Pathway commons 2019 update: integration, analysis and exploration of pathway data

Simple item page
buir.contributor.authorDoğrusöz, Uğur
dc.citation.epageD497en_US
dc.citation.issueNumberD1en_US
dc.citation.spageD489en_US
dc.citation.volumeNumber48en_US
dc.contributor.authorRodchenkov, I.en_US
dc.contributor.authorBabur, Ö.en_US
dc.contributor.authorLuna, A.en_US
dc.contributor.authorAksoy, B. A.en_US
dc.contributor.authorWong, J. V.en_US
dc.contributor.authorFong, D.en_US
dc.contributor.authorFranz, M.en_US
dc.contributor.authorSiper, M. C.en_US
dc.contributor.authorCheung, M.en_US
dc.contributor.authorWrana, M.en_US
dc.contributor.authorMistry, H.en_US
dc.contributor.authorMosier, L.en_US
dc.contributor.authorDlin, J.en_US
dc.contributor.authorWen, Q.en_US
dc.contributor.authorO’Callaghan, C.en_US
dc.contributor.authorLi, W.en_US
dc.contributor.authorElder, G.en_US
dc.contributor.authorSmith, P. T.en_US
dc.contributor.authorDallago, C.en_US
dc.contributor.authorCerami, E.en_US
dc.contributor.authorGross, B.en_US
dc.contributor.authorDoğrusöz, Uğuren_US
dc.contributor.authorDemir, E.en_US
dc.contributor.authorBader, G. D.en_US
dc.contributor.authorSander, C.en_US
dc.date.accessioned2021-03-03T10:35:39Z
dc.date.available2021-03-03T10:35:39Z
dc.date.issued2020
dc.departmentDepartment of Computer Engineeringen_US
dc.description.abstractPathway Commons (https://www.pathwaycommons.org) is an integrated resource of publicly available information about biological pathways including biochemical reactions, assembly of biomolecular complexes, transport and catalysis events and physical interactions involving proteins, DNA, RNA, and small molecules (e.g. metabolites and drug compounds). Data is collected from multiple providers in standard formats, including the Biological Pathway Exchange (BioPAX) language and the Proteomics Standards Initiative Molecular Interactions format, and then integrated. Pathway Commons provides biologists with (i) tools to search this comprehensive resource, (ii) a download site offering integrated bulk sets of pathway data (e.g. tables of interactions and gene sets), (iii) reusable software libraries for working with pathway information in several programming languages (Java, R, Python and Javascript) and (iv) a web service for programmatically querying the entire dataset. Visualization of pathways is supported using the Systems Biological Graphical Notation (SBGN). Pathway Commons currently contains data from 22 databases with 4794 detailed human biochemical processes (i.e. pathways) and ∼2.3 million interactions. To enhance the usability of this large resource for end-users, we develop and maintain interactive web applications and training materials that enable pathway exploration and advanced analysis.en_US
dc.identifier.doi10.1093/nar/gkz946en_US
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/11693/75706
dc.language.isoEnglishen_US
dc.publisherOxford University Pressen_US
dc.relation.isversionofhttps://dx.doi.org/10.1093/nar/gkz946en_US
dc.source.titleNucleic Acids Researchen_US
dc.titlePathway commons 2019 update: integration, analysis and exploration of pathway dataen_US
dc.typeArticleen_US
Files
Original bundle
Now showing 1 - 1 of 1
Thumbnail Image
Name:
Pathway_commons_2019_update_integration_analysis_and_exploration_of_pathway_data.pdf
Size:
2.12 MB
Format:
Adobe Portable Document Format
Description:
View / Download
Download
License bundle
Now showing 1 - 1 of 1
No Thumbnail Available
Name:
license.txt
Size:
1.71 KB
Format:
Item-specific license agreed upon to submission
Description:
Download
Collections
Department of Computer Engineering