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:

105KB

Simple_Full_Example.zip

archive

Open

The dataset below is a truncated example showing only the first SDF record and first three rows of each file type. The full files are available in the "Simple Example Dataset" 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
PATENT_ID
JOURNAL_NAME
YEAR	2011
VOLUME
ISSUE
FIRST_PAGE
LAST_PAGE
REF_TYPE	Dataset
TITLE	Pathogen Box Compounds Screening
AUTHORS	Bloggs, J; Smith, M
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	MMV010764	MMV026468	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_HMBS
RIDX	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs
ASSAY_DESCRIPTION	Compound was evaluated for the inhibition of human FECH at 10uM	Compound was evaluated for the inhibition of human HMBS at 100uM
ASSAY_TYPE	B	B
ASSAY_ORGANISM	Homo sapiens	Homo sapiens
ASSAY_STRAIN
ASSAY_TAX_ID	9606	9606
ASSAY_TISSUE
ASSAY_CELL_TYPE
ASSAY_SUBCELLULAR_FRACTION
ASSAY_SOURCE
TARGET_TYPE	PROTEIN	PROTEIN
TARGET_NAME	FECH	HMBS
TARGET_ACCESSION	P22830	P08397
TARGET_ORGANISM	Homo sapiens	Homo sapiens
TARGET_TAX_ID	9606	9606

ASSAY_PARAM.tsv

AIDX	PB_FECH	PB_HMBS
TYPE	CONC	CONC
RELATION	=	=
VALUE	10	100
UNITS	uM	uM
TEXT_VALUE
COMMENTS

ACTIVITY.tsv

RIDX	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs
CRIDX	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs	Pathogen_Box_Bloggs
CRIDX_DOCID
CRIDX_CHEMBLID
CIDX	MMV161996	MMV202458	MMV676395
SRC_ID_CIDX
AIDX	1	1	1
TYPE	Inhibition	Inhibition	Inhibition
ACTION_TYPE	ANTAGONIST	ANTAGONIST	ANTAGONIST
TEXT_VALUE
RELATION	=	=	=
VALUE	0	1	61
UPPER_VALUE
UNITS	%	%	%
SD_PLUS
SD_MINUS
ACTIVITY_COMMENT	Not active	Not active	Active
ACT_ID	PB_FECH_MMV161996	PB_FECH_MMV202458	PB_FECH_MMV676395
TEOID

ACTIVITY_PROPERTIES.tsv

ACT_ID	PB_FECH_MMV161996
TYPE	HILL_SLOPE
RELATION	=
VALUE
UNITS
TEXT_VALUE	1.1
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_MMV161996	PB_FECH_MMV202458	PB_FECH_MMV676395	PB_FECH_MMV676395
SAMID	0	1	2	2