Trindade Daniel, Orsine Lissur A, Barbosa-Silva Adriano, Donnard Elisa R, Ortega J Miguel
Depto. de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-010, Brazil.
Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg.
Methods. 2015 Mar;74:16-35. doi: 10.1016/j.ymeth.2014.10.006. Epub 2014 Oct 28.
Genomic information is being underlined in the format of biological pathways. Building these biological pathways is an ongoing demand and benefits from methods for extracting information from biomedical literature with the aid of text-mining tools. Here we hopefully guide you in the attempt of building a customized pathway or chart representation of a system. Our manual is based on a group of software designed to look at biointeractions in a set of abstracts retrieved from PubMed. However, they aim to support the work of someone with biological background, who does not need to be an expert on the subject and will play the role of manual curator while designing the representation of the system, the pathway. We therefore illustrate with two challenging case studies: hair and breast development. They were chosen for focusing on recent acquisitions of human evolution. We produced sub-pathways for each study, representing different phases of development. Differently from most charts present in current databases, we present detailed descriptions, which will additionally guide PESCADOR users along the process. The implementation as a web interface makes PESCADOR a unique tool for guiding the user along the biointeractions, which will constitute a novel pathway.
基因组信息正以生物途径的形式被凸显出来。构建这些生物途径是一项持续的需求，并且借助文本挖掘工具从生物医学文献中提取信息的方法对此大有裨益。在此，我们希望能在你构建系统的定制途径或图表表示的尝试中为你提供指导。我们的手册基于一组软件，这些软件旨在查看从PubMed检索到的一组摘要中的生物相互作用。然而，它们旨在支持有生物学背景的人员开展工作，这些人员无需是该领域的专家，并且在设计系统（即途径）的表示形式时将扮演人工编目的角色。因此，我们用两个具有挑战性的案例研究进行说明：毛发和乳腺发育。选择它们是为了聚焦人类进化的最新研究成果。我们为每个研究生成了子途径，代表发育的不同阶段。与当前数据库中呈现的大多数图表不同，我们给出了详细描述，这将额外指导PESCADOR用户完成整个过程。作为一个网络界面的实现方式使PESCADOR成为指导用户了解生物相互作用的独特工具，这些生物相互作用将构成一条新颖的途径。
