Representing annotation compositionality and provenance for the Semantic Web

Journal of Biomedical Semantics

Volumn 4, Issue 1, 2013, Pages

  Livingston, Kevin M ^a   Bada, Michael ^a   Hunter, Lawrence E ^a   Verspoor, Karin ^b,c  

^a UNIVERSITY OF COLORADO   (United States)

^b CSIRO   (Australia)

^c UNIVERSITY OF MELBOURNE   (Australia)

Author keywords

Annotation; Conceptual data modeling; Markup; Ontology; OWL; Provenance; RDF

Indexed keywords

EID: 84978174587     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/2041-1480-4-38     Document Type: Article

References (61)

1. Huang DW, Sherman BT, Lempicki RA: Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 2009, 37 (1): 1-13. 10.1093/nar/gkn923.
2. Aronson AR, Bodenreider O, Chang HF, Humphrey SM, Mork JG, Nelson SJ, Rindflesch TC, Wilbur WJ: The NLM indexing initiative. Proceedings American Medical Informatics Association 2000 Annual Symposium. 2000, American Medical Informatics Association, 17-21.
3. Hunter J, Cole T, Sanderson R, Van de Sompel H: The open annotation collaboration: a data model to support sharing and interoperability of scholarly annotations. Digital Humanities 2010: Conference Abstracts. Digital Humanities 2010. Edited by: Pierazzo E. 2010, London, United Kingdom, (175-178).?7-10 July 2010
4. 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.
5. Sahoo SS, Sheth A, Henson C: Semantic provenance for eScience: managing the deluge of scientific data. Internet Computing, IEEE. 2008, 12 (4): 46-54.
6. Zhao J, Sahoo SS, Missier P, Sheth A, Goble C: Extending semantic provenance into the web of data. Internet Computing, IEEE. 2011, 15 (1): 40-48.
7. Gessler DDG, Joslyn C, Verspoor K: A posteriori ontology engineering for data-driven science. Data Intensive Science. Edited by: Critchlow T, Dam KK. 2013, Boca Raton, FL: Taylor Francis CRC Press
8. Bada M, Livingston K, Hunter L: From text to knowledge: toward systematic composition of complex representations. Deep Knowledge Representation Challenge Workshop. 2011, Banff, Alberta, Canada: The Sixth International Conference on Knowledge Capture (K-CAP)
9. Dublin Core Metadata Initiative. http://dublincore.org
10. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ, et al: The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol. 2007, 25 (11): 1251-1255. 10.1038/nbt1346.
11. Coulet A, Shah NH, Garten Y, Musen M, Altman RB: Using text to build semantic networks for pharmacogenomics. J Biomed Inform. 2010, 43 (6): 1009-1019. 10.1016/j.jbi.2010.08.005.
12. Liu H, Komandur R, Verspoor K: From graphs to events: a subgraph matching approach for information extraction from biomedical text. BioNLP Shared Task 2011 Workshop. 2011, Stroudsburg, PA, USA: Association for Computational Linguistics, 164-172.
13. De Marneffe MC, Manning CD: The Stanford typed dependencies representation. COLING'08 Workshop on CrossFramework and Cross-Domain Parser Evaluation. 2008, Stroudsburg, PA: Association for Computational Linguistics, 1-8.
14. Verspoor KM, Cohen KB: Natural Language Processing. Encyclopedia of Systems Biology. Edited by: Dubitsky W, Wolkenhauer O, Yokota H, Cho K-H. 2013, New York: Springer
15. Marcus M, Santorini B, Marcinkiewicz MA: Building a large annotated corpus of English: the Penn treebank. Computational Linguistics. 1993, 19 (2): 313-330.
16. Bada M, Eckert M, Evans D, Garcia K, Shipley K, Sitnikov D, Baumgartner WA, Bretonnel Cohen K, Verspoor K, Blake JA, Hunter LE: Concept annotation in the CRAFT corpus. BMC Bioinformatics. 2012, 13: 161-10.1186/1471-2105-13-161.
17. Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S: InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res. 2012, 40 (D1): D306-D312. 10.1093/nar/gkr948.
18. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT: Gene ontology: tool for the unification of biology. Nat Genet. 2000, 25 (1): 25-10.1038/75556.
19. Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H: The protein ontology: a structured representation of protein forms and complexes. Nucleic Acids Res. 2011, 39 (suppl 1): D539-
20. Carroll JJ, Bizer C, Hayes P, Stickler P: Named graphs, provenance and trust. Internet Computing, IEEE (Volume:15, Issue: 1). 2011, ACM, 40-48.
21. Consortium TU: Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2012, 40 (D1): D71-D75.
22. Livingston KM, Johnson HL, Verspoor K, Hunter LE: Leveraging gene ontology annotations to improve a memory-based language understanding system. IEEE Internet Computing - INTERNET. 2010, 40-45.
23. Livingston KM, Bada M, Hunter L, Verspoor KM: An ontology of annotation content structure and provenance. Proc Intelligent Systems in Molecular Biology: Bio-ontologies SIG. 2011
24. Livingston KM: Language Understanding by Reference Resolution in Episodic Memory. 2009, Evanston, IL: Northwestern University
25. Verspoor K, Bretonnel Cohen K, Lanfranchi A, Warner C, Johnson HL, Roeder C, Choi JD, Funk C, Malenkiy Y, Eckert M, Xue N, Baumgartner WA, Bada M, Palmer M, Hunter LE: A corpus of full-text journal articles is a robust evaluation tool for revealing differences in performance of biomedical natural language processing tools. BMC Bioinformatics. 2012, 13: 207-10.1186/1471-2105-13-207.
26. Meyer LR, Zweig AS, Hinrichs AS, Karolchik D, Kuhn RM, Wong M, Sloan CA, Rosenbloom KR, Roe G, Rhead B, et al: The UCSC genome browser database: extensions and updates 2013. Nucleic Acids Res. 2013, 41 (D1): D64-D69. 10.1093/nar/gks1048.
27. Sherry ST, Ward M-H, Kholodov M, Baker J, Phan L, Smigielski EM, Sirotkin K: dbSNP: the NCBI database of genetic variation. Nucleic Acids Res. 2001, 29 (1): 308-311. 10.1093/nar/29.1.308.
28. Forbes SA, Bhamra G, Bamford S, Dawson E, Kok C, Clements J, Menzies A, Teague JW, Futreal PA, Stratton MR: The Catalogue of Somatic Mutations in Cancer (COSMIC). 2008, In: Current Protocols in Human Genetics. John Wiley & Sons, Inc.
29. Amberger J, Bocchini CA, Scott AF, Hamosh A: McKusick's Online Mendelian Inheritance in Man (OMIM®). Nucleic Acids Res. 2009, 37 (suppl 1): D793-D796.
30. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, Collins FS, Manolio TA: Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci. 2009, 106 (23): 9362-9367. 10.1073/pnas.0903103106.
31. Chan J, Kishore R, Sternberg P, Van Auken K: The gene ontology: enhancements for 2011. Nucleic Acids Res. 2012, 40 (D1): D559-D564.
32. Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST: The variant call format and VCFtools. Bioinformatics. 2012, 27 (15): 2156-2158.
33. Belleau F, Nolin MA, 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.
34. ISO: ISO 24612:2012 language resource management -- linguistic annotation framework (LAF). 2012, http://shop.bsigroup.com/ProductDetail/?pid=000000000030107266
35. Ferrucci D, Lally A, Verspoor K, Nyberg E: Unstructured Information Management Architecture (UIMA) Version 1.0, technical standard. OASIS, Organization for the Advancement of Structured Information Standards. 2009, http://docs.oasis-open.org/uima/v1.0/uima-v1.0.html
36. Ferrucci D, Lally A: UIMA: an architectural approach to unstructured information processing in the corporate research environment. Nat Lang Eng. 2004, 10 (3/4): 327-348.
37. Riesbeck CK, Martin C: Direct memory access parsing. Yale University Report. 1985, 354: 1-40.
38. Riesbeck CK: From conceptual analyzer to direct memory access parsing: an overview. Advances in Cognitive Science, Volume 1. Edited by: Sharkey NE. 1986, Chichester, UK: Ellis Horwood, 236-258.
39. Hunter L, Lu Z, Firby JWAB, Ogren PV, Cohen KB, Johnson HL: OpenDMAP: An open-source, ontology-driven concept analysis engine, with applications to capturing knowledge regarding protein transport, protein interactions and cell-specific gene expression. BMC Bioinformatics. 2008, 9 (78): 1-11.
40. Phillips PC: Epistasis - the essential role of gene interactions in the structure and evolution of genetic systems. Nat Rev Genet. 2008, 9 (11): 855-867. 10.1038/nrg2452.
41. Wan X, Yang C, Yang Q, Zhao H, Yu W: The complete compositional epistasis detection in genome-wide association studies. BMC Genet. 2013, 14 (1): 7-10.1186/1471-2156-14-7.
42. Goudey B, Rawlinson D, Wang Q, Shi F, Ferra H, Campbell R, Stern L, Inouye M, Ong CS, Kowalczyk A: GWIS - model-free, fast and exhaustive search for epistatic interactions in case-control GWAS. BMC Genomics. 2013, 14 (Suppl 3): S10-10.1186/1471-2164-14-S3-S10.
43. Mons B, Van Haagen H, Chichester C, Hoen PB, Den Dunnen JT, Van Ommen G, Van Mulligen E, Singh B, Hooft R, Roos M, et al: The value of data. Nat Genet. 2011, 43 (4): 281-283. 10.1038/ng0411-281.
44. Groth P, Gibson A, Velterop J: The anatomy of a nano-publication. Information Services and Use. 2010, 30: 51-56.
45. Ding L, Finin T, Peng Y, Da Silva PP, Deborah L: Tracking RDF Graph Provenance using RDF Molecules, 2005, Proceedings of the Fourth International Semantic Web Conference. 2005
46. Hill D, Smith B, McAndrews-Hill M, Blake J: Gene ontology annotations: what they mean and where they come from. BMC Bioinformatics. 2008, 9 (Suppl 5): S2-10.1186/1471-2105-9-S5-S2.
47. Ide N, Suderman K: GrAF: A graph-based format for linguistic annotations. Linguistic Annotation Workshop at ACL 2007. 2007, Prague: Association for Computational Linguistics
48. Cassidy S: Realisation of LAF in the DADA annotation server. Fifth Joint ISO-ACL/SIGSEM Workshop on Interoperable Semantic Annotation (ISA-5). 2010, Hong Kong
49. Chiarcos C: POWLA: Modeling linguistic corpora in OWL/DL. The Semantic Web: Research and Applications. 2012, Berlin, Germany: Springer, 225-239.
50. Verspoor KM, Livingston KM: Towards adaptation of linguistic annotation to scholarly annotation formalisms on the semantic web. The Sixth Linguistic Annotation Worshop (LAW VI). 2012, Jeju, Republic of Korea: Association for Computational Linguistics
51. Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M: The sequence ontology: a tool for the unification of genome annotations. Genome biology. 2005, 6 (5): R44-10.1186/gb-2005-6-5-r44.
52. Sahoo SS, Bodenreider O, Hitzler P, Sheth A, Thirunarayan K: Provenance Context Entity (PaCE): Scalable provenance tracking for scientific RDF data. Scientific and Statistical Database Management. 2010, Berlin, Germany: Springer-Verlag, 461-470.
53. Flouris G, Fundulaki I, Pediaditis P, Theoharis Y, Christophides V: Coloring RDF triples to capture provenance. The Semantic Web-ISWC 2009. 2009, Berlin, Germany: Springer-Verlag, 196-212.
54. Patrinos GP, Cooper DN, Van Mulligen E, Gkantouna V, Tzimas G, Tatum Z, Schultes E, Roos M, Mons B: Microattribution and nanopublication as means to incentivize the placement of human genome variation data into the public domain. Hum Mutat. 2012, 33 (11): 1503-1512. 10.1002/humu.22144.
55. Da Silva PP, McGuinness DL, Fikes R: A proof markup language for semantic web services. Inf Syst. 2006, 31 (4-5): 381-395.
56. Hartig O: Provenance information in the web of data. Linked Data on the Web Workshop (LDOW). 2009, Madrid, Spain
57. Provenance and Annotation of Data -International Provenance and Annotation Workshop, IPAW 2006, volume 4145 of Lecture Notes in Computer Science, May. Edited by: Moreau L, Foster I. 2006, Berlin, Germany: Springer-Verlag
58. Groth P: First OPM workshop minutes. Information Science Institute, USC (July 2008). 2008, http://twiki.ipaw.info/bin/view/Challenge/FirstOPMWorkshopMinutes
59. Moreau L, Clifford B, Freire J, Futrelle J, Gil Y, Groth P, Kwasnikowska N, Miles S, Missier P, Myers j: The open provenance model core specification (v1. 1). Futur Gener Comput Syst. 2011, 27 (6): 743-756. 10.1016/j.future.2010.07.005.
60. PROV. http://www.w3.org/2011/prov/wiki/Main_Page
61. PROV-O. http://www.w3.org/TR/2012/WD-prov-o-20120503/