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.

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 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)

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)

The two parts of this particle constitute a single chapter in H.J. Berman, Law and Revolution: The Formation of the Western Legal Tradition, published by Harvard University Press.

v. 1. Nicomachean ethics. Politics. The Athenian Constitution. Rhetoric. On Poetics.--v. 2. Logic.--v. 3. Physics. Metaphysics. On the soul. Short physical treaties.--v. 4. On the heavens. On generation and corruption. Meteorology. Biological treatises.

When the whole is greater than the sum of the parts--indeed, so great that the sum far transcends the parts and represents something utterly new and different--we call that phenomenon emergence. When the chemicals diffusing in the primordial waters came together to form the first living cell, that was emergence. When the activities of the neurons in the brain result in mind, that too is emergence. In The Emergence of Everything, one of the leading scientists involved in the study of (...) complexity, Harold J. Morowitz, takes us on a sweeping tour of the universe, a tour with 28 stops, each one highlighting a particularly important moment of emergence. For instance, Morowitz illuminates the emergence of the stars, the birth of the elements and of the periodic table, and the appearance of solar systems and planets. We look at the emergence of living cells, animals, vertebrates, reptiles, and mammals, leading to the great apes and the appearance of humanity. He also examines tool making, the evolution of language, the invention of agriculture and technology, and the birth of cities. And as he offers these insights into the evolutionary unfolding of our universe, our solar system, and life itself, Morowitz also seeks out the nature of God in the emergent universe, the God posited by Spinoza, Bruno, and Einstein, a God Morowitz argues we can know through a study of the laws of nature. Written by one of our wisest scientists, The Emergence of Everything offers a fascinating new way to look at the universe and the natural world, and it makes an important contribution to the dialogue between science and religion. (shrink)

Celebrating the remarkable career of jurist Harold J. Berman, the essays in this volume demonstrate that Berman's contributions to Russian studies, international trade law, legal history, philosophy of law, and law and religion have firmly established him as part of the tradition of our greatest American jurists.

The two parts of this article constitute a single chapter in H.J. Berman, Law and Revolution: The Formation of the Western Legal Tradition.

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)

Scientific realism is usually a thesis or theses advanced about our best natural science. In contrast, this book defends scientific realism applied to the social and behavioral sciences. It does so, however, by applying the same argument strategy that many have found convincing for the natural sciences, namely, by arguing that we can only explain the success of the sciences by postulating their approximate truth. The particular success that Trout emphasizes for the social sciences is the effective use of statistical (...) testing. Social scientists apply diverse statistical measurement tools to social reality; they are able to refine and improve those measurements over time. The best explanation for such success is that the social sciences give us an approximately true account of some of the laws and entities of the social world. (shrink)

Two overriding considerations shaped the development of early research on the biological effects of microwave radiation—possible medical application and uncertainty about the hazards of exposure to radar. Reports in the late 1940s and early 1950s of hazards resulting from microwave exposure led to the near abandonment of medical research related to microwave diathermy at the same time that military and industrial concern over hazards grew, culminating in the massive research effort known as ‘the Tri-Service program’ . Both the early focus (...) on medical application and the later search for hazards played important roles in dictating how this field of research developed as a science. (shrink)