The Protein Ontology (PRO) provides a formal, logically-based classification of specific protein classes including structured representations of protein isoforms, variants and modified forms. Initially focused on proteins found in human, mouse and Escherichia coli, PRO now includes representations of protein complexes. The PRO Consortium works in concert with the developers of other biomedical ontologies and protein knowledge bases to provide the ability to formally organize and integrate representations of precise protein forms so as to enhance accessibility to results of protein (...) research. PRO (http://pir.georgetown.edu/pro) is part of the Open Biomedical Ontologies (OBO) Foundry. (shrink)

Physics has been thought to truly represent reality since at least Galileo, and the foundations of physics are always established using philosophical ideas. In particular, the elegant naming of physical entities is usually very influential in the acceptance of physical theories. We here demonstrate (using current developments in thermodynamics as an example) that both the epistemology and the ontology of physics ultimately rest on poetic language. What we understand depends essentially on the language we use. We wish to establish our (...) knowledge securely, but strictly speaking this is impossible using only analytic language. Knowledge of the meanings of things must use a natural language designed to express meaning, that is, poetic language. Although the world is really there, and although we can indeed know it truly, this knowledge is never either complete or certain but ultimately must rest on intuition. Reading a recently discovered artefact with a palaeo-Hebrew inscription as from the first century, we demonstrate from it that this ontological understanding long predates the Hellenic period. Poetic language is primary, both logically and temporally. (shrink)

Main Response Topics ? Introduction ? Open display and public evaluation ? Publicity versus patient privacy ? Facial tissue donation ? Validity of Louisville Instrument for Risk Acceptance ? Patients' understanding of risk ? Face versus hand transplantation ? Rejection rates/risks ? Patient compliance ? Exit strategy ? Functional recovery ? Societietal implications ? Psychological implications ? Conclusion: Uncertainty likely to persist.

Biomedical ontologies are emerging as critical tools in genomic and proteomic research where complex data in disparate resources need to be integrated. A number of ontologies exist that describe the properties that can be attributed to proteins; for example, protein functions are described by Gene Ontology, while human diseases are described by Disease Ontology. There is, however, a gap in the current set of ontologies—one that describes the protein entities themselves and their relationships. We have designed a PRotein Ontology (PRO) (...) to facilitate protein annotation and to guide new experiments. The components of PRO extend from the classification of proteins on the basis of evolutionary relationships to the representation of the multiple protein forms of a gene (products generated by genetic variation, alternative splicing, proteolytic cleavage, and other post-translational modification). PRO will allow the specification of relationships between PRO, GO and other OBO Foundry ontologies. Here we describe the initial development of PRO, illustrated using human proteins from the TGF-beta signaling pathway. (shrink)

The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or posttranslational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. PRO provides a framework (...) for the formal representation of protein classes and protein forms in the OBO Foundry. It is designed to enable data retrieval and integration and machine reasoning at the molecular level of proteins, thereby facilitating cross-species comparisons, pathway analysis, disease modeling and the generation of new hypotheses. (shrink)

Transplantation continues to push the frontiers of medicine into domains that summon forth troublesome ethical questions. Looming on the frontier today is human facial transplantation. We develop criteria that, we maintain, must be satisfied in order to ethically undertake this as-yet-untried transplant procedure. We draw on the criteria advanced by Dr. Francis Moore in the late 1980s for introducing innovative procedures in transplant surgery. In addition to these we also insist that human face transplantation must meet all the ethical requirements (...) usually applied to health care research. We summarize the achievements of transplant surgery to date, focusing in particular on the safety and efficacy of immunosuppressive medications. We also emphasize the importance of risk/benefit assessments that take into account the physical, aesthetic, psychological, and social dimensions of facial disfiguration, reconstruction, and transplantation. Finally, we maintain that the time has come to move facial transplantation research into the clinical phase. (shrink)

Functional diversity holds the promise of understanding ecosystems in ways unattainable by taxonomic diversity studies. Underlying this promise is the intuition that investigating the diversity of what organisms actually do—i.e. their functional traits—within ecosystems will generate more reliable insights into the ways these ecosystems behave, compared to considering only species diversity. But this promise also rests on several conceptual and methodological—i.e. epistemic—assumptions that cut across various theories and domains of ecology. These assumptions should be clearly addressed, notably for the sake (...) of an effective comparison and integration across domains, and for assessing whether or not to use functional diversity approaches for developing ecological management strategies. The objective of this contribution is to identify and critically analyze the most salient of these assumptions. To this aim, we provide an “epistemic roadmap” that pinpoints these assumptions along a set of historical, conceptual, empirical, theoretical, and normative dimensions. (shrink)

Interactive narratives are inextricable from the way that we understand our encounters with digital technology. This is based upon the way that these encounters are processually formed into a narrative of episodic events, arranged and re-arranged by various levels of agency. After describing past research conducted at the iCinema Research Centre at the University of New South Wales, this paper sets out a framework within which to build a relational theory of interactive narrative formation, outlining future research in the area.

Each chapter heading bears a phrase from a contemporary author, held to incorporate the character of that section of the study under consideration. Chapter 1 carries the title given to early English translations of the Lettres provinciales; chapter 2 recalls the description of Pascall by Boyle and other English scientists; and chapter 3 draws from Kennett's preface to his version of the Pensees. The heading of chapter 4 is from Pope's Essay on Man. The exclamation which introduces chapter 5 concludes (...) an essay in the Gentleman's Magazine for 1789, probably by Boswell; the words for chapter 6 come from a pastoral letter of John Wesley; and chapter 7 represents the verdict of Coleridge. The title of the book itself is derived from the heading to the twenty-first chapter of Kennett's Pensees, which seems to have forecast the essence of the eighteenth-century's perplexity upon the issues raised by Pascal: 'The strange Contrarieties discoverable in Human Nature, with regard to Truth, and Happiness, and many other things.'. (shrink)