BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature

Calle, Guillermo de la; García-Remesal, Miguel; Chiesa, Stefano Della; Iglesia, Diana de la; Maojo, Víctor

doi:10.1186/1471-2105-10-320

Cited by 29 publications

(29 citation statements)

References 20 publications

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“…The ACTION-grid project (Kern et al, 2008;Martín-Sanchez et al, 2008;Chiesa et al, 2009;De La Calle et al, 2009;, expected to create a common health information infrastructure in Europe to be extended to other regions, is considering nanomedicine and nanoinformatics as cardinal points of the project.…”

Section: Nanoinformatics Has Taken Its First Stepsmentioning

confidence: 99%

Nanotechnology and human health: risks and benefits

Cattaneo

Gornati

Sabbioni

et al. 2010

J of Applied Toxicology

137

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Nanotechnology is expected to be promising in many fields of medical applications, mainly in cancer treatment. While a large number of very attractive exploitations open up for the clinics, regulatory agencies are very careful in admitting new nanomaterials for human use because of their potential toxicity. The very active research on new nanomaterials that are potentially useful in medicine has not been counterbalanced by an adequate knowledge of their pharmacokinetics and toxicity. The different nanocarriers used to transport and release the active molecules to the target tissues should be treated as additives, with potential side effects of themselves or by virtue of their dissolution or aggregation inside the body. Only recently has a systematic classification of nanomaterials been proposed, posing the basis for dedicated modeling at the nanoscale level. The use of in silico methods, such as nano-QSAR and PSAR, while highly desirable to expedite and rationalize the following stages of toxicological research, are not an alternative, but an introduction to mandatory experimental work.

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Section: Nanoinformatics Has Taken Its First Stepsmentioning

confidence: 99%

Nanotechnology and human health: risks and benefits

Cattaneo

Gornati

Sabbioni

et al. 2010

J of Applied Toxicology

137

View full text Add to dashboard Cite

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“…This is a direction where the authors have been active in Africa, working on various initiatives to teach African professionals BMI methods and tools can transfer open BMI results to these areasbut this introduces yet another topic which would require further discussion in a separate forum. We would like to mention that we have carried out extensive research in text mining methods to automatically extract information about informatics resources (software, databases, tools, services) from the scientific literature [11][12][13][14][15][16]. We originally carried out this work in BI, later expanding it to include MI.…”

Section: Figmentioning

confidence: 99%

Biomedical Informatics Publications: a Global Perspective

Maojo¹,

García-Remesal²,

Bielza³

et al. 2012

Methods Inf Med

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SummaryBackground: Biomedical Informatics (BMI) is a broad discipline, having evolved from both Medical Informatics (MI) and Bioinformatics (BI). An analysis of publications in the fieldshould provide an indication about the geographic distribution of BMI research contributions and possible lessons for the future, both for research and professional practice. Objectives: In part I of our analysis of biomedical informatics publications we presented results from BMI conferences. In this second part, we analyse BMI journals, which provide a broader perspective and comparison between data from conferences and journals that ought to confirm or suggest alternatives to the original distributional findings from the conferences.

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“…Based on text mining techniques, the authors have built a new approach to automatically create a searchable index of bioinformatics resources, with information automatically extracted from abstracts of research articles using text mining techniques (31). We are currently building a nanoinventory of resources from the literature (32), in which we have seen the great variability in how researchers report their results.…”

Section: Nanoinformatics: Informational Foundations For Nanomedicinementioning

confidence: 99%

Nanoinformatics and DNA-Based Computing: Catalyzing Nanomedicine

et al. 2010

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Five decades of research and practical application of computers in biomedicine has given rise to the discipline of medical informatics, which has made many advances in genomic and translational medicine possible. Developments in nanotechnology are opening up the prospects for nanomedicine and regenerative medicine where informatics and DNA computing can become the catalysts enabling health care applications at sub-molecular or atomic scales. Although nanomedicine promises a new exciting frontier for clinical practice and biomedical research, issues involving costeffectiveness studies, clinical trials and toxicity assays, drug delivery methods, and the implementation of new personalized therapies still remain challenging. Nanoinformatics can accelerate the introduction of nano-related research and applications into clinical practice, leading to an area that could be called "translational nanoinformatics." At the same time, DNA and RNA computing presents an entirely novel paradigm for computation. Nanoinformatics and DNA-based computing are together likely to completely change the way we model and process information in biomedicine and impact the emerging field of nanomedicine most strongly. In this article, we review work in nanoinformatics and DNA (and RNA)-based computing, including applications in nanopediatrics. We analyze their scientific foundations, current research and projects, envisioned applications and potential problems that might arise from them. O ver the past two decades, bioinformatics and systems biology have addressed informational challenges in biomedicine at the molecular and cellular level, leading to the sequencing of the Human Genome and other -omics projects. At a higher scale, or organismal level, medical informatics deals with patient information, whereas public health informatics focuses on their aggregation at the population level. Recently, Biomedical Informatics (BMI) has emerged to integrate the fields of Medical Informatics and Bioinformatics. However, new informatics methods will be needed to deal with phenomena and research at the smallest, submolecular or atomic levels. The new discipline of Nanoinformatics aims to represent and work with information at the nano level. In this review article, we use the generic name, "Nanoinformatics," to avoid any premature overspecialization in a disciplinelike medical nanoinformatics or bionanoinformatics-that still needs to be more completely defined. We include in this review the related computational field dealing with methods and devices that process biological information by using DNA and RNA.Nanoinformatics refers to the use of informatics techniques for analyzing and processing information about the structure and physico-chemical characteristics of nanoparticles, their environments, and applications. Figure 1 schematically represents some of its relationships with related disciplines.Nanoinformatics is a newly emerging informatics area, working at the intersection between informatics (computer science and information technol...

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BIRI: a new approach for automatically discovering and indexing available public bioinformatics resources from the literature

Cited by 29 publications

References 20 publications

Nanotechnology and human health: risks and benefits

Nanotechnology and human health: risks and benefits

Biomedical Informatics Publications: a Global Perspective

Nanoinformatics and DNA-Based Computing: Catalyzing Nanomedicine

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