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Victor Maojo,1 Martin Fritts,2,3 Diana de la Iglesia,1 Raul E Cachau,4 Miguel Garcia-Remesal,1 Joyce A Mitchell,5 Casimir Kulikowski61Biomedical Informatics Group, Departamento de Inteligencia Artificial, Facultad de Informática, Universidad Politécnica de Madrid, Spain; 2SAIC-Frederick Inc, National Cancer Institute at Frederick, Frederick, Maryland, 3National Institute of Standards and Technology, Gaithersburg, Maryland, 4Advanced Biomedical Computing Center, National Cancer Institute, SAIC-Frederick Inc, Frederick, Maryland, 5Department of Biomedical Informatics, University of Utah, Utah, 6Department of Computer Science, Rutgers, The State University of New Jersey, New Jersey, USAAbstract: Over a decade ago, nanotechnologists began research on applications of nanomaterials for medicine. This research has revealed a wide range of different challenges, as well as many opportunities. Some of these challenges are strongly related to informatics issues, dealing, for instance, with the management and integration of heterogeneous information, defining nomenclatures, taxonomies and classifications for various types of nanomaterials, and research on new modeling and simulation techniques for nanoparticles. Nanoinformatics has recently emerged in the USA and Europe to address these issues. In this paper, we present a review of nanoinformatics, describing its origins, the problems it addresses, areas of interest, and examples of current research initiatives and informatics resources. We suggest that nanoinformatics could accelerate research and development in nanomedicine, as has occurred in the past in other fields. For instance, biomedical informatics served as a fundamental catalyst for the Human Genome Project, and other genomic and –omics projects, as well as the translational efforts that link resulting molecular-level research to clinical problems and findings.Keywords: biomedical informatics, nanomedicine, nanotoxicology, ontologies, electronic health records

Background: 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.Methods: We manually collected data about authors and their geographical origin from various MI journals: the International Journal of Medical Informatics (IJMI), the Journal of Biomedical Informatics (JBI), Methods of In formation in Medicine (MIM) and The Journal of the American Medical Informatics Association (JAMIA). Focusing on first authors, we also compared these findings with data from the journal Bioinformatics.Results: Our results confirm those obtained in our analysis of BMI conferences - that local and regional authors favor their corresponding MI journals just as they do their conferences. Consideration of other factors, such as the increasingly open source nature of data and software tools, is consistent with these findings.Conclusions: Our analysis suggests various indicators that could lead to further, deeper analyses, and could provide additional insights for future BMI research and professional activities. [ABSTRACT FROM AUTHOR]

Background: In the past decade, Medical Informatics (MI) and Bioinformatics (BI) have converged towards a new discipline, called Biomedical Informatics (BMI) bridging informatics methods across the spectrum from genomic research to personalized medicine and global healthcare. This convergence still raises challenging research questions which are being addressed by researchers internationally, which in turn raises the question of how biomedical informatics publications reflect the contributions from around the world in documenting the research.Objectives: To analyse the worldwide participation of biomedical informatics researchers from professional groups and societies in the best-known scientific conferences in the field. The analysis is focused on their geographical affiliation, but also includes other features, such as the impact and recognition of the conferences.Methods: We manually collected data about authors of papers presented at three major MI conferences: Medinfo, MIE and the AMIA symposium. In addition, we collected data from a BI conference, ISMB, as a comparison. Finally, we analyzed the impact and recognition of these conferences within their scientific contexts.Results: Data indicate a predominance of local authors at the regional conferences (AMIA and MIE), whereas other conferences with a world-wide scope (Medinfo and ISMB) had broader participation. Our analysis shows that the influence of these conferences beyond the discipline remains somewhat limited.Conclusions: Our results suggest that for BMI to be recognized as a broad discipline, both in the geographical and scientific sense, it will need to extend the scope of collaborations and their interdisciplinary impacts worldwide. [ABSTRACT FROM AUTHOR]

Objectives: Biomedical ontologies have been very successful in structuring knowledge for many different applications, receiving widespread praise for their utility and potential. Yet, the role of computational ontologies in scientific research, as opposed to knowledge management applications, has not been extensively discussed. We aim to stimulate further discussion on the advantages and challenges presented by biomedical ontologies from a scientific perspective.Methods: We review various aspects of biomedical ontologies going beyond their practical successes, and focus on some key scientific questions in two ways. First, we analyze and discuss current approaches to improve biomedical ontologies that are based largely on classical, Aristotelian ontological models of reality. Second, we raise various open questions about biomedical ontologies that require further research, analyzing in more detail those related to visual reasoning and spatial ontologies.Results: We outline significant scientific issues that biomedical ontologies should consider, beyond current efforts of building practical consensus between them. For spatial ontologies, we suggest an approach for building "morphospatial" taxonomies, as an example that could stimulate research on fundamental open issues for biomedical ontologies.Conclusions: Analysis of a large number of problems with biomedical ontologies suggests that the field is very much open to alternative interpretations of current work, and in need of scientific debate and discussion that can lead to new ideas and research directions. [ABSTRACT FROM AUTHOR]