The ExaMode Ontology

Release February 2023

This version:
https://w3id.org/examode/ontology
Latest version:
https://w3id.org/examode/ontology
Ontology Version IRI:
https://w3id.org/examode/ontology/2.0/
Authors:
Stefano Marchesin, (University of Padua)
Laura Menotti, (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:
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License:
https://creativecommons.org/licenses/by/4.0/ License

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Cite as:
Laura Menotti, Stefano Marchesin, Gianmaria Silvello. The EXAMODE ontology, v2.0. https://doi.org/10.5281/zenodo.7669237
Ontology Specification Draft

Introduction back to ToC

The ExaMode ontology was developed in the context of the ExaMode project co-financed by the European Commission under the Horizon 2020 framework, which aims to 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.

The ExaMode project 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 focus on four largely diffused and studied diseases:

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

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 models the diagnosis process using WSIs in histopathology, defining the key concepts and properties to model diagnoses, 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. Compared to previous efforts [Serra et al., 2019; Gurcan et al., 2017], the ExaMode ontology focuses on diagnosing histopathology exams, defining components related to the annotation process of WSIs. The ontology is multilingual since components are labeled in three different languages: English, Italian, and Dutch. It comprises five semantic areas grouping components related to the same aspect of the diagnostic process: clinical case reports (i.e., general aspects), diagnosis results, other tests performed, interventions or surgical procedures employed to retrieve the specimen, and the anatomical location of the specimen. This classification provides an ontological template that can be used to model any disease in the histopathology domain. We modeled four largely diffused and studied diseases: colon cancer, uterine cervix cancer, lung cancer, and celiac disease. Thanks to the modularity of this approach, we can easily expand our ontology to include more use cases.

The ontology design followed a bottom-up approach starting from anonymized clinical reports about the four considered diseases provided by Azienda Ospedaliera per l’Emergenza Cannizzaro (AOEC) in Italy and the Radboud University Medical Center (RUMC) in The Netherlands. We analyzed these textual records and worked together with the pathologists and physicians, employing a co-design methodology to accurately identify the classes and relations to be included in the ontology. The ExaMode ontology is designed to meet the OBO principles to ease interoperability with other biomedical ontologies. Hence, we maximized the reuse of concepts defined in already available and well-known biomedical ontologies and vocabularies, thus limiting the creation of new classes and relations to a minimum.

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 today to 2040 will increase by up to 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 toady 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.

The average survival rate for metastatic lung cancer is very low, whereas early stages have higher survival rates. The treatment of low-stage lung cancer is complete surgical resection. Instead, for metastatic lung cancer, the surgical option is often impossible. An accurate diagnosis from lung biopsies targets the most correct prognostic and therapeutic management for the patient.

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.

Celiac Disease

The list of the diseases included in the ExaMode priority list also includes a non-cancerous illness, namely the celiac 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 celiac disease than undiagnosed ones [Fasano et al., 2003].

In general, routine screening for celiac 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 celiac disease relies mainly on the presence of positive celiac 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 celiac disease correctly.

Considering an increasing number of new cases of celiac 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
[Ontology NS Prefix]<https://w3id.org/examode/ontology/>
rdfs<http://www.w3.org/2000/01/rdf-schema>
dc<http://purl.org/dc/elements/1.1>
dcterms<http://purl.org/dc/terms/>
xsd<http://www.w3.org/2001/XMLSchema>
foaf<http://xmlns.com/foaf/0.1>
skos<http://www.w3.org/2004/02/skos/core>
ncit<http://purl.obolibrary.org/obo/NCIT_>
uberon<http://purl.obolibrary.org/obo/UBERON_>
fma<http://purl.obolibrary.org/obo/FMA_>
go<http://purl.obolibrary.org/obo/GO_>
mondo<http://purl.obolibrary.org/obo/MONDO_>
hpo<https://hpo.jax.org/app/browse/term/HP:>
bto<http://purl.obolibrary.org/obo/BTO_>
mp<http://purl.obolibrary.org/obo/MP_>
uniprot<https://www.uniprot.org/uniprotkb/>

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

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]. The main task for a pathologist is to detect cancerous polyps (e.g., for population screening) and to identify the answers to these main diagnostic criteria:

  1. Presence or absence of polyp;
  2. Presence of adenoma-serrated polyps/malignant polyps;
  3. Presence or absence of dysplasia;
  4. Presence of high or low-grade dysplasia.
Moreover, in the microscopic analysis of colon excisional biopsy sample, there is a minimum of data that also need to be provided by the pathologist:
  1. Type of the polyp. It is important to distinguish between the two main types of polyps: adenoma-serrated polyps and malignant polyps. From the diagnostic perspective, it can also be useful to know the number of each type of polyp.
  2. The grade of the dysplasia if a polyp is present (low, medium, 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.

This information is a prognostic factor leading to the decision about the patient's management. For example, polyps with a negative polypectomy margin, low-grade histology, and no lymphovascular invasion can be safely treated with endoscopic polypectomy. On the other hand, 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 done when previous tests provide evidence of precancerous/abnormal or neoplastic lesions in the uterine cervix. The cervical tissue removed has to be analyzed by an expert pathologist to identify if the tumor lesions are present or not. If present, the pathology report provides diagnostic information and works as a prognostic tool for the patient’s treatment. Colposcopy with directed biopsy is currently one of the “gold standard” practices for diagnosing cervical pre-cancer.

Thus, the histopathologist aims to recognize and identify these precursor lesions, known as Cervical Intraepithelial Neoplasia (CIN), which displays the 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;
  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].

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 [Travis et al., 2011]. 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.

Celiac Disease

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

Celiac disease is an immune-mediated disease with chronic outcome and genetic predisposition to an intolerance to gluten and its proteins. This intolerance leads to an abnormal immune response, followed by chronic inflammation and alteration of the small intestinal mucosa. The diagnosis of this pathology is based on the description of the histopathological alterations of the 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 The ExaMode ontology is organized into five semantic areas, each concerning different aspects of the histopathology process.:

  1. General Area: This area comprises entities that are common to all use cases, such as patients’ information and clinical case reports. As we mentioned before, to ensure modularity in the ExaMode ontology, each use case has its own classes which are subclasses of a general-purpose class. For instance, clinical case reports concerning colon cancer are instances of the Class "Colon Clinical Case Report", which is a subclass of the general-purpose class “Clinical Case”. The same reasoning is applied to most classes, such as outcomes, interventions, and locations. 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.
  2. Diagnosis: This area contains all classes related to the different outcomes one can expect from a clinical case report concerning a specific use case. All use cases have the same structure, yet the components describing positive outcomes differ based on the considered disease. In general, each clinical case report is associated with its outcome using the object property "hasOutcome" and outcomes can be negative, inconclusive, or positive. Negative and inconclusive are the same for all use cases, while positive outcomes differ based on the disease. Positive outcomes describe the type of cancer or disease that has been diagnosed in the examined specimen and it can be associated with additional information for some types of diseases.
  3. Location Area : This area models the anatomical locations where the disease detected in the specimen is located or where an intervention has been performed. All classes include locations specific for each use case and are modeled as subclasses of the general-purpose class "Anatomical Entity". The specific components, i.e. anatomical locations, of this semantic area highly depend on the different use cases.
  4. Procedure: This area cdescribes the intervention or surgical procedure performed to obtain the specimen used for the diagnosis. As for the other semantic areas, the general-purpose classes are "Intervention or Procedure" and ``Surgical Procedure", which is actually a subclass of the former. All interventions or surgeries performed for a specific clinical case are instances of the corresponding classes specific for the considered use case.
  5. Test: This area comprises all classes corresponding to additional tests on the specimen to identify additional information useful for the diagnosis. In fact, Immunohistochemistry (IHC) is an important field of study that determines the tissue distribution of antigens and it is widely used for the diagnosis of diseases, especially for identifying the type of cancer in a tissue [Duraiyan et al., 2012]. For this reason, we identify a general-purpose class called "Immunohistochemical Test" and all the specific tests for each use case are modeled as subclasses of it. We link an outcome with the additional test through the object property "hasTest" and each test can have a boolean, float or string-valued result embodied in three different data properties corresponding to the different result datatype.

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

EXAMODE General Area

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 celiac 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 (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 University Medical Center (RUMC) 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). Positive outcomes describe the type of cancer or disease that has been diagnosed in the examined specimen and it can be associated with additional information for some types of diseases. For instance, in the colon cancer use case, if the specimen has been diagnosed as "Polyp of Colon" or any of its subclasses, we might have additional information about the degree of dysplasia the polyp presents. We refer to this additional data as "Annotations to the Case" and we modeled them as subclasses of the general-purpose class called "Finding".

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. For cervical cancer, in the diagnosis, indipendently of its type, one could detect the presence of koilocytes, or the specimen could test positive for HPV. 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 or any of its subclasses, there may be additional information regarding the presence of necrosis or metastasis.

Diagnosis - Celiac Disese

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

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

In this case, a positive outcome can be enriched with information about the presence of immune cells such as granulocytes or lymphocytes, the presence of intestinal abnormalities such as edema or intestinal fibrosis, or data about the villi status, such as their atrophy degree or length. All components modeling such information are grouped in the "Annotations to the Case" area.

Procedure, Location & Test - Colon Cancer

location and procedure

As shown above, the Examode Ontology comprises three other semantic 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. We also modeled the Test area, which comprises other test performed.

In the case of the colon, the performed procedure can only be a surgical procedure which, in turn, can be a resection, an 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 - celiac Disease

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

In the case of the celiac 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 celiac 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, object properties and data properties back to ToC

This section provides details for each class and property defined by The EXAMODE ontology.

Classes

Adenomac back to ToC or Class ToC

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

A polypoid adenoma that arises from and protrudes into the lumen of the colon. Epithelial dysplasia is always present. According to the architectural pattern it is classified as tubular, tubulovillous, or villous. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0006498
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

Anatomical Entityc back to ToC or Class ToC

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

Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. [ Definition Source: FMA : 62955 http://orcid.org/0000-0001-9114-8737 ]
Is defined by
http://orcid.org/0000-0001-9114-8737
http://purl.obolibrary.org/obo/UBERON_0001062
has sub-classes
Celiac Anatomical Entity c, Cervix Anatomical Entity c, Colon Anatomical Entity c, Lung Anatomical Entity c
is in range of
has location op

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
Semantic Area 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, Cluster of Differentation 3 c, Cytokeratin 34bE12 c, Cytokeratin 5/6 c, Desmocollin-3 c, Endonuclease P40 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

Celiac Anatomical Entityc back to ToC or Class ToC

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

Class describing biological entities related to celiac disease.
has super-classes
Anatomical Entity c
has members
Antrum Pylori ni, Crypt of Lieberkuhn of Duodenum ni, Duodenal Ampulla ni, Duodenal Epithelium ni, Duodenal Gland ni, Duodenal Lamina Propria ni, Duodenal Mucosa ni, Duodenum ni, Greater Curvature of Stomach ni, Intestinal Villus of Duodenum ni, Jejunum ni, Mucosa of Pyloric Antrum ni, Small Intestine ni
is disjoint with
Cervix Anatomical Entity c, Colon Anatomical Entity c, Lung Anatomical Entity c

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.
is equivalent to
presence of op some Celiac Disease Finding c
has outcome op only Celiac Outcome c
has super-classes
Clinical Case Report c
is in domain of
has laboratory finding op
is disjoint with
Cervix Clinical Case Report c, Colon Clinical Case Report c, Lung Clinical Case Report c

Celiac Disease Findingc back to ToC or Class ToC

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

Finding in celiac outcomes.
has super-classes
Finding c
has members
Enterocyte ni, Eosinophil ni, Granulocyte ni, Leukocyte ni, Lymphocyte ni, Neutrophil ni
is disjoint with
Dysplasia c, Human Papilloma Virus Infection c, Intestinal Abnormality c, Koilocytotic Squamous Cell c, Lung Carcinoma Finding c

Celiac Disease Intervention or Procedurec back to ToC or Class ToC

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

Class describing interventions or procedures related to celiac disease.
is equivalent to
has location op only Celiac Anatomical Entity c
has super-classes
Intervention or Procedure c
has sub-classes
Celiac Disease Surgical Procedure c
is disjoint with
Cervix Cancer Intervention or Procedure c, Colon Cancer Intervention or Procedure c, Lung Cancer Intervention or Procedure c

Celiac Disease Intervention or Procedure Typec back to ToC or Class ToC

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

Class describing the type of intervention or procedure related to celiac disease.
has super-classes
Intervention or Procedure Type c
has members
Biopsy of Duodenum ni, Biopsy of Jejunum ni, Biopsy of Small Intestine ni, Biopsy of the Greater Curvature ni, Biopsy of the Pyloric Antrum ni, Endoscopic Biopsy ni

Celiac Disease Surgery Typec back to ToC or Class ToC

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

Class describing surgical procedure type related to celiac disease.
has super-classes
Surgical Procedure Type c

Celiac Disease Surgical Procedurec back to ToC or Class ToC

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

Class describing surgical procedures related to celiac disease.
has super-classes
Celiac Disease Intervention or Procedure c, Surgical Procedure c
is disjoint with
Cervix Cancer Surgical Procedure c, Colon Cancer Surgical Procedure c, Lung Cancer Surgical Procedure c

Celiac Outcomec back to ToC or Class ToC

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

Class representing all outcomes of celiac clinical case report.
is equivalent to
has intervention op only Celiac Disease Intervention or Procedure c
has location op only Celiac Anatomical Entity c
has super-classes
Outcome c
has sub-classes
Celiac Positive Outcome c
is in domain of
presence of intestinal abnormality op
is disjoint with
Cervix Outcome c, Colon Outcome c, Lung Outcome c

Celiac Positive Outcomec back to ToC or Class ToC

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

Positive Outcome, i.e., something related to celiac disease has been found in the patient.
is equivalent to
positive result type op only Celiac Positive Outcome Type c
has super-classes
Celiac Outcome c, Positive Outcome c
has sub-classes
Duodenitis c, Positive to Celiac Disease c
is disjoint with
Cervix Positive Outcome c, Colon Positive Outcome c, Lung Positive Outcome c

Celiac Positive Outcome Typec back to ToC or Class ToC

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

Class describing for which type of celiac disease the clinical case tested positive.
has super-classes
Positive Outcome Type c
is disjoint with
Cervix Positive Outcome Type c, Colon Positive Outcome Type c, Lung Positive Outcome Type c

Cervix Anatomical Entityc back to ToC or Class ToC

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

Class describing biological entities related to cervix cancer.
has super-classes
Anatomical Entity c
has members
Cervical Mucus ni, Cervical Squamo-Columnar Junction ni, Cervix Epithelium ni, Cervix Glandular Epithelium ni, Cervix Squamous Epithelium ni, Endometrium ni, Exocervical Epithelium ni, Lamina Propria ni, Mucosa ni, Pavement Epithelium ni, Simple Epithelium ni, Uterus, NOS ni
is disjoint with
Celiac Anatomical Entity c, Colon Anatomical Entity c, Lung Anatomical Entity c

Cervix Cancer Intervention or Procedurec back to ToC or Class ToC

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

Class describing interventions or procedures related to cervix cancer.
is equivalent to
has location op only Cervix Anatomical Entity c
has super-classes
Intervention or Procedure c
has sub-classes
Cervix Cancer Surgical Procedure c
is disjoint with
Celiac Disease Intervention or Procedure c, Colon Cancer Intervention or Procedure c, Lung Cancer Intervention or Procedure c

Cervix Cancer Surgical Procedurec back to ToC or Class ToC

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

Class describing surgical procedures related to cervix cancer.
has super-classes
Cervix Cancer Intervention or Procedure c, Surgical Procedure c
is disjoint with
Celiac Disease Surgical Procedure c, Colon Cancer Surgical Procedure c, Lung Cancer Surgical Procedure c

Cervix Clinical Case Reportc back to ToC or Class ToC

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

Class representing the clinical cases about cervix cancer.
is equivalent to
has outcome op only Cervix Outcome c
has super-classes
Clinical Case Report c
is disjoint with
Celiac Clinical Case Report c, Colon Clinical Case Report c, Lung Clinical Case Report c

Cervix Intervention or Procedure Typec back to ToC or Class ToC

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

Class describing the type of intervention or procedure related to cervix cancer.
has super-classes
Intervention or Procedure Type c
has sub-classes
Cervix Surgery Type c
has members
Cervical Biopsy ni

Cervix Outcomec back to ToC or Class ToC

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

Class representing all outcomes of cervix clinical case reports.
is equivalent to
has intervention op only Cervix Cancer Intervention or Procedure c
has location op only Cervix Anatomical Entity c
detected HPV op min 0 Human Papilloma Virus Infection c
detected koilocyte op min 0 Koilocytotic Squamous Cell c
detected HPV op max 1 Human Papilloma Virus Infection c
detected koilocyte op max 1 Koilocytotic Squamous Cell c
has super-classes
Outcome c
has sub-classes
Cervix Positive Outcome c
is in domain of
detected HPV op, detected koilocyte op
is disjoint with
Celiac Outcome c, Colon Outcome c, Lung Outcome c

Cervix Positive Outcomec back to ToC or Class ToC

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

Positive Outcome, i.e., something related to cervix cancer has been found in the patient.
is equivalent to
positive result type op only Cervix Positive Outcome Type c
has super-classes
Cervix Outcome c, Positive Outcome c
is disjoint with
Celiac Positive Outcome c, Colon Positive Outcome c, Lung Positive Outcome c

Cervix Surgery Typec back to ToC or Class ToC

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

Class describing surgical procedure type related to cervix cancer.
has super-classes
Cervix Intervention or Procedure Type c, Surgical Procedure Type c
has members
Conization ni, Endocervical Curettage ni, Hysterectomy ni, Loop Electrosurgical Excision ni, Radical Hysterectomy ni, Total Abdominal Hysterectomy ni

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, String Check Element c

Chromogranin-Ac back to ToC or Class ToC

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

Pancreastatin: Strongly inhibits glucose induced insulin release from the pancreas. Catestatin: Inhibits catecholamine release from chromaffin cells and noradrenergic neurons by acting as a non-competitive nicotinic cholinergic antagonist (PubMed:15326220). Displays antibacterial activity against Gram-positive bacteria S.aureus and M.luteus, and Gram-negative bacteria E.coli and P.aeruginosa (PubMed:15723172 and PubMed:24723458). Can induce mast cell migration, degranulation and production of cytokines and chemokines (PubMed:21214543). Acts as a potent scavenger of free radicals in vitro (PubMed:24723458). May play a role in the regulation of cardiac function and blood pressure (PubMed:18541522). Serpinin: Regulates granule biogenesis in endocrine cells by up-regulating the transcription of protease nexin 1 (SERPINE2) via a cAMP-PKA-SP1 pathway. This leads to inhibition of granule protein degradation in the Golgi complex which in turn promotes granule formation. Miscellaneous Binds calcium with a low-affinity. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/P10645
has super-classes
Boolean Check Element c

Clear Cell Adenocarcinomac back to ToC or Class ToC

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

A malignant neoplasm composed of glandular epithelial clear cells. Various architectural patterns may be seen, including papillary, tubulocystic, and solid. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0005004
has super-classes
Lung Adenocarcinoma c

Clinical Case Reportc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/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 equivalent to
is about disease op exactly 1 Disease or Disorder c
has sub-classes
Celiac Clinical Case Report c, Cervix Clinical Case Report c, Colon Clinical Case Report c, Lung Clinical Case Report c
is in domain of
has Internal Identifier dp, has block number dp, has image dp, has outcome op, has slide op, has textual diagnosis dp, identifier dp, is about disease op, maker op
is in range of
has clinical case report op, made op

Cluster of Differentation 3c back to ToC or Class ToC

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

Consisting of cell surface type I membrane Delta, Epsilon, Gamma, Zeta, and Eta protein subunits with ITAM domains and noncovalently associated with the disulfide bound heterodimeric alpha/beta and gamma/delta TCR, the CD3 complex couples receptor antigen recognition to signal transduction pathways during T-cell activation. During TCR engagement with MHC-associated antigen on host cell surfaces and synapse formation, CD3 activity leads to Tyr-phosphorylated CD3 subunits, Tyr phosphorylation of LAT colocalized in lipid rafts, and MAPK activation. CD3 signal transduction appears to involve LCK, ZAP70, Nck, SLA, SLA2, and DOCK2. CD3 subunits may also associate with the cytoskeleton. CD3 also mediates TCR signal transduction during the developmental transition through positive selection of immature thymocytes to mature CD4+ or CD8+ T cells. (NCI) [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C38897
has super-classes
Boolean Check Element c

Collectionc back to ToC or Class ToC

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

A meaningful collection of concepts.
Is defined by
http://www.w3.org/2004/02/skos/core
has sub-classes
Ordered Collection c
is in domain of
has member op
is disjoint with
Concept c, Concept Scheme c

Colon Anatomical Entityc back to ToC or Class ToC

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

Class describing biological entities related to colon cancer.
has super-classes
Anatomical Entity c
has members
Abdomen ni, Ascending Colon ni, Caecum ni, Colon, NOS ni, Colorectum ni, Descending Colon ni, Ileum ni, Left Colon ni, Rectal Mucous Membrane ni, Rectosigmoid Junction ni, Rectum, NOS ni, Right Colon ni, Sigmoid Colon ni, Transverse Colon ni
is disjoint with
Celiac Anatomical Entity c, Cervix Anatomical Entity c, Lung Anatomical Entity c

Colon Cancer Intervention or Procedurec back to ToC or Class ToC

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

Class describing interventions or procedures related to colon cancer.
is equivalent to
has location op only Colon Anatomical Entity c
has super-classes
Intervention or Procedure c
has sub-classes
Colon Cancer Surgical Procedure c
is disjoint with
Celiac Disease Intervention or Procedure c, Cervix Cancer Intervention or Procedure c, Lung Cancer Intervention or Procedure c

Colon Cancer Surgical Procedurec back to ToC or Class ToC

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

Class describing surgical procedures related to colon cancer.
has super-classes
Colon Cancer Intervention or Procedure c, Surgical Procedure c
is disjoint with
Celiac Disease Surgical Procedure c, Cervix Cancer Surgical Procedure c, Lung Cancer Surgical Procedure c

Colon Clinical Case Reportc back to ToC or Class ToC

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

Class representing all colon cancer cases.
is equivalent to
has outcome op only Colon Outcome c
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: https://w3id.org/examode/ontology/ColonHyperplasticPolyp

A serrated polypoid lesion that arises in the colon. It is usually found in the distant colon and it rarely produces symptoms. This group includes goblet cell rich, mucin poor, and microvesicular hyperplastic polyps. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C4930
has super-classes
Polyp of Colon c

Colon Inflammatory Polypc back to ToC or Class ToC

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

A non-neoplastic polypoid lesion in the colon. It may arise in a background of inflammatory bowel disease or colitis. It is characterized by the presence of a distorted epithelium, inflammation, and fibrosis. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0006152
has super-classes
Polyp of Colon c

Colon Intervention or Procedure Typec back to ToC or Class ToC

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

Class describing the type of intervention or procedure related to colon cancer.
has super-classes
Intervention or Procedure Type c
has sub-classes
Colon Surgery Type c
has members
Biopsy of Colon ni, Endoscopic Biopsy ni

Colon Outcomec back to ToC or Class ToC

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

Class representing all outcomes of colon clinical case reports.
is equivalent to
has intervention op only Colon Cancer Intervention or Procedure c
has location op only Colon Anatomical Entity c
has super-classes
Outcome c
has sub-classes
Colon Positive Outcome c
is disjoint with
Celiac Outcome c, Cervix Outcome c, Lung Outcome c

Colon Positive Outcomec back to ToC or Class ToC

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

Positive Outcome, i.e., something related to colon cancer has been found in the patient.
is equivalent to
positive result type op only Colon Positive Outcome Type c
has super-classes
Colon Outcome c, Positive Outcome c
has sub-classes
Polyp of Colon c
is disjoint with
Celiac Positive Outcome c, Cervix Positive Outcome c, Lung Positive Outcome c

Colon Positive Outcome Typec back to ToC or Class ToC

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

Class describing for which type of colon cancer the clinical case tested positive.
has super-classes
Positive Outcome Type c
has members
Adenocarcinoma ni, Colitis ni, Colon Adenocarcinoma ni, Granuloma ni, Metastatic Adenocarcinoma ni, Metastatic Colon Adenocarcinoma ni, Ulcer ni
is disjoint with
Celiac Positive Outcome Type c, Cervix Positive Outcome Type c, Lung Positive Outcome Type c

Colon Surgery Typec back to ToC or Class ToC

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

Class describing surgical procedure type related to colon cancer.
has super-classes
Colon Intervention or Procedure Type c, Surgical Procedure Type c
has members
Anastomosis ni, Colonoscopic Polypectomy ni, Hemicolectomy ni, Polypectomy ni, Resection ni

Colon Tubular Adenomac back to ToC or Class ToC

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

A usually polypoid neoplasm that arises from the glandular epithelium of the colonic mucosa. It is characterized by a tubular architectural pattern. The neoplastic glandular cells have dysplastic features. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C7041
has super-classes
Adenoma c

Colon Tubulovillous Adenomac back to ToC or Class ToC

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

A neoplasm that arises from the glandular epithelium of the colonic mucosa. It is characterized by tubular and villous architectural patterns. The neoplastic glandular cells have dysplastic features. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C5496
has super-classes
Adenoma c

Colon Villous Adenomac back to ToC or Class ToC

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

A villous adenoma that involves the colon. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0021271
has super-classes
Adenoma c

Conceptc back to ToC or Class ToC

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

An abstract idea or notion; a unit of thought.
An idea or notion; a unit of thought.
Is defined by
http://www.w3.org/2004/02/skos/core
is in domain of
has related op, is in semantic relation with op, is top concept in scheme op
is in range of
has related op, has top concept op, is in semantic relation with op
has members
Acanthosis ni, Adenocarcinoma ni, Adult Onset ni, Anastomosis ni, Antrum Pylori ni, Ascending Colon ni, Atrophic Vulva ni, Biopsy of Colon ni, Biopsy of Duodenum ni, Biopsy of Jejunum ni, Biopsy of Small Intestine ni, Biopsy of the Greater Curvature ni, Biopsy of the Pyloric Antrum ni, Bronchial Biopsy ni, Bronchus ni, Brunner's Gland Hyperplasia ni, Caecum ni, Celiac disease ni, Cervical Adenocarcinoma ni, Cervical Adenocarcinoma in Situ ni, Cervical Biopsy ni, Cervical Cancer ni, Cervical Carcinoma ni, Cervical Intraepithelial Neoplasia ni, Cervical Intraepithelial Neoplasia Grade 2/3 ni, Cervical Mucus ni, Cervical Polyp ni, Cervical Squamo-Columnar Junction ni, Cervical Squamous Cell Carcinoma ni, Cervical Squamous Intraepithelial Neoplasia 2 ni, Cervicitis ni, Cervix Epithelium ni, Cervix Glandular Epithelium ni, Cervix Squamous Epithelium ni, Chronic Active Inflammation ni, Chronic Cervicitis ni, Chronic Inflammation ni, Colitis ni, Colon Adenocarcinoma ni, Colon Carcinoma ni, Colon Dysplasia ni, Colon, NOS ni, Colonoscopic Polypectomy ni, Colorectum ni, Condyloma ni, Conization ni, Crohn Disease ni, Crypt of Lieberkuhn of Duodenum ni, Descending Colon ni, Duodenal Ampulla ni, Duodenal Epithelium ni, Duodenal Gland ni, Duodenal Lamina Propria ni, Duodenal Mucosa ni, Duodenum ni, Dyskeratosis ni, Edema ni, Elastofibroma ni, Endocervical Curettage ni, Endometrium ni, Endoscopic Biopsy ni, Enterocyte ni, Eosinophil ni, Erosion ni, Exocervical Epithelium ni, Female Gender ni, Focal Acute Inflammation ni, Gastric Heterotopia of the Small Intestine ni, Gastric Metaplasia ni, Glandular Atrophy ni, Granulocyte ni, Granuloma ni, Greater Curvature of Stomach ni, Hemicolectomy ni, High Grade Dysplasia ni, Human Papilloma Virus Infection ni, Hyperemia ni, Hyperkeratosis ni, Hysterectomy ni, Ileum ni, Inflammation ni, Insufficient Material ni, Intestinal Fibrosis ni, Intestinal Metaplasia ni, Intestinal Villus of Duodenum ni, Jejunum ni, Koilocytotic Squamous Cell ni, Lamina Propria ni, Late Onset ni, Left Colon ni, Left Inferior Lobar Bronchus ni, Left Main Bronchus ni, Left Superior Lobar Bronchus ni, Leukocyte ni, Lobar Bronchus ni, Loop Electrosurgical Excision ni, Low Grade Cervical Squamous Intraepithelial Neoplasia ni, Lung ni, Lung Biopsy ni, Lung cancer ni, Lymphadenitis ni, Lymphocyte ni, Main Bronchus ni, Malabsorption ni, Male Gender ni, Mediastinum ni, Metaplasia ni, Metastasis ni, Metastatic Adenocarcinoma ni, Metastatic Colon Adenocarcinoma ni, Midlle Age Onset ni, Mild Colon Dysplasia ni, Mild Dysplasia ni, Moderate Colon Dysplasia ni, Moderate Dysplasia ni, Mucosa ni, Mucosa of Pyloric Antrum ni, Necrosis ni, Neutrophil ni, Pavement Epithelium ni, Pleura ni, Polypectomy ni, Pulmonary Lymph Node ni, Radboud University Nijmegen ni, Radical Hysterectomy ni, Rectal Mucous Membrane ni, Rectosigmoid Junction ni, Rectum, NOS ni, Resection ni, Right Colon ni, Right Inferior Lobar Bronchus ni, Right Main Bronchus ni, Right Superior Lobar Bronchus ni, Sarcoidosis ni, Severe Colon Dysplasia ni, Severe Dysplasia ni, Sigmoid Colon ni, Simple Epithelium ni, Small Intestine ni, Specimen Unsatisfactory for Diagnosis ni, Squamous Carcinoma in Situ ni, Squamous Intraepithelial Neoplasia ni, Squamous Metaplasia ni, Thoracic Lymph Node ni, Tissue Congestion ni, Total Abdominal Hysterectomy ni, Transverse Colon ni, Ulcer ni, Uterus, NOS ni, Young Adult Onset ni
is disjoint with
Collection c, Concept Scheme c

Concept Schemec back to ToC or Class ToC

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

A set of concepts, optionally including statements about semantic relationships between those concepts.
Is defined by
http://www.w3.org/2004/02/skos/core
Example
Thesauri, classification schemes, subject heading lists, taxonomies, 'folksonomies', and other types of controlled vocabulary are all examples of concept schemes. Concept schemes are also embedded in glossaries and terminologies.
is in domain of
has top concept op
is in range of
is in scheme op, is top concept in scheme op
is disjoint with
Collection c, Concept c

Cytokeratin 34bE12c back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/CK34BE12

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: https://w3id.org/examode/ontology/CK56

An immunohistochemical diagnostic test utilizing an antibody to detect both cytokeratin 5 and 6 in tissues. [Definition Source: NCIT]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C80497
has super-classes
Boolean Check Element c

Desmocollin-3c back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/DSC3

Component of intercellular desmosome junctions. Involved in the interaction of plaque proteins and intermediate filaments mediating cell-cell adhesion. May contribute to epidermal cell positioning (stratification) by mediating differential adhesiveness between cells that express different isoforms. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/Q14574
has super-classes
Boolean Check Element c

Disease or Disorderc back to ToC or Class ToC

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

A disease is a disposition to undergo pathological processes that exists in an organism because of one or more disorders in that organism. [Definition Source: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C2991
is in range of
associated disease, is about disease op
has members
Celiac disease ni, Cervical Cancer ni, Colon Carcinoma ni, Lung cancer ni

Duodenitisc back to ToC or Class ToC

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

A form of inflammation
Is defined by
http://purl.obolibrary.org/obo/MONDO_0004627
has super-classes
Celiac Positive Outcome c
is in domain of
duodenitis severity dp

Dysplasiac back to ToC or Class ToC

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

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.
Is defined by
http://purl.obolibrary.org/obo/NCIT_C4086
has super-classes
Finding c
is in range of
has dysplasia op
has members
Colon Dysplasia ni, High Grade Dysplasia ni, Mild Colon Dysplasia ni, Mild Dysplasia ni, Moderate Colon Dysplasia ni, Moderate Dysplasia ni, Severe Colon Dysplasia ni, Severe Dysplasia ni
is disjoint with
Celiac Disease Finding c, Human Papilloma Virus Infection c, Intestinal Abnormality c, Koilocytotic Squamous Cell c, Lung Carcinoma Finding c

Endonuclease P40c back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/P40

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

Findingc back to ToC or Class ToC

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

A meaningful interpretation of data or observations resulting from planned evaluations. Compare to conclusion, hypothesis. See also general observation class, intervention, event. A meaningful interpretation of data or observations resulting from planned evaluations. Compare to conclusion, hypothesis. See also general observation class, intervention, event. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C3367
has sub-classes
Celiac Disease Finding c, Dysplasia c, Human Papilloma Virus Infection c, Intestinal Abnormality c, Koilocytotic Squamous Cell c, Lung Carcinoma Finding 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

Genderc back to ToC or Class ToC

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

Characteristics of people that are socially constructed, including norms, behaviors, and roles based on sex. As a social construct, gender varies from society to society and can change over time. (Adapted from WHO.) [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C17357
is in range of
has gender op
has members
Female Gender ni, Male Gender ni

HER2 (CB11)c back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/HER2

Protein tyrosine kinase that is part of several cell surface receptor complexes, but that apparently needs a coreceptor for ligand binding. Essential component of a neuregulin-receptor complex, although neuregulins do not interact with it alone. GP30 is a potential ligand for this receptor. Regulates outgrowth and stabilization of peripheral microtubules (MTs). Upon ERBB2 activation, the MEMO1-RHOA-DIAPH1 signaling pathway elicits the phosphorylation and thus the inhibition of GSK3B at cell membrane. This prevents the phosphorylation of APC and CLASP2, allowing its association with the cell membrane. In turn, membrane-bound APC allows the localization of MACF1 to the cell membrane, which is required for microtubule capture and stabilization. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprotkb/P04626/entry
has super-classes
String Check Element c
is in domain of
has test result dp

Human Papilloma Virus Infectionc back to ToC or Class ToC

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

A cervix disease may present or not the human papilloma virus.
Is defined by
http://purl.obolibrary.org/obo/MONDO_0005161
has super-classes
Finding c
is in range of
detected HPV op
has members
Human Papilloma Virus Infection ni
is disjoint with
Celiac Disease Finding c, Dysplasia c, Intestinal Abnormality c, Koilocytotic Squamous Cell c, Lung Carcinoma Finding c

Immunohistochemical Testc back to ToC or Class ToC

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

A diagnostic test in which an antibody is used to link a cellular antigen specifically to a stain that can be seen with a microscope. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C51944
has super-classes
Test c
has sub-classes
Check Element c

Immunoprecipitationc back to ToC or Class ToC

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

Antigen aggregation with antibody, in the right ratios, to cause precipitation. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C16724
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
is in domain of
inconclusive result type op

Inconclusive Outcome Typec back to ToC or Class ToC

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

Class describing why the clinical case resulted inconclusive.
is in range of
inconclusive result type op
has members
Insufficient Material ni, Specimen Unsatisfactory for Diagnosis ni

Institutionc back to ToC or Class ToC

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

has members
ExaMode Consortium ni

Intervention or Procedurec back to ToC or Class ToC

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

This general class represents the intervention performed on the patient to obtain the samples that are then studied to find the disease. In particular, this class represents the attribute 'MATERIALI' in the AOEC Database, and the attribute METHOD in the TCGA database.
Is defined by
http://purl.obolibrary.org/obo/NCIT_C25218
has sub-classes
Celiac Disease Intervention or Procedure c, Cervix Cancer Intervention or Procedure c, Colon Cancer Intervention or Procedure c, Lung Cancer Intervention or Procedure c, Surgical Procedure c
is in domain of
has intervention type op
is in range of
has intervention op

Intervention or Procedure Typec back to ToC or Class ToC

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

Class describing the type of intervention or procedure performed.
has sub-classes
Celiac Disease Intervention or Procedure Type c, Cervix Intervention or Procedure Type c, Colon Intervention or Procedure Type c, Lung Intervention or Procedure Type c, Surgical Procedure Type c
is in range of
has intervention type op

Intestinal Abnormalityc back to ToC or Class ToC

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

Abnormality in celiac outcomes.
has super-classes
Finding c
is in range of
presence of intestinal abnormality op
has members
Brunner's Gland Hyperplasia ni, Chronic Active Inflammation ni, Chronic Inflammation ni, Crohn Disease ni, Edema ni, Erosion ni, Gastric Heterotopia of the Small Intestine ni, Gastric Metaplasia ni, Glandular Atrophy ni, Hyperemia ni, Inflammation ni, Intestinal Fibrosis ni, Intestinal Metaplasia ni, Malabsorption ni, Tissue Congestion ni, Ulcer ni
is disjoint with
Celiac Disease Finding c, Dysplasia c, Human Papilloma Virus Infection c, Koilocytotic Squamous Cell c, Lung Carcinoma Finding c

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

IRI: https://w3id.org/examode/ontology/CK19

Involved in the organization of myofibers. Together with KRT8, helps to link the contractile apparatus to dystrophin at the costameres of striated muscle. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/P08727
has super-classes
Boolean Check Element c

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

IRI: https://w3id.org/examode/ontology/CK20

Plays a significant role in maintaining keratin filament organization in intestinal epithelia. When phosphorylated, plays a role in the secretion of mucin in the small intestine. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/P35900
has super-classes
Boolean Check Element c

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

IRI: https://w3id.org/examode/ontology/CK7

Blocks interferon-dependent interphase and stimulates DNA synthesis in cells. Involved in the translational regulation of the human papillomavirus type 16 E7 mRNA (HPV16 E7). [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/P08729
has super-classes
Boolean Check Element c

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

IRI: https://w3id.org/examode/ontology/CK59

In the hair cortex, hair keratin intermediate filaments are embedded in an interfilamentous matrix, consisting of hair keratin-associated protein (KRTAP), which are essential for the formation of a rigid and resistant hair shaft through their extensive disulfide bond cross-linking with abundant cysteine residues of hair keratins. The matrix proteins include the high-sulfur and high-glycine-tyrosine keratins. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/P26371
has super-classes
Boolean Check Element c

Koilocytotic Squamous Cellc back to ToC or Class ToC

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

Koilocytes are epithelial cells containing a hyperchromatic nucleus that is acentrically displaced by perinuclear vacuole(s), and these morphological alterations are used by pathologists to help identify HPV-infected epithelial cells in Pap smears. [Definition Source: PMID 18688031]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C36808
has super-classes
Finding c
is in range of
detected koilocyte op
has members
Koilocytotic Squamous Cell ni
is disjoint with
Celiac Disease Finding c, Dysplasia c, Human Papilloma Virus Infection c, Intestinal Abnormality c, Lung Carcinoma Finding c

Laboratory Findingc back to ToC or Class ToC

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

This class is used to contain information about the celiac disease, the IEL, the villli to crypt ratio and the villi status.
has sub-classes
Other Laboratory Finding c, Villi Laboratory Finding c
is in range of
has laboratory finding op

Lung Adenocarcinomac back to ToC or Class ToC

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

A carcinoma that arises from the lung and is characterized by the presence of malignant glandular epithelial cells. There is a male predilection with a male to female ratio of 2:1. Usually lung adenocarcinoma is asymptomatic and is identified through screening studies or as an incidental radiologic finding. If clinical symptoms are present they include shortness of breath, cough, hemoptysis, chest pain, and fever. Tobacco smoke is a known risk factor. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0005061
has super-classes
Non-Small Cell Lung Carcinoma c
has sub-classes
Clear Cell Adenocarcinoma c, Metastatic Neoplasm c

Lung Anatomical Entityc back to ToC or Class ToC

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

Class describing biological entities related to lung cancer.
has super-classes
Anatomical Entity c
has members
Bronchus ni, Left Inferior Lobar Bronchus ni, Left Main Bronchus ni, Left Superior Lobar Bronchus ni, Lobar Bronchus ni, Lung ni, Main Bronchus ni, Mediastinum ni, Pleura ni, Pulmonary Lymph Node ni, Right Inferior Lobar Bronchus ni, Right Main Bronchus ni, Right Superior Lobar Bronchus ni, Thoracic Lymph Node ni
is disjoint with
Celiac Anatomical Entity c, Cervix Anatomical Entity c, Colon Anatomical Entity c

Lung Cancer Intervention or Procedurec back to ToC or Class ToC

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

Class describing interventions or procedures related to lung cancer.
is equivalent to
has location op only Lung Anatomical Entity c
has super-classes
Intervention or Procedure c
has sub-classes
Lung Cancer Surgical Procedure c
is disjoint with
Celiac Disease Intervention or Procedure c, Cervix Cancer Intervention or Procedure c, Colon Cancer Intervention or Procedure c

Lung Cancer Surgical Procedurec back to ToC or Class ToC

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

Class describing surgical procedures related to lung cancer.
has super-classes
Lung Cancer Intervention or Procedure c, Surgical Procedure c
is disjoint with
Celiac Disease Surgical Procedure c, Cervix Cancer Surgical Procedure c, Colon Cancer Surgical Procedure c

Lung Carcinomac back to ToC or Class ToC

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

A carcinoma that arises from epithelial cells of the lung. [Definition Source: https://orcid.org/0000-0002-6601-2165]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0005138
is equivalent to
presence of op some Lung Carcinoma Finding c
has super-classes
Lung Positive Outcome c
has sub-classes
Non-Small Cell Lung Carcinoma c, Small Cell Lung Carcinoma c

Lung Carcinoma Findingc back to ToC or Class ToC

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

Is defined by
https://w3id.org/examode/ontology/
has super-classes
Finding c
has members
Metastasis ni, Necrosis ni
is disjoint with
Celiac Disease Finding c, Dysplasia c, Human Papilloma Virus Infection c, Intestinal Abnormality c, Koilocytotic Squamous Cell c

Lung Clinical Case Reportc back to ToC or Class ToC

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

Class representing all lung cancer cases.
is equivalent to
has outcome op only Lung Outcome c
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 Intervention or Procedure Typec back to ToC or Class ToC

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

Class describing the type of intervention or procedure related to lung cancer.
has super-classes
Intervention or Procedure Type c
has sub-classes
Lung Surgery Type c
has members
Bronchial Biopsy ni, Lung Biopsy ni

Lung Large Cell Carcinomac back to ToC or Class ToC

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

A poorly differentiated non-small cell lung carcinoma composed of large polygonal cells without evidence of glandular or squamous differentiation. There is a male predilection. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0003050
has super-classes
Non-Small Cell Lung Carcinoma c

Lung Outcomec back to ToC or Class ToC

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

Class representing all outcomes of lung clinical case reports.
is equivalent to
has intervention op only Lung Cancer Intervention or Procedure c
has location op only Lung Anatomical Entity c
has super-classes
Outcome c
has sub-classes
Lung Positive Outcome c
is disjoint with
Celiac Outcome c, Cervix Outcome c, Colon Outcome c

Lung Positive Outcomec back to ToC or Class ToC

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

Positive Outcome, i.e., something related to lung cancer has been found in the patient.
is equivalent to
positive result type op only Lung Positive Outcome Type c
has super-classes
Lung Outcome c, Positive Outcome c
has sub-classes
Lung Carcinoma c
is disjoint with
Celiac Positive Outcome c, Cervix Positive Outcome c, Colon Positive Outcome c

Lung Positive Outcome Typec back to ToC or Class ToC

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

Class describing for which type of lung cancer the clinical case tested positive.
has super-classes
Positive Outcome Type c
has members
Elastofibroma ni, Lymphadenitis ni, Sarcoidosis ni
is disjoint with
Celiac Positive Outcome Type c, Cervix Positive Outcome Type c, Colon Positive Outcome Type c

Lung Surgery Typec back to ToC or Class ToC

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

Class describing surgical procedure type related to lung cancer.
has super-classes
Lung Intervention or Procedure Type c, Surgical Procedure Type c

Malignant Lung Neoplasmc back to ToC or Class ToC

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

A primary or metastatic malignant neoplasm involving the lung. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C7377
has super-classes
Non-Small Cell Lung Carcinoma c

Metastatic Neoplasmc back to ToC or Class ToC

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

A tumor that has spread from its original (primary) site of growth to another site, close to or distant from the primary site. Metastasis is characteristic of advanced malignancies, but in rare instances can be seen in neoplasms lacking malignant morphology. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0024883
has super-classes
Lung Adenocarcinoma c

Napsin Ac back to ToC or Class ToC

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

May be involved in processing of pneumocyte surfactant precursors. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/O96009
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

Neprilysinc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/CD10

Thermolysin-like specificity, but is almost confined on acting on polypeptides of up to 30 amino acids (PubMed:15283675, PubMed:8168535). Biologically important in the destruction of opioid peptides such as Met- and Leu-enkephalins by cleavage of a Gly-Phe bond (PubMed:17101991). Able to cleave angiotensin-1, angiotensin-2 and angiotensin 1-9 (PubMed:15283675). Involved in the degradation of atrial natriuretic factor (ANF) (PubMed:2531377, PubMed:2972276). Displays UV-inducible elastase activity toward skin preelastic and elastic fibers (PubMed:20876573). [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/P08473
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

Non-Small Cell Lung Carcinomac back to ToC or Class ToC

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

A group of at least three distinct histological types of lung cancer, including non-small cell squamous cell carcinoma, adenocarcinoma, and large cell carcinoma. Non-small cell lung carcinomas have a poor response to conventional chemotherapy. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0005233
has super-classes
Lung Carcinoma c
has sub-classes
Lung Adenocarcinoma c, Lung Large Cell Carcinoma c, Malignant Lung Neoplasm c, Non-Small Cell Squamous Lung Carcinoma c

Non-Small Cell Squamous Lung Carcinomac back to ToC or Class ToC

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

A squamous cell carcinoma that arises from the lung. It is characterized by the presence of large malignant cells. It includes the clear cell and papillary variants of squamous cell carcinoma. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0056806
has super-classes
Non-Small Cell Lung Carcinoma c

Onsetc back to ToC or Class ToC

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

The age group in which disease manifestations appear. [Definition Source: HPO]
Is defined by
https://hpo.jax.org/app/browse/term/HP:0003674
is in range of
has age onset op
has members
Adult Onset ni, Late Onset ni, Midlle Age Onset ni, Young Adult Onset ni

Ordered Collectionc back to ToC or Class ToC

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

An ordered collection of concepts, where both the grouping and the ordering are meaningful.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-classes
Collection c
is in domain of
has member list op

Organizationc back to ToC or Class ToC

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

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

Other Laboratory Findingc back to ToC or Class ToC

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

This class contains information about other laboratory finding related to celiac disease, e.g. IEL or number of mitosis per crypt.
has super-classes
Laboratory Finding c
is in domain of
intraepithelial lymphocyte count dp, number of mitosis per crypt dp

Outcomec back to ToC or Class ToC

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

A class representing a general outcome, whatever it may be (positive, negative, uncertain, not enough information etc).
Is defined by
http://purl.obolibrary.org/obo/NCIT_C20200
has sub-classes
Celiac Outcome c, Cervix Outcome c, Colon Outcome c, Lung Outcome c, Positive Outcome c
is in domain of
has intervention op, has test op
is in range of
has outcome op

Patientc back to ToC or Class ToC

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

A person under health care. The person may be waiting for this care or may be receiving it or may have already received it. [Definition source: RxList]
Is defined by
https://w3id.org/examode/ontology/
is in domain of
has age dp, has age onset op, has clinical case report op, has gender op

Polyp of Colonc back to ToC or Class ToC

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

A polyp that involves the colon. [Definition Source: MONDO]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0021400
is equivalent to
has dysplasia op min 0 Dysplasia c
has dysplasia op max 1 Dysplasia c
has super-classes
Colon Positive Outcome c
has sub-classes
Adenoma c, Colon Hyperplastic Polyp c, Colon Inflammatory Polyp c
is in domain of
has dysplasia op

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
Celiac Positive Outcome c, Cervix Positive Outcome c, Colon Positive Outcome c, Lung Positive Outcome c
is in domain of
positive result type op

Positive Outcome Typec back to ToC or Class ToC

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

Class describing for what the clinical case tested positive.
has sub-classes
Celiac Positive Outcome Type c, Cervix Positive Outcome Type c, Colon Positive Outcome Type c, Lung Positive Outcome Type c
is in range of
positive result type op

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 an individual in the ontology, and it is not good practice to have entities that are both individuals and General Classes in the same ontology.
has super-classes
Celiac Positive Outcome c
is in domain of
modified Marsh classification of histologic findings in celiac disease dp

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

IRI: https://w3id.org/examode/ontology/KI67

Required to maintain individual mitotic chromosomes dispersed in the cytoplasm following nuclear envelope disassembly (PubMed:27362226). Associates with the surface of the mitotic chromosome, the perichromosomal layer, and covers a substantial fraction of the chromosome surface (PubMed:27362226). Prevents chromosomes from collapsing into a single chromatin mass by forming a steric and electrostatic charge barrier: the protein has a high net electrical charge and acts as a surfactant, dispersing chromosomes and enabling independent chromosome motility (PubMed:27362226). Binds DNA, with a preference for supercoiled DNA and AT-rich DNA (PubMed:10878551). Does not contribute to the internal structure of mitotic chromosomes (By similarity). May play a role in chromatin organization (PubMed:24867636). It is however unclear whether it plays a direct role in chromatin organization or whether it is an indirect consequence of its function in maintaining mitotic chromosomes dispersed (Probable). [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/P46013
has super-classes
Float Check Element c
is in domain of
has value dp

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

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

Pulmonary surfactant-associated proteins promote alveolar stability by lowering the surface tension at the air-liquid interface in the peripheral air spaces. SP-B increases the collapse pressure of palmitic acid to nearly 70 millinewtons per meter. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/P07988
has super-classes
Boolean Check Element c

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

IRI: https://w3id.org/examode/ontology/CD45

Protein tyrosine-protein phosphatase required for T-cell activation through the antigen receptor. Acts as a positive regulator of T-cell coactivation upon binding to DPP4. The first PTPase domain has enzymatic activity, while the second one seems to affect the substrate specificity of the first one. Upon T-cell activation, recruits and dephosphorylates SKAP1 and FYN. Dephosphorylates LYN, and thereby modulates LYN activity (By similarity). (Microbial infection) Acts as a receptor for human cytomegalovirus protein UL11 and mediates binding of UL11 to T-cells, leading to reduced induction of tyrosine phosphorylation of multiple signaling proteins upon T-cell receptor stimulation and impaired T-cell proliferation. [Definition Source: Uniprot]
Is defined by
https://www.uniprot.org/uniprot/P08575
has super-classes
Boolean Check Element c

Semantic Areac back to ToC or Class ToC

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

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
is in range of
has semantic area
has members
Anatomical Location ni, Diagnosis ni, General Entity ni, Procedure ni, Test ni

Serrated Adenomac back to ToC or Class ToC

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

An adenoma that arises from the large intestine and the appendix. It is characterized by prominent serration of the glands. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C38458
has super-classes
Adenoma c

Slide Devicec back to ToC or Class ToC

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

A flat rectangular piece of glass on which specimens can be mounted for microscopic study. [Definition Source:NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C50178
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: https://w3id.org/examode/ontology/SCLC1

Small cell lung cancer (SCLC) is a highly aggressive malignant neoplasm, accounting for 10-15% of lung cancer cases, characterized byrapid growth, and early metastasis. SCLC usually manifests as a large hilar mass with bulky mediastinal lymphadenopathy presenting clinically with chest pain, persistent cough, dyspnea, wheezing, hoarseness, hemoptysis, loss of appetite, weight loss, and neurological and endocrine paraneoplastic syndromes. SCLC is primarily reported in elderly people with a history of long-term tobacco exposure. [Definition Source Orphanet 70573]
Is defined by
http://purl.obolibrary.org/obo/MONDO_0008433
has super-classes
Lung Carcinoma c

String Check Elementc back to ToC or Class ToC

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

A set of checks controlled on an Immunohistochemical test that can only have a string result.
has super-classes
Check Element c
has sub-classes
HER2 (CB11) c

Surgical Procedurec back to ToC or Class ToC

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

A diagnostic or treatment procedure performed by manual and/or instrumental means, often involving an incision and the removal or replacement of a diseased organ or tissue; of or relating to or involving or used in surgery or requiring or amenable to treatment by surgery. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C15329
has super-classes
Intervention or Procedure c
has sub-classes
Celiac Disease Surgical Procedure c, Cervix Cancer Surgical Procedure c, Colon Cancer Surgical Procedure c, Lung Cancer Surgical Procedure c

Surgical Procedure Typec back to ToC or Class ToC

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

Class describing the type of surgical procedure performed.
has super-classes
Intervention or Procedure Type c
has sub-classes
Celiac Disease Surgery Type c, Cervix Surgery Type c, Colon Surgery Type c, Lung Surgery Type c

Synaptophysinc back to ToC or Class ToC

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

Possibly involved in structural functions as organizing other membrane components or in targeting the vesicles to the plasma membrane. Involved in the regulation of short-term and long-term synaptic plasticity. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/P08247
has super-classes
Boolean Check Element c

Testc back to ToC or Class ToC

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

A general class representing a test.
Is defined by
http://purl.obolibrary.org/obo/NCIT_C47891
has sub-classes
Immunohistochemical Test c
is in range of
has test op

TTF1 Humanc back to ToC or Class ToC

IRI: https://w3id.org/examode/ontology/TTF1

Multifunctional nucleolar protein that terminates ribosomal gene transcription, mediates replication fork arrest and regulates RNA polymerase I transcription on chromatin. Plays a dual role in rDNA regulation, being involved in both activation and silencing of rDNA transcription. Interaction with BAZ2A/TIP5 recovers DNA-binding activity. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/Q15361
has super-classes
Boolean Check Element c

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

IRI: https://w3id.org/examode/ontology/P63

Tumor protein 63 isoform 2 (586 aa, ; 66 kDa) is encoded by the human TP63 gene. This protein plays a role in the mediation of both transcription and skin development. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C128298
has super-classes
Boolean Check Element c

Villi Laboratory Findingc back to ToC or Class ToC

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

This class contains information about villi status
has super-classes
Laboratory Finding c
is in domain of
absence of villi dp, duodenum villi length dp, has flattened villi dp, villi degree of atrophy dp, villi to crypt of Lieberkuhn ratio dp

Vimentinc back to ToC or Class ToC

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

Vimentins are class-III intermediate filaments found in various non-epithelial cells, especially mesenchymal cells. Vimentin is attached to the nucleus, endoplasmic reticulum, and mitochondria, either laterally or terminally. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2. [Definition Source: UniProt]
Is defined by
https://www.uniprot.org/uniprot/P08670
has super-classes
Boolean Check Element c

Object Properties

detected HPVop back to ToC or Object Property ToC

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

If this property is present, it signals the presence of a human papilloma virus (HPV) in the outcome. It needs to have as object the HPV infection named entity.
has domain
Cervix Outcome c
has range
Human Papilloma Virus Infection c

detected koilocyteop back to ToC or Object Property ToC

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

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

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

Broader concepts are typically rendered as parents in a concept hierarchy (tree).
Relates a concept to a concept that is more general in meaning.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
has broader transitive op
has sub-properties
has broader match op
is inverse of
has narrower op

has broader matchop back to ToC or Object Property ToC

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

skos:broadMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
has broader op, is in mapping relation with op
is inverse of
has narrower match op

has broader transitiveop back to ToC or Object Property ToC

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

skos:broaderTransitive is a transitive superproperty of skos:broader.
Is defined by
http://www.w3.org/2004/02/skos/core

has characteristics: transitive

has super-properties
is in semantic relation with op
has sub-properties
has broader op
is inverse of
has narrower transitive op

has clinical case reportop back to ToC or Object Property ToC

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

Connects one patient to its clinical case report.

has characteristics: symmetric

has domain
Patient c
has range
Clinical Case Report c

has close matchop back to ToC or Object Property ToC

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

skos:closeMatch is used to link two concepts that are sufficiently similar that they can be used interchangeably in some information retrieval applications. In order to avoid the possibility of "compound errors" when combining mappings across more than two concept schemes, skos:closeMatch is not declared to be a transitive property.
Is defined by
http://www.w3.org/2004/02/skos/core

has characteristics: symmetric

has super-properties
is in mapping relation with op
has sub-properties
has exact match op

has dysplasiaop back to ToC or Object Property ToC

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

Connects an instance of Polyp of Colon to a named individual of type Dysplasia. Cardinality between 0 and 1.
has domain
Polyp of Colon c
has range
Dysplasia c

has exact matchop back to ToC or Object Property ToC

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

skos:exactMatch is disjoint with each of the properties skos:broadMatch and skos:relatedMatch.
skos:exactMatch is used to link two concepts, indicating a high degree of confidence that the concepts can be used interchangeably across a wide range of information retrieval applications. skos:exactMatch is a transitive property, and is a sub-property of skos:closeMatch.
Is defined by
http://www.w3.org/2004/02/skos/core

has characteristics: symmetric, transitive

has super-properties
has close match op

has genderop back to ToC or Object Property ToC

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

To connect a record with the gender of the corresponding person.

has characteristics: functional

has domain
Patient c
has range
Gender c

has interventionop back to ToC or Object Property ToC

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

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 intervention typeop back to ToC or Object Property ToC

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

Connects an intervention (or procedure) to its type.
has domain
Intervention or Procedure c
has range
Intervention or Procedure Type c

has laboratory findingop back to ToC or Object Property ToC

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

Connects an instance of celiac outcome to an instance of laboratory finding or any of its subclasses.
has domain
Celiac Clinical Case Report c
has range
Laboratory Finding 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) or an Intervention to a location, a member of the class anatomical entity.
has domain
Intervention or Procedure c or Outcome c
has range
Anatomical Entity c

has memberop back to ToC or Object Property ToC

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

Relates a collection to one of its members.
Is defined by
http://www.w3.org/2004/02/skos/core
has domain
Collection c
has range
Collection c or Concept c

has member listop back to ToC or Object Property ToC

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

For any resource, every item in the list given as the value of the skos:memberList property is also a value of the skos:member property.
Relates an ordered collection to the RDF list containing its members.
Is defined by
http://www.w3.org/2004/02/skos/core

has characteristics: functional

has domain
Ordered Collection c
has range
list

has narrowerop back to ToC or Object Property ToC

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

Narrower concepts are typically rendered as children in a concept hierarchy (tree).
Relates a concept to a concept that is more specific in meaning.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
has narrower transitive op
has sub-properties
has narrower match op
is inverse of
has broader op

has narrower matchop back to ToC or Object Property ToC

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

skos:narrowMatch is used to state a hierarchical mapping link between two conceptual resources in different concept schemes.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
has narrower op, is in mapping relation with op
is inverse of
has broader match op

has narrower transitiveop back to ToC or Object Property ToC

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

skos:narrowerTransitive is a transitive superproperty of skos:narrower.
Is defined by
http://www.w3.org/2004/02/skos/core

has characteristics: transitive

has super-properties
is in semantic relation with op
has sub-properties
has narrower op
is inverse of
has broader transitive op

has outcomeop back to ToC or Object Property ToC

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

Every report has an outcome, whatever it may be (positive, negative, inconclusive etc.)

has characteristics: functional

has domain
Clinical Case Report c
has range
Outcome c

has relatedop back to ToC or Object Property ToC

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

skos:related is disjoint with skos:broaderTransitive
Relates a concept to a concept with which there is an associative semantic relationship.
Is defined by
http://www.w3.org/2004/02/skos/core
https://w3id.org/examode/ontology/

has characteristics: symmetric

has super-properties
is in semantic relation with op
has sub-properties
has related match op
has domain
Concept c
has range
Concept c

has related matchop back to ToC or Object Property ToC

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

skos:relatedMatch is used to state an associative mapping link between two conceptual resources in different concept schemes.
Is defined by
http://www.w3.org/2004/02/skos/core

has characteristics: symmetric

has super-properties
has related op, is in mapping relation with op

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

The test performed.
has domain
Outcome c
has range
Test c

has top conceptop back to ToC or Object Property ToC

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

Relates, by convention, a concept scheme to a concept which is topmost in the broader/narrower concept hierarchies for that scheme, providing an entry point to these hierarchies.
Is defined by
http://www.w3.org/2004/02/skos/core
has domain
Concept Scheme c
has range
Concept c
is inverse of
is top concept in scheme op

inconclusive result typeop back to ToC or Object Property ToC

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

Connects an inconclusive outcome to its type.
has domain
Inconclusive Outcome c
has range
Inconclusive Outcome Type 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. 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.

has characteristics: functional

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

is in mapping relation withop back to ToC or Object Property ToC

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

These concept mapping relations mirror semantic relations, and the data model defined below is similar (with the exception of skos:exactMatch) to the data model defined for semantic relations. A distinct vocabulary is provided for concept mapping relations, to provide a convenient way to differentiate links within a concept scheme from links between concept schemes. However, this pattern of usage is not a formal requirement of the SKOS data model, and relies on informal definitions of best practice.
Relates two concepts coming, by convention, from different schemes, and that have comparable meanings
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
is in semantic relation with op
has sub-properties
has broader match op, has close match op, has narrower match op, has related match op

is in schemeop back to ToC or Object Property ToC

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

Relates a resource (for example a concept) to a concept scheme in which it is included.
Is defined by
http://www.w3.org/2004/02/skos/core
has sub-properties
is top concept in scheme op
has range
Concept Scheme c

is in semantic relation withop back to ToC or Object Property ToC

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

Links a concept to a concept related by meaning.
Is defined by
http://www.w3.org/2004/02/skos/core
has sub-properties
has broader transitive op, has narrower transitive op, has related op, is in mapping relation with op
has domain
Concept c
has range
Concept c

is top concept in schemeop back to ToC or Object Property ToC

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

Relates a concept to the concept scheme that it is a top level concept of.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
is in scheme op
has domain
Concept c
has range
Concept Scheme c
is inverse of
has top concept op

madeop back to ToC or Object Property ToC

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

has domain
agent c or Organization c
has range
Clinical Case Report c
is inverse of
maker op

makerop back to ToC or Object Property ToC

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

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

positive result typeop back to ToC or Object Property ToC

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

Connects a positive outcome to its type.
has domain
Positive Outcome c
has range
Positive Outcome Type 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. Such information may not be directly pertinent to the disease however it can be still linked to it.
has domain
Celiac Clinical Case Report c or Lung Carcinoma c
has range
Celiac Disease Finding c or Lung Carcinoma Finding c

presence of intestinal abnormalityop back to ToC or Object Property ToC

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

Connects one celiac outcome to the intestinal abnormality detected in the specimen.
has domain
Celiac Outcome c
has range
Intestinal Abnormality c

Data Properties

absence of villidp back to ToC or Data Property ToC

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

Whether the tissue is without villi.

has characteristics: functional

has domain
Villi Laboratory Finding c
has range
boolean

duodenitis severitydp back to ToC or Data Property ToC

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

The severity of the duodenitis.

has characteristics: functional

has domain
Duodenitis c
has range
string

duodenum villi lengthdp back to ToC or Data Property ToC

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

The distance from point to point along the longest axis of the finger-like projections of the mucosal layer of the duodenum.
Is defined by
http://purl.obolibrary.org/obo/VT_0010209
has domain
Villi Laboratory Finding c
has range
string

has agedp back to ToC or Data Property ToC

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

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

has block numberdp back to ToC or Data Property ToC

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

The block number identifies the part of the image connected to the diagnosis (for Radbound). For AOEC this property is not necessary. We use it to contain the "internal id".

has characteristics: functional

has domain
Clinical Case Report c
has range
integer

has flattened villidp back to ToC or Data Property ToC

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

Whether the specimen presents falttened villi.
has domain
Villi Laboratory Finding c
has range
boolean

has imagedp back to ToC or Data Property ToC

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

Connects a clinical case report to the name of its corresponding image (the name of the image, e.g. the name of the file).

has characteristics: functional

has domain
Clinical Case Report c
has range
string

has Internal Identifierdp back to ToC or Data Property ToC

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

Connects a clinical case with the its ID used inside the ExaMode project. This property was thought to connect a case to its id given by the hospitals. In this ontology we use the dc:identifier property to connect one case with an URL identifying it.
has domain
Clinical Case Report c
has range
any u r i

has outcomedp back to ToC or Data Property ToC

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

Connects one immunohistochemical test to its boolean value.

has characteristics: functional

has domain
Neprilysin c or Cluster of Differentation 3 c or Receptor-type tyrosine-protein phosphatase C c or Keratin, type I cytoskeletal 19 c or Keratin, type I cytoskeletal 20 c or Cytokeratin 34bE12 c or Cytokeratin 5/6 c or Keratin-associated protein 5-9 c or Keratin, type II cytoskeletal 7 c or Chromogranin-A c or Desmocollin-3 c or Immunoprecipitation c or Napsin A c or Endonuclease P40 c or Tumor Protein 63 Isoform 2 c or Pulmonary surfactant-associated protein B c or Synaptophysin c or TTF1 Human c or Vimentin c
has range
boolean

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 test resultdp back to ToC or Data Property ToC

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

Connects one immunohistochemical test to its string result.

has characteristics: functional

has domain
HER2 (CB11) 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 immunohistochemical test to its float value

has characteristics: functional

has domain
Proliferation marker protein Ki-67 c
has range
float

identifierdp back to ToC or Data Property ToC

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

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

intraepithelial lymphocyte countdp back to ToC or Data Property ToC

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

The determination of the number of the intraepithelial lymphocytes in a sample. [Definition Source: NCI]
Is defined by
http://purl.obolibrary.org/obo/NCIT_C184424
has domain
Other Laboratory Finding c
has range
string

modified Marsh classification of histologic findings in celiac diseasedp back to ToC or Data Property ToC

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

The severity of celiac disease according to Marsh classification.

has characteristics: functional

has domain
Positive to Celiac Disease c
has range
{ "0" , "1" , "2" , "3a" , "3b" , "3c" }

notationdp back to ToC or Data Property ToC

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

A notation, also known as classification code, is a string of characters such as "T58.5" or "303.4833" used to uniquely identify a concept within the scope of a given concept scheme.
Is defined by
http://www.w3.org/2004/02/skos/core

number of mitosis per cryptdp back to ToC or Data Property ToC

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

has domain
Other Laboratory Finding c
has range
string

villi degree of atrophydp back to ToC or Data Property ToC

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

The degree of atrophy of villi.
has domain
Villi Laboratory Finding c
has range
{ "focal" , "mild" , "mild to moderate" , "moderate" , "moderate-severe" , "not specified" , "severe" , "total" }

villi to crypt of Lieberkuhn ratiodp back to ToC or Data Property ToC

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

Ratio of villous height to crypt or Lieberkuhn depth
has domain
Villi Laboratory Finding c
has range
string

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
has domain
thing c
has range
string

alternative labelap back to ToC or Annotation Property ToC

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

The range of skos:altLabel is the class of RDF plain literals.
An alternative lexical label for a resource.
Is defined by
http://www.w3.org/2004/02/skos/core
Example
Acronyms, abbreviations, spelling variants, and irregular plural/singular forms may be included among the alternative labels for a concept. Mis-spelled terms are normally included as hidden labels (see skos:hiddenLabel).
has super-properties
label

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 implemented to extract entities from a clinical case record. NB: we do not guarantee that these rules are always valid, or that they are the only valid. It may be the case that they are inaccurate since we were only able to infer them from the cases that were provided to us. Treat these annotations only as a documentation of our process and for a first implementation of the entities extractor.
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 or Disorder 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 materialiap 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

change noteap back to ToC or Annotation Property ToC

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

A note about a modification to a concept.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
note ap

conforms toap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/conformsTo

creatorap back to ToC or Annotation Property ToC

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

definitionap back to ToC or Annotation Property ToC

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

A statement or formal explanation of the meaning of a concept.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
note ap

definitionap back to ToC or Annotation Property ToC

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

Property representing the definition in the ontobee website. In later versions of the ontology we prefer rdfs:comment since it is more universally used.
has sub-properties
alternative definition ap, external definition ap, structure notes ap, taxon notes ap
has domain
thing c
has range
string

descriptionap back to ToC or Annotation Property ToC

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

editorial noteap back to ToC or Annotation Property ToC

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

A note for an editor, translator or maintainer of the vocabulary.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
note ap

exampleap back to ToC or Annotation Property ToC

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

An example of the use of a concept.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
note ap

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 domain
thing c
has range
string

has exact synonymap back to ToC or Annotation Property ToC

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

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

has Ontobee annotationap back to ToC or Annotation Property ToC

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

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

has related synonymap back to ToC or Annotation Property ToC

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

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 domain
thing c
has range
string

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
Semantic Area c

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 exact synonym ap, has related synonym ap
has domain
thing c
has range
string

hidden labelap back to ToC or Annotation Property ToC

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

The range of skos:hiddenLabel is the class of RDF plain literals.
A lexical label for a resource that should be hidden when generating visual displays of the resource, but should still be accessible to free text search operations.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
label

history noteap back to ToC or Annotation Property ToC

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

A note about the past state/use/meaning of a concept.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
note ap

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 notes that may be useful to those who will work on building the ontology.
has domain
thing c
has range
string

licenseap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/license

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

nameap back to ToC or Annotation Property ToC

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

noteap back to ToC or Annotation Property ToC

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

A general note, for any purpose.
Is defined by
http://www.w3.org/2004/02/skos/core
has sub-properties
change note ap, definition ap, editorial note ap, example ap, history note ap, scope note ap

preferred labelap back to ToC or Annotation Property ToC

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

A resource has no more than one value of skos:prefLabel per language tag, and no more than one value of skos:prefLabel without language tag.
The preferred lexical label for a resource, in a given language.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
label

rightsap back to ToC or Annotation Property ToC

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

scope noteap back to ToC or Annotation Property ToC

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

A note that helps to clarify the meaning and/or the use of a concept.
Is defined by
http://www.w3.org/2004/02/skos/core
has super-properties
note ap

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
has domain
thing c
has range
string

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

term statusap back to ToC or Annotation Property ToC

IRI: http://www.w3.org/2003/06/sw-vocab-status/ns#term_status

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. [Definition Source: http://orcid.org/0000-0002-6601-2165]
belongs to
Colon Anatomical Entity c

Acanthosisni back to ToC or Named Individual ToC

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

Diffuse hypertrophy of the stratum spinosum layer of the epidermis. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c

Adenocarcinomani back to ToC or Named Individual ToC

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

A common cancer characterized by the presence of malignant glandular cells. Morphologically, adenocarcinomas are classified according to the growth pattern (e.g., papillary, alveolar) or according to the secreting product (e.g., mucinous, serous). Representative examples of adenocarcinoma are ductal and lobular breast carcinoma, lung adenocarcinoma, renal cell carcinoma, hepatocellular carcinoma (hepatoma), colon adenocarcinoma, and prostate adenocarcinoma. [Definition Source: NCI]
belongs to
Concept c
Colon Positive Outcome Type c

Adult Onsetni back to ToC or Named Individual 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. [Defintion Source: HPO probison]
belongs to
Concept c
Onset c

Anastomosisni back to ToC or Named Individual ToC

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

A natural or surgically-induced connection between tubular structures in the body. [Definition Source: NCI]
belongs to
Concept c
Colon Surgery Type c

Anatomical Locationni back to ToC or Named Individual ToC

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

belongs to
Semantic Area c

Antrum Pylorini back to ToC or Named Individual ToC

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

The initial part of the pyloric canal of the stomach. This site contains endocrine cells that produce gastrin and somatostatin. [Definition Source: NCI]
belongs to
Concept c
Celiac Anatomical Entity 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
Concept c
Colon Anatomical Entity c
is same as
Right Colon
has facts
has broader transitive op Colon, NOS

Atrophic Vulvani back to ToC or Named Individual 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.
belongs to
Concept c
Cervix Positive Outcome Type c

Biopsy of Colonni back to ToC or Named Individual ToC

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

Removal of tissue from the colon for microscopic examination, using an endoscope. [Definition Source: NCI]
belongs to
Concept c
Colon Intervention or Procedure Type c
has facts
has broader transitive op Endoscopic Biopsy

Biopsy of Duodenumni back to ToC or Named Individual ToC

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

Removal of tissue from the duodenum for microscopic examination, using an endoscope. [Definition Source: NCI]
belongs to
Concept c
Celiac Disease Intervention or Procedure Type c
has facts
has broader transitive op Biopsy of Small Intestine

Biopsy of Jejunumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51902

Removal of tissue from the jujunum for microscopic examination, using an endoscope. [Definition Source: NCI]
belongs to
Concept c
Celiac Disease Intervention or Procedure Type c
has facts
has broader transitive op Biopsy of Small Intestine

Biopsy of Small Intestineni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C51600

Removal of tissue from the small intestine for microscopic examination, using an endoscope. [Definition Source: NCI]
belongs to
Concept c
Celiac Disease Intervention or Procedure Type c
has facts
has broader transitive op Endoscopic Biopsy

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

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

Biopsy produced in the greater curvature area, a region in the stomach.
belongs to
Concept c
Celiac Disease Intervention or Procedure Type c
has facts
has broader transitive op Endoscopic Biopsy

Biopsy of the Pyloric Antrumni back to ToC or Named Individual ToC

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

Biopsy executed in the pyloric antrum, a form of endoscopic biopsy.
belongs to
Concept c
Celiac Disease Intervention or Procedure Type c
has facts
has broader transitive op Endoscopic Biopsy

Bronchial Biopsyni back to ToC or Named Individual ToC

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

Removal of tissue from the bronchus for microscopic examination. [Definition Source: NCI]
belongs to
Concept c
Lung Intervention or Procedure Type c

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
Concept c
Lung Anatomical Entity 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. [Definition Source: NCI]
belongs to
Concept c
Intestinal 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
Concept c
Colon Anatomical Entity c
has facts
has broader transitive op Colon, NOS

Cannizzaro Hospitalni back to ToC or Named Individual ToC

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

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

Celiac diseaseni back to ToC or Named Individual ToC

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

An autoimmune genetic disorder with an unknown pattern of inheritance that primarily affects the digestive tract. It is caused by intolerance to dietary gluten. Consumption of gluten protein triggers an immune response which damages small intestinal villi and prevents adequate absorption of nutrients. Clinical signs include abdominal cramping, diarrhea or constipation and weight loss. If untreated, the clinical course may progress to malnutrition, anemia, osteoporosis and an increased risk of intestinal malignancies. However, the prognosis is favorable with successful avoidance of gluten in the diet. [Definition Source: NCI]
belongs to
Concept c
Disease or Disorder c

Cervical Adenocarcinomani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C4029

An adenocarcinoma arising from the cervical epithelium. It accounts for approximately 15% of invasive cervical carcinomas. Increased numbers of sexual partners and human papillomavirus (HPV) infection are risk factors. Grossly, advanced cervical adenocarcinoma may present as an exophytic mass, an ulcerated lesion, or diffuse cervical enlargement. Microscopically, the majority of cervical adenocarcinomas are of the endocervical (mucinous) type. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c
has facts
has broader transitive op Cervical Carcinoma

Cervical Adenocarcinoma in Situni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c
has facts
has broader transitive op Cervical Adenocarcinoma

Cervical Biopsyni back to ToC or Named Individual ToC

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

Removal of tissue from the cervix for microscopic examination. [Definition Source: NCI]
belongs to
Concept c
Cervix Intervention or Procedure Type 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. [Definition Source: NCI]
belongs to
Concept c
Disease or Disorder c

Cervical Carcinomani back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c

Cervical Intraepithelial Neoplasiani back to ToC or Named Individual ToC

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

Squamous or glandular intraepithelial neoplasia that affects the cervical mucosal epithelium. There is no evidence of stromal invasion. According to the degree of cellular atypia and the associated architectural changes, it is classified as low or high grade. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c

Cervical Intraepithelial Neoplasia Grade 2/3ni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c
has facts
has broader transitive op Cervical Intraepithelial Neoplasia

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
Concept c
Cervix Anatomical Entity c

Cervical Polypni back to ToC or Named Individual ToC

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

A polyp that arises from the surface of the cervix. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type 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
Concept c
Cervix Anatomical Entity c
has facts
has broader transitive op Cervix Epithelium

Cervical Squamous Cell Carcinomani back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c
has facts
has broader transitive op Cervical Carcinoma

Cervical Squamous Intraepithelial Neoplasia 2ni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c
has facts
has broader transitive op Cervical Intraepithelial Neoplasia Grade 2/3

Cervicitisni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type 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
Concept c
Cervix Anatomical Entity 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
Concept c
Cervix Anatomical Entity c
has facts
has broader transitive op Cervix Epithelium

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
Concept c
Cervix Anatomical Entity c
has facts
has broader transitive op Cervix Epithelium

Chronic Active Inflammationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C82901

The coexistence of a chronic inflammatory process with a superimposed polymorphonuclear neutrophilic infiltration. [Definition Source: NCI]
belongs to
Concept c
Intestinal Abnormality c
has facts
has broader transitive op Inflammation

Chronic Cervicitisni back to ToC or Named Individual ToC

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

Chronic inflammation of the cervix. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c
has facts
has broader transitive op Cervicitis

Chronic Inflammationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C174450

An inflammatory process characterized by the presence of lymphocytes and plasma cells and the absence of polymorphonuclear neutrophils. [Definition Source: NCI]
belongs to
Concept c
Intestinal Abnormality c
has facts
has broader transitive op Inflammation

Colitisni back to ToC or Named Individual ToC

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

Inflammation of the colon. [Defintion Source: NCI]
belongs to
Concept c
Colon Positive Outcome Type c

Colon Adenocarcinomani back to ToC or Named Individual ToC

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

An adenocarcinoma arising from the colon. It is more frequently seen in populations with a Western type diet and in patients with a history of chronic inflammatory bowel disease. Signs and symptoms include intestinal bleeding, anemia, and change in bowel habits. According to the degree of cellular differentiation, colonic adenocarcinomas are divided into well, moderately, and poorly differentiated. Histologic variants include mucinous adenocarcinoma, signet ring cell carcinoma, medullary carcinoma, serrated adenocarcinoma, cribriform comedo-type adenocarcinoma, and micropapillary adenocarcinoma. [Definition Source: NCI]
belongs to
Concept c
Colon Positive Outcome Type c
has facts
has broader transitive op Adenocarcinoma

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 [Definition Source: https://orcid.org/0000-0002-6601-2165]
belongs to
Concept c
Disease or Disorder 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. [Definition Source: NCI]
belongs to
Concept c
Dysplasia c

Colon, NOSni back to ToC or Named Individual ToC

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

Colon, Not Otherwise Specified (NOS)
belongs to
Concept c
Colon Anatomical Entity c
has facts
has broader transitive op Colorectum

Colonoscopic Polypectomyni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Colon Surgery Type c
has facts
has broader transitive op Polypectomy

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
Concept c
Colon Anatomical Entity c

Condylomani back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c

Conizationni back to ToC or Named Individual ToC

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

Surgical removal of a cone-shaped portion of tissue from the uterine cervix. [Definition Source: NCI]
belongs to
Concept c
Cervix Surgery Type c

Crohn Diseaseni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C2965

A gastrointestinal disorder characterized by chronic inflammation involving all layers of the intestinal wall, noncaseating granulomas affecting the intestinal wall and regional lymph nodes, and transmural fibrosis. Crohn disease most commonly involves the terminal ileum; the colon is the second most common site of involvement. [Definition Source: NCI]
belongs to
Concept c
Intestinal Abnormality 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. [Definition Source: http://orcid.org/0000-0002-6601-2165]
belongs to
Concept c
Celiac Anatomical Entity c
has facts
has broader transitive op Duodenum

Dennis Dossoni back to ToC or Named Individual ToC

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

belongs to
person c

Descending Colonni back to ToC or Named Individual ToC

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

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
Concept c
Colon Anatomical Entity c
has facts
has broader transitive op Colon, NOS

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. [Definition Source: NCI]
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
Concept c
Celiac Anatomical Entity c
has facts
has broader transitive op Duodenum

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
Concept c
Celiac Anatomical Entity c
has facts
has broader transitive op Duodenum

Duodenal Glandni back to ToC or Named Individual ToC

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

Compound, tubular, submucosal glands located in the duodenum proximal to the sphincter of Oddi; these glands produce alkaline-rich secretions that function to both protect the duodenum from the acidic content of the stomach and to enable intestinal enzymes to activate, thus enabling absorption to start. [Definition Source: NCI]
belongs to
Concept c
Celiac Anatomical Entity c
has facts
has broader transitive op Duodenum

Duodenal 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
Concept c
Celiac Anatomical Entity c
has facts
has broader transitive op Duodenum

Duodenal Mucosani back to ToC or Named Individual ToC

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

The inner lining of the duodenum. [Definition Source: NCI]
belongs to
Concept c
Celiac Anatomical Entity c
has facts
has broader transitive op Duodenum

Duodenumni back to ToC or Named Individual ToC

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

A jointed tube 25-30 cm long that connects the stomach to the jejunum. [Definition Source: NCI]
belongs to
Concept c
Celiac Anatomical Entity c

Dyskeratosisni back to ToC or Named Individual 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.[Defintion Source: ISBN 0-7216-0187-1] Dyskeratosis congenita is congenital disease characterized by reticular skin pigmentation, nail degeneration, and leukoplakia on the mucous membranes associated with short telomeres. [Defintion Source: PMID 22285015]
belongs to
Concept c
Cervix Positive Outcome Type c

Edemani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3002

Accumulation of an excessive amount of fluid in cells or intercellular tissues. [Definition Source: NCI]
belongs to
Concept c
Intestinal Abnormality c

Elastofibromani back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Lung Positive Outcome Type c

Endocervical Curettageni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Surgery Type 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Anatomical Entity c
has facts
has broader transitive op Mucosa

Endoscopic Biopsyni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Celiac Disease Intervention or Procedure Type c
Colon Intervention or Procedure Type c

Enterocyteni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C12585

A type of epithelial cell that lines the intestines and colon. It participates in the absorption of water and nutrients from the intestinal lumen, and in the secretion of digestive enzymes. [Definition Source: NCI]
belongs to
Concept c
Celiac Disease Finding c

Eosinophilni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C12532

Granular leukocytes with a nucleus that usually has two lobes connected by a slender thread of chromatin, and cytoplasm containing coarse, round granules that are uniform in size and stainable by eosin. [Definition Source: NCI]
belongs to
Concept c
Celiac Disease Finding c
has facts
has broader transitive op Leukocyte
has broader transitive op Granulocyte

Erosionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C50443

An eating away or breakdown of any type of external or internal human tissue including but not limited to skin, teeth, mucosa, or somatic, which involves only the outer tissue layer. When tissue surrounds an implanted device, the tissue breakdown may result in migration and loss of the implant material and may result in further complications such as infection or abscess. [Definition Source: NCI]
belongs to
Concept c
Intestinal Abnormality c

ExaMode Consortiumni back to ToC or Named Individual ToC

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

belongs to
Institution c

Exocervical Epitheliumni back to ToC or Named Individual ToC

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

A epithelium that is part of a ectocervix.
belongs to
Concept c
Cervix Anatomical Entity c
has facts
has broader transitive op Cervix Epithelium

Female Genderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C16576

A person who belongs to the sex that normally produces ova. The term is used to indicate biological sex distinctions, or cultural gender role distinctions, or both. [Definition Source: NCI]
belongs to
Concept c
Gender c

Focal Acute Inflammationni back to ToC or Named Individual ToC

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

An inflammatory process characterized by the localized collection of polymorphonuclear neutrophils. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c

Gastric Heterotopia of the Small Intestineni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C7029

Gastric heterotopia (GH) is a rare, congenital condition where gastric tissue is found outside of its normal location in the gastric mucosa. It is usually benign and can be found throughout the gastrointestinal (GI) tract. In the duodenum, it is usually seen as multiple polyps, specifically in the duodenal bulb. [Definition Source: PMID 35607542]
belongs to
Concept c
Intestinal Abnormality c

Gastric Metaplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C8361

Precancerous change of the mucosa of the stomach with intestinal epithelium, and is associated with an increased risk of dysplasia and cancer. [Definition Source: PMID 29606921]
belongs to
Concept c
Intestinal Abnormality c

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

Gianmaria Silvelloni back to ToC or Named Individual ToC

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

belongs to
person c

Glandular Atrophyni back to ToC or Named Individual ToC

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

belongs to
Concept c
Intestinal Abnormality c

Granulocyteni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C12530

A type of leukocyte with a multilobed nucleus and cytoplasmic granules. The unique morphology of the nucleus has led to their also being known as polymorphonuclear leukocytes (PMLs or PMNs). Granulocytes are subdivided according to the staining properties of their granules into eosinophils (red with acidic dye), basophils (blue with basic dye), and neutrophils (not amenable to staining with either acidic or basic dyes). [Definition Source: NCI]
belongs to
Concept c
Celiac Disease Finding c

Granulomani back to ToC or Named Individual ToC

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

An inflammation AE that shows localized nodular inflammation found in tissues.
belongs to
Concept c
Colon Positive Outcome Type c

Greater Curvature of Stomachni back to ToC or Named Individual ToC

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

The lateral and inferior border of the stomach. Attached to it is the greater omentum. [Definition Source: NCI]
belongs to
Concept c
Celiac Anatomical Entity c

Hemicolectomyni back to ToC or Named Individual ToC

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

Surgical removal of approximately half of the colon. [Definition Source: NCI]
belongs to
Concept c
Colon Surgery Type 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. [Definition Source: NCI]
belongs to
Concept c
Dysplasia c

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
Concept c
Human Papilloma Virus Infection c

Hyperemiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C50588

The presence of an increased amount of blood in a part or organ; engorgement. [Definition Source: NCI]
belongs to
Concept c
Intestinal Abnormality c

Hyperkeratosisni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c

Hysterectomyni back to ToC or Named Individual 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). [Definition Source: NCI]
belongs to
Concept c
Cervix Surgery Type 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
Concept c
Colon Anatomical Entity c

Inflammationni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C3137

A finding of a localized protective response resulting from injury or destruction of tissues. Inflammation serves to destroy, dilute, or wall off both the injurious agent and the injured tissue. In the acute phase, inflammation is characterized by the signs of pain, heat, redness, swelling, and loss of function. Histologically, inflammation involves a complex series of events, including dilatation of arterioles, capillaries, and venules, with increased permeability and blood flow; exudation of fluids, including plasma proteins; and leukocyte migration into the site of inflammation. [Definition Source: NCI]
belongs to
Concept c
Intestinal Abnormality c

Insufficient Materialni back to ToC or Named Individual ToC

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

Inconclusive outcome where not enough material was present for the diagnosis.
belongs to
Concept c
Inconclusive Outcome Type 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
Concept c
Intestinal Abnormality c

Intestinal Metaplasiani back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C8360

A morphologic finding indicating the replacement of epithelial tissue outside the intestines by intestinal-type epithelium. [Definition Source: NCI]
belongs to
Concept c
Intestinal 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
Concept c
Celiac Anatomical Entity c
has facts
has broader transitive op Duodenum

Jejunumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002115

The portion of the small intestine that extends from the duodenum to the ileum. [Definition Source: NCI]
belongs to
Concept c
Celiac Anatomical Entity c

Koilocytotic Squamous Cellni back to ToC or Named Individual ToC

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

Koilocytes are epithelial cells containing a hyperchromatic nucleus that is acentrically displaced by perinuclear vacuole(s), and these morphological alterations are used by pathologists to help identify HPV-infected epithelial cells in Pap smears. [Definition Source: PMID 18688031]
belongs to
Concept c
Koilocytotic Squamous Cell 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Anatomical Entity c
has facts
has broader transitive op Mucosa

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. [Defintion Source: HPO probison]
belongs to
Concept c
Onset c
has facts
has broader transitive op Adult Onset

Laura Menottini back to ToC or Named Individual ToC

IRI: https://orcid.org/0000-0002-0676-682X

belongs to
person 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
Concept c
Colon Anatomical Entity c
has facts
has broader transitive op Colon, NOS

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
Concept c
Lung Anatomical Entity c
has facts
has broader transitive op Lobar Bronchus

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. [Definition Source: NCI]
belongs to
Concept c
Lung Anatomical Entity c
has facts
has broader transitive op Main Bronchus

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
Concept c
Lung Anatomical Entity c
has facts
has broader transitive op Lobar Bronchus

Leukocyteni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C12529

Blood cells that are devoid of hemoglobin, capable of ameboid motion and phagocytosis, and act as the principal components of the immune system. [Definition Source: NCI]
belongs to
Concept c
Celiac Disease Finding 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. [Definition Source: NCI]
belongs to
Concept c
Lung Anatomical Entity c
has facts
has broader transitive op Bronchus

Loop Electrosurgical Excisionni back to ToC or Named Individual ToC

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

Uses a thin, low-voltage electrified wire loop to cut out a thin layer of abnormal tissue; generally used to remove abnormal cells on the surface of the cervix. [Definition Source: NCI]
belongs to
Concept c
Cervix Surgery Type c

Low Grade Cervical Squamous Intraepithelial Neoplasiani back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c
has facts
has broader transitive op Cervical Intraepithelial Neoplasia

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
Concept c
Lung Anatomical Entity c

Lung Biopsyni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Lung Intervention or Procedure Type c

Lung cancerni back to ToC or Named Individual ToC

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

A malignant neoplasm involving the lung. [Definition Source: https://orcid.org/0000-0002-6601-2165]
belongs to
Concept c
Disease or Disorder c

Lymphadenitisni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Lung Positive Outcome Type c

Lymphocyteni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C12535

White blood cells formed in the body's lymphoid tissue. The nucleus is round or ovoid with coarse, irregularly clumped chromatin while the cytoplasm is typically pale blue with azurophilic (if any) granules. Most lymphocytes can be classified as either T or B (with subpopulations of each); those with characteristics of neither major class are called null cells. [Definition Source: NCI]
belongs to
Concept c
Celiac Disease Finding 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
Concept c
Lung Anatomical Entity c
has facts
has broader transitive op Bronchus

Malabsorptionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C113483

Inadequate absorption of nutrients in the small intestine. [Definition Source: NCI]
belongs to
Concept c
Intestinal Abnormality c

Male Genderni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C20197

A person who belongs to the sex that normally produces sperm. The term is used to indicate biological sex distinctions, cultural gender role distinctions, or both. [Definition Source: NCI]
belongs to
Concept c
Gender c

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
Concept c
Lung Anatomical Entity c

Melissa Anne Haendelni back to ToC or Named Individual ToC

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

belongs to
person c

Metaplasiani back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type 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. [Definition Source: NCI]
belongs to
Concept c
Lung Carcinoma Finding c

Metastatic Adenocarcinomani back to ToC or Named Individual ToC

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

An adenocarcinoma which has spread from its original site of growth to another anatomic site. [Definition Source: NCI]
belongs to
Concept c
Colon Positive Outcome Type c
has facts
has broader transitive op Adenocarcinoma

Metastatic Colon Adenocarcinomani back to ToC or Named Individual ToC

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

An adenocarcinoma that arises from the colon and has metastasized to another anatomic site. [Definition Source: NCI]
belongs to
Concept c
Colon Positive Outcome Type c
has facts
has broader transitive op Metastatic Adenocarcinoma
has broader transitive op Colon Adenocarcinoma

Midlle 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. [Defintion Source: HPO probison]
belongs to
Concept c
Onset c
has facts
has broader transitive op Adult Onset

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. [Definition Source: NCI]
belongs to
Concept c
Dysplasia c
has facts
has broader transitive op Colon Dysplasia
has broader transitive op Mild 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. [Definition Source: NCI]
belongs to
Concept c
Dysplasia c

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. [Definition Source: NCI]
belongs to
Concept c
Dysplasia c
has facts
has broader transitive op Colon Dysplasia
has broader transitive op Moderate 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. [Definition Source: NCI]
belongs to
Concept c
Dysplasia c
has facts
has broader transitive op High Grade Dysplasia

Mucosani back to ToC or Named Individual ToC

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

The moist, inner lining of some organs and body cavities (such as the nose, mouth, lungs, and stomach). Glands in the mucosa make mucus (a thick, slippery fluid). [Definition Source: NCI]
belongs to
Concept c
Cervix Anatomical Entity c

Mucosa of Pyloric Antrumni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/FMA_17055

Mucosa found in the gastric antrum. [Definition Source: Humpath.com - Human pathology]
belongs to
Concept c
Celiac Anatomical Entity c
has facts
has broader transitive op Antrum Pylori

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
Concept c
Lung Carcinoma Finding c

Neutrophilni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C12533

Granular leukocytes having a nucleus with three to five lobes connected by slender threads of chromatin, and cytoplasm containing fine inconspicuous granules and stainable by neutral dyes. [Definition Source: NCI]
belongs to
Concept c
Celiac Disease Finding c
has facts
has broader transitive op Leukocyte
has broader transitive op Granulocyte

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. [Defintion Source: Dorlands_Medical_Dictionary:MerckSource]
belongs to
Concept c
Cervix Anatomical Entity c
is same as
Simple Epithelium
has facts
has broader transitive op Cervix Epithelium

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).
A thin layer of tissue that covers the lungs and lines the interior wall of the chest cavity. It protects and cushions the lungs. This tissue secretes a small amount of fluid that acts as a lubricant, allowing the lungs to move smoothly in the chest cavity while breathing.; The serous membrane that lines the wall of the thoracic cavity and the surface of the lungs. [Definition Source: NCI]
belongs to
Concept c
Lung Anatomical Entity c

Polypectomyni back to ToC or Named Individual ToC

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

Complete or partial removal of a polypoid lesion from the mucosal surface. [Definition Source: NCI]
belongs to
Concept c
Colon Surgery Type c
has facts
has broader transitive op Biopsy of Colon

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

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
Concept c
Lung Anatomical Entity 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
Concept c
Organization c

Radical Hysterectomyni back to ToC or Named Individual 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.
belongs to
Concept c
Cervix Surgery Type c
has facts
has broader transitive op Hysterectomy

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
Concept c
Colon Anatomical Entity c
has facts
has broader transitive op Colon, NOS

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
Concept c
Colon Anatomical Entity c
has facts
has broader transitive op Colon, NOS

Rectum, NOSni back to ToC or Named Individual ToC

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

Rectum, Not Otherwise Specified (NOS)
belongs to
Concept c
Colon Anatomical Entity c
has facts
has broader transitive op Colorectum

Resectionni back to ToC or Named Individual ToC

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

A surgical procedure in which tissue is removed from the body. [Definition Source: NCI]
belongs to
Concept c
Colon Surgery Type 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
Concept c
Colon Anatomical Entity c
is same as
Ascending Colon
has facts
has broader transitive op Colon, NOS

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
Concept c
Lung Anatomical Entity c
has facts
has broader transitive op Lobar Bronchus

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. [Definition Source: NCI]
belongs to
Concept c
Lung Anatomical Entity c
has facts
has broader transitive op Main Bronchus

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
Concept c
Lung Anatomical Entity c
has facts
has broader transitive op Lobar Bronchus

Sarcoidosisni back to ToC or Named Individual 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. [Definition Source: Orhpanet 797]
belongs to
Concept c
Lung Positive Outcome Type 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
Concept c
Dysplasia c
has facts
has broader transitive op Colon Dysplasia
has broader transitive op Severe 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. [Definition Source: NCI]
belongs to
Concept c
Dysplasia c
has facts
has broader transitive 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
Concept c
Colon Anatomical Entity c
has facts
has broader transitive op Colon, NOS

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. [Definition Source: NCI]
belongs to
Concept c
Cervix Anatomical Entity c
is same as
Pavement Epithelium
has facts
has related op Pavement Epithelium

Small Intestineni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0002108

The section of the intestines between the pylorus and cecum. The small intestine is approximately 20 feet long and consists of the duodenum, the jejunum, and the ileum. Its main function is to absorb nutrients from food as the food is transported to the large intestine. [Definition Source: NCI]
belongs to
Concept c
Celiac Anatomical Entity c

Specimen Unsatisfactory for Diagnosisni back to ToC or Named Individual ToC

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

belongs to
Concept c
Inconclusive Outcome Type c

Squamous Carcinoma in Situni back to ToC or Named Individual ToC

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

A malignant epithelial neoplasm confined to the squamous epithelium, without invasion of the underlying tissues. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c
is same as
Squamous Intraepithelial Neoplasia
has facts
has broader transitive op Cervical Intraepithelial Neoplasia Grade 2/3

Squamous Intraepithelial Neoplasiani back to ToC or Named Individual 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.
belongs to
Concept c
Cervix Positive Outcome Type c
is same as
Squamous Carcinoma in Situ
has facts
has broader transitive op Cervical Carcinoma

Squamous Metaplasiani back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Cervix Positive Outcome Type c
has facts
has broader transitive op Metaplasia

Stefano Marchesinni back to ToC or Named Individual ToC

IRI: https://orcid.org/0000-0003-0362-5893

belongs to
person c

Testni back to ToC or Named Individual ToC

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

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

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
Concept c
Lung Anatomical Entity c

Tissue Congestionni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/NCIT_C82971

A finding indicating the presence of increased blood volume in the vascular lumen. [Definition Source: NCI]
belongs to
Concept c
Intestinal Abnormality c

Total Abdominal Hysterectomyni back to ToC or Named Individual ToC

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

Surgical removal of all of the uterus, via an abdominal approach. [Definition Source: NCI]
belongs to
Concept c
Cervix Surgery Type c
has facts
has broader transitive op Hysterectomy

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
Concept c
Colon Anatomical Entity c
has facts
has broader transitive op Colon, NOS

Ulcerni back to ToC or Named Individual 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. [Definition Source: NCI]
belongs to
Concept c
Colon Positive Outcome Type c
Intestinal Abnormality c

Uterus, NOSni back to ToC or Named Individual ToC

IRI: http://purl.obolibrary.org/obo/UBERON_0000995

The female muscular organ of gestation in which the developing embryo or fetus is nourished until birth.
belongs to
Concept c
Cervix Anatomical Entity 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. [Defintion Source: HPO DDD:hfirth]
belongs to
Concept c
Onset c
has facts
has broader transitive op Adult Onset

Legend back to ToC

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

References back to ToC

[Serra et al., 2019] Serra, L.M., Duncan, W.D., Diehl, A.D.: An ontology for representing hematologic malignancies: the cancer cell ontology. BMC Bioinform. 20-S(5), 231–236 (2019).

[Gurcan et al., 2017] Gurcan, M.N., Tomaszewski, J., Overton, J.A., Doyle, S., Ruttenberg, A., Smith, B.: Developing the quantitative histopathology image ontology (qhio): a case study using the hot spot detection problem. Journal of biomedical informatics 66, 129–135 (2017).

[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 celiac 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] celiac 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)

[Duraiyan et al., 2012] Duraiyan, J., Govindarajan, R., Kaliyappan, K., Palanisamy, M.: Applications of immunohistochemistry. Journal of pharmacy & bioallied sciences 4(Suppl 2), 307 (2012).

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.