title: Sharing and archiving nucleic acid structure mapping data.
abstract: Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public servers for storing, retrieving, and searching the data. We have also developed a consistent nomenclature (ontology) within the Ontology of Biomedical Investigations (OBI), which provides unique identifiers (termed persistent URLs, or PURLs) for classifying the data. Links to standardized data sets shared using our proposed format along with a tutorial and links to templates can be found at http://snrnasm.bio.unc.edu.
authors: Oxford e-Research Center, University of Oxford, OX1 3QG, Oxford, United Kingdom.
authors: Philippe
authors: P
authors: Rocca-Serra
authors: Stanislav
authors: S
authors: Bellaousov
authors: Amanda
authors: A
authors: Birmingham
authors: Chunxia
authors: C
authors: Chen
authors: Pablo
authors: P
authors: Cordero
authors: Rhiju
authors: R
authors: Das
authors: Lauren
authors: L
authors: Davis-Neulander
authors: Caia D S
authors: CD
authors: Duncan
authors: Matthew
authors: M
authors: Halvorsen
authors: Rob
authors: R
authors: Knight
authors: Neocles B
authors: NB
authors: Leontis
authors: David H
authors: DH
authors: Mathews
authors: Justin
authors: J
authors: Ritz
authors: Jesse
authors: J
authors: Stombaugh
authors: Kevin M
authors: KM
authors: Weeks
authors: Craig L
authors: CL
authors: Zirbel
authors: Alain
authors: A
authors: Laederach
references: Nat Protoc. 2008;3(9):1395-401
references: 18772866
references: Nucleic Acids Res. 1987 Nov 25;15(22):9109-28
references: 2446263
references: Curr Opin Chem Biol. 2008 Dec;12(6):667-73
references: 18935976
references: OMICS. 2006 Summer;10(2):199-204
references: 16901226
references: Nucleic Acids Res. 1988 Aug 25;16(16):7943-60
references: 2843807
references: Nucleic Acids Res. 2003 Jan 1;31(1):439-41
references: 12520045
references: J Biol Chem. 1979 Oct 10;254(19):9608-16
references: 114514
references: Curr Opin Struct Biol. 2003 Jun;13(3):300-8
references: 12831880
references: RNA. 1997 Jan;3(1):1-16
references: 8990394
references: Nat Methods. 2010 Apr;7(4):291-4
references: 20190761
references: FEBS Lett. 1980 Oct 20;120(1):12-6
references: 7002606
references: Science. 1991 Jan 25;251(4992):401-7
references: 1989074
references: J Mol Biol. 2003 Apr 25;328(2):463-78
references: 12691754
references: Science. 1986 Aug 15;233(4765):727-34
references: 3016894
references: RNA. 2010 Jun;16(6):1108-17
references: 20413617
references: Nat Protoc. 2006;1(3):1610-6
references: 17406453
references: Cell Mol Life Sci. 2000 May;57(5):796-808
references: 10892344
references: Bioinformatics. 2007 Jul 15;23(14):1868-70
references: 17496317
references: Nucleic Acids Res. 1981 Oct 10;9(19):5125-40
references: 7031604
references: Nucleic Acids Res. 1984 Sep 11;12(17):6763-78
references: 6207483
references: Methods Enzymol. 2009;468:47-66
references: 20946764
references: Proc Natl Acad Sci U S A. 2004 May 11;101(19):7287-92
references: 15123812
references: J Am Chem Soc. 2007 Apr 11;129(14):4144-5
references: 17367143
references: Biochemistry. 2000 Sep 12;39(36):10975-85
references: 10998234
references: RNA. 2005 Mar;11(3):344-54
references: 15701734
references: J Mol Biol. 1986 Feb 5;187(3):399-416
references: 2422386
references: Proc Natl Acad Sci U S A. 2002 Jan 8;99(1):155-60
references: 11756689
references: EMBO J. 1982;1(2):269-76
references: 16453415
references: J Mol Biol. 1987 Nov 5;198(1):91-107
references: 3323531
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21
references: 18045790
references: BMC Bioinformatics. 2007 Nov 27;8 Suppl 9:S1
references: 18047702
references: J Mol Biol. 2006 Jun 2;359(2):446-54
references: 16626736
references: Curr Protoc Bioinformatics. 2009 Jun;Chapter 14:Unit 14.9
references: 19496059
references: Methods Enzymol. 1986;130:132-81
references: 3773731
references: Curr Opin Struct Biol. 2010 Jun;20(3):295-304
references: 20447823
references: Nat Rev Mol Cell Biol. 2004 Nov;5(11):908-19
references: 15520810
references: J Mol Biol. 2001 Mar 9;306(5):1157-66
references: 11237624
references: Nat Protoc. 2008;3(2):288-302
references: 18274531
references: Biochemistry. 1994 Feb 22;33(7):1778-87
references: 8110780
references: RNA. 2006 Apr;12(4):533-41
references: 16484377
references: Nat Protoc. 2007;2(10):2608-23
references: 17948004
references: Nucleic Acids Res. 2011 Jan;39(Database issue):D539-45
references: 20935045
references: RNA. 2009 Sep;15(9):1623-31
references: 19622678
references: Biochemistry. 2005 Apr 5;44(13):4957-70
references: 15794634
references: AMIA Annu Symp Proc. 2008 Nov 06;:1223-4
references: 18999306
references: Proc Natl Acad Sci U S A. 2007 Apr 24;104(17):7045-50
references: 17438287
references: Nat Methods. 2010 Dec;7(12):995-1001
references: 21057495
references: J Biomol Struct Dyn. 1989 Apr;6(5):971-84
references: 2686708
references: Nucleic Acids Res. 1978 Sep;5(9):3157-70
references: 212715
references: J Mol Biol. 2000 May 5;298(3):539-55
references: 10772868
references: PLoS Biol. 2008 Apr 29;6(4):e96
references: 18447581
references: AMIA Annu Symp Proc. 2003;:953
references: 14728458
references: J Mol Biol. 2004 Nov 5;343(5):1195-206
references: 15491606
references: J Mol Biol. 2001 May 25;309(1):57-68
references: 11491301
references: Science. 1989 Jul 21;245(4915):276-82
references: 2501870
references: Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4144-9
references: 18322008
references: Nucleic Acids Res. 2008 Jun;36(11):e63
references: 18477638
references: Eur J Biochem. 1977 Nov 1;80(2):319-24
references: 923582
references: J Mol Biol. 2006 Oct 20;363(2):531-44
references: 16963081
references: Proc Natl Acad Sci U S A. 2009 Jan 6;106(1):97-102
references: 19109441
references: Methods Mol Biol. 2008;419:53-67
references: 18369975
references: Proc Natl Acad Sci U S A. 1984 Nov;81(22):6978-82
references: 6209709
references: RNA. 2008 Oct;14(10):1979-90
references: 18772246
references: Annu Rev Biophys Biomol Struct. 2001;30:457-75
references: 11441810
references: Proc Natl Acad Sci U S A. 1980 Aug;77(8):4679-82
references: 6159633
references: Proc Natl Acad Sci U S A. 1995 Feb 14;92(4):1113-6
references: 7862644
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D25-30
references: 18073190
references: Nature. 2010 Sep 2;467(7311):103-7
references: 20811459
references: RNA. 1999 Oct;5(10):1308-25
references: 10573122
references: Cell. 1985 Oct;42(3):713-24
references: 4053183
references: J Am Chem Soc. 2005 Mar 30;127(12):4223-31
references: 15783204
references: BMC Bioinformatics. 2002;3:2
references: 11869452
references: Genome Res. 2007 Jun;17(6):954-9
references: 17568011
references: Comput Biol Chem. 2006 Dec;30(6):395-407
references: 17123865
references: J Mol Biol. 2001 May 18;308(5):839-51
references: 11352576
references: J Am Chem Soc. 2007 Mar 7;129(9):2676-82
references: 17295487
references: Nucleic Acids Res. 2008 Jan;36(Database issue):D344-50
references: 17932057
references: Curr Protoc Nucleic Acid Chem. 2002 Feb;Chapter 6:Unit 6.7
references: 18428898
references: Nucleic Acids Res. 2005 Jan 1;33(Database issue):D121-4
references: 15608160
references: Nat Struct Biol. 2002 Dec;9(12):928-33
references: 12434149
references: Nature. 2009 Aug 6;460(7256):711-6
references: 19661910
references: Nat Biotechnol. 2010 Nov;28(11):1178-9
references: 21057487
references: Biochemistry. 1978 Oct 17;17(21):4493-9
references: 363143
references: Bioinformatics. 2010 Sep 15;26(18):2354-6
references: 20679334
references: J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S7
references: 20626927