Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

BMC Bioinformatics

Volumn 14, Issue , 2013, Pages

  Stoltzfus, Arlin ^a   Lapp, Hilmar ^b   Matasci, Naim ^c   Deus, Helena ^d   Sidlauskas, Brian ^e   Zmasek, Christian M ^f   Vaidya, Gaurav ^g   Pontelli, Enrico ^h   Cranston, Karen ^b   Vos, Rutger ⁱ   Webb, Campbell O ^j   Harmon, Luke J ^k   Pirrung, Megan ^l   O'Meara, Brian ^m   Pennell, Matthew W ^k   Mirarab, Siavash ⁿ   Rosenberg, Michael S ^o   Balhoff, James P ^b   Bik, Holly M ^p   Heath, Tracy A ^q   Midford, Peter E ^b   Brown, Joseph W ^k   McTavish, Emily Jane ^r   Sukumaran, Jeet ^s   Westneat, Mark ^t   Alfaro, Michael E ^u   Steele, Aaron ^q   Jordan, Greg ^v   more..

^a NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY   (United States)

^b NATIONAL EVOLUTIONARY SYNTHESIS CENTER   (United States)

^c UNIVERSITY OF ARIZONA   (United States)

^d NATIONAL UNIVERSITY OF IRELAND   (Ireland)

^e OREGON STATE UNIVERSITY   (United States)

^f BURNHAM INSTITUTE   (United States)

^g UNIVERSITY OF COLORADO   (United States)

^h New Mexico State University   (United States)

ⁱ NATURALIS BIODIVERSITY CENTER   (Netherlands)

^j HARVARD UNIVERSITY   (United States)

^k UNIVERSITY OF IDAHO   (United States)

^l UNIVERSITY OF COLORADO   (United States)

^m UNIVERSITY OF TENNESSEE   (United States)

ⁿ University of Texas at Austin   (United States)

^o ARIZONA STATE UNIVERSITY   (United States)

^p UNIVERSITY OF CALIFORNIA   (United States)

^q UNIVERSITY OF CALIFORNIA   (United States)

^r UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^s DUKE UNIVERSITY   (United States)

^t FIELD MUSEUM OF NATURAL HISTORY   (United States)

^u UNIVERSITY OF CALIFORNIA   (United States)

^v LONDON SCHOOL OF ECONOMICS   (United Kingdom)

more..

Author keywords

Data reuse; Hackathon; Phylogeny; Taxonomy; Tree of life; Web services

Indexed keywords

DATA REUSE; DESIGN AND IMPLEMENTATIONS; ELECTRONIC MARKETPLACES; HACKATHON; PHYLOGENY; SEMANTIC WEB TECHNOLOGY; SUSTAINABLE COMMUNITIES; TREE OF LIFE;

BIOLOGY; DATA INTEGRATION; DIGITAL STORAGE; ELECTRONIC DATA INTERCHANGE; FORESTRY; SOFTWARE ENGINEERING; TAXONOMIES; WEB SERVICES; WEBSITES;

INTEROPERABILITY;

BIOLOGY; COMPUTER PROGRAMS; DATA; ENGINEERING; FORESTRY;

ARTICLE; COMPUTER PROGRAM; INTERNET; PHYLOGENY;

INTERNET; PHYLOGENY; SOFTWARE;

EID: 84877613686     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-158     Document Type: Article

References (68)

1. Assembling the tree of life: harnessing life's history to benefit science and society 2002, Arlington: National Science Foundation, Cracraft J, Donoghue M, Dragoo J, Hillis D, Yates T, (accessed 9 May 2013 from http://ucjeps.berkeley.edu/tol.pdf).
2. Felsenstein J. Inferring Phylogenies 2004, Sunderland, Mass: Sinauer.
3. Kumar S, Dudley J. Bioinformatics software for biologists in the genomics era. Bioinformatics (Oxford, England) 2007, 23(14):1713-1717.
4. Larsen PO, von Ins M. The rate of growth in scientific publication and the decline in coverage provided by Science Citation Index. Scientometrics 2010, 84(3):575-603. 10.1007/s11192-010-0202-z, 2909426, 20700371.
5. Stoltzfus A, O'Meara B, Whitacre J, Mounce R, Gillespie EL, Kumar S, Rosauer DF, Vos RA. Sharing and Re-use of Phylogenetic Trees (and associated data) to Facilitate Synthesis. BMC Res Notes 2012, 5:574. 10.1186/1756-0500-5-574, 3583491, 23088596.
6. Sanderson MJ, Donoghue MJ, Piel WH, Eriksson T. TreeBASE: a prototype database of phylogenetic analyses and an interactive tool for browsing the phylogeny of life. Am J Bot 1994, 81(6):183.
7. Piel W, Chan L, Dominus M, Ruan J, Vos R, Tannen V. TreeBASE v. 2: A Database of Phylogenetic Knowledge 2009, London: e-BioSphere.
8. Webb CO, Donoghue MJ. Phylomatic: tree assembly for applied phylogenetics. Mol Ecol Notes 2005, 5:181-183.
9. The Angiosperm Phylogeny G An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG III. Bot J Linn Soc 2009, 16((2):105-121. The Angiosperm Phylogeny G.
10. Web of Knowledge. http://www.webofknowledge.com.
11. Bininda-Emonds OR, Cardillo M, Jones KE, MacPhee RD, Beck RM, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A. The delayed rise of present-day mammals. Nature 2007, 446(7135):507-512. 10.1038/nature05634, 17392779.
12. Smith SA, Beaulieu JM, Stamatakis A, Donoghue MJ. Understanding angiosperm diversification using small and large phylogenetic trees. Am J Bot 2011, 98(3):404-414. 10.3732/ajb.1000481, 21613134.
13. Goloboff PA, Catalano SA, Marcos Mirande J, Szumik CA, Salvador Arias J, Källersjö M, Farris JS. Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups. Cladistics 2009, 25(3):211-230.
14. McDonald D, Price MN, Goodrich J, Nawrocki EP, DeSantis TZ, Probst A, Andersen GL, Knight R, Hugenholtz P. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea. ISME J 2012, 6(3):610-618. 10.1038/ismej.2011.139, 3280142, 22134646.
15. Sayers EW, Barrett T, Benson DA, Bolton E, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Federhen S. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2011, 39(Database issue):D38-D51. 3013733, 21097890.
16. Maddison D, Schulz K-S, Maddison W. The Tree of Life Web Project. Zootaxa 2007, 1668:19-40.
17. Cannone J, Subramanian S, Schnare M, Collett J, D'Souza L, Du Y, Feng B, Lin N, Madabusi L, Muller K. The Comparative RNA Web (CRW) Site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 2002, 3(1):2. 10.1186/1471-2105-3-2, 65690, 11869452.
18. Heymans M, Singh A. Deriving phylogenetic trees from the similarity analysis of metabolic pathways. Bioinformatics (Oxford, England) 2003, 19(suppl 1):i138-i146.
19. Kummerfeld S, Teichmann S. Relative rates of gene fusion and fission in multi-domain proteins. Trends Genet 2005, 21(1):25-30. 10.1016/j.tig.2004.11.007, 15680510.
20. Ruan J, Li H, Chen Z, Coghlan A, Coin LJ, Guo Y, Heriche JK, Hu Y, Kristiansen K, Li R. TreeFam: 2008 Update. Nucleic Acids Res 2008, 36(Database issue):D735-D740. 2238856, 18056084.
21. Vilella A, Severin J, Ureta-Vidal A, Heng L, Durbin R, Birney E. EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res 2009, 19(2):327-335. 2652215, 19029536.
22. Patterson DJ, Cooper J, Kirk PM, Pyle RL, Remsen DP. Names are key to the big new biology. Trends Ecol Evol (Personal edition) 2010, 25(12):686-691.
23. Parr CS, Guralnick R, Cellinese N, Page RD. Evolutionary informatics: unifying knowledge about the diversity of life. Trends Ecol Evol 2012, 27(2):94-103. 10.1016/j.tree.2011.11.001, 22154516.
24. Page RD. Biodiversity informatics: the challenge of linking data and the role of shared identifiers. Brief Bioinform 2008, 9(5):345-354. 10.1093/bib/bbn022, 18445641.
25. Vos RA, Caravas J, Hartmann K, Jensen MA, Miller C. BIO:Phylo-phyloinformatic analysis using perl. BMC Bioinformatics 2011, 12:63. 10.1186/1471-2105-12-63, 3056726, 21352572.
26. Sukumaran J, Holder MT. DendroPy: a Python library for phylogenetic computing. Bioinformatics (Oxford, England) 2010, 26(12):1569-1571.
27. Felsenstein J. Phylogenies and the comparative method. Amer Natural 1985, 125:1-15.
28. Pagel M. The Maximum Likelihood Approach to Reconstructing Ancestral Character States of Discrete Characters on Phylogenies. Syst Biol 1999, 48(3):612-622.
29. Pagel M. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proc R Soc B 1994, 255:37-45.
30. Stewart CA, Almes GT, Wheeler BC. Cyberinfrastructure Software Sustainability and Reusability: Report from an NSF-funded workshop 2010, Bloomington, IN: Indiana University.
31. Prlić A, Procter JB. Ten Simple Rules for the Open Development of Scientific Software. PLoS Comput Biol 2012, 8(12):e1002802. 10.1371/journal.pcbi.1002802, 3516539, 23236269.
32. Vandervalk BP, McCarthy EL, Wilkinson MD. Moby and Moby 2: creatures of the deep (web). Brief Bioinform 2009, 10(2):114-128. 10.1093/bib/bbn051, 19151099.
33. Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol 2010, 11(8):R86. 10.1186/gb-2010-11-8-r86, 2945788, 20738864.
34. Hughes-Croucher T, Wilson M. Up and Running with Node.js. Up and Running 2012, 204. Sebastopol: O'Reilly, 1.
35. Page RD. A Taxonomic Search Engine: federating taxonomic databases using web services. BMC Bioinformatics 2005, 6:48. 10.1186/1471-2105-6-48, 555944, 15757517.
36. Boyle B, Hopkins N, Lu Z, Garay JAR, Mozzherin D, Rees T, Matasci N, Narro ML, Piel WH, Mckay SJ. The taxonomic name resolution service: an online tool for automated standardization of plant names. BMC Bioinformatics 2013, 14:16. 10.1186/1471-2105-14-16, 3554605, 23324024.
37. Mammal Species of the World. A Taxonomic and Geographic Reference 2005, Baltimore: Johns Hopkins University Press, Wilson DE, Reeder DM, 3.
38. Leebens-Mack J, Vision T, Brenner E, Bowers J, Cannon S, Clement M, Cunningham C, Depamphilis C, DeSalle R, Doyle J. Taking the first steps towards a standard for reporting on phylogenies: Minimum information about a phylogenetic analysis (MIAPA). Omics-A: J Integr Biol 2006, 10(2):231-237.
39. Berners-Lee T, Hendler J. Publishing on the semantic web. Nature 2001, 410(6832):1023-1024.
40. Klyne G, Carroll JJ. Resource Description Framework (RDF): Concepts and Abstract Syntax. World Wide Web Consortium 2004, : .
41. Virtuoso Universal Server. http://virtuoso.openlinksw.com.
42. World Wide Web Consortium Large Triple Stores. 2011, World Wide Web Consortium.
43. Prosdocimi F, Chisham B, Pontelli E, Thompson JD, Stoltzfus A. Initial Implementation of a Comparative Data Analysis Ontology. Evol Bioinformatics 2009, 5:47-66.
44. Smith B, Ashburner M, Rosse C, Bard J, Bug W, Ceusters W, Goldberg LJ, Eilbeck K, Ireland A, Mungall CJ. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat Biotechnol 2007, 25(11):1251-1255. 10.1038/nbt1346, 2814061, 17989687.
45. Lewis PO. NCL: a C++ class library for interpreting data files in NEXUS format. Bioinformatics (Oxford, England) 2003, 19(17):2330-2331.
46. Maddison DR, Swofford DL, Maddison WP. NEXUS: An Extensible File Format for Systematic Information. Syst Biol 1997, 46(4):590-621. 10.1093/sysbio/46.4.590, 11975335.
47. Dean J, Ghemawat S. MapReduce: Simplified Data Processing on Large Clusters. Sixth Symposium on Operating System Design and Implementation 2004, 107-113. San Francisco, CA: ACM.
48. Foundation FS GNU awk 2008, : , Foundation FS.
49. Hedges SB, Dudley J, Kumar S. TimeTree: a public knowledge-base of divergence times among organisms. Bioinformatics (Oxford, England) 2006, 22(23):2971-2972.
50. Urbanek S. FastRWeb: Fast Interactive Web Framework for Data Mining Using R. ISAC 2008 World Congress 2008, : .
51. Urbanek S. Rserve - A Fast Way to Provide R Functionality to Applications. Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003) 2003, : , Hornik K, Leisch F, Zeileis A.
52. Popescu AA, Huber KT, Paradis E. Ape 3.0: New tools for distance-based phylogenetics and evolutionary analysis in R. Bioinformatics (Oxford, England) 2012, 28(11):1536-1537.
53. Mesquite: a modular system for evolutionary analysis. Version 2.73. http://mesquiteproject.org.
54. Doyon JP, Ranwez V, Daubin V, Berry V. Models, algorithms and programs for phylogeny reconciliation. Brief Bioinform 2011, 12(5):392-400. 10.1093/bib/bbr045, 21949266.
55. Zmasek CM, Eddy SR. A simple algorithm to infer gene duplication and speciation events on a gene tree. Bioinformatics (Oxford, England) 2001, 17(9):821-828.
56. Han M, Zmasek C. PhyloXML: XML for evolutionary biology and comparative genomics. BMC Bioinformatics 2009, 10:356. 10.1186/1471-2105-10-356, 2774328, 19860910.
57. Voss RS, Jansa SA. Phylogenetic relationships and classification of didelphid marsupials, an extant radiation of New World metatherian mammals. Bull Am Mus Nat Hist 2009, 322:1-177.
58. O'Leary MA, Kaufman S. MorphoBank: phylophenomics in the" cloud" Cladistics 2011, 27:529-537.
59. Riek A. Allometry of milk intake at peak lactation. Mamm Biol 2011, 76(1):3-11.
60. Miller MA, Pfeiffer W, Schwartz T. Creating the CIPRES Science Gateway for inference of large phylogenetic trees. Gateway Computing Environments Workshop (GCE) 2010, 1-8. La Jolla, CA, USA: San Diego Supercomput. Center.
61. Sanderson M, Boss D, Chen D, Cranston K, Wehe A. The PhyLoTA Browser: processing GenBank for molecular phylogenetics research. Syst Biol 2008, 57(3):335-346. 10.1080/10635150802158688, 18570030.
62. Farris SM, Roberts NS. Coevolution of generalist feeding ecologies and gyrencephalic mushroom bodies in insects. Proc Natl Acad Sci U S A 2005, 102(48):17394-17399. 10.1073/pnas.0508430102, 1297680, 16293692.
63. Martinson H, Schneider K, Gilbert J, Hines J, Hambäck P, Fagan W. Detritivory: stoichiometry of a neglected trophic level. Ecol Res 2008, 23(3):487-491.
64. Shenoy BD, Jeewon R, Hyde KD. Impact of DNA sequence-data on the taxonomy of anamorphic fungi. Fungal Divers 2007, 26:1-54.
65. Smolenaars MM, Madsen O, Rodenburg KW, Van der Horst DJ. Molecular diversity and evolution of the large lipid transfer protein superfamily. J Lipid Res 2007, 48(3):489-502.
66. Stelkens R, Seehausen O. Genetic distance between species predicts novel trait expression in their hybrids. Evolution 2009, 63(4):884-897. 10.1111/j.1558-5646.2008.00599.x, 19220450.
67. Whitney KD, Garland T. Did genetic drift drive increases in genome complexity?. PLoS Genet 2010, 6(8): 10.1371/journal.pgen.1001080, 3009686, 21203501.
68. Matsen FA, Kodner RB, Armbrust EV. Pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree. BMC Bioinformatics 2010, 11:538. 10.1186/1471-2105-11-538, 3098090, 21034504.