The RNA tools registry

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August Jones
5 years ago
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enon-coding nces Faculty of Health and Medical Sciences University of Copenhagen university of copenhagen f a c u lt y o f h e a lt h a n d m e d i c a l sciences 32nd

1 university of copenhagen f a c u lt y o f h e a lt h a n d m e d i c a l s c i e n c e s The RNA tools registry A community effort to catalog RNA bioinformatics resources and their relationships Anne Wenzel university of copenhagen f a c u lt y o f h e a lt h a n d m e d i c a l Center for RNA in Technology and Health s c i enon-coding nces Faculty of Health and Medical Sciences University of Copenhagen university of copenhagen f a c u lt y o f h e a lt h a n d m e d i c a l sciences 32nd TBI Winterseminar Bled, Slovenia February 2017 university of copenhagen f a c u lt y o f h e a lt h a n d m e d i c a l s c i e n c e s university of copenhagen medical sciences

2 1 The Danish ELIXIR node Bioinformatics tool interoperability and integration Creation of a comprehensive tool registry Provision of tools in the form preferred by users across academia and industry Benchmarking, tool sustainability and renewal Tool interoperability

3 2 bio.tools ELIXIR Tools and Data Services Registry Collection of bioinformatics resources 5226 entries currently (goal: by the end of 2017) Mandatory attributes: Name Version Description Function Topic Homepage Free text Ontology term Ontology term URL Contact ,... Tool Type (Ison et al., Nucleic Acids Res, 2016) [Command-line tool, Database portal, Desktop application, Web service,...]

4 3 EDAM ontology Topic is a broader domain or field of interest, of study, data, or technology, e.g., MicroRNA, RNA-seq Function describes what a tool does, but not (typically) how, e.g., RNA-RNA interaction prediction Data describes the type of (input or output) data, e.g., RNA sequence or Multiple RNA sequence alignment Format of the Data, e.g., FASTA or Stockholm (Ison et al., Bioinformatics, 2013)

5 4 Search for RNA interaction in EDAM only reveals Protein-RNA interaction

6 5 Curatathon I Photo: T. Houwaart

7 Process outline 6

8 Curatathon II Photo: N. Doncheva 7

9 8 Since then... Added 20 tools Automatic validation checks Adapt to new bio.tools schema Further sanitizing entries Carefully hand-curated 90 entries

10 9 Results: Contents of the registry 389 tools currently in the registry Ten most frequently used Topic terms: RNA secondary structure RNA 3D structure RNA RNA interactions Alternative splicing RNA secondary structure alignment Read quantification MicroRNA Data visualisation Differential expression ncrna Occurrence

11 RNA structure prediction RNA 3D structure analysis Quantitative analysis Prediction Annotation RNA 3D structure determination Query and retrieval RNA sequence design RNA structure comparison Visualisation Alignment Quality control RNA 3D structure storing RNA secondary structure prediction RNA 3D structure prediction RNA 3D motif extraction RNA 3D model quality prediction RNA structure contacts Expression analysis Read quantification RNA interaction prediction RNA sequence prediction Binding site prediction RNA homology prediction Structure annotation Sequence annotation Homology annotation Database search Data retrieval RNA 3D structure-based sequence design RNA inverse folding sirna design RNA 3D structure comparison RNA secondary structure comparison RNA interaction visualisation RNA structure visualisation Sequence alignment Model alignment Structural alignment Structure alignment Sequencing quality control Multiple sequences RNA secondary structure prediction RNA global secondary structure prediction RNA local secondary structure prediction RNA consensus secondary structure prediction Single sequence RNA secondary structure prediction RNA fold recognition RNA 3D motif prediction RNA 3D structure refinement RNA 3D structure modeling RNA structure contacts classification RNA structure contacts storing Isoform quantification Differential gene expression analysis RNA-RNA interaction prediction RNA-DNA interaction prediction RNA-protein interaction prediction RNA interaction 3D modeling RNA sequence motif prediction RNA de novo prediction RNA secondary structure annotation Gene prediction RNA 3D structure annotation Splice site prediction Sequence motif annotation Orthology annotation Xenology annotation Paralogy annotation RNA 3D rigid body superposition RNA 3D flexible superposition RNA 3D model evaluation RNA secondary structure clustering RNA secondary structure distance computation RNA 3D structure visualisation RNA secondary structure visualisation Pairwise sequence alignment Nucleic acid sequence alignment Amino acid sequence alignment Multiple sequence alignment RNA family model comparison RNA secondary structural alignment RNA secondary structure alignment RNA 3D structure alignment Read pre-processing Global multiple sequences RNA secondary structure prediction Local multiple sequences RNA secondary structure prediction Global single sequence RNA secondary structure prediction Local single sequence RNA secondary structure prediction RNA 3D fragment-based structure modeling RNA 3D template-based structure modeling RNA 3D template-free structure modeling RNA-RNA intermolecular interaction prediction RNA-RNA intra-/intermolecular interaction prediction ncrna target prediction RNA-ion docking RNA-protein docking RNA-small molecule docking RNA-RNA complex modeling Machine learning Mapping assembly Sequence alignment analysis RNA secondary structure motif annotation ncrna gene prediction mrna prediction Functional mrna prediction Functional ncrna prediction RNA 3D motif annotation RNA 3D structure annotation storing Short-read alignment RNA global secondary structural alignment RNA multiple secondary structural alignment RNA pairwise secondary structural alignment RNA local secondary structural alignment sirna off-target prediction mirna target prediction srna target prediction snorna target prediction mirna gene prediction CRISPR gene prediction tmrna gene prediction circrna gene prediction trna gene prediction snorna gene prediction lncrna gene prediction RNase P gene prediction RNA global multiple secondary structural alignment RNA global pairwise secondary structural alignment RNA local multiple secondary structural alignment RNA local pairwise secondary structural alignment Results: RNA tools Function Ontology Function Protégé

12 DEMO

13 12 Conclusion For the individual resources, we provide comprehensive description systematic classification relations to other resources

14 12 Conclusion For the individual resources, we provide comprehensive description systematic classification relations to other resources To be integrated in EDAM : ontology bio.tools : registry

15 12 Conclusion For the individual resources, we provide comprehensive description systematic classification relations to other resources To be integrated in EDAM : ontology bio.tools : registry Allowing a researcher to identify the right functional class to solve the problem at hand find alternatives for certain tools

16 12 Conclusion For the individual resources, we provide comprehensive description systematic classification relations to other resources To be integrated in EDAM : ontology bio.tools : registry Allowing a researcher to identify the right functional class to solve the problem at hand find alternatives for certain tools Our approach is relevant for other community efforts

17 13 Outlook Graphical ontology-driven entry point to the tools registry Open for contributions by 3rd parties Text-mine abstracts (using existing edammap) Journal incentive to require accession before publication Interfacing with RNAcentral

18 14 Acknowledgements The RNA tools and software consortium consists of researchers from: University of Vienna, Austria University of Freiburg, Germany University of Jena, Germany University of Leipzig, Germany European Bioinformatics Institute, Hinxton, UK International Institute of Molecular and Cell Biology, Warsaw, Poland Paris-Sud University, Orsay, France École polytechnique, Palaiseau, France University of Copenhagen, Denmark We acknowledge the Danish infrastructure roadmap grant to the Danish ELIXIR node and Innovation Fund Denmark ( B) to the grant for RTH.

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