Teaching Computers to Read the Pharmacogenomics Literature … so You don‘t have to

Garten, Yael; Altman, Russ B.

doi:10.2217/pgs.10.48

Cited by 6 publications

(6 citation statements)

References 46 publications

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“…One of the applications of text mining in this area is associated to the curation the PharmaGKB database,102 where genetic variations are linked to drug responses 103. 104…”

Section: Applicationsmentioning

confidence: 99%

Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications

Vázquez

Krallinger

Leitner

et al. 2011

Molecular Informatics

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Providing prior knowledge about biological properties of chemicals, such as kinetic values, protein targets, or toxic effects, can facilitate many aspects of drug development. Chemical information is rapidly accumulating in all sorts of free text documents like patents, industry reports, or scientific articles, which has motivated the development of specifically tailored text mining applications. Despite the potential gains, chemical text mining still faces significant challenges. One of the most salient is the recognition of chemical entities mentioned in text. To help practitioners contribute to this area, a good portion of this review is devoted to this issue, and presents the basic concepts and principles underlying the main strategies. The technical details are introduced and accompanied by relevant bibliographic references. Other tasks discussed are retrieving relevant articles, identifying relationships between chemicals and other entities, or determining the chemical structures of chemicals mentioned in text. This review also introduces a number of published applications that can be used to build pipelines in topics like drug side effects, toxicity, and protein-disease-compound network analysis. We conclude the review with an outlook on how we expect the field to evolve, discussing its possibilities and its current limitations.

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“…One of the applications of text mining in this area is associated to the curation the PharmaGKB database,102 where genetic variations are linked to drug responses 103. 104…”

Section: Applicationsmentioning

confidence: 99%

Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications

Vázquez

Krallinger

Leitner

et al. 2011

Molecular Informatics

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show abstract

“…One uniform approach has been abandoned and replaced by more tailored and personalized approaches that put the learner as the center and consider an individual’s inherited factors and capabilities to empower them [ 25 , 32 – 35 ]. Many medical and health sciences colleges are embracing this evidence-based shift in paradigm by tailoring the pedagogy according to the learner’s individual traits [ 36 – 40 ].…”

Section: Discussionmentioning

confidence: 99%

Development of the pharmacogenomics and genomics literacy framework for pharmacists

et al. 2021

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Background Pharmacists play a unique role in integrating genomic medicine and pharmacogenomics into the clinical practice and to translate pharmacogenomics from bench to bedside. However, the literature suggests that the knowledge gap in pharmacogenomics is a major challenge; therefore, developing pharmacists’ skills and literacy to achieve this anticipated role is highly important. We aim to conceptualize a personalized literacy framework for the adoption of genomic medicine and pharmacogenomics by pharmacists in the United Arab Emirates with possible regional and global relevance. Results A qualitative approach using focus groups was used to design and to guide the development of a pharmacogenomics literacy framework. The Health Literacy Skills framework was used as a guide to conceptualize the pharmacogenomics literacy for pharmacists. The framework included six major components with specific suggested factors to improve pharmacists’ pharmacogenomics literacy. Major components include individual inputs, demand, skills, knowledge, attitude and sociocultural factors. Conclusion This framework confirms a holistic bottom-up approach toward the implementation of pharmacogenomics. Personalized medicine entails personalized efforts and frameworks. Similar framework can be created for other healthcare providers, patients and stakeholders.

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“…Current new efforts at PharmGKB focus on: The development of automated natural language parsing tools to extract annotation information from the literature automatically [Coulet et al, 2010; Garten and Altman, 2009, 2010]. …”

Section: The Pharmacogenomics Knowledge Base (Pharmgkb)mentioning

confidence: 99%

Databases in the area of pharmacogenetics

2011

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In the area of pharmacogenetics and personalized health care it is obvious that databases, providing important information of the occurrence and consequences of variant genes encoding drug metabolizing enzymes, drug transporters, drug targets, and other proteins of importance for drug response or toxicity, are of critical value for scientists, physicians, and industry. The primary outcome of the pharmacogenomic field is the identification of biomarkers that can predict drug toxicity and drug response, thereby individualizing and improving drug treatment of patients. The drug in question and the polymorphic gene exerting the impact are the main issues to be searched for in the databases. Here, we review the databases that provide useful information in this respect, of benefit for the development of the pharmacogenomic field.

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Teaching Computers to Read the Pharmacogenomics Literature … so You don‘t have to

Cited by 6 publications

References 46 publications

Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications

Text Mining for Drugs and Chemical Compounds: Methods, Tools and Applications

Development of the pharmacogenomics and genomics literacy framework for pharmacists

Databases in the area of pharmacogenetics

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