - coverage that is sufficiently broad to provide assistance to those engaged in building domain ontologies for purposes of data annotation.
BFO 2 Reference: BFO’s treatment of continuants and occurrents - as also its treatment of regions, rests on a dichotomy between space and time, and on the view that there are two perspectives on reality - earlier called the ‘SNAP’ and ‘SPAN’ perspectives, both of which are essential to the non-reductionist representation of reality as we understand it from the best available science
OBO Relations Ontology
The OBO Relations Ontology (RO) is a collection of OWL relations (ObjectProperties) intended for use across a wide variety of biological ontologies.