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

Publishing date: 2020-03-03

Published on: GigaScience

summary: Genome and proteome annotation pipelines are generally custom built and not easily reusable by other groups. This leads to duplication of effort, increased costs, and suboptimal annotation quality. One way to address these issues 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. Here, Bolleman et al demonstrate an approach to generate portable genome and proteome annotation pipelines that users can run without recourse to custom software. This proof of concept uses their own rule-based annotation pipeline HAMAP, which provides functional annotation for protein sequences to the same depth and quality as UniProtKB/Swiss-Prot, and the W3C standards Resource Description Framework and SPARQL.

authors: Jerven Bolleman, Edouard 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

link to paper: https://academic.oup.com/gigascience/article/9/2/giaa003/5731417

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