Tools and data services registry: a community effort to document bioinformatics resources

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, Piotr Chmura, Christian Anthon, Niall Beard, Karel Berka, Dan Bolser, Tim Booth, Anthony Bretaudeau (+57 others)
2015 Nucleic Acids Research  
Life sciences are yielding huge data sets that underpin scientific discoveries fundamental to improvement in human health, agriculture and the environment. In support of these discoveries, a plethora of databases and tools are deployed, in technically complex and diverse implementations, across a spectrum of scientific disciplines. The corpus of documentation of these resources is fragmented across the Web, with much redundancy, and has lacked a common standard of information. The outcome is
more » ... t scientists must often struggle to find, understand, compare and use the best resources for the Table 3 . Resource providers. A non-exhaustive list of collections that have contributed or will contribute to the registry. The list includes a cross-section of bioinformatics service providers including other catalogues such as SEQwiki and BioCatalogue Name, URL, Short description CBS Prediction Servers A collection of on-line prediction services from CBS-DTU. The resource contains 75 tools for gene finding and splice sites, post-translational protein modification, immunological features, protein function and structure, protein sorting, genomic epidemiology and more. The tools can be used via interactive input forms, with many available as software packages and SOAP Web services. DRCAT resource The data resource catalogue is a collection of metadata on bioinformatics Web-based data resources. The catalog contains over 600 resources including bioinformatics and biomedical databases, ontologies, taxonomies and catalogues. BiBiServ BiBiServ is a collection of bioinformatics tools that emerged from the research at Bielefeld University. It contains over 40 mainly analysis and utility tools, including RNA structure prediction, metagenomics, genome rearrangement, alignments, evolutionary relationships, primer design and suffix trees. These are available as interactive web applications, HTTP Web services and downloadable software. BINF.KU.DK Services and Software A collection of over 20 web services, databases and software packages from The Bioinformatics Centre at The University of Copenhagen. The resource covers sequence and structure analysis, prediction and modeling, gene regulation, population genetics and more. ELIXIR-CZ Services collection The Czech Bioinformatics Services resource is provided by members of ELIXIR CZ node. It contains over 30 bioinformatics tools and databases for analysis of sequence, topology and structure of nucleic acids and proteins to genomics, proteomics and benchmarks for small molecule interactions. The databases can be accessed via web GUIs while tools are available as web, standalone and command-line applications. ELIXIR eLearning Platform Orange Orange data mining suite is an open source data visualization and analysis software for data mining through visual programming or Python scripting. It consists of over 100 components for machine learning and add-ons for bioinformatics and text mining. GoMapMan GoMapMan is a database of gene functional annotations in the plant sciences based on the plant-specific MapMan ontology. ELIXIR-ITA Services collection A collection of services provided by research institutions members of the ELIXIR Italian node. The resource includes databases and analysis tools developed and maintained by Italian bioinformatics groups and institutions. University of Padova ELIXIR-ITA-PADOVA A collection of 60 bioinformatics tools from the University of Padova.It includes databases for structural bioinformatics and genome sequences as well as tools for sequence analysis, phylogenetics, structure analysis, chemioinformatics and network analysis. Bologna Biocomputing group predictors and services A collection of 22 predictors for subcellular localization, disease-related mutations and protein sequences annotation from Bologna Biocomputing Group. Most tools are accessible using a Web UI while some offer a command line interface. Sapienza University Biocomputing group resources and tools A collection of 19 resources and tools for structural bioinformatics, immunoinformatics and genomics from the Sapienza University Biocomputing Group. Molecular Genetics Group ELIXIR-ITA-TORVERGATA A collection of 7 databases and portals linking physically and functionally gene products. All databases and portals data can be searched, visualized and downloaded through Web UI interfaces. Molecular Bioinformatics Group ELIXIR-ITA-TORVERGATA A collection of tools dedicated to the analysis of protein structures, the identification of structure motifs and the comparison of RNA secondary structure. Milano-Bicocca Resources and Tools ELIXIR-ITA-BICOCCA Online services and open source software, mainly for NGS and EST analysis or to infer evolutionary histories in tumors. The majority of tools are used via a command line interface while the rest offer a graphical interface. Mobyle@Pasteur A collection of 300 bioinformatics tools covering various topics such as sequence analysis, phylogeny, integrated in an online workbench. The suite is a combination of tools developed at the Institut Pasteur and/or tools used by it, for research and education. Galaxy@Institut Pasteur A collection of 260 bioinformatics tools, mainly dedicated to NGS analysis, and integrated into the Galaxy instance available at the Institut Pasteur. This instance is only available to Pasteur researchers and collaborators. GenOuest A collection of tools dedicated to the analyses of NGS data along with bioinformatics genomic databases hosted by GenOuest. Most tools can be used via command line, while the databases and some of the tools are available through a web interface.
doi:10.1093/nar/gkv1116 pmid:26538599 pmcid:PMC4702812 fatcat:npzer6xh7fezlbcamfmdvv552m