title: A guide for building biological pathways along with two case studies: hair and breast development.
abstract: 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.
authors.affiliation: Depto. de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-010, Brazil. Electronic address: daniel-trindade@c-bio.grad.ufmg.br.
authors.forename: Daniel
authors.initials: D
authors.lastname: Trindade
authors.affiliation: Depto. de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-010, Brazil. Electronic address: lissurorsine@gmail.com.
authors.forename: Lissur A
authors.initials: LA
authors.lastname: Orsine
authors.affiliation: Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Esch-sur-Alzette 4362, Luxembourg. Electronic address: adriano.barbosa@uni.lu.
authors.forename: Adriano
authors.initials: A
authors.lastname: Barbosa-Silva
authors.affiliation: Centro de Oncologia Molecular, Instituto de Ensino e Pesquisa, Hospital Sírio-Libanês, São Paulo, SP 01308-060, Brazil. Electronic address: edonnard@mochsl.org.br.
authors.forename: Elisa R
authors.initials: ER
authors.lastname: Donnard
authors.affiliation: Depto. de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG 31270-010, Brazil. Electronic address: miguel@icb.ufmg.br.
authors.forename: J Miguel
authors.initials: JM
authors.lastname: Ortega
mesh_terms: D001940:Breast / Q000254:growth & development*; D057225:Data Mining / Q000379:methods* / Q000639:trends; D030541:Databases, Genetic / Q000639:trends; D005260:Female; D006197:Hair / Q000254:growth & development*; D006801:Humans; D039781:PubMed / Q000639:trends
keywords: Breast development; Hair development; PESCADOR; Pathway; PubMed