1,720,983 research outputs found
Protein Functional Annotation
No full textThe deluge of sequencing data needs curated association of structural and functional features to each sequence in the database. Inference of correct annotation is a major problem of sequence analysis. We highlight why it is difficult to solve the annotation task given the little amount of validated information in the database linking sequences, structure and experimental function in the most curated repository of protein sequences. We review state-of-the-art methods currently benchmarked in the Critical Assessment of protein Function Annotation algorithms (CAFA), an experiment designed to provide a large-scale assessment of computational methods dedicated to predicting protein functio
La diffusione della disinformazione scientifica: l'eco della rete
No full textLa diffusione della disinformazione ha di recente raggiunto livelli allarmanti. Emergono nuove posizioni anti-scientifiche e ne risorgono alcune superate secoli fa. Il comodo mega-libro della rete, che contiene tutte le opinioni e i loro contrari, ha finito per oscurare le fonti autorevoli.
Questa iniziativa, promossa dall'Accademia delle Scienze dell'Istituto di Bologna, vuole suscitare l’attenzione del pubblico per gli eventi di disinformazione che percolano indisturbati e con risonanza nella rete. Il fine è quello di aprire un dibattito per far emergere metodi e criteri a favore di una formazione solida e consapevole
Transmembrane Domain Prediction
No full textTransmembrane proteins constitute some 20%–30% of proteins of all prokaryotic and eukaryotic organisms and are involved in fundamental biological processes. Experimental determination of their structure is difficult due to their peculiar property of being stable in a complex environment consisting of separate hydrophilic and hydrophobic phases. Computational tools are then necessary to fill the gap between the knowledge of protein sequence and the characterization of its role in the context of biological complexity
Extended and Robust Protein Sequence Annotation over Conservative Nonhierarchical Clusters
No full textGenome annotation is one of the most important issues in the genomic era. The exponential growth rate of newly sequenced genomes and proteomes urges the development of fast and reliable annotation methods, suited to exploit all the information available in curated databases of protein sequences and structures. To this aim we developed BAR+, the Bologna Annotation Resource.1 The basic notion is that sequences with high identity value to a counterpart can inherit the same function/s and structure, if available. As a case study we describe how the ATP-binding domain of the ABC transporters can be found and modeled in over 30,000 new sequences not annotated before. We also mapped into BAR+ all the ABC transporters listed in the Transporter Classification DataBase2 and found that within our environment annotation could be extended to another 256,866 sequences
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
Full text link“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
Full text linkWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Bioschemas.org
No full textProject Website: http://bioschemas.org/Source Code: https://github.com/BioSchemas/bioschemasLicense: Creative Commons Attribution-ShareAlike License (version 3.0)AbstractSchema.org provides a way to add semantic markup to web pages. It describes ‘types’ of information, which then have ‘properties’. For example, ‘Event’ is a type that has properties like ‘startDate’, ‘endDate’ and ‘description’. Bioschemas aims to improve data interoperability in life sciences by encouraging people in life science to use schema.org markup. This structured information then makes it easier to discover, collate and analyse distributed data. Bioschemas reuses and extends schema.org in a number of ways: defining a minimum information model for the datatype being described using as few concepts as possible and only where necessary adding new properties, and the introduction of cardinalities and controlled vocabularies. The main outcome of Bioschemas is a collection of specifications that provide guidelines to facilitate a more consistent adoption of schema.org markup within the life sciences for the “Find” part of the FAIR (Findable, Accessible, Interoperable, Reusable) principles.In 2016 Bioschemas successfully piloted with training materials and events to enable the EU ELIXIR Research Infrastructure Training Portal (TeSS) to rapidly and simply harvest metadata from community sites. Encouraged by this in March 2017 we launched a 12 month project to pilot Bioschemas for data repositories and datasets. Specifically we are working on:General descriptions for datasets and data repositoriesSpecific descriptions for prioritised datatypes: Samples, Human Beacons, Plant phenotypes and Protein annotationsFacilitating discovery by registries and data aggregators, and by general search enginesFacilitate tool development for annotation and validation of compliant resourcesAll work is grounded on describing real data resources for real use cases: to this end large and small dataset are part of the project: Pfam, Interpro, PDBe, UniProt, BRENDA, EGA, COPaKB, and Gene3D. Data aggregators participating include: InterMine, BioSamples and OmicsDI. Registries include Identifiers.org, DataMed, Biosharing and the Beacon Network. Bioschemas operates as an open community initiative, sponsored by the EU ELIXIR Research Infrastructure and is supported by the NIH BD2K programme and Google
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