OntoDas——一种便于构建针对基因本体论的复杂查询的工具。

OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.

作者信息

O'Neill Kieran, Garcia Alexander, Schwegmann Anita, Jimenez Rafael C, Jacobson Dan, Hermjakob Henning

机构信息

Central Node, National Bioinformatics Network, Golf Park, Raapenberg Road, Cape Town, South Africa.

出版信息

BMC Bioinformatics. 2008 Oct 16;9:437. doi: 10.1186/1471-2105-9-437.

DOI:10.1186/1471-2105-9-437

PMID:18925933

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC2579441/

Abstract

BACKGROUND

Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms.

RESULTS

OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions.

CONCLUSION

OntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at http://ontodas.nbn.ac.za.

摘要

背景

诸如基因本体论之类的本体论能够以概念化的方式构建针对生物信息的复杂查询，然而现有的实现此目的的系统过于技术化。在生物领域，对便于灵活检索信息的软件的需求日益增长。OntoDas旨在通过允许通过选择有效的本体术语来定义查询来满足这一需求。

结果

OntoDas是一个基于网络的工具，它使用信息可视化技术来提供一个直观、交互式的环境，用于针对基因本体论数据库构建基于本体的查询。通过与生物学家合作，以参与式方式设计了一个全面的用例和界面本身，以确保界面与生物学家的工作方式相匹配。OntoDas进一步由另一组生物学家进行测试，并根据他们的建议进行了完善。