Feichen Shen, Hongfang Liu, Sunghwan Sohn, David W Larson, Yugyung Lee
In the current biomedical data movement, numerous efforts have been made to convert and normalize a large number of traditional structured and unstructured data (e.g., EHRs, reports) to semi-structured data (e.g., RDF, OWL). With the increasing number of semi-structured data coming into the biomedical community, data integration and knowledge discovery from heterogeneous domains become important research problem. In the application level, detection of related concepts among medical ontologies is an important goal of life science research. It is more crucial to figure out how different concepts are related within a single ontology or across multiple ontologies by analysing predicates in different knowledge bases. However, the world today is one of information explosion, and it is extremely difficult for biomedical researchers to find existing or potential predicates to perform linking among cross domain concepts without any support from schema pattern analysis. Therefore, there is a need for a mechanism to do predicate oriented pattern analysis to partition heterogeneous ontologies into closer small topics and do query generation to discover cross domain knowledge from each topic. In this paper, we present such a model that predicates oriented pattern analysis based on their close relationship and generates a similarity matrix. Based on this similarity matrix, we apply an innovated unsupervised learning algorithm to partition large data sets into smaller and closer topics and generate meaningful queries to fully discover knowledge over a set of interlinked data sources. We have implemented a prototype system named BmQGen and evaluate the proposed model with colorectal surgical cohort from the Mayo Clinic.
{"title":"Predicate Oriented Pattern Analysis for Biomedical Knowledge Discovery.","authors":"Feichen Shen, Hongfang Liu, Sunghwan Sohn, David W Larson, Yugyung Lee","doi":"10.4236/iim.2016.83006","DOIUrl":"10.4236/iim.2016.83006","url":null,"abstract":"In the current biomedical data movement, numerous efforts have been made to convert and normalize a large number of traditional structured and unstructured data (e.g., EHRs, reports) to semi-structured data (e.g., RDF, OWL). With the increasing number of semi-structured data coming into the biomedical community, data integration and knowledge discovery from heterogeneous domains become important research problem. In the application level, detection of related concepts among medical ontologies is an important goal of life science research. It is more crucial to figure out how different concepts are related within a single ontology or across multiple ontologies by analysing predicates in different knowledge bases. However, the world today is one of information explosion, and it is extremely difficult for biomedical researchers to find existing or potential predicates to perform linking among cross domain concepts without any support from schema pattern analysis. Therefore, there is a need for a mechanism to do predicate oriented pattern analysis to partition heterogeneous ontologies into closer small topics and do query generation to discover cross domain knowledge from each topic. In this paper, we present such a model that predicates oriented pattern analysis based on their close relationship and generates a similarity matrix. Based on this similarity matrix, we apply an innovated unsupervised learning algorithm to partition large data sets into smaller and closer topics and generate meaningful queries to fully discover knowledge over a set of interlinked data sources. We have implemented a prototype system named BmQGen and evaluate the proposed model with colorectal surgical cohort from the Mayo Clinic.","PeriodicalId":61442,"journal":{"name":"智能信息管理(英文)","volume":"8 3","pages":"66-85"},"PeriodicalIF":0.0,"publicationDate":"2016-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5626454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35478137","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Estela S Estape, Mary Helen Mays, Elizabeth A Sternke
Personalized medicine is the development of 'tailored' therapies that reflect traditional medical approaches, with the incorporation of the patient's unique genetic profile and the environmental basis of the disease. These individualized strategies encompass disease prevention, diagnosis, as well as treatment strategies. Today's healthcare workforce is faced with the availability of massive amounts of patient- and disease-related data. When mined effectively, these data will help produce more efficient and effective diagnoses and treatment, leading to better prognoses for patients at both the individual and population level. Designing preventive and therapeutic interventions for those patients who will benefit most while minimizing side effects and controlling healthcare costs, requires bringing diverse data sources together in an analytic paradigm. A resource to clinicians in the development and application of personalized medicine is largely facilitated, perhaps even driven, by the analysis of "big data". For example, the availability of clinical data warehouses is a significant resource for clinicians in practicing personalized medicine. These "big data" repositories can be queried by clinicians, using specific questions, with data used to gain an understanding of challenges in patient care and treatment. Health informaticians are critical partners to data analytics including the use of technological infrastructures and predictive data mining strategies to access data from multiple sources, assisting clinicians' interpretation of data and development of personalized, targeted therapy recommendations. In this paper, we look at the concept of personalized medicine, offering perspectives in four important, influencing topics: 1) the availability of 'big data' and the role of biomedical informatics in personalized medicine, 2) the need for interdisciplinary teams in the development and evaluation of personalized therapeutic approaches, and 3) the impact of electronic medical record systems and clinical data warehouses on the field of personalized medicine. In closing, we present our fourth perspective, an overview to some of the ethical concerns related to personalized medicine and health equity.
{"title":"Translation in Data Mining to Advance Personalized Medicine for Health Equity.","authors":"Estela S Estape, Mary Helen Mays, Elizabeth A Sternke","doi":"10.4236/iim.2016.81002","DOIUrl":"https://doi.org/10.4236/iim.2016.81002","url":null,"abstract":"<p><p>Personalized medicine is the development of 'tailored' therapies that reflect traditional medical approaches, with the incorporation of the patient's unique genetic profile and the environmental basis of the disease. These individualized strategies encompass disease prevention, diagnosis, as well as treatment strategies. Today's healthcare workforce is faced with the availability of massive amounts of patient- and disease-related data. When mined effectively, these data will help produce more efficient and effective diagnoses and treatment, leading to better prognoses for patients at both the individual and population level. Designing preventive and therapeutic interventions for those patients who will benefit most while minimizing side effects and controlling healthcare costs, requires bringing diverse data sources together in an analytic paradigm. A resource to clinicians in the development and application of personalized medicine is largely facilitated, perhaps even driven, by the analysis of \"big data\". For example, the availability of clinical data warehouses is a significant resource for clinicians in practicing personalized medicine. These \"big data\" repositories can be queried by clinicians, using specific questions, with data used to gain an understanding of challenges in patient care and treatment. Health informaticians are critical partners to data analytics including the use of technological infrastructures and predictive data mining strategies to access data from multiple sources, assisting clinicians' interpretation of data and development of personalized, targeted therapy recommendations. In this paper, we look at the concept of personalized medicine, offering perspectives in four important, influencing topics: 1) the availability of 'big data' and the role of biomedical informatics in personalized medicine, 2) the need for interdisciplinary teams in the development and evaluation of personalized therapeutic approaches, and 3) the impact of electronic medical record systems and clinical data warehouses on the field of personalized medicine. In closing, we present our fourth perspective, an overview to some of the ethical concerns related to personalized medicine and health equity.</p>","PeriodicalId":61442,"journal":{"name":"智能信息管理(英文)","volume":"8 1","pages":"9-16"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4236/iim.2016.81002","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34561592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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