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= link_to "Back to model creation", '/create'
%h2 Spreadsheets (Excel, CSV)
%p
Input files have two columns. Enter in the first column the chemical structure in
%a{:href => "http://en.wikipedia.org/wiki/Simplified_molecular_input_line_entry_specification", :rel => "external"} SMILES
format, in the second column the toxic activity. The first line contains a description of the columns and is ignored.
%dl
%dt Classification datasets
%dd Please use 1/0, active/inactive or true/false to indicate active/inactive compounds.
%dt Regression datasets
%dd
Enter a quantitative value. For optimal performance you should
%ul
%li
use
%a{:href => "http://en.wikipedia.org/wiki/Molar_(concentration)", :rel => "external"} molar
units
%li enter non-logarithmic values (logarithms are taken internally)
%li avoid 0 activities (will be ignored)
%p
Input files are accepted in
%a{:href => "http://en.wikipedia.org/wiki/Microsoft_Excel", :rel => "external"} Excel
and
%a{:href => "http://en.wikipedia.org/wiki/Comma-separated_values", :rel => "external"} CSV
formats.
%h3 Excel example
- n = 0
.code
%table
%tr
%td
%th A
%th B
%tr
- n += 1
%th= n
%td SMILES
%td Hamster Carcinogenicity
%tr
- n += 1
%th= n
%td CC(=O)Nc1ccc(O)cc1
%td 1
%tr
- n += 1
%th= n
%td O=c1[nH]cnc2[nH]ncc12
%td 1
%tr
- n += 1
%th= n
%td CCCCNc1cc(cc(c1Oc2ccccc2)S(=O)(=O)N)C(=O)O
%td 1
%tr
- n += 1
%th= n
%td CC(C)(C)NCC(O)COc1cccc2NC(=O)CCc12
%td 1
%tr
- n += 1
%th= n
%td CN(C)CCCC1(OCc2cc(C#N)ccc21)c3ccc(F)cc3
%td 1
%tr
- n += 1
%th= n
%td CCC(CC)CCN1C(=O)CN=C(C2CCCCC2F)c3cc(Cl)ccc13
%td 0
%tr
- n += 1
%th= n
%td CCN(CC)CC(=O)Nc1c(C)cccc1C
%td 0
%tr
- n += 1
%th= n
%td CC(C)(C)NCC(O)COc1cccc2CC(O)C(O)Cc12
%td 0
%tr
- n += 1
%th= n
%td CN1CCCC1c2cccnc2
%td 0
%p
Excel examples for download:
%ul
%li
= link_to "hamster_carcinogenicity.xls", "/hamster_carcinogenicity.xls"
(classification)
%li
= link_to "EPAFHM.xls", "/EPAFHM.xls"
(regression)
%h3 CSV example
.code
%pre
:preserve
SMILES, Hamster Carcinogenicity
CC(=O)Nc1ccc(O)cc1, 1
O=c1[nH]cnc2[nH]ncc12, 1
CCCCNc1cc(cc(c1Oc2ccccc2)S(=O)(=O)N)C(=O)O, 1
CC(C)(C)NCC(O)COc1cccc2NC(=O)CCc12, 1
CN(C)CCCC1(OCc2cc(C#N)ccc21)c3ccc(F)cc3, 1
CCC(CC)CCN1C(=O)CN=C(C2CCCCC2F)c3cc(Cl)ccc13, 0
CCN(CC)CC(=O)Nc1c(C)cccc1C, 0
CC(C)(C)NCC(O)COc1cccc2CC(O)C(O)Cc12, 0
CN1CCCC1c2cccnc2, 0
%p
CSV examples for download:
%ul
%li
= link_to "hamster_carcinogenicity.csv", "/hamster_carcinogenicity.csv"
(classification)
%li
= link_to "EPAFHM.csv", "/EPAFHM.csv"
(regression)
%p You can create CSV files in Excel: Create a sheet with two columns and export them as CSV file with the "Save As" option from the menu, selecting the CSV (comma delimited) format.
%h2 SDF
%p
Currently ToxCreate supports
%a{:href => "http://en.wikipedia.org/wiki/Chemical_table_file#SDF", :rel => "external"} SDF
files with a single data item as shown below (multiple data items will raise an error). You can also download an example SDF file:
= link_to "hamster_carcinogenicity.sdf", "/hamster_carcinogenicity.sdf"
.code
%pre
-# keep empty lines -they are required by SDF
:preserve
6 6 0 0 0 0 0 0 0 0 1 V2000
1.3304 -1.0738 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.1104 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.3767 -0.4086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3767 -1.7390 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.1104 -2.1509 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -1.0738 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 5 2 0 0 0 0
1 6 1 0 0 0 0
2 3 2 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
M END
> <ActivityOutcome_CPDBAS_Hamster>
inactive
$$$$
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