FALDO: A semantic standard for describing the location of nucleotide and protein feature annotation

Journal of Biomedical Semantics

Volumn 7, Issue 1, 2016, Pages

  Bolleman, Jerven T ^a   Mungall, Christopher J ^b   Strozzi, Francesco ^c   Baran, Joachim ^d   Dumontier, Michel ^e   Bonnal, Raoul J P ^f   Buels, Robert ^g   Hoehndorf, Robert ^h   Fujisawa, Takatomo ⁱ   Katayama, Toshiaki ⁱ   Cock, Peter J A ^j  

^a SWISS INSTITUTE OF BIOINFORMATICS   (Switzerland)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c PARCO TECNOLOGICO PADANO   (Italy)

^d CODAMONO ^*  (Canada)

^e STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f Istituto Nazionale di Genetica Molecolare   (Italy)

^g UNIVERSITY OF CALIFORNIA   (United States)

^h Department of Computer Science ^*  (United Kingdom)

ⁱ NATIONAL INSTITUTE OF GENETICS   (Japan)

^j SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

more..

Author keywords

Annotation; Data integration; RDF; Semantic Web; Sequence feature; Sequence ontology; SPARQL; Standardisation

Indexed keywords

NUCLEOTIDE; PROTEIN;

BIOLOGICAL ONTOLOGY; BOOK; CHEMISTRY; FUZZY LOGIC; GENETIC DATABASE; GENETICS; HUMAN; METABOLISM; MOLECULAR GENETICS; PROTEIN DATABASE; SEMANTICS; STANDARDS;

BIOLOGICAL ONTOLOGIES; DATABASES, GENETIC; DATABASES, PROTEIN; FUZZY LOGIC; HUMANS; MOLECULAR SEQUENCE ANNOTATION; NUCLEOTIDES; PROTEINS; REFERENCE BOOKS; SEMANTICS;

EID: 84973617096     PISSN: None     EISSN: 20411480     Source Type: Journal    
DOI: 10.1186/s13326-016-0067-z     Document Type: Article

References (30)

1. Sanger F. The terminal peptides of insulin. Biochem J. 1949; 45(5):563-74.
2. Dayhoff MO, Eck RV, Foundation NBR. Atlas of Protein Sequence and Structure. Silver Spring (Maryland): National Biomedical Research Foundation; 1965.
3. Reese MG, Moore B, Batchelor C, Salas F, Cunningham F, Marth GT, Stein L, Flicek P, Yandell M, Eilbeck K. A standard variation file format for human genome sequences. Genome Biol. 2010; 11(R88). doi: 10.1186/gb-2010-11-8-r88.
4. Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JGR, Korf I, Lapp H, Lehväslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E. The Bioperl toolkit: Perl modules for the life sciences. Genome Res. 2002; 12(10):1611-8. doi: 10.1101/gr.361602.
5. Cock PJA, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJL. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics. 2009; 25(11):1422-3. doi: 10.1093/bioinformatics/btp163.
6. Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T. BioRuby: bioinformatics software for the Ruby programming language. Bioinformatics. 2010; 26(20):2617-9. doi: 10.1093/bioinformatics/btq475.
7. Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S. BioJava: an open-source framework for bioinformatics in 2012. Bioinformatics. 2012; 28(20):2693-5. doi: 10.1093/bioinformatics/bts494.
8. Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T. The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J Biomed Semantics. 2010; 1:8. doi: 10.1186/2041-1480-1-8.
9. Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernández JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T. The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J Biomed Semantics. 2011; 2:6. doi: 10.1186/2041-1480-2-4.
10. Katayama T, Wilkinson MD, Micklem G, Kawashima S, Yamaguchi A, Nakao M, Yamamoto Y, Okamoto S, Oouchida K, Chun HW, Aerts J, Afzal H, Antezana E, Arakawa K, Aranda B, Belleau F, Bolleman J, Bonnal RJP, Chapman B, Cock PJA, Eriksson T, Gordon PMK, Goto N, Hayashi K, Horn H, Ishiwata R, Kaminuma E, Kasprzyk A, Kawaji H, Kido N, Kim YJ, Kinjo AR, Konishi F, Kwon KH, Labarga A, Lamprecht AL, Lin Y, Lindenbaum P, McCarthy L, Morita H, Murakami K, Nagao K, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Ono K, Oshita K, Park KJ, Prins P, Saito TL, Samwald M, Satagopam VP, Shigemoto Y, Smith R, Splendiani A, Sugawara H, Taylor J, Vos RA, Withers D, Yamasaki C, Zmasek CM, Kawamoto S, Okubo K, Asai K, Takagi T. The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies. J Biomed Semantics. 2013; 4:6. doi: 10.1186/2041-1480-4-6.
11. Katayama T, Wilkinson MD, Aoki-Kinoshita KF, Kawashima S, Yamamoto Y, Yamaguchi A, Okamoto S, Kawano S, Kim JD, Wang Y, Wu H, Kano Y, Ono H, Bono H, Kocbek S, Aerts J, Akune Y, Antezana E, Arakawa K, Aranda B, Baran J, Bolleman J, Bonnal RJP, Buttigieg PL, Campbell MP, Chen Y-A, Chiba H, Cock PJA, Cohen KB, Constantin A, Duck G, Dumontier M, Fujisawa T, Fujiwara T, Goto N, Hoehndorf R, Igarashi Y, Itaya H, Ito M, Iwasaki W, Kalaš M, Katoda T, Kim T, Kokubu A, Komiyama Y, Kotera M, Laibe C, Lapp H, Lütteke T, Marshall MS, Mori T, Mori H, Morita M, Murakami K, Nakao M, Narimatsu H, Nishide H, Nishimura Y, Nystrom-Persson J, Ogishima S, Okamura Y, Okuda S, Oshita K, Packer NH, Prins P, Ranzinger R, Rocca-Serra P, Sansone S, Sawaki H, Shin SH, Splendiani A, Strozzi F, Tadaka S, Toukach P, Uchiyama I, Umezaki M, Vos R, Whetzel PL, Yamada I, Yamasaki C, Yamashita R, York WS, Zmasek CM, Kawamoto S, Takagi T. Biohackathon series in 2011 and 2012: penetration of ontology and Linked Data in life science domains. J Biomed Semantics. 2014; 5:5. doi: 10.1186/2041-1480-5-5.
12. The UniProt Consortium. Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res. 2013; 41(D1):43-7. doi: 10.1093/nar/gks1068 http://nar.oxfordjournals.org/content/41/D1/D43.full.pdf+html.
13. Ogasawara O, Mashima J, Kodama Y, Kaminuma E, Nakamura Y, Okubo K, Takagi T. Ddbj new system and service refactoring. Nucleic Acids Res. 2013; 41(D1):25-9. doi: 10.1093/nar/gks1152. http://nar.oxfordjournals.org/content/41/D1/D25.full.pdf+html.
14. Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. Genbank. Nucleic Acids Res. 2013; 41(D1):36-42. doi: 10.1093/nar/gks1195. http://nar.oxfordjournals.org/content/41/D1/D36.full.pdf+html.
15. Cochrane G, Alako B, Amid C, Bower L, Cerdeño-Tárraga A, Cleland I, Gibson R, Goodgame N, Jang M, Kay S, Leinonen R, Lin X, Lopez R, McWilliam H, Oisel A, Pakseresht N, Pallreddy S, Park Y, Plaister S, Radhakrishnan R, Rivière S, Rossello M, Senf A, Silvester N, Smirnov D, ten Hoopen P, Toribio A, Vaughan D, Zalunin V. Facing growth in the European Nucleotide Archive. Nucleic Acids Res. 2013; 41(D1):30-5. doi: 10.1093/nar/gks1175. http://nar.oxfordjournals.org/content/41/D1/D30.full.pdf+html.
16. Toukach PV. Bacterial carbohydrate structure database 3: Principles and realization. J Chem Inform Modeling. 2011; 51(1):159-70. doi: 10.1021/ci100150d. http://pubs.acs.org/doi/pdf/10.1021/ci100150d.
17. Ranzinger R, Herget S, von der Lieth C-W, Frank M. GlycomeDB - a unified database for carbohydrate structures. Nucleic Acids Res. 2011; 39(suppl 1):373-6. doi: 10.1093/nar/gkq1014. http://nar.oxfordjournals.org/content/39/suppl_1/D373.full.pdf+html.
18. Lütteke T, Bohne-Lang A, Loss A, Goetz T, Frank M, von der Lieth C-W. Glycosciences.de: an internet portal to support glycomics and glycobiology research. Glycobiology. 2006; 16(5):71-81. doi: 10.1093/glycob/cwj049. http://glycob.oxfordjournals.org/content/16/5/71R.full.pdf+html.
19. Akune Y, Hosoda M, Kaiya S, Shinmachi D, Aoki-Kinoshita KF. The RINGS resource for glycome informatics analysis and data mining on the web. OMICS: J Integrative Biol. 2010; 14(4):475-86. doi: http://dx.doi.org/10.1089/omi.2009.0129.
20. Campbell MP, Peterson R, Mariethoz J, Gasteiger E, Akune Y, Aoki-Kinoshita KF, Lisacek F, Packer NH. Unicarbkb: Building a knowledge platform for glycoproteomics. Underconsideration NAR Databases. 2014. doi: 10.1093/nar/gkt1128.
21. 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 Biol. 2005; 6(5):44. doi: 10.1186/gb-2005-6-5-r44.
22. Vakatov D E. Biological sequence data model. Technical report, NCBI. 2013. http://www.ncbi.nlm.nih.gov/toolkit/doc/book/ch_datamod/#ch_datamod.Locations_on_Biologi.
23. Le Hors A, Solbrig H, Eric Prud'hommeaux. Rdf validation workshop report, practical assurances for quality rdf data. Technical report, W3C. 2013. http://www.w3.org/2012/12/rdf-val/report.
24. Baran J, Durgahee BSB, Eilbeck K, Antezana E, Hoehndorf R, Dumontier M. GFVO: the Genomic Feature and Variation Ontology. 2015. PeerJ3:e933. https://doi.org/10.7717/peerj.933.
25. Skinner ME, Uzilov AV, Stein LD, Mungall CJ, Holmes IH. JBrowse: A next-generation genome browser. Genome Res. 2009; 19:1630-8. doi: 10.1101/gr.094607.109.
26. Devisscher M, De Meyer T, Van Criekinge W, Dawyndt P. An ontology based query engine for querying biological sequences. EMBnet J. 2013; 19(B):51-5.
27. Mungall CJ, Emmert DB, The FlyBase Consortium. A Chado case study: an ontology-based modular schema for representing genome-associated biological information. Bioinformatics. 2007; 23(13):337-46. doi: 10.1093/bioinformatics/btm189. http://bioinformatics.oxfordjournals.org/content/23/13/i337.full.pdf+html.
28. Alekseyenko AV, Lee CJ. Nested containment list (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases. Bioinformatics. 647. 2007. doi: 10.1093/bioinformatics/btl647.
29. Beckett D, Berners-Lee T, Prud'hommeaux E, Carothers G. Rdf 1.1 turtle - terse rdf triple language. Technical report, W3C. 2014. http://www.w3.org/TR/turtle/.
30. Sporny M, Kellogg G, Lanthaler M. Json-ld 1.0 - a json-based serialization for linked data. Technical report, W3C. 2014. http://www.w3.org/TR/json-ld/.