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In Silico Drug Screening Analysis against the Overexpression of PGAM1 Gene in Different Cancer Treatments. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5515692. [PMID: 34195264 PMCID: PMC8184345 DOI: 10.1155/2021/5515692] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 04/17/2021] [Accepted: 05/24/2021] [Indexed: 01/24/2023]
Abstract
Phosphoglycerate mutase 1 (PGAM1) is considered as a novel target for multiple types of cancer drugs for the upregulation in tumor, cell prefoliation, and cell migration. During aerobic glycolysis, PGAM1 plays a critical role in cancer cell metabolism by catalyzing the conversion of 3-phosphoglycerate (3PG) to 2-phosphoglycerate (2PG). In this computational-based study, the molecular docking approach was used with the best binding active sites of PGAM1 to screen 5,000 Chinese medicinal phytochemical library. The docking results were three ligands with docking score, RMSD-refine, and residues. Docking scores were -16.57, -15.22, and -15.74. RMSD values were 0.87, 2.40, and 0.98, and binding site residues were Arg 191, Arg 191, Arg 116, Arg 90, Arg 10, and Tyr 92. The best compounds were subjected to ADMETsar, ProTox-2 server, and Molinspiration analysis to evaluate the toxicological and drug likeliness potential of such selected compounds. The UCSF-Chimera tool was used to visualize the results, which shows that the three medicinal compounds named N-Nitrosohexamethyleneimine, Subtrifloralactone-K, and Kanzonol-N in chain-A were successfully binding with the active pockets of PGAM1. The study might facilitate identifying the hit molecules that could be beneficial in the development of antidrugs against various types of cancer treatment. These hit phytochemicals could be beneficial for further investigation of a novel target for cancer.
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Gagalova KK, Leon Elizalde MA, Portales-Casamar E, Görges M. What You Need to Know Before Implementing a Clinical Research Data Warehouse: Comparative Review of Integrated Data Repositories in Health Care Institutions. JMIR Form Res 2020; 4:e17687. [PMID: 32852280 PMCID: PMC7484778 DOI: 10.2196/17687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 06/09/2020] [Accepted: 07/17/2020] [Indexed: 12/23/2022] Open
Abstract
Background Integrated data repositories (IDRs), also referred to as clinical data warehouses, are platforms used for the integration of several data sources through specialized analytical tools that facilitate data processing and analysis. IDRs offer several opportunities for clinical data reuse, and the number of institutions implementing an IDR has grown steadily in the past decade. Objective The architectural choices of major IDRs are highly diverse and determining their differences can be overwhelming. This review aims to explore the underlying models and common features of IDRs, provide a high-level overview for those entering the field, and propose a set of guiding principles for small- to medium-sized health institutions embarking on IDR implementation. Methods We reviewed manuscripts published in peer-reviewed scientific literature between 2008 and 2020, and selected those that specifically describe IDR architectures. Of 255 shortlisted articles, we found 34 articles describing 29 different architectures. The different IDRs were analyzed for common features and classified according to their data processing and integration solution choices. Results Despite common trends in the selection of standard terminologies and data models, the IDRs examined showed heterogeneity in the underlying architecture design. We identified 4 common architecture models that use different approaches for data processing and integration. These different approaches were driven by a variety of features such as data sources, whether the IDR was for a single institution or a collaborative project, the intended primary data user, and purpose (research-only or including clinical or operational decision making). Conclusions IDR implementations are diverse and complex undertakings, which benefit from being preceded by an evaluation of requirements and definition of scope in the early planning stage. Factors such as data source diversity and intended users of the IDR influence data flow and synchronization, both of which are crucial factors in IDR architecture planning.
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Affiliation(s)
- Kristina K Gagalova
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada.,Research Institute, BC Children's Hospital, Vancouver, BC, Canada
| | - M Angelica Leon Elizalde
- Research Institute, BC Children's Hospital, Vancouver, BC, Canada.,School of Population and Public Health, University of British Columbia, Vancouver, BC, Canada
| | - Elodie Portales-Casamar
- Research Institute, BC Children's Hospital, Vancouver, BC, Canada.,Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Matthias Görges
- Research Institute, BC Children's Hospital, Vancouver, BC, Canada.,Department of Anesthesiology, Pharmacology and Therapeutics, University of British Columbia, Vancouver, BC, Canada
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A rule-based semantic approach for data integration, standardization and dimensionality reduction utilizing the UMLS: Application to predicting bariatric surgery outcomes. Comput Biol Med 2019; 106:84-90. [DOI: 10.1016/j.compbiomed.2019.01.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Revised: 01/21/2019] [Accepted: 01/21/2019] [Indexed: 11/24/2022]
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Callahan A, Abeyruwan SW, Al-Ali H, Sakurai K, Ferguson AR, Popovich PG, Shah NH, Visser U, Bixby JL, Lemmon VP. RegenBase: a knowledge base of spinal cord injury biology for translational research. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2016; 2016:baw040. [PMID: 27055827 PMCID: PMC4823819 DOI: 10.1093/database/baw040] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 03/03/2016] [Indexed: 12/20/2022]
Abstract
Spinal cord injury (SCI) research is a data-rich field that aims to identify the biological mechanisms resulting in loss of function and mobility after SCI, as well as develop therapies that promote recovery after injury. SCI experimental methods, data and domain knowledge are locked in the largely unstructured text of scientific publications, making large scale integration with existing bioinformatics resources and subsequent analysis infeasible. The lack of standard reporting for experiment variables and results also makes experiment replicability a significant challenge. To address these challenges, we have developed RegenBase, a knowledge base of SCI biology. RegenBase integrates curated literature-sourced facts and experimental details, raw assay data profiling the effect of compounds on enzyme activity and cell growth, and structured SCI domain knowledge in the form of the first ontology for SCI, using Semantic Web representation languages and frameworks. RegenBase uses consistent identifier schemes and data representations that enable automated linking among RegenBase statements and also to other biological databases and electronic resources. By querying RegenBase, we have identified novel biological hypotheses linking the effects of perturbagens to observed behavioral outcomes after SCI. RegenBase is publicly available for browsing, querying and download. Database URL:http://regenbase.org
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Affiliation(s)
- Alison Callahan
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305
| | | | - Hassan Al-Ali
- Miami Project to Cure Paralysis, University of Miami School of Medicine, Miami, FL 33136
| | - Kunie Sakurai
- Miami Project to Cure Paralysis, University of Miami School of Medicine, Miami, FL 33136
| | - Adam R Ferguson
- Brain and Spinal Injury Center (BASIC), Department of Neurological Surgery, University of California, San Francisco; San Francisco Veterans Affairs Medical Center, San Francisco, CA 94143
| | - Phillip G Popovich
- Center for Brain and Spinal Cord Repair and the Department of Neuroscience, The Ohio State University, Columbus, OH 43210
| | - Nigam H Shah
- Stanford Center for Biomedical Informatics Research, Stanford University, Stanford, CA 94305
| | - Ubbo Visser
- Department of Computer Science, University of Miami, Coral Gables, FL 33146
| | - John L Bixby
- Miami Project to Cure Paralysis, University of Miami School of Medicine, Miami, FL 33136 Center for Computational Science, University of Miami, Coral Gables, FL 33146 Department of Cellular and Molecular Pharmacology, University of Miami School of Medicine, Miami, FL 33136, USA
| | - Vance P Lemmon
- Miami Project to Cure Paralysis, University of Miami School of Medicine, Miami, FL 33136 Center for Computational Science, University of Miami, Coral Gables, FL 33146
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Sun H, Depraetere K, De Roo J, Mels G, De Vloed B, Twagirumukiza M, Colaert D. Semantic processing of EHR data for clinical research. J Biomed Inform 2015; 58:247-259. [PMID: 26515501 DOI: 10.1016/j.jbi.2015.10.009] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 09/10/2015] [Accepted: 10/17/2015] [Indexed: 11/24/2022]
Abstract
There is a growing need to semantically process and integrate clinical data from different sources for clinical research. This paper presents an approach to integrate EHRs from heterogeneous resources and generate integrated data in different data formats or semantics to support various clinical research applications. The proposed approach builds semantic data virtualization layers on top of data sources, which generate data in the requested semantics or formats on demand. This approach avoids upfront dumping to and synchronizing of the data with various representations. Data from different EHR systems are first mapped to RDF data with source semantics, and then converted to representations with harmonized domain semantics where domain ontologies and terminologies are used to improve reusability. It is also possible to further convert data to application semantics and store the converted results in clinical research databases, e.g. i2b2, OMOP, to support different clinical research settings. Semantic conversions between different representations are explicitly expressed using N3 rules and executed by an N3 Reasoner (EYE), which can also generate proofs of the conversion processes. The solution presented in this paper has been applied to real-world applications that process large scale EHR data.
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Affiliation(s)
- Hong Sun
- Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium.
| | - Kristof Depraetere
- Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium
| | - Jos De Roo
- Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium
| | - Giovanni Mels
- Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium
| | - Boris De Vloed
- Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium
| | - Marc Twagirumukiza
- Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium
| | - Dirk Colaert
- Advanced Clinical Applications Research Group, Agfa HealthCare, Moutstraat 100, 9000 Gent, Belgium
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Smith B, Arabandi S, Brochhausen M, Calhoun M, Ciccarese P, Doyle S, Gibaud B, Goldberg I, Kahn CE, Overton J, Tomaszewski J, Gurcan M. Biomedical imaging ontologies: A survey and proposal for future work. J Pathol Inform 2015; 6:37. [PMID: 26167381 PMCID: PMC4485195 DOI: 10.4103/2153-3539.159214] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Accepted: 04/30/2015] [Indexed: 12/24/2022] Open
Abstract
Background: Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical definitions thereby also supporting reasoning over the tagged data. Aim: This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. Results and Conclusions: The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data.
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Affiliation(s)
- Barry Smith
- Department of Philosophy, The State University of New York at Buffalo, Buffalo, NY 14260, USA
| | | | - Mathias Brochhausen
- Division of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
| | - Michael Calhoun
- Department of Health and Human Performance, Elon University, Elon, NC 27244, USA
| | - Paolo Ciccarese
- Harvard Medical School, Massachusetts General Hospital, PerkinElmer Innovation Labs, Boston, MA 02115, USA
| | - Scott Doyle
- Department of Pathology and Anatomical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
| | - Bernard Gibaud
- Laboratoire du Traitement du Signal et de l'Image (LTSI), Inserm Unit 1099, University of Rennes 1, Rennes, France
| | - Ilya Goldberg
- National Institute on Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - Charles E Kahn
- Department of Radiology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - John Tomaszewski
- Department of Pathology and Anatomical Sciences, University at Buffalo, The State University of New York, Buffalo, NY 14214, USA
| | - Metin Gurcan
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, USA
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Robson B, Caruso TP, Balis UG. Suggestions for a web based universal exchange and inference language for medicine. Continuity of patient care with PCAST disaggregation. Comput Biol Med 2015; 56:51-66. [DOI: 10.1016/j.compbiomed.2014.10.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Revised: 10/23/2014] [Accepted: 10/25/2014] [Indexed: 10/24/2022]
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Meldolesi E, van Soest J, Dinapoli N, Dekker A, Damiani A, Gambacorta MA, Valentini V. An umbrella protocol for standardized data collection (SDC) in rectal cancer: a prospective uniform naming and procedure convention to support personalized medicine. Radiother Oncol 2014; 112:59-62. [PMID: 24853366 DOI: 10.1016/j.radonc.2014.04.008] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 04/17/2014] [Accepted: 04/18/2014] [Indexed: 01/01/2023]
Abstract
Predictive models allow treating physicians to deliver tailored treatment moving from prescription by consensus to prescription by numbers. The main features of an umbrella protocol for standardizing data and procedures to create a consistent dataset useful to obtain a trustful analysis for a Decision Support System for rectal cancer are reported.
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Affiliation(s)
- Elisa Meldolesi
- Sacred Heart University, Radiotherapy Department, Rome, Italy.
| | - Johan van Soest
- Maastricht University Medical Centre+, Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Developmental Biology, The Netherlands
| | - Nicola Dinapoli
- Sacred Heart University, Radiotherapy Department, Rome, Italy
| | - Andre Dekker
- Maastricht University Medical Centre+, Department of Radiation Oncology (MAASTRO), GROW School for Oncology and Developmental Biology, The Netherlands
| | - Andrea Damiani
- Sacred Heart University, Radiotherapy Department, Rome, Italy
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Systems genetics in "-omics" era: current and future development. Theory Biosci 2012; 132:1-16. [PMID: 23138757 DOI: 10.1007/s12064-012-0168-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 10/25/2012] [Indexed: 02/06/2023]
Abstract
The systems genetics is an emerging discipline that integrates high-throughput expression profiling technology and systems biology approaches for revealing the molecular mechanism of complex traits, and will improve our understanding of gene functions in the biochemical pathway and genetic interactions between biological molecules. With the rapid advances of microarray analysis technologies, bioinformatics is extensively used in the studies of gene functions, SNP-SNP genetic interactions, LD block-block interactions, miRNA-mRNA interactions, DNA-protein interactions, protein-protein interactions, and functional mapping for LD blocks. Based on bioinformatics panel, which can integrate "-omics" datasets to extract systems knowledge and useful information for explaining the molecular mechanism of complex traits, systems genetics is all about to enhance our understanding of biological processes. Systems biology has provided systems level recognition of various biological phenomena, and constructed the scientific background for the development of systems genetics. In addition, the next-generation sequencing technology and post-genome wide association studies empower the discovery of new gene and rare variants. The integration of different strategies will help to propose novel hypothesis and perfect the theoretical framework of systems genetics, which will make contribution to the future development of systems genetics, and open up a whole new area of genetics.
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Wu D, Rice CM, Wang X. Cancer bioinformatics: a new approach to systems clinical medicine. BMC Bioinformatics 2012; 13:71. [PMID: 22549015 PMCID: PMC3424139 DOI: 10.1186/1471-2105-13-71] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 05/01/2012] [Indexed: 11/10/2022] Open
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