The EXAMODE ontology
type: Ontology
imports: core
creator: Laura Menotti
creator: Stefano Marchesin
creator: Gianmaria Silvello
description: ExaMode focuses on histopathological diagnosis of tissues with the aim of detecting diseases. We take into account the future cancer incidence and mortality burden worldwide which is predicted to be increasing (by 63% from 2018 until 2040); hence, we decided to focus our attention mainly on four use-cases: Colon cancer, Cervix cancer, Lung cancer, Celiac disease In this ontology we model the main aspects concerning these diseases and the patients' histopathological reports concerning them. The focus of the ontology is on the pathological report and not on the diseases and their modeling. The reports can have a positive, negative or inconclusive outcome. The ExaMode ontology defines a formal classification schema to encode the medical reports in histopathology and to define the formal relationships between diseases, their anatomical locations and the procedures to withdrawn and analyse the human tissues. We model the anatomical location of the disease, the main information about the disease itself and the procedure adopted to withdraw and analyse the tissues.
rights: Copyright 2020-2022 University of Padua, Italy Licensed under the Creative Commons Attribution-ShareAlike 4.0 International License https://creativecommons.org/licenses/by-sa/4.0/ You may obtain a copy of the License at https://creativecommons.org/licenses/by-sa/4.0/legalcode This work has been supported by the EXAMODE project https://www.examode.eu/ funded by the European Union’s Horizon 2020 research and innovation programme under the grant agreement No 825292
comment: EXAMODE stands for Extreme-scale Analytics via Multimodal Ontology Discovery & Enhancement
version info: This ontology is encoded in OWL 2 DL

has semantic type
type: AnnotationProperty
has exact synonym: Semantic_Type
comment: In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. NB: this property is different from hasSemanticArea since this property serves as an annotation to give, when possible, a label indicating the semantic type. This label is taken from Ontobee. hasSemanticArea is used instead to give a tag to every entity, identifying what type of entity that is.
comment: Used to specify the semantic type of something.
label: ha tipo semantico @it
label: heeft een semantisch type @nl
definition: A property that represents a description of the sort of thing or category to which a concept belongs in the context of the UMLS semantic network.
range: string
domain: Thing

alternative definition
type: AnnotationProperty
comment: To give an alternative definition (coming from another authoritative source) to the annotated entity.
label: alternatieve definitie @nl
label: definzione alternativa @it
sub property of: definition
range: string
domain: Thing

external definition
type: AnnotationProperty
comment: A definition coming from a source external to the ones commonly used in Examode, or from a non-authoritative one.
label: definizione esterna @it
label: externe definitie @nl
sub property of: definition

structure notes
type: AnnotationProperty
comment: Notes about the structure of some entity, e.g. a location or an intervention.
label: note strutturali @it
label: structurele opmerkingen @nl
sub property of: definition
range: string
domain: Thing

has broad synonym
type: AnnotationProperty
comment: A property to connect an entity to broad synobyms.
label: ha sinonimi generici @it
label: heeft een breed synoniem @nl
sub property of: has synonym
range: string
domain: Thing

has exact synonym
type: AnnotationProperty
comment: An alias in which the alias exhibits true synonymy.
label: ha sinonimi esatti @it
label: heeft een exact synoniem @nl
sub property of: has synonym
range: string
domain: Thing

has related synonym
type: AnnotationProperty
comment: To connect an entity to sinonims that are only related to it, and not completely equivalent to it.
label: ha sinonimi correlati @it
label: heeft verwant synoniem @nl
sub property of: has synonym
range: string
domain: Thing

has synonym
type: AnnotationProperty
comment: To connect an entity to strings representing synonims to the xsd:string given as label. They should be accompanies by the annotation specifying the corresponding language.
label: ha sinonimo @it
label: heeft synoniem @nl
range: string
domain: Thing

cardinality
type: AnnotationProperty
comment: The cardinality constraint owl:cardinality is a built-in OWL property that links a restriction class to a data value belonging to the range of the XML Schema datatype nonNegativeInteger. A restriction containing an owl:cardinality constraint describes a class of all individuals that have exactly N semantically distinct values (individuals or data values) for the property concerned, where N is the value of the cardinality constraint. Syntactically, the cardinality constraint is represented as an RDF property element with the corresponding rdf:datatype attribute. This construct is in fact redundant as it can always be replaced by a pair of matching owl:minCardinality and owl:maxCardinality constraints with the same value. It is included as a convenient shorthand for the user. The following example describes a class of individuals that have exactly two parents: <owl:Restriction> <owl:onProperty rdf:resource="#hasParent" /> <owl:cardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:cardinality> </owl:Restriction>
range: nonNegativeInteger
domain: Thing

maxCardinality
type: AnnotationProperty
comment: The cardinality constraint owl:maxCardinality is a built-in OWL property that links a restriction class to a data value belonging to the value space of the XML Schema datatype nonNegativeInteger. A restriction containing an owl:maxCardinality constraint describes a class of all individuals that have at most N semantically distinct values (individuals or data values) for the property concerned, where N is the value of the cardinality constraint. Syntactically, the cardinality constraint is represented as an RDF property element with the corresponding rdf:datatype attribute. The following example describes a class of individuals that have at most two parents: <owl:Restriction> <owl:onProperty rdf:resource="#hasParent" /> <owl:maxCardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:maxCardinality> </owl:Restriction>
range: nonNegativeInteger
domain: Thing

minCardinality
type: AnnotationProperty
comment: The cardinality constraint owl:minCardinality is a built-in OWL property that links a restriction class to a data value belonging to the value space of the XML Schema datatype nonNegativeInteger. A restriction containing an owl:minCardinality constraint describes a class of all individuals that have at least N semantically distinct values (individuals or data values) for the property concerned, where N is the value of the cardinality constraint. Syntactically, the cardinality constraint is represented as an RDF property element with the corresponding rdf:datatype attribute. The following example describes a class of individuals that have at least two parents: <owl:Restriction> <owl:onProperty rdf:resource="#hasParent" /> <owl:minCardinality rdf:datatype="&xsd;nonNegativeInteger">2</owl:minCardinality> </owl:Restriction> Note that an owl:minCardinality of one or more means that all instances of the class must have a value for the property.
range: nonNegativeInteger
domain: Thing

annotated rule
type: AnnotationProperty
comment: This property is used to annotated classes with a comment representing the rule that we inferred during the process of definition of this ontology. This rule may be implemented to extract entities from a clinical case record. NB: we do not guarantee that these rules are always valid, or that they are the only valid. It may be the case that they are inaccurate since we were only able to infer them from the cases that were provided to us. Treat these annotations only as a documentation of our process and for a first implementation of the entities extractor.
label: annotatieregel @nl
label: regola per l'annotazione @it
range: string
domain: Thing

associated disease
type: AnnotationProperty
comment: In this ontologies different entities were developed to deal with specific entities. This property is used to link one entity to the corresponding disease it was defined for. It is just some more information to keep track of the nature of entities and to what disease they originally belong.
label: geassocieerde ziekte @nl
label: malattia associata @it
range: Disease or Disorder
domain: Thing

associated keyword in diagnosis
type: AnnotationProperty
comment: Property to take notes (for reminding us/ help us define rule/ maybe do some reasoning in the future) about which keywords to look for in the Diagnosis
label: bijbehorende trefwoorden in de diagnose @nl
label: parole chiave associate nella diagnosi @it
range: string
domain: Thing

associated keyword in materiali
type: AnnotationProperty
comment: Connects one class (a location or a intervention) to the keyword in the field Materiali that, if found, indicates the presence of that class.
label: bijbehorende trefwoorden in het veld materialen @nl
label: parole chiave associate nel field materiali @it
range: string
domain: Thing

definition
type: AnnotationProperty
comment: Property representing the definition in the ontobee website. In later versions of the ontology we prefer rdfs:comment since it is more universally used.
label: definitie @nl
label: definizione @it
range: string
domain: Thing

has Ontobee annotation
type: AnnotationProperty
comment: A property to connect one entity to the annotations found for that entitiy in the corresponding page in Ontobee (http://www.ontobee.org/).
label: ha annotazione da Ontobee @it
label: heeft een record van Ontobee @nl
range: string
domain: Thing

has SNOMED code
type: AnnotationProperty
comment: Use this property to annotate one entity with its corresponding SNOMED code.
label: ha codice SNOMED @it
label: heeft SNOMED-code @nl
range: string
domain: Thing

has semantic area
type: AnnotationProperty
comment: Connects one ontology class or Individual to the semantic area to which it belongs. For example, a Poly is a diagnosis, therefore the Polyp belongs to the semantic area of Diagnosis.
label: presenta area semantica @it
label: presenteert semantisch gebied @nl
range: Semantic Area
domain: Thing

internal notes
type: AnnotationProperty
comment: Use this property to annotate a resource with some notes that may be useful to those who will work on building the ontology.
label: interne notities @nl
label: note interne @it
range: string
domain: Thing

taxon notes
type: AnnotationProperty
comment: A field found sometimes for entities taken from Ontobee's ontologies. You can treat it as an ulterior/alternative definition.
label: note tassonomiche @it
label: structurele opmerkinegen @nl
sub property of: definition
range: string
domain: Thing

related
type: ObjectProperty
type: SymmetricProperty
domain: Concept
range: Concept
is defined by: skos vocabulary

maker
type: ObjectProperty
domain: Clinical Case Report
range: Class
  union of: Agent
  union of: Organization
comment: An agent that made this thing.
comment: In this ontology the property maker is used to connect a clinical case report to the organization that produced it. For future possibilities, we put domain and range to owl:Thing.
label: producent @nl
label: produttore @it
term status: stable
definition: The maker property relates something to a Agent that made it. As such it is an inverse of the made property. The name (or other rdfs:label) of the maker of something can be described as the dc:creator of that thing. For example, if the thing named by the URI http://danbri.org/ has a maker that is a Person whose name is 'Dan Brickley', we can conclude that http://danbri.org/ has a dc:creator of 'Dan Brickley'.
has semantic area: General Entity

detected HPV
type: ObjectProperty
domain: Cervix Outcome
range: Human Papilloma Virus Infection
comment: If this property is present, it signals the presence of a human papilloma virus (HPV) in the outcome. It needs to have as object the HPV infection named entity.
label: gedetecteerd HPV @nl
label: identificato HPV @it
associated disease: Cervical Cancer
has semantic area: Diagnosis

detected koilocyte
type: ObjectProperty
domain: Cervix Outcome
range: Koilocytotic Squamous Cell
comment: Signals the presence of Koilocytotic Squamous Cell. It needs to have as object the Koilocytotic Squamous Cell named entity.
label: gedetecteerd koylocite @nl
label: rilevati coilociti @it
associated disease: Cervical Cancer
has semantic area: Diagnosis

has age onset
type: ObjectProperty
type: FunctionalProperty
domain: Patient
range: Onset
comment: Links one record to its age group, or "onset".
label: ha gruppo d'età @it
label: heeft leeftijdsgroep @nl
has semantic area: General Entity

has clinical case report
type: ObjectProperty
type: SymmetricProperty
domain: Patient
range: Clinical Case Report
comment: Connects one patient to its clinical case report.
label: ha caso clinico @it
label: heeft een klinische casus @nl
has semantic area: General Entity

has dysplasia
type: ObjectProperty
domain: Polyp of Colon
range: Dysplasia
comment: Connects an instance of Polyp of Colon to a named individual of type Dysplasia. Cardinality between 0 and 1.
label: heeft dysplasie @nl
label: presenta displasia @it
associated disease: Colon Carcinoma
has semantic area: Diagnosis

has gender
type: ObjectProperty
type: FunctionalProperty
domain: Patient
range: Gender
comment: To connect a record with the gender of the corresponding person.
label: heeft geslacht @nl
label: presenta genere @it
has semantic area: General Entity

has intervention
type: ObjectProperty
domain: Outcome
range: Intervention or Procedure
comment: A report is associated to an intervention (or procedure) that was performed to the patient to obtain the tissue used to study the presence (or absence) of the disease.
label: heeft tussenkomst @nl
label: intervento associato @it
has semantic area: Procedure

has intervention type
type: ObjectProperty
domain: Intervention or Procedure
range: Intervention or Procedure Type
comment: Connects an intervention (or procedure) to its type.
label: soort tussenkomst @nl
label: tipo di intervento @it
has semantic area: Procedure

has laboratory finding
type: ObjectProperty
domain: Celiac Clinical Case Report
range: Laboratory Finding
comment: Connects an instance of celiac outcome to an instance of laboratory finding or any of its subclasses.
label: heeft laboratorium bevindingen @nl
label: presenta risultati di laboratorio @it
has semantic area: Diagnosis

has location
type: ObjectProperty
domain: Class
  union of: Intervention or Procedure
  union of: Outcome
range: Anatomical Entity
comment: A clinical case record has a location where it is positioned. This property connects an instance of clinical case report (of whatever type) or an Intervention to a location, a member of the class anatomical entity.
label: heeft locatie @nl
label: è localizzato in @it
has semantic area: Anatomical Location

has outcome
type: ObjectProperty
type: FunctionalProperty
domain: Clinical Case Report
range: Outcome
comment: Every report has an outcome, whatever it may be (positive, negative, inconclusive etc.)
label: heeft uitkomst @nl
label: presenta risultato @it
has semantic area: Diagnosis

has slide
type: ObjectProperty
domain: Clinical Case Report
range: Slide Device
comment: Connects a clinical case report to one slide. This Slide class was generated due to the way Radbound deals with its data. Each patient is associated to one block. Each block is a diagnosis, and it can be associated to one or more slides that helped the medic to reach that diagnosis.
label: heeft glijbaan @nl
label: presenta vetrino @it
has semantic area: General Entity

has test
type: ObjectProperty
domain: Outcome
range: Test
comment: The test performed.
label: heeft toets @nl
label: presenta test @it
has semantic area: Test

inconclusive result type
type: ObjectProperty
domain: Inconclusive Outcome
range: Inconclusive Outcome Type
comment: Connects an inconclusive outcome to its type.
label: onduidelijk resultaattype @nl
label: tipo di risultato inconclusivo @it
has semantic area: Diagnosis

is about disease
type: ObjectProperty
type: FunctionalProperty
domain: Clinical Case Report
range: Disease or Disorder
comment: This property is used to connect an instance of a clinical case to an instance of Disease. Thus, this property has as a range the disease and you should expect, every time you have a report, to have this property pointing to one of the four instances of disease.
label: connesso alla malattia @it
label: handler om sygdom @nl
has semantic area: General Entity

positive result type
type: ObjectProperty
domain: Positive Outcome
range: Positive Outcome Type
comment: Connects a positive outcome to its type.
label: positief resultaattype @nl
label: tipo di risultato positivo @it
has semantic area: Diagnosis

presence of
type: ObjectProperty
domain: Class
  union of: Celiac Clinical Case Report
  union of: Lung Carcinoma
range: Class
  union of: Celiac Disease Finding
  union of: Lung Carcinoma Finding
comment: This property is used to connect an outcome instance to a generic annotation which signals the presence of some more information correlating the clinical case. Such information may not be directly pertinent to the disease however it can be still linked to it.
label: aanwezigheid van @nl
label: individuata presenza di @it
has semantic area: Diagnosis

presence of intestinal abnormality
type: ObjectProperty
domain: Celiac Outcome
range: Intestinal Abnormality
comment: Connects one celiac outcome to the intestinal abnormality detected in the specimen.
label: aanwezigheid van darm afwijkingen @nl
label: individuata anomalia intestinale @it
associated disease: Celiac disease
has semantic area: Diagnosis

identifier
type: DatatypeProperty
domain: Clinical Case Report
range: string
comment: An unambiguous reference to the resource within a given context. Property connecting a case to its id. It follows dublin core specification http://www.ukoln.ac.uk/metadata/dcmi-ieee/identifiers/, that says: Recommended practice is to identify the resource by means of a string conforming to an identification system. Examples include International Standard Book Number (ISBN), Digital Object Identifier (DOI), and Uniform Resource Name (URN). Persistent identifiers should be provided as HTTP URIs. In this ontology it is supposed that this property connects a clinical case to a string representing an URL.
label: identificatore @it
has semantic area: General Entity

modified Marsh classification of histologic findings in celiac disease
type: DatatypeProperty
type: FunctionalProperty
domain: Positive to Celiac Disease
range: Datatype
  one of: 0
  one of: 1
  one of: 2
  one of: 3a
  one of: 3b
  one of: 3c
comment: The severity of celiac disease according to Marsh classification.
label: classificazione di Marsh della malattia celiaca @it
label: gewijzigde Marsh-classificatie van histologische bevindingen bij coeliakie @nl
associated disease: Celiac disease
has semantic area: Diagnosis

duodenitis severity
type: DatatypeProperty
type: FunctionalProperty
domain: Duodenitis
range: string
comment: The severity of the duodenitis.
label: ernst van duodenitis @nl
label: gravità della duodenite @it
associated disease: Celiac disease
has semantic area: Diagnosis

has age
type: DatatypeProperty
domain: Patient
range: integer
comment: Connects the Report to the age of the patient.
label: età @it
label: heeft leeftijd @nl
has semantic area: General Entity

has block number
type: DatatypeProperty
type: FunctionalProperty
domain: Clinical Case Report
range: integer
comment: The block number identifies the part of the image connected to the diagnosis (for Radbound). For AOEC this property is not necessary. We use it to contain the "internal id".
label: ha numero di blocco @it
label: heeft bloknummer @nl
has semantic area: General Entity

has textual diagnosis
type: DatatypeProperty
domain: Clinical Case Report
range: string
comment: Connects an instance of clinical case to its diagnosis, i.e. the text written by the doctor. @nl
label: presenta campo diagnosi @it
label: presenteert diagnoseveld @nl
has semantic area: General Entity

has flattened villi
type: DatatypeProperty
domain: Villi Laboratory Finding
range: boolean
conforms to: http://linkedlifedata.com/resource/umls/id/C2673838
comment: Whether the specimen presents falttened villi.
label: heeft afgeplatte villi @nl
label: presenta villi appiattiti @it
associated disease: Celiac disease
associated keyword in diagnosis: villi appiattiti, appiattimento dei villi
has semantic area: Diagnosis

intraepithelial lymphocyte count
type: DatatypeProperty
domain: Other Laboratory Finding
range: string
conforms to: http://linkedlifedata.com/resource/umls/id/C5669280
comment: The determination of the number of the intraepithelial lymphocytes in a sample. [Definition Source: NCI]
label: intra-epitheliale lymfocythoeveelheid @nl
label: quantità di linfociti intraeppiteliali @it
associated disease: Celiac disease
associated keyword in diagnosis: LIE, ILE, “linfociti intraepiteliali pari a”, “linfociti”, ”entorociti" @it
has semantic area: Diagnosis

has image
type: DatatypeProperty
type: FunctionalProperty
domain: Clinical Case Report
range: string
comment: Connects a clinical case report to the name of its corresponding image (the name of the image, e.g. the name of the file).
label: huidige afbeelding @nl
label: presenta immagine @it
has semantic area: General Entity

has Internal Identifier
type: DatatypeProperty
domain: Clinical Case Report
range: anyURI
comment: Connects a clinical case with the its ID used inside the ExaMode project. This property was thought to connect a case to its id given by the hospitals. In this ontology we use the dc:identifier property to connect one case with an URL identifying it. @nl
label: heeft interne ID @nl
label: presenta identificatore interno @it
has semantic area: General Entity

has slide diagnosis
type: DatatypeProperty
domain: Slide Device
range: string
comment: Each slide can be associated to its own diagnosis.
label: heeft dia-geassocieerde diagnose @nl
label: presenta diagnosi associata al vetrino @it
has semantic area: General Entity

has slide id
type: DatatypeProperty
domain: Slide Device
range: string
comment: Each slide is associated to its own id
label: presenta id vetrino @it
label: presenteert dia-id @nl
has semantic area: General Entity

has value
type: DatatypeProperty
type: FunctionalProperty
domain: Proliferation marker protein Ki-67
range: float
comment: Connects a immunohistochemical test to its float value
label: presenta valore @it
has semantic area: Test

villi to crypt of Lieberkuhn ratio
type: DatatypeProperty
domain: Villi Laboratory Finding
range: string
comment: Ratio of villous height to crypt or Lieberkuhn depth
label: rapporto villi / cripte di Lieberkhun @it
label: villi tot crypte van Lieberkuhn ratio @nl
associated disease: Celiac disease
associated keyword in diagnosis: check the presence of keywords “Rapporto villo cripta”
has semantic area: Diagnosis

number of mitosis per crypt
type: DatatypeProperty
domain: Other Laboratory Finding
range: string
label: aantal mitoses per crypte @nl
label: numero di mitosi per cripta @it
associated disease: Celiac disease
associated keyword in diagnosis: numero di mitosi per cripta
has semantic area: Diagnosis

has outcome
type: DatatypeProperty
type: FunctionalProperty
domain: Class
  union of: Neprilysin
  union of: Cluster of Differentation 3
  union of: Receptor-type tyrosine-protein phosphatase C
  union of: Keratin, type I cytoskeletal 19
  union of: Keratin, type I cytoskeletal 20
  union of: Cytokeratin 34bE12
  union of: Cytokeratin 5/6
  union of: Keratin-associated protein 5-9
  union of: Keratin, type II cytoskeletal 7
  union of: Chromogranin-A
  union of: Desmocollin-3
  union of: Immunoprecipitation
  union of: Napsin A
  union of: Endonuclease P40
  union of: Tumor Protein 63 Isoform 2
  union of: Pulmonary surfactant-associated protein B
  union of: Synaptophysin
  union of: TTF1 Human
  union of: Vimentin
range: boolean
comment: Connects one immunohistochemical test to its boolean value.
label: presenta outcome @it
label: presenteert resultaten @nl
has semantic area: Test

has test result
type: DatatypeProperty
type: FunctionalProperty
domain: HER2 (CB11)
range: string
comment: Connects one immunohistochemical test to its string result.
label: heeft een testresultaat @nl
label: presenta risultato @it
has semantic area: Test

absence of villi
type: DatatypeProperty
type: FunctionalProperty
domain: Villi Laboratory Finding
range: boolean
comment: Whether the tissue is without villi.
label: afwezigheid van villi @nl
label: assenza di villi @it
associated disease: Celiac disease
associated keyword in diagnosis: priva di villi
has semantic area: Diagnosis

villi degree of atrophy
type: DatatypeProperty
domain: Villi Laboratory Finding
range: Datatype
  one of: focal
  one of: mild
  one of: mild to moderate
  one of: moderate
  one of: moderate-severe
  one of: not specified
  one of: severe
  one of: total
conforms to: http://linkedlifedata.com/resource/umls/id/C0877518
comment: The degree of atrophy of villi.
label: grado di atrofia dei villi @it
label: villi atrofie graad @nl
associated disease: Celiac disease
associated keyword in diagnosis: atrofia dei villi
has semantic area: Diagnosis

duodenum villi length
type: DatatypeProperty
domain: Villi Laboratory Finding
range: string
comment: The distance from point to point along the longest axis of the finger-like projections of the mucosal layer of the duodenum.
label: duodenum villi lengte @nl
label: lunghezza dei villi del duodeno @it
associated disease: Celiac disease
associated keyword in diagnosis: "villi" + characterization
has semantic area: Diagnosis

Concept
type: Class
comment: An abstract idea or notion; a unit of thought.

Organization
type: Class
has semantic type: General
comment: An organization that, in the context of the ExaMode program, provides clinical case records. It is usually an Hospital (e.g. AOEC or Radbound).
label: Organisatie @nl
label: Organizzazione @it
has semantic area: General
has semantic area: General Entity

Institution
type: Class
label: Instelling @nl
label: Instituzione @it
has semantic area: General Entity

Adenoma
type: Class
subclass of: Polyp of Colon
conforms to: http://linkedlifedata.com/resource/umls/id/C0007131
has exact synonym: colonic adenomatous polyp; adenomatous polyp of colon; colon adenomatous polyp; adenomatous polyp of the colon; Adenomatous polyp
comment: A polypoid adenoma that arises from and protrudes into the lumen of the colon. Epithelial dysplasia is always present. According to the architectural pattern it is classified as tubular, tubulovillous, or villous. [Definition Source: NCI]
label: Adenoom @nl
associated disease: Colon Carcinoma
has SNOMED code: M814000
has semantic area: Diagnosis

Anatomical Entity
type: Class
conforms to: http://linkedlifedata.com/resource/umls/id/C1515976
comment: 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. [ Definition Source: FMA : 62955 http://orcid.org/0000-0001-9114-8737 ]
label: Anatomische Entiteit @nl
label: Entità Anatomica @it
has semantic area: Anatomical Location

Annotation
type: Class
comment: A general class to represent all the kionds of annnotations that may be needed in an ExaMode report.
label: Annotatie @nl
label: Annotazione @it
has semantic area: General Entity

Boolean Check Element
type: Class
subclass of: Check Element
comment: A set of checks controlled on an Immunohistochemical test that can only have a boolean result (positive - negative).
label: Booleaans Controle-Element @nl
label: Elemento di Controllo Booleano @it
has semantic area: Test

Neprilysin
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C0025250
comment: Thermolysin-like specificity, but is almost confined on acting on polypeptides of up to 30 amino acids (PubMed:15283675, PubMed:8168535). Biologically important in the destruction of opioid peptides such as Met- and Leu-enkephalins by cleavage of a Gly-Phe bond (PubMed:17101991). Able to cleave angiotensin-1, angiotensin-2 and angiotensin 1-9 (PubMed:15283675). Involved in the degradation of atrial natriuretic factor (ANF) (PubMed:2531377, PubMed:2972276). Displays UV-inducible elastase activity toward skin preelastic and elastic fibers (PubMed:20876573). [Definition Source: UniProt]
associated disease: Lung cancer
associated keyword in diagnosis: CD10
associated keyword in diagnosis: Neprilysin
has semantic area: Test

Cluster of Differentation 3
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C0108779
comment: Consisting of cell surface type I membrane Delta, Epsilon, Gamma, Zeta, and Eta protein subunits with ITAM domains and noncovalently associated with the disulfide bound heterodimeric alpha/beta and gamma/delta TCR, the CD3 complex couples receptor antigen recognition to signal transduction pathways during T-cell activation. During TCR engagement with MHC-associated antigen on host cell surfaces and synapse formation, CD3 activity leads to Tyr-phosphorylated CD3 subunits, Tyr phosphorylation of LAT colocalized in lipid rafts, and MAPK activation. CD3 signal transduction appears to involve LCK, ZAP70, Nck, SLA, SLA2, and DOCK2. CD3 subunits may also associate with the cytoskeleton. CD3 also mediates TCR signal transduction during the developmental transition through positive selection of immature thymocytes to mature CD4+ or CD8+ T cells. (NCI) [Definition Source: NCI]
associated disease: Celiac disease
associated keyword in diagnosis: Presence of the word "CD3"
has semantic area: Test

Receptor-type tyrosine-protein phosphatase C
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C0054961
comment: Protein tyrosine-protein phosphatase required for T-cell activation through the antigen receptor. Acts as a positive regulator of T-cell coactivation upon binding to DPP4. The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one. Upon T-cell activation, recruits and dephosphorylates SKAP1 and FYN. Dephosphorylates LYN, and thereby modulates LYN activity (By similarity). (Microbial infection) Acts as a receptor for human cytomegalovirus protein UL11 and mediates binding of UL11 to T-cells, leading to reduced induction of tyrosine phosphorylation of multiple signaling proteins upon T-cell receptor stimulation and impaired T-cell proliferation. [Definition Source: Uniprot]
label: Fosfatasi tirosina-proteina tipo recettore C @it
label: Receptor-type tyrosine-eiwitfosfatase C. @nl
associated disease: Lung cancer
associated keyword in diagnosis: CD45
has semantic area: Test

Keratin, type I cytoskeletal 19
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C4082253
comment: Involved in the organization of myofibers. Together with KRT8, helps to link the contractile apparatus to dystrophin at the costameres of striated muscle. [Definition Source: UniProt]
associated disease: Lung cancer
associated keyword in diagnosis: CK19
has semantic area: Test

Keratin, type I cytoskeletal 20
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C1433368
comment: Plays a significant role in maintaining keratin filament organization in intestinal epithelia. When phosphorylated, plays a role in the secretion of mucin in the small intestine. [Definition Source: UniProt]
associated disease: Lung cancer
associated keyword in diagnosis: CK20
has semantic area: Test

Cytokeratin 34bE12
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C0908867
comment: One of the tests that can be made for the lung cancer.
associated disease: Lung cancer
associated keyword in diagnosis: CK34BE12
has semantic area: Test

Cytokeratin 5/6
type: Class
subclass of: Boolean Check Element
has semantic type: Laboratory Procedure
conforms to: http://linkedlifedata.com/resource/umls/id/C2825225
has exact synonym: Cytokeratin 5/6 Expression; CK 5/6 Immunohistochemical Expression; CK 5/6 Expression; CK5/6; Cytokeratin 5/6 Immunohistochemical Expression
comment: An immunohistochemical diagnostic test utilizing an antibody to detect both cytokeratin 5 and 6 in tissues. [Definition Source: NCIT]
associated disease: Lung cancer
associated keyword in diagnosis: CK5/6
has semantic area: Test

Keratin-associated protein 5-9
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C1956465
comment: In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated protein (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high-sulfur and high-glycine-tyrosine keratins. [Definition Source: UniProt]
associated disease: Lung cancer
associated keyword in diagnosis: CK5
has semantic area: Test

Keratin, type II cytoskeletal 7
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C3272783
comment: Blocks interferon-dependent interphase and stimulates DNA synthesis in cells. Involved in the translational regulation of the human papillomavirus type 16 E7 mRNA (HPV16 E7). [Definition Source: UniProt]
associated disease: Lung cancer
associated keyword in diagnosis: CK7
has semantic area: Test

Chromogranin-A
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C0055633
comment: Pancreastatin: Strongly inhibits glucose induced insulin release from the pancreas. Catestatin: Inhibits catecholamine release from chromaffin cells and noradrenergic neurons by acting as a non-competitive nicotinic cholinergic antagonist (PubMed:15326220). Displays antibacterial activity against Gram-positive bacteria S.aureus and M.luteus, and Gram-negative bacteria E.coli and P.aeruginosa (PubMed:15723172 and PubMed:24723458). Can induce mast cell migration, degranulation and production of cytokines and chemokines (PubMed:21214543). Acts as a potent scavenger of free radicals in vitro (PubMed:24723458). May play a role in the regulation of cardiac function and blood pressure (PubMed:18541522). Serpinin: Regulates granule biogenesis in endocrine cells by up-regulating the transcription of protease nexin 1 (SERPINE2) via a cAMP-PKA-SP1 pathway. This leads to inhibition of granule protein degradation in the Golgi complex which in turn promotes granule formation. Miscellaneous Binds calcium with a low-affinity. [Definition Source: UniProt]
associated disease: Lung cancer
associated keyword in diagnosis: Chromogranina @it
has semantic area: Test

Celiac Anatomical Entity
type: Class
subclass of: Anatomical Entity
disjoint with: Cervix Anatomical Entity
disjoint with: Colon Anatomical Entity
disjoint with: Lung Anatomical Entity
comment: Class describing biological entities related to celiac disease.
label: Coeliakie Anatomische Entiteit @nl
label: Entità Anatomica relativa alla Celiachia @it
has semantic area: Anatomical Location

Celiac Clinical Case Report
type: Class
equivalent class: Restriction
  on property: presence of
  some values from: Celiac Disease Finding
equivalent class: Restriction
  on property: has outcome
  all values from: Celiac Outcome
subclass of: Clinical Case Report
disjoint with: Cervix Clinical Case Report
disjoint with: Colon Clinical Case Report
disjoint with: Lung Clinical Case Report
comment: Class representing all the celiac disease clinical cases.
label: Caso Clinico di Malattia Celiaca @it
label: Klinisch Geval van Coeliakie @nl
has semantic area: General Entity

Celiac Disease Finding
type: Class
subclass of: Finding
disjoint with: Dysplasia
disjoint with: Human Papilloma Virus Infection
disjoint with: Intestinal Abnormality
disjoint with: Koilocytotic Squamous Cell
disjoint with: Lung Carcinoma Finding
comment: Finding in celiac outcomes.
label: Coeliakie Vinden @nl
label: Scoperta riguardo la Malattia Celiaca @it
associated disease: Celiac disease
has semantic area: Diagnosis

Celiac Disease Intervention or Procedure
type: Class
equivalent class: Restriction
  on property: has location
  all values from: Celiac Anatomical Entity
subclass of: Intervention or Procedure
disjoint with: Cervix Cancer Intervention or Procedure
disjoint with: Colon Cancer Intervention or Procedure
disjoint with: Lung Cancer Intervention or Procedure
comment: Class describing interventions or procedures related to celiac disease.
label: Coeliakie Tussenkomst of Procedure @nl
label: Intervento o Procedura relativa allla Malattia Celiaca @it
has semantic area: Procedure

Celiac Disease Intervention or Procedure Type
type: Class
subclass of: Intervention or Procedure Type
comment: Class describing the type of intervention or procedure related to celiac disease.
label: Tipo di Intervento o Procedura relativa allla Malattia Celiaca @it
label: Type Coeliakie Tussenkomst of Procedure @nl
has semantic area: Procedure

Celiac Outcome
type: Class
equivalent class: Restriction
  on property: has intervention
  all values from: Celiac Disease Intervention or Procedure
equivalent class: Restriction
  on property: has location
  all values from: Celiac Anatomical Entity
subclass of: Outcome
disjoint with: Cervix Outcome
disjoint with: Colon Outcome
disjoint with: Lung Outcome
comment: Class representing all outcomes of celiac clinical case report.
label: Resultaat van Coeliakie @nl
label: Risultato di Malattia Celiaca @it
has semantic area: Diagnosis

Celiac Positive Outcome Type
type: Class
subclass of: Positive Outcome Type
disjoint with: Cervix Positive Outcome Type
disjoint with: Colon Positive Outcome Type
disjoint with: Lung Positive Outcome Type
comment: Class describing for which type of celiac disease the clinical case tested positive.
label: Tipo di Risultato Positivo alla Malattia Celiaca @it
label: Type Coeliakie Positief Resultaat @nl
has semantic area: Diagnosis

Celiac Positive Outcome
type: Class
equivalent class: Restriction
  on property: positive result type
  all values from: Celiac Positive Outcome Type
subclass of: Celiac Outcome
subclass of: Positive Outcome
disjoint with: Cervix Positive Outcome
disjoint with: Colon Positive Outcome
disjoint with: Lung Positive Outcome
comment: Positive Outcome, i.e., something related to celiac disease has been found in the patient.
label: Positieve Uitkomst van Coeliakie @nl
label: Risultato Positivo di Malattia Celiaca @it
has semantic area: Diagnosis

Celiac Disease Surgical Procedure
type: Class
subclass of: Celiac Disease Intervention or Procedure
subclass of: Surgical procedure
disjoint with: Cervix Cancer Surgical Procedure
disjoint with: Colon Cancer Surgical Procedure
disjoint with: Lung Cancer Surgical Procedure
comment: Class describing surgical procedures related to celiac disease.
label: Coeliakie Chirurgische Ingreep @nl
label: Intervento Chirurgico relativo allla Malattia Celiaca @it
has semantic area: Procedure

Celiac Disease Surgery Type
type: Class
subclass of: Surgical Procedure Type
comment: Class describing surgical procedure type related to celiac disease.
label: Tipo di Intervento Chirurgico relativo alla Malattia Celiaca @it
label: Type Coeliakie Chirurgische Ingreep @nl
has semantic area: Procedure

Cervix Anatomical Entity
type: Class
subclass of: Anatomical Entity
disjoint with: Colon Anatomical Entity
disjoint with: Lung Anatomical Entity
comment: Class describing biological entities related to cervix cancer.
label: Baarmoederhals Anatomische Entiteit @nl
label: Entità Anatomica relativa al Tumore alla Cervice @it
has semantic area: Anatomical Location

Cervix Clinical Case Report
type: Class
equivalent class: Restriction
  on property: has outcome
  all values from: Cervix Outcome
subclass of: Clinical Case Report
disjoint with: Colon Clinical Case Report
disjoint with: Lung Clinical Case Report
comment: Class representing the clinical cases about cervix cancer.
label: Caso Clinico di Cancro alla Cervice @it
label: Klinisch Geval van Baarmoederhalskanker @nl
has semantic area: General Entity

Cervix Cancer Intervention or Procedure
type: Class
equivalent class: Restriction
  on property: has location
  all values from: Cervix Anatomical Entity
subclass of: Intervention or Procedure
disjoint with: Colon Cancer Intervention or Procedure
disjoint with: Lung Cancer Intervention or Procedure
comment: Class describing interventions or procedures related to cervix cancer.
label: Baarmoederhalskanker Tussenkomst of Procedure @nl
label: Intervento o Procedura relativa al Cancro alla Cervice @it
has semantic area: Procedure

Cervix Intervention or Procedure Type
type: Class
subclass of: Intervention or Procedure Type
comment: Class describing the type of intervention or procedure related to cervix cancer.
label: Tipo di Intervento o Procedura relativa al Cancro alla Cervice @it
label: Type Baarmoederhalskanker Tussenkomst of Procedure @nl
has semantic area: Procedure

Cervix Outcome
type: Class
equivalent class: Restriction
  on property: has intervention
  all values from: Cervix Cancer Intervention or Procedure
equivalent class: Restriction
  on property: has location
  all values from: Cervix Anatomical Entity
equivalent class: Restriction
  on property: detected HPV
  min qualified cardinality: 0
  on class: Human Papilloma Virus Infection
equivalent class: Restriction
  on property: detected koilocyte
  min qualified cardinality: 0
  on class: Koilocytotic Squamous Cell
equivalent class: Restriction
  on property: detected HPV
  max qualified cardinality: 1
  on class: Human Papilloma Virus Infection
equivalent class: Restriction
  on property: detected koilocyte
  max qualified cardinality: 1
  on class: Koilocytotic Squamous Cell
subclass of: Outcome
disjoint with: Colon Outcome
disjoint with: Lung Outcome
comment: Class representing all outcomes of cervix clinical case reports.
label: Resultaat van Baarmoederhalskanker @nl
label: Risultato di Cancro alla Cervice @it
has semantic area: Diagnosis

Cervix Positive Outcome Type
type: Class
subclass of: Positive Outcome Type
disjoint with: Colon Positive Outcome Type
disjoint with: Lung Positive Outcome Type
comment: Class describing for which type of cervix cancer the clinical case tested positive.
label: Tipo di Risultato Positivo al Cancro alla Cervice @it
label: Type Baarmoederhalskanker Positief Resultaat @nl
has semantic area: Diagnosis

Cervix Positive Outcome
type: Class
equivalent class: Restriction
  on property: positive result type
  all values from: Cervix Positive Outcome Type
subclass of: Cervix Outcome
subclass of: Positive Outcome
disjoint with: Colon Positive Outcome
disjoint with: Lung Positive Outcome
comment: Positive Outcome, i.e., something related to cervix cancer has been found in the patient.
label: Positieve Uitkomst van Baarmoederhalskanker @nl
label: Risulato Positivo di Cancro alla Cervice @it
has semantic area: Diagnosis

Cervix Cancer Surgical Procedure
type: Class
subclass of: Cervix Cancer Intervention or Procedure
subclass of: Surgical procedure
disjoint with: Colon Cancer Surgical Procedure
disjoint with: Lung Cancer Surgical Procedure
comment: Class describing surgical procedures related to cervix cancer.
label: Baarmoederhalskanker Chirurgische Ingreep @nl
label: Intervento Chirurgico relativo al Cancro alla Cervice @it
has semantic area: Procedure

Cervix Surgery Type
type: Class
subclass of: Cervix Intervention or Procedure Type
subclass of: Surgical Procedure Type
comment: Class describing surgical procedure type related to cervix cancer.
label: Tipo di Intervento Chirurgico relativo al Tumore alla Cervice @it
label: Type Baarmoederhalskanker Chirurgische Ingreep @nl
has semantic area: Procedure

Check Element
type: Class
subclass of: Immunohistochemical Test
comment: This is a set of elements containing all the possible checks that a patient may do for a generic disease.
label: Controleer Element @nl
label: Controllo @it
has semantic area: Test

Clear Cell Adenocarcinoma
type: Class
subclass of: Lung Adenocarcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0206681
comment: A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid. [Definition Source: NCI]
label: Adenocarcinoma a Cellule Chiare @it
label: Heldercellig Adenocarcinoom @nl
associated disease: Lung cancer
definition: MSH: An adenocarcinoma characterized by the presence of varying combinations of clear and hobnail-shaped tumor cells. There are three predominant patterns described as tubulocystic, solid, and papillary. These tumors, usually located in the female reproductive organs, have been seen more frequently in young women since 1970 as a result of the association with intrauterine exposure to diethylstilbestrol. (From Holland et al., Cancer Medicine, 3d ed),NCI: A rare type of tumor, usually of the female genital tract, in which the insides of the cells look clear when viewed under a microscope.,NCI: A malignant neoplasm comprising glandular epithelial clear cells.,NCI: A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid.
has SNOMED code: M831030
has semantic area: Diagnosis

Clinical Case Report
type: Class
equivalent class: Restriction
  on property: is about disease
  qualified cardinality: 1
  on class: Disease or Disorder
comment: This is the main class of the ontology. The Clinical Case is one record in the database, and in this version of the ontology may be of one of four diseases: celiac disease, lung cancer, cervix cancer, colon cancer. This class is sub-instantiated to the other different sub-classes
label: Caso clinico @it
label: Klinisch Casusrapport @nl
has semantic area: General Entity

Colon Anatomical Entity
type: Class
subclass of: Anatomical Entity
disjoint with: Lung Anatomical Entity
comment: Class describing biological entities related to colon cancer.
label: Dikke Darm Anatomische Entiteit @nl
label: Entità Anatomica relativa al Tumore al Colon @it
has semantic area: Anatomical Location

Colon Clinical Case Report
type: Class
equivalent class: Restriction
  on property: has outcome
  all values from: Colon Outcome
subclass of: Clinical Case Report
disjoint with: Lung Clinical Case Report
comment: Class representing all colon cancer cases.
label: Caso Clinico di Cancro al Colon @it
label: Klinisch Geval van Darmkanker @nl
has semantic area: General Entity

Colon Hyperplastic Polyp
type: Class
subclass of: Polyp of Colon
has semantic type: Disease or Syndrome
conforms to: http://linkedlifedata.com/resource/umls/id/C0742608
has exact synonym: Hyperplastic Colonic Polyp; Colon HP; Metaplastic Polyp of the Colon; Metaplastic Polyp of Colon; Metaplastic Colonic Polyp; Hyperplastic Polyp of the Colon; Metaplastic Colon Polyp; Hyperplastic Polyp of Colon; Colon Metaplastic Polyp; Colon MP; Colon Hyperplastic Polyp; Colonic Hyperplastic Polyp
comment: A serrated polypoid lesion that arises in the colon. It is usually found in the distant colon and it rarely produces symptoms. This group includes goblet cell rich, mucin poor, and microvesicular hyperplastic polyps. [Definition Source: NCI]
label: Polipo Iperplastico del Colon @it
associated disease: Colon Carcinoma
has SNOMED code: M720400
has semantic area: Diagnosis
internal notes: old SNOMED M72040

Colon Inflammatory Polyp
type: Class
subclass of: Polyp of Colon
conforms to: http://linkedlifedata.com/resource/umls/id/C0267392
has exact synonym: inflammatory polyp of colon; inflammatory polyp of the colon; colonic inflammatory polyp.
comment: A non-neoplastic polypoid lesion in the colon. It may arise in a background of inflammatory bowel disease or colitis. It is characterized by the presence of a distorted epithelium, inflammation, and fibrosis. [Definition Source: NCI]
label: Colon Ontstekingspoliep @nl
label: Polipo Infiammatorio del Colon @it
associated disease: Colon Carcinoma
has semantic area: Diagnosis

Colon Cancer Intervention or Procedure
type: Class
equivalent class: Restriction
  on property: has location
  all values from: Colon Anatomical Entity
subclass of: Intervention or Procedure
disjoint with: Lung Cancer Intervention or Procedure
comment: Class describing interventions or procedures related to colon cancer.
label: Darmkanker Tussenkomst of Procedure @nl
label: Intervento o Procedura relativa al Cancro al Colon @it
has semantic area: Procedure

Colon Intervention or Procedure Type
type: Class
subclass of: Intervention or Procedure Type
comment: Class describing the type of intervention or procedure related to colon cancer.
label: Tipo di Intervento o Procedura relativa al Cancro al Colon @it
label: Type Darmkanker Tussenkomst of Procedure @nl
has semantic area: Procedure

Colon Outcome
type: Class
equivalent class: Restriction
  on property: has intervention
  all values from: Colon Cancer Intervention or Procedure
equivalent class: Restriction
  on property: has location
  all values from: Colon Anatomical Entity
subclass of: Outcome
disjoint with: Lung Outcome
comment: Class representing all outcomes of colon clinical case reports.
label: Resultaat van Darmkanker @nl
label: Risultato di Cancro al Colon @it
has semantic area: Diagnosis

Colon Positive Outcome Type
type: Class
subclass of: Positive Outcome Type
disjoint with: Lung Positive Outcome Type
comment: Class describing for which type of colon cancer the clinical case tested positive.
label: Tipo di Risultato Positivo al Cancro al Colon @it
label: Type Darmkanker Positief Resultaat @nl
has semantic area: Diagnosis

Polyp of Colon
type: Class
equivalent class: Restriction
  on property: has dysplasia
  min qualified cardinality: 0
  on class: Dysplasia
equivalent class: Restriction
  on property: has dysplasia
  max qualified cardinality: 1
  on class: Dysplasia
subclass of: Colon Positive Outcome
conforms to: http://linkedlifedata.com/resource/umls/id/C0009376
has exact synonym: colon polyp; polyp of the colon; colonic polyp
comment: A polyp that involves the colon. [Definition Source: MONDO]
label: Poliep van de Dikke Darm @nl
label: Polipo del Colon @it
associated disease: Colon Carcinoma
has semantic area: Diagnosis

Colon Positive Outcome
type: Class
equivalent class: Restriction
  on property: positive result type
  all values from: Colon Positive Outcome Type
subclass of: Colon Outcome
subclass of: Positive Outcome
disjoint with: Lung Positive Outcome
comment: Positive Outcome, i.e., something related to colon cancer has been found in the patient.
label: Positieve Uitkomst van Darmkanker @nl
label: Risulato Positivo di Cancro al Colon @it
has semantic area: Diagnosis

Colon Cancer Surgical Procedure
type: Class
subclass of: Colon Cancer Intervention or Procedure
subclass of: Surgical procedure
disjoint with: Lung Cancer Surgical Procedure
comment: Class describing surgical procedures related to colon cancer.
label: Darmkanker Chirurgische Ingreep @nl
label: Intervento Chirurgico relativo al Cancro al Colon @it
has semantic area: Procedure

Colon Surgery Type
type: Class
subclass of: Colon Intervention or Procedure Type
subclass of: Surgical Procedure Type
comment: Class describing surgical procedure type related to colon cancer.
label: Tipo di Intervento Chirurgico relativo al Tumore al Colon @it
label: Type Darmkanker Chirurgische Ingreep @nl
has semantic area: Procedure

Colon Tubular Adenoma
type: Class
subclass of: Adenoma
conforms to: http://linkedlifedata.com/resource/umls/id/C1112503
has exact synonym: Colon Tubular Adenoma
comment: A usually polypoid neoplasm that arises from the glandular epithelium of the colonic mucosa. It is characterized by a tubular architectural pattern. The neoplastic glandular cells have dysplastic features. [Definition Source: NCI]
label: Adenoma Tubulare del Colon @it
label: Colon Tubulair Adenoom @nl
associated disease: Colon Carcinoma
has SNOMED code: M821100
has semantic area: Diagnosis

Colon Tubulovillous Adenoma
type: Class
subclass of: Adenoma
has semantic type: Gene or Genome
conforms to: http://linkedlifedata.com/resource/umls/id/C1112748
has exact synonym: Tubulovillous Adenoma of Colon; Colon Tubulovillous Adenoma; Tubulovillous Adenoma of the Colon; Colonic Tubulovillous Adenoma
comment: A neoplasm that arises from the glandular epithelium of the colonic mucosa. It is characterized by tubular and villous architectural patterns. The neoplastic glandular cells have dysplastic features. [Definition Source: NCI]
label: Adenoma Tubulovilloso del Colon @it
label: Colon Tubulovillous Adenoom @nl
associated disease: Colon Carcinoma
has SNOMED code: M826300
has semantic area: Diagnosis

Colon Villous Adenoma
type: Class
subclass of: Adenoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0149862
has exact synonym: villous adenoma of colon
comment: A villous adenoma that involves the colon. [Definition Source: NCI]
label: Adenoma del Colon Villoso @it
label: Colon Villous Adenoom @nl
associated disease: Colon Carcinoma
has SNOMED code: M826110
has semantic area: Diagnosis
internal notes: previous SNOMED code M82611

Desmocollin-3
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C1448860
comment: Component of intercellular desmosome junctions. Involved in the interaction of plaque proteins and intermediate filaments mediating cell-cell adhesion. May contribute to epidermal cell positioning (stratification) by mediating differential adhesiveness between cells that express different isoforms. [Definition Source: UniProt]
associated disease: Lung cancer
has semantic area: Test

Disease or Disorder
type: Class
conforms to: http://linkedlifedata.com/resource/umls/id/C0012634
comment: A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. [Definition Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/]
label: Malattia o Disturbo @it
label: Ziekte of Aandoening @nl
has semantic area: General Entity

Duodenitis
type: Class
subclass of: Celiac Positive Outcome
conforms to: http://linkedlifedata.com/resource/umls/id/C0013298
has exact synonym: duodenitis; duodenum inflammation; inflammation of duodenum
has related synonym: hemorragic duodenitis
comment: A form of inflammation
comment: Acute or chronic inflammation of the duodenum. Causes include bacterial and viral infections and gastroesophageal reflux disease. Symptoms include vomiting and abdominal pain. [Definition Source: NCI]
label: Duodenite @it
associated disease: Celiac disease
has SNOMED code: M400000
has semantic area: Diagnosis

Dysplasia
type: Class
subclass of: Finding
disjoint with: Human Papilloma Virus Infection
disjoint with: Intestinal Abnormality
disjoint with: Koilocytotic Squamous Cell
disjoint with: Lung Carcinoma Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C0334044
has exact synonym: Dyscrasia; Dysplasia; Dysplastic; dyscrasia; dysplasia
comment: A usually neoplastic transformation of the cell, associated with altered architectural tissue patterns. The cellular changes include nuclear and cytoplasmic abnormalities. Molecular genetic abnormalities are also often found and, in some instances, may lead to cancer.
comment: A usually neoplastic transformation of the cell, associated with altered architectural tissue patterns. The cellular changes include nuclear and cytoplasmic abnormalities. Molecular genetic abnormalities are also often found and, in some instances, may lead to cancer. [Definition Source: NCI]
label: Displasia @it
label: Dysplasie @nl
associated disease: Colon Carcinoma
has SNOMED code: M740000
has semantic area: Diagnosis
internal notes: original SNOMED M74000

Finding
type: Class
conforms to: http://linkedlifedata.com/resource/umls/id/C1285578
comment: A meaningful interpretation of data or observations resulting from planned evaluations. Compare to conclusion, hypothesis. See also general observation class, intervention, event. A meaningful interpretation of data or observations resulting from planned evaluations. Compare to conclusion, hypothesis. See also general observation class, intervention, event. [Definition Source: NCI]
label: Scoperta @it
label: Vinden @nl
has semantic area: Diagnosis

Float Check Element
type: Class
subclass of: Check Element
comment: A set of checks that can be performed on a Immunohistochemical Test that present a float as output value.
label: Elemento di Controllo del Galleggiante @it
label: Voltter Controle-Element @nl
has semantic area: Test

Gender
type: Class
conforms to: http://linkedlifedata.com/resource/umls/id/C0079399
comment: Characteristics of people that are socially constructed, including norms, behaviors, and roles based on sex. As a social construct, gender varies from society to society and can change over time. (Adapted from WHO.) [Definition Source: NCI]
label: Genere Biologico @it
label: Geslacht @nl
has semantic area: General Entity

HER2 (CB11)
type: Class
subclass of: String Check Element
comment: Protein tyrosine kinase that is part of several cell surface receptor complexes, but that apparently needs a coreceptor for ligand binding. Essential component of a neuregulin-receptor complex, although neuregulins do not interact with it alone. GP30 is a potential ligand for this receptor. Regulates outgrowth and stabilization of peripheral microtubules (MTs). Upon ERBB2 activation, the MEMO1-RHOA-DIAPH1 signaling pathway elicits the phosphorylation and thus the inhibition of GSK3B at cell membrane. This prevents the phosphorylation of APC and CLASP2, allowing its association with the cell membrane. In turn, membrane-bound APC allows the localization of MACF1 to the cell membrane, which is required for microtubule capture and stabilization. [Definition Source: UniProt]
associated disease: Celiac disease
associated keyword in diagnosis: HER2
has semantic area: Test

Human Papilloma Virus Infection
type: Class
subclass of: Finding
disjoint with: Intestinal Abnormality
disjoint with: Koilocytotic Squamous Cell
disjoint with: Lung Carcinoma Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C0343641
comment: A cervix disease may present or not the human papilloma virus.
comment: An infectious process caused by a human papillomavirus. This infection can cause abnormal tissue growth.
label: Humaan Papillomavirus-Infectie @nl
label: Infezione da Papillomavirus Umano @it
annotated rule: presence of code D0445** in field 'Diagnosi'
associated disease: Cervical Cancer
has Ontobee annotation: Human papilloma Virus infection; Human papillomavirus disease or disorder; Human Papillomavirus infection; Human papillomavirus infectious disease; Human papillomavirus caused disease or disorder
has SNOMED code: D044500
has semantic area: Diagnosis
internal notes: original SNOMED D0445

Immunohistochemical Test
type: Class
subclass of: Test
has semantic type: Occupational Activity
conforms to: http://linkedlifedata.com/resource/umls/id/C1708472
comment: A diagnostic test in which an antibody is used to link a cellular antigen specifically to a stain that can be seen with a microscope. [Definition Source: NCI]
label: Immunohistochemische Test @nl
label: Test Immunoistochimico @it
associated disease: Colon Carcinoma
associated keyword in diagnosis: presence of word “CD3”/“test immunoistochimico” /“colorazione immunoistochimica”
has semantic area: Test

Immunoprecipitation
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C0021069
comment: Antigen aggregation with antibody, in the right ratios, to cause precipitation. [Definition Source: NCI]
label: Immunoprecipitatie @nl
label: Immunoprecipitazione @it
has SNOMED code: P382000
has semantic area: Test

Inconclusive Outcome
type: Class
subclass of: Class
  union of: Celiac Outcome
  union of: Cervix Outcome
  union of: Colon Outcome
  union of: Lung Outcome
comment: Inconclusive Outcome. Not enough tissue or not enough evidence was present to decide for a negative or positive outcome.
label: Onduidelijk Resultaat @nl
label: Risultato Inconcludente @it
has semantic area: Diagnosis

Inconclusive Outcome Type
type: Class
comment: Class describing why the clinical case resulted inconclusive.
label: Onduidelijk Resultaattype @nl
label: Tipo di Risultato Inconcludente @it
has semantic area: Diagnosis

Intervention or Procedure
type: Class
alternative definition: The drug, device, therapy, or process under investigation in a clinical study that is believed to have an effect on outcomes of interest in a study (e.g., health-related quality of life, efficacy, safety, pharmacoeconomics). See also: test articles; devices; drug product; medicinal product; combination product.; In medicine, a treatment or action taken to prevent or treat disease, or improve health in other ways.
conforms to: http://linkedlifedata.com/resource/umls/id/C0184661
has exact synonym: interventionDescription; intervention; Intervention; Procedure; Intervention Strategies; Interventional; Intervention or Procedure
comment: This general class represents the intervention performed on the patient to obtain the samples that are then studied to find the disease. In particular, this class represents the attribute 'MATERIALI' in the AOEC Database, and the attribute METHOD in the TCGA database.
label: Intervento o Procedura @it
label: Tussenkomst of Procedure @nl
definition: An activity that produces an effect, or that is intended to alter the course of a disease in a patient or population. This is a general term that encompasses the medical, social, behavioral, and environmental acts that can have preventive, therapeutic, or palliative effects.
has semantic area: General
has semantic area: Procedure

Intervention or Procedure Type
type: Class
comment: Class describing the type of intervention or procedure performed.
label: Tipo di intervento o procedura @it
label: Type Tussenkomst of Procedure @nl
has semantic area: Procedure

Intestinal Abnormality
type: Class
subclass of: Finding
disjoint with: Koilocytotic Squamous Cell
disjoint with: Lung Carcinoma Finding
comment: Abnormality in celiac outcomes.
label: Anomalia relativa all'Intestino @it
label: Intestinale Afwijking @nl
has semantic area: Diagnosis

Proliferation marker protein Ki-67
type: Class
subclass of: Float Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C4742498
comment: Required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly (PubMed:27362226). Associates with the surface of the mitotic chromosome, the perichromosomal layer, and covers a substantial fraction of the chromosome surface (PubMed:27362226). Prevents chromosomes from collapsing into a single chromatin mass by forming a steric and electrostatic charge barrier: the protein has a high net electrical charge and acts as a surfactant, dispersing chromosomes and enabling independent chromosome motility (PubMed:27362226). Binds DNA, with a preference for supercoiled DNA and AT-rich DNA (PubMed:10878551). Does not contribute to the internal structure of mitotic chromosomes (By similarity). May play a role in chromatin organization (PubMed:24867636). It is however unclear whether it plays a direct role in chromatin organization or whether it is an indirect consequence of its function in maintaining mitotic chromosomes dispersed (Probable). [Definition Source: UniProt]
label: Marcatore di proliferazione della proteina Ki-67 @it
label: Proliferatie marker proteïne Ki-67 @nl
associated disease: Lung cancer
associated keyword in diagnosis: Ki-67
has semantic area: Test

Koilocytotic Squamous Cell
type: Class
subclass of: Finding
disjoint with: Lung Carcinoma Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C1517678
has exact synonym: Koilocyte; Koilocytotic Squamous Cell
comment: Koilocytes are epithelial cells containing a hyperchromatic nucleus that is acentrically displaced by perinuclear vacuole(s), and these morphological alterations are used by pathologists to help identify HPV-infected epithelial cells in Pap smears. [Definition Source: PMID 18688031]
label: Cellula Squamosa Cilocitotica @it
label: Koilocytotische Plaveiselcel @nl
associated disease: Cervical Cancer
has semantic area: Diagnosis

Lung Large Cell Carcinoma
type: Class
subclass of: Non-Small Cell Lung Carcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0345958
has exact synonym: lung large cell carcinoma; large cell lung carcinoma; large cell lung cancer; large cell undifferentiated lung carcinoma; large cell carcinoma of the lung; large cell carcinoma of lung; anaplastic lung carcinoma
has related synonym: LCLC
comment: A poorly differentiated non-small cell lung carcinoma composed of large polygonal cells without evidence of glandular or squamous differentiation. There is a male predilection. [Definition Source: NCI]
label: Carcinoma Polmonare a Grandi Cellule @it
label: Grootcellig Longcarcinoom @nl
associated disease: Lung cancer
has SNOMED code: M801090
has semantic area: Diagnosis

Laboratory Finding
type: Class
comment: This class is used to contain information about the celiac disease, the IEL, the villli to crypt ratio and the villi status.
label: Laboratorium Bevinding @nl
label: Risultati di Laboratorio @it
has semantic area: Diagnosis

Lung Adenocarcinoma
type: Class
subclass of: Non-Small Cell Lung Carcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0152013
has exact synonym: lung adenocarcinoma; bronchogenic lung adenocarcinoma; nonsmall cell adenocarcinoma; non-small cell lung adenocarcinoma; adenocarcinoma of the lung; adenocarcinoma of lung
comment: A carcinoma that arises from the lung and is characterized by the presence of malignant glandular epithelial cells. There is a male predilection with a male to female ratio of 2:1. Usually lung adenocarcinoma is asymptomatic and is identified through screening studies or as an incidental radiologic finding. If clinical symptoms are present they include shortness of breath, cough, hemoptysis, chest pain, and fever. Tobacco smoke is a known risk factor. [Definition Source: NCI]
label: Adenocarcinoma Polmonare @it
label: Long Adenocarcinoom @nl
associated disease: Lung cancer
has SNOMED code: M814030
has semantic area: Diagnosis

Lung Anatomical Entity
type: Class
subclass of: Anatomical Entity
comment: Class describing biological entities related to lung cancer.
label: Entità Anatomica relativa al Tumore ai Polmoni @it
label: Long Anatomische Entiteit @nl
has semantic area: Anatomical Location

Lung Carcinoma
type: Class
equivalent class: Restriction
  on property: presence of
  some values from: Lung Carcinoma Finding
subclass of: Lung Positive Outcome
conforms to: http://linkedlifedata.com/resource/umls/id/C0684249
has broad synonym: cancer of lung; cancer of the lung; lung cancer; lung cancer, NOS
has exact synonym: lung carcinoma; carcinoma of lung; carcinoma of the lung
comment: A carcinoma that arises from epithelial cells of the lung. [Definition Source: https://orcid.org/0000-0002-6601-2165]
label: Carcinoma Polmonare @it
label: Longcarcinoom @nl
associated disease: Lung cancer
has SNOMED code: M801030
has semantic area: Diagnosis

Lung Carcinoma Finding
type: Class
subclass of: Finding
is defined by: Finding in outcomes that tested positive for Lung Carcinoma or any of its subclasses.
label: Longcarcinoom Vinden @nl
label: Scoperta nel Carcinoma Polmonare @it
associated disease: Lung cancer
has semantic area: Diagnosis

Lung Clinical Case Report
type: Class
equivalent class: Restriction
  on property: has outcome
  all values from: Lung Outcome
subclass of: Clinical Case Report
comment: Class representing all lung cancer cases.
label: Caso Clinico di Cancro ai Polmoni @it
label: Klinisch Geval van Longkanker @nl
has semantic area: General Entity

Lung Cancer Intervention or Procedure
type: Class
equivalent class: Restriction
  on property: has location
  all values from: Lung Anatomical Entity
subclass of: Intervention or Procedure
comment: Class describing interventions or procedures related to lung cancer.
label: Intervento o Procedura relativa al Cancro ai Polmoni @it
label: Longkanker tussenkomst of procedure @nl
has semantic area: Procedure

Lung Intervention or Procedure Type
type: Class
subclass of: Intervention or Procedure Type
comment: Class describing the type of intervention or procedure related to lung cancer.
label: Tipo di Intervento o Procedura relativa al Cancro ai Polmoni @it
label: Type Longkanker Tussenkomst of Procedure @nl
has semantic area: Procedure

Lung Outcome
type: Class
equivalent class: Restriction
  on property: has intervention
  all values from: Lung Cancer Intervention or Procedure
equivalent class: Restriction
  on property: has location
  all values from: Lung Anatomical Entity
subclass of: Outcome
comment: Class representing all outcomes of lung clinical case reports.
label: Resultaat van Longkanker @nl
label: Risultato di Cancro ai Polmoni @it
has semantic area: Diagnosis

Lung Positive Outcome Type
type: Class
subclass of: Positive Outcome Type
comment: Class describing for which type of lung cancer the clinical case tested positive.
label: Tipo di Risultato Positivo al Cancro ai Polmoni @it
label: Type Longkanker Positief Resultaat @nl
has semantic area: Diagnosis

Lung Positive Outcome
type: Class
equivalent class: Restriction
  on property: positive result type
  all values from: Lung Positive Outcome Type
subclass of: Lung Outcome
subclass of: Positive Outcome
comment: Positive Outcome, i.e., something related to lung cancer has been found in the patient.
label: Positieve Uitkomst van Longkanker @nl
label: Risulato Positivo di Cancro ai Polmoni @it
has semantic area: Diagnosis

Lung Cancer Surgical Procedure
type: Class
subclass of: Lung Cancer Intervention or Procedure
subclass of: Surgical procedure
comment: Class describing surgical procedures related to lung cancer.
label: Intervento Chirurgico relativo al Cancro ai Polmoni @it
label: Longkanker Chirurgische Ingreep @nl
has semantic area: Procedure

Lung Surgery Type
type: Class
subclass of: Lung Intervention or Procedure Type
subclass of: Surgical Procedure Type
comment: Class describing surgical procedure type related to lung cancer.
label: Tipo di Intervento Chirurgico relativo al Tumore ai Polmoni @it
label: Type Longkanker Chirurgische Ingreep @nl
has semantic area: Procedure

Malignant Lung Neoplasm
type: Class
subclass of: Non-Small Cell Lung Carcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0242379
has exact synonym: Malignant Lung Tumor; Malignant Lung Neoplasm; Malignant Tumor of the Lung; Malignant Neoplasm of Lung; Malignant Neoplasm of the Lung; Malignant Tumor of Lung
comment: A primary or metastatic malignant neoplasm involving the lung. [Definition Source: NCI]
label: Kwaadaardige Longneoplasma @nl
label: Neoplasia Polmonare Maligna @it
associated disease: Lung cancer
has SNOMED code: M800034
has SNOMED code: M800130
has semantic area: Diagnosis

Metastatic Neoplasm
type: Class
subclass of: Lung Adenocarcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C2939420
has exact synonym: Metastatic Tumor; metastasis; Neoplasm, metastatic; Metastatic Disease; Tumor, metastatic; Metastatic; Metastatic Neoplasm; Metastasis
has exact synonym: metastatic disease; metastatic neoplasm; metastatic tumor
comment: A tumor that has spread from its original (primary) site of growth to another site, close to or distant from the primary site. Metastasis is characteristic of advanced malignancies, but in rare instances can be seen in neoplasms lacking malignant morphology. [Definition Source: NCI]
label: Neoplasia Metastatica @it
label: Uitgezaaide Neoplasma @nl
associated disease: Lung cancer
has SNOMED code: M800060
has SNOMED code: M814060
has semantic area: Diagnosis

Napsin A
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C1538038
comment: May be involved in processing of pneumocyte surfactant precursors. [Definition Source: UniProt]
associated disease: Lung cancer
associated keyword in diagnosis: Napsina
has semantic area: Test

Non-Small Cell Lung Carcinoma
type: Class
subclass of: Lung Carcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0007131
has exact synonym: NSCLC - non-small cell lung cancer; non-small cell lung carcinoma; non-small cell carcinoma of lung; non-small cell carcinoma of the lung; non-small cell cancer of lung; non-small cell lung cancer; non-small cell cancer of the lung; NSCLC
has related synonym: non-small cell lung cancer, NOS; non small cell lung cancer NOS
comment: A group of at least three distinct histological types of lung cancer, including non-small cell squamous cell carcinoma, adenocarcinoma, and large cell carcinoma. Non-small cell lung carcinomas have a poor response to conventional chemotherapy. [Definition Source: NCI]
label: Carcinoma Polmonare Non a Piccole Cellule @it
label: Niet-Kleincellig Longcarcinoom @nl
associated disease: Lung cancer
has SNOMED code: M807030
has semantic area: Diagnosis

Negative Result
type: Class
subclass of: Class
  union of: Celiac Outcome
  union of: Cervix Outcome
  union of: Colon Outcome
  union of: Lung Outcome
comment: The presence of a negative result, i.e. normal tissue
label: Negatief Resultaat @nl
label: Risultato Negativo @it
has SNOMED code: M010100
has semantic area: Diagnosis

No Malignancy
type: Class
subclass of: Class
  union of: Celiac Outcome
  union of: Cervix Outcome
  union of: Colon Outcome
  union of: Lung Outcome
comment: No present of malignancy for one of the diseases included in the ExaMode ontology.
label: Geen Maligniteit @nl
label: Nessuna Malignità @it
has SNOMED code: M094500
has semantic area: Diagnosis

Onset
type: Class
conforms to: http://linkedlifedata.com/resource/umls/id/C0206132
comment: The age group in which disease manifestations appear. [Definition Source: HPO]
comment: This class represents a generic age group.
label: Gruppo d'età @it
label: Leeftijdsgroep @nl
has semantic area: General Entity

Other Laboratory Finding
type: Class
subclass of: Laboratory Finding
comment: This class contains information about other laboratory finding related to celiac disease, e.g. IEL or number of mitosis per crypt.
label: Altri Risultati di Laboratorio @it
label: Andere Laboratorium Bevindingen @nl
associated disease: Celiac disease
has semantic area: Diagnosis

Outcome
type: Class
has semantic type: Finding
alternative definition: A specific result or effect that can be measured. Examples of outcomes include decreased pain, reduced tumor size, and improvement of disease.; 1. events or experiences that clinicians or investigators examining the impact of an intervention or exposure measure because they believe such events or experiences may be influenced by the intervention or exposure. 2. (SDTM) The result of carrying out a mathematical or statistical procedure. NOTE: 1. such events and experiences are called clinical outcomes independently of whether they are part of the original question/protocol of the investigation. [1. Guyatt, G., Schunemann H., Dept. epidemiology & statistics, McMaster University-personal communication] See also variable; outcome can be a result of analysis; outcome is more general than endpoint in that it does not necessarily relate to a planned objective of the study.outcome. The measureable characteristic (clinical outcome assessment, biomarker) that is influenced or affected by an individual's baseline state or an intervention as in a clinical trial or other exposure.
conforms to: http://linkedlifedata.com/resource/umls/id/C1274040
has exact synonym: OUT; result; Result; Outcome; outcome
comment: A class representing a general outcome, whatever it may be (positive, negative, uncertain, not enough information etc).
label: Resultaat @nl
label: Risultato @it
definition: The result of an action.
has semantic area: Diagnosis

Endonuclease P40
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C0909069
comment: One of the tests that can be performed to check lung cancer.
associated disease: Lung cancer
associated keyword in diagnosis: P40
has semantic area: Test

Tumor Protein 63 Isoform 2
type: Class
subclass of: Boolean Check Element
has semantic type: Amino Acid, Peptide, or Protein
structure notes: Tumor protein 63 isoform 2 is the product of an alternative promoter and start codon located in exon 3 of the human TP63 gene. It also has an N-terminally truncated transactivation domain. Expression of isoform 2 may be tissue specific and aberrant expression may be associated with head and neck squamous cell carcinoma. (Atlas of Genetics and Cytogenetics in Oncology and Haematology)
conforms to: http://linkedlifedata.com/resource/umls/id/C4284135
has exact synonym: Delta Np63 Alpha; Tumor Protein 63 Isoform 2; Delta-N p63-Alpha; p51; DeltaN-Alpha; P51delNalpha; DeltaNp63 Alpha
comment: Tumor protein 63 isoform 2 (586 aa, ; 66 kDa) is encoded by the human TP63 gene. This protein plays a role in the mediation of both transcription and skin development. [Definition Source: NCI]
associated disease: Lung cancer
associated keyword in materiali: P63
has semantic area: Test

Pulmonary surfactant-associated protein B
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C0072599
comment: Pulmonary surfactant-associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces. SP-B increases the collapse pressure of palmitic acid to nearly 70 millinewtons per meter. [Definition Source: UniProt]
label: Proteina associata ai tensioattivi polmonari B @it
label: Pulmonale surfactant-geassocieerd proteïne B. @nl
associated disease: Lung cancer
has semantic area: Test

Patient
type: Class
conforms to: http://linkedlifedata.com/resource/umls/id/C0030705
comment: A person under health care. The person may be waiting for this care or may be receiving it or may have already received it. [Definition source: RxList]
label: Geduldig @nl
label: Paziente @it
has semantic area: General Entity

Positive Outcome
type: Class
subclass of: Outcome
comment: Positive Outcome, i.e., something has been found in the patient. This is the higher class for the positive outcome.
label: Positieve Uitkomst @nl
label: Risultato Positivo @it
has semantic area: Diagnosis

Positive Outcome Type
type: Class
comment: Class describing for what the clinical case tested positive.
label: Positieve Uitkomst Type @nl
label: Tipo di Risultato Positivo @it
has semantic area: Diagnosis

Positive to Celiac Disease
type: Class
subclass of: Celiac Positive Outcome
conforms to: http://linkedlifedata.com/resource/umls/id/C0007570
comment: Represents the fact that the patient is actually positive to celiac disease. We use a different entity, instead of the entity "celiac disease", because that one is an individual in the ontology, and it is not good practice to have entities that are both individuals and General Classes in the same ontology.
label: Positief voor Coealiakie @nl
label: Positivo alla Celiachia @it
associated disease: Celiac disease
has SNOMED code: D547100
has semantic area: Diagnosis

Small Cell Lung Carcinoma
type: Class
subclass of: Lung Carcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0149925
has exact synonym: oat cell carcinoma of the lung; small cell neuroendocrine carcinoma of the lung; small cell neuroendocrine carcinoma of lung; small cell lung carcinoma; small cell carcinoma of lung; oat cell carcinoma of lung; lung oat cell carcinoma; oat cell lung carcinoma; lung small cell carcinoma; small cell lung cancer; small cell carcinoma of the lung; lung small cell neuroendocrine carcinoma
has related synonym: small cell cancer of the lung; SCLC1
comment: Small cell lung cancer (SCLC) is a highly aggressive malignant neoplasm, accounting for 10-15% of lung cancer cases, characterized byrapid growth, and early metastasis. SCLC usually manifests as a large hilar mass with bulky mediastinal lymphadenopathy presenting clinically with chest pain, persistent cough, dyspnea, wheezing, hoarseness, hemoptysis, loss of appetite, weight loss, and neurological and endocrine paraneoplastic syndromes. SCLC is primarily reported in elderly people with a history of long-term tobacco exposure. [Definition Source Orphanet 70573]
label: Carcinoma Polmonare a Piccole Cellule @it
label: Kleincellig Longcarcinoom @nl
associated disease: Lung cancer
has SNOMED code: M804130
has semantic area: Diagnosis

Synaptophysin
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C0085255
comment: Possibly involved in structural functions as organizing other membrane components or in targeting the vesicles to the plasma membrane. Involved in the regulation of short-term and long-term synaptic plasticity. [Definition Source: UniProt]
label: Synaptofysin @nl
associated disease: Lung cancer
associated keyword in diagnosis: Sinaptoﬁsina
associated keyword in diagnosis: Syph Human
has semantic area: Test

Semantic Area
type: Class
subclass of: Annotation
comment: A general container for entities that represent semantical areas. Examples of semantical areas include "General" (common to all diseases), "Anatomic Site", "Procedure", "Diagnosis".
label: Area Semantica @it
label: Semantisch Gebied @nl
has semantic area: General Entity

Serrated Adenoma
type: Class
subclass of: Adenoma
conforms to: http://linkedlifedata.com/resource/umls/id/C1266025
has exact synonym: Traditional Serrated Adenoma; Serrated Adenoma; TSA; Serrated Adenoma Type II; Serrated adenoma; Traditional serrated adenoma
comment: An adenoma that arises from the large intestine and the appendix. It is characterized by prominent serration of the glands. [Definition Source: NCI]
label: Adenoma Seghettato @it
label: Gekarteld Adenoom @nl
associated disease: Colon Carcinoma
has semantic area: Diagnosis

Slide Device
type: Class
conforms to: http://linkedlifedata.com/resource/umls/id/C1705201
has exact synonym: Slide; Slide Device Component; Slide Device; Microscope Slide
comment: A flat rectangular piece of glass on which specimens can be mounted for microscopic study. [Definition Source:NCI]
label: Schuif @nl
label: Vetrino @it
has semantic area: General Entity

Non-Small Cell Squamous Lung Carcinoma
type: Class
subclass of: Non-Small Cell Lung Carcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C4324656
has exact synonym: non-small cell squamous lung cancer; non-small cell squamous lung carcinoma; squamous non-small cell lung carcinoma
comment: A squamous cell carcinoma that arises from the lung. It is characterized by the presence of large malignant cells. It includes the clear cell and papillary variants of squamous cell carcinoma. [Definition Source: NCI]
label: Carcinoma Polmonare Squamoso Non a Piccole Cellule @it
label: Niet-Kleincellig Plaveiselcelcarcinoom @nl
associated disease: Lung cancer
has SNOMED code: M807030
has semantic area: Diagnosis

String Check Element
type: Class
subclass of: Check Element
comment: A set of checks controlled on an Immunohistochemical test that can only have a string result.
label: Elemento di Controllo Testuale @it
label: Tekenreeks Controle-Element @nl
has semantic area: Test

Surgical Procedure Type
type: Class
subclass of: Intervention or Procedure Type
comment: Class describing the type of surgical procedure performed.
label: Tipo di Intervento Chirurgico @it
label: Type Chirurgische Ingreep @nl
has semantic area: Procedure

Surgical procedure
type: Class
subclass of: Intervention or Procedure
conforms to: http://linkedlifedata.com/resource/umls/id/C0543467
comment: A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. [Definition Source: NCI]
label: Chirurgische Ingreep @nl
label: Intervento Chirurgico @it
has semantic area: Procedure

TTF1 Human
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C1610981
has exact synonym: Transcription termination factor 1
comment: Multifunctional nucleolar protein that terminates ribosomal gene transcription, mediates replication fork arrest and regulates RNA polymerase I transcription on chromatin. Plays a dual role in rDNA regulation, being involved in both activation and silencing of rDNA transcription. Interaction with BAZ2A/TIP5 recovers DNA-binding activity. [Definition Source: UniProt]
associated disease: Lung cancer
associated keyword in diagnosis: Transcription termination factor 1
has semantic area: Test

Test
type: Class
has semantic type: Activity
conforms to: http://linkedlifedata.com/resource/umls/id/C0392366
comment: A general class representing a test.
definition: A procedure for critical evaluation; a means of determining the presence, quality, or truth of something
has semantic area: Test

Vimentin
type: Class
subclass of: Boolean Check Element
conforms to: http://linkedlifedata.com/resource/umls/id/C0042666
comment: Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. [Definition Source: UniProt]
associated disease: Lung cancer
has semantic area: Test

Villi Laboratory Finding
type: Class
subclass of: Laboratory Finding
comment: This class contains information about villi status
label: Risultati di Laboratorio relativi ai Vilii @it
label: Villi Laboratorium Bevinding @nl
associated disease: Celiac disease
has semantic area: Diagnosis

Radboud University Nijmegen
type: NamedIndividual
type: Concept
type: Organization
comment: Radboud University Nijmegen (abbreviated as RU, Dutch: Radboud Universiteit Nijmegen, formerly Katholieke Universiteit Nijmegen) is a public university with a strong focus on research located in Nijmegen, the Netherlands. It was established on 17 October 1923 and is situated in the oldest city of the Netherlands. The RU has seven faculties and enrolls over 19,900 students. It was internationally ranked 156th by the QS World University Rankings.
label: Radboud Universiteit Nijmegen @it
has semantic area: General

Melissa Anne Haendel
type: NamedIndividual
type: Person

Pavement Epithelium
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
broader transitive: Cervix Epithelium
alternative definition: FMA: Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.,UWDA: Epithelium which consists of a single layer of epithelial cells. Examples: endothelium, mesothelium, glandular squamous epithelium.,NCI: Epithelium composed of a single layer of cells attached to a basement membrane.
conforms to: http://linkedlifedata.com/resource/umls/id/C0682574
comment: Squamous epithelium composed of a single layer of cells. [Defintion Source: Dorlands_Medical_Dictionary:MerckSource]
label: Bestrating Epitheel @nl
label: Epitelio della Pavimentazione @it
associated disease: Cervical Cancer
has semantic area: Anatomical Location

Mucosa of Pyloric Antrum
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
broader transitive: Antrum Pylori
conforms to: http://linkedlifedata.com/resource/umls-concept/C0735812
comment: Mucosa found in the gastric antrum. [Definition Source: Humpath.com - Human pathology]
label: Mucosa dell'Antro Pilorico @it
label: Mucosa van Pylorus Antrum @nl
associated disease: Celiac disease
has semantic area: Diagnosis

Right Superior Lobar Bronchus
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
broader transitive: Lobar Bronchus
conforms to: http://linkedlifedata.com/resource/umls/id/C0225610
has exact synonym: Right upper lobar bronchus; Right upper lobe bronchus
comment: Part of the right bronchus.
label: Bronco Lobare Superiore Destro @it
label: Rechter Superieure Lobaire Bronchus @nl
associated disease: Lung cancer
has semantic area: Anatomical Location

Right Inferior Lobar Bronchus
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
broader transitive: Lobar Bronchus
conforms to: http://linkedlifedata.com/resource/umls/id/C0225621
has exact synonym: Bronchus of right lower lobe; Right lower lobe bronchus; Right lower lobar bronchus.
comment: A region of the bronchus in the lung.
label: Bronco Lobare Inferiore Destro @it
label: Rechter Inferieure Lobaire Bronchus @nl
associated disease: Lung cancer
has semantic area: Anatomical Location

Left Superior Lobar Bronchus
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
broader transitive: Lobar Bronchus
conforms to: http://linkedlifedata.com/resource/umls/id/C0225632
has exact synonym: Left upper lobar bronchus; Bronchus of left upper lobe; Left upper lobe bronchus
comment: Part of the left bronchus.
label: Bronco Lobare Superiore Sinistro @it
label: Linker Superieure Lobaire Bronchus @nl
associated disease: Lung cancer
has semantic area: Anatomical Location

Left Inferior Lobar Bronchus
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
broader transitive: Lobar Bronchus
conforms to: http://linkedlifedata.com/resource/umls/id/C0225641
has exact synonym: Bronchus of left lower lobe; Left lower lobe bronchus; Left lower lobar bronchus
comment: A region of the bronchus in the lungs.
label: Bronco Lobare Inferiore Sinistro @it
label: Links Inferieure Lobaire Bronchus @nl
associated disease: Lung cancer
has semantic area: Anatomical Location

Necrosis
type: NamedIndividual
type: Concept
type: Lung Carcinoma Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C0027540
has broad synonym: necrosis
has exact synonym: cellular necrosis; necrotic cell death
has exact synonym: metastasize; Metastasis, NOS; metastasis; Tumor Cell Migration; Metastasize; Metastasis
comment: Note that the word necrosis has been widely used in earlier literature to describe forms of cell death which are now known by more precise terms, such as apoptosis. Necrosis can occur in a regulated fashion, involving a precise sequence of signals.
label: Necrose @nl
label: Necrosi @it
associated disease: Lung cancer
definition: A type of cell death that is morphologically characterized by an increasingly translucent cytoplasm, swelling of organelles, minor ultrastructural modifications of the nucleus (specifically, dilatation of the nuclear membrane and condensation of chromatin into small, irregular, circumscribed patches) and increased cell volume (oncosis), culminating in the disruption of the plasma membrane and subsequent loss of intracellular contents. Necrotic cells do not fragment into discrete corpses as their apoptotic counterparts do. Moreover, their nuclei remain intact and can aggregate and accumulate in necrotic tissues. [Defintion Source: PMID:18846107, PMID:20823910]
has semantic area: Diagnosis

Cervical Polyp
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0007855
has exact synonym: polyp of the cervix uteri; adenomatous polyp of the uterine cervix; uterine cervix polyp; cervical polyp; adenomatous polyp of cervix; uterine cervix adenomatous polyp; adenomatous polyp of uterine cervix; cervix uteri polyp; polyp of cervix; polyp of the uterine cervix; cervix adenomatous polyp; cervix polyp; polyp of cervix uteri; polyp of uterine cervix; cervix uteri adenomatous polyp; polyp of the cervix; adenomatous polyp of the cervix
comment: A polyp that arises from the surface of the cervix. [Definition Source: NCI]
label: Cervicale Poliep @nl
label: Polipo Cervicale @it
associated disease: Cervical Cancer
has SNOMED code: M768002
has SNOMED code: M768003
has semantic area: Diagnosis

Athrophic Vulva
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0156393
has exact synonym: atrophy of vulva; atrophic vulva
has related synonym: atrophic vulvitis
comment: Vaginal atrophy (atrophic vaginitis) is thinning, drying and inflammation of the vaginal walls that may occur when your body has less estrogen. Vaginal atrophy occurs most often after menopause. For many women, vaginal atrophy not only makes intercourse painful but also leads to distressing urinary symptoms. Because the condition causes both vaginal and urinary symptoms, doctors use the term "genitourinary syndrome of menopause (GSM)" to describe vaginal atrophy and its accompanying symptoms.
label: Atrofische Vulva @nl
label: Vulva Atrofica @it
associated disease: Cervical Cancer
has SNOMED code: M580000
has semantic area: Diagnosis

Colon Carcinoma
type: NamedIndividual
type: Concept
type: Disease or Disorder
conforms to: http://linkedlifedata.com/resource/umls/id/C0699790
comment: A carcinoma that arises from epithelial cells of the colon [Definition Source: https://orcid.org/0000-0002-6601-2165]
label: Carcinoma del Colon @it
label: Coloncarcinoom @nl
has semantic area: General Entity

Lymphadenitis
type: NamedIndividual
type: Concept
type: Lung Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0024205
has broad synonym: lymph gland infection
has exact synonym: inflammation of lymph node; acute adenitis; chronic lymphadenitis; lymphadenitis; Inflammation of lymph node; acute lymphadenitis; adenitis; lymph node inflammation; chronic adenitis; lymph nodeitis
comment: Acute or chronic inflammation of one or more lymph nodes. It is usually caused by an infectious process. [Definition Source: NCI]
label: Linfoadenite @it
label: Lymfadenitis @nl
associated disease: Lung cancer
has SNOMED code: M400000
has semantic area: Diagnosis

Cervical Cancer
type: NamedIndividual
type: Concept
type: Disease or Disorder
conforms to: http://linkedlifedata.com/resource/umls/id/C0007847
has broad synonym: cervical neoplasm; tumor of the cervix uteri; uterine cervical neoplasm
has exact synonym: malignant tumor of uterine cervix; uterine cervix cancer; malignant neoplasm of cervix; malignant neoplasm of uterine cervix; malignant tumor of the uterine cervix; malignant tumor of cervix uteri; malignant cervical neoplasm; cervix cancer; malignant neoplasm of cervix uteri; neoplasm of uterine cervix; malignant neoplasm of the uterine cervix; malignant cervix uteri neoplasm; malignant uterine cervix neoplasm; malignant tumor of cervix; malignant cervix neoplasm; malignant tumor of the cervix uteri; malignant neoplasm of the cervix uteri; malignant cervix uteri tumor; malignant cervix tumor; malignant uterine cervix tumor; cancer of uterine cervix; cervix uteri cancer; malignant cervical tumor; malignant tumor of the cervix; malignant neoplasm of the cervix
comment: A primary or metastatic malignant neoplasm involving the cervix. [Definition Source: NCI]
label: Baarmoederhalskanker @nl
label: Cancro Cervicale @it
has semantic area: General Entity

Squamous Carcinoma in Situ
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
broader transitive: Cervical Intraepithelial Neoplasia Grade 2/3
conforms to: http://linkedlifedata.com/resource/umls/id/C0334245
has exact synonym: squamous carcinoma in situ; cervical intraepithelial neoplasia grade III with severe dysplasia; stage 0 uterine cervix carcinoma; severe dysplasia of the cervix uteri; stage 0 squamous cell carcinoma; CIN III - carcinoma in situ of cervix; squamous cell carcinoma in-situ; epidermoid cell carcinoma in situ; CIN III - severe dyskaryosis; grade III SIN; carcinoma in situ of uterine cervix; carcinoma, squamous cell, in situ, malignant; grade 3 SIN; uterine cervix in situ carcinoma; squamous intraepithelial neoplasia, grade III; carcinoma in situ of cervix; CIN III; intraepithelial squamous cell carcinoma; grade 3 squamous intraepithelial neoplasia; squamous cell carcinoma in situ; epidermoid carcinoma in situ; grade III squamous intraepithelial neoplasia; severe dysplasia of cervix; cervix Ca in situ
has related synonym: squamous carcinoma in situ
comment: A malignant epithelial neoplasm confined to the squamous epithelium, without invasion of the underlying tissues. [Definition Source: NCI]
label: Cervicale Squameuze Intra-Epitheliale Neoplasie Graad 3 @nl
label: Neoplasia Cervicale Squamosa Intraepiteliale di Grado 3 @it
associated disease: Cervical Cancer
has SNOMED code: M740080
has SNOMED code: M801020
has semantic area: Diagnosis
internal notes: originally the SNOMED code was M74008*

Celiac disease
type: NamedIndividual
type: Concept
type: Disease or Disorder
conforms to: http://linkedlifedata.com/resource/umls/id/C0007570
has exact synonym: coeliac disease; non tropical sprue; idiopathic steatorrhea; gluten-induced enteropathy; celiac sprue
comment: An autoimmune genetic disorder with an unknown pattern of inheritance that primarily affects the digestive tract. It is caused by intolerance to dietary gluten. Consumption of gluten protein triggers an immune response which damages small intestinal villi and prevents adequate absorption of nutrients. Clinical signs include abdominal cramping, diarrhea or constipation and weight loss. If untreated, the clinical course may progress to malnutrition, anemia, osteoporosis and an increased risk of intestinal malignancies. However, the prognosis is favorable with successful avoidance of gluten in the diet. [Definition Source: NCI]
label: Celiachia @it
label: Coeliakie @nl
has semantic area: General Entity

Cervical Carcinoma
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0302592
has broad synonym: cervix cancer; cervical cancer, NOS; cervical cancer; cancer of cervix; uterine cervix cancer
has exact synonym: cancer of the uterine cervix; carcinoma of the cervix; carcinoma of cervix; carcinoma of the cervix uteri; carcinoma cervix uteri; cancer of uterine cervix; cervical carcinoma; carcinoma of uterine cervix; cervix carcinoma; uterine cervix carcinoma; carcinoma of cervix uteri; cancer of the cervix; cervix uteri carcinoma; carcinoma of the uterine cervix; cancer of cervix
comment: A carcinoma arising from either the exocervical squamous epithelium or the endocervical glandular epithelium. The major histologic types of cervical carcinoma are: squamous carcinoma, adenocarcinoma, adenosquamous carcinoma, adenoid cystic carcinoma and undifferentiated carcinoma. [Definition Source: NCI]
label: Carcinoma Cervicale @it
label: Cervicaal Carcinoom @nl
associated disease: Cervical Cancer
has SNOMED code: M801030
has semantic area: Diagnosis

Human Papilloma Virus Infection
type: NamedIndividual
type: Concept
conforms to: http://linkedlifedata.com/resource/umls/id/C0343641
comment: A cervix disease may present or not the human papilloma virus.
comment: An infectious process caused by a human papillomavirus. This infection can cause abnormal tissue growth. [Definition Source: NCI]
label: Humaan Papillomavirus-Infectie @nl
label: Infezione da Papillomavirus Umano @it
annotated rule: presence of code D0445** in field 'Diagnosi'
associated disease: Cervical Cancer
has Ontobee annotation: Human papilloma Virus infection; Human papillomavirus disease or disorder; Human Papillomavirus infection; Human papillomavirus infectious disease; Human papillomavirus caused disease or disorder
has SNOMED code: D044500
has semantic area: Diagnosis
internal notes: original SNOMED D0445

Cervical Intraepithelial Neoplasia Grade 2/3
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
broader transitive: Cervical Intraepithelial Neoplasia
conforms to: http://linkedlifedata.com/resource/umls/id/C2986622
has exact synonym: cervical intraepithelial neoplasia grade 2/3; high grade dysplasia; moderate or severe dysplasia
comment: A neoplastic process in the cervix characterized by morphologic features of both moderate and severe intraepithelial neoplasia. [Definition Source: NCI]
label: Cervicale Intra-Epitheliale Neoplasie Graad 2/3 @nl
label: Neoplasia Intraepiteliale Cervicale di Grado 2/3 @it
associated disease: Cervical Cancer
has semantic area: Diagnosis

Cervical Squamous Cell Carcinoma
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
broader transitive: Cervical Carcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0279671
has exact synonym: squamous cervical cancer; cervical squamous cell cancer; squamous cell carcinoma of cervix uteri; squamous cell carcinoma of cervix; squamous cell carcinoma of the uterine cervix; cervix uteri squamous cell carcinoma; uterine cervix squamous cell carcinoma; cervical squamous cell carcinoma; cervix squamous cell carcinoma; squamous cell carcinoma of the cervix uteri; squamous cell carcinoma of the cervix; squamous cell carcinoma of uterine cervix has_related_synonym: cervical squamous cell carcinoma, NOS; CESC; cervical squamous cell carcinoma, not otherwise specified
comment: A squamous cell carcinoma arising from the cervical epithelium. It usually evolves from a precancerous cervical lesion. Increased numbers of sexual partners and human papillomavirus (HPV) infection are risk factors for cervical squamous cell carcinoma. The following histologic patterns have been described: conventional squamous cell carcinoma, papillary squamous cell carcinoma, transitional cell carcinoma, lymphoepithelioma-like carcinoma, verrucous carcinoma, condylomatous carcinoma and spindle cell carcinoma. Survival is most closely related to the stage of disease at the time of diagnosis. [Definition Source: NCI]
label: Carcinoma a Cellule Squamose Cervicali @it
label: Cervicaal Plaveiselcelcarcinoom @nl
associated disease: Cervical Cancer
has SNOMED code: M807030
has semantic area: Diagnosis
internal notes: previous SNOMED M80703*

Lung cancer
type: NamedIndividual
type: Concept
type: Disease or Disorder
conforms to: http://linkedlifedata.com/resource/umls/id/C0684249
has exact synonym: malignant neoplasm of the lung; lung cancer; malignant lung neoplasm; cancer of lung; malignant tumor of the lung; malignant tumor of lung; malignant neoplasm of lung; malignant lung tumor.
has related synonym: lung neoplasm; Nonsmall cell lung cancer; alveolar cell carcinoma; lung cancer, protection against.
comment: A malignant neoplasm involving the lung. [Definition Source: https://orcid.org/0000-0002-6601-2165]
label: Cancro ai Polmoni @it
label: Longkanker @nl
has semantic area: General Entity

Sarcoidosis
type: NamedIndividual
type: Concept
type: Lung Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0036202
has broad synonym: benign lymphogranulomatosis of Schaumann; lupus pernio of Besnier; miliary lupoid of boeck
has exact synonym: besnier-Boeck-Schaumann syndrome; sarcoid; Darier-Roussy sarcoid; Boeck's sarcoid; Besnier-Boeck-Schaumann disease; Boeck's sarcoidosis; lymphogranulomatosis; sarcoidosis; Boeck sarcoid
comment: Sarcoidosis is a multisystemic disorder of unknown cause characterized by the formation of immune granulomas in involved organs. [Definition Source: Orhpanet 797]
label: Sarcoidosi @it
label: Sarcoïdose @nl
associated disease: Lung cancer
has SNOMED code: D028280
has semantic area: Diagnosis

Cervical Intraepithelial Neoplasia
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0206708
has exact synonym: cervical intraepithelial neoplasia
has related synonym: Intraepithelial Neoplasia of the Uterine Cervix; Intraepithelial Neoplasms, Cervical; Neoplasm, Cervical Intraepithelial; Intraepithelial Neoplasm, Cervical; Cervix Intraepithelial Neoplasia; Cervical Intraepithelial Neoplasms; Intraepithelial Neoplasia of the Cervix Uteri; Neoplasms, Cervical Intraepithelial; Intraepithelial Neoplasia of Uterine Cervix; Neoplasia, Cervical Intraepithelial; Cervical Intraepithelial Neoplasm; Intraepithelial Neoplasia, Cervical; Cervical intraepithelial neoplasia; NEOPL CERVICAL INTRAEPITHELIAL; Uterine Cervix Intraepithelial Neoplasia; Intraepithelial Neoplasia of Cervix Uteri; Intraepithelial Neoplasia of the Cervix; Cervix Uteri Intraepithelial Neoplasia; Intraepithelial Neoplasia of Cervix; Cervical Dysplasia; Cervical Intraepithelial Neoplasia
comment: Squamous or glandular intraepithelial neoplasia that affects the cervical mucosal epithelium. There is no evidence of stromal invasion. According to the degree of cellular atypia and the associated architectural changes, it is classified as low or high grade. [Definition Source: NCI]
label: Cervicale intra-epitheliale neoplasie @nl
label: Neoplasia Intraepiteliale Cervicale @it
associated disease: Cervical Cancer
has semantic area: Diagnosis

Squamous Intraepithelial Neoplasia
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
broader transitive: Cervical Carcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0851140
has exact synonym: severe dysplasia of the cervix uteri aJCC v6; uterine cervix intraepithelial neoplasia grade 3 aJCC v6; intraepithelial neoplasia of the cervix grade 3 aJCC v6; carcinoma in situ of the uterine cervix aJCC v6; intraepithelial neoplasia of the cervix uteri grade 3 aJCC v6; severe dysplasia of cervix aJCC v6; severe dysplasia of cervix; intraepithelial neoplasia of uterine cervix grade 3 aJCC v6; cervical intraepithelial neoplasia grade 3 aJCC v6; uterine cervix carcinoma in situ aJCC v6; carcinoma in situ of the cervix aJCC v6; FIGO stage 0 carcinoma of uterine cervix; severe dysplasia of cervix uteri aJCC v6; cervix uteri intraepithelial neoplasia grade 3 aJCC v6; grade 3 cervical intraepithelial neoplasia aJCC v6; stage 0 uterine cervix carcinoma; carcinoma in situ of uterine cervix aJCC v6; CIN III - severe dyskaryosis; cervix uteri Severe dysplasia aJCC v6; FIGO stage 0 cervical carcinoma; cervix uteri carcinoma in situ aJCC v6; stage 0 cervical cancer aJCC v6; FIGO stage 0 carcinoma of the cervix uteri; cervical carcinoma in situ aJCC v6; uterine cervix Severe dysplasia aJCC v6; carcinoma in situ of the cervix uteri aJCC v6; severe cervical dysplasia aJCC v6; FIGO stage 0 carcinoma of cervix uteri; carcinoma in situ of cervix aJCC v6; carcinoma in situ of uterine cervix; carcinoma in situ of cervix uteri aJCC v6; cervix intraepithelial neoplasia grade 3 aJCC v6; FIGO stage 0 carcinoma of the uterine cervix; CIN III; cervical intraepithelial neoplasia grade III with severe dysplasia; cervical Severe dysplasia aJCC v6; CIN III - carcinoma in situ of cervix; FIGO stage 0 uterine cervix carcinoma; CIN 3 aJCC v6; severe dysplasia of the uterine cervix aJCC v6; carcinoma of cervix stage 0; intraepithelial neoplasia of cervix uteri grade 3 aJCC v6; squamous intraepithelial neoplasia, grade III; stage 0 cervical cancer; cervix Severe dysplasia aJCC v6; FIGO stage 0 carcinoma of the cervix; carcinoma in situ of cervix; CIN grade 3 aJCC v6; cervical cancer stage 0 aJCC v6…
has related synonym: cervix uteri carcinoma in situ
has related synonym: uterine cervix carcinoma in situ
comment: Slightly abnormal cells are found on the surface of the cervix. Cervical squamous intraepithelial neoplasia 1 is usually caused by infection with certain types of human papillomavirus (HPV) and is found when a cervical biopsy is done. Cervical squamous intraepithelial neoplasia 1 is not cancer and usually goes away on its own without treatment, but sometimes it can become cancer and spread into nearby tissue. Cervical squamous intraepithelial neoplasia 1 is sometimes called low-grade or mild dysplasia. Also called CIN 1.
label: Neoplasia Intraepiteliale Squamosa @it
label: Squameuze Intra-Epitheliale Neoplasie @nl
associated disease: Cervical Cancer
has semantic area: Diagnosis

Intestinal Fibrosis
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C3544347
has exact synonym: intestinal synechia; intestinal adhesions
comment: Formation of fibrous tissue in any part of the intestine as a result of repair or a reactive process.
label: Fibrosi Intestinale @it
label: Intestinale Fibrose @nl
associated disease: Celiac disease
associated keyword in diagnosis: fibrosi @it
has semantic area: Diagnosis

Malabsorption
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C3714745
comment: Inadequate absorption of nutrients in the small intestine. [Definition Source: NCI]
label: Malabsorptie @nl
label: Malassorbimento @it
associated disease: Celiac disease
associated keyword in diagnosis: malassorbimento
has semantic area: Diagnosis

Main Bronchus
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
broader transitive: Bronchus
conforms to: http://linkedlifedata.com/resource/umls/id/C0024496
has exact synonym: Mainstem bronchus; Main Bronchus
comment: The left and right main bronchi considered as a group.
label: Belangrijkste Bronchus @nl
label: Bronco Principale @it
associated disease: Lung cancer
has semantic area: Anatomical Location

Endometrium
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
broader transitive: Mucosa
alternative definition: MSH: The mucous membrane lining of the uterine cavity that is hormonally responsive during the MENSTRUAL CYCLE and PREGNANCY. The endometrium undergoes cyclic changes that characterize MENSTRUATION. After successful FERTILIZATION, it serves to sustain the developing embryo.,CSP: tissue lining the uterus, it is sloughed off during the woman's menstrual period, and afterward grows back and slowly gets thicker and thicker until the next period.,NCI: The layer of tissue that lines the uterus.,NCI: The endometrium, or tunica mucosa, is the mucous membrane comprising the inner layer of the uterine wall; it consists of a simple columnar epithelium and a lamina propria that contains simple tubular uterine glands. The structure, thickness, and state of the endometrium undergo marked change with the menstrual cycle.,NCI: The mucous membrane comprising the inner layer of the uterine wall; it consists of a simple columnar epithelium and a lamina propria that contains simple tubular uterine glands. The structure, thicknes
alternative definition: The layer of tissue that lines the uterus.; The mucous membrane comprising the inner layer of the uterine wall.
conforms to: http://linkedlifedata.com/resource/umls/id/C0014180
conforms to: http://linkedlifedata.com/resource/umls/id/C0334186
comment: The mucous membrane comprising the inner layer of the uterine wall; it consists of a simple columnar epithelium and a lamina propria that contains simple tubular uterine glands. The structure, thickness, and state of the endometrium undergo marked change with the menstrual cycle. [Definition Source: NCI]
label: Baarmoederslijmvlies @nl
label: Endometrio @it
associated disease: Cervical Cancer
has SNOMED code: M793100
has semantic area: Anatomical Location

Leukocyte
type: NamedIndividual
type: Concept
type: Celiac Disease Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C0023516
comment: Blood cells that are devoid of hemoglobin, capable of ameboid motion and phagocytosis, and act as the principal components of the immune system. [Definition Source: NCI]
label: Leucocita @it
label: Leukocyt @nl
associated disease: Celiac disease
associated keyword in diagnosis: "leucocitario"
has semantic area: Diagnosis

Granulocyte
type: NamedIndividual
type: Concept
type: Celiac Disease Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C0018183
has exact synonym: polymorphonuclear leukocyte; granular leucocyte; granular leukocyte
comment: A type of leukocyte with a multilobed nucleus and cytoplasmic granules. The unique morphology of the nucleus has led to their also being known as polymorphonuclear leukocytes (PMLs or PMNs). Granulocytes are subdivided according to the staining properties of their granules into eosinophils (red with acidic dye), basophils (blue with basic dye), and neutrophils (not amenable to staining with either acidic or basic dyes). [Definition Source: NCI]
label: Granulocita @it
associated disease: Celiac disease
associated keyword in diagnosis: “inﬁltrato” + “granulociti”/“granulocitario"
has semantic area: Diagnosis

Eosinophil
type: NamedIndividual
type: Concept
type: Celiac Disease Finding
broader transitive: Leukocyte
broader transitive: Granulocyte
conforms to: http://linkedlifedata.com/resource/umls/id/C0014467
comment: Granular leukocytes with a nucleus that usually has two lobes connected by a slender thread of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and stainable by eosin. [Definition Source: NCI]
label: Eosinofiel @nl
label: Eosinofilo @it
associated disease: Celiac disease
associated keyword in diagnosis: eosinofili, eosinofilo
has semantic area: Diagnosis

Neutrophil
type: NamedIndividual
type: Concept
type: Celiac Disease Finding
broader transitive: Leukocyte
broader transitive: Granulocyte
conforms to: http://linkedlifedata.com/resource/umls/id/C0027950
comment: Granular leukocytes having a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. [Definition Source: NCI]
label: Neutrofiel @nl
label: Neutrofilo @it
associated disease: Celiac disease
associated keyword in diagnosis: neutrofilo
has semantic area: Diagnosis

Lymphocyte
type: NamedIndividual
type: Concept
type: Celiac Disease Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C0024264
comment: White blood cells formed in the body's lymphoid tissue. The nucleus is round or ovoid with coarse, irregularly clumped chromatin while the cytoplasm is typically pale blue with azurophilic (if any) granules. Most lymphocytes can be classified as either T or B (with subpopulations of each); those with characteristics of neither major class are called null cells. [Definition Source: NCI]
label: Linfocita @it
label: Lymfocyt @nl
associated disease: Celiac disease
associated keyword in diagnosis: “inﬁltrato” + “linfociti”/“linfocitario"
has semantic area: Diagnosis

Enterocyte
type: NamedIndividual
type: Concept
type: Celiac Disease Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C0682610
comment: A type of epithelial cell that lines the intestines and colon. It participates in the absorption of water and nutrients from the intestinal lumen, and in the secretion of digestive enzymes. [Definition Source: NCI]
label: Enterocita @it
label: Enterocyt @nl
associated disease: Celiac disease
associated keyword in diagnosis: enterociti
has semantic area: Diagnosis

Mucosa
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
alternative definition: The moist, inner lining of some organs and body cavities (such as the nose, mouth, lungs, and stomach). Glands in the mucosa make mucus (a thick, slippery fluid).
conforms to: http://linkedlifedata.com/resource/umls/id/C0026724
has exact synonym: Mucosal; MUCOSA; Mucous Membrane; mucous membrane; Mucosa; mucosa
comment: The moist, inner lining of some organs and body cavities (such as the nose, mouth, lungs, and stomach). Glands in the mucosa make mucus (a thick, slippery fluid). [Definition Source: NCI]
label: Slijmvlies @nl
associated disease: Cervical Cancer
has semantic area: Anatomical Location

Brunner's Gland Hyperplasia
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
has semantic type: Pathologic Function
conforms to: http://linkedlifedata.com/resource/umls/id/C0341253
comment: A rare hyperplastic lesion of Brunner's gland in the duodenum. Although it is usually asymptomatic and discovered incidentally during upper gastrointestinal endoscopy, it may cause hemorrhage. [Definition Source: NCI]
label: Hyperplasie van de Klier van Brunner @nl
label: Iperplasia della Ghiandola di Brunner @it
associated disease: Celiac disease
associated keyword in diagnosis: “Brunner” + “iperplasia” + “ghiandole” @it
definition: Usually hyperplasia of Brunner’s glands. NB: the mere Presence of Brunner’s glands is not automatically an hyperplasia. Rather, hyperplasia Is something the glands may have or not. If they have it, it may be a problem
has semantic area: Diagnosis

Anatomical Location
type: NamedIndividual
type: Semantic Area
conforms to: http://linkedlifedata.com/resource/umls/id/C1515974
has exact synonym: Location; Anatomic Site
label: Anatomische Locatie @nl
label: Posizione Anatomica @it
definition: Named locations of or within the body. [Definition Source: NCI]

Diagnosis
type: NamedIndividual
type: Semantic Area
conforms to: http://linkedlifedata.com/resource/umls/id/C0011900
comment: The investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such an investigation. [Definition Source: NCI]
label: Diagnose @nl
label: Diagnosi @it

Hysterectomy
type: NamedIndividual
type: Concept
type: Cervix Surgery Type
alternative definition: Surgery to remove the uterus and, sometimes, the cervix. When the uterus and the cervix are removed, it is called a total hysterectomy. When only the uterus is removed, it is called a partial hysterectomy.
conforms to: http://linkedlifedata.com/resource/umls/id/C0020699
comment: A surgical procedure to remove the uterine body (partial hysterectomy) or the uterine body and cervix (total hysterectomy). [Definition Source: NCI]
label: Hysterectomie @nl
label: Isterectomia @it
associated disease: Cervical Cancer
has semantic area: Procedure

Endoscopic Biopsy
type: NamedIndividual
type: Concept
type: Celiac Disease Intervention or Procedure Type
type: Colon Intervention or Procedure Type
has semantic type: Diagnostic Procedure
conforms to: http://linkedlifedata.com/resource/umls/id/C0184980
has exact synonym: Endoscopy and Biopsy; Endoscopic Biopsy
comment: The removal of tissue specimens or fluid from the living body for microscopic examination, performed to establish a diagnosis. In the case of an endoscopic biopsy, an endoscope is used to obtain the sample. [Definition Source: NCI]
label: Biopsia Endoscopica @it
label: Endoscopische Biopsie @nl
associated disease: Colon Carcinoma
associated disease: Celiac disease
has SNOMED code: P410000
has semantic area: Procedure
internal notes: previous SNOMED P41

Conization
type: NamedIndividual
type: Concept
type: Cervix Surgery Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0195324
has exact synonym: cone biopsy; LEEP
has related synonym: Bx; BIOPSY; biopsy; Biopsy
comment: Surgical removal of a cone-shaped portion of tissue from the uterine cervix. [Definition Source: NCI]
label: Conizzazione @it
associated disease: Cervical Cancer
has semantic area: Procedure

Endocervical Curettage
type: NamedIndividual
type: Concept
type: Cervix Surgery Type
has semantic type: Diagnostic Procedure
alternative definition: A procedure in which the mucous membrane of the cervical canal is scraped using a spoon-shaped instrument called a curette.
conforms to: http://linkedlifedata.com/resource/umls/id/C0195344
comment: A procedure in which the mucous membrane of the cervical canal is scraped using a curette. [Definition Source: NCI]
label: Curettage Endocervicale @it
label: Endocervicale Curettage @nl
associated disease: Cervical Cancer
has semantic area: Procedure

High Grade Dysplasia
type: NamedIndividual
type: Concept
type: Dysplasia
has semantic type: Finding
conforms to: C156083
comment: A subjective characterization of the phenomenon of dysplasia, based on microscopic examination of the architectural and/or cytological changes in a tissue sample, that is determined to be high. [Definition Source: NCI]
label: Displasia di Alto Grado @it
label: Hoogwaardige Dysplasie @nl
associated disease: Colon Carcinoma
has semantic area: Diagnosis

Anastomosis
type: NamedIndividual
type: Concept
type: Colon Surgery Type
has semantic type: Therapeutic or Preventive Procedure
alternative definition: A procedure to connect healthy sections of tubular structures in the body after the diseased portion has been surgically removed.; A natural or surgically-induced connection between tubular structures in the body.
conforms to: http://linkedlifedata.com/resource/umls/id/C0677554
comment: A natural or surgically-induced connection between tubular structures in the body. [Definition Source: NCI]
label: Anastomose @nl
label: Anastomosi @it
associated disease: Colon Carcinoma
has SNOMED code: M182000
has semantic area: Procedure
internal notes: previous snomed was M18200

Resection
type: NamedIndividual
type: Concept
type: Colon Surgery Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0015252
has exact synonym: Removal Technique; Resection; Surgical Resection
comment: A surgical procedure in which tissue is removed from the body. [Definition Source: NCI]
label: Resectie @nl
label: Resezione @it
associated disease: Colon Carcinoma
has SNOMED code: P110000
has semantic area: Procedure
internal notes: previous SNOMED was P11000

Metastatic Colon Adenocarcinoma
type: NamedIndividual
type: Concept
type: Colon Positive Outcome Type
broader transitive: Metastatic Adenocarcinoma
broader transitive: Colon Adenocarcinoma
conforms to: https://uts.nlm.nih.gov/uts/umls/concept/C4324497
comment: An adenocarcinoma that arises from the colon and has metastasized to another anatomic site. [Definition Source: NCI]
label: Adenocarcinoma Metastatico del Colon @it
label: Gemetastaseerd Colon Adenocarcinoom @nl
associated disease: Colon Carcinoma
has semantic area: Diagnosis

Female Gender
type: NamedIndividual
type: Concept
type: Gender
conforms to: http://linkedlifedata.com/resource/umls/id/C0015780
has exact synonym: Female Gender, Self Reported; Female Gender, Self Report; Female; Female Gender
comment: A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both. [Definition Source: NCI]
label: Genere Femminile @it
label: Vrouwlijk Geslacht @nl
has semantic area: General Entity

Chronic Inflammation
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
broader transitive: Inflammation
conforms to: http://linkedlifedata.com/resource/umls/id/C0021376
comment: An inflammatory process characterized by the presence of lymphocytes and plasma cells and the absence of polymorphonuclear neutrophils. [Definition Source: NCI]
label: Chronische Ontsteking @nl
label: Infiammazione Cronica @it
associated disease: Celiac disease
associated keyword in diagnosis: flogosi cronica, flogosi cronica non attiva
has semantic area: Diagnosis

Metastasis
type: NamedIndividual
type: Concept
type: Lung Carcinoma Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C0027627
comment: The spread of cancer from one part of the body to another. A tumor formed by cells that have spread is called a "metastatic tumor" or a "metastasis." The metastatic tumor contains cells that are like those in the original (primary) tumor. [Definition Source: NCI]
label: Metastase @nl
label: Metastasi @it
associated disease: Lung cancer
has semantic area: Diagnosis

Male Gender
type: NamedIndividual
type: Concept
type: Gender
has semantic type: Qualitative Concept
conforms to: http://linkedlifedata.com/resource/umls/id/C1706180
has exact synonym: Male Gender, Self Report; Male; Male Gender; Male Gender, Self Reported
comment: A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both. [Definition Source: NCI]
label: Genere Maschile @it
label: Mannelijk Geslacht @nl
has semantic area: General Entity

Polypectomy
type: NamedIndividual
type: Concept
type: Colon Surgery Type
broader transitive: Biopsy of Colon
conforms to: http://linkedlifedata.com/resource/umls/id/C0149684
has exact synonym: Polypectomy
comment: Complete or partial removal of a polypoid lesion from the mucosal surface. [Definition Source: NCI]
label: Polipectomia @it
label: Polypectomie @nl
annotated rule: Presence of jeyword "polipectomia" in "Materiali"
associated disease: Colon Carcinoma
has semantic area: Procedure
has semantic area: Complete or partial removal of a polypoid lesion from the mucosal surface.

Cervicitis
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
has semantic type: Disease or Syndrome
conforms to: http://linkedlifedata.com/resource/umls/id/C0007860
conforms to: http://linkedlifedata.com/resource/umls/id/C0007861
has exact synonym: Cervicitis
comment: An acute or chronic inflammatory process that affects the cervix. Causes include sexually transmitted diseases and bacterial infections. Clinical manifestations include abnormal vaginal bleeding and vaginal discharge. [Definition Source: NCI]
label: Cervicite @it
associated disease: Cervical Cancer
has SNOMED code: M400000
has SNOMED code: M430000
has semantic area: Diagnosis
internal notes: Previously, this class presented SNOMED coded M40000 and M30000*

Colitis
type: NamedIndividual
type: Concept
type: Colon Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0009319
has exact synonym: Lymphadenitis; colitis; colon inflammation; inflammation of colon
comment: Inflammation of the colon. [Defintion Source: NCI]
label: Colite @it
associated disease: Colon Carcinoma
has SNOMED code: M400000
has SNOMED code: M400700
has semantic area: Diagnosis
internal notes: previously it had snomed codes M40000 and M40070

Chronic Cervicitis
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
broader transitive: Cervicitis
conforms to: http://linkedlifedata.com/resource/umls/id/C0269062
comment: Chronic inflammation of the cervix. [Definition Source: NCI]
label: Cervicite Cronica @it
label: Chronische Cervicitis @nl
associated disease: Cervical Cancer
has semantic area: Diagnosis

Adenocarcinoma
type: NamedIndividual
type: Concept
type: Colon Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C2750272
comment: A common cancer characterized by the presence of malignant glandular cells. Morphologically, adenocarcinomas are classified according to the growth pattern (e.g., papillary, alveolar) or according to the secreting product (e.g., mucinous, serous). Representative examples of adenocarcinoma are ductal and lobular breast carcinoma, lung adenocarcinoma, renal cell carcinoma, hepatocellular carcinoma (hepatoma), colon adenocarcinoma, and prostate adenocarcinoma. [Definition Source: NCI]
label: adenocarcinoom @nl
has semantic area: Diagnosis

Condyloma
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
alternative definition: A raised growth on the surface of the genitals caused by human papillomavirus (HPV) infection. The HPV in genital warts is very contagious and can be spread by skin-to-skin contact, usually during oral, anal, or genital sex with an infected partner.; A wart of the perianal region or genitalia that is caused by sexual transmission of the human papillomavirus.
conforms to: http://linkedlifedata.com/resource/umls/id/C0302180
has exact synonym: genital wart; condyloma; Genital Warts; Condyloma Acuminatum; Condyloma Acuminata; Genital Wart; Condyloma; Venereal Wart
comment: A sexually transmitted papillary growth caused by the human papillomavirus. It usually arises in the skin and mucous membranes of the perianal region and external genitalia. [Definition Source: NCI]
label: Condiloma @it
associated disease: Cervical Cancer
has SNOMED code: M767000
has semantic area: Diagnosis
internal notes: previous SNOMED was M76700

Crohn Disease
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C0010346
comment: A gastrointestinal disorder characterized by chronic inflammation involving all layers of the intestinal wall, noncaseating granulomas affecting the intestinal wall and regional lymph nodes, and transmural fibrosis. Crohn disease most commonly involves the terminal ileum; the colon is the second most common site of involvement. [Definition Source: NCI]
label: Morbo di Crohn @it
label: Ziekte van Crohn @nl
associated disease: Celiac disease
associated keyword in diagnosis: Crohn
has semantic area: Diagnosis

Edema
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C0013604
comment: Accumulation of an excessive amount of fluid in cells or intercellular tissues. [Definition Source: NCI]
label: Oedeem @nl
associated disease: Celiac disease
associated keyword in diagnosis: Edema @it
has semantic area: Diagnosis

Granuloma
type: NamedIndividual
type: Concept
type: Colon Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0018188
comment: An inflammation AE that shows localized nodular inflammation found in tissues.
label: Granuloom @nl
associated disease: Colon Carcinoma
has SNOMED code: M440000
has semantic area: Diagnosis
internal notes: old SNOMED M44000

Inflammation
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C0021368
comment: A finding of a localized protective response resulting from injury or destruction of tissues. Inflammation serves to destroy, dilute, or wall off both the injurious agent and the injured tissue. In the acute phase, inflammation is characterized by the signs of pain, heat, redness, swelling, and loss of function. Histologically, inflammation involves a complex series of events, including dilatation of arterioles, capillaries, and venules, with increased permeability and blood flow; exudation of fluids, including plasma proteins; and leukocyte migration into the site of inflammation. [Definition Source: NCI]
label: Infiammazione @it
label: Ontsteking @nl
associated disease: Celiac disease
associated keyword in diagnosis: flogosi
has semantic area: Diagnosis

Metaplasia
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
alternative definition: Conversion of a mature, normal cell or groups of mature cells to other forms of mature cells.; A change of cells to a form that does not normally occur in the tissue in which it is found.
conforms to: http://linkedlifedata.com/resource/umls/id/C0025568
has exact synonym: Metaplasia; METAPLASIA; Metaplastic Change; metaplasia
comment: Transformation of a mature, normal cell or groups of mature cells to other forms of mature cells. The capacity for malignant transformation of metaplastic cells is a subject of controversy. [Definition Source: NCI]
label: Metaplasie @nl
associated disease: Cervical Cancer
definition: MSH: A condition in which there is a change of one adult cell type to another similar adult cell type.,CSP: transformation of a normal to a similar but abnormal mature cell type.,NCI: A change of cells to a form that does not normally occur in the tissue in which it is found.,CHV: a change in the type of cells in a tissue to a form that is not normal for that tissue,CHV: a change in the type of cells in a tissue to a form that is not normal for that tissue,NCI: Transformation of a mature, normal cell or groups of mature cells to other forms of mature cells. The capacity for malignant transformation of metaplastic cells is a subject of controversy.
has SNOMED code: M730000
has semantic area: Diagnosis

Squamous Metaplasia
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
broader transitive: Metaplasia
conforms to: http://linkedlifedata.com/resource/umls/id/C0025570
comment: A morphologic finding indicating the transformation of glandular or transitional epithelial cells to, usually, mature squamous epithelial cells. Representative examples include squamous metaplasia of bronchial epithelium, cervix, urinary bladder, and prostate gland. [Definition Source: NCI]
label: Metaplasia Squamosa @it
label: Plaveiselcelmetaplasie @nl
associated disease: Cervical Cancer
has SNOMED code: M732200
has semantic area: Diagnosis

Lamina Propria
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
broader transitive: Mucosa
conforms to: http://linkedlifedata.com/resource/umls/id/C1179187
has exact synonym: cassock
comment: The connective tissue coat of a mucous membrane including the epithelium and basement membrane. [Definition Source: NCI]
associated disease: Cervical Cancer
definition: A type of connective tissue found under the thin layer of tissues covering a mucous membrane.,NCI: The connective tissue coat of a mucous membrane including the epithelium and basement membrane. [Definition Source: NCI]
has semantic area: Anatomical Location

Left Main Bronchus
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
broader transitive: Main Bronchus
conforms to: http://linkedlifedata.com/resource/umls/id/C0225630
has exact synonym: MAIN BRONCHUS, LEFT; Left Main Bronchus
comment: One of the two main bronchi. It is narrower but longer than the right main bronchus and connects to the left lung. [Definition Source: NCI]
label: Bronco Principale Sinistro @it
label: Linker Hoofdbronchus @nl
associated disease: Lung cancer
has semantic area: Anatomical Location

Lobar Bronchus
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
broader transitive: Bronchus
conforms to: http://linkedlifedata.com/resource/umls/id/C0225653
has exact synonym: Lobar Bronchus; Secondary Bronchus
comment: A part the bronchial tree, arising from the primary bronchi, with each one serving as the airway to a specific lobe of the lung. [Definition Source: NCI]
label: Bronco Lobare @it
label: Lobaire Bronchus @nl
associated disease: Lung cancer
has semantic area: Anatomical Location

Right Main Bronchus
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
broader transitive: Main Bronchus
conforms to: http://linkedlifedata.com/resource/umls/id/C0225608
has exact synonym: Right Main Bronchus; MAIN BRONCHUS, RIGHT
comment: One of the two main bronchi. It is wider but shorter than the left main bronchus and connects to the right lung. [Definition Source: NCI]
label: Bronco Principale Destro @it
label: Rechter Hoofdbronchus @nl
associated disease: Lung cancer
has semantic area: Anatomical Location

Simple Epithelium
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
related: Pavement Epithelium
conforms to: http://linkedlifedata.com/resource/umls/id/C0682574
has exact synonym: Simple Epithelium
has exact synonym: Unilaminar epithelium
comment: Epithelium composed of a single layer of cells attached to a basement membrane. [Definition Source: NCI]
label: Eenlagig Epitheel @nl
label: Epitelio Semplice @it
associated disease: Cervical Cancer
has semantic area: Anatomical Location

Ulcer
type: NamedIndividual
type: Concept
type: Colon Positive Outcome Type
type: Intestinal Abnormality
alternative definition: A circumscribed loss of integrity of the skin or mucous membrane.; Destruction of an epithelial surface extending into or beyond the basement membrane.
conforms to: http://linkedlifedata.com/resource/umls/id/C0041582
has exact synonym: Ulcerative Inflammation; Ulcer; Ulceration; Ulcers; Ulcerated; ulcer; ULCER; Ulcerative
comment: A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue. [Definition Source: NCI]
label: Ulcera @it
label: Zweer @nl
associated disease: Colon Carcinoma
associated disease: Celiac disease
associated keyword in diagnosis: ulcerativa, ulcerata
has SNOMED code: 400300
has semantic area: Diagnosis
internal notes: previous SNOMED was M40030

Acanthosis
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C4230612
comment: Diffuse hypertrophy of the stratum spinosum layer of the epidermis. [Definition Source: NCI]
label: Acantosi @it
associated disease: Cervical Cancer
has SNOMED code: G000900
has SNOMED code: M727100
has semantic area: Diagnosis
internal notes: previous SNOMED G0009

Hyperkeratosis
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
alternative definition: Thickening of the outermost layer of stratified squamous epithelium.; A condition marked by thickening of the outer layer of the skin, which is made of keratin (a tough, protective protein). It can result from normal use (corns, calluses), chronic inflammation (eczema), or genetic disorders (X-linked ichthyosis, ichthyosis vulgaris).
conforms to: http://linkedlifedata.com/resource/umls/id/C0870082
comment: Hypertrophy of the outermost layer of the epidermis. It may be caused by physical or chemical irritants, irradiation, infection, or neoplastic processes. [Definition Source: NCI]
label: Hyperkeratose @nl
label: Ipercheratosi @it
associated disease: Cervical Cancer
has semantic area: Diagnosis

Koilocytotic Squamous Cell
type: NamedIndividual
type: Concept
conforms to: http://linkedlifedata.com/resource/umls/id/C1517678
has exact synonym: Koilocyte; Koilocytotic Squamous Cell
comment: Koilocytes are epithelial cells containing a hyperchromatic nucleus that is acentrically displaced by perinuclear vacuole(s), and these morphological alterations are used by pathologists to help identify HPV-infected epithelial cells in Pap smears. [Definition Source: PMID 18688031]
label: Cellula Squamosa Cilocitotica @it
label: Koilocytotische Plaveiselcel @nl
associated disease: Cervical Cancer
has semantic area: Diagnosis

Low Grade Cervical Squamous Intraepithelial Neoplasia
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
broader transitive: Cervical Intraepithelial Neoplasia
conforms to: http://linkedlifedata.com/resource/umls/id/C1518005
has exact synonym: Mild Squamous Dysplasia of the Cervix; Low Grade Cervical Squamous Intraepithelial Neoplasia; Low-Grade Cervical SIL; Low-Grade Cervical Squamous Intraepithelial Lesion; Low Grade Cervical Squamous Intraepithelial Lesion; Low-Grade CIN; Cervical Squamous Intraepithelial Neoplasia 1; Low Grade Cervical Squamous Intraepithelial Neoplasia; LSIL; low grade dysplasia; mild dysplasia
comment: A precancerous neoplastic process that affects the cervical squamous epithelium without evidence of invasion. It is usually associated with human papillomavirus infection. It is characterized by the presence of mild atypia in the superficial epithelial layer that may be associated with koilocytosis. Maturation is present in the upper two thirds of the epithelium. Mitotic figures are not numerous and are present in the basal third of the epithelium. [Definition Source: NCI]
label: Cervicale Squameuze Intra-Epitheliale Neoplasie Graad 1 @nl
label: Neoplasia Cervicale Squamosa Intraepiteliale di Grado 1 @it
associated disease: Cervical Cancer
has SNOMED code: M740060
has semantic area: Diagnosis
internal notes: old SNOMED M74006*

Cervical Squamous Intraepithelial Neoplasia 2
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
broader transitive: Cervical Intraepithelial Neoplasia Grade 2/3
conforms to: http://linkedlifedata.com/resource/umls/id/C0349459
has exact synonym: CIN 2; Cervical Squamous Intraepithelial Neoplasia 2; Moderate Squamous Dysplasia of the Cervix; cervical squamous intraepithelial neoplasia 2
comment: Cervical squamous intraepithelial neoplasia characterized by the presence of maturation in the upper half of the squamous epithelium and conspicuous nuclear atypia which is present in all epithelial layers. Mitotic figures are present in the basal two thirds of the epithelium. [Definition Source: NCI]
label: Cervicale Squameuze Intra-Epitheliale Neoplasie Graad 2 @nl
label: Neoplasia Cervicale Squamosa Intraepiteliale di Grado 2 @it
associated disease: Cervical Cancer
has SNOMED code: M740070
has semantic area: Diagnosis
internal notes: original SNOMED M74007*

Cervical Adenocarcinoma
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
broader transitive: Cervical Carcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0279672
has exact synonym: adenocarcinoma of the uterine cervix; uterine cervix adenocarcinoma; adenocarcinoma of cervix; adenocarcinoma of cervix uteri; adenocarcinoma - cervix; cervix adenocarcinoma; adenocarcinoma of the cervix; adenocarcinoma of the cervix uteri; adenocarcinoma cervix uteri; adenocarcinoma of uterine cervix; cervix uteri adenocarcinoma; cervical adenocarcinoma
has related synonym: cervical adenocarcinoma, NOS; cervical adenocarcinoma, not otherwise specified
comment: An adenocarcinoma arising from the cervical epithelium. It accounts for approximately 15% of invasive cervical carcinomas. Increased numbers of sexual partners and human papillomavirus (HPV) infection are risk factors. Grossly, advanced cervical adenocarcinoma may present as an exophytic mass, an ulcerated lesion, or diffuse cervical enlargement. Microscopically, the majority of cervical adenocarcinomas are of the endocervical (mucinous) type. [Definition Source: NCI]
label: Adenocarcinoma Cervicale @it
label: Cervicaal Adenocarcinoom @nl
associated disease: Cervical Cancer
has semantic area: Diagnosis

Metastatic Adenocarcinoma
type: NamedIndividual
type: Concept
type: Colon Positive Outcome Type
broader transitive: Adenocarcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0334277
has exact synonym: Metastatic Adenocarcinoma
comment: An adenocarcinoma which has spread from its original site of growth to another anatomic site. [Definition Source: NCI]
label: Adenocarcinoma Metastatico @it
label: Gemetastaseerd Adenocarcinoom @nl
associated disease: Colon Carcinoma
has SNOMED code: M80106
has SNOMED code: M814060
has semantic area: Diagnosis
internal notes: old SNOMED M81406

Elastofibroma
type: NamedIndividual
type: Concept
type: Lung Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0334460
comment: A benign, slow-growing tumor arising from the soft tissues usually in the mid-thoracic region of the elderly. It is characterized by the presence of paucicellular collagenous tissue, adipocytes and a predominance of large coarse elastic fibers arranged in globules. [Definition Source: NCI]
associated disease: Lung cancer
has semantic area: Diagnosis

Colon Adenocarcinoma
type: NamedIndividual
type: Concept
type: Colon Positive Outcome Type
broader transitive: Adenocarcinoma
conforms to: http://linkedlifedata.com/resource/umls/id/C0338106
has exact synonym: colonic adenocarcinoma; adenocarcinoma of the colon; colon adenocarcinoma; adenocarcinoma of colon; adenocarcinoma - colon
has related synonym: COAD
comment: An adenocarcinoma arising from the colon. It is more frequently seen in populations with a Western type diet and in patients with a history of chronic inflammatory bowel disease. Signs and symptoms include intestinal bleeding, anemia, and change in bowel habits. According to the degree of cellular differentiation, colonic adenocarcinomas are divided into well, moderately, and poorly differentiated. Histologic variants include mucinous adenocarcinoma, signet ring cell carcinoma, medullary carcinoma, serrated adenocarcinoma, cribriform comedo-type adenocarcinoma, and micropapillary adenocarcinoma. [Definition Source: NCI]
label: Adenocarcinoma del Colon @it
label: Colon Adenocarcinoom @nl
associated disease: Colon Carcinoma
has SNOMED code: M80102
has SNOMED code: M814030
has semantic area: Diagnosis

Cervical Adenocarcinoma in Situ
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
broader transitive: Cervical Adenocarcinoma
has semantic type: Neoplastic Process
conforms to: http://linkedlifedata.com/resource/umls/id/C0346203
has exact synonym: Uterine Cervix Adenocarcinoma in situ; Adenocarcinoma in situ of the Uterine Cervix; Cervix Uteri Adenocarcinoma in situ; Adenocarcinoma in situ of Uterine Cervix; Cervical Adenocarcinoma In Situ AJCC v7; Adenocarcinoma in situ of the Cervix; Cervix Adenocarcinoma in situ; Adenocarcinoma in situ of Cervix Uteri; Adenocarcinoma in situ of Cervix; Adenocarcinoma in situ of the Cervix Uteri; Cervical Adenocarcinoma In Situ
comment: Adenocarcinoma in situ (AIS) represents a pre-cancerous condition that can progress to cervical adenocarcinoma. Cervical adenocarcinoma in situ occurs in the glandular tissue of the cervix and is the condition which leads to invasive adenocarcinoma. [Definition Source: NCI]
label: Adenocarcinoma Cervicale in Situ @it
label: Cervicaal Adenocarcinoom in Situ @nl
associated disease: Cervical Cancer
definition: tage 0 includes: (Tis, N0, M0). Tis: Carcinoma in situ. N0: No regional lymph node metastasis. M0: No distant metastasis. FIGO no longer includes stage 0.
has semantic area: Diagnosis

Colon Dysplasia
type: NamedIndividual
type: Concept
type: Dysplasia
has semantic type: Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C1302363
has exact synonym: Dysplasia of the Colon; Colonic Dysplasia; Dysplasia of Colon; Colon Dysplasia
comment: A morphologic finding indicating the presence of dysplastic glandular epithelial cells in the colonic mucosa. There is no evidence of invasion. [Definition Source: NCI]
label: Colon Dysplasie @nl
label: Displasia del Colon @it
associated disease: Colon Carcinoma
has semantic area: Diagnosis

Mild Colon Dysplasia
type: NamedIndividual
type: Concept
type: Dysplasia
broader transitive: Colon Dysplasia
broader transitive: Mild Dysplasia
conforms to: http://linkedlifedata.com/resource/umls/id/C0586367
has exact synonym: Low Grade Dysplasia of the Colon; Low-Grade Dysplasia of Colon; Low-Grade Dysplasia of the Colon; Mild Dysplasia of Colon; Low-Grade Colon Dysplasia; Mild Colon Dysplasia; Low-Grade Colonic Dysplasia; Mild Colonic Dysplasia; Mild Dysplasia of the Colon; Low Grade Colon Dysplasia; Low Grade Colonic Dysplasia; Low Grade Dysplasia of Colon
comment: A morphologic finding indicating the presence of mild dysplastic cellular changes and mild architectural changes in the glandular epithelium of the colonic mucosa. There is no evidence of invasion. [Definition Source: NCI]
label: Displasia del Colon Lieve @it
label: Milde Colondysplasie @nl
associated disease: Colon Carcinoma
has semantic area: Diagnosis

Moderate Colon Dysplasia
type: NamedIndividual
type: Concept
type: Dysplasia
broader transitive: Colon Dysplasia
broader transitive: Moderate Dysplasia
has semantic type: Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C0586368
has exact synonym: Moderate Dysplasia of the Colon; Moderate Colonic Dysplasia; Moderate Colon Dysplasia; Moderate Dysplasia of Colon
comment: A morphologic finding indicating the presence of moderate dysplastic cellular changes and moderate architectural changes in the glandular epithelium of the colonic mucosa. There is no evidence of invasion. [Definition Source: NCI]
label: Displasia Moderata del colon @it
label: Matige Colondysplasie @nl
associated disease: Colon Carcinoma
has semantic area: Diagnosis

Erosion
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C1959609
comment: An eating away or breakdown of any type of external or internal human tissue including but not limited to skin, teeth, mucosa, or somatic, which involves only the outer tissue layer. When tissue surrounds an implanted device, the tissue breakdown may result in migration and loss of the implant material and may result in further complications such as infection or abscess. [Definition Source: NCI]
label: Erosie @nl
label: Erosione @it
associated disease: Celiac disease
associated keyword in diagnosis: erosioni, erosivo, erosiva
has semantic area: Diagnosis

Hyperemia
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C0020452
has exact synonym: hyperaemia; hyperemic
comment: The presence of an increased amount of blood in a part or organ; engorgement. [Definition Source: NCI]
label: Hyperemie @nl
label: Iperemia @it
associated disease: Celiac disease
associated keyword in diagnosis: iperemia @it
has semantic area: Diagnosis

Biopsy of Small Intestine
type: NamedIndividual
type: Concept
type: Celiac Disease Intervention or Procedure Type
broader transitive: Endoscopic Biopsy
conforms to: http://linkedlifedata.com/resource/umls/id/C0399943
comment: Removal of tissue from the small intestine for microscopic examination, using an endoscope. [Definition Source: NCI]
label: Biopsia dell'Intestino Tenue @it
label: Biopsie van de Dunne Darm @nl
associated disease: Celiac disease
has semantic area: Procedure

Cervical Biopsy
type: NamedIndividual
type: Concept
type: Cervix Intervention or Procedure Type
has semantic type: Diagnostic Procedure
conforms to: http://linkedlifedata.com/resource/umls/id/C0195314
has exact synonym: Biopsy (cervical); Other method, specify: ECC
comment: Removal of tissue from the cervix for microscopic examination. [Definition Source: NCI]
label: Biopsia Cervicale @it
label: Cervicale Biopsie @nl
associated disease: Cervical Cancer
has semantic area: Procedure

Biopsy of Colon
type: NamedIndividual
type: Concept
type: Colon Intervention or Procedure Type
broader transitive: Endoscopic Biopsy
conforms to: http://linkedlifedata.com/resource/umls/id/C0192867
has exact synonym: Colonoscopic Biopsy; Colonoscopy and Biopsy; Biopsy of Colon
comment: Removal of tissue from the colon for microscopic examination, using an endoscope. [Definition Source: NCI]
label: Biopsia del Colon @it
label: Biopsie van de Dikke Darm @nl
associated disease: Colon Carcinoma
has SNOMED code: P114000
has SNOMED code: P400000
has semantic area: Procedure
internal notes: previous SNOMED was P11400, P40

Biopsy of Duodenum
type: NamedIndividual
type: Concept
type: Celiac Disease Intervention or Procedure Type
broader transitive: Biopsy of Small Intestine
has semantic type: Diagnostic Procedure
conforms to: http://linkedlifedata.com/resource/umls/id/C0399805
has exact synonym: Endoscopic Biopsy of Duodenum; Duodenal Biopsy; Biopsy of Duodenum
comment: Removal of tissue from the duodenum for microscopic examination, using an endoscope. [Definition Source: NCI]
label: Biopsia del Duodeno @it
label: Biopsie van de Twaalfvingerige Darm @nl
associated disease: Celiac disease
associated keyword in materiali: Biopsia duodeno
has semantic area: Procedure
has semantic area: Intervention

Colonoscopic Polypectomy
type: NamedIndividual
type: Concept
type: Colon Surgery Type
broader transitive: Polypectomy
conforms to: http://linkedlifedata.com/resource/umls/id/C0589347
has exact synonym: Colonoscopic Polypectomy; Colonic Polypectomy
comment: Complete or partial removal of a polypoid lesion from the mucosal surface of the large intestine. [Definition Source: NCI]
label: Colonoscopische Polypectomie @nl
label: Polipectomia Colonscopica @it
associated disease: Colon Carcinoma
has semantic area: Procedure

Total Abdominal Hysterectomy
type: NamedIndividual
type: Concept
type: Cervix Surgery Type
broader transitive: Hysterectomy
has semantic type: Therapeutic or Preventive Procedure
conforms to: http://linkedlifedata.com/resource/umls/id/C0404079
comment: Surgical removal of all of the uterus, via an abdominal approach. [Definition Source: NCI]
label: Isterectomia Addominale Totale @it
label: Totale Abdominale Hysterectomie @nl
annotated rule: Other method, specify: total Abdominal Hysterectomy
associated disease: Cervical Cancer
has semantic area: Procedure

Lung Biopsy
type: NamedIndividual
type: Concept
type: Lung Intervention or Procedure Type
has semantic type: Diagnostic Procedure
alternative definition: Removal of tissue from the lung, for microscopic examination.
conforms to: http://linkedlifedata.com/resource/umls/id/C0189485
comment: The removal of a small piece of lung tissue to be checked by a pathologist for cancer or other diseases. The tissue may be removed using a bronchoscope (a thin, lighted, tube-like instrument that is inserted through the trachea and into the lung). It may also be removed using a fine needle inserted through the chest wall, by surgery guided by a video camera inserted through the chest wall, or by an open biopsy. In an open biopsy, a doctor makes an incision between the ribs, removes a sample of lung tissue, and closes the wound with stitches. [Definition Source: NCI]
label: Biopsia Polmonare @it
label: Long Biopsie @nl
associated disease: Lung cancer
has semantic area: Procedure

Loop Electrosurgical Excision
type: NamedIndividual
type: Concept
type: Cervix Surgery Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0184930
comment: Uses a thin, low-voltage electrified wire loop to cut out a thin layer of abnormal tissue; generally used to remove abnormal cells on the surface of the cervix. [Definition Source: NCI]
label: Cervicale Sprong @nl
label: Leep Cervicale @it
associated disease: Cervical Cancer
has semantic area: Procedure

Bronchial Biopsy
type: NamedIndividual
type: Concept
type: Lung Intervention or Procedure Type
has semantic type: Diagnostic Procedure
conforms to: http://linkedlifedata.com/resource/umls/id/C0740463
has exact synonym: Bronchial Biopsy; Biopsy of Bronchus
comment: Removal of tissue from the bronchus for microscopic examination. [Definition Source: NCI]
label: Biopsia Bronchiale @it
label: Bronchiale Biopsie @nl
associated disease: Lung cancer
definition: Removal of tissue from the bronchus for microscopic examination.
has semantic area: Procedure

Biopsy of Jejunum
type: NamedIndividual
type: Concept
type: Celiac Disease Intervention or Procedure Type
broader transitive: Biopsy of Small Intestine
conforms to: http://linkedlifedata.com/resource/umls/id/C0576452
comment: Removal of tissue from the jujunum for microscopic examination, using an endoscope. [Definition Source: NCI]
label: Biopsia del Digiuno @it
label: Biopsie van Jejunum @nl
associated disease: Celiac disease
has semantic area: Procedure

Dyskeratosis
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0334061
comment: Dyskeratosis is abnormal keratinization occurring prematurely within individual cells or groups of cells below the stratum granulosum.[Defintion Source: ISBN 0-7216-0187-1] Dyskeratosis congenita is congenital disease characterized by reticular skin pigmentation, nail degeneration, and leukoplakia on the mucous membranes associated with short telomeres. [Defintion Source: PMID 22285015]
label: Discheratosi @it
label: Dyskeratose @nl
associated disease: Cervical Cancer
has SNOMED code: M740100
has semantic area: Diagnosis

Gastric Heterotopia of the Small Intestine
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C1333772
comment: Gastric heterotopia (GH) is a rare, congenital condition where gastric tissue is found outside of its normal location in the gastric mucosa. It is usually benign and can be found throughout the gastrointestinal (GI) tract. In the duodenum, it is usually seen as multiple polyps, specifically in the duodenal bulb. [Definition Source: PMID 35607542]
label: Eterotopia Gastrica @it
label: Maag Heterotopie van de Dunne Darm @nl
associated disease: Celiac disease
associated keyword in diagnosis: eterotopia
has semantic area: Diagnosis

Chronic Active Inflammation
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
broader transitive: Inflammation
conforms to: http://linkedlifedata.com/resource/umls/id/C0333383
comment: The coexistence of a chronic inflammatory process with a superimposed polymorphonuclear neutrophilic infiltration. [Definition Source: NCI]
label: Chronische Actieve Ontsteking @nl
label: Infiammazione Cronica Attiva @it
associated disease: Celiac disease
associated keyword in diagnosis: flogosi cronica attiva
has semantic area: Diagnosis

Focal Acute Inflammation
type: NamedIndividual
type: Concept
type: Cervix Positive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C1265832
comment: An inflammatory process characterized by the localized collection of polymorphonuclear neutrophils. [Definition Source: NCI]
label: Focale Acute Ontsteking @nl
label: Infiammazione Acuta Focale @it
associated disease: Cervical Cancer
has SNOMED code: M410000
has semantic area: Diagnosis
internal notes: old SNOMED M41000

Tissue Congestion
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C2826600
comment: A finding indicating the presence of increased blood volume in the vascular lumen. [Definition Source: NCI]
label: Congestione @it
label: Weefsel Congestie @nl
associated disease: Celiac disease
associated keyword in diagnosis: congestione
has semantic area: Diagnosis

Intestinal Metaplasia
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C0334037
comment: A morphologic finding indicating the replacement of epithelial tissue outside the intestines by intestinal-type epithelium. [Definition Source: NCI]
label: Intestinale Metaplasie @nl
label: Metaplasia Intestinale @it
associated disease: Celiac disease
associated keyword in diagnosis: metaplasia intestinale
has semantic area: Diagnosis

Gastric Metaplasia
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C0334038
comment: Precancerous change of the mucosa of the stomach with intestinal epithelium, and is associated with an increased risk of dysplasia and cancer. [Definition Source: PMID 29606921]
label: Maagmetaplasie @nl
label: Metaplasia Gastrica @it
associated disease: Celiac disease
associated keyword in diagnosis: metaplasia gastrica
has semantic area: Diagnosis

Mild Dysplasia
type: NamedIndividual
type: Concept
type: Dysplasia
conforms to: http://linkedlifedata.com/resource/umls/id/C0334046
has exact synonym: CIN 1; DYSPLASIA, MILD; MILD DYSPLASIA, CIN 1
comment: A morphologic finding indicating the presence of mild cellular atypia associated with mild architectural changes in a tissue sample. [Definition Source: NCI]
label: Displasia Lieve @it
label: Milde Dysplasie @nl
associated disease: Colon Carcinoma
has SNOMED code: M740060
has semantic area: Diagnosis
internal notes: original SNOMED M74006

Moderate Dysplasia
type: NamedIndividual
type: Concept
type: Dysplasia
broader transitive: High Grade Dysplasia
conforms to: http://linkedlifedata.com/resource/umls/id/C0334047
has exact synonym: Moderate Dysplasia; CIN 2; DYSPLASIA, MODERATE; MODERATE DYSPLASIA, CIN 2
comment: A morphologic finding indicating the presence of moderate cellular atypia associated with moderate architectural changes in a tissue sample. [Definition Source: NCI]
label: Displasia Moderata @it
label: Matige Dysplasie @nl
associated disease: Colon Carcinoma
has SNOMED code: M740070
has semantic area: Diagnosis

Severe Dysplasia
type: NamedIndividual
type: Concept
type: Dysplasia
broader transitive: High Grade Dysplasia
has semantic type: Finding
conforms to: http://linkedlifedata.com/resource/umls/id/C0334048
has exact synonym: Severe Dysplasia; CIN 3; DYSPLASIA, SEVERE; SEVERE DYSPLASIA, CIN 3
comment: A morphologic finding indicating the presence of severe cellular atypia associated with severe architectural changes in a tissue sample. [Definition Source: NCI]
label: Displasia Grave @it
label: Ernstige Dysplasie @nl
associated disease: Colon Carcinoma
has semantic area: Diagnosis

Hemicolectomy
type: NamedIndividual
type: Concept
type: Colon Surgery Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0546535
has exact synonym: Hemicolectomy
comment: Surgical removal of approximately half of the colon. [Definition Source: NCI]
label: Emicolectomia @it
label: Hemicolectomie @nl
associated disease: Colon Carcinoma
has SNOMED code: P111500
has semantic area: Procedure
internal notes: old SNOMED P11150

Radical Hysterectomy
type: NamedIndividual
type: Concept
type: Cervix Surgery Type
broader transitive: Hysterectomy
conforms to: http://linkedlifedata.com/resource/umls/id/C2987682
comment: Radical hysterectomy refers to the excision of the uterus en bloc with the parametrium (ie, round, broad, cardinal, and uterosacral ligaments) and the upper one-third to one-half of the vagina. The surgeon usually also performs a bilateral pelvic lymph node dissection. The procedure requires a thorough knowledge of pelvic anatomy, meticulous attention to sharp dissection, and careful technique to allow dissection of the ureters and mobilization of both bladder and rectum from the vagina. Particular care must be taken with the vasculature of the pelvic side walls and the venous plexuses at the lateral corners of the bladder to avoid excessive blood loss. Removal of the ovaries and fallopian tubes is not part of a radical hysterectomy; they may be preserved if clinically appropriate.
label: Isterectomia Radicale @it
label: Radicale Hysterectomie @nl
associated disease: Cervical Cancer
has semantic area: Procedure

Cervical Mucus
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C0007872
conforms to: http://linkedlifedata.com/resource/umls/id/C1619816
has exact synonym: cervix mucus
comment: A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation [WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
label: Baarmoederhalsslijm @nl
label: Muco Cervicale @it
associated disease: Cervical Cancer
has semantic area: Anatomical Location

Duodenal Mucosa
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
broader transitive: Duodenum
conforms to: http://linkedlifedata.com/resource/umls/id/C0227284
has exact synonym: doudenal mucosa; mucosa of duodenum; mucous membrane of duodenum; duodenal mucous membrane
has related synonym: duodenum mucosa
comment: The inner lining of the duodenum. [Definition Source: NCI]
label: Mucosa Duodenale @it
label: Slijmvlies van de Twaalfvingerige Darm @nl
associated disease: Celiac disease
associated keyword in diagnosis: mucosa duodenale
has semantic area: Anatomical Location

Abdomen
type: NamedIndividual
type: Colon Anatomical Entity
structure notes: Vertebrate specific. In arthropods 'abdomen' is the most distal section of the body which lies behind the thorax or cephalothorax. If need be we can introduce some grouping class
conforms to: http://linkedlifedata.com/resource/umls/id/C0000726
has exact synonym: abdominopelvis; abdominopelvic region
has related synonym: belly; celiac region; adult abdomen
comment: The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column. [Definition Source: http://orcid.org/0000-0002-6601-2165]
label: Addome @it
label: Buik @nl
associated disease: Colon Carcinoma
has SNOMED code: TY4100
has semantic area: Anatomical Location
internal notes: original SNOMED TY4100

Pleura
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
description: A thin layer of tissue that covers the lungs and lines the interior wall of the chest cavity. It protects and cushions the lungs. This tissue secretes a small amount of fluid that acts as a lubricant, allowing the lungs to move smoothly in the chest cavity while breathing.; The serous membrane that lines the wall of the thoracic cavity and the surface of the lungs. [Definition Source: NCI]
conforms to: http://linkedlifedata.com/resource/umls/id/C0032225
comment: The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
label: Borstvlies @nl
associated disease: Lung cancer
has SNOMED code: T29000
has semantic area: Anatomical Location

Uterus, NOS
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
external definition: he 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.
conforms to: http://linkedlifedata.com/resource/umls/id/C0042149
has related synonym: Uterus
comment: The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
label: Baarmoeder, Niet Anders Gespecificeerd @nl
label: Utero, Non Altrimenti Specificato @it
associated disease: Cervical Cancer
has semantic area: Anatomical Location
taxon notes: 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.

Rectum, NOS
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colorectum
conforms to: http://linkedlifedata.com/resource/umls/id/C0034896
has exact synonym: terminal portion of intestine
has related synonym: terminal portion of large intestine; rectal sac; intestinum rectum
comment: Rectum, Not Otherwise Specified (NOS)
label: Rectum, Niet Anders Gespecificeerd @nl
label: Retto, Non Altrimenti Specificato @it
annotated rule: Presence of keyword "Rectum NOS" in "Materiali" field in AOEC Database.
associated disease: Colon Carcinoma
definition: The terminal portion of the intestinal tube, terminating with the anus. [Definition Source: NCI]
has SNOMED code: T680000
has semantic area: Anatomical Location
internal notes: original SNOMED T68000

Caecum
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colon, NOS
conforms to: http://linkedlifedata.com/resource/umls/id/C0007531
has exact synonym: caecum; cecum; intestinum crassum caecum
has related synonym: intestinum crassum cecum; intestinum caecum; blindgut; blind intestine
comment: A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
label: Blinde Darm @nl
label: Cieco @it
annotated rule: Keyword Caecum in "Materiali" field
associated disease: Colon Carcinoma
has SNOMED code: T671000
has semantic area: Anatomical Location
internal notes: original SNOMED T67100

Colon, NOS
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colorectum
conforms to: http://linkedlifedata.com/resource/umls/id/C0009368
has exact synonym: large bowel
has related synonym: hindgut
comment: Colon, Not Otherwise Specified (NOS)
label: Colon, Non Altrimenti Specificato @it
label: Dikke Darm, Niet Anders Gespecificeerd @nl
associated disease: Colon Carcinoma
definition: Last portion of the large intestine before it becomes the rectum.
has SNOMED code: T670000
has semantic area: Anatomical Location
internal notes: original SNOMED T67000

Ascending Colon
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colon, NOS
conforms to: http://linkedlifedata.com/resource/umls/id/C0227375
has exact synonym: colon ascendens
has related synonym: spiral colon
comment: Section of colon which is distal to the cecum and proximal to the transversecolon.
label: Colon Ascendente @it
label: Oplopende Dubbele Punt @nl
associated disease: Colon Carcinoma
has SNOMED code: T672000
has semantic area: Anatomical Location
internal notes: original SNOMED T67200

Transverse Colon
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colon, NOS
conforms to: http://linkedlifedata.com/resource/umls/id/C0227386
has exact synonym: colon transversum
comment: The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon.
label: Colon Trasverso @it
label: Dwars Dubbele Punt @nl
annotated rule: Keyword "trasverso" in "Materiali" field.
associated disease: Colon Carcinoma
has SNOMED code: T674000
has semantic area: Anatomical Location
internal notes: original SNOMED T67400

Descending Colon
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colon, NOS
conforms to: http://linkedlifedata.com/resource/umls/id/C0227389
has exact synonym: colon descendens
comment: The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
label: Aflopende Dubbele Punt @nl
label: Colon Discendente @it
associated disease: Colon Carcinoma
has SNOMED code: T676000
has semantic area: Anatomical Location

Sigmoid Colon
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colon, NOS
conforms to: http://linkedlifedata.com/resource/umls/id/C0227391
has related synonym: colon sigmoideum; pelvic colon; sigmoid colon; sigmoid flexure
comment: The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
label: Colon Sigmoideo @it
associated disease: Colon Carcinoma
has SNOMED code: T677000
has semantic area: Anatomical Location
internal notes: original SNOMED T67700

Greater Curvature of Stomach
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C0227223
has exact synonym: stomach greater curvature
comment: The lateral and inferior border of the stomach. Attached to it is the greater omentum. [Definition Source: NCI]
label: Curvatura Maggiore dello Stomaco @it
label: Grotere Kromming van de Maag @nl
associated disease: Celiac disease
associated keyword in materiali: Corpo
has semantic area: Anatomical Location

Antrum Pylori
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C0034193
has broad synonym: antrum
has exact synonym: antrum of stomach; stomach pyloric antrum
has related synonym: antrum pyloricum; antrum of Willis; stomach antrum; antrum pylori; gastric antrum
comment: The initial part of the pyloric canal of the stomach. This site contains endocrine cells that produce gastrin and somatostatin. [Definition Source: NCI]
label: Antro Pilorico @it
label: Pylorus Antrum @nl
associated disease: Celiac disease
associated keyword in materiali: Antro
has semantic area: Anatomical Location

Duodenal Gland
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
broader transitive: Duodenum
conforms to: http://linkedlifedata.com/resource/umls/id/C0006323
comment: Compound, tubular, submucosal glands located in the duodenum proximal to the sphincter of Oddi; these glands produce alkaline-rich secretions that function to both protect the duodenum from the acidic content of the stomach and to enable intestinal enzymes to activate, thus enabling absorption to start. [Definition Source: NCI]
label: Duodenale Klier @nl
label: Ghiandola Duodenale @it
associated disease: Celiac disease
has Ontobee annotation: editor note: currently defined as equivalent to any submucosal gland in the duodenum. database_cross_reference: EMAPA:36522; GAID:314; NCIT:C13010; FMA:15060; http://www.snomedbrowser.com/Codes/Details/41298001; http://en.wikipedia.org/wiki/Brunner's_glands; MESH:A03.492.411.620.270.322; UMLS:C0006323; MA:0001551; http://linkedlifedata.com/resource/umls/id/C0006323; BTO:0002376 has_exact_synonym: submucosal gland of duodenum; Brunner's gland; gland of Brunner has_obo_namespace: uberon has_related_synonym: glandula duodenales Brunneri; glandula duodenales http://www.geneontology.org/formats/oboInOwl#id: UBERON:0001212 in_subset: http://purl.obolibrary.org/obo/uberon/core#organ_slim; http://purl.obolibrary.org/obo/uberon/core#pheno_slim; http://purl.obolibrary.org/obo/uberon/core#uberon_slim taxon_notes: Said to be absent outside mammlian (Andrew 1959) but Ziswiler and Farner (1972) noted similar glands at the gastroduodenal junction of some birds
has semantic area: Anatomical Location

Lung
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
alternative definition: Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.
conforms to: http://linkedlifedata.com/resource/umls/id/C0024109
has exact synonym: pulmo
comment: Respiration organ that develops as an oupocketing of the esophagus.
label: Long @nl
label: Polmone @it
associated disease: Lung cancer
has SNOMED code: T280000
has semantic area: Anatomical Location
internal notes: original SNOMED T28000
taxon notes: 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

Small Intestine
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C0021852
comment: The section of the intestines between the pylorus and cecum. The small intestine is approximately 20 feet long and consists of the duodenum, the jejunum, and the ileum. Its main function is to absorb nutrients from food as the food is transported to the large intestine. [Definition Source: NCI]
label: Dunne Darm @nl
label: Intestino Tenue @it
associated disease: Celiac disease
has semantic area: Anatomical Location

Duodenum
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
external definition: The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum.
conforms to: C001330
has related synonym: upper intestine; proximal intestine
comment: A jointed tube 25-30 cm long that connects the stomach to the jejunum. [Definition Source: NCI]
label: Duodeno @it
label: Twaalfvingerige darm @nl
associated disease: Celiac disease
has SNOMED code: T643000
has semantic area: Anatomical Location
internal notes: original SNOMED T-64300
taxon notes: In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum.; In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz.

Jejunum
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C0022378
comment: The portion of the small intestine that extends from the duodenum to the ileum. [Definition Source: NCI]
label: Digiuno @it
associated disease: Celiac disease
has semantic area: Anatomical Location

Ileum
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C0020885
has related synonym: intestinum ileum; lower intestine; posterior intestine; distal intestine
comment: The portion of the small intestine that extends from the jejunum to the colon
label: Ileo @it
associated disease: Colon Carcinoma
has SNOMED code: T65200
has SNOMED code: T679210
has semantic area: Anatomical Location
taxon notes: The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum.

Bronchus
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C0006255
has exact synonym: bronchi; bronchial trunk
has related synonym: bronchial tissue
comment: The upper conducting airways of the lung; these airways arise from the terminus of the trachea
label: Bronco @it
associated disease: Lung cancer
has SNOMED code: T260000
has semantic area: Anatomical Location
internal notes: original SNOMED T26000
taxon notes: In humans, the main bronchus is histologically identical to trachea; 2ary and 3ary bronchi are not; epithelium becomes simple columnar, goblet cell number decreases, elastic fibers in lamina propria increases, distribution more uniform. Muscular layer between mucosa and submucosa appears. cartilage rings become discontinuous plates connected by fibrous connective tissue

Rectal Mucous Membrane
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colon, NOS
conforms to: http://linkedlifedata.com/resource/umls/id/C0227395
has exact synonym: mucous membrane of rectum; rectum mucous membrane; mucosa of organ of rectum; rectal mucosa; rectum mucosa; rectal mucous membrane; rectum mucosa of organ; organ mucosa of rectum; rectum organ mucosa
comment: A mucosa that is part of a rectum
label: Membrana Mucosa Rettale @it
label: Rectaal Slijmvlies @nl
associated disease: Colon Carcinoma
has SNOMED code: T680100
has semantic area: Anatomical Location

Mediastinum
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C0025066
has exact synonym: mediastinal part of chest
comment: The central part of the thoracic cavity enclosed by the left and right pleurae.
label: Mediastino @it
associated disease: Lung cancer
has SNOMED code: TY2300
has semantic area: Anatomical Location
internal notes: original SNOMED TY2300, I decided to left it untouched since it is quite peculiar

Cervix Epithelium
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
structure notes: The epithelium of the cervix is varied. The ectocervix (more distal, by the vagina) is composed of nonkeratinized stratified squamous epithelium. The endocervix (more proximal, within the uterus) is composed of simple columnar epithelium.
conforms to: http://linkedlifedata.com/resource/umls/id/C1711358
has exact synonym: cervical epithelium; epithelium of cervix; cervix epithelial tissue; cervical canal epithelial tissue; cervical canal epithelium
comment: An epithelium that is part of a uterine cervix
label: Cervix Epitheel @nl
label: Epitelio della Cervice @it
associated disease: Cervical Cancer
has semantic area: Anatomical Location

Cervix Squamous Epithelium
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
broader transitive: Cervix Epithelium
conforms to: http://linkedlifedata.com/resource/umls/id/C1707351
has exact synonym: cervical squamous epithelium
comment: The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane.
label: Cervix Plaveiselepitheel @nl
label: Epitelio Squamoso della Cervice @it
associated disease: Cervical Cancer
has semantic area: Anatomical Location

Thoracic Lymph Node
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C0229745
has exact synonym: lymph node of thorax
has related synonym: deep thoracic lymph node
comment: A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes
label: Linfonodo Toracico @it
label: Thoracale Lymfeknoop @nl
associated disease: Lung cancer
has SNOMED code: T083000
has semantic area: Anatomical Location

Intestinal Villus of Duodenum
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
broader transitive: Duodenum
conforms to: http://linkedlifedata.com/resource/umls/id/C1179669
comment: An intestinal villus in the duodenum.
label: Intestinale Villus van de Twaalfvingerige Darm @nl
label: Villi Intestinali del Duodeno @it
associated disease: Celiac disease
has semantic area: Anatomical Location

Duodenal Epithelium
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
broader transitive: Duodenum
conforms to: http://linkedlifedata.com/resource/umls/id/C0227286
has exact synonym: epithelium of duodenum
comment: An epithelium that is part of a duodenum.
label: Duodenaal Epitheel @nl
label: Epitelio Duodenale @it
associated disease: Celiac disease
has semantic area: Anatomical Location

Left Colon
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colon, NOS
conforms to: http://linkedlifedata.com/resource/umls/id/C0227388
has related synonym: distal colon
comment: The distal portion of the colon; it develops embryonically from the hindgut and functions in the storage and elimination of waste.
label: Colon Sinistro @it
label: Linker Dubbele Punt @nl
associated disease: Colon Carcinoma
has SNOMED code: T679950
has semantic area: Anatomical Location
internal notes: previous SNOMED T67995

Right Colon
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colon, NOS
conforms to: http://linkedlifedata.com/resource/umls/id/C1305188
has related synonym: proximal colon
comment: The proximal portion of the colon, extending from the ileocecal valve usually to a point proximal to the left colic flexure; it develops embryonically from the terminal portion of the midgut and functions in absorption.
label: Colon Destro @it
label: Rechter Dubbele Punt @nl
associated disease: Colon Carcinoma
has SNOMED code: T679650
has semantic area: Anatomical Location
internal notes: original SNOMED T67965

Cervix Glandular Epithelium
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
broader transitive: Cervix Epithelium
structure notes: The 'glandular' or columnar epithelium of the cervix is located cephalad to the squamocolumnar junction. It covers a variable amount of the ectocervix and lines the endocervical canal. It is comprised of a single layer of mucin-secreting cells. The epithelium is thrown into longitudinal folds and invaginations that make up the so-called endocervical glands (they are not true glands). These infolding crypts and channels make the cytologic and colposcopic detection of neoplasia less reliable and more problematic. The complex architecture of the endocervical glands gives the columnar epithelium a papillary appearance through the colposcope and a grainy appearance upon gross visual inspection. The single cell layer allows the coloration of the underlying vasculature to be seen more easily. Therefore, the columnar epithelium appears more red in comparison with the more opaque squamous epithelium.
conforms to: http://linkedlifedata.com/resource/umls/id/C1707350
has related synonym: cervix columnar epithelium
comment: A glandular epithelium that is part of a uterine cervix.
label: Cervix Glandulair Epitheel @nl
label: Epitelio Ghiandolare della Cervice @it
associated disease: Cervical Cancer
has semantic area: Anatomical Location

Exocervical Epithelium
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
broader transitive: Cervix Epithelium
conforms to: http://linkedlifedata.com/resource/umls/id/C1283920
has exact synonym: ectocervical epithelium; exocervical epithelium
comment: A epithelium that is part of a ectocervix.
label: Epitelio Esocervicale @it
label: Exocervicaal Epitheel @nl
associated disease: Cervical Cancer
has semantic area: Anatomical Location

Cervical Squamo-Columnar Junction
type: NamedIndividual
type: Concept
type: Cervix Anatomical Entity
broader transitive: Cervix Epithelium
conforms to: http://linkedlifedata.com/resource/umls/id/C3273256
has broad synonym: squamocolumnar junction
has exact synonym: squamocolumnar junction of uterine cervix; squamo-columnar junction of uterine cervix
comment: Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet
label: Cervicale Squamocolumnaire Overgang @nl
label: Giunzione Squamocolonnare Cervicale @it
associated disease: Cervical Cancer
has semantic area: Anatomical Location

Colorectum
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C1711309
comment: The subdivision of the digestive tract that consists of the colon and the rectum @nl
label: Coloretto @it
associated disease: Colon Carcinoma
has semantic area: Anatomical Location

Crypt of Lieberkuhn of Duodenum
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
broader transitive: Duodenum
conforms to: http://linkedlifedata.com/resource/umls/id/C2951230
has exact synonym: duodenal crypt; duodenal crypt of Lieberkuhn
comment: An intestinal crypt that is located in the duodenum. [Definition Source: http://orcid.org/0000-0002-6601-2165]
label: Cripta di Lieberkuhn del Duodeno @it
label: Crypte van Lieberkuhn van de Twaalfvingerige Darm @nl
associated disease: Celiac disease
has Ontobee annotation: database_cross_reference: EMAPA:37838; FMA:269063 has_exact_synonym: duodenal crypt; duodenal crypt of Lieberkuhn has_obo_namespace: uberon http://www.geneontology.org/formats/oboInOwl#id: UBERON:0013482 in_subset: http://purl.obolibrary.org/obo/uberon/core#pheno_slim
has semantic area: Anatomical Location

Duodenal Ampulla
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
broader transitive: Duodenum
conforms to: http://linkedlifedata.com/resource/umls/id/C0227300
has exact synonym: duodenal cap; bulbus (duodenum); ampulla duodeni; duodenal cap viewed radiologically; bulbus duodeni; ampulla (duodenum); ampulla of duodenum
comment: The very first part of the duodenum which is slightly dilated.
label: Ampolla Duodenale @it
label: Duodenale Ampulla @nl
associated disease: Celiac disease
has semantic area: Anatomical Location

Duodenal Lamina Propria
type: NamedIndividual
type: Concept
type: Celiac Anatomical Entity
broader transitive: Duodenum
conforms to: http://linkedlifedata.com/resource/umls/id/C0227287
has exact synonym: lamina propria of duodenum; duodenal lamina propria; lamina propria mucosae of duodenum
comment: A lamina propria that is part of a duodenum.
label: Lamina Propria del Duodeno @it
associated disease: Celiac disease
has semantic area: Diagnosis

Pulmonary Lymph Node
type: NamedIndividual
type: Concept
type: Lung Anatomical Entity
conforms to: http://linkedlifedata.com/resource/umls/id/C0229749
comment: Pulmonary lymph nodes are a common and underrecognized cause of a peripheral SPN. These lymph nodes are usually found at the bifurcation of the bronchi, before the fourth branch, where they are referred to as peribronchial lymph nodes. Lymph nodes are occasionally present within the lung parenchyma, where they are designated intrapulmonary lymph nodes (IPLNs) or perifissural nodules (PFNs).
label: Linfonodo Polmonare @it
label: Pulmonale Lymfeknoop @nl
associated disease: Lung cancer
has SNOMED code: T080000
has SNOMED code: T083110
has SNOMED code: T083120
has SNOMED code: T083200
has SNOMED code: T083210
has semantic area: Anatomical Location
internal notes: previous SNOMED was T08311, T08312, T08320, T08321, T08000

Rectosigmoid Junction
type: NamedIndividual
type: Concept
type: Colon Anatomical Entity
broader transitive: Colon, NOS
conforms to: http://linkedlifedata.com/resource/umls/id/C1709868
has related synonym: rectosigmoid region
comment: An anatomical junction that is between the sigmoid colon and rectum.
label: Giunzione Rettosigmoidea @it
label: Rectosigmoid Junctie @nl
associated disease: Colon Carcinoma
has SNOMED code: T679210
has semantic area: Anatomical Location

Adult Onset
type: NamedIndividual
type: Concept
type: Onset
conforms to: http://linkedlifedata.com/resource/umls/id/C1853562
comment: Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later. [Defintion Source: HPO probison]
label: Gruppo d'Età Adulta @it
label: Volwassen Aanvang @nl
has semantic area: General Entity

Late Onset
type: NamedIndividual
type: Concept
type: Onset
broader transitive: Adult Onset
conforms to: http://linkedlifedata.com/resource/umls/id/C4025592
comment: A type of adult onset with onset of symptoms after the age of 60 years. [Defintion Source: HPO probison]
label: Gruppo d'Età Tarda @it
label: Laat Begin @nl
has semantic area: General Entity

Midlle Age Onset
type: NamedIndividual
type: Concept
type: Onset
broader transitive: Adult Onset
conforms to: http://linkedlifedata.com/resource/umls/id/C1969363
comment: A type of adult onset with onset of symptoms at the age of 40 to 60 years. [Defintion Source: HPO probison]
label: Begin op Middelbare Leeftijd @nl
label: Gruppo d'Età della Mezza Età @it
has semantic area: General Entity

Young Adult Onset
type: NamedIndividual
type: Concept
type: Onset
broader transitive: Adult Onset
conforms to: http://linkedlifedata.com/resource/umls/id/C3554568
comment: Onset of disease at the age of between 16 and 40 years. [Defintion Source: HPO DDD:hfirth]
label: Begin bij Jonge Volwassenen @nl
label: Gruppo d'Età Giovane Adulto @it
has semantic area: General Entity

Dennis Dosso
type: NamedIndividual
type: Person

Laura Menotti
type: NamedIndividual
type: Person

Stefano Marchesin
type: NamedIndividual
type: Person

Gianmaria Silvello
type: NamedIndividual
type: Person

Biopsy of the Pyloric Antrum
type: NamedIndividual
type: Concept
type: Celiac Disease Intervention or Procedure Type
broader transitive: Endoscopic Biopsy
comment: Biopsy executed in the pyloric antrum, a form of endoscopic biopsy.
label: Biopsia dell'Antro Pilorico @it
label: Biopsie van Het Pylorusantrum @nl
associated disease: Celiac disease
associated keyword in materiali: “Biopsia” + “STOMACO” + “Antro”
has semantic area: Procedure

Cannizzaro Hospital
type: NamedIndividual
type: Organization
comment: Entity representing the Cannizzaro Hospital as producer of medical report
label: Ospedale Cannizzaro @it
label: Ziekenhuis Cannizzaro @nl
has semantic area: General

Biopsy of the Greater Curvature
type: NamedIndividual
type: Concept
type: Celiac Disease Intervention or Procedure Type
broader transitive: Endoscopic Biopsy
comment: Biopsy produced in the greater curvature area, a region in the stomach.
label: Biopsia della Grande Curvatura @it
label: Biopsie van de Grotere Kromming @nl
associated disease: Celiac disease
associated keyword in materiali: Biopsia + Stomaco + Corpo @it
has semantic area: Procedure

Severe Colon Dysplasia
type: NamedIndividual
type: Concept
type: Dysplasia
broader transitive: Colon Dysplasia
broader transitive: Severe Dysplasia
conforms to: http://linkedlifedata.com/resource/umls/id/C0586369
has exact synonym: Severe Colon Dysplasia; Severe dysplasia of colon
comment: Dysplasia is a term that describes how much your polyp looks like cancer under the microscope. Polyps that are more abnormal and look more like cancer are said to have high-grade (severe) dysplasia.
label: Ernstige Colondysplasie @nl
label: Grave Displasia del Colon @it
associated disease: Colon Carcinoma
has semantic area: Diagnosis

Specimen Unsatisfactory for Diagnosis
type: NamedIndividual
type: Concept
type: Inconclusive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0702119
label: Campione Insoddisfacente per la Diagnosi @it
label: Specimen Onbevredigend voor Diagnose @nl
has SNOMED code: M090000
has semantic area: Diagnosis

General Entity
type: NamedIndividual
type: Semantic Area
comment: In this ontology there are different semantic areas. These are: diagnosis, procedure, test, anatomical location, and general. General is the area of entities that are common to all clinical cases. Organization, clinical case reports, diseases, are classes with entities that do not belong to the other 4 semantic areas, therefore we classified them in general. These are the classes that, in our documentation, are contained in the green box.
label: Algemene Entiteit @nl
label: Entità Generica @it

Glandular Atrophy
type: NamedIndividual
type: Concept
type: Intestinal Abnormality
conforms to: http://linkedlifedata.com/resource/umls/id/C1389050
label: Atrofia Ghiandolare @it
label: Glandulaire Atrofie @nl
associated disease: Celiac disease
has semantic area: Diagnosis

Insufficient Material
type: NamedIndividual
type: Concept
type: Inconclusive Outcome Type
conforms to: http://linkedlifedata.com/resource/umls/id/C0332630
comment: Inconclusive outcome where not enough material was present for the diagnosis.
label: Materiale Insufficiente @it
label: Onvoldoende Materiaal @nl
has SNOMED code: M010100
has semantic area: Diagnosis

Procedure
type: NamedIndividual
type: Semantic Area
has exact synonym: Intervention
comment: Semantic class to describe the semantic area of the interventions. We defined our own class (and not used the ncit one) because we wanted to keep the two separated to not entangle too much queries and also because here we are using it with a slightly different semantic meaning.
label: Procedura @it

Test
type: NamedIndividual
type: Semantic Area
comment: Test is a semantic area encompassing all those entities representing one test. One example are the immunistochemical tests like the immunoprecipitation. These tests may have different outcome, like being true or false, or a non-negative integer.

ExaMode Consortium
type: NamedIndividual
type: Institution