Biotea: RDFizing PubMed Central in support for the paper as an interface to the Web of Data

Journal of Biomedical Semantics

Volumn 4, Issue 1, 2013, Pages

  Garcia Castro, L Jael ^a   McLaughlin, C ^b   Garcia, A ^b  

^a UNIVERSITAT JAUME I   (Spain)

^b FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84923845958     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-4-S1-S5     Document Type: Article

References (51)

1. Swan A: Overview of scholarly communication. Open Access: Key Strategic, Technical and Economic Aspects. Edited by: Jacobs N: Chandos. 2006
2. Borgman CL: Scholarship in the Digital Age: Information, Infrastructure, and the Internet. 2007, Cambridge, MA, and London: MIT Press
3. D'Arcus B, Giasson F: Bibliographic Ontology Specification. 2009, [ http://bibliontology.com/specification ]
4. DCMI Usage Board: DCMI Metadata Terms. 2012, [ http://dublincore.org/documents/dcmi-terms/ ]
5. Weibel S: The Dublin core metadata initiative - The Frankfurt focus and the year 2000. Zeitschrift Fur Bibliothekswesen Und Bibliographie. 2000, 47 (1): 3-13.
6. The Friend of a Friend (FOAF) project. [ http://www.foaf-project.org/ ]
7. Brickley D, Miller L: FOAF Vocabulary Specification 0.98. 2010, [ http://xmlns.com/foaf/spec/ ]
8. IDEAlliance: Publishing Requirements for Industry Standard Metadata. [ http://www.idealliance.org/specifications/prism/ ]
9. Carpenter P: Nature Publishing Group releases linked data platform. 2012, [ http://www.nature.com/press_releases/linkeddata.html ]
10. Elsevier BV: Elsevier Developers. [ http://www.developers.elsevier.com/ ]
11. Kruk SR, Woroniecki T, Gzella A, Dabrowski M: JeromeDL - a Semantic Digital Library. International Semantic Web Conference - Semantic Web Challenge. 2007, Busan, Korea
12. Kruk S, Haslhofer B, Piotr P, Westerski A, Woroniecki T: The Role of Ontologies in Semantic Digital Libraries. European Networked Knowledge Organization Systems (NKOS) Workshop. 2006, Alicante, Spain
13. BRICKS Project: Building Resources for Integrated Cultural Knowledge Services. [ http://www.brickscommunity.org/ ]
14. Ciccarese P, Ocana M, Clark T: DOMEO: a web-based tool for semantic annotation of online documents. Bio-Ontologies. 2011, Vienna, Austria
15. Garcia-Castro A, Labarga A, Garcia L, Giraldo O, Montaña C, Bateman JA: Semantic Web and Social Web heading towards Living Documents in the Life Sciences. Web Semantics: Science, Services and Agents on the World Wide Web. 2010, 8 (2-3): 155-162. 10.1016/j.websem.2010.03.006.
16. Attwood TK, Kell DB, Mcdermott P, Marsh J, Pettifer SR, Thorne D: Utopia Documents and The Semantic Biochemical Journal experiment. EMBNet News. 2010, 15 (4):
17. U.S. National Institutes of Health's National Library of Medicine: PubMed Central. [ http://www.ncbi.nlm.nih.gov/pmc/ ]
18. Belleau F, Nolin M-A, Tourigny N, Rigault P, Morissette J: Bio2RDF: Towards a mashup to build bioinformatics knowledge systems. Journal of Biomedical Informatics. 2008, 41 (5): 706-716. 10.1016/j.jbi.2008.03.004.
19. Callahan A, Cruz-Toledo J, Ansell P, Klassen D, Tumarello G, Dumontier M: Improved dataset coverage and interoperability with Bio2RDF Release 2. Semantic Web Applications and Tools for Life Sciences; Paris, France. 2012
20. Shoton D, Peroni S: DoCO, the Document Components Ontology. 2011, [ http://purl.org/spar/doco ]
21. Ciccarese P, Ocana M, Garcia Castro L, Das S, Clark T: An open annotation ontology for science on web 3.0. Journal of Biomedical Semantics. 2011, 2 (Suppl 2): S4-10.1186/2041-1480-2-S2-S4.
22. Berners-Lee T: Design issues: Linked data. 2009, [ http://www.w3.org/DesignIssues/LinkedData ]
23. Koch J, Velasco CA, Ackermann P: Representing Content in RDF 1.0. 2011, [ http://www.w3.org/TR/Content-in-RDF10/ ]
24. Kirsch H, Rebholz-Schuhmann D: Distributed modules for text annotation and IE applied to the biomedical domain. International Joint Workshop on Natural Language Processing in Biomedicine and its Applications; Geneva, Switzerland. 2004, Association for Computational Linguistics, 50-53.
25. Rebholz-Schuhmann D, Arregui M, Gaudan M, Kirsch H, Jimeno A: Text processing through Web Services: Calling Whatizit. Bioinformatics. 2007, 24 (2): 296-298.
26. Jonquet C, Shah NH, Youn CH, Callendar C, Storey M-A, Musen MA: NCBO Annotator: Semantic Annotation of Biomedical Data. International Semantic Web Conference, Poster and Demo session. 2009
27. Juty N, Le Novère N, Laibe C: Identifiers.org and MIRIAM Registry: community resources to provide persistent identification. Nucleic Acids Research. 2012, 40 (D1): D580-D586. 10.1093/nar/gkr1097.
28. The JQuery Foundation: JQuery. [ http://jquery.com ]
29. Gómez J, Jiménez R: Biojs, a library of JavaScript components to represent biological data. Bioinformatics. 2013, [ http://code.google.com/p/biojs/ ]
30. Huss JW, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, Su AI: The Gene Wiki: community intelligence applied to human gene annotation. Nucleic Acids Research. 38 (suppl 1): D633-D639.
31. Magrane M, UniProt Consortium: UniProt Knowledgebase: a hub of integrated protein data. Database. 2011
32. Pafilis E, O'Donoghue SI, Jensen LJ, Horn H, Kuhn M, Brown NP, Schneider R: Reflect: augmented browsing for the life scientist. Nat Biotech. 2009, 27 (6): 508-510. 10.1038/nbt0609-508.
33. SameAs - Interlinking the web of data. [ http://sameas.org ]
34. Saha B, Hoch A, Khuller S, Raschid L, Zhang X-N: Dense subgraphs with restrictions and applications to gene annotation graphs. 14th Annual international conference on Research in Computational Molecular Biology. 2010, Lisbon, Portugal. Springer-Verlag
35. Thor A, Anderson P, Raschid L, Navlakha S, Saha B, Khuller S, Zhang X-N: Link prediction for annotation graphs using graph summarization. International Conference on the Semantic Web. 2011, Bonn, Germany. Springer-Verlag
36. Srinivasan P, Libbus B, Sehgal AK: Mining MEDLINE: Postulating a Beneficial Role for Curcumin Longa in Retinal Diseases. Workshop BioLINK, Linking Biological Literature, Ontologies and Databases at HLT NAACL. 2004
37. Hummon NP, Dereian P: Connectivity in a citation network: The development of DNA theory. Social Networks. 1989, 11 (1): 39-63. 10.1016/0378-8733(89)90017-8.
38. Boyack KW, Newman D, Duhon RJ, Klavans R, Patek M, Biberstine JR, Schijvenaars B, Skupin A, Ma N, Börner K: Clustering More than Two Million Biomedical Publications: Comparing the Accuracies of Nine Text-Based Similarity Approaches. PLoS ONE. 1802, 6 (3): e9-
39. Lewis J, Ossowski S, Hicks J, Errami M, Garner HR: Text similarity: an alternative way to search MEDLINE. Bioinformatics. 2006, 22 (18): 2298-2304. 10.1093/bioinformatics/btl388.
40. Medline Fact Sheet. [ http://www.nlm.nih.gov/pubs/factsheets/medline.html ]
41. Yamamoto Y, Takagi T: Biomedical knowledge navigation by literature clustering. Journal of Biomedical Informatics. 2007, 40 (2): 114-130. 10.1016/j.jbi.2006.07.004.
42. Theodosiou T, Darzentas N, Angelis L, Ouzounis CA: PuReD-MCL: a graph-based PubMed document clustering methodology. Bioinformatics. 2008, 24 (17): 1935-1941. 10.1093/bioinformatics/btn318.
43. Belhajjame K, Cheney J, Corsar D, Garijo D, Soiland-Reyes S, Zednik S, Zhao J: The PROV ontology. 2012, [ http://www.w3.org/TR/prov-o/ ]
44. Brickley D, Guha RV: RDF Vocabulary Description Language 1.0: RDF Schema. 2004, World Wide Web Consortium W3C, http://www.w3.org/TR/rdf-schema/
45. Monq.jfa. [ http://freecode.com/projects/monq_jfa ]
46. Dai M, Shah NH, Xuan W, Musen MA, Watson SJ, Athey B, Meng F: An Efficient Solution for Mapping Free Text to Ontology Terms. AMIA Summit on Translational Bioinformatics. 2008, San Francisco, CA, U.S.A.
47. Völkel M: RDFReactor - From Ontologies to Programatic Data Access. Jena User Conference:. 2006, Bristol, UK
48. Mendeley, reference manager and academic social network. [ http://www.mendeley.com/ ]
49. CrossRef. [ http://www.crossref.org/ ]
50. Sayers E: E-utilities Quick Start. [ http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi ]
51. OBO Foundry: OBO Foundry Identifier Policy. [ http://obofoundry.org/id-policy.shtml ]