NeXML: Rich, extensible, and verifiable representation of comparative data and metadata

Systematic Biology

Volumn 61, Issue 4, 2012, Pages 675-689

  Vos, Rutger A ^a   Balhoff, James P ^b,c   Caravas, Jason A ^d   Holder, Mark T ^e   Lapp, Hilmar ^b   Maddison, Wayne P ^f   Midford, Peter E ^b   Priyam, Anurag ^g   Sukumaran, Jeet ^e   Xia, Xuhua ^h   Stoltzfus, Arlin ⁱ  

^a NATURALIS BIODIVERSITY CENTER   (Netherlands)

^b NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

^c UNIVERSITY OF NORTH CAROLINA SCHOOL OF MEDICINE   (United States)

^d WAYNE STATE UNIVERSITY   (United States)

^e UNIVERSITY OF KANSAS   (United States)

^f UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^g INDIAN INSTITUTE OF TECHNOLOGY   (India)

^h UNIVERSITY OF OTTAWA   (Canada)

ⁱ NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

Author keywords

Data standards; evolutionary informatics; interoperability; phyloinformatics; semantic web; syntax format

Indexed keywords

ARTICLE; BIODIVERSITY; BIOLOGICAL MODEL; BIOLOGY; CLASSIFICATION; COMPUTER LANGUAGE; COMPUTER PROGRAM; EVALUATION; EVOLUTION; INFORMATION SCIENCE; PHYLOGENY; STANDARD;

BIODIVERSITY; BIOLOGICAL EVOLUTION; CLASSIFICATION; COMPUTATIONAL BIOLOGY; INFORMATICS; MODELS, BIOLOGICAL; PHYLOGENY; PROGRAMMING LANGUAGES; SOFTWARE;

EID: 84862498268     PISSN: 10635157     EISSN: 1076836X     Source Type: Journal    
DOI: 10.1093/sysbio/sys025     Document Type: Article

References (60)

1. Adida B., Birbeck M., McCarron S., Pemberton S. 2008. RDFa in XHTML: Syntax and Processing. Available from: http://www.w3.org/TR/rdfa-syntax/. [Wed Sep 21, 2011].
2. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., Davis A.P., Dolinski K., Dwight S.S., Eppig J.T., Harris M.A., Hill D.P., Issel-Tarver L., Kasarskis A., Lewis S., Matese J.C., Richardson J.E., Ringwald M., Rubin G.M., Sherlock G. 2000. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 25:25-29. (Pubitemid 30257031)
3. Balhoff J.P., Dahdul W.M., Kothari C.R., Lapp H., Lundberg J.G., Mabee P., Midford P.E., Westerfield M., Vision T.J. 2010. Phenex: ontological annotation of phenotypic diversity. PLoS One 5:e10500.
4. Beaman R.S., Cellinese N. 2010. The tree of life knowledge and information network. Available from: http://www.tolkin.org. [Wed Sep 21, 2011].
5. Beckett D. 2004. RDF/XML syntax specification (revised). W3C Recommendation. Available from: http://www.w3.org/TR/RECrdf-syntax/. [Wed Sep 28, 2011].
6. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. 2009. GenBank. Nucleic Acids Res. 37:D26-31.
7. Biron P.V., Malhotra A. 2004. XML schema part 2: datatypes second edition. W3C Recommendation. Available from: http://www.w3.org/TR/xmlschema-2/. [Wed Sep 21, 2011].
8. Bisby F.A. 2000. The quiet revolution: biodiversity informatics and the internet. Science. 289:2309-2312.
9. Brandes U., Eiglsperger M., Herman I., Himsolt M., Marshall M.S. 2002. GraphML progress report: structural layer proposal. In: Mutzel P., Junger M., Leipert S., editors. Proceedings of the 9th International Symposium on Graph Drawing (GD 2001); 2001 Sep. 23-26; Berlin/Heidelberg: Springer. p. 109-112.
10. Cardona G., Rossello F., Valiente G. 2008. Extended Newick: it is time for a standard representation of phylogenetic networks. BMC Bioinformatics 9:532.
11. Connelly T., Sharp P., Ausiello D., Bronner-Fraser M., Burke I., Eisen J., Janetos A., Karp R., Kim P., Lauffenburger D., Lidstrom M., LimW., McFall-Ngai M., Meyerowitz E., Yamamoto K. 2009. A new biology for the 21st century: ensuring the United States leads the coming biology revolution. Washington (DC): National Academies Press. p. 112.
12. Constable H., Guralnick R., Wieczorek J., Spencer C., Peterson A.T. 2010. VertNet: a new model for biodiversity data sharing. PLoS Biol. 8:e1000309.
13. Dahdul W.M., Balhoff J.P., Engeman J., Grande T., Hilton E.J., Kothari C., Lapp H., Lundberg J.G., Midford P.E., Vision T.J., Westerfield M., Mabee P.M. 2010a. Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature. PLoS One 5:e10708.
14. Dahdul W.M., Lundberg J.G., Midford P.E., Balhoff J.P., Lapp H., Vision T.J., Haendel M.A., Westerfield M., Mabee P.M. 2010b. The teleost anatomy ontology: anatomical representation for the genomics age. Syst. Biol. 59:369-383.
15. Drummond A.J., Rambaut A. 2007. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol. 7:214.
16. Fallside D.C., Walmsley P. 2004. XML schema part 0: primer second edition. W3C recommendation. Available from: http://www. w3.org/TR/xmlschema-0/. [Thu Sep 22, 2011].
17. Felsenstein J. 1989. PHYLIP-phylogeny inference package (version 3.2). Cladistics 5:164-166.
18. Felsenstein J. 2004. Inferring phylogenies. Sunderland (MA): Sinauer.
19. Gkoutos G.V., Green E.C.J., Mallon A.-M., Hancock J.M., Davidson D. 2004. Using ontologies to describe mouse phenotypes. Genome Biol. 6:R8.
20. Gopalan V., Qiu W.-G., Chen M.Z., Stoltzfus A. 2006. Nexplorer: phylogeny-based exploration of sequence family data. Bioinformatics 22:120-121. (Pubitemid 43057019)
21. Han M.V., Zmasek C.M. 2009. phyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 10:356.
22. Hladish T., Gopalan V., Liang C., Qiu W., Yang P., Stoltzfus A. 2007. Bio::NEXUS: a Perl API for the NEXUS format for comparative biological data. BMC Bioinformatics 8:191.
23. Hyam R. 2008. TDWG technical roadmap 2008. Available from: http://www.tdwg.org/fileadmin/subgroups/tag/TAG Roadmap 2008.pdf. [Wed Sep 21, 2011].
24. Johnson N.F. 2007. Biodiversity informatics. Annu. Rev. Entomol. 52:421-438. (Pubitemid 46133578)
25. Jordan G.E., Piel W.H. 2008. PhyloWidget: web-based visualizations for the tree of life. Bioinformatics 24:1641-1642. (Pubitemid 351966165)
26. Leary P.R., Remsen D.P., Norton C.N., Patterson D.J., Sarkar I.N. 2007. uBioRSS: tracking taxonomic literature using RSS. Bioinformatics 23:1434-1436. (Pubitemid 47050530)
27. Leebens-Mack J., Vision T.J., Brenner E., Bowers J.E., Cannon S., Clement M.J., Cunningham C.W., dePamphilis C., deSalle R., Doyle J.J., Eisen J.A., Gu X., Harshman J., Jansen R.K., Kellogg E.A., Koonin E.V., Mishler B.D., Philippe H., Pires J.C., Qiu Y.L., Rhee S.Y., Sjolander K., Soltis D.E., Soltis P.S., Stevenson D.W., Wall K., Warnow T., Zmasek C. 2006. Taking the first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis (MIAPA). Omics 10: 231-237. (Pubitemid 44298612)
28. Lewis P.O. 2003. NCL: a C++ class library for interpreting data files in NEXUS format. Bioinformatics 19:2330-2331. (Pubitemid 37483996)
29. Li H., Coghlan A., Ruan J., Coin L.J., Hrich J.-K., Osmotherly L., Li R., Liu T., Zhang Z., Bolund L., Wong G.K.-S., Zheng W., Dehal P., Wang J., Durbin R. 2006. TreeFam: a curated database of phylogenetic trees of animal gene families. Nucleic Acids Res. 34:D572-D580.
30. Maddison D.R., Maddison W.P. 2005. MacClade 4: analysis of phylogeny and character evolution. Version 4.08a. Available from: http://macclade.org/. [Thu Sep 22, 2011].
31. Maddison D.R., Schulz K.-S., MaddisonW.P. 2007. The tree of life web project. Zootaxa 1668:19-40.
32. Maddison D.R., Swofford D.L., Maddison W.P. 1997. NEXUS: an extensible file format for systematic information. Syst. Biol. 46: 590-621.
33. Maddison W.P., Maddison D.R. 2011. Mesquite: a modular system for evolutionary analysis. Version 2.74. Available from: http://mesquiteproject.org. [Wed Sep 21, 2011].
34. Matthews S.J., Sul S.-J., Williams T.L. 2010. A Novel Approach for Compressing Phylogenetic Trees . In: Borodovsky, M., Gogarten J., Przytycka T., Rajasekaran S., editors. Bioinformatics research and applications. Berlin (Germany): Springer. p. 113-124.
35. McEntire R., Karp P., Abernethy N., Benton D., Helt G., DeJongh M., Kent R., Kosky A., Lewis S., Hodnett D., Neumann E., Olken F., Pathak D., Tarczy-Hornoch P., Toldo L., Topaloglou T. 2000. An evaluation of ontology exchange languages for bioinformatics. Proc. Int. Conf. Intell. Syst. Mol. Biol. 8:239-250.
36. Miller M.A., Pfeiffer W., Schwarz T. 2010. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE). 2010. p. 1-8.
37. Moore A.J., McPeek M.A., Rausher M.D., Rieseberg L., Whitlock M.C. 2010. The need for archiving data in evolutionary biology. J. Evol. Biol. 23:659-660.
38. Mungall C.J., Gkoutos G.V., Smith C.L., Haendel M.A., Lewis S.E., Ashburner M. 2010. Integrating phenotype ontologies across multiple species. Genome Biol. 11:R2.
39. O'Leary M.A., Kaufman S.G. 2007 MorphoBank 2.5: web application for morphological phylogenetics and taxonomy. Available from: http://www.morphobank. org. [Wed Sep 21, 2011].
40. Page R.D.M. 2008. Biodiversity informatics: the challenge of linking data and the role of shared identifiers. Brief. Bioinform. 9: 345-354.
41. Parks D.H., Porter M., Churcher S., Wang S., Blouin C., Whalley J., Brooks S., Beiko R.G. 2009. GenGIS: a geospatial information system for genomic data. Genome Res. 19:1896-1904.
42. Piel W.H., Chan L., Dominus M.J., Ruan J., Vos R.A., Tannen V. 2009. TreeBASE v. 2: a database of phylogenetic knowledge. London: e-BioSphere.
43. Prosdocimi F., Chisham B., Pontelli E., Thompson J.D., Stoltzfus A. 2009. Initial implementation of a comparative data analysis ontology. Evol. Bioinform. Online 5:47-66.
44. Rausher M.D., McPeek M.A., Moore A.J., Rieseberg L., Whitlock M.C. 2010. Data archiving. Evolution 64:603-604.
45. Rice K.A., Donoghue M.J., Olmstead R.G. 1997. Analyzing large data sets: rbcL 500 revisited. Syst. Biol. 46:554-563. (Pubitemid 127386651)
46. Ronquist F., Huelsenbeck J.P. 2003. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572-1574. (Pubitemid 37038874)
47. Sanderson M.J., Boss D., Chen D., Cranston K.A., Wehe A. 2008. The PhyLoTA browser: processing GenBank for molecular phylogenetics research. Syst. Biol. 57:335-346. (Pubitemid 351882201)
48. Schmitt T., Messina D.N., Schreiber F., Sonnhammer E.L. 2011. SeqXML and OrthoXML: standards for sequence and orthology information. Brief. Bioinform. 12:485-488.
49. Sidlauskas B., Ganapathy G., Hazkani-Covo E., Jenkins K.P., Lapp H., McCall L.W., Price S., Scherle R., Spaeth P.A., Kidd D.M. 2010. Linking big: the continuing promise of evolutionary synthesis. Evolution 64:871-880.
50. Smits S.A., Ouverney C.C. 2010. jsPhyloSVG: a javascript library for visualizing interactive and vector-based phylogenetic trees on the web. PLoS One 5:e12267.
51. Stoesser G., Sterk P., Tuli M.A., Stoehr P.J., Cameron G.N. 1997. The EMBL nucleotide sequence database. Nucleic Acids Res. 25: 7-14.
52. Sukumaran J., Holder M.T. 2010. DendroPy: a Python libary for phylogenetic computing. Bioinformatics 26:1569-1571.
53. Swofford D.L. 2002. PAUP*: phylogenetic analysis using parsimony (and other methods), 4.0 beta. Sunderland (MA): Sinauer.
54. Taylor C.F., Field D., Sansone S.A., Aerts J., Apweiler R., Ashburner M., Ball C.A., Binz P.A., Bogue M., Booth T., Brazma A., Brinkman R.R., Michael Clark A., Deutsch E.W., Fiehn O., Fostel J., Ghazal P., Gibson F., Gray T., Grimes G., Hancock J.M., Hardy N.W., Hermjakob H., Julian R.K. Jr., Kane M., Kettner C., Kinsinger C., Kolker E., Kuiper M., Le Novere N., Leebens-Mack J., Lewis S.E., Lord P., Mallon A.M., Marthandan N., Masuya H., McNally R., Mehrle A., Morrison N., Orchard S., Quackenbush J., Reecy J.M., Robertson D.G., Rocca-Serra P., Rodriguez H., Rosenfelder H., Santoyo-Lopez J., Scheuermann R.H., Schober D., Smith B., Snape J., Stoeckert C.J. Jr., Tipton K., Sterk P., Untergasser A., Vandesompele J., Wiemann S. 2008. Promoting coherent minimum reporting guidelines for biological and biomedical investigations: the MIBBI project. Nat. Biotechnol 26:889-896.
55. Than C., Ruths D., Nakhleh L. 2008. PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 9:322.
56. Thompson H.S., Beech D., Maloney M., Mendelsohn N. 2004 XML schema part 1: structures second edition. W3C Recommendation. Available from: http://www.w3.org/TR/xmlschema-1/. [Wed Sep 21, 2011].
57. Whelan S., de Bakker P.I.W., Quevillon E., Rodriguez N., Goldman N. 2006. PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res. 34: D327-D331.
58. Whitlock M.C., McPeek M.A., Rausher M.D., Rieseberg L., Moore A.J. 2010. Data archiving. Am. Nat. 175: 145-146.
59. Xia X., Xie Z. 2001. DAMBE: software package for data analysis in molecular biology and evolution. J. Hered. 92: 371-373. (Pubitemid 32848767)
60. Zmasek C.M., Eddy S.R. 2001. ATV: display and manipulation of annotated phylogenetic trees. Bioinformatics 17: 383-384. (Pubitemid 32421939)