Ontologies and Knowledge Graphs in Cancer Research

A special issue of Cancers (ISSN 2072-6694). This special issue belongs to the section "Cancer Informatics and Big Data".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 6812

Special Issue Editors


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Guest Editor
LASIGE, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
Interests: biomedical ontologies; semantic web; ontology matching; semantic similarity; ontology evolution; knowledge management; data mining
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Research and Development Pharmaceuticals, Bayer AG, Berlin Area, 13353 Berlin, Germany
Interests: biomarker development in oncology; DNA damage response; semantic data integration; biomedical ontologies
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Cancer research relies on a large number of diverse datasets generated by different omics technologies. Electronic health record data, which are gathered at the point-of-care, are increasingly utilized in pre-clinical and clinical research as well as health management and analyzed in unison with genomic data.

Curation, management, and analysis of these data present unique challenges arising from data heterogeneity, complexity, and size. Ontologies and knowledge graphs are being increasingly adopted to address these issues, and have great potential to support multidisciplinary cancer research efforts. Moreover, ontology-based approaches for genomics, machine learning, and clinical decision support are a growing hot topic due to their potential to support explainability.

This Issue will focus on the use of ontologies in the context of cancer research and care, including but not limited to ontology development and evolution, genomic data analysis, ontology-based machine learning and artificial intelligence, semantic data integration using knowledge graphs and other methods, semantic data resources, use of ontologies in translational medicine, and clinical decision support.

Prof. Dr. Cátia Pesquita
Dr. Andreas Schlicker
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Cancers is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2900 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • ontologies
  • knowledge graphs
  • semantic data integration
  • artificial intelligence

Published Papers (1 paper)

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Review

27 pages, 511 KiB  
Review
Ontologies and Knowledge Graphs in Oncology Research
by Marta Contreiras Silva, Patrícia Eugénio, Daniel Faria and Catia Pesquita
Cancers 2022, 14(8), 1906; https://doi.org/10.3390/cancers14081906 - 10 Apr 2022
Cited by 10 | Viewed by 5596
Abstract
The complexity of cancer research stems from leaning on several biomedical disciplines for relevant sources of data, many of which are complex in their own right. A holistic view of cancer—which is critical for precision medicine approaches—hinges on integrating a variety of heterogeneous [...] Read more.
The complexity of cancer research stems from leaning on several biomedical disciplines for relevant sources of data, many of which are complex in their own right. A holistic view of cancer—which is critical for precision medicine approaches—hinges on integrating a variety of heterogeneous data sources under a cohesive knowledge model, a role which biomedical ontologies can fill. This study reviews the application of ontologies and knowledge graphs in cancer research. In total, our review encompasses 141 published works, which we categorized under 14 hierarchical categories according to their usage of ontologies and knowledge graphs. We also review the most commonly used ontologies and newly developed ones. Our review highlights the growing traction of ontologies in biomedical research in general, and cancer research in particular. Ontologies enable data accessibility, interoperability and integration, support data analysis, facilitate data interpretation and data mining, and more recently, with the emergence of the knowledge graph paradigm, support the application of Artificial Intelligence methods to unlock new knowledge from a holistic view of the available large volumes of heterogeneous data. Full article
(This article belongs to the Special Issue Ontologies and Knowledge Graphs in Cancer Research)
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