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

PLoS Computational Biology

Volumn 12, Issue 6, 2016, Pages

  Waagmeester, Andra ^a   Kutmon, Martina ^a   Riutta, Anders ^b   Miller, Ryan ^a   Willighagen, Egon L ^a   Evelo, Chris T ^a   Pico, Alexander R ^b  

^a MAASTRICHT UNIVERSITY   (Netherlands)

^b GLADSTONE INSTITUTES   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DATA INTEGRATION; HTTP; INFORMATION USE;

BIOINFORMATICIANS; BIOLOGICAL DATA; BIOLOGICAL PATHWAYS; BIOLOGICAL RESOURCES; DATA RESOURCES; GRAPHICAL REPRESENTATIONS; KNOWLEDGE INTEGRATION; ONLINE DATA; ONLINE RESOURCES; SEMANTIC-WEB;

SEMANTIC WEB;

ARTICLE; BIOLOGY; COMPUTER PROGRAM; DATA PROCESSING; GENE; INFORMATION PROCESSING; LINGUISTICS; METABOLITE; ONLINE SYSTEM; PROTEIN DETERMINATION; SEMANTIC WEB; STATISTICAL ANALYSIS; BIOLOGICAL ONTOLOGY; HUMAN; INFORMATION RETRIEVAL; INTERNET; MEDICAL RESEARCH; PROCEDURES; SEMANTICS;

BIOLOGICAL ONTOLOGIES; BIOMEDICAL RESEARCH; COMPUTATIONAL BIOLOGY; HUMANS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; SEMANTICS;

EID: 84978910838     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1004989     Document Type: Article

References (38)

1. Jennen DGJ, Gaj S, Giesbertz PJ, van Delft JHM, Evelo CT, et al. (2010) Biotransformation pathway maps in wikipathways enable direct visualization of drug metabolism related expression changes. Drug Discov Today15: 851–858. doi: 10.1016/j.drudis.2010.08.00220708095
2. Khatri P, Sirota M, Butte AJ, (2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol8: e1002375. doi: 10.1371/journal.pcbi.100237522383865
3. van Iersel MP, Kelder T, Pico AR, Hanspers K, Coort S, et al. (2008) Presenting and exploring biological pathways with PathVisio. BMC Bioinformatics9: 399. doi: 10.1186/1471-2105-9-39918817533
4. Kelder T, Conklin BR, Evelo CT, Pico AR, (2010) Finding the right questions: exploratory pathway analysis to enhance biological discovery in large datasets. PLoS Biol8. doi: 10.1371/journal.pbio.100047220824171
5. Kelder T, van Iersel MP, Hanspers K, Kutmon M, Conklin BR, et al. (2012) WikiPathways: building research communities on biological pathways. Nucleic Acids Res40: D1301–1307. doi: 10.1093/nar/gkr107422096230
6. Kutmon M, Riutta A, Nunes N, Hanspers K, Willighagen EL, et al. (2016) WikiPathways: capturing the full diversity of pathway knowledge. Nucleic Acids Research44: D488–D494. doi: 10.1093/nar/gkv102426481357
7. Maglott D, Ostell J, Pruitt KD, Tatusova T, (2011) Entrez gene: gene-centered information at NCBI. Nucleic Acids Research39: D52–D57. doi: 10.1093/nar/gkq123721115458
8. Yates A, Akanni W, Amode MR, Barrell D, Billis K, et al. (2016) Ensembl 2016. Nucleic Acids Research44: D710–D716. doi: 10.1093/nar/gkv115726687719
9. The UniProt Consortium (2015) UniProt: a hub for protein information. Nucleic Acids Research43: D204–D212. doi: 10.1093/nar/gku98925348405
10. Wishart DS, Jewison T, Guo AC, Wilson M, Knox C, et al. (2013) HMDB 3.0—The human metabolome database in 2013. Nucleic Acids Research41: D801–D807. doi: 10.1093/nar/gks106523161693
11. Pence HE, Williams A, (2010) ChemSpider: An online chemical information resource. J Chem Educ87: 1123–1124. doi: 10.1021/ed100697w
12. Kim S, Thiessen PA, Bolton EE, Chen J, Fu G, et al. (2016) PubChem substance and compound databases. Nucleic Acids Research44: D1202–D1213. doi: 10.1093/nar/gkv95126400175
13. Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, et al. (2014) The ChEMBL bioactivity database: an update. Nucleic Acids Research42: D1083–D1090. doi: 10.1093/nar/gkt103124214965
14. van Iersel MP, Pico AR, Kelder T, Gao J, Ho I, et al. (2010) The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC Bioinformatics11: 5. doi: 10.1186/1471-2105-11-520047655
15. Semantic web. URL http://www.w3.org/standards/semanticweb/.
16. Berners-Lee T, Fielding R, Irvine U, and LM. Uniform resource identifiers (uri): Generic syntax. URL http://www.faqs.org/rfcs/rfc2396.html.
17. Juty N, Le Novere N, Laibe C, (2012) Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Res40: D580–586. doi: 10.1093/nar/gkr109722140103
18. Miles A, Bechhofer S. Skos simple knowledge organization system reference. URL http://www.w3.org/TR/skos-reference/.
19. Piñero J, Queralt-Rosinach N, Bravo A, Deu-Pons J, Bauer-Mehren A, et al. (2015) DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes. Database2015: bav028+. doi: 10.1093/database/bav02825877637
20. Luciano JS, (2005) Pax of mind for pathway researchers. Drug Discov Today10: 937–942. doi: 10.1016/S1359-6446(05)03501-415993813
21. Le Novere N, Hucka M, Mi H, Moodie S, Schreiber F, et al. (2009) The Systems Biology Graphical Notation. Nat Biotechnol27: 735–741. doi: 10.1038/nbt0909-864d19668183
22. Kohn KW, Aladjem MI, Weinstein JN, Pommier Y, (2006) Molecular interaction maps of bioregulatory networks: a general rubric for systems biology. Mol Biol Cell17: 1–13. doi: 10.1091/mbc.E05-09-082416267266
23. Finney A, Hucka M, (2003) Systems biology markup language: Level 2 and beyond. Biochem Soc Trans31: 1472–1473. doi: 10.1042/bst031147214641091
24. Juty N, Ali R, Glont M, Keating S, Rodriguez N, et al. (2015) BioModels: Content, Features, Functionality and Use. CPT: Pharmacometrics & Systems Pharmacology.
25. OWL 2 Web Ontology Language Document Overview (Second Edition). URL http://www.w3.org/TR/owl2-overview/.
26. Luna A, Sunshine ML, van Iersel MP, Aladjem MI, Kohn KW, (2011) PathVisio-MIM: PathVisio plugin for creating and editing Molecular Interaction Maps (MIMs). Bioinformatics27: 2165–2166. doi: 10.1093/bioinformatics/btr33621636591
27. Ratnam J, Zdrazil B, Digles D, Cuadrado-Rodriguez E, Neefs JM, et al. (2014) The application of the open pharmacological concepts triple store (open PHACTS) to support drug discovery research. PLoS ONE9: e115460. doi: 10.1371/journal.pone.011546025522365
28. 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.
29. Prud x2019;Hommeaux E, Seaborne A, et al. (2008) SPARQL query language for RDF. W3C recommendation 15.
30. (2015). Help:WikiPathways Sparql queries. URL http://www.wikipathways.org/index.php/Help:WikiPathways_Sparql_queries.
31. van Hage WR, Kauppinen T, Davis C (2015) SPARQL Package for R.
32. Bohler A, Eijssen LM, van Iersel MP, Leemans C, Willighagen EL, et al. (2015) Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment. BMC Bioinformatics16: 267. doi: 10.1186/s12859-015-0708-826298294
33. Waagmeester A (2015). DifExInsullinSIgnalling.R. https://gist.github.com/andrawaag/6989c8c218862a912ef6.
34. Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, et al. (2011) Pathway commons, a web resource for biological pathway data. Nucleic Acids Research39: D685–D690. doi: 10.1093/nar/gkq103921071392
35. Waagmeester A (2015). BioSystems2RDF. https://github.com/andrawaag/BioSystems2RDF.
36. Williams AJ, Harland L, Groth P, Pettifer S, Chichester C, et al. (2012) Open PHACTS: semantic interoperability for drug discovery. Drug Discovery Today17: 1188–98. doi: 10.1016/j.drudis.2012.05.01622683805
37. Haupt C, Waagmeester A, Zimmermann M, Willighagen E (2013). Guidelines for exposing data as RDF in Open PHACTS. URL http://www.openphacts.org/specs/2013/WD-rdfguide-20131007/.
38. McBride B, (2002) Jena: a semantic web toolkit. Internet Computing, IEEE6: 55–59. doi: 10.1109/MIC.2002.1067737