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Redaschi, N.

Publications and source records attributed to Redaschi, N..

2 recordsLinked to original sources
bioRxiv2019

HAMAP rules as SPARQL - A portable annotation pipeline for genomes and proteomes

MotivationGenome and proteome annotation pipelines are generally custom built and therefore not easily reusable by other groups, which leads to duplication of effort, increased costs, and suboptimal results. One cost-effective way to increase the data quality in public databases is to encourage the adoption of annotation standards and technological solutions that enable the sharing of biological knowledge and tools for genome and proteome annotation.\n\nResultsWe have translated the rules of our HAMAP proteome annotation pipeline to queries in the W3C standard SPARQL 1.1 syntax and applied them with two off-the-shelf SPARQL engines to UniProtKB/Swiss-Prot protein sequences described in RDF format. This approach is applicable to any genome or proteome annotation pipeline and greatly simplifies their reuse.\n\nAvailabilityHAMAP SPARQL rules and documentation are freely available for download from the HAMAP FTP site ftp://ftp.expasy.org/databases/hamap/hamapsparql.tar.gz under a CC-BY-ND 4.0 license. The annotations generated by the rules are under the CC-BY 4.0 license.\n\nContacthamap@sib.swiss\n\nSupplementary informationSupplementary data are included at the end of this document.

bioinformatics↗
bioRxiv2019

The ELIXIR Core Data Resources: fundamental infrastructure for the life sciences

MotivationLife science research in academia, industry, agriculture, and the health sector depends critically on free and open data resources. ELIXIR (www.elixir-europe.org), the European Research Infrastructure for life sciences data, has identified a set of Core Data Resources within Europe that are of most fundamental importance for the long-term preservation of biological data. We explore characteristics of their usage, impact and assured funding horizon to assess their value and importance as an infrastructure, to understand sustainability of the infrastructure, and to demonstrate a model for assessing Core Data Resources worldwide. ResultsThe nineteen resources currently designated ELIXIR Core Data Resources form a data infrastructure in Europe which is a subset of the worldwide open life science data infrastructure. We show that, from 2014 to 2018, data managed by the Core Data Resources more than tripled while staff numbers increased by less than a tenth. Additionally, support for the Core Data Resources is precarious: together they have assured funding for less than a third of current staff after four years. Our findings demonstrate the importance of the ELIXIR Core Data Resources as repositories for research data and knowledge, while also demonstrating the uncertain nature of the funding environment for this infrastructure. ELIXIR is working towards longer-term support for the Core Data Resources and, through the Global Biodata Coalition, aims to ensure support for the worldwide life science data resource infrastructure of which the ELIXIR Core Data Resources are a subset. Contactrachel.drysdale@elixir-europe.org Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗