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

View ORCID ProfileJerven Bolleman, View ORCID ProfileEduoard de Castro, View ORCID ProfileDelphine Baratin, View ORCID ProfileSebastien Gehant, View ORCID ProfileBeatrice A. Cuche, View ORCID ProfileAndrea H. Auchincloss, View ORCID ProfileElisabeth Coudert, View ORCID ProfileChantal Hulo, View ORCID ProfilePatrick Masson, View ORCID ProfileIvo Pedruzzi, View ORCID ProfileCatherine Rivoire, View ORCID ProfileIoannis Xenarios, View ORCID ProfileNicole Redaschi, View ORCID ProfileAlan Bridge
doi: https://doi.org/10.1101/615294
Jerven Bolleman
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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  • For correspondence: jerven.bolleman@sib.swiss
Eduoard de Castro
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Delphine Baratin
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Sebastien Gehant
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Beatrice A. Cuche
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Andrea H. Auchincloss
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Elisabeth Coudert
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Chantal Hulo
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Patrick Masson
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Ivo Pedruzzi
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Catherine Rivoire
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Ioannis Xenarios
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
2CHUV/LICR, Agora Centre, CH-1005 Lausanne, Switzerland
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Nicole Redaschi
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Alan Bridge
1Swiss-Prot Group, SIB Swiss Institute of Bioinformatics, CMU, 1 rue Michel-Servet, CH-1211 Geneva 4, Switzerland
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Abstract

Motivation Genome 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.

Results We 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.

Availability HAMAP 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.

Contact hamap{at}sib.swiss

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted April 24, 2019.
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HAMAP rules as SPARQL A portable annotation pipeline for genomes and proteomes
Jerven Bolleman, Eduoard de Castro, Delphine Baratin, Sebastien Gehant, Beatrice A. Cuche, Andrea H. Auchincloss, Elisabeth Coudert, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Ioannis Xenarios, Nicole Redaschi, Alan Bridge
bioRxiv 615294; doi: https://doi.org/10.1101/615294
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HAMAP rules as SPARQL A portable annotation pipeline for genomes and proteomes
Jerven Bolleman, Eduoard de Castro, Delphine Baratin, Sebastien Gehant, Beatrice A. Cuche, Andrea H. Auchincloss, Elisabeth Coudert, Chantal Hulo, Patrick Masson, Ivo Pedruzzi, Catherine Rivoire, Ioannis Xenarios, Nicole Redaschi, Alan Bridge
bioRxiv 615294; doi: https://doi.org/10.1101/615294

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