Cells are cognitive entities possessing great computational power. DNA serves as a multivalent information storage medium for these computations at various time scales. Information is stored in sequences, epigenetic modifications, and rapidly changing nucleoprotein complexes. Because DNA must operate through complexes formed with other molecules in the cell, genome functions are inherently interactive and involve two-way communication with various cellular compartments. Both coding sequences and repetitive sequences contribute to the hierarchical systemic organization of the genome. By virtue of nucleoprotein complexes, (...) epigenetic modifications, and natural genetic engineering activities, the genome can serve as a read-write storage system. An interactive informatic conceptualization of the genome allows us to understand the functional importance of DNA that does not code for protein or RNA structure, clarifies the essential multidirectional and systemic nature of genomic information transfer, and emphasizes the need to investigate how cellular computation operates in reproduction and evolution. (shrink)

Informatics is generally understood as a “new technology” and is therewith discussed according to technological aspects such as speed, data retrieval, information control and so on. Its widespread use from home appliances to enterprises and universities is not the result of a clear-cut analysis of its inner possibilities but is rather dependent on all sorts of ideological promises of unlimited progress. We will discuss the theoretical definition of informatics proposed in 1936 by Alan Turing in order to show (...) that it should be taken as final and complete. This definition has no relation to the technology because Turing defines computers as doing the work of solving problems with numbers. This formal definition implies nonetheless a relation to the non-formalized elements around informatics, which we shall discuss through the Greek notion of téchne. (shrink)

The current informal practice of pharmacometrics as a combination art and science makes it hard to appreciate the role that informatics can and should play in the future of the discipline and to comprehend the gaps that exist because of its absence. The development of pharmacometric informatics has important implications for expediting decision making and for improving the reliability of decisions made in model-based development. We argue that well-defined informatics for pharmacometrics can lead to much needed improvements (...) in the efficiency, effectiveness, and reliability of the pharmacometrics process. The purpose of this paper is to provide a description of the pervasive yet often poorly appreciated role of informatics in improving the process of data assembly, a critical task in the delivery of pharmacometric analysis results. First, we provide a brief description of the pharmacometric analysis process. Second, we describe the business processes required to create analysis-ready data sets for the pharmacometrician. Third, we describe selected informatic elements required to support the pharmacometrics and data assembly processes. Finally, we offer specific suggestions for performing a systematic analysis of existing challenges as an approach to defi ning the next generation of pharmacometric informatics. (shrink)

An explicit formal-ontological representation of entities existing at multiple levels of granularity is an urgent requirement for biomedical information processing. We discuss some fundamental principles which can form a basis for such a representation. We also comment on some of the implicit treatments of granularity in currently available ontologies and terminologies (GO, FMA, SNOMED CT).

This article is part of a For-Discussion-Section of Methods of Information in Medicine about the paper "Biomedical Informatics: We Are What We Publish", written by Peter L. Elkin, Steven H. Brown, and Graham Wright. It is introduced by an editorial. This article contains the combined commentaries invited to independently comment on the Elkin et al. paper. In subsequent issues the discussion can continue through letters to the editor.

This article clarifies three principles that should guide the development of any cognitive ontology. First, that an adequate cognitive ontology depends essentially on an adequate task ontology; second, that the goal of developing a cognitive ontology is independent of the goal of finding neural implementations of the processes referred to in the ontology; and third, that cognitive ontologies are neutral regarding the metaphysical relationship between cognitive and neural processes.

This article is an overview of the philosophy of informatics with a special regard to some Polish philosophers. It juxtaposes the informationistic worldview with the long-prevailing mechanical conceptualization of nature before introducing the metaphysical perspective of the information revolution in sciences. The article shows also how ontic pancomputationalism – regarded as an update to structural realism – could enrich the philosophical research in some classical topics. The paper concludes with a discussion of the philosophy of Jan Salamucha, a philosopher (...) from the Cracow Circle whose ideas could be inspiring for today’s philosophy of informatics in Cracow. (shrink)

The automatic integration of rapidly expanding information resources in the life sciences is one of the most challenging goals facing biomedical research today. Controlled vocabularies, terminologies, and coding systems play an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources – for example pertaining to genes and proteins, drugs and diseases – secure in the knowledge that the same terms will also represent the same entities on all occasions of use. In the (...) naming of genes, proteins, and other molecular structures, considerable efforts are under way to reduce the effects of the different naming conventions which have been spawned by different groups of researchers. Electronic patient records, too, increasingly involve the use of standardized terminologies, and tremendous efforts are currently being devoted to the creation of terminology resources that can meet the needs of a future era of personalized medicine, in which genomic and clinical data can be aligned in such a way that the corresponding information systems become interoperable. (shrink)

Objective: There are benefits and risks of giving patients more granular control of their personal health information in electronic health record (EHR) systems. When designing EHR systems and policies, informaticists and system developers must balance these benefits and risks. Ethical considerations should be an explicit part of this balancing. Our objective was to develop a structured ethics framework to accomplish this. -/- Methods: We reviewed existing literature on the ethical and policy issues, developed an ethics framework called a “Points to (...) Consider” (P2C) document, and convened a national expert panel to review and critique the P2C. -/- Results: We developed the P2C to aid informaticists designing an advanced query tool for an electronic health record (EHR) system in Indianapolis. The P2C consists of six questions (“Points”) that frame important ethical issues, apply accepted principles of bioethics and Fair Information Practices, comment on how questions might be answered, and address implications for patient care. -/- Discussion: The P2C is intended to clarify whatis at stake when designers try to accommodate potentially competing ethical commitments and logistical realities. The P2C was developed to guide informaticists who were designing a query tool in an existing EHR that would permit patient granular control. While consideration of ethical issues is coming to the forefront of medical informatics design and development practices, more reflection is needed to facilitate optimal collaboration between designers and ethicists. This report contributes to that discussion. (shrink)

Initially the problems of data integration, for example in the field of medicine, were resolved in case by case fashion. Pairs of databases were cross-calibrated by hand, rather as if one were translating from French into Hebrew. As the numbers and complexity of database systems increased, the idea arose of streamlining these efforts by constructing one single benchmark taxonomy, as it were a central switchboard, into which all of the various classification systems would need to be translated only once. By (...) serving as a lingua franca for database integration this benchmark taxonomy would ensure that all databases calibrated in its terms would be automatically compatible with each other. We describe one strategy for creating such a lingua franca, in which philosophical ontology plays a central role. (shrink)

How do we find what is clinically significant in the swarms of data being generated by today’s diagnostic technologies? As electronic records become ever more prevalent – and digital imaging and genomic, proteomic, salivaomics, metabalomics, pharmacogenomics, phenomics and transcriptomics techniques become commonplace – fdifferent clinical and biological disciplines are facing up to the need to put their data houses in order to avoid the consequences of an uncontrolled explosion of different ways of describing information. We describe a new strategy to (...) advance the consistency of data in the dental research community. The strategy is based on the idea that existing systems for data collection in dental research will continue to be used, but proposes a methodology in which past, present and future data will be described using a consensus-based controlled structured vocabulary called the Ontology for Dental Research (ODR). (shrink)

Abstract— The term Health Informatics represent a huge volume of data that is collected from different source of health sector. Because of its’ diversity in nature, quite a big number of attributes, numerous amount data, health informatics can be considered as Big Data. Therefore, different techniques used for analyzing Big Data will also fit for Health Informatics. In recent years, implementation of Data Mining on Health Informatics brings a lot of fruitful outcomes that improve the overall (...) healthcare system both in analyzing disease and improving healthcare services which eventually reduce expenses. This paper will define the term the health informatics with a detail discussion about different source of heath informatics. Finally, some case study will be illustrated as examples where data mining techniques are applied to produce more efficient, in depth outcomes in analyzing disease. (shrink)

My original contribution to knowledge is : Any weapon that exhibits intended and/or untended lethal autonomy in targeting and interdiction – does so by way of design and/or recessive flaw(s) in its systems of control – any such weapon is capable of war-fighting and other battle-space interaction in a manner that its Human Commander does not anticipate. Even with the complexity of Lethal Autonomy issues there is nothing particular to gain from being a low-tech Military. Lethal autonomous weapons are therefore (...) independently capable of exhibiting positive or negative recessive norms of targeting in its perceptions of Discrimination between Civilian and Military Objects, Proportionality of Methods and Outcomes, Feasible Precaution before interdiction and its underlying Concepts of Humanity. Additionally Lethal Autonomy in Human-interacting Autonomous Robots is ubiquitous[designed and/or recessive]. This marks the completion of an Open PhD ( #openphd ) project done in sui generis form. (shrink)

Abstract Introduction Logically valid deductive arguments are clear examples of abstract recursive computational proce‐ dures on propositions or on probabilities. However, it is not known if the cortical time‐consuming inferential pro‐ cesses in which logical arguments are eventually realized in the brain are in fact physically different from other kinds of inferential processes. Methods In order to determine whether an electrical EEG discernible pattern of logical deduction exists or not, a new experimental paradigm is proposed contrasting logically valid and invalid (...) inferences with exactly the same content (same premises and same relational variables) and distinct logical complexity (propositional truth‐functional operators). Electroencephalographic signals from 19 subjects (24.2 ± 3.3 years) were acquired in a two‐condition para‐ digm (100 trials for each condition). After the initial general analysis, a trial‐by‐trial approach in beta‐2 band allowed to uncover not only evoked but also phase asynchronous activity between trials. Results showed that (i) deductive inferences with the same content evoked the same response pattern in logically valid and invalid conditions, (ii) mean response time in logically valid inferences is 61.54% higher, (iii) logically valid inferences are subjected to an early (400 ms) and a late reprocessing (600 ms) verified by two distinct beta‐2 activa‐ tions (p‐value < 0,01, Wilcoxon signed rank test). Conclusion We found evidence of a subtle but measurable electrical trait of logical validity. Results put forward the hypothesis that some logically valid deductions are recursive or computational cortical events. Keywords Beta‐2 band, Evoked potentials, Induced potentials, Deductive inference, Logical validity, Cortical bases of logical reasoning. (shrink)

The Foundational Model of Anatomy (FMA) symbolically represents the structural organization of the human body from the macromolecular to the macroscopic levels, with the goal of providing a robust and consistent scheme for classifying anatomical entities that is designed to serve as a reference ontology in biomedical informatics. Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems. We diagnose certain characteristic errors in the treatment of these (...) relations and show how these errors can be avoided through adoption of the formalism we describe. We then illustrate how a consistently applied formal treatment of taxonomy and partonomy can support the alignment of ontologies. (shrink)

The collaboration of Language and Computing nv (L&C) and the Institute for Formal Ontology and Medical Information Science (IFOMIS) is guided by the hypothesis that quality constraints on ontologies for software ap-plication purposes closely parallel the constraints salient to the design of sound philosophical theories. The extent of this parallel has been poorly appreciated in the informatics community, and it turns out that importing the benefits of phi-losophical insight and methodology into application domains yields a variety of improvements. L&C’s (...) LinKBase® is one of the world’s largest medical domain ontologies. Its current primary use pertains to natural language processing ap-plications, but it also supports intelligent navigation through a range of struc-tured medical and bioinformatics information resources, such as SNOMED-CT, Swiss-Prot, and the Gene Ontology (GO). In this report we discuss how and why philosophical methods improve both the internal coherence of LinKBase®, and its capacity to serve as a translation hub, improving the interoperability of the ontologies through which it navigates. (shrink)

We introduce the Vital Sign Ontology (VSO), an extension of the Ontology for General Medical Science (OGMS) that covers the consensus human vital signs: blood pressure, body temperature, respiratory rate, and pulse rate. VSO provides a controlled structured vocabulary for describing vital sign measurement data, the processes of measuring vital signs, and the anatomical entities participating in such measurements. VSO is implemented in OWL-DL and follows OBO Foundry guidelines and best practices. If properly developed and extended, we believe the VSO (...) will find applications for the EMR, clinical informatics, and medical device communities. (shrink)

Taking as an assumption the existence of an informatics revolution nowadays and that the examination of studies and debates related to it may allow the identification of questions of a philosophical nature, the present study aims to identify and formulate some of these questions, as well as to investigate whether the historical controversy about monopsychism, which occurred at the University of Paris in 1270, can be considered a theoretical framework capable of providing contributions to these philosophical questions. The answer (...) to this research problem may be positive, insofar as the aforementioned theoretical framework allows to identify contributions to the solution of the above mentioned questions. Or negative, otherwise. Or even in terms, to the extent that such subsidies only partially meet their objectives or raise, in turn, new questions. (shrink)

Letter commenting on the paper Barry Smith, Louis J. Goldberg, Alan Ruttenberg & Michael Glick, "Ontology and the Future of Dental Research Informatics", Journal of the American Dental Association 141 2010;(10):1173-75 with responses by the authors of the paper.

The "second-generation indigenization" hypothesis of Huntington's phenomenological observations on totalitarianism in Cold War regime collapse subtly portrayed the realpolitik interest groups' political influences with autocracy disbandment processes. The research puts democratization as the premise and globalization as purpose for the analysis, with the cultural anthropological psychopathology & criminological elements of genocide and crime against humanity explained, underlying some of the Communist Party of China (CPC)’s organizational behaviors. With the regionalism purposes & approaches to multilateralism by People's Republic of China (PRC), (...) the end of democratization is leveraged against the procedural means with power politics of declared “decmocracy”. Between quantitative autocratic controls and realpolitik local-regional interest groups, the connotation of democratization in liberal international globalization has either been used for militant purposes or pushed the landscape of regime collapse into realpolitik local groups and autocratic controls in the process of globalization, with a case study on a local branch of Argricultural Bank of China on supply-side hijacking by the State-owned Assets Supervision and Administration Commission of the State Council (SASAC). With the industrial interests omposed on realpolitik local groups, autocratic regionalism becomes of the "best interest scenario" for the realpolitik local groups with psychopathological spread of the criminological behaviors, by the cyber organizational criminal operations correlated with PRC’s approaches to international relations and multilateralism through bilateral trade & finance in monetary and currency domains, developed into the digitization of economies with criminological schemes in telecommunication, information, and informatics systems. However, the diminishing autonomy & freedom of the territorial population in turn derogated the real economy that wielded the prisoners' dilemma between autocracy and totalitarianism in a negative sum game deterioration cycle, with the censorship practices by the illicit regimes for propaganda controls sustaining "ideology security". In the democratization process of the dictatorial regime, "second-generation indigenization" is thus mapped to the sectarian interests respondent to dictatorial propaganda generation, other than a natural phenomenon out of autonomy and freedom premises in decision theory. The article recaps the coup d'état between Xi Jinping and Bo Xilai before Xi took the autocratic power, and analyzes the human rights situation in the obstacle of democratization and by the coercion mechanism imposed on the mainland China civil society for the militant purposes, with its behaviral spread of censorship to the “internet platforms” in liberal democratic countries by financial interest incentives and avoidance from war threats, whereby military backends in the cyber systems already indicate otherwise. (shrink)

We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) (...) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. (shrink)

Biomedical ontologies exist to serve integration of clinical and experimental data, and it is critical to their success that they be put to widespread use in the annotation of data. How, then, can ontologies achieve the sort of user-friendliness, reliability, cost-effectiveness, and breadth of coverage that is necessary to ensure extensive usage? Methods: Our focus here is on two different sets of answers to these questions that have been proposed, on the one hand in medicine, by the SNOMED CT community, (...) and on the other hand in biology, by the OBO Foundry. We address more specifically the issue as to how adherence to certain development principles can advance the usability and effectiveness of an ontology or terminology resource, for example by allowing more accurate maintenance, more reliable application, and more efficient interoperation with other ontologies and information resources. Results: SNOMED CT and the OBO Foundry differ considerably in their general approach.Nevertheless, a general trend towards more formal rigor and cross-domain interoperability can be seen in both and we argue that this trend should be accepted by all similar initiatives in the future. Conclusions: Future efforts in ontology development have to address the need for harmonization and integration of ontologies across disciplinary borders, and for this, coherent formalization of ontologies is a prerequisite. (shrink)

In the first wave of the COVID-19 pandemic, healthcare workers in some countries were forced to make distressing triaging decisions about which individual patients should receive potentially life-saving treatment. Much of the ethical discussion prompted by the pandemic has concerned which moral principles should ground our response to these individual triage questions. In this paper we aim to broaden the scope of this discussion by considering the ethics of broader structural allocation decisions raised by the COVID-19 pandemic. More specifically, we (...) consider how nations ought to distribute a scarce life-saving resource across healthcare regions in a public health emergency, particularly in view of regional differences in projected need and existing capacity. We call this the regional triage question. Using the case study of ventilators in the COVID-19 pandemic, we show how the moral frameworks that we might adopt in response to individual triage decisions do not translate straightforwardly to this regional-level triage question. Having outlined what we take to be a plausible egalitarian approach to the regional triage question, we go on to propose a novel way of operationalising the ‘save the most lives’ principle in this context. We claim that the latter principle ought to take some precedence in the regional triage question, but also note important limitations to the extent of the influence that it should have in regional allocation decisions. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is (...) of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

Vaccination can protect vaccinated individuals and often also prevent them from spreading disease to other people. This opens up the possibility of getting vaccinated for the sake of others. In fact, altruistic vaccination has recently been conceptualized as a kind of vaccination that is undertaken primary for the benefit of others. In order to better understand the potential role of altruistic motives in people’s vaccination decisions, we conducted two focus group studies with a total of 37 participants. Study 1 included (...) three focus groups on the subject of HPV vaccination for boys. Study 2 included three focus groups on the subject of pertussis and measles vaccination for childcare workers. We found substantial evidence of other-regarding motives across all focus groups, which suggests that altruistic motives could be an important factor when it comes to people’s vaccination decisions. We address the significance of these findings for vaccination policy surrounding HPV vaccination for boys and vaccination for childcare workers. We also extend the findings to normative work on vaccination for the sake of others more generally. (shrink)

In Spanish, on Internet as the new god of all us.

The National Cancer Institute’s Thesaurus (NCIT) has been created with the goal of providing a controlled vocabulary which can be used by specialists in the various sub-domains of oncology. It is intended to be used for purposes of annotation in ways designed to ensure the integration of data and information deriving from these various sub-domains, and thus to support more powerful cross-domain inferences. In order to evaluate its suitability for this purpose, we examined the NCIT’s treatment of the kinds of (...) entities which are fundamental to an ontology of colon carcinoma. We here describe the problems we uncovered concerning classification, synonymy, relations and definitions, and we draw conclusions for the work needed to establish the NCIT as a reference ontology for the cancer domain in the future. (shrink)

The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support (...) the Foundry’s goal of consistent and non-redundant annotation if appropriate mappings of data annotated with their aid can be achieved. To construct such mappings in reliable fashion, however, it is necessary to analyze terminological resources from an ontologically realistic perspective in such a way as to identify the exact import of the ‘concepts’ and associated terms which they contain. We propose a framework for such analysis that is designed to maximize the degree to which legacy terminologies and the data coded with their aid can be successfully used for information-driven clinical and translational research. (shrink)

Ontology is a burgeoning field, involving researchers from the computer science, philosophy, data and software engineering, logic, linguistics, and terminology domains. Many ontology-related terms with precise meanings in one of these domains have different meanings in others. Our purpose here is to initiate a path towards disambiguation of such terms. We draw primarily on the literature of biomedical informatics, not least because the problems caused by unclear or ambiguous use of terms have been there most thoroughly addressed. We advance (...) a proposal resting on a distinction of three levels too often run together in biomedical ontology research: 1. the level of reality; 2. the level of cognitive representations of this reality; 3. the level of textual and graphical artifacts. We propose a reference terminology for ontology research and development that is designed to serve as common hub into which the several competing disciplinary terminologies can be mapped. We then justify our terminological choices through a critical treatment of the ‘concept orientation’ in biomedical terminology research. (shrink)

Ontologies, as the term is used in informatics, are structured vocabularies comprised of human- and computer-interpretable terms and relations that represent entities and relationships. Within informatics fields, ontologies play an important role in knowledge and data standardization, representation, integra- tion, sharing and analysis. They have also become a foundation of artificial intelligence (AI) research. In what follows, we outline the Coronavirus Infectious Disease Ontology (CIDO), which covers multiple areas in the domain of coronavirus diseases, including etiology, transmission, epidemiology, (...) pathogenesis, diagnosis, prevention, and treatment. We emphasize CIDO development relevant to COVID-19. (shrink)

The study, design and development of a low-cost digital braille printer is boarded with a transdisciplinary approach. The main challenge was focused on reducing significantly the high cost of this type of printers and their printing services. This context is aggravated with the low commercialization of these products in the country, a factor that makes the access of these tools -that are essential to much of the low and middle sectors of the Argentine social structure- even more difficult. An interdisciplinary (...) group of teachers, graduates and students of the careers of industrial design and informatics degree from the National University of La Plata, developed the design and prototype of a braille printer. The work was carried out according to the principles of Gandhian Engineering, based on the reuse of ink-jet printers. The project consists of the design, development and generation of a low-cost Braille printer, produced locally, which prioritizes the use of nationally manufactured components for assembly. To achieve this, an electronic and electromechanical system was designed and manufactured to adapt any Inkjet printer to the objectives of the project, enabling the recycling of obsolete printers. This means, it is proposed to resolve through the use of text printers, applying technical knowledge of computer science and industrial design, to adapt the technological components to the Braille lexicon printer. They also developed, on the one hand, software that controls the printer and allows its use in a simple and accessible way. On the other hand, the hardware and external components were adapted with 3D printing technology and thermoforming, producing a housing that contains the entire printer. Finally, a systematization of the assembly process of the printer prototype was carried out, making it possible to replicate it. Using methodologies of Gandhian Design, a prototype and two alternative proposals of carcasses were obtained. The main objective, which guided this work, was that blind people can access low-cost braille printers promoting by this a favorable impact on the cultural development of their daily lives. (shrink)

Responding to Danaher et al. on self-tracking technologies, I argue that human lived experience is becoming increasingly mediated by generalized, statistical information, which I term our "infotality." Drawing on the work of Foucault, I argue that infotality is historically novel and best understood as the product of biopolitics, healthism, and informatics. I then critique the authors' "stance of cautious openness,” which misunderstands the aims of the technology in question and the fundamental ambiguity of the role information plays in the (...) achievement of human wellbeing. Self-tracking technologies are not primarily designed to change behavior; they are designed to create and sustain the desire for their use. I conclude by suggesting that infotality names a new way to fall for an old ruse: the promise that more information means more wellbeing. (shrink)

In recent years, neuroscience has begun to transform itself into a “big data” enterprise with the importation of computational and statistical techniques from machine learning and informatics. In addition to their translational applications such as brain-computer interfaces and early diagnosis of neuropathology, these tools promise to advance new solutions to longstanding theoretical quandaries. Here I critically assess whether these promises will pay off, focusing on the application of multivariate pattern analysis (MVPA) to the problem of reverse inference. I argue (...) that MVPA does not inherently provide a new answer to classical worries about reverse inference, and that the method faces pervasive interpretive problems of its own. Further, the epistemic setting of MVPA and other decoding methods contributes to a potentially worrisome shift towards prediction and away from explanation in fundamental neuroscience. (shrink)

This book is written for middle and high school students, for teachers and for those with a passion for math, containing 150+1 problems (which are followed by solutions) to make it more accessible to the reader. The last problem (150+1), a very interesting one, leaves some space for comments and generalizations. The book is a collaboration between a multi-awarded student at Romania’s National Mathematics Olympiad (Carina Maria Viespescu, student in year 10 at Liceul International of Informatics Bucuresti), a teacher (...) from Colegiul National “Fratii Buzesti” din Cravoia and prof. Dr. Emeritus Florentin Smarandache from the University of New Mexico. A couple of problems are proposed by colleagues, and their names indicated in footnotes. (shrink)

The issue of the definition and position of archaeology as a discipline is examined in relation to the dispute which took place from 1980 to 2009 between the archaeologist Jean-Claude Gardin and the sociologist Jean-Claude Passeron. This case study enables us to explore the actual conceptual relationships between archaeology and the other sciences (as opposed to those wished for or prescribed). The contrasts between the positions declared by the two researchers and the rooting of their arguments in their disciplines are (...) examined: where the sociologist makes use of his philosophical training, the archaeologist relies mainly on his work on semiology and informatics. Archaeology ultimately plays a minor role in the arguments proposed. This dispute therefore cannot be considered as evidence for the movement of concepts between archaeology and the social sciences. A blind spot in the debate, relating to the ontological specificities of archaeological objects, nevertheless presents itself as a possible way of implementing this movement. (shrink)

We begin at the beginning, with an outline of Aristotle’s views on ontology and with a discussion of the influence of these views on Linnaeus. We move from there to consider the data standardization initiatives launched in the 19th century, and then turn to investigate how the idea of computational ontologies developed in the AI and knowledge representation communities in the closing decades of the 20th century. We show how aspects of this idea, particularly those relating to the use of (...) the term 'concept' in ontology development, influenced SNOMED CT and other medical terminologies. Against this background we then show how the Foundational Model of Anatomy, the Gene Ontology, Basic Formal Ontology and other OBO Foundry ontologies came into existence and discuss their role in the development of contemporary biomedical informatics. (shrink)

In a world that is overflowing with journals and other outlets for scientific publication, the appearance of any new periodical requires some justification. There are already more journals than we can read and more conferences than we can attend. In the case of applied Ontology, we believe that the creation of anew journal not only is completely justifiable, it is downright exciting. For too long, workers in computer science have assumed that content comes for free. “Theory” in computer science has (...) always meant the theory of processes and of computation. We measure the complexity of computer programs in terms of how long it takes machines to execute them, not in terms of how long it takes people to understand and to represent the data on which those programs might operate. We typically describe computer code in terms of algorithms that operate on formal parameters, often without pausing to discuss where the data that might satisfy those parameters come from. This journal was founded on the premise that workers in computer science, informatics, and information science are overdue in paying as much attention to contents as they do to algorithms. (shrink)

Representing species-specific proteins and protein complexes in ontologies that are both human and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although existing protin-centric informatics resources provide the biomedical research community with well-curated compendia of protein sequence and structure, these resources lack formal ontological representations of the relationships among the proteins themselves. The Protein Ontology (PRO) Consortium is filling this informatics resource gap by developing ontological representations and relationships among proteins and their variants and modified (...) forms. Because proteins are often functional only as members of stable protein complexes, the PRO Consortium, in collaboration with existing protein and pathway databases, has launched a new initiative to implement logical and consistent representation of protein complexes. We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein complexes and comparative biology, and how PRO is being integrated into existing community bioinformatics resources. The PRO resource is accessible at http://pir.georgetown.edu/pro/. (shrink)

Vaccine research, as well as the development, testing, clinical trials, and commercial uses of vaccines involve complex processes with various biological data that include gene and protein expression, analysis of molecular and cellular interactions, study of tissue and whole body responses, and extensive epidemiological modeling. Although many data resources are available to meet different aspects of vaccine needs, it remains a challenge how we are to standardize vaccine annotation, integrate data about varied vaccine types and resources, and support advanced vaccine (...) data analysis and inference. To address these problems, the community-based Vaccine Ontology (VO) has been developed through collaboration with vaccine researchers and many national and international centers and programs, including the National Center for Biomedical Ontology (NCBO), the Infectious Disease Ontology (IDO) Initiative, and the Ontology for Biomedical Investigations (OBI). VO utilizes the Basic Formal Ontology (BFO) as the top ontology and the Relation Ontology (RO) for definition of term relationships. VO is represented in the Web Ontology Language (OWL) and edited using the Protégé-OWL. Currently VO contains more than 2000 terms and relationships. VO emphasizes on classification of vaccines and vaccine components, vaccine quality and phenotypes, and host immune response to vaccines. These reflect different aspects of vaccine composition and biology and can thus be used to model individual vaccines. More than 200 licensed vaccines and many vaccine candidates in research or clinical trials have been modeled in VO. VO is being used for vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI). Multiple VO applications will be presented. (shrink)

Investigation into the sequence structure of the genetic code by means of an informatic approach is a real success story. The features of human language are also the object of investigation within the realm of formal language theories. They focus on the common rules of a universal grammar that lies behind all languages and determine generation of syntactic structures. This universal grammar is a depiction of material reality, i.e., the hidden logical order of things and its relations determined by natural (...) laws. Therefore mathematics is viewed not only as an appropriate tool to investigate human language and genetic code structures through computer sciencebased formal language theory but is itself a depiction of material reality. This confusion between language as a scientific tool to describe observations/experiences within cognitive constructed models and formal language as a direct depiction of material reality occurs not only in current approaches but was the central focus of the philosophy of science debate in the twentieth century, with rather unexpected results. This article recalls these results and their implications for more recent mathematical approaches that also attempt to explain the evolution of human language. (shrink)

The desideratum of semantic interoperability has been intensively discussed in medical informatics circles in recent years. Originally, experts assumed that this issue could be sufficiently addressed by insisting simply on the application of shared clinical terminologies or clinical information models. However, the use of the term ‘ontology’ has been steadily increasing more recently. We discuss criteria for distinguishing clinical ontologies from clinical terminologies and information models. Then, we briefly present the role clinical ontologies play in two multicentric research projects. (...) Finally, we discuss the interactions between these different kinds of knowledge representation artifacts and the stakeholders involved in developing interoperational real-world clinical applications. We provide ontology engineering examples from two EU-funded projects. (shrink)

Ethics should guide the design of electronic health records (EHR), and recognized principles of bioethics can play an important role. This approach was adopted recently by a team of informaticists designing and testing a system where patients exert granular control over who views their personal health information. While this method of building ethics in from the start of the design process has significant benefits, questions remain about how useful the application of bioethics principles can be in this process, especially when (...) principles conflict. For instance, while the ethical principle of respect for autonomy supports a robust system of granular control, the principles of beneficence and non-maleficence counsel restraint due to the danger of patients being harmed by restrictions on provider access to data. Conflict between principles has long been recognized by ethicists and has even motivated attacks on approaches that state and apply principles. In this paper we show how using ethical principles can help in the design of EHRs by first, explaining how ethical principles can and should be used generally, and then by, discuss how attention to details in specific cases can show that the tension between principles is not as bad as it initially appeared. We conclude by suggesting further ways in which the application of these (and other) principles can add value to the ongoing discussion of patient involvement in their health care. This is a new approach to linking principles to informatics design that we expect will stimulate further interest. (shrink)

Objectives: Machine learning (ML) has the potential to facilitate “continual learning” in medicine, in which an ML system continues to evolve in response to exposure to new data over time, even after being deployed in a clinical setting. In this article, we provide a tutorial on the range of ethical issues raised by the use of such “adaptive” ML systems in medicine that have, thus far, been neglected in the literature. -/- Target audience: The target audiences for this tutorial are (...) the developers of ML AI systems, healthcare regulators, the broader medical informatics community, and practicing clinicians. -/- Scope: Discussions of adaptive ML systems to date have overlooked the distinction between 2 sorts of variance that such systems may exhibit—diachronic evolution (change over time) and synchronic variation (difference between cotemporaneous instantiations of the algorithm at different sites)—and underestimated the significance of the latter. We highlight the challenges that diachronic evolution and synchronic variation present for the quality of patient care, informed consent, and equity, and discuss the complex ethical trade-offs involved in the design of such systems. (shrink)

In the era of “big data,” science is increasingly information driven, and the potential for computers to store, manage, and integrate massive amounts of data has given rise to such new disciplinary fields as biomedical informatics. Applied ontology offers a strategy for the organization of scientific information in computer-tractable form, drawing on concepts not only from computer and information science but also from linguistics, logic, and philosophy. This book provides an introduction to the field of applied ontology that is (...) of particular relevance to biomedicine, covering theoretical components of ontologies, best practices for ontology design, and examples of biomedical ontologies in use. After defining an ontology as a representation of the types of entities in a given domain, the book distinguishes between different kinds of ontologies and taxonomies, and shows how applied ontology draws on more traditional ideas from metaphysics. It presents the core features of the Basic Formal Ontology (BFO), now used by over one hundred ontology projects around the world, and offers examples of domain ontologies that utilize BFO. The book also describes Web Ontology Language (OWL), a common framework for Semantic Web technologies. Throughout, the book provides concrete recommendations for the design and construction of domain ontologies. (shrink)

This volume presents research that integrates decision making and creativity within the social contexts in which these processes occur. The volume is an essential addition to and expansion of recent approaches to decision making. Such approaches attempt to incorporate more of the psychological and socio-cultural context in which human decision making takes place. The authors come from different disciplines and also belong to a broad spectrum of research traditions. They present innovative chapters dealing with both theoretical and empirical aspects of (...) decision making in different personal and organizational contexts. All chapters are written from the perspective that human decision making is inherently social and more or less creative. The volume addresses fundamental questions about the nature of human decision making as it occurs in different social contexts. Thereby, it becomes essential reading for researchers in decision making and for advanced students in psychology, management science, informatics, and related disciplines. (shrink)

The article is devoted to the increasing role of tourism in the world economy. The dynamics of international tourism indicators is investigated. The main global innovations in the tourism industry are identified: the growth of tourism types; the application of qualitatively new solutions of scientific and methodological and applied character; growing of tourism influence on the society; the existence of synergistic effect in the tourist industry as a result of combination of subjects efforts at all management levels; changing of the (...) role of internal and external factors that encourage innovative tourism development. In the article, the interaction of global processes on tourism innovations is defined. These processes are: intellectualization, informatization, cooperation, formation of the global tourism market, liberalization of the national tourism markets, increased competition and the spread of transnationalization. (shrink)

The 21st century imposed many challenges on mankind, among them there is a very important problem of entrepreneurial leadership transformation. Entrepreneurship gradual modification under the pressure of factors of innovation, informatization of the environment and the need for socialization of the relations between businessmen and society has led to the need of new understanding of leadership positions. The purpose of this scientific research is to substantiate the style of entrepreneurial leadership, which will become dominant in the 21st century. Analyzing and (...) systematizing the scientific works of many modern scholars by the methods of theoretical synthesis, analysis and synthesis, we have solved the problems of entrepreneurial leadership transformation. The use of the historical and logical method has revealed the relationship between the entrepreneurial leadership development and entrepreneurial types. The study found that the global business environment requires new leaders, whose key competences will meet the needs of society, educational space, ethical requirements, etc. Studying the similarities and differences of various leadership styles has become the basis for the allocation of a new style – the leadership of conscious influence, the main characteristics of which are given in this research. In order to achieve the goals, set by the leader-entrepreneur, it is proposed to systematize the leadership opportunities on tactical and strategic, the factors of influence on their realization in the future are generalized. By the method of scientific and theoretical prediction the portrait of an entrepreneur in a global perspective has been formed. Prospects for further research in this area are the development of a methodology for evaluating the effectiveness of business leaders' actions and systematization of ways to increase their effectiveness in the future. (shrink)

This article is a modified version of a paper I gave to the conference Philosophy & Informatics - First Italian Conference on the use of ICT in philosophical disciplines, promoted by the Italian Philosophical Association (University of Rome "La Sapienza", 23-24 November, 1995).

The integration of standardized biomedical terminologies into a single, unified knowledge representation system has formed a key area of applied informatics research in recent years. The Unified Medical Language System (UMLS) is the most advanced and most prominent effort in this direction, bringing together within its Metathesaurus a large number of distinct source-terminologies. The UMLS Semantic Network, which is designed to support the integration of these source-terminologies, has proved to be a highly successful combination of formal coherence and broad (...) scope. We argue here, however, that its organization manifests certain structural problems, and we describe revisions which we believe are needed if the network is to be maximally successful in realizing its goals of supporting terminology integration. (shrink)

The automatic integration of information resources in the life sciences is one of the most challenging goals facing biomedical informatics today. Controlled vocabularies have played an important role in realizing this goal, by making it possible to draw together information from heterogeneous sources secure in the knowledge that the same terms will also represent the same entities on all occasions of use. One of the most impressive achievements in this regard is the Gene Ontology (GO), which is rapidly acquiring (...) the status of a de facto standard in the field of gene and gene product annotations, and whose methodology has been much intimated in attempts to develop controlled vocabularies for shared use in different domains of biology. The GO Consortium has recognized, however, that its controlled vocabulary as currently constituted is marked by several problematic features - features which are characteristic of much recent work in bioinformatics and which are destined to raise increasingly serious obstacles to the automatic integration of biomedical information in the future. Here, we survey some of these problematic features, focusing especially on issues of compositionality and syntactic regimentation. (shrink)