Article

PathBuilder - Open Source Software for Annotating and Developing Pathway Resources

Institute of Bioinformatics, International Tech Park, Bangalore 560066, India.
Bioinformatics (Impact Factor: 4.98). 08/2009; 25(21):2860-2. DOI: 10.1093/bioinformatics/btp453
Source: PubMed

ABSTRACT

We have developed PathBuilder, an open-source web application to annotate biological information pertaining to signaling pathways and to create web-based pathway resources. PathBuilder enables annotation of molecular events including protein-protein interactions, enzyme-substrate relationships and protein translocation events either manually or through automated importing of data from other databases. Salient features of PathBuilder include automatic validation of data formats, built-in modules for visualization of pathways, automated import of data from other pathway resources, export of data in several standard data exchange formats and an application programming interface for retrieving existing pathway datasets.
PathBuilder is freely available for download at http://pathbuilder.sourceforge.net/ under the terms of GNU lesser general public license (LGPL: http://www.gnu.org/copyleft/lesser.html). The software is platform independent and has been tested on Windows and Linux platforms.
pandey@jhmi.edu
Supplementary data are available at Bioinformatics online.

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Available from: Shivakumar Keerthikumar
    • "Studies describing the downstream signaling events induced upon binding of IL-10 to its receptor were screened for annotation of this pathway. The information was then manually curated and cataloged using PathBuilder (Kandasamy et al. 2009), an annotation tool developed in-house for the curation of signaling pathways. Annotation criteria, previously employed for generation of RANK/RANKL (Raju et al. 2011a), Interleukin-17 (Sharma et al. 2015), CRH (Subbannayya et al. 2013), Gastrin (Subbannayya et al. 2014), BDNF (Brain derived neurotrophic factor) (Subbannayya et al. 2013) and TSLP (Thymic stromal lymphopoietin) (Zhong et al. 2014) signaling pathways, were followed for mapping IL-10 signaling molecules. "
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    ABSTRACT: Interleukin-10 (IL-10) is an anti-inflammatory cytokine with important immunoregulatory functions. It is primarily secreted by antigen-presenting cells such as activated T-cells, monocytes, B-cells and macrophages. In biologically functional form, it exists as a homodimer that binds to tetrameric heterodimer IL-10 receptor and induces downstream signaling. IL-10 is associated with survival, proliferation and anti-apoptotic activities of various cancers such as Burkitt lymphoma, non-Hodgkins lymphoma and non-small scell lung cancer. In addition, it plays a central role in survival and persistence of intracellular pathogens such as Leishmania donovani, Mycobacterium tuberculosis and Trypanosoma cruzi inside the host. The signaling mechanisms of IL-10 cytokine are not well explored and a well annotated pathway map has been lacking. To this end, we developed a pathway resource by manually annotating the IL-10 induced signaling molecules derived from literature. The reactions were categorized under molecular associations, activation/inhibition, catalysis, transport and gene regulation. In all, 37 molecules and 76 reactions were annotated. The IL-10 signaling pathway can be freely accessed through NetPath, a resource of signal transduction pathways previously developed by our group.
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    • "The articles were screened for information pertaining to molecular association (protein-protein interactions), catalysis (post-translational modifications), transport (translocation of proteins between sub-cellular compartments), activation/inhibition and gene regulation events that have been reported under stimulation by IL- 17 and its subtypes. The pathway data were annotated using PathBuilder, a curation tool developed by our group (Kandasamy et al. 2009). The annotation criteria were followed as described in IL-11 (Balakrishnan et al. 2013), RANKL (Raju et al. 2011) and TSLP (Zhong et al. 2014) signaling pathways. "
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    ABSTRACT: Interleukin-17 (IL-17) belongs to a relatively new family of cytokines that has garnered attention as the signature cytokine of Th17 cells. This cytokine family consists of 6 ligands, which bind to 5 receptor subtypes and induce downstream signaling. Although the receptors are ubiquitously expressed, cellular responses to ligands vary across tissues. The cytokine family is associated with various autoimmune disorders including rheumatoid arthritis, multiple sclerosis, inflammatory bowel disease, asthma and psoriasis in addition to being implicated in the pathogenesis of cancer. In addition, this family plays a role in host defense against bacterial and fungal infections. The signaling mechanisms of the IL-17 family of proinflammatory cytokines are not well explored. In this study, we present a resource of literature-annotated reactions induced by IL-17. The reactions are catalogued under 5 categories, namely; molecular association, catalysis, transport, activation/inhibition and gene regulation. A total of 93 molecules and 122 reactions have been annotated. The IL-17 pathway is freely available through NetPath, a resource of signal transduction pathways previously developed by our group.
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    • "For manual curation of these events, we considered the NetPath annotation criteria as previously described for the series of NetPath pathways (Raju et al. 2011a; Soman et al. 2013). We used the software PathBuilder, developed by our group, to manually document the signaling events (Kandasamy et al. 2009). Information pertaining to protein–protein interactions, enzyme-catalyzed 166 Y. Subbannayya et al. "
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    ABSTRACT: Abbreviations CCKAR Cholecystokinin A receptor CCKBR Cholecystokinin B receptor ECL Enterochromaffin-like PPI Protein-protein interaction PTM Post-translational modification HPRD Human protein reference database SBML Systems biology markup language PSI-MI Proteomics standards initiative for molecular interaction BioPax Biological pathway exchange Yashwanth Subbannayya and Kumari Anuja contributed equally. Y. Subbannayya : J. Advani : V. Nanjappa : B. George : B. L. Somani : R. Raju (*)
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