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)
Vitalism was long viewed as the most grotesque view in biological theory: appeals to a mysterious life-force, Romantic insistence on the autonomy of life, or worse, a metaphysics of an entirely living universe. In the early twentieth century, attempts were made to present a revised, lighter version that was not weighted down by revisionary metaphysics: “organicism”. And mainstream philosophers of science criticized Driesch and Bergson’s “neovitalism” as a too-strong ontological commitment to the existence of certain entities or “forces”, over and (...) above the system of causal relations studied by mechanistic science, rejecting the weaker form, organicism, as well. But there has been some significant scholarly “push-back” against this orthodox attitude, notably pointing to the 18th-century Montpellier vitalists to show that there are different historical forms of vitalism, including how they relate to mainstream scientific practice. Additionally, some trends in recent biology that run counter to genetic reductionism and the informational model of the gene present themselves as organicist. Here, we examine some cases of vitalism in the twentieth century and today, not just as a historical form but as a significant metaphysical and scientific model. We argue for vitalism’s conceptual originality without either reducing it to mainstream models of science or presenting it as an alternate model of science, by focusing on historical forms of vitalism, logical empiricist critiques thereof and the impact of synthetic biology on current theorizing of vitalism. (shrink)
El año 2011 remeció a Chile con un despertar de los movimientos sociales que levantaron sus demandas para la reestructuración del modelo educacional y social chileno heredado de la dictadura. El libro recopila columnas en prensa, artículos de discusión y material de información elaborado por autores y colectivos diversos que desde una perspectiva crítica al modelo y de compromiso con los movimientos sociales activan algunas de las discusiones de este proceso.
No matter how it is viewed, as a plausible version of anti-utilitarianism or of non-consequentialist, or even as a plausible version of deontology, the theory of prima facie duties certainly makes W. D. Ross one of the most important moral philosopher of the twentieth-century. By outlining his pluralistic deontology, this paper attempts to argue for a positive answer to the question of whether Ross’s theory can offer a solution to the issue of conflicting duties. If such a solution is convincing, (...) as I believe it is, it would indicate the possibility to justify within the deontological framework, i.e., without committing to the principle of good-maximizing, those “hard cases” where people should break a promise or other (prima facie) duty in order to prevent a disastrous outcome. The theory of prima facie duties might then suggest that deontology and utilitarianism would likely be reconcilable. (shrink)
The Protein Ontology (PRO) provides terms for and supports annotation of species-specific protein complexes in an ontology framework that relates them both to their components and to species-independent families of complexes. Comprehensive curation of experimentally known forms and annotations thereof is expected to expose discrepancies, differences, and gaps in our knowledge. We have annotated the early events of innate immune signaling mediated by Toll-Like Receptor 3 and 4 complexes in human, mouse, and chicken. The resulting ontology and annotation data set (...) has allowed us to identify species-specific gaps in experimental data and possible functional differences between species, and to employ inferred structural and functional relationships to suggest plausible resolutions of these discrepancies and gaps. (shrink)
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)
The paper attempts to outline the actual academic debates around the concept of PR ethics. The first part aims to show the intimate link between professionalism and ethics as well as their bearing on the reputation of the PR field. Whether and how ethical public relations are possible is the main issue analyzed in the second part of the article. The two paradigms of public relations, “the attorney-adversary system” and “the two-way symmetrical model”, are put face to face in order (...) to better understand the arguments of their proponents as to the way of approaching to the ethical matters. A main concern of the third part is to answer the question if something is wrong with situational ethics. The problem is approached in the light of virtue ethics, which is itself situational in Aristotel’s sense of the term. In the final part, the paper suggests the possibility to use W. D. Ross’s pluralist deontology as a conceptual structure from which to build a practical model for the analysis of moral dilemmas in the PR practice. (shrink)
The Protein Ontology (PRO; http://proconsortium.org) formally defines protein entities and explicitly represents their major forms and interrelations. Protein entities represented in PRO corresponding to single amino acid chains are categorized by level of specificity into family, gene, sequence and modification metaclasses, and there is a separate metaclass for protein complexes. All metaclasses also have organism-specific derivatives. PRO complements established sequence databases such as UniProtKB, and interoperates with other biomedical and biological ontologies such as the Gene Ontology (GO). PRO relates to (...) UniProtKB in that PRO’s organism-specific classes of proteins encoded by a specific gene correspond to entities documented in UniProtKB entries. PRO relates to the GO in that PRO’s representations of organism-specific protein complexes are subclasses of the organism-agnostic protein complex terms in the GO Cellular Component Ontology. The past few years have seen growth and changes to the PRO, as well as new points of access to the data and new applications of PRO in immunology and proteomics. Here we describe some of these developments. (shrink)
The Protein Ontology (PRO) web resource provides an integrative framework for protein-centric exploration and enables specific and precise annotation of proteins and protein complexes based on PRO. Functionalities include: browsing, searching and retrieving, terms, displaying selected terms in OBO or OWL format, and supporting URIs. In addition, the PRO website offers multiple ways for the user to request, submit, or modify terms and/or annotation. We will demonstrate the use of these tools for protein research and annotation.
Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological ontologies, including the Cell Ontology (CL), designed to provide a standardized representation of cell types for data annotation. Ontologies have been shown to have significant benefits for computational analyses of large data sets and for automated reasoning applications, leading to organized attempts to improve the structure and formal (...) rigor of ontologies to better support computation. Currently, the CL employs multiple is_a relations, defining cell types in terms of histological, functional, and lineage properties, and the majority of definitions are written with sufficient generality to hold across multiple species. This approach limits the CL's utility for computation and for cross-species data integration. Results: To enhance the CL's utility for computational analyses, we developed a method for the ontological representation of cells and applied this method to develop a dendritic cell ontology (DC-CL). DC-CL subtypes are delineated on the basis of surface protein expression, systematically including both species-general and species-specific types and optimizing DC-CL for the analysis of flow cytometry data. We avoid multiple uses of is_a by linking DC-CL terms to terms in other ontologies via additional, formally defined relations such as has_function. This approach brings benefits in the form of increased accuracy, support for reasoning, and interoperability with other ontology resources. Accordingly, we propose our method as a general strategy for the ontological representation of cells. DC-CL is available from http://www.obofoundry.org. (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)
[No hay resumen disponible, se incluyen los primerso párrafos del texto] Hace ya mucho tiempo algunos amigos de alrededor de treinta años comenzamos a estudiar filosofía bajo la dirección de Gregorio Klimovsky. Muy pronto uno de nosotros se destacó por su capacidad creadora y su curiosidad filosófica: era Juan Larreta. Es así que, a pesar de haber iniciado tarde su formación, descolló como filósofo de mérito tanto en la Argentina como en el exterior. Presidente de la Sociedad Argentina de Análisis (...) Filosófico (SADAF) durante dos períodos, obtuvo el Diploma al M érito en Filosofía de la Fundación Konex en el 2006 y fue nombrado miembro honorario de la Sociedad Española de Filosofía Analítica (SEFA) en 2010. Organizó seminarios y dictó conferencias en centros de estudios filosóficos y en universidades argentinas y extranjeras, en cuyas publicaciones escribió numerosos artículos de singular valía, todos ellos caracterizados por su originalidad, su irreverente desafío al sentido común y sus ingeniosos experimentos mentales (thought experiments). Esta despedida dolorosa se empeña en acercar a la memoria recuerdos queridos de circunstancias compartidas con este amigo excepcional. fue nuestro centro: en su casa organizó, durante muchos años, seminarios de filosofía, de economía y, junto con María Elisa, esas reuniones cinéfilas de divertidas, sorprendentes y variadas interpretaciones... (shrink)
The Protein Ontology (PRO; http://purl.obolibrary.org/obo/pr) formally defines and describes taxon-specific and taxon-neutral protein-related entities in three major areas: proteins related by evolution; proteins produced from a given gene; and protein-containing complexes. PRO thus serves as a tool for referencing protein entities at any level of specificity. To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference and PSI-MOD as a post-translational modification (...) reference. We illustrate its use in facilitating an alignment between PRO and Reactome protein entities. We also address issues of scalability, describing our first steps into the use of text mining to identify protein-related entities, the large-scale import of proteoform information from expert curated resources, and our ability to dynamically generate PRO terms. Web views for individual terms are now more informative about closely-related terms, including for example an interactive multiple sequence alignment. Finally, we describe recent improvement in semantic utility, with PRO now represented in OWL and as a SPARQL endpoint. These developments will further support the anticipated growth of PRO and facilitate discoverability of and allow aggregation of data relating to protein entities. (shrink)
A 25 años de su muerte, los escritos de Louis Althusser continúan siendo tan polémicos y controvertidos como lo fueron en el momento de su publicación. La siguiente investigación se propone analizar uno de los temas que más controversias y críticas suscitó en la década de los sesenta, momento por demás polémico dentro de su producción intelectual: la relación entre la ciencia e ideología. ¿Se trata de una llana oposición?, ¿son la ciencia y la ideología dos estructuras claramente diferenciadas?, ¿es (...) acaso la ciencia la salida de la ideología?, ¿es la ciencia la verdad y la ideología el error? A través de un estudio pormenorizado de los textos publicados en la década señalada, este trabajo buscará dar cuenta del pensamiento de Althusser en relación con esta temática en el marco de sus valiosos aportes al pensamiento marxista. -/- . (shrink)
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
The members of the International Network for the Analysis of Intergenerational Relations proudly present the most recent issue of the jointly produced compendium "Generations, Intergenerational Relations and Generational Policy". This new version includes 17 languages: English, French, German, Italian, Spanish, Polish, Portuguese, Swedish, Hungarian, Turkish, Romanian, Lithuanian, Slovenian, Bosnian, Ukrainian, Russian and Chinese. The layout of the compendium is designed for using it to translate the specific concepts and terminology of research on generations and intergenerational relations from one language into (...) another. **** K. Lüscher, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 17 languages, Universität Konstanz, Konstanz 2017, 428pp. (shrink)
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
K. Lüscher, M. Sánchez, A. Klimczuk, Generations, intergenerational relationships, generational policy: A multilingual compendium, 12 languages, Universität Konstanz, Konstanz 2016, 300pp.
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