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The ExaMode Ontology (colon version)

Release June 2020

This version:
https://w3id.org/examode/ontology
Latest version:
https://w3id.org/examode/ontology
External repository (Zenodo):
Examode Ontology (Colon Cancer) v0.2
DOI: 10.5281/zenodo.3907400
Revision:
0.2
Authors:
Dennis Dosso, (University of Padua)
Gianmaria Silvello, (University of Padua)
Contributors:
Members of the EXAMODE project, EXAMODE H2020
Publisher:
EXAMODE project
This project is funded from the European Union's Horizon 2020 research and innovation programme under grant agreement no 825292
Download serialization:
JSON-LD RDF/XML N-Triples TTL
License:
http://creativecommons.org/licenses/by/1.0/ License
Visualization:
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Cite as:
Dennis Dosso and Gianmaria Silvello, 2020. The ExaMode Ontology, v0.2, colon cancer.

Ontology Specification Draft

Introduction back to ToC

One of the main objectives of the ExaMode project financed by the European Commission under the Horizon 2020 framework, is to provide a computer aided system which will improve the diagnosis performance and reduce the pathologists workload.

As most of the samples analyzed for histopathological diagnosis consist of cancer biopsies and future cancer incidence and mortality burden worldwide is predicted to be increasing (by 63% from 2018 until 2040), we decided to focus our attention mainly on cancer diseases.

ExaMode focuses on four use cases:

  • Colon cancer
  • Cervix cancer
  • Lung cancer
  • Celiac disease

The current version of the ontology models only the Colon cancer case. The ontology is going to be extended in the next months and will maintain retro-compatibility with the previously released version.

Colon Cancer

The estimated number of colon cancer incidence from 2018 to 2040 is going to increase by up 75%, for both sexes and all ages. The American Cancer Society (ACS) recommends regular screening for colon cancer for people over 45 years. The screening can be done either with a stool-based molecular tests or with a visual exams, so the at this stage the screening process does not include histopathological examination.

However, with the increase number of screenings, the number of cases that need further investigation or confirmation of initial findings by histopathological analysis will raise. Therefore, the colon cancer-associated workload for histopathologists will constantly and significantly increase in the next years. Cancer detection in biopsies is not very difficult for pathologists, but given the large amount of tested samples, it is very time-consuming and has a substantial impact on the histopathologist workload.

From the scientific point of view, computer-aided colon cancer diagnosis appears to be very interesting, as suggested by the number of scientific articles available in the largest research publication database. Computer-aided diagnosis tools are mostly based on data-hungry prediction algorithms. In this context data is typically composed of annotated WSIs for colon biopsy samples; nevertheless, the annotation process is expensive and time-consuming. An alternative is to automatically annotate WSIs by using the medical reports related to them; ExaMode is working on automatic methods to extract key pathological concepts from the medical reports to (weakly) annotate the WSIs to be used for the training of prediction algorithms.

Hence, prediction algorithms can be fed by strongly (manually) annotated data as well as by weakly annotated data. The present ontology is useful in both cases by providing a common ground for identifying key concepts and the consistent terminology to be used by the algorithms.

The ExaMode ontology defines the key concepts and properties to model the diagnosis of colon cancer cases, the anatomical location where the disease might be located, the procedure employed to obtain the tissue to be analysed and the tests conducted on the tissue.

Despite the existence of many medical ontologies focusing specifically on cancer, there are not a comprehensive ontology comprehensively modeling all colon cancer related disease, anatomical location, topography and pathology laboratory process. For this reason, the ExaMode ontology build upon a large number of existing and widely-used ontologies and provides the missing classes and relationships to make them work seamlessly together. The ExaMode ontology defines its own classes and terms when they are not available in any other publicly well-known ontology.

Namespace declarations

Table 1: Namespaces used in the document
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owl<http://www.w3.org/2002/07/owl>
fabio<http://purl.org.spar/fabio>
xsd<http://www.w3.org/2001/XMLSchema>
doid<https://www.ebi.ac.uk/ols/ontologies/doid>
skos<http://www.w3.org/2004/02/skos/core>
rdfs<http://www.w3.org/2000/01/rdf-schema>
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rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns>
term<https://hpo.jax.org/app/browse/term>
id<http://linkedlifedata.com/resource/umls/id>
page<http://dbpedia.org/page>
obo<http://purl.obolibrary.org/obo>
default namespace<https://w3id.org/examode/ontology>
dc<http://purl.org/dc/elements/1.1>

The ExaMode Ontology: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

Annotation Properties

Named Individuals

The ExaMode Ontology: Description back to ToC

The goal of this document is to define an OWL 2 ontology for the ExaMode project whose overall goal is to build predictive algorithms to help pathologist in the diagnosis of cancer cases. The starting point of ExaMode are medical diagnostic reports associated with WSIs of examined tissues.

The present ontology models the diagnostic reports associated to a (series of) WSI and enable a structured encoding of the main concepts of a diagnosis. These concepts and their relations can be used to automatically annotate WSI as well as to do some reasoning over diagnostic reports about colon cancer.

The majority of colon-rectal cancers derives from precursor lesions which can be identified using endoscopic procedure (colonoscopy), leading to excision of these lesions, well known as polyps.

Therefore, good endoscopic practice together with an accurate histopathological diagnosis decreases the incidence of colorectal cancer. There are different precursor lesions with different diagnostic and prognostic significance. In this ontology we focus on the most important features and measurements for polyps. Considering all these aspects, in the microscopic analysis of colon excisional biopsy sample, there is a minimum of data that need to be provided by the pathologist:

  1. Type of the polyp, as well as the number of polyps of a given type - it is important distinguish between the two main types of polyps : adenoma-serrated polyps and malignant polyps. From the diagnostic perspective, it can be also useful to know the number of each type of polyps.
  2. It is valuable to identify dysplasia and grade it (low grade, medium grade or high grade). In some cases, coexistent pathological abnormalities can be observed and they have to be reported, i.e. described as present/not present.
  3. In case of malignant polyps (considered as cancer), several critical histologic features need to be assessed, which include tumor type, histological tumor grade, lymphovascular invasion and margin involvement.

This information is a prognostic factor leading patient's management: polyps with a negative polypectomy margin, low grade histology, and no lymphovascular invasion can be safely treated with endoscopic polypectomy, whereas positive margin, high grade (poorly differentiated) histology, and lymphovascular invasion are associated with an increased risk of adverse outcomes and surgical resection is indicated.

We represent the ontology as a graph where nodes are classes and edges are typed relationships amongst the classes. Classes (nodes) represent real-world objects such as a person, a project, a tissue or an anatomical part. Relationships (edges) describe how classes interact one with the other. In ExaMode we limit the creation of new classes to a minimum and we re-use existing ontologies as much as possible.

The EXAMODE ontology describes the medical reports and it is organized in five main conceptual areas:

  1. EXAMODE cancer cases: This area contains all the classes common to the four cancer cases considered in EXAMODE. In this area we classify each use case on the basis of the disease it analyses, so we have: “cervical cancer”, “lung cancer”, “colon carcinoma” and “celiac disease” as four diseases assigned to four use cases. Each “dataset” contains several “Clinical Case Report”. The Clinical Case Report class has four children, one for each disease; for instance, we can see that for the colon the Clinical Case Report class has a child called Colon Clinical Case Report.
  2. Diagnosis: This area contains the classes related to the diagnosis which are extracted from the medical report. The main class is the “Outcome” which is specialized into three main sub-classes “Negative result”, “Positive outcome” and “Inconclusive outcome”. “Positive outcome” has many subclasses, one for each type of issues detected in the diagnosis (e.g., “Carcinoma” or “Sarcoidosis”). As you can see, this is a taxonomy of the possible diagnoses we can find in the reports. The subclass property is disjunctive, meaning that only one positive outcome subclass can be instantiated at each time.
  3. Anatomical location/Topography : This area contains the classes modelling the taxonomy of the possible anatomical locations where the “disease” can be located. This information is extracted from the medical reports. For the lung, the main locations are lung, bronchus, mediastinum and thoracic lymph node. Bronchus is specialized into more areas. The same can be done, if necessary, for the lung. This area describes also where the tissue was withdrawn for the analyses via the hasTopography property.
  4. Procedure: This area contains the classes that model the procedure adopted to obtain the material where the analysis was performed. The main class is “Intervention or Procedure” and corresponds to the “Material” column in the AOEC reports. For the colon we have one main class “Biopsy of Colon” with two subclasses: Polypectomy and Colonscopic Polypectomy. The code “P-40” identifies a biopsy, but in the “Materiale” column we may find some keywords specifying that we are talking about a polypectomy.

    EXAMODE cancer cases

    EXAMODE cases

    The central class of this part of the ontology is Clinical Case Report. All the medical reports modeled through this ontology are part of this class that can be instantiated for specific cases such as the Colon Clinical Case Report. As we can see there is a clinical case report for each one of the EXAMODE cancer cases.

    All medical reports are associated with a Patient (normally anonymized) because a single patient can have more than one associated medical report. We model minimal patient information: age at the time of the report, gender and an age onset to classify the patients into three categories: young adult, middle age and late.

    All medical reports are associated with the Organization which produced it. In EXAMODE there are two organizations: the Cannizzaro Hospital in Italy and the Radboud Medical Center in the Netherlands.

    Each medical report can be related to an image file about the report. The block number refers to internal ids related to the reports or the images.

    Colon Cancer: Diagnosis

    Colon cancer diagnosis

    This is the central area of the EXAMODE Colon Cancer ontology. Each medical report is connected to an Outcome. The Outcome class represents a general outcome that be positive (PositiveOutcome), negative (NegativeOutcome), inconclusive (InconclusiveOutcome) due to insufficient material (NegativeOutcome) or specimen unsatisfactory for diagnosis (SpecimenUnsatisfactory), and without the evidence of malignancy (NoMalignancy).

    The positive outcome is specialized into a taxonomy of diseases ranging from benign to malignant states as shown in the figure below. Colon disease

    The main task for a pathologist is to detect cancerous polyps (e.g. for population screening). The high objectiveness of the diagnostic criteria are:

    1. Polyp / No polyp
    2. Adenoma-Serrated Polyps / Malignant Polyps
    3. The number of polyps observed (for each type)
    4. Dysplasia present / not present
    5. High grade dysplasia / Low grade dysplasia

    The majority of colon-rectal cancers derives from precursor lesions which can be identified using endoscopic procedure (Colonoscopy), leading to excision of these lesions, well known as polyps. Therefore, good endoscopic practice together with an accurate histopathological diagnosis decreases the incidence of colorectal cancer.

    There are different precursor lesions with different diagnostic and prognostic significance. In this ontology, we focus on the most important features and measurements for polyps. Considering all these aspects, in the microscopic analysis of colon excisional biopsy sample, there is a minimum of data that need to be provided by the pathologist:

    1. Type of the polyp, as well as the number of polyps of a given type - it is important distinguish between the two main types of polyps: adenoma-serrated polyps and malignant polyps. From the diagnostic perspective, it can be also useful to know the number of each type of polyps.
    2. It could be valuable to identify dysplasia and grade it (low grade, medium grade or high grade).
    3. In case of malignant polyps (considered as cancer, e.g. Colon Adenocarcinoma or Metastatic Adenocarcinoma), several critical histological features need to be assessed, which include tumor type, histological tumor grade, lymphovascular invasion and margin involvement.

    The EXAMODE ontology for the colon cancer has two other main areas as shown below. One detailing the performed surgical procedure to collect the tissue and the other relating the tissue and the, potential, detected disease to an anatomical location. Note that the anatomical location where the disease might be located can be more specific than the location where the tissue was withdrawn. location and procedure

Cross reference for The ExaMode Ontology classes, properties and dataproperties back to ToC

This section provides details for each class and property defined by The ExaMode Ontology.

Classes

Adenomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0006498

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.
has super-classes
Polyp of Colon c
has sub-classes
Colon Tubular Adenoma c, Colon Tubulovillous Adenoma c, Colon Villous Adenoma c

Adult onsetc back to ToC or Class ToC

IRI: https://hpo.jax.org/app/browse/term/HP:0003581

Onset of disease manifestations in adulthood, defined here as at the age of 16 years or later.
has super-classes
Onset c
has members
Late onset ni, Middle age onset ni, Young adult onset ni

Anastomosisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C15609

A natural or surgically-induced connection between tubular structures in the body.
has super-classes
Surgical Procedure c

Annotationc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#Annotation

A general class to represent all the kinds of annotations that may be needed in a medical report.
has sub-classes
Disease Annotation c, Onset c, Semantic Area c
is in domain of
is specification of op
is in range of
is specification of op

Biopsyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C15189

The removal of cells or tissues for examination by a pathologist. The pathologist may study the tissue under a microscope or perform other tests on the cells or tissue. There are many different types of biopsy procedures. The most common types include: (1) incisional biopsy, in which only a sample of tissue is removed; (2) excisional biopsy, in which an entire lump or suspicious area is removed; and (3) needle biopsy, in which a sample of tissue or fluid is removed with a needle.; The removal of tissue specimens or fluid from the living body for microscopic examination, performed to establish a diagnosis.
has super-classes
Surgical Procedure c
has sub-classes
Endoscopic Biopsy c

Biopsy of Colonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51678

Removal of tissue from the colon for microscopic examination, using an endoscope.
has super-classes
Endoscopic Biopsy c
has sub-classes
Colonoscopic polypectomy c, Polypectomy c

Boolean Check Elementc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#BooleanCheckElement

A set of checks controlled on an Immunohistochemical test that can only have a boolean result (positive - negative).
has super-classes
Check Element c
has sub-classes
Immunoprecipitation c
is in domain of
outcome dp

Check Elementc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#CheckElement

This is a set of elements containing all the possible checks that a patient may do for a disease.
has super-classes
Immunohistochemical Test c
has sub-classes
Boolean Check Element c, Float Check Element c

Clinical Case Reportc back to ToC or Class ToC

IRI: http://purl.org.spar/fabio/ClinicalCaseReport

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
Is defined by
https://www.examode.dei.unipd.it/ontology/
has sub-classes
Colon Clinical Case Report c
is in domain of
has block number dp, has outcome op, has textual diagnosis dp, identifier dp, is about disease op, test used op
is in range of
has Clinical Case Report op

Colitisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0005292

Inflammation of the colon.
has super-classes
Positive outcome c

Colon Adenocarcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0002271

A carcinoma that arises from glandular epithelial cells of the colon.
has super-classes
Positive outcome c

Colon Annotationc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#ColonAnnotation

A class that is a container for elements that may or may not be found in a colon case. Originally thought to have Dysplasia.
has super-classes
Disease Annotation c
is in range of
has dysplasia
has members
Colon Dysplasia ni, Mild Colon Dysplasia ni, Moderate Colon Dysplasia ni, Severe Colon Dysplasia ni

Colon Clinical Case Reportc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#ColonClinicalCaseReport

Class representing all colon cancer cases.
has super-classes
Clinical Case Report c

Colon Hyperplastic Polypc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4930

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.
has super-classes
Polyp of Colon c

Colon Inflammatory Polypc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0006152

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.
has super-classes
Polyp of Colon c

Colon Tubular Adenomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C7041

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.
has super-classes
Adenoma c

Colon Tubulovillous Adenomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C5496

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
has super-classes
Adenoma c

Colon Villous Adenomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0021271

A villous adenoma that involves the colon.
has super-classes
Adenoma c

Colonoscopic polypectomyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51688

Complete or partial removal of a polypoid lesion from the mucosal surface of the large intestine.
has super-classes
Biopsy of Colon c

Diseasec back to ToC or Class ToC

IRI: https://www.ebi.ac.uk/ols/ontologies/doid/Disease

General class representing one disease.
is in range of
associated disease, is about disease op
has members
colon carcinoma ni

Disease Annotationc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#DiseaseAnnotation

A container class for elements that may or may not be present in diseases. One disease may present some elements that are not exaclty directly correlated to the presence/absence of the disease. or elements that are just there, and it is useful to note their presence/absence. This is the class of all elements that can be considered a sort of addendum, information extracted from the clinical case record but not directly related to the presence outcome. The inspiration for this class first came when we had to deal with the Annotations to the Case of the Celiac Disease. You can also think of this class as a superclass for other containers.
has super-classes
Annotation c
has sub-classes
Colon Annotation c
is in range of
presence of op
has members
Dysplasia ni, High Grade Dysplasia ni, Mild Dysplasia ni, Moderate Dysplasia ni, Pre-Cancerous Dysplasia ni, Severe Dysplasia ni

Endoscopic Biopsyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C15389

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.
has super-classes
Biopsy c
has sub-classes
Biopsy of Colon c

Float Check Elementc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#FloatCheckElement

A set of checks that can be performed on a Immunohistochemical Test that present a float as output value.
has super-classes
Check Element c
is in domain of
has value dp

genderc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C17357

The assemblage of properties that distinguish people on the basis of the societal roles expected for the two sexes.
is equivalent to
{ male , female gender }
is in range of
has gender op

Granulomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OAE_0001850

An inflammation AE that shows localized nodular inflammation found in tissues.
has super-classes
Positive outcome c

Hemicolectomyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C86074

Surgical removal of approximately half of the colon.
has super-classes
Surgical Procedure c

Immunohistochemical Testc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51944

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.
has super-classes
test c
has sub-classes
Check Element c

Immunoprecipitationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C16724

Antigen aggregation with antibody, in the right ratios, to cause precipitation. [def-source: NCI]
has super-classes
Boolean Check Element c

Inconclusive Outcomec back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#InconclusiveOutcome

Inconclusive Outcome. Not enough tissue or not enough evidence was present to decide for a negative or positive outcome.
has super-classes
Outcome c
has sub-classes
Insufficient Material c, Specimen unsatisfactory for diagnosis c

Insufficient Materialc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#InsufficientMaterial

Inconclusive outcome where not enough material was present for the diagnosis.
has super-classes
Inconclusive Outcome c

Metastatic Adenocarcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4124

An adenocarcinoma which has spread from its original site of growth to another anatomic site.
has super-classes
Positive outcome c

Negative Resultc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#NegativeResult

The presence of a negative result, i.e. normal tissue
has super-classes
Outcome c

No Malignancyc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#NoMalignancy

has super-classes
Outcome c

Onsetc back to ToC or Class ToC

IRI: https://hpo.jax.org/app/browse/term/HP:0003674

The age group in which disease manifestations appear.
has super-classes
Annotation c
has sub-classes
Adult onset c
is in range of
has age onset op

Organizationc back to ToC or Class ToC

IRI: http://xmlns.com/foaf/0.1/organization

An organization that, in the context of the ExaMode program, provides clinical case records. It is usually an Hospital (e.g. AOEC or Radbound).
Is defined by
https://www.examode.dei.unipd.it/ontology/
has members
Cannizzaro Hospital ni, Radboud Universiteit Nijmegen ni

Outcomec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C20200

A class representing a general outcome, whatever it may be (positive, negative, uncertain, not enough information etc).
has sub-classes
Inconclusive Outcome c, Negative Result c, No Malignancy c, Positive outcome c
is in domain of
Has Intervention op, has location op, has test op, presence of op
is in range of
has outcome op

Patientc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/IDOMAL_0000603

A person under health care. The person may be waiting for this care or may be receiving it or may have already received it.
is in domain of
has Clinical Case Report op, has age dp, has age onset op, has gender op, has image dp

Polyp of Colonc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0021400

A polyp that involves the colon.
has super-classes
Positive outcome c
has sub-classes
Adenoma c, Colon Hyperplastic Polyp c, Colon Inflammatory Polyp c

Polypectomyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C25349

Complete or partial removal of a polypoid lesion from the mucosal surface.
is equivalent to
Colonoscopic polypectomy c
has super-classes
Biopsy of Colon c

Positive outcomec back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#PositiveOutcome

Positive Outcome, i.e., something has been found in the patient. This is the higher class for the positive outcome.
has super-classes
Outcome c
has sub-classes
Colitis c, Colon Adenocarcinoma c, Granuloma c, Metastatic Adenocarcinoma c, Polyp of Colon c, Ulcer c
is in domain of
has dysplasia

Resectionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C158758

A surgical procedure in which tissue is removed.
has super-classes
Surgical Procedure c

Semantic Areac back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#SemantcArea

A general container for entities that represent semantical areas. Examples of semantical areas include "general" (common to all diseases), "Anatomic Site", "Procedure", "Diagnosis".
has super-classes
Annotation c
has members
Anatomical Location ni, Diagnosis ni, General Entity ni, Procedure ni, Test ni

Specimen unsatisfactory for diagnosisc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology#SpecimenUnsatisfactory

has super-classes
Inconclusive Outcome c

Surgical Procedurec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C15329

Type of Intervention that is a surgical procedure.
has super-classes
Intervention or Procedure c
has sub-classes
Anastomosis c, Biopsy c, Hemicolectomy c, Resection c

testc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C47891

A general class representing a test.
has sub-classes
Immunohistochemical Test c
is in range of
has test op, test used op

Topographyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C38034

The description of an anatomical region or of a body part.
is in range of
has location op, intervention has topography op
has members
Abdomen ni, Ascending Colon ni, Caecum ni, Colon, NOS ni, Descending colon ni, Ileum ni, Left colon ni, Rectal mucous membrane ni, Rectosigmoid junction ni, Rectum, NOS ni, Right colon ni, Sigmoid colon ni, Transverse Colon ni

Ulcerc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3426

A circumscribed inflammatory and often suppurating lesion on the skin or an internal mucous surface resulting in necrosis of tissue.
has super-classes
Positive outcome c

Object Properties

has age onsetop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#hasAgeOnset

Links one record to its age group, or 'onset'.
has domain
Patient c
has range
Onset c

has Clinical Case Reportop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#hasClinicalCaseReport

Coonects one patient to its clinical case report.
has domain
Patient c
has range
Clinical Case Report c

has genderop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#hasGender

To connect a record with the gender of the corresponding person.
has domain
Patient c
has range
gender c

Has Interventionop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#hasIntervention

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.
has domain
Outcome c
has range
Intervention or Procedure c

has locationop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#hasLocation

A clinical case record is focused on an anatomical location. This property connects an instance of clinical case report (of whatever type) to an anatomical location, a member of the class topology.
has domain
Outcome c
has range
Topography c

has outcomeop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#hasOutcome

Every report has an outcome, whatever it may be (positive, negative, inconclusive etc.)
has domain
Clinical Case Report c
has range
Outcome c

has testop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#hasTest

connects an instance of intervention to some trait found in the patient.
has domain
Outcome c
has range
test c

intervention has topographyop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#InterventionHasLocation

every intervention/procedure is performed in an anatomical location. We use the topology entities to encode the information about this location. We use this property supposing to reference one subclass of Topography.
has domain
Intervention or Procedure c
has range
Topography c

is about diseaseop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#isAboutDisease

This property is used to connect an instance of a clinical case to an instance of Disease. We want to note here, since we found ourselves thinking about this, that one disease, e.g. colon cancer, is itself a subclass of Disease, but also an instance of Disease (there may be many different types of colon cancer, but also colon cancer is a disease by itself). 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. In the future this decision may change.
has domain
Clinical Case Report c
has range
Disease c

is specification ofop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#isSpecificationOf

We may have certain hyerarchies that are not exactly in a relation of type subClassOf or partOf. These are usually determined by specification of more general concepts. We use this property to express such hyerarchies. One example (the only one for now in ExaMode) is the one of the Dysplasia.

has characteristics: transitive

has domain
Annotation c
has range
Annotation c

makerop back to ToC or Object Property ToC

IRI: http://xmlns.com/foaf/0.1/maker

An agent that made this thing.
has domain
thing c
has range
thing c

presence ofop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#presenceOf

This property is used to connect an outcome instance to a generic annotation which signals the presence of more information correlating the clinical case and which may not be directly pertinent to the disease but however still linked to it.
has domain
Outcome c
has range
Disease Annotation c

same asop back to ToC or Object Property ToC

IRI: http://www.w3.org/2002/07/owl#sameAs

has characteristics: symmetric

has domain
thing c
has range
thing c

test usedop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology#testUsed

the test being used in this report
has domain
Clinical Case Report c
has range
test c

Data Properties

has agedp back to ToC or Data Property ToC

IRI: https://w3id.org/examode/ontology#hasAge

Connects the Report to the age of the patient.
has domain
Patient c
has range
integer

has block numberdp back to ToC or Data Property ToC

IRI: https://w3id.org/examode/ontology#hasBlockNumber

The block number identifies the part of the image connected to the diagnosis (for Radbound). For AOC this property is not necessary. We use it to contain the "internal id".
has domain
Clinical Case Report c
has range
int

has imagedp back to ToC or Data Property ToC

IRI: https://w3id.org/examode/ontology#hasImage

Connects a clinical case report to the name of its corresponding image.
has domain
Patient c
has range
string

has textual diagnosisdp back to ToC or Data Property ToC

IRI: https://w3id.org/examode/ontology#hasDiagnosisText

Connects an instance of clinical case to its diagnosis, i.e. the text written by the medical doctor.
has domain
Clinical Case Report c
has range
string

has valuedp back to ToC or Data Property ToC

IRI: https://w3id.org/examode/ontology#hasValue

Connects a test annotation to its float value
has domain
Float Check Element c
has range
float

identifierdp back to ToC or Data Property ToC

IRI: http://purl.org/dc/elements/1.1/identifier

Property connecting a case to its id
has domain
Clinical Case Report c
has range
has ID

outcomedp back to ToC or Data Property ToC

IRI: https://w3id.org/examode/ontology#checkOutcome

Connects one annotation to its boolean value
has domain
Boolean Check Element c
has range
boolean

Annotation Properties

Alternative Definitionap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/NCIT_P325

has super-properties
Definition ap

annotated ruleap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#annotatedRule

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 impkemented 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.
has domain
thing c
has range
string

associated diseaseap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#AssociatedDisease

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.
has domain
thing c
has range
Disease c

associated keyword in diagnosisap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#associatedKeywordInDiagnosis

property to take notes (for reminding us/ help us define rule/ do some reasoning) about which keywords to look for in the Diagnosis field of a medical record
has domain
thing c
has range
string

associated keyword in Materialsap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#associatedKeywordInMateriali

Connects one class (a location or a intervention) to the keyword in the field 'Material' that, if found, indicates the presence of that class.
has domain
thing c
has range
string

broaderap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2004/02/skos/core#broader

Property used to build a hierarchy among the elements of an annotation. When one thing that can be an annotation to an outcome is inside a hierarchy, it is connected to its parent through this property.
has domain
thing c
has range
thing c

cardinalityap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2002/07/owl#cardinality

has domain
thing c
has range
non negative integer

Definitionap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#definition

Property representing the definition in the ontobee website. In later versions of the ontology we prefer rdfs:comment since it is more universally used.

External definitionap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/UBPROP_0000001

has super-properties
Definition ap

has broad synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym

A property to connect an entity to broad synonyms.
has super-properties
has synonym ap

has dysplasiaap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#hasDysplasia

This property connects an instance of outcome for a case of Colon cancer to a presence of Dysplasia (if it is present). Cardinality between 0 and 1.
has domain
Positive outcome c
has range
Colon Annotation c

has Exact Synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasExactSynonym

An alias in which the alias exhibits true synonymy.
has super-properties
has synonym ap
has domain
thing c
has range
string

has ontobee annotationap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#hasOntobeeAnnotation

A property to connect one entity to the annotations found for that entitiy in the corresponding page in Ontobee (http://www.ontobee.org/).
has domain
thing c
has range
string

has related synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym

has super-properties
has synonym ap

has Semantic Areaap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#hasSemanticArea

Connects one ontology class or Individual to the semantic area to which it belongs. For example, a Polyp is a diagnosis, therefore the Polyp belongs to the semantic area of Diagnosis.
has domain
thing c
has range
area annotation

has semantic typeap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/NCIT_P106

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.
has domain
thing c
has range
string

has SNOMED codeap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#hasSNOMEDCode

Use this property to annotate one entity with its corresponding SNOMED code.
has domain
thing c
has range
string

has synonymap back to ToC or Annotation Property ToC

IRI: http://www.geneontology.org/formats/oboInOwl#hasSynonym

has sub-properties
has Exact Synonym ap, has broad synonym ap, has related synonym ap
has domain
thing c
has range
string

has synonym labelap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#hasSynonymLabel

Use this property when you want to add a synonim label. You should not use this property when you want to add synonims that are going to be used in some algorithm or methodlogy. You should use hasSynonim instead.
has domain
thing c
has range
string

has UMLS codeap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#hasUMLS

This property connects an element to its UMLS code
has domain
thing c
has range
string
thing c

max cardinalityap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2002/07/owl#maxCardinality

has domain
thing c
has range
non negative integer

min cardinalityap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2002/07/owl#minCardinality

has domain
thing c
has range
non negative integer

partOfap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2002/07/owl#partOf

has domain
thing c
has range
thing c

Preferred Nameap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/NCIT_P108

A property representing the word or phrase that NCI uses by preference to refer to the concept.
has domain
thing c
has range
string

structure notesap back to ToC or Annotation Property ToC

IRI: http://purl.obolibrary.org/obo/UBPROP_0000010

has super-properties
Definition ap

taxon notesap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology#taxonNotes

An additional field that may be present in medical reports to describe entities taken from Ontobee's ontologies. You can consider it as an alternative definition.
has super-properties
Definition ap
has domain
thing c
has range
string

titleap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/elements/1.1/title

Named Individuals

Abdomenni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000916

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.
belongs to
Topography c

Anatomical Locationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C13717

Named locations of or within the body.
belongs to
Semantic Area c

Ascending Colonni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001156

Section of colon which is distal to the cecum and proximal to the transversecolon.
belongs to
Topography c

Bagni back to ToC or Named Individual ToC

IRI: http://www.w3.org/1999/02/22-rdf-syntax-ns#Bag

Caecumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001153

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.
belongs to
Topography c

Cannizzaro Hospitalni back to ToC or Named Individual ToC

IRI: https://w3id.org/examode/ontology#Cannizzaro_Hospital

Entity representing the Cannizzaro Hospital as producer of medical report
belongs to
Organization c

colon carcinomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0002032

A carcinoma that arises from epithelial cells of the colon [database_cross_reference: MONDO:DesignPattern]
belongs to
Disease c

Colon Dysplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4847

A morphologic finding indicating the presence of dysplastic glandular epithelial cells in the colonic mucosa. There is no evidence of invasion.
belongs to
Colon Annotation c

Colon, NOSni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001155

Colon, Not Otherwise Specified
belongs to
Topography c

Descending colonni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001158

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.
belongs to
Topography c

Diagnosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C15220

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.
belongs to
Semantic Area c

Disease or Disorderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0000001

A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism.

Dysplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4086

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.
belongs to
Disease Annotation c

female genderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C46110

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. [def-source: NCI]

General Entityni back to ToC or Named Individual ToC

IRI: https://w3id.org/examode/ontology#General

generisk enhed
belongs to
Semantic Area c

High Grade Dysplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C156083

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.
belongs to
Disease Annotation c
has facts
is specification of op Dysplasia

Ileumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002116

The portion of the small intestine that extends from the jejunum to the colon
belongs to
Topography c

Late onsetni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/app/browse/term/HP:0003584

A type of adult onset with onset of symptoms after the age of 60 years.
belongs to
Adult onset c

Left colonni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0008971

The distal portion of the colon; it develops embryonically from the hindgut and functions in the storage and elimination of waste.
belongs to
Topography c

maleni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C46109

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.

Middle age onsetni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/app/browse/term/HP:0003596

A type of adult onset with onset of symptoms at the age of 40 to 60 years.
belongs to
Adult onset c

Mild Colon Dysplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4848

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.
belongs to
Colon Annotation c
has facts
is specification of op Colon Dysplasia

Mild Dysplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C8362

A morphologic finding indicating the presence of mild cellular atypia associated with mild architectural changes in a tissue sample.
belongs to
Disease Annotation c
has facts
is specification of op Dysplasia

Moderate Colon Dysplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4849

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.
belongs to
Colon Annotation c
has facts
is specification of op Colon Dysplasia

Moderate Dysplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C8363

A morphologic finding indicating the presence of moderate cellular atypia associated with moderate architectural changes in a tissue sample.
belongs to
Disease Annotation c
has facts
is specification of op High Grade Dysplasia

Pre-Cancerous Dysplasiani back to ToC or Named Individual ToC

IRI: http://linkedlifedata.com/resource/umls/id/C0521191

belongs to
Disease Annotation c
has facts
is specification of op Dysplasia

Procedureni back to ToC or Named Individual ToC

IRI: https://w3id.org/examode/ontology#Procedure

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.
belongs to
Semantic Area c
has facts
is specification of op Severe Dysplasia

Radboud Universiteit Nijmegenni back to ToC or Named Individual ToC

IRI: http://dbpedia.org/page/Radboud_University_Nijmegen

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.
belongs to
Organization c

Rectal mucous membraneni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0003346

A mucosa that is part of a rectum
belongs to
Topography c

Rectosigmoid junctionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0036214

An anatomical junction that is between the sigmoid colon and rectum.
belongs to
Topography c

Rectum, NOSni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001052

Rectum, Not Otherwise Specified.
belongs to
Topography c

Right colonni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0008972

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.
belongs to
Topography c

Severe Colon Dysplasiani back to ToC or Named Individual ToC

IRI: https://w3id.org/examode/ontology#SevereColonDysplasia

belongs to
Colon Annotation c
has facts
is specification of op Colon Dysplasia

Severe Dysplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C8364

A morphologic finding indicating the presence of severe cellular atypia associated with severe architectural changes in a tissue sample.
belongs to
Disease Annotation c
has facts
is specification of op High Grade Dysplasia

Sigmoid colonni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001159

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.
belongs to
Topography c

Testni back to ToC or Named Individual ToC

IRI: https://w3id.org/examode/ontology#Test

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.
belongs to
Semantic Area c

Transverse Colonni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001157

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.
belongs to
Topography c

Young adult onsetni back to ToC or Named Individual ToC

IRI: https://hpo.jax.org/app/browse/term/HP:0011462

Onset of disease at the age of between 16 and 40 years.
belongs to
Adult onset c

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties
ni: Named Individuals

Acknowledgements back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.