The ImmunoPeptidomics Ontology : design and evaluation

Bibliographic Details
Main Author: Eugénio, Patrícia Raquel dos Anjos
Publication Date: 2022
Format: Master thesis
Language: eng
Source: Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
Download full: http://hdl.handle.net/10451/59210
Summary: Tese de Mestrado, Bioinformática e Biologia Computacional, 2022, Universidade de Lisboa, Faculdade de Ciências
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spelling The ImmunoPeptidomics Ontology : design and evaluationOntologiaImunopeptidómicaImPOTeses de mestrado - 2023Domínio/Área Científica::Engenharia e Tecnologia::Engenharia Eletrotécnica, Eletrónica e InformáticaTese de Mestrado, Bioinformática e Biologia Computacional, 2022, Universidade de Lisboa, Faculdade de CiênciasThere is significant hardship in manipulating the complex and variable data generated by biomedical subdomains such as immunopeptidomics. Therefore, ontologies are often used to express knowledge in a domain to help establish a standard nomenclature to help handle and integrate medical data. As a new field, immunopeptidomics lacks standardization: there is no recognized vocabulary or explicitly defined meanings. Hundreds of ontologies cover the biomedical domain, including neighboring subdomains like proteomics and immunology, but none adequately cover immunopeptidomics. This shortcoming needed to be addressed so cancer research in this domain could start to affect clinical practice. This dissertation details the development of the ImmunoPeptidomics Ontology, ImPO, to allow later integration of data produced by immunopeptidomics in personalized oncology. For this purpose, ImPO was designed following a process that comprised: capturing domain specialist knowledge in immunopeptidomics; iterative conceptual modeling of the domain through an Entity-Relationship model, semantic modeling by OWL formalization of the ER, cross-referencing ImPO with 28 external ontologies, and evaluation with competency questions and construction pitfalls. Unlike most biomedical ontologies currently accessible, ImPO was created to be populated with data and function as the semantic backbone of a knowledge graph (KG). ImPO was created as part of the KATY project, which aims to apply “AI-empowered knowledge” to clinical practice in Clear Cell Renal Cell Carcinoma. ImPO is one of the KATY KG components that will facilitate data integration in the project and give explainability to the AI techniques created in the project. Nonetheless, the ImPO ontology was created to be utilized independently of the KATY KG as a stand-alone knowledge model to aid in data integration and knowledge discovery in immunopeptidomics.Pesquita, Cátia Luísa Santana CalistoFaria, Daniel Pedro de JesusRepositório da Universidade de LisboaEugénio, Patrícia Raquel dos Anjos2023-09-11T16:57:47Z202320222023-01-01T00:00:00Zinfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/masterThesisapplication/pdfhttp://hdl.handle.net/10451/59210TID:203485556enginfo:eu-repo/semantics/openAccessreponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiainstacron:RCAAP2025-03-17T15:01:05Zoai:repositorio.ulisboa.pt:10451/59210Portal AgregadorONGhttps://www.rcaap.pt/oai/openaireinfo@rcaap.ptopendoar:https://opendoar.ac.uk/repository/71602025-05-29T03:31:43.298023Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologiafalse
dc.title.none.fl_str_mv The ImmunoPeptidomics Ontology : design and evaluation
title The ImmunoPeptidomics Ontology : design and evaluation
spellingShingle The ImmunoPeptidomics Ontology : design and evaluation
Eugénio, Patrícia Raquel dos Anjos
Ontologia
Imunopeptidómica
ImPO
Teses de mestrado - 2023
Domínio/Área Científica::Engenharia e Tecnologia::Engenharia Eletrotécnica, Eletrónica e Informática
title_short The ImmunoPeptidomics Ontology : design and evaluation
title_full The ImmunoPeptidomics Ontology : design and evaluation
title_fullStr The ImmunoPeptidomics Ontology : design and evaluation
title_full_unstemmed The ImmunoPeptidomics Ontology : design and evaluation
title_sort The ImmunoPeptidomics Ontology : design and evaluation
author Eugénio, Patrícia Raquel dos Anjos
author_facet Eugénio, Patrícia Raquel dos Anjos
author_role author
dc.contributor.none.fl_str_mv Pesquita, Cátia Luísa Santana Calisto
Faria, Daniel Pedro de Jesus
Repositório da Universidade de Lisboa
dc.contributor.author.fl_str_mv Eugénio, Patrícia Raquel dos Anjos
dc.subject.por.fl_str_mv Ontologia
Imunopeptidómica
ImPO
Teses de mestrado - 2023
Domínio/Área Científica::Engenharia e Tecnologia::Engenharia Eletrotécnica, Eletrónica e Informática
topic Ontologia
Imunopeptidómica
ImPO
Teses de mestrado - 2023
Domínio/Área Científica::Engenharia e Tecnologia::Engenharia Eletrotécnica, Eletrónica e Informática
description Tese de Mestrado, Bioinformática e Biologia Computacional, 2022, Universidade de Lisboa, Faculdade de Ciências
publishDate 2022
dc.date.none.fl_str_mv 2022
2023-09-11T16:57:47Z
2023
2023-01-01T00:00:00Z
dc.type.status.fl_str_mv info:eu-repo/semantics/publishedVersion
dc.type.driver.fl_str_mv info:eu-repo/semantics/masterThesis
format masterThesis
status_str publishedVersion
dc.identifier.uri.fl_str_mv http://hdl.handle.net/10451/59210
TID:203485556
url http://hdl.handle.net/10451/59210
identifier_str_mv TID:203485556
dc.language.iso.fl_str_mv eng
language eng
dc.rights.driver.fl_str_mv info:eu-repo/semantics/openAccess
eu_rights_str_mv openAccess
dc.format.none.fl_str_mv application/pdf
dc.source.none.fl_str_mv reponame:Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
instname:FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron:RCAAP
instname_str FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
instacron_str RCAAP
institution RCAAP
reponame_str Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
collection Repositórios Científicos de Acesso Aberto de Portugal (RCAAP)
repository.name.fl_str_mv Repositórios Científicos de Acesso Aberto de Portugal (RCAAP) - FCCN, serviços digitais da FCT – Fundação para a Ciência e a Tecnologia
repository.mail.fl_str_mv info@rcaap.pt
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