PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle data Article Swipe
Chunjiang Yu
,
Hui Zong
,
Yalan Chen
,
Yibin Zhou
,
Xingyun Liu
,
Yuxin Lin
,
Jiakun Li
,
Xiaonan Zheng
,
Hua Min
,
Bairong Shen
·
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/bib/bbae136
YOU?
·
· 2024
· Open Access
·
· DOI: https://doi.org/10.1093/bib/bbae136
Disease ontologies facilitate the semantic organization and representation of domain-specific knowledge. In the case of prostate cancer (PCa), large volumes of research results and clinical data have been accumulated and needed to be standardized for sharing and translational researches. A formal representation of PCa-associated knowledge will be essential to the diverse data standardization, data sharing and the future knowledge graph extraction, deep phenotyping and explainable artificial intelligence developing. In this study, we constructed an updated PCa ontology (PCAO2) based on the ontology development life cycle. An online information retrieval system was designed to ensure the usability of the ontology. The PCAO2 with a subclass-based taxonomic hierarchy covers the major biomedical concepts for PCa-associated genotypic, phenotypic and lifestyle data. The current version of the PCAO2 contains 633 concepts organized under three biomedical viewpoints, namely, epidemiology, diagnosis and treatment. These concepts are enriched by the addition of definition, synonym, relationship and reference. For the precision diagnosis and treatment, the PCa-associated genes and lifestyles are integrated in the viewpoint of epidemiological aspects of PCa. PCAO2 provides a standardized and systematized semantic framework for studying large amounts of heterogeneous PCa data and knowledge, which can be further, edited and enriched by the scientific community. The PCAO2 is freely available at https://bioportal.bioontology.org/ontologies/PCAO, http://pcaontology.net/ and http://pcaontology.net/mobile/.
Related Topics
Concepts
Computer science
Ontology
Information retrieval
Open Biomedical Ontologies
Standardization
Data integration
Ontology-based data integration
Data science
Data mining
Semantic Web
Suggested Upper Merged Ontology
Philosophy
Operating system
Epistemology
Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/bib/bbae136
- https://academic.oup.com/bib/article-pdf/25/3/bbae136/57129860/bbae136.pdf
- OA Status
- gold
- Cited By
- 11
- References
- 48
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W4393392255
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W4393392255Canonical identifier for this work in OpenAlex
- DOI
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https://doi.org/10.1093/bib/bbae136Digital Object Identifier
- Title
-
PCAO2: an ontology for integration of prostate cancer associated genotypic, phenotypic and lifestyle dataWork title
- Type
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articleOpenAlex work type
- Language
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enPrimary language
- Publication year
-
2024Year of publication
- Publication date
-
2024-03-27Full publication date if available
- Authors
-
Chunjiang Yu, Hui Zong, Yalan Chen, Yibin Zhou, Xingyun Liu, Yuxin Lin, Jiakun Li, Xiaonan Zheng, Hua Min, Bairong ShenList of authors in order
- Landing page
-
https://doi.org/10.1093/bib/bbae136Publisher landing page
- PDF URL
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https://academic.oup.com/bib/article-pdf/25/3/bbae136/57129860/bbae136.pdfDirect link to full text PDF
- Open access
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YesWhether a free full text is available
- OA status
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goldOpen access status per OpenAlex
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https://academic.oup.com/bib/article-pdf/25/3/bbae136/57129860/bbae136.pdfDirect OA link when available
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Computer science, Ontology, Information retrieval, Open Biomedical Ontologies, Standardization, Data integration, Ontology-based data integration, Data science, Data mining, Semantic Web, Suggested Upper Merged Ontology, Philosophy, Operating system, EpistemologyTop concepts (fields/topics) attached by OpenAlex
- Cited by
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11Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 5, 2024: 6Per-year citation counts (last 5 years)
- References (count)
-
48Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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| referenced_works | https://openalex.org/W2266617708, https://openalex.org/W2060427373, https://openalex.org/W90362830, https://openalex.org/W2996636445, https://openalex.org/W2025349319, https://openalex.org/W2404369708, https://openalex.org/W3153565604, https://openalex.org/W3091797093, https://openalex.org/W2547822643, https://openalex.org/W6750697081, https://openalex.org/W2166516661, https://openalex.org/W2085333314, https://openalex.org/W1782193986, https://openalex.org/W3147142721, https://openalex.org/W2164111029, https://openalex.org/W3119005666, https://openalex.org/W4206841660, https://openalex.org/W4315754639, https://openalex.org/W906421731, https://openalex.org/W6683984977, https://openalex.org/W2953358308, https://openalex.org/W2331619795, https://openalex.org/W2329366499, https://openalex.org/W1989881917, https://openalex.org/W2010227770, https://openalex.org/W1974313714, https://openalex.org/W2152915862, https://openalex.org/W1490161904, https://openalex.org/W6603694148, https://openalex.org/W2087779040, https://openalex.org/W6713634263, https://openalex.org/W2162151166, https://openalex.org/W2159092541, https://openalex.org/W1933028489, https://openalex.org/W2100133323, https://openalex.org/W1984761526, https://openalex.org/W3097762503, https://openalex.org/W3000329625, https://openalex.org/W2048612925, https://openalex.org/W2110301462, https://openalex.org/W2168120333, https://openalex.org/W2154829072, https://openalex.org/W1973465852, https://openalex.org/W4283360637, https://openalex.org/W4213051433, https://openalex.org/W3103867242, https://openalex.org/W2798343740, https://openalex.org/W4205810721 |
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| abstract_inverted_index.A | 40 |
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| abstract_inverted_index.study, | 71 |
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| abstract_inverted_index.(PCAO2) | 78 |
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| abstract_inverted_index.http://pcaontology.net/mobile/. | 210 |
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| corresponding_author_ids | https://openalex.org/A5081095213, https://openalex.org/A5026168109 |
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