HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes
HAMAP as SPARQL rules-A portable annotation pipeline for genomes and proteomes
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DOI：
10.1093/gigascience/giaa003
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发表时间：
2020-02-01
期刊：
影响因子：
9.2
通讯作者：
Bridge, Alan
中科院分区：
文献类型：
--
作者：
Bolleman, Jerven;de Castro, Edouard;Bridge, Alan
背景：基因组和蛋白质组注释管道通常是定制的，不容易被其他组重用。这会导致重复的工作、增加的成本和次优的注释质量。解决这些问题的一种方法是鼓励采用注释标准和技术解决方案，使基因组和蛋白质组注释的生物学知识和工具能够共享。结果：在这里，我们展示了一种生成便携式基因组和蛋白质组注释管道的方法，用户可以在不依赖自定义软件的情况下运行。这个概念验证使用了我们自己的基于规则的注释管道HAMAP，它为蛋白质序列提供了与UniProtKB/Swiss-Prot相同深度和质量的功能性注释，以及万维网联盟（W3C）标准资源描述框架（RDF）和SPARQL （SPARQL协议和RDF查询语言的递归缩写）。我们将复杂的HAMAP规则转换为W3C标准SPARQL 1.1语法，然后使用免费的SPARQL引擎将它们应用于RDF格式的蛋白质序列。这种方法支持生成与我们自己的内部管道生成的注释相同的注释，使用标准的、现成的解决方案，并且适用于任何基因组或蛋白质组注释管道。结论：在CC-BY-ND 4.0许可下，HAMAP SPARQL规则可以从HAMAP FTP站点ftp://ftp.expasy.org/databases/hamap/sparql/免费下载。规则生成的注释采用CC-BY 4.0许可协议。使用HAMAP作为SPARQL的教程和补充代码可以在GitHub上找到https://github.com/sib-swiss/HAMAP- SPARQL，关于HAMAP的一般文档可以在HAMAP网站上找到https://hamap.expasy.org。
Background: 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. Results: Here we demonstrate one approach to generate portable genome and proteome annotation pipelines that users can run without recourse to custom software. This proof of concept uses our 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 World Wide Web Consortium (W3C) standards Resource Description Framework (RDF) and SPARQL (a recursive acronym for the SPARQL Protocol and RDF Query Language). We translate complex HAMAP rules into the W3C standard SPARQL 1.1 syntax, and then apply them to protein sequences in RDF format using freely available SPARQL engines. This approach supports the generation of annotation that is identical to that generated by our own in-house pipeline, using standard, off-the-shelf solutions, and is applicable to any genome or proteome annotation pipeline. Conclusions: HAMAP SPARQL rules are freely available for download from the HAMAP FTP site, ftp://ftp.expasy.org/databases/hamap/sparql/, under the CC-BY-ND 4.0 license. The annotations generated by the rules are under the CC-BY 4.0 license. A tutorial and supplementary code to use HAMAP as SPARQL are available on GitHub at https://github.com/sib-swiss/HAMAP- SPARQL, and general documentation about HAMAP can be found on the HAMAP website at https://hamap.expasy.org.