SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database
The Small Molecule Pathway Database (SMPDB, http://www.smpdb.ca) is a comprehensive, colorful, fully searchable and highly interactive database for visualizing human metabolic, drug action, drug metabolism, physiological activity and metabolic disease pathways. SMPDB contains >600 pathways with n...
| Main Authors: | , , , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Online |
| Language: | English |
| Published: |
Oxford University Press
2014
|
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965088/ |
| id |
pubmed-3965088 |
|---|---|
| recordtype |
oai_dc |
| spelling |
pubmed-39650882014-03-25 SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database Jewison, Timothy Su, Yilu Disfany, Fatemeh Miri Liang, Yongjie Knox, Craig Maciejewski, Adam Poelzer, Jenna Huynh, Jessica Zhou, You Arndt, David Djoumbou, Yannick Liu, Yifeng Deng, Lu Guo, An Chi Han, Beomsoo Pon, Allison Wilson, Michael Rafatnia, Shahrzad Liu, Philip Wishart, David S. III. Metabolic and signalling pathways, enzymes The Small Molecule Pathway Database (SMPDB, http://www.smpdb.ca) is a comprehensive, colorful, fully searchable and highly interactive database for visualizing human metabolic, drug action, drug metabolism, physiological activity and metabolic disease pathways. SMPDB contains >600 pathways with nearly 75% of its pathways not found in any other database. All SMPDB pathway diagrams are extensively hyperlinked and include detailed information on the relevant tissues, organs, organelles, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Since its last release in 2010, SMPDB has undergone substantial upgrades and significant expansion. In particular, the total number of pathways in SMPDB has grown by >70%. Additionally, every previously entered pathway has been completely redrawn, standardized, corrected, updated and enhanced with additional molecular or cellular information. Many SMPDB pathways now include transporter proteins as well as much more physiological, tissue, target organ and reaction compartment data. Thanks to the development of a standardized pathway drawing tool (called PathWhiz) all SMPDB pathways are now much more easily drawn and far more rapidly updated. PathWhiz has also allowed all SMPDB pathways to be saved in a BioPAX format. Significant improvements to SMPDB’s visualization interface now make the browsing, selection, recoloring and zooming of pathways far easier and far more intuitive. Because of its utility and breadth of coverage, SMPDB is now integrated into several other databases including HMDB and DrugBank. Oxford University Press 2014-01-01 2013-11-06 /pmc/articles/PMC3965088/ /pubmed/24203708 http://dx.doi.org/10.1093/nar/gkt1067 Text en © The Author(s) 2013. Published by Oxford University Press. http://creativecommons.org/licenses/by/3.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
| repository_type |
Open Access Journal |
| institution_category |
Foreign Institution |
| institution |
US National Center for Biotechnology Information |
| building |
NCBI PubMed |
| collection |
Online Access |
| language |
English |
| format |
Online |
| author |
Jewison, Timothy Su, Yilu Disfany, Fatemeh Miri Liang, Yongjie Knox, Craig Maciejewski, Adam Poelzer, Jenna Huynh, Jessica Zhou, You Arndt, David Djoumbou, Yannick Liu, Yifeng Deng, Lu Guo, An Chi Han, Beomsoo Pon, Allison Wilson, Michael Rafatnia, Shahrzad Liu, Philip Wishart, David S. |
| spellingShingle |
Jewison, Timothy Su, Yilu Disfany, Fatemeh Miri Liang, Yongjie Knox, Craig Maciejewski, Adam Poelzer, Jenna Huynh, Jessica Zhou, You Arndt, David Djoumbou, Yannick Liu, Yifeng Deng, Lu Guo, An Chi Han, Beomsoo Pon, Allison Wilson, Michael Rafatnia, Shahrzad Liu, Philip Wishart, David S. SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database |
| author_facet |
Jewison, Timothy Su, Yilu Disfany, Fatemeh Miri Liang, Yongjie Knox, Craig Maciejewski, Adam Poelzer, Jenna Huynh, Jessica Zhou, You Arndt, David Djoumbou, Yannick Liu, Yifeng Deng, Lu Guo, An Chi Han, Beomsoo Pon, Allison Wilson, Michael Rafatnia, Shahrzad Liu, Philip Wishart, David S. |
| author_sort |
Jewison, Timothy |
| title |
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database |
| title_short |
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database |
| title_full |
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database |
| title_fullStr |
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database |
| title_full_unstemmed |
SMPDB 2.0: Big Improvements to the Small Molecule Pathway Database |
| title_sort |
smpdb 2.0: big improvements to the small molecule pathway database |
| description |
The Small Molecule Pathway Database (SMPDB, http://www.smpdb.ca) is a comprehensive, colorful, fully searchable and highly interactive database for visualizing human metabolic, drug action, drug metabolism, physiological activity and metabolic disease pathways. SMPDB contains >600 pathways with nearly 75% of its pathways not found in any other database. All SMPDB pathway diagrams are extensively hyperlinked and include detailed information on the relevant tissues, organs, organelles, subcellular compartments, protein cofactors, protein locations, metabolite locations, chemical structures and protein quaternary structures. Since its last release in 2010, SMPDB has undergone substantial upgrades and significant expansion. In particular, the total number of pathways in SMPDB has grown by >70%. Additionally, every previously entered pathway has been completely redrawn, standardized, corrected, updated and enhanced with additional molecular or cellular information. Many SMPDB pathways now include transporter proteins as well as much more physiological, tissue, target organ and reaction compartment data. Thanks to the development of a standardized pathway drawing tool (called PathWhiz) all SMPDB pathways are now much more easily drawn and far more rapidly updated. PathWhiz has also allowed all SMPDB pathways to be saved in a BioPAX format. Significant improvements to SMPDB’s visualization interface now make the browsing, selection, recoloring and zooming of pathways far easier and far more intuitive. Because of its utility and breadth of coverage, SMPDB is now integrated into several other databases including HMDB and DrugBank. |
| publisher |
Oxford University Press |
| publishDate |
2014 |
| url |
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965088/ |
| _version_ |
1612071059967705088 |