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  1. Wilfried Allaerts (1991). On the Role of Gravity and Positional Information in Embryological Axis Formation and Tissue Compartmentalization. Acta Biotheoretica 39 (1).
    The idea that gravity affects dorso-ventral polarization in anouran development contrasts with the theories of self-organization through reaction-diffusion processes. As a result of a literature study we discuss the role of gravity in embryological axis formation and speculate on an influence of gravity on tissue compartmentalization. The involvement of compartmentalization in tissue homeostasis is discussed in the light of the recent progress in mammalian cell culture studies.
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  2. Lydia Arianova (1996). The Information Processing Organisms. Acta Biotheoretica 44 (2).
    In spite of the tremendous progress in recent decades of biological science, many aspects of the behaviour of organisms in general and of humans in particular remain still somewhat obscure. A new approach towards the study of the behaviour of man was presented by Heisenberg when he emphasized that a Cartesian view of nature as an object out there is an illusion in so far as the observer is always part of the formula, the man viewing nature must be figured (...)
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  3. Gennaro Auletta (2011). Cognitive Biology: Dealing with Information From Bacteria to Minds. Oxford University Press, Usa.
    Machine generated contents note: -- 1. Quantum Mechanics as a General Framework -- 2. Classical and Quantum Information and Entropy -- 3. The Brain: An Outlook -- 4. Vision -- 5. Dealing with Target's Motion and Our Own Movement -- 6. Complexity: A Necessary Condition -- 7. General Features of Life -- 8. The Organism as a Semiotic and Cybernetic System -- 9. Phylogeny -- 10. Ontogeny -- 11. Epigeny -- 12. Representational Semiotics -- 13. The Brain as an Information-Control (...)
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  4. Christopher J. Austin (2014). The Dispositional Genome: Primus Inter Pares. Biology and Philosophy:1-20.
    According to the proponents of Developmental Systems Theory and the Causal Parity Thesis, the privileging of the genome as “first among equals” with respect to the development of phenotypic traits is more a reflection of our own heuristic prejudice than of ontology - the underlying causal structures responsible for that specified development no more single out the genome as primary than they do other broadly “environmental” factors. Parting with the methodology of the popular responses to the Thesis, this paper offers (...)
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  5. Francisco J. Ayala (1989). Thermodynamics, Information, and Evolution: The Problem of Reductionism. [REVIEW] History and Philosophy of the Life Sciences 11 (1):115 - 120.
  6. Marcello Barbieri (forthcoming). From Biosemiotics to Code Biology. Biological Theory.
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  7. Marcello Barbieri (2003). Biology with Information and Meaning. History and Philosophy of the Life Sciences 25 (2):243 - 254.
    It is shown that information and meaning can be defined by operative procedures, and that we need to recognize them as new types of natural entities. They are not quantities (neither fundamental nor derived) because they cannot be measured, and they are not qualities because they are not subjective features. Here it is proposed to call them nominable entities, i.e., entities which can be specified only by naming their components in their natural order.
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  8. Lluís Barceló-Coblijn (2013). Biology: A Newcomer in Linguistics. [REVIEW] Biological Theory 7 (3):281-284.
  9. J. Bard (2005). Bioinformatics Ain't What It Used to Be By Arthur M. Lesk. Bioessays 27 (9):981.
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  10. J. Bard (2002). An Introduction to BioInformatics By Lesk M. Bioessays 24 (9):867-868.
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  11. Scott Barolo (2012). Shadow Enhancers: Frequently Asked Questions About Distributed Cis‐Regulatory Information and Enhancer Redundancy. Bioessays 34 (2):135-141.
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  12. Carl T. Bergstrom & Martin Rosvall (2011). The Transmission Sense of Information. Biology and Philosophy 26 (2):159-176.
    Biologists rely heavily on the language of information, coding, and transmission that is commonplace in the field of information theory developed by Claude Shannon, but there is open debate about whether such language is anything more than facile metaphor. Philosophers of biology have argued that when biologists talk about information in genes and in evolution, they are not talking about the sort of information that Shannon’s theory addresses. First, philosophers have suggested that Shannon’s theory is only useful for developing a (...)
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  13. Carl Bergstrom & Martin Rosvall (2011). Response to Commentaries on “The Transmission Sense of Information”. Biology and Philosophy 26 (2):195-200.
    Response to commentaries on “The Transmission Sense of Information” Content Type Journal Article Pages 195-200 DOI 10.1007/s10539-011-9257-3 Authors Carl T. Bergstrom, Department of Biology, University of Washington, Seattle, WA 98195-1800, USA Martin Rosvall, Integrated Science Lab, Department of Physics, Umeå University, 901 87 Umeå, Sweden Journal Biology and Philosophy Online ISSN 1572-8404 Print ISSN 0169-3867 Journal Volume Volume 26 Journal Issue Volume 26, Number 2.
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  14. Jesse M. Bering & Todd K. Shackelford (2004). Supernatural Agents May Have Provided Adaptive Social Information. Behavioral and Brain Sciences 27 (6):732-733.
    Atran & Norenzayan's (A&N's) target article effectively combines the insights of evolutionary biology and interdisciplinary cognitive science, neither of which alone yields sufficient explanatory power to help us fully understand the complexities of supernatural belief. Although the authors' ideas echo those of other researchers, they are perhaps the most squarely grounded in neo-Darwinian terms to date. Nevertheless, A&N overlook the possibility that the tendency to infer supernatural agents' communicative intent behind natural events served an ancestrally adaptive function.
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  15. Thomas Bittner & Barry Smith (2004). Normalizing Medical Ontologies Using Basic Formal Ontology. In Proceedings of GMDS 2004.
    Description Logics are nowadays widely accepted as formalisms which provide reasoning facilities which allow us to discover inconsistencies in ontologies in an automatic fashion. Where ontologies are developed in modular fashion, they allow changes in one module to propogated through the system of ontologies automatically in a way which helps to maintain consistency and stability. For this feature to be utilized effectively, however, requires that domain ontologies be represented in a normalized form.
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  16. OIivier Bodenreider, Barry Smith & Anita Burgun (2004). The Ontology-Epistemology Divide: A Case Study in Medical Terminology. In Achille Varzi & Laure Vieu (eds.), Formal Ontology in Information Systems. Proceedings of the Third International Conference (FOIS 2004),. IOS Press.
    Medical terminology collects and organizes the many different kinds of terms employed in the biomedical domain both by practitioners and also in the course of biomedical research. In addition to serving as labels for biomedical classes, these names reflect the organizational principles of biomedical vocabularies and ontologies. Some names represent invariant features (classes, universals) of biomedical reality (i.e., they are a matter for ontology). Other names, however, convey also how this reality is perceived, measured, and understood by health professionals (i.e., (...)
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  17. Olivier Bodenreider, Barry Smith, Anand Kumar & Anita Burgun (2007). Investigating Subsumption in SNOMED CT: An Exploration Into Large Description Logic-Based Biomedical Terminologies”,. Artificial Intelligence in Medicine 39:183-195.
    Formalisms based on one or other flavor of Description Logic (DL) are sometimes put forward as helping to ensure that terminologies and controlled vocabularies comply with sound ontological principles. The objective of this paper is to study the degree to which one DL-based biomedical terminology (SNOMED CT) does indeed comply with such principles. We defined seven ontological principles (for example: each class must have at least one parent, each class must differ from its parent) and examined the properties of SNOMED (...)
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  18. Robert N. Brandon & Norbert Hornstein (1986). From Icons to Symbols: Some Speculations on the Origins of Language. [REVIEW] Biology and Philosophy 1 (2):169-189.
    This paper is divided into three sections. In the first section we offer a retooling of some traditional concepts, namely icons and symbols, which allows us to describe an evolutionary continuum of communication systems. The second section consists of an argument from theoretical biology. In it we explore the advantages and disadvantages of phenotypic plasticity. We argue that a range of the conditions that selectively favor phenotypic plasticity also favor a nongenetic transmission system that would allow for the inheritance of (...)
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  19. Pier Luigi Buttigieg, Norman Morrison, Barry Smith, Christopher J. Mungall & Suzanna E. Lewis (2013). The Environment Ontology. Journal of Biomedical Semantics 4 (43).
    As biological and biomedical research increasingly reference the environmental context of the biological entities under study, the need for formalisation and standardisation of environment descriptors is growing. The Environment Ontology (ENVO; www.environmentontology.org) is a community-led, open project which seeks to provide an ontology for specifying a wide range of environments relevant to multiple life science disciplines and, through an open participation model, to accommodate the terminological requirements of all those needing to annotate data using ontology classes. This paper summarises ENVO’s (...)
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  20. Werner Callebaut & John Collier (2006). Biological Information. Biological Theory 1 (3):221-223.
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  21. Fernando Castro-Chavez (2012). The Rules of Variation Expanded, Implications for the Research on Compatible Genomics. Biosemiotics 5 (1):121-145.
    The main focus of this article is to present the practical aspect of the code rules of variation and the search for a second set of genomic rules, including comparison of sequences to understand how to preserve compatible organisms in danger of extinction and how to generate biodiversity. Three new rules of variation are introduced: 1) homologous recombination, 2) a healthy fertile offspring, and 3) comparison of compatible genomes. The novel search in the natural world for fully compatible genomes capable (...)
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  22. Werner Ceusters & Barry Smith (2010). A Unified Framework for Biomedical Terminologies and Ontologies. Studies in Health Technology and Informatics 160:1050-1054.
    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 (...)
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  23. Werner Ceusters & Barry Smith (2010). Foundations for a Realist Ontology of Mental Disease. Journal of Biomedical Semantics 1 (10):1-23.
    While classifications of mental disorders have existed for over one hundred years, it still remains unspecified what terms such as 'mental disorder', 'disease' and 'illness' might actually denote. While ontologies have been called in aid to address this shortfall since the GALEN project of the early 1990s, most attempts thus far have sought to provide a formal description of the structure of some pre-existing terminology or classification, rather than of the corresponding structures and processes on the side of the patient. (...)
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  24. Werner Ceusters & Barry Smith (2006). A Realism-Based Approach to the Evolution of Biomedical Ontologies. In Proceedings of the Annual AMIA Symposium. AMIA.
    We present a novel methodology for calculating the improvements obtained in successive versions of biomedical ontologies. The theory takes into account changes both in reality itself and in our understanding of this reality. The successful application of the theory rests on the willingness of ontology authors to document changes they make by following a number of simple rules. The theory provides a pathway by which ontology authoring can become a science rather than an art, following principles analogous to those that (...)
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  25. Werner Ceusters & Barry Smith (2006). Referent Tracking for Treatment Optimisation in Schizophrenic Patients. Journal of Web Semantics 4 (3):229-236.
    The IPAP Schizophrenia Algorithm was originally designed in the form of a flow chart to help physicians optimise the treatment of schizophrenic patients. We examined the current version from the perspective of recent work on terminologies and ontologies thereby drawing on the resources of Basic Formal Ontology, and this with the objective to make the algorithm appropriate for Semantic Web applications. We found that Basic Formal Ontology is a rich enough theory to represent all the entities involved and that applying (...)
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  26. Werner Ceusters & Barry Smith (2005). Tracking Referents in Electronic Health Records. Studies in Health Technology and Informatics 116:71–76.
    Electronic Health Records (EHRs) are organized around two kinds of statements: those reporting observations made, and those reporting acts performed. In neither case does the record involve any direct reference to what such statements are actually about. They record not: what is happening on the side of the patient, but rather: what is said about what is happening. While the need for a unique patient identifier is generally recognized, we argue that we should now move to an EHR regime in (...)
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  27. Werner Ceusters, Barry Smith & James Matthew Fielding (2004). LinkSuite™: Software Tools for Formally Robust Ontology-Based Data and Information Integration. In Proceedings of DILS 2004 (Data Integration in the Life Sciences), (Lecture Notes in Bioinformatics, 2994). Springer.
    The integration of information resources in the life sciences is one of the most challenging problems facing bioinformatics today. We describe how Language and Computing nv, originally a developer of ontology-based natural language understanding systems for the healthcare domain, is developing a framework for the integration of structured data with unstructured information contained in natural language texts. L&C’s LinkSuite™ combines the flexibility of a modular software architecture with an ontology based on rigorous philosophical and logical principles that is designed to (...)
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  28. Werner Ceusters, Barry Smith & Louis Goldberg (2005). A Terminological and Ontological Analysis of the NCI Thesaurus. Methods of Information in Medicine 44:498-507.
    We performed a qualitative analysis of the Thesaurus in order to assess its conformity with principles of good practice in terminology and ontology design. We used both the on-line browsable version of the Thesaurus and its OWL-representation (version 04.08b, released on August 2, 2004), measuring each in light of the requirements put forward in relevant ISO terminology standards and in light of ontological principles advanced in the recent literature. Version 04.08b of the NCI Thesaurus suffers from the same broad range (...)
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  29. Laurel Cooper, Ramona Walls, Justin Elser, Maria A. Gandolfo, Dennis W. Stevenson & Barry Smith (2013). The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant and Cell Physiology 54:1-23..
    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly-available, collaborative effort to develop and maintain a controlled, structured vocabulary (“ontology”) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded (...)
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  30. Soraya De Chadarevian (1996). Sequences, Conformation, Information: Biochemists and Molecular Biologists in the 1950s. [REVIEW] Journal of the History of Biology 29 (3):361-386.
  31. William Dembski, Evolution of Biological Information.
    National Cancer Institute, Frederick Cancer Research and Development Center, Laboratory of Experimental and Computational Biology, PO Box B, Frederick, MD 21702-1201, USA..
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  32. William Dembski, If Only Darwinists Scrutinized Their Own Work as Closely: A Response to "Erik".
    An Internet persona known as "Erik" reviewed those aspects of my book No Free Lunch dealing with the Law of Conservation of Information and specificational resources. Erik's review is titled "On Dembski's Law of Conservation of Information" and is available at http://www.talkreason.org/articles/dembski_LCI.pdf. I respond to the review here.
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  33. Stephen M. Downes, Biological Information.
    This paper discussses various concepts of biological information with particular attention being paid to genetic information.
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  34. Arantza Etxeberria Agiriano & Tomás Garcia Azkonobieta (2004). Sobre la noción de información genética: seméntica y excepcionalidad (On the notion of genetic information: semantics and exceptionality). Theoria 19 (2):209-230.
    EI objetivo de este artículo es analizar ciertas críticas a la aplicación de la nocion de informacíon en biología, teniendo en cuenta tanto la historia del concepto como las diferentes posiciones actuales. Creemos que la motivacíon principal de las críticas es negar que los genes sean un factor causal excepcional en el desarrollo, y favorecer la imagen de la vida como un sistema organizado que requiere diferentes recursos. Aunque compartimos el rechazo deI reduccionismo genetico, argumentamos que éste no es atribuible (...)
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  35. Keith D. Farnsworth, John Nelson & Carlos Gershenson (forthcoming). Living is Information Processing: From Molecules to Global Systems. Acta Biotheoretica.
    We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by both molecular states and ecological states as well as the more obvious nucleic acid coding; (b) this information processing has one overall function—to perpetuate itself; and (c) the processing method is filtration (cognition) of, and synthesis of, information at lower levels to appear at (...)
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  36. James M. Fielding, Jonathan Simon, Werner Ceusters & Barry Smith (2004). Ontological Theory for Ontological Engineering: Biomedical Systems Information Integration. In Proceedings of the Ninth International Conference on the Principles of Knowledge Representation and Reasoning. AMIA.
    Software application ontologies have the potential to become the keystone in state-of-the-art information management techniques. It is expected that these ontologies will support the sort of reasoning power required to navigate large and complex terminologies correctly and efficiently. Yet, there is one problem in particular that continues to stand in our way. As these terminological structures increase in size and complexity, and the drive to integrate them inevitably swells, it is clear that the level of consistency required for such navigation (...)
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  37. K. M. Franks & T. J. Sejnowski (2002). Communication in Neuronal Networks. Bioessays 12:1130.
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  38. Georg Fuellen, Melanie Börries, Hauke Busch, Aubrey de Grey, Udo Hahn, Thomas Hiller, Andreas Hoeflich, Ludger Jansen, Georges E. Janssens, Christoph Kaleta, Anne C. Meinema, Sascha Schäuble, Paul N. Schofield, Barry Smith & Daniel Wuttke (2013). In-Silico-Approaches and the Role of Ontologies in Aging Research. Rejuvenation Research 16 (6):540-546.
    The 2013 Rostock Symposium on Systems Biology and Bioinformatics in Aging Research was again dedicated to dissecting the aging process using in silico means. A particular focus was on ontologies, as these are a key technology to systematically integrate heterogeneous information about the aging process. Related topics were databases and data integration. Other talks tackled modeling issues and applications, the latter including talks focussed on marker development and cellular stress as well as on diseases, in particular on diseases of kidney (...)
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  39. Philippe Gagnon (2013). An Improbable God Between Simplicity and Complexity: Thinking About Dawkins's Challenge. International Philosophical Quarterly 53 (4):409-433.
    Richard Dawkins has popularized an argument that he thinks sound for showing that there is almost certainly no God. It rests on the assumptions (1) that complex and statistically improbable things are more difficult to explain than those that are not and (2) that an explanatory mechanism must show how this complexity can be built up from simpler means. But what justifies claims about the designer’s own complexity? One comes to a different understanding of order and of simplicity when one (...)
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  40. Maciej Giertych (2001). Rola informacji w funkcjonowaniu przyrody w kontekście sporu o ewolucję. Filozofia Nauki 2.
    Biological reality does not consist of chemistry and physics of organism alone. It also includes their information content. This information regulates developmental and reproductive processes. Its quantity is finite. We observe mixing of information (mating patterns, reduction division, hybridisation, genetic engineering), its loss (species extinction, reduction of genetic diversity in domestication, isolation, inbreeding) and increase of useless or injurious information (duplications, neutral and harmful mutations, genetic load). On the other hand we do not observe new useful biological information arising (positive (...)
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  41. Peter Godfrey-Smith, Information and the Argument From Design.
    William Dembski holds that "the origin of information is best sought in intelligent causes" ("Intelligent Design as a Theory of Information", 1997). In particular, Dembski argues that Darwinism is not able to explain the existence of biological structures that contain a certain kind of information – "complex specified information" (CSI). To explain these informational features of living systems, we must instead appeal to the choices made by an intelligent designer.
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  42. Peter Godfrey-Smith (2014). Signs and Symbolic Behavior. Biological Theory 9 (1):78-88.
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  43. Peter Godfrey-Smith (2011). Senders, Receivers, and Genetic Information: Comments on Bergstrom and Rosvall. Biology and Philosophy 26 (2):177-181.
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  44. Peter Godfrey-Smith (2007). Information in Biology. In David L. Hull & Michael Ruse (eds.), The Cambridge Companion to the Philosophy of Biology. Cambridge University Press. 103--119.
    The concept of information has acquired a strikingly prominent role in contemporary biology. This trend is especially marked within genetics, but it has also become important in other areas, such as evolutionary theory and developmental biology, particularly where these fields border on genetics. The most distinctive biological role for informational concepts, and the one that has generated the most discussion, is in the description of the relations between genes and the various structures and processes that genes play a role in (...)
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  45. Peter Godfrey-Smith (2001). The Role of Information and Replication in Selection Processes. Behavioral and Brain Sciences 24 (3):538-538.
    Hull et al. argue that information and replication are both essential ingredients in any selection process. But both information and replication are found in only some selection processes, and should not be included in abstract descriptions of selection intended to help researchers discover and describe selection processes in new domains.
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  46. Albert Goldfain, Barry Smith & Lindsay Cowell (2010). Dispositions and the Infectious Disease Ontology. In Formal Ontology in Information Systems. Proceedings of the Sixth International Conference (FOIS 2010). IOS Press.
    This paper addresses the use of dispositions in the Infectious Disease Ontology (IDO). IDO is an ontology constructed according to the principles of the Open Biomedical Ontology (OBO) Foundry and uses the Basic Formal Ontology (BFO) as an upper ontology. After providing a brief introduction to disposition types in BFO and IDO, we discuss three general techniques for representing combinations of dispositions under the headings blocking dispositions, complementary dispositions, and collective dispositions. Motivating examples for each combination of dispositions is given (...)
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  47. Albert Goldfain, Barry Smith & Lindsay G. Cowell (2011). Towards an Ontological Representation of Resistance: The Case of MRSA. Journal of Biomedical Informatics 44 (1):35-41.
    This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. The treatments of resistance terms in various existing ontologies are examined and found to be either overly narrow, internally inconsistent, or otherwise problematic. We propose a more coherent characterization of resistance in terms of what we shall call blocking dispositions, which are collections of mutually coordinated dispositions which are of such a sort that they cannot undergo simultaneous realization within a single (...)
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  48. R. Gorelick (2007). Werner Callebaut and John Collier-Editorial: Biological Information When Information Theory Is No Longer Theory. Biological Theory 2 (2).
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  49. Root Gorelick (2007). Werner Callebaut and John Collier—Editorial: Biological Information (Biological Theory 1: 221–223, 2006). Biological Theory 2 (2):180-182.
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  50. Root Gorelick & Manfred D. Laubichler (2008). Genetic= Heritable (Genetic# DNA). Biological Theory 3 (1):79-84.
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