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

摘要

Background: Genome and proteome annotation pipelines are generally custom built and not easily reusable by othergroups. This leads to duplication of effort, increased costs, and suboptimal annotation quality. One way to address theseissues is to encourage the adoption of annotation standards and technological solutions that enable the sharing ofbiological knowledge and tools for genome and proteome annotation. Results: Here we demonstrate one approach togenerate portable genome and proteome annotation pipelines that users can run without recourse to custom software. Thisproof of concept uses our own rule-based annotation pipeline HAMAP, which provides functional annotation for proteinsequences to the same depth and quality as UniProtKB/Swiss-Prot, and the World Wide Web Consortium (W3C) standardsResource Description Framework (RDF) and SPARQL (a recursive acronym for the SPARQL Protocol and RDF QueryLanguage). We translate complex HAMAP rules into the W3C standard SPARQL 1.1 syntax, and then apply them to proteinsequences in RDF format using freely available SPARQL engines. This approach supports the generation of annotation thatis identical to that generated by our own in-house pipeline, using standard, off-the-shelf solutions, and is applicable to anygenome or proteome annotation pipeline. Conclusions: HAMAP SPARQL rules are freely available for download from theHAMAP FTP site, ftp://ftp.expasy.org/databases/hamap/sparql/, under the CC-BY-ND 4.0 license. The annotations generatedby the rules are under the CC-BY 4.0 license. A tutorial and supplementary code to use HAMAP as SPARQL are available onGitHub at https://github.com/sib-swiss/HAMAP-SPARQL, and general documentation about HAMAP can be found on theHAMAP website at https://hamap.expasy.org.