[Version 2015-04-29]

Links to the examples of files which can be used to submit information about chemical samples to ChemGenDB database are presented below.

Use any of those example files as templates, remove the example values, fill in information about your samples, put them into a zip archive file and rename the final archive according the file name mask:

SupplierName_ISODate_BatchName.zip

The parts ISODate and BatchName of the file name are optional. They must be separated by uderscore character ("_") if they are specified. BatchName can be description of the set of the samples contained in the zip file. Please do not use any special characters in SupplierName or BatchName to prevent problems with file names (especially space, "/", ":", "\" should be avoided). If no BatchName is specified the ISODate part will be used instead. If no ISODate is specified, the date when the upload was performed is used.

1) CEG_2009-04-11_cdx-only.zip (only .cdx files)

Samples submitted by supplier CEG on 04/11/2009 (or 11.4.2009)

Contains:

just .cdx files

  • each file contains full structure (no abbreviations) of one compound drawn in ChemDraw, no additional text (the structure will be used to calculate molecular formula and molecular weight of the compound)
  • the name of each .cdx file must be a unique code of the sample
  • .cdx files only can be used if samples are delivered in solid form. For solutions .xls file (see 2), 3) below) must be added specifying the solvent and concentration of the samples and positions of the samples in plates

2) LOX_2009-01-30_xls-only.zip (only .xls file)

Samples submitted by supplier LOX on 1/30/2009 (or 30.1.2009)

Contains:

LOX_2009-01-30.xls (or just one .xls file with any name)

file containing information about the samples.

  • the first row of the xls file contains names of sample properties
  • all subsequent rows must contain the properties values for individual samples, one sample per row
  • the first property "id" (in the first column) must hold a unique code of the sample, the code must be unique among all samples ever sent by the given supplier
  • properties "platename" (any text unique for each rack from the supplier) and "position" (e.g. A1, C12, ...) should be filled if the samples are submitted in well plates
  • properties "solvent" and "conc" should be filled if the samples are supplied in solution. For solvent use usually "DMSO" or "H2O". Concentration should be in mol/L. Please see information about submission of samples in solution. (If samples are submitted in the solid form specify "weight" property, see below.)
  • property "mw" (molecular weight) should be filled if no structure is submitted or if the molecular weight of the sample is different from the one calculated from the structure
  • any number of additional properties (columns) can be added
  • .xls file alone is used only if no samples structures are supplied or the structures can be specified in textual SMILES format in "smiles" property column
  • property "weight" should specify amount of a solid sample in miligrams, if solid samples were submitted. Please read information about submission of solid samples.
  • property "volume" can be specified (in microliters), if samples are delivered in solution, but the value is not mandatory. Please see information about submission of samples in solution.

3) Gren_2009-05-20_xls-and-cdx.zip (.xls and .cdx files)

Samples submitted by supplier Gren on 05/20/2009 (or 20.5.2009)

Contains:

  • Gren_2009-05-20.xls (or just one .xls file with any name)

    see 2) above

    • value of the id field must be equal to the base name of the .cdx file (i.e. file name without the .cdx extension)

  • .cdx files (see 1) above)

4) SDH_2009-01-13_xls-and-sdf.zip (.xls and .sdf files)

Samples submitted by supplier SDH on 01/13/2009 (i.e. 13.1.2009)

Contains:

  • SDH_2009-01-13.xls (or just one .xls file with any name)

    file containing additional information about the samples (see 2) above

    • Property "sdfid" should be filled with ID (unique identifiers of the structures) values used in .sdf file. If they are equal to "id" values, just copy the values from "id" column into the "sdfid" column.

    • If the .xls file does not contain ID values from .sdf file, then the name of the field in .sdf file which holds sample id values used in the .xls file must be specified during the import (in the input line "SDF ID name"). In this case no "sdfid" field should be specified in .xls file.

      EXAMPLE:
      For .sdf and .xls files delivered by Sigma for the Lopac library compounds you should use "CATNUM" as the "SDF ID name" (and "Lopac" for "Library name"). Both files should be placed in the .zip archive with the name starting with "Sigma_".

  • SDH_2009-01-13.sdf

    file containing structures of the samples.

    • The sdf file must contain ID field holding identifier which equals to the value specified in "sdfid" column in SDH_2009-01-13.xls
    • If the .xls file does not contain ID values from .sdf file, then the "SDF ID name" must be specified during the import (see above).