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The ExaMode Ontology

Release October 2020

This version:
https://w3id.org/examode/ontology
Latest version:
https://w3id.org/examode/ontology
Revision:
0.4
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, 2020. The ExaMode Ontology, v0.4. 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>
0-1<http://xmlns.com/foaf/0.1>
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

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

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 members
Late onset ni, Middle age onset ni, Young adult onset ni

Anastomosisc back to ToC or Class ToC

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

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

Annotationc back to ToC or Class ToC

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

A general class to represent all the kionds of annnotations that may be needed in an ExaMode report.
has sub-classes
Disease Annotation c, Onset c, Semantic Area c
is in domain of
is specification of op
is in range of
is specification of op

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

Biopsyc back to ToC or Class ToC

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

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

Biopsy of Colonc back to ToC or Class ToC

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

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

Biopsy of Duodenumc back to ToC or Class ToC

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

Removal of tissue from the duodenum for microscopic examination, using an endoscope.
has super-classes
Endoscopic Biopsy c

Biopsy of the Greater Curvaturec back to ToC or Class ToC

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

Biopsy produced in the greater curvature area, a region in the stomach.
has super-classes
Endoscopic Biopsy c

Biopsy of the pyloric antrumc back to ToC or Class ToC

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

Biopsy executed in the pyloric antrum, a form of endoscopic biopsy.
has super-classes
Endoscopic Biopsy c

Boolean Check Elementc back to ToC or Class ToC

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

A set of checks controlled on an Immunohistochemical test that can only have a boolean result (positive - negative).
has super-classes
Check Element c
has sub-classes
Chromogranin-A c, Cytokeratin 5/6 c, Desmocollin-3 c, Immunoprecipitation c, Keratin, type I cytoskeletal 19 c, Keratin, type I cytoskeletal 20 c, Keratin, type II cytoskeletal 7 c, Keratin-associated protein 5-9 c, Napsin A c, Neprilysin c, Pulmonary surfactant-associated protein B c, Receptor-type tyrosine-protein phosphatase C c, Synaptophysin c, TTF1 Human c, Tumor Protein 63 Isoform 2 c, Vimentin c, cytokeratin 34bE12 c, endonuclease P40 c
is in domain of
outcome dp

Bronchial Biopsyc back to ToC or Class ToC

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

Removal of tissue from the bronchus for microscopic examination.
has super-classes
Endoscopic Biopsy c

Celiac Abnormalityc back to ToC or Class ToC

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

Class for abnormalities that can be found in a patient looking for the celiac disease. Some of these include the Edema, Hyperemia, Intestinal fibrosis, Brunner's Gland Hyperplasia.
has super-classes
Disease Annotation c
is in range of
presence of celiac abnormality op
has members
Brunner's Gland Hyperplasia ni, Edema ni, hyperemia ni, intestinal fibrosis ni

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 in domain of
has celiac annotation op, presence of celiac element op
is disjoint with
Cervix Clinical Case Report c, Colon Clinical Case Report c, Lung Clinical Case Report c

Celiac Disease Annotationc back to ToC or Class ToC

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

A subclass containing Annotations only for the celiac disease.
has super-classes
Disease Annotation c
is in range of
presence of celiac element op
has members
granulocyte ni, lymphocyte ni

Celiac Disease Annotation Bagc back to ToC or Class ToC

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

has super-classes
Disease Annotation c
is in domain of
has IEL dp, has villi to crypt ratio dp, villi status dp
is in range of
has celiac annotation op
is same as
Bag
is also defined as
named individual

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

Removal of tissue from the cervix for microscopic examination.
has super-classes
Endoscopic Biopsy c, Intervention or Procedure c

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.
has super-classes
Positive Outcome c
has sub-classes
Cervical Squamous Cell Carcinoma c, cervical adenocarcinoma c, squamous intraepithelial neoplasia 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
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

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 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

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
has sub-classes
Chronic Cervicitis c

Cervix Annotationc back to ToC or Class ToC

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

A class that is intended to be a set for information that may or may not be found in a cervix case. Instances of this class are 'things' that may be found (or not) in a patient with cervix cancer. For example, the Human Papilloma Virus. The HPV is an instance of this class and every time we annotate a case with HPV we use that instance, of type this class, without every time creating a HPV instance.
has super-classes
Disease Annotation c
is in range of
Koylocite Detected op, detected human papilloma virus op
has members
Human Papilloma Virus Infection ni, Koilocytotic Squamous Cell ni

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

Check Elementc back to ToC or Class ToC

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

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

Chromogranin-Ac back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P10645

Pancreastatin: Strongly inhibits glucose induced insulin release from the pancreas. Catestatin: Inhibits catecholamine release from chromaffin cells and noradrenergic neurons by acting as a non-competitive nicotinic cholinergic antagonist (PubMed:15326220). Displays antibacterial activity against Gram-positive bacteria S.aureus and M.luteus, and Gram-negative bacteria E.coli and P.aeruginosa (PubMed:15723172 and PubMed:24723458). Can induce mast cell migration, degranulation and production of cytokines and chemokines (PubMed:21214543). Acts as a potent scavenger of free radicals in vitro (PubMed:24723458). May play a role in the regulation of cardiac function and blood pressure (PubMed:18541522). Serpinin: Regulates granule biogenesis in endocrine cells by up-regulating the transcription of protease nexin 1 (SERPINE2) via a cAMP-PKA-SP1 pathway. This leads to inhibition of granule protein degradation in the Golgi complex which in turn promotes granule formation. Miscellaneous Binds calcium with a low-affinity.
has super-classes
Boolean Check Element 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, ha numero di blocco dp, has image dp, has outcome op, has slide op, has textual diagnosis dp, identifier dp, is about disease op, maker op, presence of celiac abnormality op, test used op
is in range of
has Clinical Case Report op

Colitisc back to ToC or Class ToC

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

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

Colon Adenocarcinomac back to ToC or Class ToC

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

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

Colon Annotationc back to ToC or Class ToC

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

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

Colon Clinical Case Reportc back to ToC or Class ToC

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

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

Colon Hyperplastic Polypc back to ToC or Class ToC

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

A serrated polypoid lesion that arises in the colon. It is usually found in the distant colon and it rarely produces symptoms. This group includes goblet cell rich, mucin poor, and microvesicular hyperplastic polyps.
has super-classes
Polyp of Colon c

Colon Inflammatory Polypc back to ToC or Class ToC

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

A non-neoplastic polypoid lesion in the colon. It may arise in a background of inflammatory bowel disease or colitis. It is characterized by the presence of a distorted epithelium, inflammation, and fibrosis.
has super-classes
Polyp of Colon c

Colon Tubular Adenomac back to ToC or Class ToC

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

A usually polypoid neoplasm that arises from the glandular epithelium of the colonic mucosa. It is characterized by a tubular architectural pattern. The neoplastic glandular cells have dysplastic features.
has super-classes
Adenoma c

Colon Tubulovillous Adenomac back to ToC or Class ToC

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

A neoplasm that arises from the glandular epithelium of the colonic mucosa. It is characterized by tubular and villous architectural patterns. The neoplastic glandular cells have dysplastic features
has super-classes
Adenoma c

Colon Villous Adenomac back to ToC or Class ToC

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

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

Colonoscopic polypectomyc back to ToC or Class ToC

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

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

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

Conizationc back to ToC or Class ToC

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

Surgical removal of a cone-shaped portion of tissue from the uterine cervix.
has super-classes
Biopsy c, Surgical Procedure c

cytokeratin 34bE12c back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/C0908867

One of the tests that can be made for the lung cancer.
has super-classes
Boolean Check Element c

Cytokeratin 5/6c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C80497

An immunohistochemical diagnostic test utilizing an antibody to detect both cytokeratin 5 and 6 in tissues.
has super-classes
Boolean Check Element c

Desmocollin-3c back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/Q14574

Component of intercellular desmosome junctions. Involved in the interaction of plaque proteins and intermediate filaments mediating cell-cell adhesion. May contribute to epidermal cell positioning (stratification) by mediating differential adhesiveness between cells that express different isoforms.
has super-classes
Boolean Check Element c

Diseasec back to ToC or Class ToC

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

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

Disease Annotationc back to ToC or Class ToC

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

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

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 c

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

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

A procedure in which the mucous membrane of the cervical canal is scraped using a curette.
has super-classes
Surgical Procedure c

endonuclease P40c back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/C0909069

One of the tests that can be performed to check lung cancer.
has super-classes
Boolean Check Element c

Endoscopic Biopsyc back to ToC or Class ToC

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

The removal of tissue specimens or fluid from the living body for microscopic examination, performed to establish a diagnosis. In the case of an endoscopic biopsy, an endoscope is used to obtain the sample.
has super-classes
Biopsy c
has sub-classes
Biopsy of Colon c, 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

Float Check Elementc back to ToC or Class ToC

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

A set of checks that can be performed on a Immunohistochemical Test that present a float as output value.
has super-classes
Check Element c
has sub-classes
Proliferation marker protein Ki-67 c
is in domain of
has value dp

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

genderc back to ToC or Class ToC

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

We defined our gender as one of two: male or female.
is equivalent to
{ male gender , female gender }
is in range of
has gender op

Granulomac back to ToC or Class ToC

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

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

Hemicolectomyc back to ToC or Class ToC

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

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

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

Hysterectomyc back to ToC or Class ToC

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

A surgical procedure to remove the uterine body (partial hysterectomy) or the uterine body and cervix (total hysterectomy).
has super-classes
Intervention or Procedure c
has sub-classes
Radical Hysterectomy c, Total Abdominal Hysterectomy c

Immunohistochemical Testc back to ToC or Class ToC

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

A diagnostic test in which an antibody is used to link a cellular antigen specifically to a stain that can be seen with a microscope.
has super-classes
test c
has sub-classes
Check Element c
has members
CD3 ni

Immunoprecipitationc back to ToC or Class ToC

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

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

Inconclusive Outcomec back to ToC or Class ToC

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

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

Insufficient Materialc back to ToC or Class ToC

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

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

Keratin, type I cytoskeletal 19c back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P08727

Involved in the organization of myofibers. Together with KRT8, helps to link the contractile apparatus to dystrophin at the costameres of striated muscle.
has super-classes
Boolean Check Element c

Keratin, type I cytoskeletal 20c back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P35900

Plays a significant role in maintaining keratin filament organization in intestinal epithelia. When phosphorylated, plays a role in the secretion of mucin in the small intestine.
has super-classes
Boolean Check Element c

Keratin, type II cytoskeletal 7c back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P08729

Blocks interferon-dependent interphase and stimulates DNA synthesis in cells. Involved in the translational regulation of the human papillomavirus type 16 E7 mRNA (HPV16 E7).
has super-classes
Boolean Check Element c

Keratin-associated protein 5-9c back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P26371

In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated protein (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high-sulfur and high-glycine-tyrosine keratins.
has super-classes
Boolean Check Element c

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.
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

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 Annotationc back to ToC or Class ToC

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

This class, as the others, is used to instantiate annotations over clinical cases.
has super-classes
Disease Annotation c
has members
Metastasis ni, necrosis ni

Lung Biopsyc back to ToC or Class ToC

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

The removal of a small piece of lung tissue to be checked by a pathologist for cancer or other diseases. The tissue may be removed using a bronchoscope (a thin, lighted, tube-like instrument that is inserted through the trachea and into the lung). It may also be removed using a fine needle inserted through the chest wall, by surgery guided by a video camera inserted through the chest wall, or by an open biopsy. In an open biopsy, a doctor makes an incision between the ribs, removes a sample of lung tissue, and closes the wound with stitches.
has super-classes
Endoscopic Biopsy c

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

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

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
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
Positive Outcome 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

Napsin Ac back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/O96009

May be involved in processing of pneumocyte surfactant precursors.
has super-classes
Boolean Check Element c

Negative Resultc back to ToC or Class ToC

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

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

Neprilysinc back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P08473

Thermolysin-like specificity, but is almost confined on acting on polypeptides of up to 30 amino acids (PubMed:15283675, PubMed:8168535). Biologically important in the destruction of opioid peptides such as Met- and Leu-enkephalins by cleavage of a Gly-Phe bond (PubMed:17101991). Able to cleave angiotensin-1, angiotensin-2 and angiotensin 1-9 (PubMed:15283675). Involved in the degradation of atrial natriuretic factor (ANF) (PubMed:2531377, PubMed:2972276). Displays UV-inducible elastase activity toward skin preelastic and elastic fibers (PubMed:20876573).
has super-classes
Boolean Check Element 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 super-classes
Annotation c
has sub-classes
Adult onset c
is in range of
has age onset op

Organizationc back to ToC or Class ToC

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

An organization that, in the context of the ExaMode program, provides clinical case records. It is usually an Hospital (e.g. AOEC or Radbound).
Is defined by
https://www.examode.dei.unipd.it/ontology/
is in range of
maker op
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, Koylocite Detected op, detected human papilloma virus op, has location op, has test op, presence of op
is in range of
has outcome op

Patientc back to ToC or Class ToC

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

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

Polyp of Colonc back to ToC or Class ToC

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

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

Polypectomyc back to ToC or Class ToC

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

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

Positive Outcomec back to ToC or Class ToC

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

Positive Outcome, i.e., something has been found in the patient. This is the higher class for the positive outcome.
has super-classes
Outcome c
has sub-classes
Acanthosis c, Atrophic vulva c, Cervical Intraepithelial Neoplasia c, Cervicitis c, Colitis c, Colon Adenocarcinoma c, Condyloma c, Duodenitis c, Dyskeratosis c, Elastofibroma c, Focal Acute Inflammation 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
is in domain of
has dysplasia

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

Proliferation marker protein Ki-67c back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P46013

Required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly (PubMed:27362226). Associates with the surface of the mitotic chromosome, the perichromosomal layer, and covers a substantial fraction of the chromosome surface (PubMed:27362226). Prevents chromosomes from collapsing into a single chromatin mass by forming a steric and electrostatic charge barrier: the protein has a high net electrical charge and acts as a surfactant, dispersing chromosomes and enabling independent chromosome motility (PubMed:27362226). Binds DNA, with a preference for supercoiled DNA and AT-rich DNA (PubMed:10878551). Does not contribute to the internal structure of mitotic chromosomes (By similarity). May play a role in chromatin organization (PubMed:24867636). It is however unclear whether it plays a direct role in chromatin organization or whether it is an indirect consequence of its function in maintaining mitotic chromosomes dispersed (Probable).
has super-classes
Float Check Element c

Pulmonary surfactant-associated protein Bc back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P07988

Pulmonary surfactant-associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces. SP-B increases the collapse pressure of palmitic acid to nearly 70 millinewtons per meter.
has super-classes
Boolean Check Element c

Radical Hysterectomyc back to ToC or Class ToC

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

Radical hysterectomy refers to the excision of the uterus en bloc with the parametrium (ie, round, broad, cardinal, and uterosacral ligaments) and the upper one-third to one-half of the vagina. The surgeon usually also performs a bilateral pelvic lymph node dissection. The procedure requires a thorough knowledge of pelvic anatomy, meticulous attention to sharp dissection, and careful technique to allow dissection of the ureters and mobilization of both bladder and rectum from the vagina. Particular care must be taken with the vasculature of the pelvic side walls and the venous plexuses at the lateral corners of the bladder to avoid excessive blood loss. Removal of the ovaries and fallopian tubes is not part of a radical hysterectomy; they may be preserved if clinically appropriate.
has super-classes
Hysterectomy c

Receptor-type tyrosine-protein phosphatase Cc back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P08575

Protein tyrosine-protein phosphatase required for T-cell activation through the antigen receptor. Acts as a positive regulator of T-cell coactivation upon binding to DPP4. The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one. Upon T-cell activation, recruits and dephosphorylates SKAP1 and FYN. Dephosphorylates LYN, and thereby modulates LYN activity (By similarity). (Microbial infection) Acts as a receptor for human cytomegalovirus protein UL11 and mediates binding of UL11 to T-cells, leading to reduced induction of tyrosine phosphorylation of multiple signaling proteins upon T-cell receptor stimulation and impaired T-cell proliferation.
has super-classes
Boolean Check Element c

Resectionc back to ToC or Class ToC

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

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

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

Semantic Areac back to ToC or Class ToC

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

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

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

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

Specimen Unsatisfactory for Diagnosisc back to ToC or Class ToC

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

has super-classes
Inconclusive Outcome 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

A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery.
has super-classes
Intervention or Procedure c
has sub-classes
Anastomosis c, Biopsy c, Conization c, Endocervical curettage c, Hemicolectomy c, Resection c

Synaptophysinc back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P08247

Possibly involved in structural functions as organizing other membrane components or in targeting the vesicles to the plasma membrane. Involved in the regulation of short-term and long-term synaptic plasticity.
has super-classes
Boolean Check Element 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

Total Abdominal Hysterectomyc back to ToC or Class ToC

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

Surgical removal of all of the uterus, via an abdominal approach.
has super-classes
Hysterectomy c

TTF1 Humanc back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/Q15361

Multifunctional nucleolar protein that terminates ribosomal gene transcription, mediates replication fork arrest and regulates RNA polymerase I transcription on chromatin. Plays a dual role in rDNA regulation, being involved in both activation and silencing of rDNA transcription. Interaction with BAZ2A/TIP5 recovers DNA-binding activity.
has super-classes
Boolean Check Element c

Tumor Protein 63 Isoform 2c back to ToC or Class ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C128298

Tumor protein 63 isoform 2 (586 aa, ; 66 kDa) is encoded by the human TP63 gene. This protein plays a role in the mediation of both transcription and skin development.
has super-classes
Boolean Check Element c

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

Vimentinc back to ToC or Class ToC

IRI: https://www.uniprot.org/uniprot/P08670

Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.
has super-classes
Boolean Check Element c

Object Properties

detected human papilloma virusop back to ToC or Object Property ToC

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

If this property is present, it signals the presence of a human papilloma virus in the outcome.
has domain
Outcome c
has range
Cervix Annotation c

has age onsetop back to ToC or Object Property ToC

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

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

has broaderop back to ToC or Object Property ToC

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

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

has celiac annotationop back to ToC or Object Property ToC

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

Connects a celiac clinical case to an annotation bag created to contain information about thecase.

has Clinical Case Reportop back to ToC or Object Property ToC

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

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

has genderop back to ToC or Object Property ToC

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

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

Has Interventionop back to ToC or Object Property ToC

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

A report is associated to an intervention (or procedure) that was performed to the patient to obtain the tissue used to study the presence (or absence) of the disease.
has domain
Outcome c
has range
Intervention or Procedure c

has locationop back to ToC or Object Property ToC

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

A clinical case record has a location where it is positioned. This property connects an instance of clinical case report (of whatever type) to a location, a member of the class topology. NB: since we are connecting a report to a location, we asked ourselves if a Topography location can be considered member of itself. For now, we are saying yes, that a subclass of topography is itself a topography, and can be directly referenced by this property.
has domain
Outcome c
has range
Topography c

has outcomeop back to ToC or Object Property ToC

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

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

has Relatedop back to ToC or Object Property ToC

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

The property skos:related is used to assert an associative link between two SKOS concepts. skos:related enables the representation of associative (non-hierarchical) links, such as the relationship between one type of event and a category of entities which typically participate in it. Another use for skos:related is between two categories where neither is more general or more specific. Note that skos:related enables the representation of associative (non-hierarchical) links, which can also be used to represent part-whole links that are not meant as hierarchical relationships. Note that, although skos:related is a symmetric property, this condition does not place any restrictions on sub-properties of skos:related (i.e., sub-properties of skos:related could be symmetric, not symmetric or antisymmetric, and still be consistent with the SKOS data model).

has characteristics: symmetric

has domain
thing c
has range
thing 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 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

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

intervention has topographyop back to ToC or Object Property ToC

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

every intervention/procedure is performed in a location. We use the topology entities to codify the information about this location. We use this property supposing to reference one subclass of Topography. We need to check that it is possible to use as range the whole class topography or if we need to go to a superclass.
has domain
Intervention or Procedure c
has range
Topography c

is about diseaseop back to ToC or Object Property ToC

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

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

is specification ofop back to ToC or Object Property ToC

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

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

has characteristics: transitive

has domain
Annotation c
has range
Annotation c

Koylocite Detectedop back to ToC or Object Property ToC

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

Signals the presence of Koilocytotic Squamous Cell. It needs to have as object the Koilocytotic Squamous Cell named entity
has domain
Outcome c
has range
Cervix Annotation c

makerop back to ToC or Object Property ToC

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

An agent that made this thing.
has domain
Clinical Case Report c
has range
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
Disease Annotation c

presence of celiac abnormalityop back to ToC or Object Property ToC

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

Connets a celiac clinical case to an annotation containing information about celiac abnormalities regarding that case.
has domain
Clinical Case Report c
has range
Celiac Abnormality c

presence of celiac elementop back to ToC or Object Property ToC

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

This property connects a celiac disease clinical case to annotations that may or may not be found in the patient.

same asop back to ToC or Object Property ToC

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

The property that determines that two given individuals are equal.
Is defined by
http://www.w3.org/2002/07/owl#

has characteristics: symmetric

has domain
thing c
has range
thing c

test usedop back to ToC or Object Property ToC

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

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

Data Properties

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 AOC this property is not necessary. We use it to contain the "internal id".
has domain
Clinical Case Report c
has range
int

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 IELdp back to ToC or Data Property ToC

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

Connects an annotation about a celiac disease to the corresponding intraepithelial lympochyte amount.
has domain
Celiac Disease Annotation Bag c
has range
intraepithelial lymphocyte amount

has imagedp back to ToC or Data Property ToC

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

Connects a clinical case report to the name of its corresponding image.
has domain
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
internal ID

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 domain
Float Check Element c
has range
float

has villi to crypt ratiodp back to ToC or Data Property ToC

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

Connects one annotation about a celiac disease case to its villi to Crypt of Lieberkuhn ratio value.
has domain
Celiac Disease Annotation Bag c
has range
Villi to crypt of Lieberkuhn Ratio

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
literal

outcomedp back to ToC or Data Property ToC

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

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

villi statusdp back to ToC or Data Property ToC

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

connects one bag of annotations for the celiac disease to the length of the villi.
has domain
Celiac Disease Annotation Bag c
has range
duodenum villi length

Annotation Properties

Alternative Definitionap back to ToC or Annotation Property ToC

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

To give an alternative definition (coming from another authoritative source) to the annotated entity.
has super-properties
Definition ap

annotated ruleap back to ToC or Annotation Property ToC

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

This property is used to annotated classes with a comment representing the rule that we inferred during the process of definition of this ontology. This rule may be impkemented to extract entities from a clinical case record. NB: we do not guarantee that these rules are always valid, or that they are the only valid. It may be the case that they are inaccurate since we were only able to infer them from the cases that were provided to us. Treat these annotations only as a documentation of our process and for a first implementation of the entities extractor.
has domain
thing c
has range
string

associated diseaseap back to ToC or Annotation Property ToC

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

In this ontologies different entities were developed to deal with specific entities. This property is used to link one entity to the corresponding disease it was defined for. It is just some more information to keep track of the nature of entities and to what disease they originally belong.
has domain
thing c
has range
Disease c

associated keyword in diagnosisap back to ToC or Annotation Property ToC

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

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

associated keyword in Materialsap back to ToC or Annotation Property ToC

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

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

cardinalityap back to ToC or Annotation Property ToC

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

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

Definitionap back to ToC or Annotation Property ToC

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

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

external definitionap back to ToC or Annotation Property ToC

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

A definition coming from a source external to the ones commonly used in Examode, or from a non-authoritative one.
has super-properties
Definition ap

has broad synonymap back to ToC or Annotation Property ToC

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

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

has dysplasiaap back to ToC or Annotation Property ToC

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

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

has ontobee annotationap back to ToC or Annotation Property ToC

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

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

has related synonymap back to ToC or Annotation Property ToC

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

To connect an entity to sinonims that are only related to it, and not completely equivalent to it.
has super-properties
has synonym ap

has Semantic Areaap back to ToC or Annotation Property ToC

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

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

has semantic typeap back to ToC or Annotation Property ToC

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

In general, applying semantic types aids in allowing users (or computer programs) to draw conclusions about concepts by virtue of the categories to which they have been assigned. We use a set of semantic types developed for the UMLS Metathesaurus. There are currently 134 semantic types in the UMLS. NB: this property is different from hasSemanticArea since this property serves as an annotation to give, when possible, a label indicating the semantic type. This label is taken from Ontobee. hasSemanticArea is used instead to give a tag to every entity, identifying what type of entity that is.
has domain
thing c
has range
string

has SNOMED codeap back to ToC or Annotation Property ToC

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

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

has synonymap back to ToC or Annotation Property ToC

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

To connect an entity to strings representing synonims to the xsd:string given as label. They should be accompanies by the annotation specifying the corresponding language.
has sub-properties
has broad synonym ap, has related synonym ap, hasExactSynonym ap
has domain
thing c
has range
string

has synonym labelap back to ToC or Annotation Property ToC

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

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

has UMLS codeap back to ToC or Annotation Property ToC

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

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

hasExactSynonymap back to ToC or Annotation Property ToC

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

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

internal notesap back to ToC or Annotation Property ToC

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

Use this property to annotate a resource with some not that may be usefult to those who will work on building the ontology.
has domain
thing c
has range
string

max cardinalityap back to ToC or Annotation Property ToC

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

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

min cardinalityap back to ToC or Annotation Property ToC

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

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

partOfap back to ToC or Annotation Property ToC

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

Tells that an object is part of another object.
has domain
thing c
has range
thing c

Preferred Nameap back to ToC or Annotation Property ToC

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

When something has a preferred name, you should specify it.
has domain
thing c
has range
string

structure notesap back to ToC or Annotation Property ToC

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

Notes about the structure of some entity, e.g. a location or an intervention.
has super-properties
Definition ap

taxon notesap back to ToC or Annotation Property ToC

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

A field found sometimes for entities taken from Ontobee's ontologies. You can treat it as an ulterior/alternative definition.
has super-properties
Definition ap
has domain
thing c
has range
string

titleap back to ToC or Annotation Property ToC

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

Named Individuals

Abdomenni back to ToC or Named Individual ToC

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

The subdivision of the vertebrate body between the thorax and pelvis. The ventral part of the abdomen contains the abdominal cavity and visceral organs. The dorsal part includes the abdominal section of the vertebral column.
belongs to
Topography c

Anatomical Locationni back to ToC or Named Individual ToC

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

We use this as a semantical class for a location of the body. Similar to Topology, but since we are already using that as a class, we did not want to use the same class for this role.
belongs to
Semantic Area c

Ascending Colonni back to ToC or Named Individual ToC

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

Section of colon which is distal to the cecum and proximal to the transversecolon.
belongs to
Topography c
is same as
Right colon
has facts
same as op Right colon

Bagni back to ToC or Named Individual ToC

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

The rdf:Bag class is the class of RDF 'Bag' containers. It is a subclass of rdfs:Container. Whilst formally it is no different from an rdf:Seq or an rdf:Alt, the rdf:Bag class is used conventionally to indicate to a human reader that the container is intended to be unordered.
is same as
Celiac Disease Annotation Bag
has facts
same as op Celiac Disease Annotation Bag

Bronchusni back to ToC or Named Individual ToC

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

The upper conducting airways of the lung; these airways arise from the terminus of the trachea
belongs to
Topography c

Brunner's Gland Hyperplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C135565

A rare hyperplastic lesion of Brunner's gland in the duodenum. Although it is usually asymptomatic and discovered incidentally during upper gastrointestinal endoscopy, it may cause hemorrhage.
belongs to
Celiac Abnormality c

Caecumni back to ToC or Named Individual ToC

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

A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction.
belongs to
Topography c

Cannizzaro Hospitalni back to ToC or Named Individual ToC

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

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

CD3ni back to ToC or Named Individual ToC

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

Cluster of Differentiation 3
belongs to
Immunohistochemical Test 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 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

A substance produced by the cervix and endocervical glands[BTO]. Thick acidic mucus that blocks the cervical os after mestruation [WP]. This 'infertile' mucus blocks spermatozoa from entering the uterus.
belongs to
Topography c

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

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

Region of cervical epithelium where columnar epithelium of endocervic and the stratified non-keratinising squamous epithelium of the ectocervic meet
belongs to
Topography c

cervix epitheliumni back to ToC or Named Individual ToC

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

An epithelium that is part of a uterine cervix
belongs to
Topography c

cervix glandular epitheliumni back to ToC or Named Individual ToC

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

A glandular epithelium that is part of a uterine cervix.
belongs to
Topography c

cervix squamous epitheliumni back to ToC or Named Individual ToC

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

The squamous epithelium of the cervical portio is similar to that of the vagina, except that it is generally smooth and lacks rete pegs. Colposcopically, it appears featureless except for a fine network of vessels which is sometimes visible. The relative opacity and pale pink coloration of the squamous epithelium derives from its multi-layered histology and the location of its supporting vessels below the basement membrane.
belongs to
Topography c

colon carcinomani back to ToC or Named Individual ToC

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

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

Colon Dysplasiani back to ToC or Named Individual ToC

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

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

Colon, NOSni back to ToC or Named Individual ToC

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

Colon, Not Otherwise Specified
belongs to
Topography c

colorectumni back to ToC or Named Individual ToC

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

The subdivision of the digestive tract that consists of the colon and the rectum
belongs to
Topography c

crypt of Lieberkuhn of duodenumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0013482

An intestinal crypt that is located in the duodenum.
belongs to
Topography c

Descending colonni back to ToC or Named Individual ToC

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

The portion of the colon between the left colic flexure and the sigmoid colon at the pelvic brim; the portion of the descending colon lying in the left iliac fossa is sometimes called the iliac colon.
belongs to
Topography c

Diagnosisni back to ToC or Named Individual ToC

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

The investigation, analysis and recognition of the presence and nature of disease, condition, or injury from expressed signs and symptoms; also, the scientific determination of any kind; the concise results of such an investigation.
belongs to
Semantic Area c

duodenal ampullani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0013644

The very first part of the duodenum which is slightly dilated.
belongs to
Topography c

duodenal epitheliumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0008346

An epithelium that is part of a duodenum.
belongs to
Topography c

duodenal glandni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001212

A compound tubular submucosal gland found in that portion of the duodenum which is above the hepatopancreatic sphincter (Sphincter of Oddi). The main function of these glands is to produce a mucus-rich alkaline secretion (containing bicarbonate)[WP]. [database_cross_reference: http://en.wikipedia.org/wiki/Brunner's_glands]
belongs to
Topography c

duodenal mucosani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000320

A mucosa that is part of a duodenum.
belongs to
Topography c

Duodenumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002114

The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one).
belongs to
Topography c

duodenum lamina propriani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0015834

A lamina propria that is part of a duodenum.
belongs to
Topography c

Dysplasiani back to ToC or Named Individual ToC

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

A usually neoplastic transformation of the cell, associated with altered architectural tissue patterns. The cellular changes include nuclear and cytoplasmic abnormalities. Molecular genetic abnormalities are also often found and, in some instances, may lead to cancer.
belongs to
Disease Annotation c

Edemani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/OMIT_0005738

Buildup of fluid in the body's tissue.
belongs to
Celiac Abnormality c

Endometriumni back to ToC or Named Individual ToC

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

The mucous membrane comprising the inner layer of the uterine wall; it consists of a simple columnar epithelium and a lamina propria that contains simple tubular uterine glands. The structure, thickness, and state of the endometrium undergo marked change with the menstrual cycle.
belongs to
Topography c
is same as
endometrium
has facts
same as op endometrium

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

exocervical epitheliumni back to ToC or Named Individual ToC

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

A epithelium that is part of a ectocervix.
belongs to
Topography c

female genderni back to ToC or Named Individual ToC

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

A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both. [def-source: NCI]

General Entityni back to ToC or Named Individual ToC

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

In this ontology there are different semantic areas. These are: diagnosis, procedure, test, anatomical location, and general. General is the area of entities that are common to all clinical cases. Organization, clinical case reports, diseases, are classes with entities that do not belong to the other 4 semantic areas, therefore we classified them in general. These are the classes that, in our documentation, are contained in the green box.
belongs to
Semantic Area c

granulocyteni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/CL_0000094

A leukocyte with abundant granules in the cytoplasm.
belongs to
Celiac Disease Annotation 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

High Grade Dysplasiani back to ToC or Named Individual ToC

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

A subjective characterization of the phenomenon of dysplasia, based on microscopic examination of the architectural and/or cytological changes in a tissue sample, that is determined to be high.
belongs to
Disease Annotation c
has facts
is specification of op Dysplasia

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

hyperemiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/SYMP_0000299

Hyperemia is a hemic system symptom consisting of an excess of blood in a body part as from an increased flow of blood due to vasodilation.
belongs to
Celiac Abnormality c

Ileumni back to ToC or Named Individual ToC

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

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

intestinal fibrosisni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/MP_0011748

Formation of fibrous tissue in any part of the intestine as a result of repair or a reactive process.
belongs to
Celiac Abnormality c

intestinal villus of duodenumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0008342

An intestinal villus in the duodenum.
belongs to
Topography c

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

The connective tissue coat of a mucous membrane including the epithelium and basement membrane.
belongs to
Topography c

Late onsetni back to ToC or Named Individual ToC

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

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

Left colonni back to ToC or Named Individual ToC

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

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

Left inferior lobar bronchusni back to ToC or Named Individual ToC

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

A region of the bronchus in the lungs.
belongs to
Topography c

Left Main Bronchusni back to ToC or Named Individual ToC

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

One of the two main bronchi. It is narrower but longer than the right main bronchus and connects to the left lung.
belongs to
Topography c

Left superior lobar bronchusni back to ToC or Named Individual ToC

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

Part of the left bronchus.
belongs to
Topography c

Lobar Bronchusni back to ToC or Named Individual ToC

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

A part the bronchial tree, arising from the primary bronchi, with each one serving as the airway to a specific lobe of the lung.
belongs to
Topography c

Lungni back to ToC or Named Individual ToC

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

Respiration organ that develops as an oupocketing of the esophagus.
belongs to
Topography c

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

lymphocyteni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/CL_0000542

A lymphocyte is a leukocyte commonly found in the blood and lymph that has the characteristics of a large nucleus, a neutral staining cytoplasm, and prominent heterochromatin.
belongs to
Celiac Disease Annotation c

Main Bronchusni back to ToC or Named Individual ToC

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

The left and right main bronchi considered as a group.
belongs to
Topography c

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.

Mediastinumni back to ToC or Named Individual ToC

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

The central part of the thoracic cavity enclosed by the left and right pleurae.
belongs to
Topography c

Metastasisni back to ToC or Named Individual ToC

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

The spread of cancer from one part of the body to another. A tumor formed by cells that have spread is called a "metastatic tumor" or a "metastasis." The metastatic tumor contains cells that are like those in the original (primary) tumor.
belongs to
Lung Annotation c

Middle age onsetni back to ToC or Named Individual ToC

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

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

Mild Colon Dysplasiani back to ToC or Named Individual ToC

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

A morphologic finding indicating the presence of mild dysplastic cellular changes and mild architectural changes in the glandular epithelium of the colonic mucosa. There is no evidence of invasion.
belongs to
Colon Annotation c
has facts
has broader op Mild Dysplasia
is specification of op Colon Dysplasia

Mild Dysplasiani back to ToC or Named Individual ToC

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

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

Moderate Colon Dysplasiani back to ToC or Named Individual ToC

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

A morphologic finding indicating the presence of moderate dysplastic cellular changes and moderate architectural changes in the glandular epithelium of the colonic mucosa. There is no evidence of invasion.
belongs to
Colon Annotation c
has facts
has broader op Moderate Dysplasia
is specification of op Colon Dysplasia

Moderate Dysplasiani back to ToC or Named Individual ToC

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

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

Mucosani back to ToC or Named Individual ToC

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

MSH: An EPITHELIUM with MUCUS-secreting cells, such as GOBLET CELLS. It forms the lining of many body cavities, such as the DIGESTIVE TRACT, the RESPIRATORY TRACT, and the reproductive tract. Mucosa, rich in blood and lymph vessels, comprises an inner epithelium, a middle layer (lamina propria) of loose CONNECTIVE TISSUE, and an outer layer (muscularis mucosae) of SMOOTH MUSCLE CELLS that separates the mucosa from submucosa.,CSP: mucus-secreting membrane lining all body cavities or passages that communicate with the exterior.,NCI: The moist, inner lining of some organs and body cavities (such as the nose, mouth, lungs, and stomach). Glands in the mucosa make mucus (a thick, slippery fluid).,NCI: Mucous membrane. (NCI),NCI: Mucous membrane.
belongs to
Topography c

necrosisni back to ToC or Named Individual ToC

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

Note that the word necrosis has been widely used in earlier literature to describe forms of cell death which are now known by more precise terms, such as apoptosis. Necrosis can occur in a regulated fashion, involving a precise sequence of signals.
belongs to
Lung Annotation c

pavement epitheliumni back to ToC or Named Individual ToC

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

Squamous epithelium composed of a single layer of cells.
belongs to
Topography c

Pleurani back to ToC or Named Individual ToC

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

The invaginated serous membrane that surrounds the lungs (the visceral portion) and lines the walls of the pleural cavity (parietal portion).
belongs to
Topography c

Pre-Cancerous Dysplasiani back to ToC or Named Individual ToC

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

Precancerous conditions of the cervix are changes to cervical cells that make them more likely to develop into cancer. These conditions are not yet cancer. But if they aren’t treated, there is a chance that these abnormal changes may become cervical cancer. If left untreated, it may take 10 years or more for precancerous conditions of the cervix to turn into cervical cancer, but in rare cases this can happen in less time. Precancerous conditions of the cervix happen in an area called the transformation zone. This is where columnar cells (a type of glandular cell) are constantly being changed into squamous cells. The transformation of columnar cells into squamous cells is a normal process, but it makes the cells more sensitive to the effect of the human papillomavirus (HPV).
belongs to
Disease Annotation c
has facts
is specification of op Dysplasia

Procedureni back to ToC or Named Individual ToC

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

Semantic class to describe the semantic area of the interventions. We defined our own class (and not used the ncit one) because we wanted to keep the two separated to not entangle too much queries and also because here we are using it with a slightly different semantic meaning.
belongs to
Semantic Area c
has facts
is specification of op Severe Dysplasia

pulmonary lymph nodeni back to ToC or Named Individual ToC

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

Pulmonary lymph nodes are a common and underrecognized cause of a peripheral SPN. These lymph nodes are usually found at the bifurcation of the bronchi, before the fourth branch, where they are referred to as peribronchial lymph nodes. Lymph nodes are occasionally present within the lung parenchyma, where they are designated intrapulmonary lymph nodes (IPLNs) or perifissural nodules (PFNs).
belongs to
Topography c

pyloric antrumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0001165

The area at the bottom of the stomach on the caudal side of the pyloric canal that contains gastrin-producing G cells, which stimulate acid production, and the luminal pH-sensitive population of somatostatin-producing D cells.
belongs to
Topography c

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
Organization c

Rectal mucous membraneni back to ToC or Named Individual ToC

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

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

Rectosigmoid junctionni back to ToC or Named Individual ToC

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

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

Rectum, NOSni back to ToC or Named Individual ToC

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

Rectum, Not Otherwise Specified.
belongs to
Topography c

Right colonni back to ToC or Named Individual ToC

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

The proximal portion of the colon, extending from the ileocecal valve usually to a point proximal to the left colic flexure; it develops embryonically from the terminal portion of the midgut and functions in absorption.
belongs to
Topography c
is same as
Ascending Colon

Right inferior lobar bronchusni back to ToC or Named Individual ToC

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

A region of the bronchus in the lung.
belongs to
Topography c

Right Main Bronchusni back to ToC or Named Individual ToC

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

One of the two main bronchi. It is wider but shorter than the left main bronchus and connects to the right lung.
belongs to
Topography c

Right superior lobar bronchusni back to ToC or Named Individual ToC

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

Part of the right bronchus.
belongs to
Topography c

Severe Colon Dysplasiani back to ToC or Named Individual ToC

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

Dysplasia is a term that describes how much your polyp looks like cancer under the microscope. Polyps that are more abnormal and look more like cancer are said to have high-grade (severe) dysplasia.
belongs to
Colon Annotation c
has facts
has broader op Severe Dysplasia
is specification of op Colon Dysplasia

Severe Dysplasiani back to ToC or Named Individual ToC

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

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

Sigmoid colonni back to ToC or Named Individual ToC

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

The part of the large intestine that is closest to the rectum and anus. It forms a loop that averages about 40 cm. in length, and normally lies within the pelvis, but on account of its freedom of movement it is liable to be displaced into the abdominal cavity.
belongs to
Topography c

Simple Epitheliumni back to ToC or Named Individual ToC

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

Epithelium composed of a single layer of cells attached to a basement membrane.
belongs to
Topography c
has facts
has Related op pavement epithelium

Testni back to ToC or Named Individual ToC

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

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

Thoracic lymph nodeni back to ToC or Named Individual ToC

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

A lymph node that is part of a thorax. Includes lymph nodes of the lungs and mediastinal lymph nodes
belongs to
Topography c

Transverse Colonni back to ToC or Named Individual ToC

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

The proximal-distal subdivision of colon that runs transversely across the upper part of the abdomen, from the right to the left colic flexure. Continuous with the descending colon.
belongs to
Topography c

uterus, NOSni back to ToC or Named Individual ToC

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

The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
belongs to
Topography c

Young adult onsetni back to ToC or Named Individual ToC

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

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

Legend back to ToC

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

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.