Annotating the human proteome

Comunicaciones a congreso

Aspekte der russischen Literaturwissenschaft aus komparatistischer Sicht

Die russische Literaturwissenschaft entwickelte sich auf der Basis der russischen Literaturkritik des 19. Jahrhunderts und setzte sich schon früh mit Problemen der komparatistischen Einfluss- und Beziehungsforschung auseinander. Sie war von Beginn an supranational und interdisziplinär ausgerichtet. Hingegen hatten die Einzelphilologien in der russischen universitären Tradition einen schweren Stand. So war z. B. anlässlich des erst im Jahre 2003 gegründeten russischen Germanistenverbandes festzustellen, dass die Vertreter der russischen Germanistik Probleme hatten, ein fachdisziplinäres Zusammengehörigkeitsgefühl zu entwickeln und sich eher als allgemeine Literaturwissenschaftler oder Komparatisten definierten. Während sich die Komparatistik in Deutschland erst nach der Überwindung eines langwierigen und schwierigen Prozesses der Abgrenzung in Bezug auf die Einzelphilologien in der wissenschaftlichen Forschung und Lehre einen festen Platz eroberte, nahm die russische Komparatistik eine völlig andere Entwicklung, da es dort einer besonderen Legitimation der vergleichenden literaturwissenschaftlichen Forschung nicht bedurfte

The SWISS-PROT protein sequence data bank and its supplement TrEMBL in 1999

SWISS-PROT is a curated protein sequence database which strives to provide a high level of annotation (such as the description of the function of a protein, its domain structure, post-translational modifications, variants, etc.), a minimal level of redundancy and high level of integration with other databases. Recent developments of the database include: cross-references to additional databases; a variety of new documentation files and improvements to TrEMBL, a computer annotated supplement to SWISS-PROT. TrEMBL consists of entries in SWISS-PROT-like format derived from the translation of all coding sequences (CDS) in the EMBL nucleotide sequence database, except the CDS already included in SWISS-PROT. The URLs for SWISS-PROT on the WWW are: http://www.expasy.ch/sprot and http://www.ebi.ac.uk/spro

Macroscopic ordering of polystyrene carboxylate-modified nanospheres self-assembled at the water-air interface

Copyright © 2010 American Chemical SocietyThis document is the Accepted Manuscript version of a Published Work that appeared in final form in Langmuir, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see http://dx.doi.org/10.1021/la1009658We present results from an experimental study of ordering characteristics in monolayers of polystyrene nanospheres self-assembled at a water-air interface. We demonstrate that the interaction of spheres, governed by the dissemination of surface charge, leads to the formation of macroscopic close-packed ordered areas or "domains" with a well-defined orientation of the lattice axes over areas of 25 mm(2). It was found that by changing the surface chemistry of the spheres it is possible to modify the balance between the attractive and repulsive forces and thus to control the ordering characteristics. We implemented a model that simulates the process of self-assembly and examines the ordering characteristics for layers with different ratio between attractive and repulsive forces. A good qualitative agreement was found between the simulations and experiment. These studies are technologically relevant as a method of producing nanosphere templates for large area patterned materials

The HUPO Proteomics Standards Initiative Meeting: Towards Common Standards for Exchanging Proteomics Data

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Initially the fields of protein–protein interactions (PPI) and mass spectroscopy have been targeted and the inaugural meeting of the PSI addressed the questions of data storage and exchange in both of these areas. The PPI group rapidly reached consensus as to the minimum requirements for a data exchange model; an XML draft is now being produced. The mass spectroscopy group have achieved major advances in the definition of a required data model and working groups are currently taking these discussions further. A further meeting is planned in January 2003 to advance both these projects

Improved Core Genes Prediction for Constructing well-supported Phylogenetic Trees in large sets of Plant Species

The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies, many similarity based algorithms, mainly dependent on calculating sequence alignment matrices, have been proposed to find them. In these kinds of approaches, a significantly high similarity score between two coding sequences extracted from a given annotation tool means that one has the same genes. In a previous work article, we presented a quality test approach (QTA) that improves the core genes quality by combining two annotation tools (namely NCBI, a partially human-curated database, and DOGMA, an efficient annotation algorithm for chloroplasts). This method takes the advantages from both sequence similarity and gene features to guarantee that the core genome contains correct and well-clustered coding sequences (\emph{i.e.}, genes). We then show in this article how useful are such well-defined core genes for biomolecular phylogenetic reconstructions, by investigating various subsets of core genes at various family or genus levels, leading to subtrees with strong bootstraps that are finally merged in a well-supported supertree.Comment: 12 pages, 7 figures, IWBBIO 2015 (3rd International Work-Conference on Bioinformatics and Biomedical Engineering

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries

BACKGROUND: With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. RESULTS: The Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. CONCLUSION: The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format. It can be accessed interactively or programmatically at