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PathBuilder specifications

Information


Unique identifier OMICS_16938
Name PathBuilder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Python
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Stability Beta
Maintained Yes

Versioning


No version available

Documentation


Maintainer


  • person_outline Akhilesh Pandey

Publication for PathBuilder

PathBuilder citations

 (5)
library_books

Differential ligand signaling network of CCL19/CCL21 CCR7 system

2015
PMCID: 4620938
PMID: 26504105
DOI: 10.1093/database/bav106

[…] irect enzyme–substrate reactions should also be considered as protein–protein interactions. For each of the reactions, the specific cell types in which the reactions are studied were also documented. PathBuilder, an in-house pathway curation tool that facilitates quality check and thereby error-free curation was used to document all the reactions systematically (). […]

library_books

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

2015
PMCID: 4309023
PMID: 25632107
DOI: 10.1093/database/bau126

[…] ons with the other information or database links, it is very much essential to have an automatic and dynamic tool which will perform the job with more accuracy and less time. To overcome such issues, PathBuilder—an open source web-based application—has received the attention to the pathway curator communities for its advanced feature to annotate biological reaction mechanisms/translocation procedu […]

library_books

Signaling Network Map of Endothelial TEK Tyrosine Kinase

2014
PMCID: 4211299
PMID: 25371820
DOI: 10.1155/2014/173026

[…] modifications (PTMs) (catalytic events). Activation/inhibition status of proteins, alterations in protein localization, and also genes regulated at mRNA level by TIE2 signaling were also documented. PathBuilder, an in-house pathway annotation tool, was used for the curation of these reactions []. Each curated reaction was internally reviewed by trained biocurators followed by an external review b […]

library_books

A Network Map of FGF 1/FGFR Signaling System

2014
PMCID: 4009234
PMID: 24829797
DOI: 10.1155/2014/962962

[…] on of proteins, (d) activation or inhibition of specific proteins, and (e) regulation of gene expression. Relevant information from research articles were manually documented using the curation tool, PathBuilder. To streamline and organize data collection from literature, we followed the previously described criteria for the inclusion/exclusion of pathway specific reactions [, ]. The data accumula […]

library_books

A Bioinformatics Resource for TWEAK Fn14 Signaling Pathway

2012
PMCID: 3357548
PMID: 22649723
DOI: 10.1155/2012/376470

[…] es were screened to capture molecular reactions stimulated by TWEAK in mammalian cells as compared to the corresponding unstimulated state. Thereafter, with the use of an in-house developed software, PathBuilder [] that enables conversion of pathway data into standard community formats, namely, PSI-MI, BioPAX, and SBML formats, we annotated biological information and reactions pertaining to TWEAK […]


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PathBuilder institution(s)
Institute of Bioinformatics, International Tech Park, Bangalore, India; Department of Biotechnology and Bioinformatics, Kuvempu University, Shankarghatta, India; McKusick-Nathans Institute of Genetic Medicine and the Departments of Biological Chemistry, Pathology and Oncology, Johns Hopkins University, Baltimore, MA, USA; Research Unit for Immunoinformatics, Research Center for Allergy and Immunology, RIKEN Yokohama Institute, Kanagawa, Japan
PathBuilder funding source(s)
This work was supported by National Institute of Health Roadmap Initiative (grant U54RR020839); National Heart Lung and Blood Institute (contract N01-HV-28180); Department of Defense Era of Hope Scholar award (W81XWH-06-1-0428).

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