The files in the subdirectories of extdata provide additional thermodynamic data and other data to support the examples in the package documentation and vignettes.
See thermo for a description of the files in extdata/OBIGT, which are used to generate the thermodynamic database.
Files in Berman contain thermodynamic data for minerals using the Berman formulation:
Ber88_1988.csv contains thermodynamic data for minerals taken from Berman (1988).
Other files with names like xxx_yyyy.csv contain thermodynamic data from other sources; xxx in the filename corresponds to the reference in thermo$obigt and yyyy gives the year of publication.
berman uses these data for the calculation of thermodynamic properties at specified and , which are then available for use in subcrt.
If there are any duplicated mineral names in the files, only the most recent data are used, as determined by the year in the file name.
Following conventions used in other data files, the names of sanidine and microcline were changed to K-feldspar,high and K-feldspar,low.
sympy.R is an R script that uses rSymPy to symbolically integrate Bermans's equations for heat capacity and volume to write experessions for enthalpy, entropy and Gibbs energy.
The testing directory contains data files based on Berman and Aranovich (1996). These are used to demonstrate the addition of data from a user-supplied file (see berman).
Files in abundance contain protein abundance and microbial occurrence data:
TBD+05.csv lists genes with transcriptomic expression changes in carbon limitation stress response experiments in yeast (Tai et al., 2005). See yeast.aa for an example that uses this file.
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 and demo("yeastgfp") for examples that use this file.
microbes.csv has data for microbial occurrence (i.e. relative enrichement) in colorectal cancer and normal tissue. The file is from the Supporting Information of Dick (2016). This file is used by demo("bugstab").
Files in bison contain BLAST results and taxonomic information for an environmental metagenome from the Bison Pool hot spring in Yellowstone National Park:
bisonN_vs_refseq57.blast.xz, bisonS..., bisonR..., bisonQ..., bisonP... are 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. 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 sequence similarity (percent identity) at least 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.
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 is not a subset of the complete ‘gi_taxid_prot.dmp.gz’ available at ftp://ftp.ncbi.nih.gov/pub/taxonomy/ but instead is a subset of ‘gi.taxid.txt’ generated from the RefSeq release catalog using ‘gencat.sh’ in the refseq directory. See id.blast for an example that uses this file and the BLAST files described above.
Files in cpetc contain experimental and calculated thermodynamic and environmental data:
PM90.csv Heat capacities of four unfolded aqueous proteins taken from Privalov and Makhatadze, 1990. Temperature in C is in the first column, and heat capacities of the proteins in J mol\(^{-1}\) K\(^{-1}\) in the remaining columns. See ionize.aa and the vignette anintro.Rmd for examples that use this file.
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.
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.aa for an example that uses this file.
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. See demo("NaCl") for an example that uses this file.
Cp.CH4.HW97.csv, V.CH4.HWM96.csv Apparent molar heat capacities and volumes of CH4 in dilute aqueous solutions reported by Hn<U+011B>dkovsk<U+00FD> and Wood, 1997 and Hn<U+011B>dkovsk<U+00FD> et al., 1996. See EOSregress and the vignette eos-regress.Rmd for examples that use these files.
SC10_Rainbow.csv Values of temperature (C, pH and logarithms of activity of , , , and for mixing of seawater and hydrothermal fluid at Rainbow field (Mid-Atlantic Ridge), taken from Shock and Canovas, 2010. See the vignette anintro.Rmd for an example that uses this file.
SS98_Fig5a.csv, SS98_Fig5b.csv Values of logarithm of fugacity of and pH as a function of temperature for mixing of seawater and hydrothermal fluid, digitized from Figs. 5a and b of Shock and Schulte, 1998. See the vignette anintro.Rmd for an example that uses this file.
rubisco.csv UniProt IDs for Rubisco, ranges of optimal growth temperature of organisms, domain and name of organisms, and URL of reference for growth temperature, from Dick, 2014. See the vignette anintro.Rmd for an example that uses this file.
bluered.txt Blue - light grey - red color palette, computed using colorspace::diverge_hcl(1000, c = 100, l = c(50, 90), power = 1). This is used by ZC.col.
AD03_Fig1?.csv Experimental data points digitized from Figure 1 of Akinfiev and Diamond, 2003, used in demos("AkDi").
TKSS14_Fig2.csv Experimental data points digitized from Figure 2 of Tutolo et al., 2014, used in demos("aluminum").
Mer75_Table4.csv Values of log(aK+/aH+) and log(aNa+/aH+) from Table 4 of Merino, 1975, used in demos("aluminum").
Files in fasta contain protein sequences:
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 read.fasta for an example that uses this file.
rubisco.fasta Sequences of Rubisco obtained from UniProt (see Dick, 2014). See the vignette anintro.Rmd for an example that uses this file.
Files in protein contain amino acid compositions for proteins.
Sce.csv.xz
Data frame of amino acid composition of 6716 proteins from the Saccharomyces Genome Database (SGD).
Values in the first three columns are the ORF names of proteins, SGDID, and GENE names. The remaining twenty columns (ALA..VAL) contain the numbers of the respective amino acids in each protein.
The sources of data for Sce.csv are the files protein_properties.tab and SGD_features.tab (for the gene names), downloaded from http://www.yeastgenome.org on 2013-08-24.
See yeast.aa for an example.
DS11.csv, DS13.csv
These two files contain amino acid compositions of metagenomically encoded proteins, averaged together according to functional annotation (DS11) or taxonomic affiliation (DS13).
The data are from Dick and Shock, 2011 and 2013.
They are used in the vignette Hot-spring proteins in CHNOSZ.
microbial.aa.csv
Overall protein compositions of microbial species reported to be positively or negatively enriched in colorectal cancer.
This file is taken from Dick, 2016.
It is used by demo("bugstab").
Files in refseq contain code and results of processing NCBI Reference Sequences (RefSeq) for microbial proteins, using RefSeq release 61 of 2013-09-09:
README.txt Instructions for producing the data files.
gencat.sh Bash script to extract microbial protein records from the RefSeq catalog.
gi.taxid.txt Output from above. The complete file is too large to distribute with CHNOSZ, but a portion is included in extdata/bison to support processing example BLAST files for the Bison Pool metagenome (based on RefSeq 57, 2013-01-08).
mkfaa.sh Combine the contents of .faa.gz files into a single FASTA file (to use e.g. for making a BLAST database).
protein.refseq.R Calculate average amino acid composition of all proteins for each organism identified by a taxonomic ID.
trim_refseq.R Keep only selected organism names (reduces number of taxa from 6758 to 779, helps to control package size).
protein_refseq.csv.xz Output from above. See example in pinfo.
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.csv.xz Output from above.
NOTE: For backward compatibility with the example BLAST files for the Bison Pool metagenome, the packaged file merges records for taxids found in either RefSeq 57 or 61.
NOTE 2: To save space for the package, the file has been trimmed to hold only those taxids listed in extdata/bison/gi.taxid.txt.
Certain taxids in release 57 were not located in the current RefSeq catalog, probably related to the transition to the “WP” multispecies accessions (ftp://ftp.ncbi.nlm.nih.gov/refseq/release/announcements/WP-proteins-06.10.2013.pdf).
See example for id.blast.
Files in supcrt contain scripts for reading and comparing SUPCRT files (including slop98.dat and newer slop files from GEOPIG (http://geopig.asu.edu)) with the database in CHNOSZ:
read.supcrt.R defines the function read.supcrt that can be used to read SUPCRT files.
compare.R uses read.supcrt to compare data in the SUPCRT file with that in thermo()$obigt.
newnames.csv maps names generated by read.supcrt, based on names present in the source SUPCRT files, to names used in thermo()$obigt.
Files in taxonomy contain taxonomic data files:
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 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 these files.
Files in adds contain additional thermodynamic data and group additivity definitions:
BZA10.csv contains supplementary thermodynamic data taken from Bazarkina et al. (2010). The data can be added to the database in the current session using add.obigt. See add.obigt for an example that uses this file.
obigt_check.csv contains the results of running check.obigt to check the internal consistency of entries in the default and optional datafiles.
RH98_Table15.csv Group stoichiometries for high molecular weight crystalline and liquid organic compounds taken from Table 15 of Richard and Helgeson, 1998. The first three columns have the compound name, formula and physical state (cr or liq). The remaining columns have the numbers of each group in the compound; the names of the groups (columns) correspond to species in thermo$obigt. The compound named 5a(H),14a(H)-cholestane in the paper has been changed to 5a(H),14b(H)-cholestane here to match the group stoichiometry given in the table. See RH2obigt for a function that uses this file.
DLEN67.csv Standard Gibbs energies of formation, in kcal/mol, from Dayhoff et al., 1967, for nitrogen (N2) plus 17 compounds shown in Fig. 2 of Dayhoff et al., 1964, at 300, 500, 700 and 1000 K. See demo("wjd") and the vignette wjd.Rmd for examples that use this file.
SK95.csv contains thermodynamic data for alanate, glycinate, and their complexes with metals, taken from Shock and Koretsky (1995) as corrected in slop98.dat. The data are used in the package tests (test-recalculate.R) to check the recalculated values of G, H, and S in thermo()$obigt using properties for alanate and glycinate from Amend and Helgeson (1997).
Akinfiev, N. N. and Diamond, L. W. (2003) Thermodynamic description of aqueous nonelectrolytes at infinite dilution over a wide range of state parameters. Geochim. Cosmochim. Acta 67, 613--629. https://doi.org/10.1016/S0016-7037(02)01141-9
Amend, J. P. and Helgeson, H. C. (1997) Calculation of the standard molal thermodynamic properties of aqueous biomolecules at elevated temperatures and pressures. Part 1. L--amino acids. J. Chem. Soc., Faraday Trans. 93, 1927--1941. https://doi.org/10.1039/A608126F
Bazarkina, E. F., Zotov, A. V. and Akinfiev, N. N. (2010) Pressure-dependent stability of cadmium chloride complexes: Potentiometric measurements at 1<U+2013>1000 bar and 25<U+00B0>C. Geol. Ore Deposits 52, 167--178. https://doi.org/10.1134/S1075701510020054
Berman, R. G. (1988) Internally-consistent thermodynamic data for minerals in the system NaO-KO-CaO-MgO-FeO-FeO-AlO-SiO-TiO-HO-CO. J. Petrol. 29, 445-522. https://doi.org/10.1093/petrology/29.2.445
Berman, R. G. and Aranovich, L. Ya. (1996) Optimized standard state and solution properties of minerals. I. Model calibration for olivine, orthopyroxene, cordierite, garnet, and ilmenite in the system FeO-MgO-CaO-AlO-TiO-SiO. Contrib. Mineral. Petrol. 126, 1-24. https://doi.org/10.1007/s004100050233
Dayhoff, M. O. and Lippincott, E. R. and Eck, R. V. (1964) Thermodynamic Equilibria In Prebiological Atmospheres. Science 146, 1461--1464. https://doi.org/10.1126/science.146.3650.1461
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.
Dick, J. M. (2014) Average oxidation state of carbon in proteins. J. R. Soc. Interface 11, 20131095. https://doi.org/10.1098/rsif.2013.1095
Dick, J. M. (2016) Proteomic indicators of oxidation and hydration state in colorectal cancer. PeerJ 4:e2238. https://doi.org/10.7717/peerj.2238
Dick, J. M. and Shock, E. L. (2011) Calculation of the relative chemical stabilities of proteins as a function of temperature and redox chemistry in a hot spring. PLoS ONE 6, e22782. https://doi.org/10.1371/journal.pone.0022782
Dick, J. M. and Shock, E. L. (2013) A metastable equilibrium model for the relative abundance of microbial phyla in a hot spring. PLoS ONE 8, e72395. https://doi.org/10.1371/journal.pone.0072395
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. https://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. https://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. https://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. https://doi.org/10.1038/nature02026
Hn<U+011B>dkovsk<U+00FD>, L., Wood, R. H. and Majer, V. (1996) Volumes of aqueous solutions of , , , and at temperatures from 298.15 K to 705 K and pressures to 35 MPa. J. Chem. Thermodyn. 28, 125--142. https://doi.org/10.1006/jcht.1996.0011
Hn<U+011B>dkovsk<U+00FD>, L. and Wood, R. H. (1997) Apparent molar heat capacities of aqueous solutions of , , , and at temperatures from 304 K to 704 K at a pressure of 28 MPa. J. Chem. Thermodyn. 29, 731--747. https://doi.org/10.1006/jcht.1997.0192
Joint Genome Institute (2007) Bison Pool Environmental Genome. Protein sequence files downloaded from IMG/M (https://img.jgi.doe.gov/)
Merino, E. (1975) Diagenesis in teriary sandstones from Kettleman North Dome, California. II. Interstitial solutions: distribution of aqueous species at 100°C and chemical relation to diagenetic mineralogy. Geochim. Cosmochim. Acta 39, 1629--1645. https://doi.org/10.1016/0016-7037(75)90085-X
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. https://doi.org/10.1016/S0022-2836(05)80198-6
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. https://doi.org/10.1016/S0016-7037(97)00345-1
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. http://www.worldcat.org/oclc/32590140
Roxby, R. and Tanford, C. (1971) Hydrogen ion titration curve of lysozyme in 6 M guanidine hydrochloride. Biochemistry 10, 3348--3352. https://doi.org/10.1021/bi00794a005
SGD project. Saccharomyces Genome Database, http://www.yeastgenome.org
Shock, E. and Canovas, P. (2010) The potential for abiotic organic synthesis and biosynthesis at seafloor hydrothermal systems. Geofluids 10, 161--192. https://doi.org/10.1111/j.1468-8123.2010.00277.x
Shock, E. L. and Koretsky, C. M. (1995) Metal-organic complexes in geochemical processes: Estimation of standard partial molal thermodynamic properties of aqueous complexes between metal cations and monovalent organic acid ligands at high pressures and temperatures. Geochim. Cosmochim. Acta 59, 1497--1532. https://doi.org/10.1016/0016-7037(95)00058-8
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 C and 5 kbar. J. Chem. Soc. Faraday Trans. 88, 803--826. https://doi.org/10.1039/FT9928800803
Shock, E. L. and Schulte, M. D. (1998) Organic synthesis during fluid mixing in hydrothermal systems. J. Geophys. Res. 103, 28513--28527. https://doi.org/10.1029/98JE02142
Tai, S. L., Boer, V. M., Daran-Lapujade, P., Walsh, M. C., de Winde, J. H., Daran, J.-M. and Pronk, J. T. (2005) Two-dimensional transcriptome analysis in chemostat cultures: Combinatorial effects of oxygen availability and macronutrient limitation in Saccharomyces cerevisiae. J. Biol. Chem. 280, 437--447. https://doi.org/10.1074/jbc.M410573200
Tutolo, B. M., Kong, X.-Z., Seyfried, W. E., Jr. and Saar, M. O. (2014) Internal consistency in aqueous geochemical data revisited: Applications to the aluminum system. Geochim. Cosmochim. Acta 133, 216--234. https://doi.org/10.1016/j.gca.2014.02.036
YeastGFP project. Yeast GFP Fusion Localization Database, http://yeastgfp.ucsf.edu; Current location: http://yeastgfp.yeastgenome.org