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 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)

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) 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)

Mysteries: remains of a hidden life -- Words on paper -- In search of a person behind the words -- A France of broken families -- Families -- Politiques -- Breaking with his father -- Aristocratic Paris -- Libertine Paris -- A political education -- Gearing up for war: mathematical inspirations -- Breda -- Military engineering -- Meeting Isaac Beeckman -- The Holy Roman empire -- Anxious dreams -- Curious meetings -- War and diplomacy in Europe -- Into Bohemia -- (...) To Hungary and disaster -- The Baltic and return to the Netherlands -- Again in France -- Paris and the rosicrucian scare -- The Valtellina and Rome -- The struggle for France -- Problems with the cardinal -- The campaign for La Rochelle -- Confrontation and departure -- The meetings -- Confrontation and conversation -- Becoming a sectarian -- Feeling threatened -- Exile -- Not yet concluded. (shrink)

The decree establishing an Athenian colony at Brea in the north Aegaean area was firmly placed by the editors ofThe Athenian Tribute Listsin 446 B.C.; they identified the troops mentioned in lines 26 ff. with the men then serving in Euboia. In 1952, however, Woodhead proposed redating the decree c. 439/8 B.C. and explained lines 26 ff. by reference to the Samian revolt. A decade later I put forward a more radical theory, which seems to have won no adherents. I (...) cannot really complain of this, since my arguments were inevitably far from cogent. For some Thucydides' silence alone will have been decisive. I would like to think that the issue has at least been clarified by now. TheA.T.L.dating appears rather less plausible. Demokleides' generalship in 439/8 B.C. would fit excellently with his role as founder of Brea. This strongly supports Woodhead. It is doubtful whether Demokleides was general as early as 446 B.C, though conceivable that he returned to the board as late as 426/5 B.C. Woodhead may well be right in locating Brea on the inner Thermaic Gulf and, if so, this too tells against theA.T.L.dating. All our evidence suggests that real Athenian involvement in this area began in the 430's. (shrink)

The series of decrees concerning Methone throws welcome light on Athenian foreign policy and the imperialism of Pericles' successors. Here is historical evidence of the highest quality. Are we using it as fully and accurately as we should? This paper is written in the belief that we are being hampered by unsound presuppositions. Chronologically the second decree is our main fixed point. It was passed in the first prytany of 426/5 B.C. The third and fourth decrees followed in the next (...) two archon-years. They can be ignored in this discussion, since one is hopelessly mutilated and the other is missing from the stone as it stands now. The real problem rises over the first decree. What is its date? It used commonly to be put in 428/7 B.C. until West argued powerfully for January/February 429/8 B.C. His view won considerable support, but the editors of The Athenian Tribute Lists have since succeeded in establishing the summer of 430 B.C. as the orthodox dating. Now those who accept this should recognize that it creates an awkwardly long gap between the first and second decrees. By the first decree Methone was permitted to pay the quota alone, instead of its full tribute, and was promised separate, favourable treatment of its arrears in return for continued loyalty. (shrink)

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