PathBuilder - Open Source Software for Annotating and Developing Pathway Resources
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.
Supplementary data are available at Bioinformatics online.
Full-textDOI: · Available from: Shivakumar Keerthikumar, Sep 29, 2015
- SourceAvailable from: Jyoti Sharma
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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. "
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.Journal of Cell Communication and Signaling 06/2015; DOI:10.1007/s12079-015-0297-3
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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. "
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 (*)Journal of Cell Communication and Signaling 01/2014; 8(2):165-170. DOI:10.1007/s12079-014-0224-z
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- "The reactions stimulated by TSLP as compared with an unstimulated state (reactions induced on co-stimulation with TSLP and any other stimuli were excluded) in human or other mammalian systems were included. We used PathBuilder (36), a pathway annotation tool developed by our group, to annotate reactions in TSLP signaling. Reactions were captured under the following categories: "
ABSTRACT: Thymic stromal lymphopoietin (TSLP) is a four-helix bundle cytokine that plays a critical role in the regulation of immune responses and in the differentiation of hematopoietic cells. TSLP signals through a heterodimeric receptor complex consisting of an interleukin-7 receptor α chain and a unique TSLP receptor (TSLPR) [also known as cytokine receptor-like factor 2 (CRLF2)]. Cellular targets of TSLP include dendritic cells, B cells, mast cells, regulatory T (Treg) cells and CD4+ and CD8+ T cells. The TSLP/TSLPR axis can activate multiple signaling transduction pathways including the JAK/STAT pathway and the PI-3 kinase pathway. Aberrant TSLP/TSLPR signaling has been associated with a variety of human diseases including asthma, atopic dermatitis, nasal polyposis, inflammatory bowel disease, eosinophilic eosophagitis and, most recently, acute lymphoblastic leukemia. A centralized resource of the TSLP signaling pathway cataloging signaling events is not yet available. In this study, we present a literature-annotated resource of reactions in the TSLP signaling pathway. This pathway map is publicly available through NetPath (http://www.netpath.org/), an open access signal transduction pathway resource developed previously by our group. This map includes 236 molecules and 252 reactions that are involved in TSLP/TSLPR signaling pathway. We expect that the TSLP signaling pathway map will provide a rich resource to study the biology of this important cytokine as well as to identify novel therapeutic targets for diseases associated with dysregulated TSLP/TSLPR signaling. Database URL: http://www.netpath.org/pathways?path_id=NetPath_24Database The Journal of Biological Databases and Curation 01/2014; 2014:bau007. DOI:10.1093/database/bau007 · 3.37 Impact Factor