extdata support the examples in the package documentation and vignettes.thermoOBIGT-2.csvcontains supplementary thermodynamic data in the same format as the primary database indata/OBIGT.csv. Data for some entries in the primary database are taken from different literature sources in this file. The default action ofadd.obigtis to add the contents of this file to CHNOSZ's working database inthermo$obigt. Seediagramand the code ofanim.TCAfor examples that use this file.obigt_check.csvcontains the results of runningcheck.obigtto check the internal consistency of entries in the primary and supplementary databases.groups_big.csvGroup contribution matrix: five structural groups on the columns ([-CH3],[-CH2-],[-CH2OH],[-CO-],[-COOH]) and 24 compounds on the rows (alkanes, alcohols, ketones, acids, multiply substituted compounds).groups_small.csvGroup contribution matrix: twelve bond-specific groups on the columns, and 25 compounds on the rows (as above, plus isocitrate). Group identity and naming conventions adapted from Benson and Buss (1958) and Domalski and Hearing (1993). See thegroups_big.csv.RH98_Table15.csvGroup stoichiometries for high molecular weight crystalline and liquid organic compounds taken from Table 15 of Richard and Helgeson, 1998. The first three columns have thecompoundname,formulaand physicalstate(crorliq). The remaining columns have the numbers of each group in the compound; the names of the groups (columns) correspond to species inthermo$obigt. The compound named5a(H),14a(H)-cholestanein the paper has been changed to5a(H),14b(H)-cholestanehere to match the group stoichiometry given in the table. SeeRH2obigtfor a function that uses this file.DLEN67.csvStandard Gibbs energies of formation, in kcal/mol, from Dayhoff et al., 1967, for nitrogen (N2) plus 17 compounds shown in Fig. 2 of Dayhoff et al., 1964, at 300, 500, 700 and 1000 K.abundance contain protein abundance data:
stressis a data frame listing proteins identified in selected proteomic stress response experiments. The names of proteins begin at row 3, and columns are all the same length (padded as necessary at the bottom byNAs). Names correspond to ordered locus names (forSce) or gene names (forEco). The column names identify the experiments, the first row contains the name of the organism (SceorEco) and the third row has the reference key for the source of the data (listed inthermo$refs).AA03.csvhas reference abundances for 71 proteins taken from Fig. 3 of Anderson and Anderson, 2002 (as corrected in Anderson and Anderson, 2003). The columns with data taken from these sources are type (hemoglobin, plasma, tissue, or interleukin), description (name used in the original figure), log10(pg/ml) (upper limitof abundance interval shown in Anderson and Anderson, 2003, log10 of concentration in pg/ml). The additional columns are data derived from a search of the SWISS-PROT/UniProtKB database based on the descriptions of the proteins: name (nominal UniProtKB name for this protein), name2 (other UniProtKB names(s) that could apply to the protein), and note (notes based on searching for a protein of this description). The amino acid compositions of all proteins whose names are not NA are included inthermo$protein. Theabbrvcolumn 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. Seeproteinandread.exprfor examples that use this file.ISR+08.csvhas columns excerpted from Additional File 2 of Ishihama et al. (2008) for protein abundances inE. colicytosol. 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). Seeread.exprfor examples that use this file.
%% \item \code{GLL+98.csv} has columns "oln" for ordered locus name and "ratio" for change in expression of yeast proteins in response to H2O2 treatment, from Godon et al., 1998. One protein, YMR108W, was listed as both induced and repressed in the original data set and is not included in this table.yeastgfp.csv.xzHas 28 columns; the names of the first five areyORF,gene name,GFP tagged?,GFP visualized?, andabundance. 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 eitherTorFfor each protein.yeastgfp.csvwas 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. Seeyeastgfpfor examples that use this file. Files in bison contain BLAST results and taxonomic information for a metagenome:
bisonN_vs_refseq57.blast.xz,bisonS_vs_refseq57.blast.xz,bisonR_vs_refseq57.blast.xz,bisonQ_vs_refseq57.blast.xz,bisonP_vs_refseq57.blast.xzare partial tabular BLAST results for proteins in the Bison Pool Environmental Genome. Protein sequences predicted in the metagenome 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 57, representing 7415 microbial genomes. Theread.blastwas used to extract only those hits with E values less than or equal to 1e-5 and with sequence similarity (percent identity) at least 30 percent, and to keep only the first hit for each query sequence. The functionwrite.blastwas 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.gi.taxid.txt.xzis 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 isnota subset of the completerefseqdirectory. Seeid.blastfor an example that uses this file and the BLAST files described above.
Files in cpetc contain heat capacity data and other thermodynamic properties:
PM90.csvHeat capacities of four unfolded aqueous proteins taken from Privalov and Makhatadze, 1990. Names of proteins are in the first column, temperature in$^{\circ}$C in the second, and heat capacities in J mol$^{-1}$K$^{-1}$in the third. Seeionize.aafor an example that uses this file.RH95.csvHeat 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. Seesubcrtfor an example that uses this file.RT71.csvpH titration measurements for unfolded lysozyme (LYSC_CHICK) taken from Roxby and Tanford, 1971. pH is in the first column, net charge in the second. Seeionize.aafor an example that uses this file.SOJSH.csvExperimental 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 (waterfor an example that uses this file.Cp.CH4.HW97.csv,V.CH4.HWM96.csvApparent molar heat capacities and volumes of CH4 in dilute aqueous solutions reported by Hnedkovsky and Wood, 1997 and Hnedkovsky et al., 1996. SeeEOSregressfor examples that use these files.BKM60_Fig7.datEh-pH values for normal, wet and waterlogged soils from Fig. 7 of Baas Becking et al., 1960. See theSC10_Rainbow.csvValues of temperature ($^{\circ}$C), pH and logarithms of activity of$\mathrm{CO_2}$,$\mathrm{H_2}$,$\mathrm{NH_4^+}$,$\mathrm{H_2S}$and$\mathrm{CH_4}$for mixing of seawater and hydrothermal fluid at Rainbow field (Mid-Atlantic Ridge), taken from Shock and Canovas, 2010. Files in fasta contain protein sequences:
HTCC1062.faa.xzis a FASTA file of 1354 protein sequences in the organismPelagibacter ubiqueHTCC1062 downloaded from the NCBI RefSeq collection on 2009-04-12. The search term was Protein: txid335992[Organism:noexp] AND "refseq"[Filter]. Seeutil.fastaandrevisitfor examples that use this file.EF-Tu.alnconsists 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 Files in protein contain protein composition data for model organisms:
Sce.csv.xzData frame of amino acid composition of proteins from theSaccharomycesGenome 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 forSce.csvis the fileprotein_properties.tabfound on the FTP site of the SGD project on 2008-08-04. Blank entries were replaced with "NA" and column headings were added. Seeread.exprfor examples that use this file.Eco.csv.xzContains 24 columns. Values in the first column correspond to rownumbers, the second column {ACName) 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 more.aa as well as read.expr. 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.
Baas Becking, L. G. M., Kaplan, I. R. and Moore, D. (1960) Limits of the natural environment in terms of pH and oxidation-reduction potentials. Journal of Geology 68(3), 243--284.
Benson, S. W. and Buss, J. H. (1958) Additivity rules for the estimation of molecular properties. Thermodynamic properties. J. Chem. Phys. 29, 546--572.
Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V. (1964) Thermodynamic Equilibria In Prebiological Atmospheres. Science 146, 1461--1464.
Dayhoff, M. O. and Lippincott, E. R., Eck, R. V. and Nagarajan (1967) Thermodynamic Equilibrium In Prebiological Atmospheres of C, H, O, N, P, S, and Cl. Report SP-3040, National Aeronautics and Space Administration.
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.
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.
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.
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.
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.
HAMAP system. HAMAP FTP directory,
Hnedkovsky, L., Wood, R. H. and Majer, V. (1996) Volumes of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 298.15 K to 705 K and pressures to 35 MPa. J. Chem. Thermodyn. 28, 125--142.
Hnedkovsky, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of CH4, CO2, H2S, and NH3 at temperatures from 304 K to 704 K at a pressure of 28 MPa. J. Chem. Thermodyn. 29, 731--747.
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.
Joint Genome Institute (2007) Bison Pool Environmental Genome. Protein sequence files downloaded from IMG/M (
Privalov, P. L. and Makhatadze, G. I. (1990) Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: Protein unfolding effects. J. Mol. Biol. 213, 385--391.
Richard, L. and Helgeson, H. C. (1998) Calculation of the thermodynamic properties at elevated temperatures and pressures of saturated and aromatic high molecular weight solid and liquid hydrocarbons in kerogen, bitumen, petroleum, and other organic matter of biogeochemical interest. Geochim. Cosmochim. Acta 62, 3591--3636.
Robie, R. A. and Hemingway, B. S. (1995) Thermodynamic Properties of Minerals and Related Substances at 298.15 K and 1 Bar ($10^5$ Pascals) Pressure and at Higher Temperatures. U. S. Geol. Surv., Bull. 2131, 461 p.
Roxby, R. and Tanford, C. (1971) Hydrogen ion titration curve of lysozyme in 6 M guanidine hydrochloride. Biochemistry 10, 3348--3352.
SGD project. Saccharomyces Genome Database,
Shock, E. L., Oelkers, E. H., Johnson, J. W., Sverjensky, D. A. and Helgeson, H. C. (1992) Calculation of the thermodynamic properties of aqueous species at high pressures and temperatures: Effective electrostatic radii, dissociation constants and standard partial molal properties to 1000 $^{\circ}$C and 5 kbar. J. Chem. Soc. Faraday Trans. 88, 803--826.
Shock, E. and Canovas, P. (2010) The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems. Geofluids 10, 161--192.
YeastGFP project. Yeast GFP Fusion Localization Database, http://yeastgfp.ucsf.edu; Current location: