Biomedical ontologies: toward scientific debate

Coordinating dissent as an alternative to consensus classification: insights from systematics for bio-ontologies

The collection and classification of data into meaningful categories is a key step in the process of knowledge making. In the life sciences, the design of data discovery and integration tools has relied on the premise that a formal classificatory system for expressing a body of data should be grounded in consensus definitions for classifications. On this approach, exemplified by the realist program of the Open Biomedical Ontologies Foundry, progress is maximized by grounding the representation and aggregation of data on settled knowledge. We argue that historical practices in systematic biology provide an important and overlooked alternative approach to classifying and disseminating data, based on a principle of coordinative rather than definitional consensus. Systematists have developed a robust system for referring to taxonomic entities that can deliver high quality data discovery and integration without invoking consensus about reality or "settled" science.

On determining factors for good research in biomedical and health informatics. Some lessons learned

OBJECTIVE

What are the determining factors for good research in medical informatics or, from a broader perspective, in biomedical and health informatics?

METHOD

From the many lessons learned during my professional career, I tried to identify a fair sampling of such factors. On the occasion of giving the IMIA Award of Excellence lecture during MedInfo 2013, they were presented for discussion.

RESULTS

Sixteen determining factors (df) have been identified: early identification and promotion (df1), appropriate education (df2), stimulating persons and environments (df3), sufficient time and backtracking opportunities (df4), breadth of medical informatics competencies (df5), considering the necessary preconditions for good medical informatics research (df6), easy access to high-quality knowledge (df7), sufficient scientific career opportunities (df8), appropriate conditions for sustainable research (df9), ability to communicate and to solve problems (df10), as well as to convey research results (df11) in a highly inter- and multidisciplinary environment, ability to think for all and, when needed, taking the lead (df12), always staying unbiased (df13), always keeping doubt (df14), but also always trying to provide solutions (df15), and, finally, being aware that life is more (df16).

CONCLUSIONS

Medical Informatics is an inter- and multidisciplinary discipline "avant la lettre". Compared to monodisciplinary research, inter- and multidisciplinary research does not only provide significant opportunities for solving major problems in science and in society. It also faces considerable additional challenges for medical informatics as a scientific field. The determining factors, presented here, are in my opinion crucial for conducting successful research and for developing a research career. Since medical informatics as a field has today become an important driving force for research progress, especially in biomedicine and health care, but also in fields like computer science, it may be helpful to consider such factors in relation with research and education in our discipline.

Nanoinformatics knowledge infrastructures: bringing efficient information management to nanomedical research

Nanotechnology represents an area of particular promise and significant opportunity across multiple scientific disciplines. Ongoing nanotechnology research ranges from the characterization of nanoparticles and nanomaterials to the analysis and processing of experimental data seeking correlations between nanoparticles and their functionalities and side effects. Due to their special properties, nanoparticles are suitable for cellular-level diagnostics and therapy, offering numerous applications in medicine, e.g. development of biomedical devices, tissue repair, drug delivery systems and biosensors. In nanomedicine, recent studies are producing large amounts of structural and property data, highlighting the role for computational approaches in information management. While in vitro and in vivo assays are expensive, the cost of computing is falling. Furthermore, improvements in the accuracy of computational methods (e.g. data mining, knowledge discovery, modeling and simulation) have enabled effective tools to automate the extraction, management and storage of these vast data volumes. Since this information is widely distributed, one major issue is how to locate and access data where it resides (which also poses data-sharing limitations). The novel discipline of nanoinformatics addresses the information challenges related to nanotechnology research. In this paper, we summarize the needs and challenges in the field and present an overview of extant initiatives and efforts.

On the ontology based representation of cell lines

Cell lines are frequently used as highly standardized and reproducible in vitro models for biomedical analyses and assays. Cell lines are distributed by cell banks that operate databases describing their products. However, the description of the cell lines' properties are not standardized across different cell banks. Existing cell line-related ontologies mostly focus on the description of the cell lines' names, but do not cover aspects like the origin or optimal growth conditions. The objective of this work is to develop an ontology that allows for a more comprehensive description of cell lines and their metadata, which should cover the data elements provided by cell banks. This will provide the basis for the standardized annotation of cell lines and corresponding assays in biomedical research. In addition, the ontology will be the foundation for automated evaluation of such assays and their respective protocols in the future. To accomplish this, a broad range of cell bank databases as well as existing ontologies were analyzed in a comprehensive manner. We identified existing ontologies capable of covering different aspects of the cell line domain. However, not all data fields derived from the cell banks' databases could be mapped to existing ontologies. As a result, we created a new ontology called cell culture ontology (CCONT) integrating existing ontologies where possible. CCONT provides classes from the areas of cell line identification, origin, cell line properties, propagation and tests performed.

Nanoinformatics: a new area of research in nanomedicine

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.

Biomedical informatics--a confluence of disciplines?

BACKGROUND

Biomedical informatics is a broad discipline that borrows many methods and techniques from other disciplines.

OBJECTIVE

To reflect a) on the character of biomedical informatics and to determine whether it is multi-disciplinary or inter-disciplinary; b) on the question whether biomedical informatics is more than the sum of its supporting disciplines and c) on the position of biomedical informatics with respect to related disciplines.

METHOD

Inviting an international group of experts in biomedical informatics and related disciplines on the occasion of the 50th anniversary of Methods of Information in Medicine to present their viewpoints.

RESULTS AND CONCLUSIONS

This paper contains the reflections of a number of the invited experts on the character of biomedical informatics. Most of the authors agree that biomedical informatics is an interdisciplinary field of study where researchers with different scientific backgrounds alone or in combination carry out research. Biomedical informatics is a very broad scientific field and still expanding, yet comprised of a constructive aspect (designing and building systems). One author expressed that the essence of biomedical informatics, as opposed to related disciplines, lies in the modelling of the biomedical content. Interdisciplinarity also has consequences for education. Maintaining rigid disciplinary structures does not allow for sufficient adaptability to capitalize on important trends nor to leverage the influences these trends may have on biomedical informatics. It is therefore important for students to become aware of research findings in related disciplines. In this respect, it was also noted that the fact that many scientific fields use different languages and that the research findings are stored in separate bibliographic databases makes it possible that potentially connected findings will never be linked, despite the fact that these findings were published. Bridges between the sciences are needed for the success of biomedical informatics.

Nanoinformatics: developing new computing applications for nanomedicine

Nanoinformatics has recently emerged to address the need of computing applications at the nano level. In this regard, the authors have participated in various initiatives to identify its concepts, foundations and challenges. While nanomaterials open up the possibility for developing new devices in many industrial and scientific areas, they also offer breakthrough perspectives for the prevention, diagnosis and treatment of diseases. In this paper, we analyze the different aspects of nanoinformatics and suggest five research topics to help catalyze new research and development in the area, particularly focused on nanomedicine. We also encompass the use of informatics to further the biological and clinical applications of basic research in nanoscience and nanotechnology, and the related concept of an extended "nanotype" to coalesce information related to nanoparticles. We suggest how nanoinformatics could accelerate developments in nanomedicine, similarly to what happened with the Human Genome and other -omics projects, on issues like exchanging modeling and simulation methods and tools, linking toxicity information to clinical and personal databases or developing new approaches for scientific ontologies, among many others.

Biomedical informatics publications: a global perspective. Part II: Journals

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.