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Ontology-Based Queries over Cancer Data

Alejandra Gonzalez-Beltran, Alejandra Gonzalez-Beltran
2010 Nature Precedings  
Overview • Motivation: queries over cancer data • Background: caGrid infrastructure • caGrid query language (CQL) • Objective: ontology-based queries over the caGrid infrastructure • Approach: • OWL representation  ...  of caGrid models • Overview • Motivation: queries over cancer data • Background: caGrid infrastructure • caGrid query language (CQL) • Objective: ontology-based queries over the caGrid infrastructure  ...  Acknowledgments • National Cancer Research Institute (NCRI) Informatics Initiative, UK  ... 
doi:10.1038/npre.2010.5406 fatcat:rckbdihnwjelnazgiwvw6aeefm

Ontology-Based Queries over Cancer Data

Alejandra Gonzalez-Beltran, Alejandra Gonzalez-Beltran
2010 Nature Precedings  
Overview • Motivation: queries over cancer data • Background: caGrid infrastructure • caGrid query language (CQL) • Objective: ontology-based queries over the caGrid infrastructure • Approach: • OWL representation  ...  of caGrid models • Overview • Motivation: queries over cancer data • Background: caGrid infrastructure • caGrid query language (CQL) • Objective: ontology-based queries over the caGrid infrastructure  ...  Acknowledgments • National Cancer Research Institute (NCRI) Informatics Initiative, UK  ... 
doi:10.1038/npre.2010.5406.1 fatcat:ryx5dvw3fnhnjnt7j6t55a32sy

Ontology-based Queries over Cancer Data [article]

Alejandra Gonzalez-Beltran, Ben Tagger, Anthony Finkelstein
2010 arXiv   pre-print
In this paper, we present the design and development of an ontology-based querying functionality that consists of: the generation of OWL2 ontologies from the underlying data resources metadata and a query  ...  rewriting and translation process based on reasoning, which converts a query at the domain ontology level into queries at the software infrastructure level.  ...  Acknowledgements The authors are grateful to the National Cancer Research Institute Informatics Initiative for support for their research.  ... 
arXiv:1012.5506v1 fatcat:q4wl7lzb5rgbfidloh4wavgpza

Federated ontology-based queries over cancer data

Alejandra González-Beltrán, Ben Tagger, Anthony Finkelstein
2011 BMC Bioinformatics  
This paper presents the design of and theoretical foundations for distributed ontology-based queries over cancer research data.  ...  This paper provides an ontology-based solution for querying distributed databases over service-oriented, model-driven infrastructures.  ...  BT wrapped the ontology generation code as a caGrid service and developed the graphical user interface to expose the query system.  ... 
doi:10.1186/1471-2105-13-s1-s9 pmid:22373043 pmcid:PMC3471355 fatcat:phmg4phaf5dm5mbznahbenpfyq

Domain concept-based queries for cancer research data sources

Alejandra Gonzalez Beltran, Anthony Finkelstein, J. Max Wilkinson, Jeff Kramer
2009 2009 22nd IEEE International Symposium on Computer-Based Medical Systems  
Acknowledgements Cancer Research UK UK National Cancer Research Institute Informatics Initiative  ...  resource Descriptive, we mean that the query gives the criteria for the desired data (instead of the procedure to find the data) Approach 2) Express the concept-based query over the generated ontology  ...  Part of the generated ontology Approach 2) Express the concept-based query over the generated ontology Find objects that have concept Single_Nucleotide_Polymorphism and have an association with objects  ... 
doi:10.1109/cbms.2009.5255343 dblp:conf/cbms/BeltranFWK09 fatcat:jhcsz2iavje3nhe3jr53xwsiui

Analysis and visualization of disease courses in a semantically-enabled cancer registry

Angel Esteban-Gil, Jesualdo Tomás Fernández-Breis, Martin Boeker
2017 Journal of Biomedical Semantics  
Data stored in a cancer registry database were transformed into RDF employing a process driven by OWL ontologies.  ...  Based on the requirements analysis, we have produced a draft of an ontology that models the semantics of a local cancer registry in a pragmatic extensible way.  ...  provides the meaning for the content; and (2) those which permit ontology-based data access using data in traditional formats but querying with semantic web query languages.  ... 
doi:10.1186/s13326-017-0154-9 pmid:28962670 pmcid:PMC5622544 fatcat:qh4fa5eewbga5mrfk5qttobxly

Integration of prostate cancer clinical data using an ontology

Hua Min, Frank J. Manion, Elizabeth Goralczyk, Yu-Ning Wong, Eric Ross, J. Robert Beck
2009 Journal of Biomedical Informatics  
As the results of the integration process, the semantic query language SPARQL is applied to perform the integrated queries across the two database systems based on PCO.  ...  As a proof of concept, the Prostate Cancer Ontology (PCO) is created for the development of the Prostate Cancer Information System (PCIS).  ...  Acknowledgments This work was supported by American Cancer Society grant #IRG-92-027-14 and NIH grant P30 CA 06927.  ... 
doi:10.1016/j.jbi.2009.05.007 pmid:19497389 pmcid:PMC2784120 fatcat:5u56d3zm6jbwlh72l2hodp77aq

Using Semantic Web Technologies to Enable Cancer Genomics Discovery at Petabyte Scale

Jovan Cejovic, Jelena Radenkovic, Vladimir Mladenovic, Adam Stanojevic, Milica Miletic, Stevan Radanovic, Dragan Bajcic, Dragan Djordjevic, Filip Jelic, Milos Nesic, Jessica Lau, Patrick Grady (+3 others)
2018 Cancer Informatics  
In response, we have developed a Semantic Web-based Data Browser, a tool allowing users to visually build and execute ontology-driven queries.  ...  Although initially implemented on top of The Cancer Genome Atlas (TCGA) data set, the Data Browser's architecture allows for seamless integration of other data sets.  ...  The authors are grateful to the patients who donated their samples to TCGA and the many researchers who have generated this data.  ... 
doi:10.1177/1176935118774787 pmid:30283230 pmcid:PMC6166304 fatcat:hkm5z2dckvcbjilynfnvfakc6u

An ontology-guided semantic data integration framework to support integrative data analysis of cancer survival

Hansi Zhang, Yi Guo, Qian Li, Thomas J. George, Elizabeth Shenkman, François Modave, Jiang Bian
2018 BMC Medical Informatics and Decision Making  
Results: Based on our use cases in the cancer survival IDA, we created tailored ontological structures in OCRV to facilitate the data integration tasks.  ...  Thus, we proposed an ontology-based approach to integrate heterogeneous datasets addressing key data integration challenges.  ...  Based on the semantic mapping axioms defined in the OBDA model, Ontop's Quest-a SPARQL query engine-can translate a SPARQL query over the ontology into a union of sub-queries over the data sources.  ... 
doi:10.1186/s12911-018-0636-4 pmid:30066664 pmcid:PMC6069766 fatcat:fpazk2lv65b2pargb4qfrll3pi

Data integration through ontology-based data access to support integrative data analysis: A case study of cancer survival

Hansi Zhang, Yi Guo, Qian Li, Thomas J. George, Elizabeth A. Shenkman, Jiang Bian
2017 2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
Prior research has suggested that cancer survival is influenced by multiple factors from multiple levels. Most of existing analyses of cancer survival used data from a single source.  ...  To improve cancer survival rates and prognosis, one of the first steps is to improve our understanding of contributory factors associated with cancer survival.  ...  Acknowledgments This work was supported in part by NIH grants UL1TR001427, the OneFlorida Cancer Control Alliance (funded by James and Esther King Biomedical Research Program, Florida Department of Health  ... 
doi:10.1109/bibm.2017.8217849 pmid:29707415 pmcid:PMC5918275 dblp:conf/bibm/ZhangGLGSB17 fatcat:l5rxomjjtncq7myrvjyoqddslm

ProKinO: An Ontology for Integrative Analysis of Protein Kinases in Cancer

Gurinder Gosal, Krys J. Kochut, Natarajan Kannan, Fazlul H. Sarkar
2011 PLoS ONE  
We also provide examples of how ontology-based data analysis can be used to generate testable hypotheses regarding cancer mutations.  ...  Navigation and analysis of ontology data can be performed using the ontology browser available at:  ...  We thank members of the NK lab for feedback on the ontology browser. Author Contributions Conceived and designed the experiments: NK KK. Performed the experiments: GG. Analyzed the data: GG KK NK.  ... 
doi:10.1371/journal.pone.0028782 pmid:22194913 pmcid:PMC3237543 fatcat:3cbi54j5p5cqpafmxswe557b6m

OMIT: A Domain-Specific Knowledge Base for MicroRNA Target Prediction

Jingshan Huang, Christopher Townsend, Dejing Dou, Haishan Liu, Ming Tan
2011 Pharmaceutical Research  
KEY WORDS human cancer . knowledge acquisition . knowledge base . microRNA (miRNA) target . ontology Electronic supplementary material The online version of this article (  ...  We describe the ontology design, semantic annotation and data integration, and user-friendly interface and conclude that the OMIT system can assist biologists in unraveling the important roles of miRNAs  ...  over the original query.  ... 
doi:10.1007/s11095-011-0573-8 pmid:21879385 fatcat:jreqhtferffmrket6lr6oujfjq

Ontologies and Knowledge Graphs in Oncology Research

Marta Contreiras Silva, Patrícia Eugénio, Daniel Faria, Catia Pesquita
2022 Cancers  
This study reviews the application of ontologies and knowledge graphs in cancer research.  ...  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  ...  The immense potential of ontologies and the knowledge graph paradigm to support cancer research data management and analysis is increasingly recognized by the oncology research community as an essential  ... 
doi:10.3390/cancers14081906 pmid:35454813 pmcid:PMC9029532 fatcat:t6erzohmvnextkix4infnk7kza

Building a European biomedical grid on cancer: the ACGT Integrated Project

M Tsiknakis, D Kafetzopoulos, G Potamias, A Analyti, K Marias, A Manganas
2006 Studies in Health Technology and Informatics  
The ultimate objective of the ACGT project is the development of a European biomedical grid for cancer research, based on the principles of open access and open source, enhanced by a set of interoperable  ...  tools and services which will facilitate the seamless and secure access to and analysis of multi-level clinico-genomic data, enriched with high-performing knowledge discovery operations and services.  ...  Each wrapper receives queries from the mediator in terms of the local ontology, transforms them in the format of the underlying data source, submits the query to the data source, and translates the results  ... 
pmid:16823143 fatcat:y5z67zykjfeydiemgb6emr5oou

Dark kinase annotation, mining and visualization using the Protein Kinase Ontology [article]

Saber Soleymani, Nathan Gravel, Liang-Chin Huang, Wayland Yeung, Elika Bozorgi, Nathaniel G Bendzunas, Krzysztof J Kochut, Natarajan Kannan
2022 bioRxiv   pre-print
Specifically, through graph mining and aggregate SPARQL queries, we identify the p21-activated protein kinase 5 (PAK5) as one of the most frequently mutated dark kinase in human cancers with abnormal expression  ...  in multiple cancers, including an unappreciated role in acute myeloid leukemia.  ...  Having identified PAK5 as the most frequently mutated dark kinase in cancers, one can further query the ontology to explore the role of this kinase in various cancers.  ... 
doi:10.1101/2022.02.25.482021 fatcat:d36wv3hcgvgsjfvxp6cweqor7a
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