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The ExaMode Ontology

Release May 2022

This version:
https://w3id.org/examode/ontology
Latest version:
https://w3id.org/examode/ontology
Revision:
0.9
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:
Visualize with WebVowl
Cite as:
Dennis Dosso and Gianmaria Silvello, 2022. The ExaMode Ontology, v0.9. https://w3id.org/examode/ontology

Ontology Specification Draft

Introduction back to ToC

One of the main objectives of the ExaMode project co-financed by the European Commission under the Horizon 2020 framework, is to provide automatic and semi-automatic methods to improve the efficiency and the effectiveness of the diagnoses in the pathology domain with the positive effect of reducing the pathologists' workload.

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

Colon disease
Schematic illustration showing the process of a polyp transformation into malignant cancer.

Computer-aided diagnosis tools today are mostly based on data-hungry prediction algorithms. In this context data is typically composed of annotated WSIs (Whole Slide Images) 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 to train 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 algorithms' consistent terminology.

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

Despite the existence of many medical ontologies focusing specifically on cancer, there is not an ontology comprehensively modeling all the diseases related to the cases mentioned above, their anatomical location, topography, and pathology laboratory process. The ExaMode ontology has been built upon many existing and widely-used ontologies and adds all the missing classes and relationships to make them seamlessly work together. Hence, the ExaMode ontology defines its classes and terms when they are not available in any other publicly well-known ontology.

In the following paragraphs, we better describe the four diseases covered by this ontology, their current scientific relevance, how they impact the well-being of the patients, and how the AI systems built using ExaMode can help prevent and help to diagnose them.

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. The number of cases is large and increasing, screenings are becoming more popular, and therefore the number of histopathological analyses is also increasing.

Uterine Cervix Carcinoma

Cervical cancer is the fourth most common cancer in women, and the eight most commonly occurring cancer overall. The estimated number of cervical cancer cases is predicted to increase by 27% until 2040, regardless of the age.

Nearly all cases of uterine cervix cancer are associated with human papillomavirus (HPV) [An et al., 2005; Kurman et al., 2014]. Although there are currently vaccines that can protect against high-cancer risk types of HPV, significantly reducing the risk of cervical cancer, these vaccines are not commonly available to low- and middle-income countries, where, according to the WHO, approximatively 90% of deaths from cervical cancer occur.

There is a great demand for histopathologists who can provide the diagnosis in these countries, and their current number is not sufficient, especially in remote locations. An algorithm-based software system that could support pathologists' work in such countries would thus be very beneficial.

Even though the screening tests for cervical cancer include mainly the Pap Smear Test (Papanicolaou test) and the colposcopic examination of the cervix, the ultimate diagnosis of ambiguous and suspicious cases requires standard histopathological assessments. Algorithmic solutions can thus also help facilitate the diagnosis of cervical cancer as a final part of the screening procedure.

Lung Cancer

According to the International Agency for Research on Cancer, the number of lung cancer in both sexes and at all ages is estimated to increase by 72% from 2018 to 2040. In general, lung cancer is the second most common cancer in both men and women - about 13% of all new cancers diagnoses are lung cancers. Moreover, lung cancer is the leading cause of cancer death among both men and women.

Taken into account the large number of deaths caused by lung cancer, this disease is perceived as a severe problem. However, some people with early-stage lung cancer can be successfully treated. Thus, it is essential to perform screenings to find cancerous lesions at an earlier stage, before they have spread, and when they are largely treatable. The most common type of screening for lung cancer is regular chest x-rays and low dose computed tomography scans (LDTC).

The screening is currently a recommended measure that should be taken to lower the risk of dying from cancer, whether it is lung cancer, colon, or cervical cancer (or others). Therefore, the histopathological diagnosis will become more and more often a final examination undertaken to unequivocally discriminant between cancerous and non-cancerous lesions found during the screening. As of today, there are no official recommendations for a screening program for lung cancer in Europe. However, the American Cancer Society recommends yearly lung cancer screening with LDCT for people with high lung cancer risk. These recommendations are the result of the National Lung Screening Trial, NLST, performed between 2002 and 2010 in the USA.

There are two main types of lung cancer: about 80-85% of lung cancers are non-small cell lung cancer (NSCLC), and about 10-15% are small cell lung cancer (SCLC). Therefore, the most common type of lung cancer is NSCLC, and its subtypes include squamous cell (epidermoid) carcinoma (25-30%), adenocarcinoma (40%), and large cell carcinoma (10-15%). The diagnosis between lung adenocarcinoma and squamous cell lung cancer is difficult, but it is important for further treatment. For the therapy, additional molecular tests are often needed, which cost money and require more samples to be taken during the biopsy. Therefore, an algorithm helping to distinguish between adenocarcinoma and squamous cell lung cancer could save time, biopsied tissues, and money.

Coeliac Disease

The list of the diseases included in the ExaMode priority list also includes a non-cancerous illness, namely the coeliac disease (CD). CD is an immune-mediated disease, with the chronic outcome and genetic predisposition to an intolerance to gluten and its proteins. It is a serious autoimmune, genetic disease where gluten ingestion leads to chronic inflammation, alterations, and damage in the small intestinal mucosa. It is estimated to affect 1 in 100 people worldwide and its prevalence has significantly increased over the past 20 years [Lohi et al., 2007]. The increase in the number of new cases is partly due to better diagnostics and screening of individuals at high risk for the disorder [Marsh, 1992]. However, it is estimated that there are far more undiagnosed cases of coeliac disease than undiagnosed ones [Fasano et al., 2003].

In general, routine screening for coeliac disease is not carried out. Testing is usually only recommended for people at a higher risk of developing this disease, such as those with a family history of the condition. In adults and children, the diagnosis of the coeliac disease relies mainly on the presence of positive coeliac disease-specific autoantibodies and further diagnostic small intestine biopsies [Fasano et al., 2001]. Intestinal biopsies are always necessary if the antibodies are low or negative, and if there are no signs/ symptoms of malabsorption. A second biopsy may be necessary if there is no clinical improvement after shifting to a strict gluten-free diet. Another biopsy is sometimes recommended in the follow-up period. Finding in the bioptic samples are characteristic, not specific, so it might be challenging for an unexperienced pathologist (and for an algorithm) to diagnose coeliac disease correctly.

Considering an increasing number of new cases of coeliac disease and an important role of small intestine biopsies in the diagnosis, the market size for the exploitation of product prototypes developed in ExaMode seems very promising.

Namespace declarations

Table 1: Namespaces used in the document
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oboInOwl<http://www.geneontology.org/formats/oboInOwl>
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>
uniprot<https://www.uniprot.org/uniprot>
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 ultimate aim of the analysis performed by a histopathologist is to complete the clinical report. A histopathological clinical report is a document that contains the results of a series of measurements and analyses performed on specific cells or tissues in order to:

  • Obtain a pathological-clinical diagnosis (disease/not disease);
  • lead to the best treatment options in case of a disease.

The goal of this document is to define an OWL 2 ontology for the ExaMode project whose overall aim 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 four cases considered in the ontology.

In the following sections we provide essential information required to understand the reports of each of the four cases. Subsequently, we describe the the ontology in its different components.

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 [Zauber et al., 2012]. 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 [Butte et al., 2012].

Uterine Cervix Cancer

The cervical biopsy (colposcopy) is a procedure made when previous tests provide evidence of precancerous/abnormal or neoplastic lesions in uterine cervix. The cervical tissue removed has to be analyzed by an expert pathologist to identify if the tumor lesions are present or not. In this case, the pathology report provides not only the diagnostic information, but it is also a prognostic tool for the patient’s treatment. Colposcopy with directed biopsy is currently the “gold standard” for the diagnosis of cervical precancer.

Thus, the aim of the histopathologist is to recognize and identify these precursor lesions well known as Cervical Intraepithelial Neoplasia (CIN), which displays proliferation of atypical basaloid cells [Lax, 2011]. Based on proliferation spread, WHO classification categorizes this dysplasia into three grades:

  1. CIN 1 (Mild Dysplasia)
  2. CIN 2 (Moderate Dysplasia)
  3. CIN 3 (Severe Dysplasia or Carcinoma in Situ)

CIN1 corresponds to Low-Grade Squamous Intraepithelial Lesion (LSIL), whereas CIN2-3 correspond to High-Grade Squamous Intraepithelial Lesion (HSIL). A strong association between these precursor lesions and HPV infection has been investigated, where LSIL is strongly associated with lowintermediate risk HPV, and HSIL is associated to high risk HPV. Therefore, the first feature that has to be identified and reported is the presence and the grade of dysplasia with possible HPV association.In the presence of cervical carcinoma we identify main microscopic features and measurements of uterine cervix colposcopy biopsy, which should be provided in the pathology report:

  1. Histologic Type<;/li>
  2. Histologic Grade;
  3. Stromal Invasion – provides information about cancer invasion into stromal tissue
  4. Margins - indicate a negative outcome;
  5. Lymphovascular Invasion – provides information about vascular/lymphatic vessel invasion.

Also, the immunohistochemistry (p16 and Ki-67 staining) assists in the histological differential diagnosis of precursors to reactive and metaplastic epithelium. For invasive cervical carcinoma, stage is the strongest prognostic factor [Lax, 2011]. Therefore, both the information retrieved from the sample stained with H&E, as well as from the sample stained immunohistochemically is important for the diagnosis and the management of a patient.

Lung Cancer

Lung cancer (LC) has a high mortality rate and is the most common cause of cancer death worldwide, accounting for 19.4% of cancer-related deaths [10]. The average overall survival rate for metastatic lung cancer is very low, whereas early stage has higher survival rates. The treatment of low-stage LC is complete surgical resection. Instead, for metastatic LC the surgical option is often impossible. An accurate diagnosis from lung biopsies targets the most correct prognostic and therapeutic management of the patients.

Moreover, a correct WHO classification is very important for metastatic tumors since there is therapeutic implication of distinguishing histological subtypes such as adenocarcinoma and squamous cell carcinoma. The identification of new therapeutic targets over the past decade resulted in an urgent need for a classification system for both non-resection specimens (particularly small biopsies) and cytology samples. For this reason an accurate and specific pathology report is important to establish diagnosis and patient’s treatment.

Starting from the analysis of lung biopsies, microscopic analysis section of the clinical report on lung cancer biopsy sample must provide the following information, with prognostic and predictive implications:

  1. Histologic Type;
  2. Histologic Grade;
  3. Spread Through Air Spaces (STAS) – information about the presence of micropapillary clusters, solid nests or single cells of tumor extending beyond the edge of the tumor into the air spaces of the surrounding lung parenchyma;
  4. Visceral Pleura Invasion
  5. Direct Invasion of Adjacent Structures;
  6. Margins – information about involvement of the tissue margins, indicating a negative outcome;
  7. Lymphovascular Invasion - provides information about vascular/lymphatic vessel invasion;
  8. Pathologic Stage Classification – based on the classification system proposed by the WHO;
  9. Extranodal Extension – indicates presence of metastasis.

Coeliac Disease

The list of the diseases included in the ExaMode priority list includes also a non-cancerous disease, namely the celiac disease (CD).

CD is an immune-mediated disease with chronic outcome and genetic predisposition to an intolerance to gluten and its proteins. This intolerance leads to abnormal immune response, followed by a chronic inflammation and alteration of the small intestinal mucosa. The diagnosis of this pathology is based on the description of the histopathological alterations of small intestine (after duodenal biopsy) by expert pathologists [GIPAD, 2011].

Microscopic analysis of small colon biopsy sample for celiac disease provides information about:

  1. Orientation of biopsy – indicates biopsy position on cellulose acetate filter and is very important for the diagnostic criteria;
  2. Normal intestinal mucosa description, includes information about: villi, enterocytes, intra-epithelial lymphocytic infiltrate and Glandular crypts. The absence or alteration of these structures must be reported;
  3. Pathological intestinal mucosa – including features which have to be reported and well described, with particular attention to increased intraepithelial T lymphocytes, decreased enterocyte height, crypt hyperplasia and villous atrophy;
  4. Pathologic Stage Classification – based on the classification system proposed by Marsh-Oberhuber and Corazza-Villanacci, in presence of intestinal mucosa alterations previously described.

The Ontology

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 subclasses, as of now, one for each disease. For instance, we can see that for the colon the Clinical Case Report class has a subclass called Colon Clinical Case Report. The instances of this class are all the instances of a colon cancer clinical record.
  2. Diagnosis: This area contains the classes related to the diagnosis which are extracted from the medical report. The main class is “Outcome”, 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, for example, the main locations are lung, bronchus, mediastinum and thoracic lymph node. Bronchus is specialized into more areas. This area also describes 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. The code “P-40” identifies a biopsy, but in the “Material” column we may find some keywords specifying that we are talking about a polypectomy.
  5. Annotation: this area is composed by sub-classes of the Annotation class. These classes represent additional information that can be attached to the Outcome of a report, which may or may not be found by doctors. For example, in the case of colon cancer, a positive outcome which finds a Polyp of the Colon may also present dysplasia which, in turn, may be present in different forms, such as Mild, Moderate or Severe.

In the following sections we discuss in detail the semantic areas, dividing them by disease when necessary.

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. Each clinical case is associated to one Disease, a general class which represent one disease. In this ontology, more specifically, a Disease is then instantiated in one of the four diseases considered in Examode, that is Cervical Cancer, Lung Cancer, Colon Carcinoma, and Coeliac Disease. The image above represents a case of Colon Clinical Case Report, thus the class is associated with the Colon Carcinoma disease through the isAboutDisease relationship. Each Clinical Case Report presents a unique identifier, obtained through the clinical cases, and a diagnosis, i.e. the text in the "Diagnosis" field found in the reports. Each medical report can also be related to an image file about the report. The block number refers to internal ids related to the reports or the images.

All medical reports are associated with a Patient (normally anonymized), since 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 also associated with the Organization that produced it. In EXAMODE there are two organizations: the Cannizzaro Hospital (AOEC) in Italy and the Radboud Medical Center in the Netherlands.

Diagnosis - Colon Cancer

Colon cancer diagnosis

The diagnosis is the central area of the EXAMODE ontology. Even though the structure of this semantic area differs from disease to disease, certain classes are shared. In particular, each medical report is connected to an Outcome. The Outcome class represents a general outcome that be positive (PositiveOutcome), negative (NegativeOutcome), without the evidence of malignancy (NoMalignancy), and inconclusive (InconclusiveOutcome) that, in turns, can be due to the presence of insufficient material (InsufficientMaterial) to reach a conclusion or to an unsatisfactory specimen for a diagnosis (SpecimenUnsatisfactory).

The positive outcome for the colon cancer is specialized into a taxonomy of states ranging from benign to malignant states.

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.

Therefore, when a patient is found positive, the diagnosis can be one among the subclasses of the class Positive Outcome in the figure above. When the outcome is an instance of the class Polyp of Colon, or one of its subclasses, it can be "annotated" with a form of Dysplasia. In this particular case, the ontology contains classes, such as Moderate Colon Dysplasia, that specifically refer to a dysplasia of the colon.

Classes such as Colon Dysplasia or High Grade Dysplasia are part of the Annotation conceptual area. These classes are used as additional information that may or may not be found through the diagnosis.

Diagnosis - Uterine Cervix Cancer

Colon cancer diagnosis
Structure of the diagnosis part of the ontology for the uterine cervix cancer.

The figure above represents the structure of the ontology for the Uterine Cervix Cancer. In the case of the Cervix, the outcome, indipendently of its type, may or may not be annotated with the presence of Human Papilloma Virus Infection. The possible positive outcome here include cervical polyp, cervicitis, one of the possible types of Cervical Intraepithaelial neoplasia (CIN), or one of the possible types of cervical carcinoma. We note that a case of cervix cancer does not present possibilities for annotations.

Diagnosis - Lung Cancer

Colon cancer diagnosis
Structure of the diagnosis part of the ontology for the lung cancer.

The figure above describe the structure of the diagnosis area for the lung cancer. In this case, the patient, when positive, may present Sarcoidosis, Lymphadenitis or Lung Carcinoma (and its possible subclasses). In the case of Lung Carcinoma, there may be the presence of Necrosis. We note that a case of lung cancer does not present possibilities for annotations.

Diagnosis - Coealiac Disese

Colon cancer diagnosis
Structure of the diagnosis and annotation part of the ontology for the coealiac disease

For the diagnosis of the coeliac disease, as described in the image above, the outcome is fairly simpler that the one of the other three diseases: if the patient is potivite, s/he can either have the coeliac disease or Duodenitis (an inflammation which does not necessarily imply coeliac disease). The outcome may be correlated with the information about the Immunohistochemical Test carried on the patient.

In the figure we also reported the annotations that may correlate a clinical case and that are derived from the information present in the "Diagnosis" field of the clinical reports. These information help to understand if the patient presents the disease, and they are specific to each report. We inferred a sub-classification of areas for this conceptual area.

  1. The first one, connected via the exa:presenceOf property to the report resource, regards the types of white blood cells that can be present (‘infiltrato’) in the tissue (e.g. in the lamina propria). There are two types of white cells: lymphocytes and granulocytes. Their presence does not imply the presence of the disease.
  2. The second set of information regards the characteristics of the samples found but that do not imply the presence of the disease. The RDF classes in this set are: (i) Brunner’s Gland Hyperplasia; (ii) edema; (iii) hyperaemia; (iv) intestinal fibrosis. These classes are connected to report resource via the exa:presenceOfCeliacAbnormality property.
  3. The third set of information is about the outcome of the analysis of the villi and comprehends three measures each one specified by a class. They are grouped in a RDF bag related to the celiac medical report via the exa:hasCeliacAnnotations property:
    1. the intraepithelial lymphocyte amount (in the AOEC reports it is specified as the amount of ‘linfociti intraepiteliali’) i.e. the lymphocytes to epithelial cells ratio. This is connected to the RDF bag through the exa:hasIEL property, where IEL stands for Intra Epithelial Lymphocytes. This amount is represented as a string because the values in the reports are expressed in heterogeneous ways.
    2. the duodenum villi length regards the status of the villi in the duodenum connected to the RDF bag via the exa:VilliStatus property. The length is represented as a string because the values are reported in words such as "normal", "reduced", etc. There is not an exhausted controlled vocabulary that can be used to represent the length.
    3. the villus crypt ratio which is the villi to crypt of Lieberkuhn ratio. This ratio is represented as a string because the values in the reports are expressed in heterogeneous ways.

Procedure, Location & Test - Colon Cancer

location and procedure

As shown above, the Examode Ontology presents other two main areas, here presented for the case of the colon cancer, i.e. the Procedure and the Anatomical Location. The former details the surgical procedure performed to collect the tissue; the latter represents an anatomical location, that can be both the area from where the tissue was taken, or where the disease is located in the patient.

In the case of the colon, the performed procedure can only be a surgical procedure which, in turn, can be a resection, a anastomosis, a hemiectomy or a form of Endoscopic Biopsy.

The contemplated anatomical location are the different areas of the colon. The class Colon, NOS (Not Otherwise Specified) describes a general area of the colon, and can be better specified by one of its subclasses. Other locations included in this area that are not in the Colon are the Rectum, the Abdomen and the Ileum.

Procedure & Location - Uterine Cervix Cancer

Colon cancer diagnosis
Structure of the anatomical location, procedure and test parts of the ontology for the cervix cancer.

In this case, the possible procedures include the cervical biopsy, an hysterectomy (and its specifications), and different types of surgical procedures, including conization and endocervical curettage.

The locations where the cancer can be located and the tissues be withdrawn include the uterus, the cervix epitelium and its different parts, and the cervical mucus.

Procedure, Location & Test - Lung Cancer

Lung cancer diagnosis
Structure of the anatomical location, procedure and test parts of the ontology for the lung cancer.

In the case of the lung cancer, the possible procedures include different types of Biopsies. It is also possible to perform different types of immunohistochemical tests, that can usually return a true/false result or a numerical one, in the case of the test on the proliferation marker protein Ki-67.

The locations for the lung cancer include the whole lung, the bronchus and their parts, the mediastinum and the Thoracic lymph nodes.

Procedure & Location - Coeliac Disease

Coealiac disease diagnosis
Structure of the anatomical location, procedure and test parts of the ontology for the coealiac disease.

In the case of the coeliac disease the surgical procedure can be a form of biopsy, performed in different locations (a biopsy in the greater curvature, a biopsy in the pyloric antrum and one in the duodenum). As such, these cases are naturally connected to their locations.

The anatomical locations for the coeliac disease include the Duodenum and its different parts, where the disease is located. Since the biopsy that allows to diagnose the disease can also be performed in the pyloric antrum and the greater curvature, they are included among the locations.

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

Abdomenc back to ToC or Class ToC

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

has super-classes
Anatomical entity c
has members
Abdomen ni
is also defined as
named individual

Acanthosisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35265

Diffuse hypertrophy of the stratum spinosum layer of the epidermis.
has super-classes
Positive Outcome c, positive outcome c

Adenocarcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2852

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]
has super-classes
Positive Outcome c
has sub-classes
Colon Adenocarcinoma c, Metastatic Adenocarcinoma c

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, Serrated 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 sub-classes
Late onset c, Middle age onset c, Young adult onset c

Anastomosisc back to ToC or Class ToC

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

has super-classes
Surgical procedure c
has members
Anastomosis ni
is also defined as
named individual

Ascending Colonc back to ToC or Class ToC

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

is equivalent to
Right colon c
has super-classes
Colon, NOS c
has members
Ascending Colon ni
is same as
Right colon c
is also defined as
named individual

Atrophic vulvac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0001932

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.
has super-classes
Positive Outcome c, positive outcome c

Biopsyc back to ToC or Class ToC

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

has super-classes
Intervention or Procedure c
has sub-classes
Endoscopic Biopsy c
has members
Biopsy ni
is also defined as
named individual

Biopsy of Colonc back to ToC or Class ToC

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

has super-classes
Endoscopic Biopsy c
has sub-classes
Colonoscopic polypectomy c, Polypectomy c
has members
Biopsy of Colon ni
is also defined as
named individual

Biopsy of Duodenumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51683

has super-classes
Endoscopic Biopsy c
has members
Biopsy of Duodenum ni
is also defined as
named individual

Biopsy of the Greater Curvaturec back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/GreaterCurvatureBiopsy

has super-classes
Endoscopic Biopsy c
has members
Biopsy of the Greater Curvature ni
is also defined as
named individual

Biopsy of the pyloric antrumc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/AntrumPyloriBiopsy

has super-classes
Endoscopic Biopsy c
has members
Biopsy of the pyloric antrum ni
is also defined as
named individual

Bronchial Biopsyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51782

has super-classes
Endoscopic Biopsy c
has members
Bronchial Biopsy ni
is also defined as
named individual

Bronchusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002185

has super-classes
Anatomical entity c
has sub-classes
Lobar Bronchus c, Main Bronchus c
has members
Bronchus ni
is also defined as
named individual

Caecumc back to ToC or Class ToC

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

has super-classes
Colon, NOS c
has members
Caecum ni
is also defined as
named individual

Celiac Clinical Case Reportc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/CeliacClinicalCaseReport

Class representing all the celiac disease clinical cases.
has super-classes
Clinical Case Report c
is disjoint with
Cervix Clinical Case Report c, Colon Clinical Case Report c, Lung Clinical Case Report c

cervical adenocarcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0005153

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.
has super-classes
cervical carcinoma c
has sub-classes
cervical adenocarcinoma in situ c

cervical adenocarcinoma in situc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4520

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.
has super-classes
cervical adenocarcinoma c

Cervical biopsyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51628

has super-classes
Endoscopic Biopsy c
has members
Cervical biopsy ni
is also defined as
named individual

cervical carcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0005131

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.
is equivalent to
Cervical Carcinoma c
has super-classes
Positive Outcome c, positive outcome c
has sub-classes
Cervical Squamous Cell Carcinoma c, cervical adenocarcinoma c, squamous intraepithelial neoplasia c

Cervical Carcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C9039

A carcinoma arising from either the exocervical squamous epithelium or the endocervical glandular epithelium. The major histologic types of cervical carcinoma are squamous cell carcinoma and adenocarcinoma. [Definition Source: NCI]
has super-classes
positive outcome c

cervical intraepithelial neoplasiac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0022394

Cervical intraepithelial neoplasia (CIN), also known as cervical dysplasia, is the abnormal growth of cells on the surface of the cervix that could potentially lead to cervical cancer. More specifically, CIN refers to the potentially precancerous transformation of cells of the cervix. CIN most commonly occurs at the squamocolumnar junction of the cervix, a transitional area between the squamous epithelium of the vagina and the columnar epithelium of the endocervix. It can also occur in vaginal walls and vulvar epithelium. CIN is graded on a 1-3 scale, with 3 being the most abnormal (see classification section below). Human papilloma virus (HPV) infection is necessary for the development of CIN, but not all with this infection develop cervical cancer.[3] Many women with HPV infection never develop CIN or cervical cancer. Typically, HPV resolves on its own. However, those with an HPV infection that lasts more than one or two years have a higher risk of developing a higher grade of CIN. Like other intraepithelial neoplasias, CIN is not cancer and is usually curable.[3] Most cases of CIN either remain stable or are eliminated by the person's immune system without need for intervention. However, a small percentage of cases progress to cervical cancer, typically cervical squamous cell carcinoma (SCC), if left untreated.
is equivalent to
Cervical Intraepithelial Neoplasia c
has super-classes
Positive Outcome c, positive outcome c
has sub-classes
Low Grade Cervical Squamous Intraepithelial Neoplasia c, cervical intraepithelial neoplasia grade 2/3 c

Cervical Intraepithelial Neoplasiac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/OMIT_0018522

has super-classes
Positive Outcome c, positive outcome c

cervical intraepithelial neoplasia grade 2/3c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0006137

A neoplastic process in the cervix characterized by morphologic features of both moderate and severe intraepithelial neoplasia.
has super-classes
cervical intraepithelial neoplasia c
has sub-classes
Cervical Squamous Intraepithelial Neoplasia 2 c, squamous carcinoma in situ c

cervical mucusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000316

has super-classes
Anatomical entity c
has members
cervical mucus ni
is also defined as
named individual

cervical polypc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0000751

A polyp that arises from the surface of the cervix.
has super-classes
Positive Outcome c, positive outcome c

cervical squamo-columnar junctionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0012253

has super-classes
cervix epithelium c
has members
cervical squamo-columnar junction ni
is also defined as
named individual

Cervical Squamous Cell Carcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0006143

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.
has super-classes
cervical carcinoma c

Cervical Squamous Intraepithelial Neoplasia 2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C40198

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.
has super-classes
cervical intraepithelial neoplasia grade 2/3 c

Cervicitisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26716

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. [def-source: NCI]
has super-classes
Positive Outcome c, positive outcome c
has sub-classes
Chronic Cervicitis c

Cervix Clinical Case Reportc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/CervixClinicalCaseReport

Class representing the clinical cases about cervix cancer.
has super-classes
Clinical Case Report c
is disjoint with
Celiac Clinical Case Report c, Colon Clinical Case Report c, Lung Clinical Case Report c

cervix epitheliumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0004801

has super-classes
Anatomical entity c
has sub-classes
Simple Epithelium c, cervical squamo-columnar junction c, cervix glandular epithelium c, cervix squamous epithelium c, exocervical epithelium c, pavement epithelium c
has members
cervix epithelium ni
is also defined as
named individual

cervix glandular epitheliumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0012250

has super-classes
cervix epithelium c
has members
cervix glandular epithelium ni
is also defined as
named individual

cervix squamous epitheliumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0006922

has super-classes
cervix epithelium c
has members
cervix squamous epithelium ni
is also defined as
named individual

check elementc back to ToC or Class ToC

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

has super-classes
Immunohistochemical Test c

Chronic Cervicitisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C27057

Chronic inflammation of the cervix.
has super-classes
Cervicitis c

clear cell adenocarcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0005004

A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid.
has super-classes
lung adenocarcinoma 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
Celiac Clinical Case Report c, Cervix Clinical Case Report c, Colon Clinical Case Report c, Lung Clinical Case Report c
is in domain of
has Internal Identifier dp, has image dp, has outcome op, has slide op, has textual diagnosis dp, identifier dp, is about disease op, maker 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.
is equivalent to
Colitis c
has super-classes
Positive Outcome c

Colitisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C26723

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.
is equivalent to
Colon Adenocarcinoma c
has super-classes
Positive Outcome c

Colon Adenocarcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4349

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]
Is defined by
https://w3id.org/examode/ontology/
has super-classes
Adenocarcinoma c, Positive Outcome c
has sub-classes
Metastatic Colon Adenocarcinoma c

Colon carcinomac back to ToC or Class ToC

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

A carcinoma that arises from epithelial cells of the colon [database_cross_reference: MONDO:DesignPattern]
has super-classes
Disease or Disorder c
has members
colon carcinoma 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
is disjoint with
Celiac Clinical Case Report c, Cervix Clinical Case Report c, Lung Clinical Case Report c

Colon Dysplasiac back to ToC or Class ToC

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

has super-classes
Dysplasia c
has sub-classes
Mild Colon Dysplasia c, Moderate Colon Dysplasia c, Severe Colon Dysplasia c
has members
Colon Dysplasia ni
is also defined as
named individual

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

Colon, NOSc back to ToC or Class ToC

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

has super-classes
Colorectum c
has sub-classes
Ascending Colon c, Caecum c, Descending colon c, Left colon c, Rectal mucous membrane c, Rectosigmoid junction c, Right colon c, Sigmoid colon c, Transverse Colon c
has members
Colon, NOS ni
is also defined as
named individual

Colonoscopic polypectomyc back to ToC or Class ToC

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

has super-classes
Biopsy of Colon c
has members
Colonoscopic polypectomy ni
is also defined as
named individual

Colorectumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0012652

has super-classes
Anatomical entity c
has sub-classes
Colon, NOS c, Rectum, NOS c
has members
Colorectum ni
is also defined as
named individual

Condylomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2960

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.
has super-classes
Positive Outcome c, positive outcome c

Conizationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C15402

has super-classes
Surgical procedure c
has members
Conization ni
is also defined as
named individual

Descending colonc back to ToC or Class ToC

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

has super-classes
Colon, NOS c
has members
Descending colon ni
is also defined as
named individual

Diseasec back to ToC or Class ToC

IRI: http://identifiers.org/snomedct/64572001

Disease - Clinical disease AND/OR syndrome - Disorder - Syndrome - Disease AND/OR syndrome present - Clinical disease AND/OR syndrome present - Disorders - Diseases - Disease (disorder)
is equivalent to
Disease c
Disease_DOID c
Disease or Disorder c
Disease_NCIT c

Diseasec back to ToC or Class ToC

IRI: http://linkedlifedata.com/resource/umls/id/C0012634

is equivalent to
Disease_DOID c
Disease or Disorder c
Disease_NCIT c

Disease or Disorderc back to ToC or Class 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.
is equivalent to
Disease_NCIT c
has sub-classes
Colon carcinoma c
is in range of
is about disease op

Disease_DOIDc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/DOID_4

A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. [dc:type: http://purl.obolibrary.org/obo/ECO_0007645][dc:type: http://purl.obolibrary.org/obo/ECO_0007645][database_cross_reference: url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/][database_cross_reference: url:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/]
is equivalent to
Disease or Disorder c
Disease_NCIT c

Disease_NCITc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2991

Any abnormal condition of the body or mind that causes discomfort, dysfunction, or distress to the person affected or those in contact with the person. The term is often used broadly to include injuries, disabilities, syndromes, symptoms, deviant behaviors, and atypical variations of structure and function. [Definition Source: NCI]

Duodenitisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0004627

A form of inflammation
has super-classes
Positive Outcome c

Dyskeratosisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C62570

Dyskeratosis is abnormal keratinization occurring prematurely within individual cells or groups of cells below the stratum granulosum.[1] Dyskeratosis congenita is congenital disease characterized by reticular skin pigmentation, nail degeneration, and leukoplakia on the mucous membranes associated with short telomeres.
has super-classes
Positive Outcome c, positive outcome c

Dysplasiac back to ToC or Class ToC

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

has super-classes
Finding c
has sub-classes
Colon Dysplasia c, High Grade Dysplasia c, Mild Dysplasia c, Pre-Cancerous Dysplasia c
is in range of
has dysplasia op
has members
Dysplasia ni
is also defined as
named individual

Elastofibromac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4245

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.
has super-classes
Positive Outcome c

Endocervical curettagec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C15403

has super-classes
Surgical procedure c
has members
Endocervical curettage ni
is also defined as
named individual

Endometriumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C12313

has super-classes
Mucosa c
has members
Endometrium ni
is same as
endometrium
is also defined as
named individual

Endoscopic Biopsyc back to ToC or Class ToC

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

has super-classes
Biopsy c
has sub-classes
Biopsy of Colon c, Biopsy of Duodenum c, Biopsy of the Greater Curvature c, Biopsy of the pyloric antrum c, Bronchial Biopsy c, Cervical biopsy c, Lung Biopsy c
has members
Endoscopic Biopsy ni
is also defined as
named individual

exocervical epitheliumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0012251

has super-classes
cervix epithelium c
has members
exocervical epithelium ni
is also defined as
named individual

Findingc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3367

A meaningful interpretation of data or observations resulting from planned evaluations. Compare to conclusion, hypothesis. See also general observation class, intervention, event.
has sub-classes
Dysplasia c

Focal Acute Inflammationc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C82967

An inflammatory process characterized by the localized collection of polymorphonuclear neutrophils.
has super-classes
Positive Outcome c, positive outcome c

Genderc back to ToC or Class ToC

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

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]
is equivalent to
{ male gender , female gender }
is in range of
has gender op
has members
female gender ni, male gender ni

Granulomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3064

An inflammation AE that shows localized nodular inflammation found in tissues.
is equivalent to
Granuloma c
has super-classes
Positive Outcome c

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

has super-classes
Surgical procedure c
has members
Hemicolectomy ni
is also defined as
named individual

High Grade Dysplasiac back to ToC or Class ToC

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

has super-classes
Dysplasia c
has sub-classes
Moderate Dysplasia c, Severe Dysplasia c
has members
High Grade Dysplasia ni
is also defined as
named individual

Hyperkeratosisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C35541

Hypertrophy of the outermost layer of the epidermis. It may be caused by physical or chemical irritants, irradiation, infection, or neoplastic processes.
has super-classes
Positive Outcome c, positive outcome c

Hysterectomyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C15256

has super-classes
Intervention or Procedure c
has sub-classes
Radical Hysterectomy c, Total Abdominal Hysterectomy c
is also defined as
named individual

Ileumc back to ToC or Class ToC

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

has super-classes
Anatomical entity c
has members
Ileum ni
is also defined as
named individual

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
has members
c d3 ni

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

Institutionc back to ToC or Class ToC

IRI: https://dbpedia.org/ontology/institution

has members
ExaMode Consortium ni

Lamina Propriac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C32918

has super-classes
Mucosa c
has members
Lamina Propria ni
is also defined as
named individual

Late onsetc back to ToC or Class ToC

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

has super-classes
Adult onset c
is also defined as
named individual

Left colonc back to ToC or Class ToC

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

has super-classes
Colon, NOS c
has members
Left colon ni
is also defined as
named individual

Left inferior lobar bronchusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/FMA_7432

has super-classes
Lobar Bronchus c
has members
Left inferior lobar bronchus ni
is also defined as
named individual

Left Main Bronchusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C32968

has super-classes
Main Bronchus c
has members
Left Main Bronchus ni
is also defined as
named individual

Left superior lobar bronchusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/FMA_7423

has super-classes
Lobar Bronchus c
has members
Left superior lobar bronchus ni
is also defined as
named individual

Lobar Bronchusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C32998

has super-classes
Bronchus c
has sub-classes
Left inferior lobar bronchus c, Left superior lobar bronchus c, Right inferior lobar bronchus c, Right superior lobar bronchus c
has members
Lobar Bronchus ni
is also defined as
named individual

Loop Electrosurgical Excisionc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51760

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]
has super-classes
Intervention or Procedure c

Low Grade Cervical Squamous Intraepithelial Neoplasiac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C40196

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.
has super-classes
cervical intraepithelial neoplasia c

Lungc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002048

has super-classes
Anatomical entity c
has members
Lung ni
is also defined as
named individual

lung adenocarcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0005061

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.
has super-classes
non-small cell lung carcinoma c
has sub-classes
clear cell adenocarcinoma c, metastatic neoplasm c

Lung Biopsyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51748

has super-classes
Endoscopic Biopsy c
has members
Lung Biopsy ni
is also defined as
named individual

lung carcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0005138

A carcinoma that arises from epithelial cells of the lung
has super-classes
Positive Outcome c
has sub-classes
non-small cell lung carcinoma c, small cell lung carcinoma c

Lung Clinical Case Reportc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/LungClinicalCaseReport

Class representing all lung cancer cases.
has super-classes
Clinical Case Report c
is disjoint with
Celiac Clinical Case Report c, Cervix Clinical Case Report c, Colon Clinical Case Report c

lung large cell carcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0003050

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.
has super-classes
non-small cell lung carcinoma c

Lymphadenitisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0002052

Acute or chronic inflammation of one or more lymph nodes. It is usually caused by an infectious process.
has super-classes
Positive Outcome c

Main Bronchusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C12284

has super-classes
Bronchus c
has sub-classes
Left Main Bronchus c, Right Main Bronchus c
has members
Main Bronchus ni
is also defined as
named individual

Malignant Lung Neoplasmc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C7377

A primary or metastatic malignant neoplasm involving the lung.
has super-classes
non-small cell lung carcinoma c

Mediastinumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0003728

has super-classes
Anatomical entity c
has members
Mediastinum ni
is also defined as
named individual

Metaplasiac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3236

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 super-classes
Positive Outcome c, positive outcome c
has sub-classes
Squamous Metaplasia 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
Adenocarcinoma c, Positive Outcome c
has sub-classes
Metastatic Colon Adenocarcinoma c

Metastatic Colon Adenocarcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C160819

has super-classes
Colon Adenocarcinoma c, Metastatic Adenocarcinoma c

metastatic neoplasmc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0024883

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.
has super-classes
lung adenocarcinoma c

Middle age onsetc back to ToC or Class ToC

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

has super-classes
Adult onset c
has members
Middle age onset ni
is also defined as
named individual

Mild Colon Dysplasiac back to ToC or Class ToC

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

has super-classes
Colon Dysplasia c, Mild Dysplasia c
has members
Mild Colon Dysplasia ni
is also defined as
named individual

Mild Dysplasiac back to ToC or Class ToC

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

has super-classes
Dysplasia c
has sub-classes
Mild Colon Dysplasia c
has members
Mild Colon Dysplasia ni, Mild Dysplasia ni
is also defined as
named individual

Moderate Colon Dysplasiac back to ToC or Class ToC

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

has super-classes
Colon Dysplasia c, Moderate Dysplasia c
has members
Moderate Colon Dysplasia ni
is also defined as
named individual

Moderate Dysplasiac back to ToC or Class ToC

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

has super-classes
High Grade Dysplasia c
has sub-classes
Moderate Colon Dysplasia c
has members
Moderate Colon Dysplasia ni, Moderate Dysplasia ni
is also defined as
named individual

Mucosac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C13166

has super-classes
Anatomical entity c
has sub-classes
Endometrium c, Lamina Propria c
has members
Mucosa ni
is also defined as
named individual

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

No present of malignancy for one of the diseases included in the ExaMode ontology.
has super-classes
Outcome c

non-small cell lung carcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0005233

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.
has super-classes
lung carcinoma c
has sub-classes
Malignant Lung Neoplasm c, lung adenocarcinoma c, lung large cell carcinoma c, non-small cell squamous lung carcinoma c

non-small cell squamous lung carcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0056806

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.
has super-classes
non-small cell lung carcinoma 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 sub-classes
Adult onset c

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 University 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 test 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

pavement epitheliumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/BTO_0002073

has super-classes
cervix epithelium c
has members
pavement epithelium ni
is also defined as
named individual

Pleurac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000977

has super-classes
Anatomical entity c
has members
Pleura ni
is also defined as
named individual

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
is in domain of
has dysplasia op

Polypectomyc back to ToC or Class ToC

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

is equivalent to
Colonoscopic polypectomy c
has super-classes
Biopsy of Colon c
has members
Polypectomy ni
is also defined as
named individual

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
Acanthosis c, Adenocarcinoma c, Atrophic vulva c, Cervical Intraepithelial Neoplasia c, Cervicitis c, Colitis c, Colitis c, Colon Adenocarcinoma c, Colon Adenocarcinoma c, Condyloma c, Duodenitis c, Dyskeratosis c, Elastofibroma c, Focal Acute Inflammation c, Granuloma c, Granuloma c, Hyperkeratosis c, Lymphadenitis c, Metaplasia c, Metastatic Adenocarcinoma c, Polyp of Colon c, Positive to Celiac Disease c, Ulcer c, cervical carcinoma c, cervical intraepithelial neoplasia c, cervical polyp c, lung carcinoma c, sarcoidosis c

Positive to Celiac Diseasec back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/PositiveToCeliacDisease

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 a Individual in this ontology, and it is not good to have entities that are both Individuals and General Classes in the same ontology.
has super-classes
Positive Outcome c

Pre-Cancerous Dysplasiac back to ToC or Class ToC

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

has super-classes
Dysplasia c
has members
Pre-Cancerous Dysplasia ni
is also defined as
named individual

pulmonary lymph nodec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0035764

has super-classes
Anatomical entity c
has members
pulmonary lymph node ni
is also defined as
named individual

Radical Hysterectomyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C94470

has super-classes
Hysterectomy c
is also defined as
named individual

Rectal mucous membranec back to ToC or Class ToC

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

has super-classes
Colon, NOS c
has members
Rectal mucous membrane ni
is also defined as
named individual

Rectosigmoid junctionc back to ToC or Class ToC

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

has super-classes
Colon, NOS c
has members
Rectosigmoid junction ni
is also defined as
named individual

Rectum, NOSc back to ToC or Class ToC

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

has super-classes
Colorectum c
is also defined as
named individual

Resectionc back to ToC or Class ToC

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

has super-classes
Surgical procedure c
has members
Resection ni
is also defined as
named individual

Right colonc back to ToC or Class ToC

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

has super-classes
Colon, NOS c
has members
Right colon ni
is same as
Ascending Colon c
is also defined as
named individual

Right inferior lobar bronchusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/FMA_7404

has super-classes
Lobar Bronchus c
has members
Right inferior lobar bronchus ni
is also defined as
named individual

Right Main Bronchusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C33486

has super-classes
Main Bronchus c
has members
Right Main Bronchus ni
is also defined as
named individual

Right superior lobar bronchusc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/FMA_7397

has super-classes
Lobar Bronchus c
has members
Right superior lobar bronchus ni
is also defined as
named individual

sarcoidosisc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0019338

Sarcoidosis is a multisystemic disorder of unknown cause characterized by the formation of immune granulomas in involved organs.
has super-classes
Positive Outcome c

Serrated Adenomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C38458

An adenoma that arises from the large intestine and the appendix. It is characterized by prominent serration of the glands.
has super-classes
Adenoma c

Severe Colon Dysplasiac back to ToC or Class ToC

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

has super-classes
Colon Dysplasia c, Severe Dysplasia c
has members
Severe Colon Dysplasia ni
is also defined as
named individual

Severe Dysplasiac back to ToC or Class ToC

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

has super-classes
High Grade Dysplasia c
has sub-classes
Severe Colon Dysplasia c
has members
Severe Colon Dysplasia ni, Severe Dysplasia ni
is also defined as
named individual

Sigmoid colonc back to ToC or Class ToC

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

has super-classes
Colon, NOS c
has members
Sigmoid colon ni
is also defined as
named individual

Simple Epitheliumc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C33554

has super-classes
cervix epithelium c
has members
Simple Epithelium ni
is also defined as
named individual

Slide Devicec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C50178

A flat rectangular piece of glass on which specimens can be mounted for microscopic study.
is in domain of
has slide diagnosis dp, has slide id dp
is in range of
has slide op

small cell lung carcinomac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0008433

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.
has super-classes
lung carcinoma c

squamous carcinoma in situc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0004693

A malignant epithelial neoplasm confined to the squamous epithelium, without invasion of the underlying tissues.
is equivalent to
squamous intraepithelial neoplasia c
has super-classes
cervical intraepithelial neoplasia grade 2/3 c

squamous intraepithelial neoplasiac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0042487

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.
has super-classes
cervical carcinoma c

Squamous Metaplasiac back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3237

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.
has super-classes
Metaplasia c

Surgical procedurec back to ToC or Class ToC

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

has super-classes
Intervention or Procedure c
has sub-classes
Anastomosis c, Conization c, Endocervical curettage 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

Thoracic lymph nodec back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0007644

has super-classes
Anatomical entity c
has members
Thoracic lymph node ni
is also defined as
named individual

Total Abdominal Hysterectomyc back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51695

has super-classes
Hysterectomy c
is also defined as
named individual

Transverse Colonc back to ToC or Class ToC

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

has super-classes
Colon, NOS c
has members
Transverse Colon ni
is also defined as
named individual

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

uterus, NOSc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/old/uterusNOS

has super-classes
Anatomical entity c
has members
uterus, NOS ni
is also defined as
named individual

Young adult onsetc back to ToC or Class ToC

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

has super-classes
Adult onset c
is also defined as
named individual

Object Properties

has age onsetop back to ToC or Object Property ToC

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

has domain
Patient 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 characteristics: symmetric

has domain
Patient c
has range
Clinical Case Report c

has dysplasiaop back to ToC or Object Property ToC

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

Connects an instance of Outcome (more precisely, Polyp of Colon) to a named individual of type Dysplasia. Cardinality between 0 and 1.
has domain
Polyp of Colon c
has range
Dysplasia 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 characteristics: functional

has domain
Patient c
has range
Gender c

has interventionop back to ToC or Object Property ToC

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

has domain
Outcome c
has range
Intervention or Procedure c

has interventionop back to ToC or Object Property ToC

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

has range
Intervention or Procedure c

has locationop back to ToC or Object Property ToC

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

has domain
Surgical procedure c or Outcome c
has range
Anatomical entity 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 characteristics: functional

has domain
Clinical Case Report c
has range
Outcome c

has slideop back to ToC or Object Property ToC

IRI: https://w3id.org/examode/ontology/hasSlide

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.

has characteristics: symmetric

has domain
Clinical Case Report c
has range
Slide Device c

has testop back to ToC or Object Property ToC

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

has domain
Outcome c

has testop back to ToC or Object Property ToC

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

has domain
Outcome c
has range
Test c

intervention has locationop back to ToC or Object Property ToC

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

has domain
Intervention or Procedure c

intervention has locationop back to ToC or Object Property ToC

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

has domain
Intervention or Procedure c

is about diseaseop back to ToC or Object Property ToC

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

represent the relationship between a general Report and and a Disease

has characteristics: functional

has domain
Clinical Case Report c
has range
Disease or Disorder c

makerop back to ToC or Object Property ToC

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

An agent that made this thing.
Is defined by
http://xmlns.com/foaf/0.1/
Term status
stable
has domain
Clinical Case Report c
has range
agent or Organization 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 some 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
necrosis c or Metastasis c

relatedop back to ToC or Object Property ToC

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

Is defined by
https://w3id.org/examode/ontology/

has characteristics: symmetric

has domain
concept c
has range
concept c

test usedop back to ToC or Object Property ToC

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

has range
Test c

Data Properties

ha numero di bloccodp 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 AOEC this property is not necessary. We use it to contain the "internal id".

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 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 (the name of the image, e.g. the name of the file).

has characteristics: functional

has domain
Clinical Case Report c
has range
string

has Internal Identifierdp back to ToC or Data Property ToC

IRI: https://w3id.org/examode/ontology/hasInternalIdentifier

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.
has domain
Clinical Case Report c
has range
any u r i

has slide diagnosisdp back to ToC or Data Property ToC

IRI: https://w3id.org/examode/ontology/hasSlideDiagnosis

Each slide can be associated to its own diagnosis.
has domain
Slide Device c
has range
string

has slide iddp back to ToC or Data Property ToC

IRI: https://w3id.org/examode/ontology/hasSlideId

Each slide is associated to its own id
has domain
Slide Device 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 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 range
float

identifierdp back to ToC or Data Property ToC

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

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.
has domain
Clinical Case Report c
has range
string

outcomedp back to ToC or Data Property ToC

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

Connects one annotation to its boolean value.
has range
boolean

Annotation Properties

annotated ruleap back to ToC or Annotation Property ToC

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

annotated ruleap back to ToC or Annotation Property ToC

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

associated diseaseap back to ToC or Annotation Property ToC

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

associated diseaseap back to ToC or Annotation Property ToC

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

associated keyword in diagnosisap back to ToC or Annotation Property ToC

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

associated keyword in diagnosisap back to ToC or Annotation Property ToC

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

associated keyword in materialiap back to ToC or Annotation Property ToC

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

cardinalityap back to ToC or Annotation Property ToC

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

creatorap back to ToC or Annotation Property ToC

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

definitionap back to ToC or Annotation Property ToC

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

definitionap back to ToC or Annotation Property ToC

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

descriptionap back to ToC or Annotation Property ToC

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

has broad synonymap back to ToC or Annotation Property ToC

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

has exact synonymap back to ToC or Annotation Property ToC

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

has ontobee annotationap back to ToC or Annotation Property ToC

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

has related synonymap back to ToC or Annotation Property ToC

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

has s n o m e d codeap back to ToC or Annotation Property ToC

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

has s n o m e d codeap back to ToC or Annotation Property ToC

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

has semantic areaap back to ToC or Annotation Property ToC

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

has semantic areaap back to ToC or Annotation Property ToC

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

has u m l sap back to ToC or Annotation Property ToC

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

has u m l sap back to ToC or Annotation Property ToC

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

internal notesap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology/internalNotes

internal notesap back to ToC or Annotation Property ToC

IRI: https://w3id.org/examode/ontology/old/internalNotes

n c i t p106ap back to ToC or Annotation Property ToC

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

n c i t p325ap back to ToC or Annotation Property ToC

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

nameap back to ToC or Annotation Property ToC

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

part ofap back to ToC or Annotation Property ToC

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

rightsap back to ToC or Annotation Property ToC

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

taxon notesap back to ToC or Annotation Property ToC

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

taxon notesap back to ToC or Annotation Property ToC

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

titleap back to ToC or Annotation Property ToC

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

u b p r o p 0000001ap back to ToC or Annotation Property ToC

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

u b p r o p 0000010ap back to ToC or Annotation Property ToC

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

Named Individuals

Abdomenni back to ToC or Named Individual ToC

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

belongs to
Topography c
Abdomen c
is also defined as
class

Anastomosisni back to ToC or Named Individual ToC

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

belongs to
Anastomosis c
is also defined as
class

Anatomical entityni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001062

belongs to
Anatomical entity c
concept c
has facts
related op Topography
is also defined as
class

Ascending Colonni back to ToC or Named Individual ToC

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

belongs to
Topography c
Ascending Colon c
concept c
is same as
Right colon
is also defined as
class

Biopsyni back to ToC or Named Individual ToC

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

belongs to
Biopsy c
is also defined as
class

Biopsy of Colonni back to ToC or Named Individual ToC

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

belongs to
Biopsy of Colon c
is also defined as
class

Biopsy of Duodenumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51683

belongs to
Biopsy of Duodenum c
is also defined as
class

Biopsy of the Greater Curvatureni back to ToC or Named Individual ToC

IRI: https://w3id.org/examode/ontology/GreaterCurvatureBiopsy

belongs to
Biopsy of the Greater Curvature c
is also defined as
class

Biopsy of the pyloric antrumni back to ToC or Named Individual ToC

IRI: https://w3id.org/examode/ontology/AntrumPyloriBiopsy

belongs to
Biopsy of the pyloric antrum c
is also defined as
class

Bronchial Biopsyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51782

belongs to
Bronchial Biopsy c
is also defined as
class

Bronchusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002185

belongs to
Topography c
Bronchus c
concept c
is also defined as
class

c d3ni back to ToC or Named Individual ToC

IRI: https://w3id.org/examode/ontology/old/CD3

belongs to
Immunohistochemical Test c

Caecumni back to ToC or Named Individual ToC

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

belongs to
Topography c
Caecum c
concept c
is also defined as
class

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

celiac diseaseni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0005130

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.
belongs to
disease c

Cervical biopsyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51628

belongs to
Cervical biopsy c
is also defined as
class

cervical cancerni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0002974

A primary or metastatic malignant neoplasm involving the cervix.
belongs to
disease c

cervical mucusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000316

belongs to
Topography c
cervical mucus c
concept c
is also defined as
class

cervical squamo-columnar junctionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0012253

belongs to
Topography c
cervical squamo-columnar junction c
concept scheme
is also defined as
class

cervix epitheliumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0004801

belongs to
Topography c
cervix epithelium c
concept c
is also defined as
class

cervix glandular epitheliumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0012250

belongs to
Topography c
cervix glandular epithelium c
concept c
is also defined as
class

cervix squamous epitheliumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0006922

belongs to
Topography c
cervix squamous epithelium c
concept c
is also defined as
class

colon carcinomani back to ToC or Named Individual ToC

IRI: https://w3id.org/examode/ontology/colon_carcinoma

belongs to
Colon carcinoma c
concept c

Colon Dysplasiani back to ToC or Named Individual ToC

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

belongs to
Colon Dysplasia c
concept c
is also defined as
class

Colon, NOSni back to ToC or Named Individual ToC

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

belongs to
Topography c
Colon, NOS c
is also defined as
class

Colonoscopic polypectomyni back to ToC or Named Individual ToC

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

belongs to
Colonoscopic polypectomy c
has facts
related op Polypectomy
is also defined as
class

Colorectumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0012652

belongs to
Topography c
Colorectum c
concept c
is also defined as
class

Conizationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C15402

belongs to
Conization c
is also defined as
class

Dennis Dossoni back to ToC or Named Individual ToC

IRI: https://orcid.org/0000-0001-7307-4607

belongs to
person c

Descending colonni back to ToC or Named Individual ToC

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

belongs to
Topography c
Descending colon c
concept c
is also defined as
class

Dysplasiani back to ToC or Named Individual ToC

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

belongs to
Dysplasia c
concept c
is also defined as
class

Endocervical curettageni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C15403

belongs to
Endocervical curettage c
is also defined as
class

Endometriumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C12313

belongs to
Endometrium c
Topography c
concept c
is same as
endometrium
is also defined as
class

endometriumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001295

The glandular mucous membrane lining of the uterine cavity that is hormonally responsive during the estrous/menstrual cycle and during pregnancy
is same as
Endometrium

Endoscopic Biopsyni back to ToC or Named Individual ToC

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

belongs to
Endoscopic Biopsy c
is also defined as
class

ExaMode Consortiumni back to ToC or Named Individual ToC

IRI: https://www.examode.eu/

belongs to
Institution c

exocervical epitheliumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0012251

belongs to
Topography c
exocervical epithelium c
concept c
is also defined as
class

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]
belongs to
Gender c

Gianmaria Silvelloni back to ToC or Named Individual ToC

IRI: https://orcid.org/0000-0003-4970-4554

belongs to
person c

Greater curvature of stomachni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001164

The greater curvature of the stomach is directed mainly forward, and is four or five times as long as the lesser curvature.
belongs to
Topography c
concept c

Hemicolectomyni back to ToC or Named Individual ToC

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

belongs to
Hemicolectomy c
is also defined as
class

High Grade Dysplasiani back to ToC or Named Individual ToC

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

belongs to
High Grade Dysplasia c
concept c
is also defined as
class

Human Papilloma Virus Infectionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0005161

A cervix disease may present or not the human papilloma virus.
belongs to
cervix annotation c

Ileumni back to ToC or Named Individual ToC

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

belongs to
Topography c
Ileum c
concept c
is also defined as
class

Intervention or Procedureni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C25218

belongs to
Intervention or Procedure c
concept c
is also defined as
class

Koilocytotic Squamous Cellni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C36808

belongs to
cervix annotation c

Lamina Propriani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C32918

belongs to
Lamina Propria c
Topography c
concept c
is also defined as
class

Late onsetni back to ToC or Named Individual ToC

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

belongs to
concept c
is also defined as
class

Left colonni back to ToC or Named Individual ToC

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

belongs to
Topography c
Left colon c
concept c
is also defined as
class

Left inferior lobar bronchusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/FMA_7432

belongs to
Left inferior lobar bronchus c
Topography c
concept c
is also defined as
class

Left Main Bronchusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C32968

belongs to
Left Main Bronchus c
Topography c
concept c
is also defined as
class

Left superior lobar bronchusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/FMA_7423

belongs to
Left superior lobar bronchus c
Topography c
concept c
is also defined as
class

Lobar Bronchusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C32998

belongs to
Lobar Bronchus c
Topography c
concept c
is also defined as
class

Lungni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002048

belongs to
Topography c
Lung c
concept c
is also defined as
class

Lung Biopsyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51748

belongs to
Lung Biopsy c
is also defined as
class

lung cancerni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MONDO_0008903

A malignant neoplasm involving the lung.
belongs to
disease c

Main Bronchusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C12284

belongs to
Main Bronchus c
Topography c
concept c
is also defined as
class

male genderni 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.
belongs to
Gender c

Mediastinumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0003728

belongs to
Topography c
Mediastinum c
concept c
is also defined as
class

Melissa Anne Haendelni back to ToC or Named Individual ToC

IRI: http://orcid.org/0000-0001-9114-8737

belongs to
person c

Metastasisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C19151

belongs to
Metastasis c
is also defined as
class

Middle age onsetni back to ToC or Named Individual ToC

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

belongs to
concept c
Middle age onset c
is also defined as
class

Mild Colon Dysplasiani back to ToC or Named Individual ToC

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

belongs to
Mild Colon Dysplasia c
Mild Dysplasia c
concept c
is also defined as
class

Mild Dysplasiani back to ToC or Named Individual ToC

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

belongs to
Mild Dysplasia c
concept c
is also defined as
class

Moderate Colon Dysplasiani back to ToC or Named Individual ToC

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

belongs to
Moderate Colon Dysplasia c
Moderate Dysplasia c
concept c
is also defined as
class

Moderate Dysplasiani back to ToC or Named Individual ToC

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

belongs to
Moderate Dysplasia c
concept c
is also defined as
class

Mucosani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C13166

belongs to
Mucosa c
Topography c
concept c
is also defined as
class

necrosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/GO_0070265

belongs to
necrosis c
is also defined as
class

pavement epitheliumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/BTO_0002073

belongs to
pavement epithelium c
Topography c
concept c
is also defined as
class

Pleurani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000977

belongs to
Topography c
Pleura c
concept c
is also defined as
class

Polypectomyni back to ToC or Named Individual ToC

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

belongs to
Polypectomy c
is also defined as
class

Pre-Cancerous Dysplasiani back to ToC or Named Individual ToC

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

belongs to
Pre-Cancerous Dysplasia c
concept c
is also defined as
class

pulmonary lymph nodeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0035764

belongs to
Topography c
pulmonary lymph node c
concept c
is also defined as
class

Radboud University 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
concept c
Organization c

Rectal mucous membraneni back to ToC or Named Individual ToC

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

belongs to
Topography c
Rectal mucous membrane c
concept c
is also defined as
class

Rectosigmoid junctionni back to ToC or Named Individual ToC

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

belongs to
Topography c
Rectosigmoid junction c
concept c
is also defined as
class

Rectum, NOSni back to ToC or Named Individual ToC

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

belongs to
Topography c
concept c
is also defined as
class

Resectionni back to ToC or Named Individual ToC

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

belongs to
Resection c
is also defined as
class

Right colonni back to ToC or Named Individual ToC

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

belongs to
Topography c
Right colon c
concept c
is same as
Ascending Colon
is also defined as
class

Right inferior lobar bronchusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/FMA_7404

belongs to
Right inferior lobar bronchus c
Topography c
concept c
is also defined as
class

Right Main Bronchusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C33486

belongs to
Right Main Bronchus c
Topography c
concept c
is also defined as
class

Right superior lobar bronchusni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/FMA_7397

belongs to
Right superior lobar bronchus c
Topography c
concept c
is also defined as
class

Severe Colon Dysplasiani back to ToC or Named Individual ToC

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

belongs to
Severe Dysplasia c
concept c
Severe Colon Dysplasia c
is also defined as
class

Severe Dysplasiani back to ToC or Named Individual ToC

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

belongs to
Severe Dysplasia c
concept c
is also defined as
class

Sigmoid colonni back to ToC or Named Individual ToC

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

belongs to
Topography c
Sigmoid colon c
concept c
is also defined as
class

Simple Epitheliumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C33554

belongs to
Simple Epithelium c
Topography c
concept c
has facts
related op pavement epithelium
is also defined as
class

Thoracic lymph nodeni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0007644

belongs to
Topography c
Thoracic lymph node c
concept c
is also defined as
class

Topographyni back to ToC or Named Individual ToC

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

belongs to
Topography c
concept c
has facts
related op Anatomical entity
is also defined as
class

Total Abdominal Hysterectomyni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51695

belongs to
concept c
is also defined as
class

Transverse Colonni back to ToC or Named Individual ToC

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

belongs to
Topography c
Transverse Colon c
concept c
is also defined as
class

uterus, NOSni back to ToC or Named Individual ToC

IRI: https://w3id.org/examode/ontology/old/uterusNOS

belongs to
Topography c
concept c
uterus, NOS c
is also defined as
class

Young adult onsetni back to ToC or Named Individual ToC

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

belongs to
concept c
is also defined as
class

Legend back to ToC

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

References back to ToC

[An et al., 2005] H.J. An, K.R. Kim, I.S. Kim, D.W. Kim, M.H. Park, I.A. Park, K.S. Suh, E.J. Seo, S.H. Sung, J.H. Sohn, H.K. Yoon, E.D. Chang, H.I. Cho, J.Y. Han, S.R. Hong and Ahn GH (2005). Prevalence of human papillomavirus DNA in various histological subtypes of cervical adenocarcinoma: a population-based study. Mod Pathol 18(4):528-534.

[Kurman et al., 2014] R.J. Kurman, M.L. Carcangiu, C.S. Herrington and R.H. Young (2014). WHO classification of tumours of the female reproductive organs. IARC press, Lyon.

[Lohi et al., 2007] S. Lohi, K. Mustalahti, K. Kaukinen, K. Laurila, P. Collin, H. Rissanen, et al. Increasing prevalence of coeliac disease over time. Aliment Pharmacol Ther 2007;26(9):1217–25.

[Marsh et al., 1992] M.N. Marsh. Gluten, major histocompatibility complex, and the small intestine. A molecular and immunobiologic approach to the spectrum of gluten sensitivity (“celiac sprue”). Gastroenterology 1992;102(1):330–54.

[Fasano et al., 2003] A. Fasano, I. Berti, T. Gerarduzzi, T. Not, R.B. Colletti, S. Drago, et al. Prevalence of celiac disease in at-risk and not-at-risk groups in the United States: a large multicenter study. Arch Intern Med 2003;163(3):286–92.

[Fasano et al., 2001] A. Fasano, C. Catassi. Current approaches to diagnosis and treatment of celiac disease: an evolving spectrum. Gastroenterology 2001;120(3):636–51.

[Zauber et al., 2011] A.G. Zauber, S.J. Winawer, M.J. O’Brien, et al. Colonoscopic polypectomy and long-term prevention of colorectalcancer deaths. 2011. N Engl J Med 2012;366:687-96.

[Butte et al., 2012] J.M. Butte, P. Tang, M. Gonen, et al. Rate of residual disease after complete endoscopic resection of malignant colonic polyp. Dis Colon Rectum 2012;55:122-7.

[Lax, 2011] S. Lax. Histopathology of cervical precursor lesions and cancer. Acta Dermatovenerol Alp Pannonica Adriat. 2011 Sep;20(3):125-33.

[Travis et al., 2011] W.D. Travis, E. Brambilla and M. Noguchi et al. International Association for the Study of Lung cancer/American Thoracic Society/European Respiratory Society international multidisciplinary classification of lung adenocarcinoma. J Thorac Oncol 2011, 6:244-285.

[GIPAD, 2011] Coeliac Disease: The Histology Report (2011) On behalf of the “Gruppo Italiano Patologi Apparato Digerente (GIPAD)” and of the “Società Italiana di Anatomia Patologica e Citopatologia Diagnostica”/International Academy of Pathology, Italian division (SIAPEC/IAP)

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.