Field names and data types - basic submission

The following files are necessary for a minimum data deposition of simple data, such as those describing experiments where 'compound X has affinity (Ki) of Y uM in assay Z.' For most depositors, this data model is sufficient to capture their data. Such depositors need only deposit their data using the files in this section. These must all be tab-separated files.

Additional files required to describe more complex data are found in the Complex results sets section.

Comparatively large datasets may need splitting into subsets in order to ensure timely feedback and loading. We will let you know if this applies to yours.

PLEASE NOTE: For ease of viewing the column headers have been formatted as rows. 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

The REFERENCE file describes the provenance of the deposition, including the title, authors and abstract. It can contain the details of a published reference, or a submitted paper pre-publication, or without being associated with a publication.

The file should contain sufficient details for a user to locate your publication or project by reading the reference. For example, data associated with a project the ABSTRACT field could contain a short description of the dataset and a link to the project site.

• RIDX, TITLE, YEAR, ABSTRACT, AUTHORS and REF_TYPE are mandatory, all other fields are optional.

• For a deposited dataset, YEAR should be the year we received the file.

• It is mandatory to have either a PMID or DOI, if your data do not have one please contact us before submission. We can provide a temporary ChEMBL DOI for datasets until an external DOI has been generated.

The TITLE, ABSTRACT and AUTHORS fields of the REFERENCE file should be populated for datasets, as well as publications. These can be brief (i.e. an organisation name can be provided for the AUTHORS field) and the abstract can be a simple summary of the experiments and their overall purpose. It should contain sufficient details for a user to locate your publication or project by reading the reference; the ABSTRACT field could contain a short description of the dataset and a link to the project site.

Header	Description	Existence	Data Type
RIDX	The RIDX set by the depositor - a primary key	Mandatory	Any character up to a length of 200. Should not start with 0
PUBMED_ID	PubMed ID	Mandatory (if the document has a PMID)	Any positive integer up to a length of 11.
JOURNAL_NAME	Journal name	Optional	Any character up to a length of 50
YEAR	Year of publication	Mandatory	Any integer up to a length of 4 between 1900 and 2050
VOLUME	The volume of the publication	Optional	Any character upt o a length of 50
ISSUE	The issue of the publication	Optional	Any character up to a length of 50
FIRST_PAGE	The first page of the article	Mandatory if it is a Publication	Any positive integer up to a length of 50
LAST_PAGE	The last page of the article	Optional	Any positive integer up to a length of 50
REF_TYPE	The type of reference (Publication, Patent, Dataset, Book)	Mandatory	One of Patent, Publication, Dataset or Book
TITLE	The title of the reference	Mandatory	Any character up to a length of 500
DOI	The Digital Object Identifier	Mandatory - Must be present, may be empty if there is a PUBMED_ID	Any DOI up to a length of 200
PATENT_ID	The Patent Identifier	Optional	Any Patent Identifier up to a length of 200
ABSTRACT	The abstract of the article. For a dataset, include a description of the dataset here	Mandatory	A very large text field
AUTHORS	A list of the authors of the publication	Mandatory	Any character up to a length of 4000
CONTACT		Recommended	Any character up to a length of 200

COMPOUND_RECORD.tsv

COMPOUND_RECORD files provide links between a record ID and a compound ID. If a CIDX-RIDX combination does not yet exist in the COMPOUND_RECORDS table for this src_id, then one will be created. If one already exists, then this existing one will be updated with the COMPOUND_NAME, etc, present in the incoming file. The CIDX is then referenced in ACTIVITY files, to identify which compounds were used.

You must provide at least one of COMPOUND_NAME, COMPOUND_KEY or COMPOUND_SOURCE in order to make the compound searchable. RIDX is optional, but if included it must be an RIDX owned by the depositor.

Header	Description	Existence	Data Type
CIDX	The CIDX set by the depositor - a primary key	Mandatory	Any character up to a length of 200
RIDX	The RIDX cited by the depositor. MUST be owned by the same depositor	Optional	Any character up to a length of 200
COMPOUND_KEY	The local synonym used for this compound in the RIDX referenced	Mandatory	Any character up to a length of 250
COMPOUND_NAME	The name used for this compound in the RIDX referenced	Mandatory	Any character up to a length of 4000
COMPOUND_SOURCE	The source of this compound in the RIDX referenced	Optional	Any character up to a length of 400

COMPOUND_CTAB.sdf

The COMPOUND_CTAB file (a Chemical Table file) defines the structure of a compound. 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 the ACTIVITY.tsv file.

This must be in V2000 molfile format. The InChI binaries we use currently do not accept V3000 molfiles. We cannot accept V3000 InChIs as we need an InChI Key for ChEMBL.

Header	Description	Existence	Data type
CIDX	The CIDX established by the depositor in the COMPOUNDS file - a foreign key	Mandatory	Any character up to a length of 200
CTAB	The CTAB (Connection table) assigned to this CIDX	Optional	A very large text field

ASSAY.tsv

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

• RIDX is optional, but if included it must be an RIDX owned by the depositor.

• The RIDX can be included in the current deposition files or can be one already loaded into ChEMBL. CRIDX should generally be identical to RIDX.

• ASSAY_TAX_ID and TARGET_TAX_ID must be the NCBI Taxon ID for the organism, not the strain. The strain for the assay organism can be given in ASSAY_STRAIN.

• ACT_ID is mandatory if providing an ACTIVITY_PROPERTIES or ACTIVITY_SUPPLEMENTARY record

• AIDX, ASSAY_DESCRIPTION and ASSAY_TYPE are all mandatory.

• TARGET_TYPE must be one from the defined list.

• Activity files must cite only existing DDIs.

An ASSAY record is a single instance of an assay, not an assay protocol record. If the same assay protocol is used in multiple datasets, it is still a new ASSAY in each dataset. Each assay can only have a single target; in the case of a panel assay, there will need to be one assay record per target.

Header	Description	Existence	Data type
AIDX	The AIDX set by the depositor - a primary key	Mandatory	Any character up to a length of 200
RIDX	The RIDX cited by the depositor. MUST be owned by the depositor	Optional	Any character up to a length of 200
ASSAY_DESCRIPTION	A description of the assay	Mandatory	Any character up to a length of 4000
ASSAY_TYPE	The type of the assay. B (Binding) ,F (Functional),A (ADMET),U (Unassigned),P (Physicochemical) or T (toxicity)	Mandatory	Accepted Assay types (ADMET, A, Functional, F, Binding, B, Unassigned, U, Physiochemical, P, Toxicity, T)
ASSAY_GROUP	Assays deposited across multiple datasets/releases that are considered comparable by the depositor are mapped to the same ASSAY GROUP. Allows depositors to group comparable assays, and users to identify assays that can be considered identical.	Optional, unless you plan to submit further data using the same assays.	Any character up to a length of 200
ASSAY_ORGANISM	The assay organism	Optional (Mandatory if ASSAY_TAXON_ID is populated)	Any character up to a length of 250
ASSAY_STRAIN	The strain of the assay organism	Optional	Any character up to a length of 200
ASSAY_TAX_ID	NCBI taxonomy ID for the assay organism	Optional	Any positive integer up to a length of 11 or '0'
ASSAY_SOURCE	The original source of the assay	Optional	Any character up to a length of 100
ASSAY_TISSUE	The type of tissue used in the assay	Optional	Any character up to a length of 100
ASSAY_CELL_TYPE		Optional	Any character up to a length of 100
ASSAY_SUBCELLULAR_FRACTION	The subcellular fraction used in the assay	Optional	Any character up to a length of 100
	The type of target	Optional
TARGET_NAME	The name of the target	Optional	Any character up to a length of 400
TARGET_ACCESSION	A UniProt accession for the target where the target is a protein. Otherwise to be left blank.	Optional	An integer or a UniProt ID up to a length of 255
TARGET_ORGANISM	The target organism	Optional	Any character up to a length of 100
TARGET_TAX_ID	The NCBI taxonomy ID of the target organism	Optional	Any positive integer up to a length of 11 of '0'

ASSAY_CELL_TYPE rules

The asssay_cell_type is either a cell-line name (e.g. MRC-5) or endogenous cell type (e.g. fibroblasts). You can see this in an example cell report card from ChEMBL: https://www.ebi.ac.uk/chembl/cell_line_report_card/CHEMBL3308499/

For cells that are within ChEMBL, the cell report card cell name can be used to populate the 'ASSAY_CELL_TYPE' field, the CHEMBL_ID to populate the MC_CELL_LINE_CHEMBL_ID field and the Cellosaurus_ID can be used to populate the MC_CELLOSAURUS_ID field.

For cell lines that are not found within ChEMBL, Cellosaurus is a good resource. For endogenous cells please try to use the Experimental Factor Ontology (EFO) which can be searched on the Ontology Lookup Service. Otherwise, a depositor-defined name can be provided as the ASSAY_CELL_TYPE.

ASSAY_PARAM.tsv

The ASSAY_PARAM file describes the assay parameters. For example the concentration of compound used, the pH of the buffer, the instrument used for data collection or the timepoints of the experiment.

Thus the ASSAY_PARAM file can be used to assign a list of parameters to an AIDX, which must have either been previously deposited in ChEMBL, or be defined in the ASSAY file, or both.

It is possible to store multiple parameters for one assay. Depositors can set their own parameters, but should use the same description for a type of data every time it is entered; for example, you must not use both CONC and CONCENTRATION if they are both referring to the same sort of concentration data.

Either a numeric VALUE or a TEXT_VALUE can be given for a single parameter; if a numeric value is given then it must include a relation, for example =, < or >.

Header	Description	Existence	Data Type
AIDX	The AIDX established by the depositor in the ASSAY file - a foreign key	Mandatory	Any character up to a length of 200
TYPE	The type of parameter. Must be unique within an AIDX	Mandatory	Any character up to a length of 250
RELATION	Symbol indicating relationship between the Type and the Value (permitted: '>','<','=','~','<=','>=','<<','>>')	Optional (Mandatory if VALUE is given)	Any relation symbol (=, >, <, ~, <=, >=, >>, <<) up to a length of 50
VALUE	The numerical value of the parameter.	Optional	Any number (including decimals, negatives and scientific notation (e.g. 3×10^2))
UNITS	The units of the parameter measurement	Optional	Any character up to a length of 100
TEXT_VALUE	The text value of non-numerical values	Optional	Any character up to a length of 4000
COMMENTS	A comment on the parameter.	Optional	Any character up to a length of 4000

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

• AIDX and TYPE are both mandatory.

• A VALUE requires an entry in the RELATION field. A TEXT_VALUE requires that RELATION is empty.

• It is a many-to-one mapping, so you can store multiple parameters for one assay.

• Depositors can set their own TYPE, but you need to use the same TYPE string for each form of data. 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 must match an existing AIDX owned by the depositor.

ACTIVITY.tsv

The ACTIVITY file outlines the numerical or text value of the data arising from a compound (CIDX) used in an assay (AIDX). If a source is updated and includes the previously loaded ACTIVITY file, existing activities will need to be wiped before loading these supplementary files.

For more complex data types, discussed in Complex results sets, supplementary ACTIVITY_PROPERTIES, ACTIVITY_SUPPLEMENTARY and ACTIVITY_SUPP_MAP files can be used to append additional data to the activities using the activity ID (ACT_ID) and test occasion ID (TEOID) set in this file to link them.

• CIDX, AIDX, ACT_ID , CRIDX , TYPE and ACTIVITY are mandatory.

• A VALUE is numeric and requires an entry in the RELATION field.

• TEXT_VALUEs should not have a RELATION sign.

• ACTION_TYPE must be one from the defined list.

• ACT_ID is mandatory if providing an ACTIVITY_PROPERTIES or ACTIVITY_SUPPLEMENTARY record that maps to a given line.

• 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.

• CRIDX should generally be identical to RIDX, unless you need to reference a separate paper for the activity and the compound.

• SRC_ID_AIDX and SRC_ID_CIDX are used when depositing against other depositor’s entities, as discussed in a later section.

Header	Description	Existence	Data type
CIDX	The CIDX established by the depositor in the COMPOUNDS file - a foreign key	Mandatory	Any character up to a length of 200
CRIDX	The RIDX to be associated with the CIDX in the creation of the compound record. Must belong to SRC_ID_CIDX.	Mandatory	Any character up to a length of 200
SRC_ID_CIDX	The SRC_ID for the CIDX. If not specified, then value is assumed to be the SRC_ID for the depositor - this field can be used to reference compounds deposited by other depositors	Optional	Any positive integer up to a length of 4
AIDX	The AIDX established by the depositor in the ASSAY file - a foreign key	Mandatory	Any character up to a length of 200
SRC_ID_AIDX	The SRC_ID for the AIDX. If not specified, then value is assumed to be the SRC_ID for the depositor	Optional	Any positive integer up to a length of 4
RIDX	The RIDX established by the depositor in the REFERENCE file - a foreign key	Deprecated. Not visible to end-users	Any character up to a length of 200
TEXT_VALUE	The text value of non-numerical values. Do not use for value ranges. Provide these as upper and lower bounds, as VALUE fields.	Optional	Any character up to a length of 1000
RELATION	Symbol indicating relationship between the Type and the Value (permitted: '>','<','=','~','<=','>=','<<','>>')	Optional (Mandatory if a VALUE is given)	Any Relation symbol (=, >, <, ~, <=, >=, >>, <<) up to a length of 50
VALUE	The numerical value of the activity measurement (see ACTIVITY_COMMENT for non-numerical values)	Optional	Any number (including decimals, negatives and scientific notation (e.g. 3×10^2))
UPPER_VALUE	Where the activity is a range, this represents the highest value of the range (numerically), while the VALUE column represents the lower value	Optional	Any number (including decimals, negatives and scientific notation (e.g. 3×10^2))
UNITS	The units of the measurement	Optional	Any character up to a length of 100
SD_MINUS	Standard Deviation Lower limit	Optional	Any number (including decimals, negatives and scientific notation (e.g. 3x10^2))
SD_PLUS	Standard Deviation Upper limit	Optional	Any number (including decimals, negatives and scientific notation (e.g. 3x10^2))
ACTIVITY_COMMENT	A comment on the activity measurement. Non-numerical 'values' should be given here. Equivalent to 'TEXT_VALUE' field in many other tables.	Optional	Any character up to a length of 4000
CRIDX_CHEMBLID	The CHEMBLID for the CRIDX. Must belong to the SRC_ID_CIDX	Optional	Any character up to a length of 200
CRIDX_DOCID	The DOCID for the CRIDX. Must belong to the SRC_ID_CIDX	Optional	Any character up to a length of 200
ACT_ID	A local ID used to relate records in ACTIVITY_PROPERTIES and Supplementary tables. A primary key in this table. Not required unless depositing such data.	Optional (Mandatory if there are ACTIVITY_PROPERTIES or ACTIVITY SUPPLEMENTARY files)	VARCHAR(50) Must be unique for each activity line, even if they have identical Properties.
TEOID	TEst Occasion ID, grouping together related Activity records. Usually used to group activities by time point and treatment. A primary key in this table.	Optional	Any integer up to a length of 11
TYPE	The type of measurement	Mandatory	Any character up to a length of 250
ACTION_TYPE		Optional	Any character up to a length of 50 - must be in the ACTION_TYPE table (see below)

INFO.txt

An INFO file can be included in a deposition to contain any additional information you might want to include with the deposited data. The INFO file will be stored but not entered into the database.