Lampa Samuel, Willighagen Egon, Kohonen Pekka, King Ali, Vrandečić Denny, Grafström Roland, Spjuth Ola
Department of Pharmaceutical Biosciences, Uppsala University, Uppsala, SE-751 24, Sweden.
Department of Bioinformatics - BiGCaT, NUTRIM, Maastricht University, P.O. Box 616, UNS50 Box 19, Maastricht, NL-6200, MD, The Netherlands.
J Biomed Semantics. 2017 Sep 4;8(1):35. doi: 10.1186/s13326-017-0136-y.
Biological sciences are characterised not only by an increasing amount but also the extreme complexity of its data. This stresses the need for efficient ways of integrating these data in a coherent description of biological systems. In many cases, biological data needs organization before integration. This is not seldom a collaborative effort, and it is thus important that tools for data integration support a collaborative way of working. Wiki systems with support for structured semantic data authoring, such as Semantic MediaWiki, provide a powerful solution for collaborative editing of data combined with machine-readability, so that data can be handled in an automated fashion in any downstream analyses. Semantic MediaWiki lacks a built-in data import function though, which hinders efficient round-tripping of data between interoperable Semantic Web formats such as RDF and the internal wiki format.
To solve this deficiency, the RDFIO suite of tools is presented, which supports importing of RDF data into Semantic MediaWiki, with metadata needed to export it again in the same RDF format, or ontology. Additionally, the new functionality enables mash-ups of automated data imports combined with manually created data presentations. The application of the suite of tools is demonstrated by importing drug discovery related data about rare diseases from Orphanet and acid dissociation constants from Wikidata. The RDFIO suite of tools is freely available for download via pharmb.io/project/rdfio .
Through a set of biomedical demonstrators, it is demonstrated how the new functionality enables a number of usage scenarios where the interoperability of SMW and the wider Semantic Web is leveraged for biomedical data sets, to create an easy to use and flexible platform for exploring and working with biomedical data.
生物科学的特点不仅在于数据量的不断增加，还在于其数据的极端复杂性。这凸显了以连贯的方式整合这些数据的有效方法的必要性。在许多情况下，生物数据在整合之前需要进行整理。这往往是一项协作性的工作，因此数据集成工具支持协作式工作方式非常重要。具有结构化语义数据创作支持的维基系统，如语义维基百科（Semantic MediaWiki），为数据的协作编辑提供了一个强大的解决方案，并结合了机器可读性，以便在任何下游分析中都能以自动化方式处理数据。然而，语义维基百科缺乏内置的数据导入功能，这阻碍了在诸如RDF等可互操作的语义网格式与内部维基格式之间进行高效的数据往返。
为了解决这一缺陷，我们提出了RDFIO工具套件，它支持将RDF数据导入语义维基百科，并带有以相同RDF格式再次导出所需的元数据或本体。此外，新功能还实现了自动数据导入与手动创建的数据展示的混搭。通过从孤儿药网（Orphanet）导入与罕见病相关的药物发现数据以及从维基数据（Wikidata）导入酸解离常数，展示了该工具套件的应用。RDFIO工具套件可通过pharmb.io/project/rdfio免费下载。
通过一系列生物医学示例，展示了新功能如何实现多种使用场景，其中利用语义维基百科和更广泛的语义网的互操作性来处理生物医学数据集，从而创建一个易于使用且灵活的平台，用于探索和处理生物医学数据。
