extdata(CHNOSZ)
extdata()所属R语言包：CHNOSZ
Extra Data
额外数据
译者：生物统计家园网 机器人LoveR
描述----------Description----------
The files in the subdirectories of extdata support the examples in the package documentation and vignettes.
文件中的子目录extdata支持包中的文件和护身符的例子。
Details
详细信息----------Details----------
Files in abundance contain protein abundance data:
文件中的abundance含蛋白质丰富的数据：
AA03.csv has reference abundances for 71 proteins taken from Fig. 3 of Anderson and Anderson, 2002 (as corrected in Anderson and Anderson, 2003). The columns with data taken from these sources are type (hemoglobin, plasma, tissue, or interleukin), description (name used in the original figure), log10(pg/ml) (upper limit of abundance interval shown in Anderson and Anderson, 2003, log10 of concentration in pg/ml). The additional columns are data derived from a search of the SWISS-PROT/UniProtKB database based on the descriptions of the proteins: name (nominal UniProtKB name for this protein), name2 (other UniProtKB names(s) that could apply to the protein), and note (notes based on searching for a protein of this description). The amino acid compositions of all proteins whose names are not NA are included in thermo$protein. The abbrv column for the proteins contains the description given by Anderson and Anderson, 2003, followed by (in parentheses) the UniProtKB accession number. Annotated initiator methionines (e.g. for ferritin, myoglobin, ENOG), signal peptides or propeptides were removed from the proteins (except where they are not annotated in UniProtKB: IGHG1, IGHA1, IGHD, MBP). In cases were multiple isoforms are present in UniProtKB (e.g. Albumin) only the first isoform was taken. In the case of C4 Complement (CO4A) and C5 Complement (CO5), the amino acid composition of only the alpha chains are listed. In the case of the protein described as iC3b, the amino acid sequence is taken to be that of Complement C3c alpha' chain fragment 1 from CO3, and is given the name CO3.C3c. The non-membrane (soluble) chains of TNF-binding protein (TNR1A) and TNF-alpha (TNFA) were used. Rantes, MIP-1 beta and MIP-1 alpha were taken from C-C motif chemokines (CCL5, CCL4, CCL3 respectively). C-peptide was taken from the corresponding annotation for insulin and here is named INS.C. See the "protactiv" vignette for an example that uses this file.
AA03.csv71蛋白取自图的丰度。 3安德森和安德森，2002年（纠正安德森和安德森，2003年）。从这些来源的数据类型的列（血红蛋白，血浆，组织，或白单元介素），描述（原来的图中使用的名称），LOG10（皮克/毫升）（上限丰富间隔安德森和安德森，2003年LOG10在PG /毫升的浓度）。额外的列数据，来自一个搜索的数据库的基础上描述的蛋白质SWISS-PROT/UniProtKB：名称（对这种蛋白质的的名义UniProtKB名），NAME2（其他的UniProtKB名称（S）的蛋白质，可以适用于） ，并注意（基于搜索本说明书中的蛋白质的票据）。 NA的氨基酸组成的蛋白质，其名称不包含在thermo$protein。 abbrv列的蛋白质包含安德森和安德森，2003年，其次是（括号内）UniProtKB加入数给出的描述。或注释的引发剂的蛋氨酸（例如铁蛋白，肌红蛋白，ENOG），信号肽，前肽的蛋白质从（除非它们未标注UniProtKB：IGHG1，IGHA1，IGHD，MBP）。的情况下，存在多种亚型在UniProtKB（如白蛋白）第一亚型。以C4的补（CO4A）和C5补体（CO5）的情况下，仅在α链的氨基酸组合物，被列出。的氨基酸序列的蛋白质的情况下，描述为IC3B，采取的是补体补体C3cα链片段1从CO3，给出的名称CO3.C3c。非膜（可溶性）链的TNF-α结合的蛋白（TNR1A）和TNF-α（TNFA）被使用。 RANTES，MIP-1β和MIP-1α的CC图案趋化因子（CCL5，CCL4，CCL3）。相应的注释胰岛素和C-肽是从这里被命名为INS.C.请参阅“protactiv一个例子，它使用这个文件的小插曲。
ISR+08.csv has columns excerpted from Additional File 2 of Ishihama et al. (2008) for protein abundances in E. coli cytosol. The columns in this file are ID (Swiss-Prot ID), accession (Swiss-Prot accession), emPAI (exponentially modified protein abundance index), copynumber (emPAI-derived copy number/cell), GRAVY (Kyte-Doolittel), FunCat (FunCat class description), PSORT (PSORT localisation), ribosomal (yes/no). See get.expr and the "protactiv" vignette for examples that use this file.
ISR+08.csv列摘自石浜等其他文件。 （2008），大肠杆菌单元质中的蛋白质丰度。此文件中的列ID（SWISS-PROT ID），加入（SWISS-PROT加入），emPAI的（指数修饰蛋白丰度指数），copynumber（emPAI衍生拷贝数/单元），的GRAVY（凯特 - Doolittel），FunCat （FunCat类的描述），PSORT（PSORT本地化），核糖体（是/否）。见get.expr和“protactiv”这个文件的例子，使用的小插曲。
yeastgfp.csv.xz Has 28 columns; the names of the first five are yORF, gene name, GFP tagged?, GFP visualized?, and abundance. The remaining columns correspond to the 23 subcellular localizations considered in the YeastGFP project (Huh et al., 2003 and Ghaemmaghami et al., 2003) and hold values of either T or F for each protein. yeastgfp.csv was downloaded on 2007-02-01 from http://yeastgfp.ucsf.edu using the Advanced Search, setting options to download the entire dataset and to include localization table and abundance, sorted by orf number. See yeastgfp for examples that use this file. </ul>
yeastgfp.csv.xz有28列的名字的第一个五年yORF，gene name，GFP tagged?，GFP visualized?和abundance。其余各列对应的23个亚单元定位在YeastGFP项目（咦等。，2003年和Ghaemmaghami等人，2003）认为，每个蛋白质是T或F值。 yeastgfp.csv被下载2007-02-01从http://yeastgfp.ucsf.edu使用高级搜索，下载整个数据集，包括定位表和丰富，由ORF数排序设置选项。见yeastgfp使用此文件的例子。 </ ul>
Files in bison contain BLAST results and taxonomic information for a metagenome:
文件中的bison包含的宏基因组的的BLAST结果和分类信息：
bisonN_vs_refseq47.blast.xz, bisonS_vs_refseq47.blast.xz, bisonR_vs_refseq47.blast.xz, bisonQ_vs_refseq47.blast.xz, bisonP_vs_refseq47.blast.xz are partial tabular BLAST results for proteins in the Bison Pool Environmental Genome. Predicted protein sequences were downloaded from the Joint Genome Institute's IMG/M system on 2009-05-13. The target database for the searches was constructed from microbial protein sequences in National Center for Biotechnology Information (NCBI) RefSeq database version 47, representing 3266 microbial genomes. The "blastall" command was used with the default setting for E value cuttoff (10.0) and options to make a tabular output file consisting of the top 20 hits for each query sequence. The function read.blast was used to extract only those hits with E values less than or equal to 1e-5 and with similarity greater than 30 percent, and to keep only the first hit for each query sequence. The function write.blast was used to save partial BLAST files (only selected columns). The files provided with CHNOSZ contain the first 5,000 hits for each sampling site at Bison Pool, representing between about 7 to 15 percent of the first BLAST hits after similarity and E value filtering.
bisonN_vs_refseq47.blast.xz，bisonS_vs_refseq47.blast.xz，bisonR_vs_refseq47.blast.xz，bisonQ_vs_refseq47.blast.xz，bisonP_vs_refseq47.blast.xz是的部分表格BLAST结果野牛泳池的环境基因组的蛋白质。预测的蛋白质序列进行了联合基因组研究所的IMG / M系统下载2009-05-13。国家生物技术信息（NCBI）RefSeq数据库版本47，较3266微生物基因组中心从微生物的蛋白质序列构建的目标数据库的搜索。 blastall“命令使用的默认设置的E值cuttoff（10.0）和选项，使一个表格输出文件为每个查询序列的前20名点击。函数read.blast只提取E值小于或等于1E-5和相似性大于30％的命中，并为每个查询序列，只保留第一次打。该功能write.blast用来保存部分的BLAST文件（只选择列）。与CHNOSZ提供的文件包含5000点击每个采样点在野牛泳池，占约7％至15％之间的相似和E值过滤后的第一起爆炸命中。
gi.taxid.txt.xz is a table that lists the sequence identifiers (gi numbers) that appear in the example BLAST files (see above), together with the corresponding taxon ids used in the NCBI databases. This file was extracted from the complete "gi_taxid_prot.dmp.gz" downloaded from ftp://ftp.ncbi.nih.gov/pub/taxonomy/ on 2011-06-16. A small number (about 0.2 percent) of the gi numbers appearing in the BLAST results were not found in "gi_taxid_prot.dmp.gz" and therefore are also excluded from gi.taxid.txt. See id.blast for an example that uses this file and the BLAST files described above. </ul>
gi.taxid.txt.xz是一个表，列出的序列标识符（GI号）出现在例如BLAST文件的（见上文），连同相应的类群IDS在NCBI数据库中使用。从该文件中提取完整的“gi_taxid_prot.dmp.gz”从ftp://ftp.ncbi.nih.gov/pub/taxonomy/下载于2011-06-16。的GI号出现在BLAST结果的一小部分（约0.2％），未发现在“gi_taxid_prot.dmp.gz”，也因此被排除gi.taxid.txt。见id.blast一个例子，它使用这个文件和BLAST上述文件。 </ ul>
Files in cpetc contain heat capacity data and other thermodynamic properties:
文件中的cpetc热容量数据和其他热力学性质：
PM90.csv Heat capacities of four unfolded aqueous proteins taken from Privalov and Makhatadze, 1990. Names of proteins are in the first column, temperature in degrees C in the second, and heat capacities in J mol^-1 K^-1 in the third. See ionize for an example that uses this file.
展开PM90.csv热容四Privalov，Makhatadze，1990从水的蛋白质。蛋白质的名称在第一列中，温度在degrees C在第二，在J摩尔热容^-1K^-1在第三位。见ionize使用该文件的一个例子。
RH95.csv Heat capacity data for iron taken from Robie and Hemingway, 1995. Temperature in Kelvin is in the first column, heat capacity in J K^-1 mol^-1 in the second. See subcrt for an example that uses this file.
RH95.csv的热容量数据的铁罗比和海明威，1995年。开尔文温度是在第一列中，JK^-1摩尔^-1在所述第二热容量。见subcrt使用该文件的一个例子。
RT71.csv pH titration measurements for unfolded lysozyme (LYSC_CHICK) taken from Roxby and Tanford, 1971. pH is in the first column, net charge in the second. See ionize for an example that uses this file.
RT71.csvpH值滴定测量展开溶菌酶（LYSC_CHICK），Roxby Tanford，1971年。 pH值是在第一列中，在第二个的净电荷。见ionize使用该文件的一个例子。
SOJSH.csv Experimental equilibrium constants for the reaction NaCl(aq) = Na+ + Cl- as a function of temperature and pressure taken from Fig. 1 of Shock et al., 1992. Data were extracted from the figure using g3data (http://www.frantz.fi/software/g3data.php). See water for an example that uses this file.
SOJSH.csv实验对于该反应的平衡常数NaCl（水溶液）=的Na +和Cl-作为温度和压力的函数的取自图。 1的冲击等，1992。提取数据从图中使用g3data的相关（http://www.frantz.fi/software/g3data.php）。见water使用该文件的一个例子。
Cp.CH4.HW97.csv, V.CH4.HWM96.csv Apparent molar heat capacities and volumes of CH4 in dilute aqueous solutions reported by Hnedkovsky and Wood, 1997 and Hnedkovsky et al., 1996. See EOSregress for examples that use these files. </ul>
Cp.CH4.HW97.csv，V.CH4.HWM96.csv表观摩尔热容量和体积的甲烷在稀水溶液中的Hnedkovsky和木材，1997年和Hnedkovsky等人，1996年报告。见EOSregress使用这些文件的例子。 </ ul>
Files in fasta contain protein sequences:
文件中的fasta所含的蛋白质序列：
HTCC1062.faa.xz is a FASTA file of 1354 protein sequences in the organism Pelagibacter ubique HTCC1062 downloaded from the NCBI RefSeq collection on 2009-04-12. The search term was Protein: txid335992[Organism:noexp] AND "refseq"[Filter]. See util.fasta and revisit for examples that use this file.
HTCC1062.faa.xz是一个FASTA文件1354的的有机体Pelagibacter ubique HTCC1062的蛋白质序列从NCBI RefSeq的收集下载2009-04-12。搜索字词蛋白质：txid335992 [生物：noexp“和”RefSeq的“过滤器]。 util.fasta和revisit使用此文件的例子。
EF-Tu.aln consists of aligned sequences (394 amino acids) of elongation factor Tu (EF-Tu). The sequences correspond to those taken from UniProtKB for ECOLI (Escherichia coli), THETH (Thermus thermophilus) and THEMA (Thermotoga maritima), and reconstructed ancestral sequences taken from Gaucher et al., 2003 (maximum likelihood bacterial stem and mesophilic bacterial stem, and alternative bacterial stem). See the "formation" vignette for an example that uses this file. </ul>
EF-Tu.aln由对齐的序列（394个氨基酸）的伸长因子Tu（EF-Tu的）组成。该序列对应于那些取自UniProtKB大肠杆菌（大肠杆菌），THETH（Thermus嗜热菌）和THEMA（海栖热袍）和重建祖先序列取自高雪氏等人，2003（最大似然细菌干和嗜温细菌干，并另一种细菌干）。请参阅“形成的一个例子，它使用这个文件的小插曲。 </ ul>
Files in protein contain protein composition data:
文件中的protein所含的蛋白质成分数据：
SGD.csv.xz Dataframe of amino acid composition of proteins from the Saccharomyces Genome Database. Contains twenty-two columns. Values in the first column are the rownumbers, the second column (OLN) has the ordered locus names of proteins, and the remaining twenty columns (Ala..Val) contain the numbers of the respective amino acids in each protein; the columns are arranged in alphabetical order based on the three-letter abbreviations for the amino acids. The source of data for SGD.csv is the file protein_properties.tab found on the FTP site of the SGD project on 2008-08-04. Blank entries were replaced with "NA" and column headings were added. See get.protein for examples that use this file.
SGD.csv.xz从酵母基因组数据库中的蛋白质的氨基酸组合物的数据框。包含22列。在第一列中的值是rownumbers，第二列（OLN）具有有序的轨迹名称蛋白质，和其余的20列（Ala..Val）包含的数字各自在每个蛋白的氨基酸;列被布置在按字母顺序排列的基础上的氨基酸的三字母缩写。的数据源SGD.csv的文件protein_properties.tab2008-08-04上的SGD项目的FTP站点上找到。空白项替换“NA”标题和列标题。见get.protein使用此文件的例子。
ECO.csv.xz Contains 24 columns. Values in the first column correspond to rownumbers, the second column AC holds the accession numbers of the proteins, the third column (Name) has the names of the corresponding genes, and the fourth column OLN lists the ordered locus names of the proteins. The remaining twenty columns (A..Y) give the numbers of the respective amino acids in each protein and are ordered alphabetically by the one-letter abbreviations of the amino acids. The sources of data for ECO.csv are the files ECOLI.dat ftp://ftp.expasy.org/databases/hamap/complete_proteomes/entries/bacteria and ECOLI.fas ftp://ftp.expasy.org/databases/hamap/complete_proteomes/fasta/bacteria downloaded from the HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes system) FTP site (Gattiker et al., 2003) on 2007-12-20. The proteins can be included in calculations using get.protein as well as get.expr; see the "protactiv" vignette for an example that uses the latter function. </ul>
ECO.csv.xz包含24列。在第一列中的值对应于rownumbers，第二列AC持有的蛋白质登录号，第三列（Name）具有相应的基因的名称，并且将第四列<X 列出了有序的轨迹名称的蛋白质。其余的20列（OLN..A）给在每个蛋白质的各个氨基酸的数目和的字母顺序排列的氨基酸的一个字母缩写。来源的数据Y的文件ECO.csvftp://ftp.expasy.org/databases/hamap/complete_proteomes/entries/bacteria和ECOLI.datftp://ftp.expasy的.org /数据库/ HAMAP的/ complete_proteomes /的fasta格式/细菌从HAMAP（高品质的自动和手动注释微生物蛋白质组的系统）FTP站点（Gattiker等，2003）下载2007-12-20。的蛋白质可以包含在计算中使用ECOLI.fas和get.protein;请参阅“protactiv”的一个例子，使用后者的功能的小插曲。 </ ul>
Files in refseq contain code and results of processing NCBI Reference Sequences (RefSeq) for microbial proteins:
文件中的refseq包含代码和结果处理NCBI参考序列（RefSeq的）微生物蛋白质：
README.txt Instructions for producing the data files.
README.txt生成数据文件的说明。
gencat.sh Bash script to microbial protein records from the RefSeq catalog.
gencat.sh Bash脚本微生物的蛋白质RefSeq的目录记录的。
mkfaa.sh Combine the contents of .faa.gz files into a single FASTA file.
mkfaa.sh相结合的内容。faa.gz文件到一个单一的FASTA文件。
protein.refseq.R Calculate average amino acid composition of all proteins for each organism identified by a taxonomic ID.
protein.refseq.R计算平均所有的蛋白质的氨基酸组成的确定的一个分类ID为每个生物体。
protein_refseq.csv.xz Output from above. See example for ZC.
protein_refseq.csv.xz从上面的输出。见的例子ZC。
taxid.names.R Generate a table of scientific names for the provided taxids. Requires the complete names.dmp and nodes.dmp from NCBI taxonomy files.
taxid.names.R生成的表格所提供的taxids的学名。需要完整的names.dmp和nodes.dmp从NCBI的分类文件。
taxid_names.csv.xz Output from above. See example for id.blast. </ul>
taxid_names.csv.xz从上面的输出。见的例子id.blast。 </ ul>
Files in taxonomy contain example taxonomic data files:
文件中的taxonomy包含分类数据文件例如：
names.dmp and nodes.dmp are excerpts of the taxonomy files available on the NCBI ftp site (ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz, accessed 2010-02-15). These example files contain only the entries for Escherichia coli K-12, Saccharomyces cerevisiae, Homo sapiens, Pyrococcus furisosus and Methanocaldococcus jannaschii (taxids 83333, 4932, 9606, 186497, 243232) and the higher-ranking nodes (genus, family, etc.) in the respective lineages. See taxonomy for examples that use this file. </ul>
names.dmp和nodes.dmp是摘录的分类文件可在NCBI ftp站点（ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz，访问2010年02 -15）。这些示例文件包含的条目大肠杆菌K-12，酿酒酵母（Saccharomyces cerevisiae），智人（Homo sapiens），：焦酚furisosus和Methanocaldococcus jannaschii（taxids 83333，4932，9606，186497，243232）和更高级别的节点（属，科，等。在各自的谱系）。见taxonomy使用此文件的例子。 </ ul>
Files in thermo contain additional thermodynamic data and group additivity definitions:
文件中的thermo包含额外的热力学数据和基团加和定义：
OBIGT-2.csv contains supplementary thermodynamic data in the same format as the primary database in data/OBIGT.csv. Data for some entries in the primary database are taken from different literature sources in this file. The default action of add.obigt is to add the contents of this file to CHNOSZ's working database in thermo$obigt. See diagram and the code of anim.TCA for examples that use this file.
OBIGT-2.csv包含在相同的格式中的主数据库data/OBIGT.csv补充热力学数据。某些项在主数据库中的数据是从不同的文献来源，在这个文件中。 add.obigt的默认操作是该文件的内容添加到CHNOSZ数据库中thermo$obigt的工作。见diagram和anim.TCA使用此文件为例子的代码。
obigt_check.csv contains the results of running check.obigt to check the internal consistency of entries in the primary and supplementary databases.
obigt_check.csv运行check.obigt来检查项目的内部一致性在小学和补充数据库的结果。
groups_big.csv Group contribution matrix: five structural groups on the columns ([-CH3],[-CH2-],[-CH2OH],[-CO-],[-COOH]) and 24 compounds on the rows (alkanes, alcohols, ketones, acids, multiply substituted compounds).
groups_big.csv基团贡献矩阵：5的列（[-CH 3]，[-CH 2-]，[-CH 2 OH]，[-CO-]，[-COOH]）和24的化合物的行的结构基团（烷烃，醇，酮，羧酸，多取代的化合物）。
groups_small.csv Group contribution matrix: twelve bond-specific groups on the columns, and 25 compounds on the rows (as above, plus isocitrate). Group identity and naming conventions adapted from Benson and Buss (1958) and Domalski and Hearing (1993). See the "xadditivity" vignette for examples that use this file and groups_big.csv. </ul>
groups_small.csv集团贡献矩阵：12列上的特定债券组，25个化合物的行（如上图，加异柠檬酸）。改编自森和Buss（1958）和Domalski和听证会（1993年）的组标识和命名约定。使用此文件的例子和groups_big.csv请参阅“xadditivity”小插曲。 </ ul>
参考文献----------References----------
Anderson, N. L. and Anderson, N. G. (2002) The human plasma proteome: History, character and diagnostic prospects. Molecular and Cellular Proteomics 1, 845–867. http://dx.doi.org/10.1074/mcp.R200007-MCP200
Anderson, N. L. and Anderson, N. G. (2003) The human plasma proteome: History, character and diagnostic prospects (Vol. 1 (2002) 845-867). Molecular and Cellular Proteomics 2, 50. http://dx.doi.org/10.1074/mcp.A300001-MCP200
Benson, S. W. and Buss, J. H. (1958) Additivity rules for the estimation of molecular properties. Thermodynamic properties. J. Chem. Phys. 29, 546–572. http://dx.doi.org/10.1063/1.1744539
Domalski, E. S. and Hearing, E. D. (1993) Estimation of the thermodynamic properties of C-H-N-O-S-Halogen compounds at 298.15 K J. Phys. Chem. Ref. Data 22, 805–1159. http://dx.doi.org/10.1063/1.555927
Gattiker, A., Michoud, K., Rivoire, C., Auchincloss, A. H., Coudert, E., Lima, T., Kersey, P., Pagni, M., Sigrist, C. J. A., Lachaize, C., Veuthey, A.-L., Gasteiger, E. and Bairoch, A. (2003) Automatic annotation of microbial proteomes in Swiss-Prot. Comput. Biol. Chem. 27, 49–58. http://dx.doi.org/10.1016/S1476-9271(02)00094-4
Gaucher, E. A., Thomson, J. M., Burgan, M. F. and Benner, S. A (2003) Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins. Nature 425(6955), 285–288. http://dx.doi.org/10.1038/nature01977
Ghaemmaghami, S., Huh, W., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K. and Weissman, J. S. (2003) Global analysis of protein expression in yeast. Nature 425(6959), 737–741. http://dx.doi.org/10.1038/nature02046
Huh, W. K., Falvo, J. V., Gerke, L. C., Carroll, A. S., Howson, R. W., Weissman, J. S. and O'Shea, E. K. (2003) Global analysis of protein localization in budding yeast. Nature 425(6959), 686–691. http://dx.doi.org/10.1038/nature02026
Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M., Hartl, F. U., Kerner, M. J. and Frishman, D. (2008) Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 9:102. http://dx.doi.org/10.1186/1471-2164-9-102
HAMAP system. HAMAP FTP directory, ftp://ftp.expasy.org/databases/hamap/
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发表于 2012-9-16 10:22:49
