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Cited by 39

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

Using the Semantic Web for Rapid Integration of WikiPathways with Other Biological Online Data Resources

Waagmeester, Andra, Kutmon, Martina, Riutta, Anders, Miller, Ryan, Willighagen, Egon L., Evelo, Chris T., Pico, Alexander R.·2016·PLOS Computational Biology
DOI 10.1371/journal.pcbi.1004989PMC PMC4918977
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Crossref · 10.1371/journal.pcbi.1004989

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Claims other papers make about this one

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  • The nanopublication model has been used to represent statements from different fields, especially in the life science domain.

    “The nanopublication model has been used to represent statements from different fields, especially in the life science domain.”

    From Provenance-driven nanopublications: representing source lineage and trust networks for multi-source assertions (2025) · cites this paper as [6]

    The Introduction describes representing WikiPathways content as triple-based statements about biological entities, and Materials and Methods describes RDF guidelines for biomedical data. Neither passage addresses the nanopublication model or its use across different fields; searches for “nanopublication” and related terms found no passage that does. (LLM, conf=0.76)

    Experimental — accuracy not yet measured

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Citations

Cites

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Research works printed but not linked: 27

  1. DGJ Jennen, 2010, Biotransformation pathway maps in wikipathways enable direct visualization of drug metabolism related expression changes, Drug Discov Today, 15, 851, 10.1016/j.drudis.2010.08.002 · DOI
  2. P Khatri, 2012, Ten years of pathway analysis: current approaches and outstanding challenges, PLoS Comput Biol, 8, e1002375, 10.1371/journal.pcbi.1002375 · DOI
  3. MP van Iersel, 2008, Presenting and exploring biological pathways with PathVisio, BMC Bioinformatics, 9, 399, 10.1186/1471-2105-9-399 · DOI
  4. T Kelder, 2010, Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets, PLoS Biol, 8, 10.1371/journal.pbio.1000472 · DOI
  5. T Kelder, 2012, WikiPathways: building research communities on biological pathways, Nucleic Acids Res, 40, D1301, 10.1093/nar/gkr1074 · DOI
  6. M Kutmon, 2016, WikiPathways: capturing the full diversity of pathway knowledge, Nucleic Acids Research, 44, D488, 10.1093/nar/gkv1024 · DOI
  7. D Maglott, 2011, Entrez gene: gene-centered information at NCBI, Nucleic Acids Research, 39, D52, 10.1093/nar/gkq1237 · DOI
  8. A Yates, 2016, Ensembl 2016, Nucleic Acids Research, 44, D710, 10.1093/nar/gkv1157 · DOI
  9. 2015, UniProt: a hub for protein information, Nucleic Acids Research, 43, D204, 10.1093/nar/gku989 · DOI · Paper page
  10. DS Wishart, 2013, HMDB 3.0—The human metabolome database in 2013, Nucleic Acids Research, 41, D801, 10.1093/nar/gks1065 · DOI
  11. HE Pence, 2010, ChemSpider: An online chemical information resource, J Chem Educ, 87, 1123, 10.1021/ed100697w · DOI
  12. S Kim, 2016, PubChem substance and compound databases, Nucleic Acids Research, 44, D1202, 10.1093/nar/gkv951 · DOI · Paper page
  13. AP Bento, 2014, The ChEMBL bioactivity database: an update, Nucleic Acids Research, 42, D1083, 10.1093/nar/gkt1031 · DOI
  14. MP van Iersel, 2010, The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services, BMC Bioinformatics, 11, 5, 10.1186/1471-2105-11-5 · DOI
  15. N Juty, 2012, Identifiers.org and MIRIAM Registry: community resources to provide persistent identification, Nucleic Acids Res, 40, D580, 10.1093/nar/gkr1097 · DOI
  16. J Piñero, 2015, DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes, Database, 2015, bav028+, 10.1093/database/bav028 · DOI · Paper page
  17. JS Luciano, 2005, Pax of mind for pathway researchers, Drug Discov Today, 10, 937, 10.1016/S1359-6446(05)03501-4 · DOI
  18. N Le Novere, 2009, The Systems Biology Graphical Notation, Nat Biotechnol, 27, 735, 10.1038/nbt.1558 · DOI · Paper page
  19. KW Kohn, 2006, Molecular interaction maps of bioregulatory networks: a general rubric for systems biology, Mol Biol Cell, 17, 1, 10.1091/mbc.E05-09-0824 · DOI
  20. N Juty, 2015, BioModels: Content, Features, Functionality and Use, CPT: Pharmacometrics & Systems Pharmacology
  21. A Luna, 2011, PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs), Bioinformatics, 27, 2165, 10.1093/bioinformatics/btr336 · DOI
  22. J Ratnam, 2014, The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research, PLoS ONE, 9, e115460, 10.1371/journal.pone.0115460 · DOI
  23. Halpin H, Hayes PJ, McCusker JP, McGuinness DL, Thompson HS (2010) When owl:sameAs Isn’t the Same: An Analysis of Identity in Linked Data. In: International Semantic Web Conference. Springer, volume 6496 of LNCS, pp. 305–320. · DOI
  24. A Bohler, 2015, Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment, BMC Bioinformatics, 16, 267, 10.1186/s12859-015-0708-8 · DOI
  25. EG Cerami, 2011, Pathway commons, a web resource for biological pathway data, Nucleic Acids Research, 39, D685, 10.1093/nar/gkq1039 · DOI · Paper page
  26. AJ Williams, 2012, Open PHACTS: semantic interoperability for drug discovery, Drug Discovery Today, 17, 1188, 10.1016/j.drudis.2012.05.016 · DOI · Paper page
  27. B McBride, 2002, Jena: a semantic web toolkit, Internet Computing, IEEE, 6, 55, 10.1109/MIC.2002.1067737 · DOI

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Metadata

Authors
Waagmeester, A., Kutmon, M., Riutta, A., Miller, R., Willighagen, E. L., Evelo, C. T., & Pico, A. R.
Venue
PLOS Computational Biology
Publisher
Public Library of Science (PLoS)
Published
2016-06-23
Volume
12
Issue
6
Pages
e1004989
ISSN
1553-7358
DOI
10.1371/journal.pcbi.1004989
PMC
PMC4918977
Cited by
39
References
1
Language
en
Licence
creativecommons.org/licenses/by/4.0/ (vor)
Funders
  • Innovative Medicines Initiative (no115191)
  • National Institutes of Health (R01-GM100039)

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