Example dataset

An example dataset, showing the structure of all required files and advice on avoiding common issues.

A simple set of example data files suitable for use as a template are available below:

Simple_Full_Example.zip

archive · 12KB

Open

The dataset below is a truncated example showing only the first SDF record and first rows of each file type. The full files are available in the "Simple_Full_Example" download. Mandatory fields are in bold.

PLEASE NOTE: For ease of viewing the column headers have been formatted as rows in this example. When submitting data to ChEMBL the formatting should be rotated by 90 degrees so that the fields are column headers and each row below is a data entry point.

REFERENCE.tsv

RIDX	Pathogen_Box_Bloggs
PUBMED_ID
DOI	10.1016/S0960-894X(01)81052-0
DATA_LICENCE	This has been left as a placeholder string. In order to include your data, it must be filled with CC0, in order to show you consent to your data being released as Public Domain. If this is not possible for you, contact us, and we may be able to permit an alternative free/open licence.
CONTACT	https://orcid.org/0000-0002-0343-0319
PATENT_ID
JOURNAL_NAME
YEAR	2022
VOLUME
ISSUE
FIRST_PAGE
LAST_PAGE
REF_TYPE	Dataset
TITLE	Pathogen Box Compounds Screening
AUTHORS	Bloggs, J; Smith, M
DOI	10.1016/S0960-894X(01)81052-0
ABSTRACT	400 compounds from the Pathogen box were screened for inhibitory activity against two human proteins.

COMPOUND_RECORD.tsv

CIDX	MMV010764	MMV026468	MMV011229
RIDX	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs
COMPOUND_NAME	MMV010764	MMV026468	MMV011229
COMPOUND_KEY	1a	2b	MMV011229
COMPOUND_SOURCE

COMPOUND_CTAB.sdf

  Mrv0541 04191616472D          

 27 28  0  0  0  0            999 V2000
   -5.0013   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2868    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5724   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8579   -0.8250    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434   -1.2375    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5559   -1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7309   -0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.6500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434   -3.7125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -2.4750    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7158   -4.1250    0.0000 Cl  0  0  0  0  0  0  0  0  0  0  0  0
    4.2868   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579   -4.1250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7145   -2.8875    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  2  0  0  0  0
  6  8  2  0  0  0  0
  6  9  1  0  0  0  0
  9 10  2  0  0  0  0
 10 11  1  0  0  0  0
 11 12  2  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 15 16  2  0  0  0  0
 15 17  1  0  0  0  0
 17 18  1  0  0  0  0
 18 19  2  0  0  0  0
 19 20  1  0  0  0  0
 20 21  2  0  0  0  0
 21 22  1  0  0  0  0
 21 23  1  0  0  0  0
 23 24  2  0  0  0  0
 18 24  1  0  0  0  0
 24 25  1  0  0  0  0
 12 26  1  0  0  0  0
 26 27  2  0  0  0  0
  9 27  1  0  0  0  0
M  END
> <CIDX>
MMV161996

$$$$

ASSAY.tsv

AIDX	PB_FECH	PB_CAVIA
RIDX	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs
ASSAY_DESCRIPTION	Compound was evaluated for the inhibition of human FECH at 10uM	Half life in Dunkin-Hartley guinea pig plasma at 5 mM by HPLC analysis
ASSAY_TYPE	B	A
ASSAY_ORGANISM	Homo sapiens	Cavia porcellus
ASSAY_STRAIN		Dunkin-Hartley
ASSAY_TAX_ID	9606	10141
ASSAY_TISSUE		Plasma
ASSAY_CELL_TYPE
ASSAY_SUBCELLULAR_FRACTION
ASSAY_SOURCE
TARGET_TYPE	PROTEIN	ADMET
TARGET_NAME	FECH
TARGET_ACCESSION	P22830
TARGET_ORGANISM	Homo sapiens
TARGET_TAX_ID	9606

ASSAY_PARAM.tsv

AIDX	PB_VIRUS	PB_VIRUS
TYPE	CONC	TIMEPOINT
RELATION	=	=
VALUE	10	2
UNITS	uM	hr
TEXT_VALUE
COMMENTS

ACTIVITY.tsv

CIDX	MMV161996	MMV161996	MMV202458	MMV202458	MMV676395	MMV676395
CRIDX	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs
AIDX	1		1		1
TYPE	Inhibition	Inhibition	Inhibition	Inhibition	Inhibition	Inhibition
ACTION_TYPE	ANTAGONIST	ANTAGONIST	ANTAGONIST	ANTAGONIST	ANTAGONIST	ANTAGONIST
TEXT_VALUE		Active		Not Active		Not Active
RELATION	=		=		=
VALUE	2		2		0
UNITS	%		%		%
ACTIVITY_COMMENT
ACT_ID	PB_FECH_MMV161996	PB_FECH_MMV161996	PB_FECH_MMV202458	PB_FECH_MMV202458	PB_FECH_MMV676395	PB_FECH_MMV676395

ACTIVITY_PROPERTIES.tsv

ACT_ID	PB_FECH_MMV161996
TYPE	HILL_SLOPE
RELATION	=
VALUE	1.1
UNITS
TEXT_VALUE
COMMENTS
RESULTS_FLAG

ACTIVITY_SUPP.tsv

REGID	0	1	2	2
SAMID	0	1	2	2
TYPE	Treatment	Treatment	Treatment	"Side Effect (Y,N)"
RELATION	=	=	=
TEXT_VALUE				Y
UNITS
VALUE
COMMENTS	1	1	1	"Y,N"

ACTIVITY_SUPP_MAP.tsv

ACT_ID	PB_FECH_MMV010764	PB_FECH_MMV675997	PB_FECH_MMV026468
SAMID	0	1	2