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Centre for Translational Bioinformatics
  1. Centre for Translational Bioinformatics
  2. Team
  3. Adriano Barbosa da Silva
  4. Systems Biology

Systems Biology

Approach to build systems biology pathways using text-mining and biological graphical notation

Textmining

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. We published a guide to build 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.

References:

  • Piereck B, Oliveira-Lima M, Benko-Iseppon AM, Diehl S, Schneider R, Brasileiro-Vidal AC, Barbosa-Silva A. LAITOR4HPC: A text mining pipeline based on HPC for building interaction networks. BMC Bioinformatics. 2020 Aug 24;21(1):365. doi: 10.1186/s12859-020-03620-4.
  • Trindade D, Orsine LA, Barbosa-Silva A, Donnard ER, Ortega JM. A guide for building biological pathways along with two case studies: hair and breast development. Methods. 2015 Mar;74:16-35. doi.org/10.1016/j.ymeth.2014.10.006
  • Donnard E, Barbosa-Silva A, Guedes RL, Fernandes GR, Velloso H, Kohn MJ, Andrade-Navarro MA, Ortega JM. Preimplantation development regulatory pathway construction through a text-mining approach. BMC Genomics. 2011 Dec 22;12 Suppl 4(Suppl 4):S3. doi: 10.1186/1471-2164-12-S4-S3.
  • Barbosa-Silva A, Fontaine JF, Donnard ER, Stussi F, Ortega JM, Andrade-Navarro MA. PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. BMC Bioinformatics. 2011 Nov 9;12:435. doi: 10.1186/1471-2105-12-435.
  • Barbosa-Silva A, Soldatos TG, Magalhães IL, Pavlopoulos GA, Fontaine JF, Andrade-Navarro MA, Schneider R, Ortega JM. LAITOR--Literature Assistant for Identification of Terms co-Occurrences and Relationships. BMC Bioinformatics. 2010 Feb 1;11:70. doi: 10.1186/1471-2105-11-70.

 

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