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

Example Load Dataset

Introduction to the load process

You can find the full specifications for the files here. This page will cover the mandatory fields, foreign keys, and how the files relate to each other.

REFERENCE.tsv

RIDX	PUBMED_ID	JOURNAL_NAME	YEAR	VOLUME	ISSUE	FIRST_PAGE	LAST_PAGE	REF_TYPE	TITLE	AUTHORS	ABSTRACT
1								Dataset	Pathogen Box Compounds Screening 	Bloggs, J; Smith, M	400 compounds from the Pathogen box were screened for inhibitory activity against two human proteins...

The Reference file describes the deposition itself. Whether it currently has a published reference, or has been submitted pre-publication or without being associated with a publication.

  • RIDX and REF_TYPE are mandatory, all other fields are optional. So for example if you do not yet have a DOI, you can leave it blank. It can be added once your data are published.
  • REF_TYPE must be either "Publication" or "Deposited".

ASSAY.tsv

AIDX	RIDX	ASSAY_DESCRIPTION	ASSAY_TYPE	ASSAY_TEST_TYPE	ASSAY_ORGANISM	ASSAY_STRAIN	ASSAY_TAX_ID	ASSAY_TISSUE	ASSAY_CELL_TYPE	ASSAY_SUBCELLULAR_FRACTION	TARGET_TYPE	TARGET_NAME	TARGET_ACCESSION	TARGET_ORGANISM	TARGET_TAX_ID
1	1	Compound was evaluated for the inhibition of human FECH at 10uM	B	In vitro	Homo sapiens		9606				PROTEIN	FECH	P22830	Homo sapiens	9606
2	1	Compound was evaluated for the inhibition of human HMBS at  100uM	B	In vitro	Homo sapiens		9606				PROTEIN	HMBS	P08397	Homo sapiens	9606

This file provides a brief description of the assay, along with the target organism, tissue, cellular fraction etc.

  • AIDX, ASSAY_DESCRIPTION and ASSAY_TYPE are all mandatory.
  • RIDX is optional, but if included it must be an RIDX owned by the depositor. Either one in this set of files or one already loaded into ChEMBL.
  • This table describes what the assay is and what it targets.

AIDX Definition

ASSAY_PARAM.tsv

AIDX	TYPE	RELATION	VALUE	UNITS	TEXT_VALUE	COMMENTS
1	CONC	=	10	uM		
2	CONC	=	100	uM

This file describes the assay parameters. For example, here the first two records show the concentration of compound used.

  • It is a many-to-one mapping, so you can store multiple parameters for one assay.
  • Depositors can set their own TYPE, but the type must uniquely match to a data type. For example, you may not use both CONC and CONCENTRATION as TYPEs if they are both referring to the same sort of concentration data.
  • AIDX and ASSAY_PARAM are both mandatory.
  • AIDX must match an existing AIDX owned by the depositor.

COMPOUND_RECORD.tsv

This is a truncated example showing only the first 3 rows. The full file is available in the "Simple Example Dataset" download.

CIDX	RIDX	COMPOUND_NAME	COMPOUND_KEY
MMV010764	1	MMV010764	MMV010764
MMV026468	1	MMV026468	MMV026468
MMV011229	1	MMV011229	MMV011229
  • The CIDX field is mandatory.
  • RIDX is optional, but if included it must be an RIDX owned by the depositor.

ACTIVITY.tsv

This is a truncated example showing only the first 3 rows. The full file is available in the "Simple Example Dataset" download.

RIDX	CRIDX	CIDX	AIDX	TYPE	RELATION	VALUE	UPPER_VALUE	UNITS	ACTIVITY_COMMENT
1	1	MMV161996	1	Inhibition		0		%	Not active
1	1	MMV202458	1	Inhibition		1		%	Not active
1	1	MMV676395	1	Inhibition		12		%	Not active
  • CIDX, AIDX and ACTIVITY are mandatory.
  • It is possible to load data without a CTAB file. If you include a CTAB file or will be loading structure data later, the CIDX fields in the CTAB must match the CIDX IDs here.
  • RIDX is optional, but if included it must be an RIDX owned by the depositor.
  • This table will take non-numerical activity values is submitted in the ACTIVITY_COMMENT field. CRIDX should generally be identical to RIDX.

ACTIVITY_PROPERTIES.tsv

ACT_ID	TYPE	RELATION	TEXT_VALUE	UNITS
1	HILL_SLOPE	=	1.1

Not a mandatory file, and omitted from the simple test set.
Can be used to supply additional activity information, for example the Hill slope of a curve.
Should contain information that is neccessary for interpretation of the ACTIVITY table data. Raw results and other supporting information belongs in

  • ACT_ID and TYPE are mandatory.
  • TYPE descripes the type of measurement.
    • Depositors can set their own categories for TYPE, but should not use the same TYPE value for different sorts of data.
    • E.g. PB_HILL_SLOPE __and PB_R_SQUARED would be valid, but storing both Hill slope and R-Squared data as PB would not be. Even if they had different UNITS or COMMENTS.
  • Can contain dependent or independent variables. If RESULT_FLAG is set to 1, it shows the record is a dependent variable/result (e.g., slope) rather than an independent variable/parameter.

ACTIVITY_SUPP

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

Not a mandatory file, and omitted from the simple test set.
This contains supplementary data on the ACTIVITY file.

  • It is not necessary to supply, for example, all the points on a curve.
  • It is more useful with datasets such as in vivo studies where animal-level data is submitted.
  • In this case, it shows the treatment group for each sample. And for any sample where a side effect on the cells was recorded, it notes this.

ACTIVITY_SUPP_MAP.

ACT_ID	SAMID
0	0
1	1
2	2

Not a mandatory file, and omitted from the simple test set.
This table maps activity IDs in the ACTIVITY file to sample IDs in the ACTIVITY_SUPP file. Both fields are mandatory.

COMPOUND_CTAB.sdf

This is a truncated example showing only the first SDF record. The full file is available in the "Simple Example Dataset" download.

  • It is possible to load data without a CTAB file. If you include a CTAB file or will be loading structure data later, the CIDX fields in the CTAB must match the CIDX IDs in ACTIVITY.tsv.

  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

$$$$

{% file src=".gitbook/assets/simple_full_example.zip" %}