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PubChem BioAssay Description CSV Tags


The PubChem Deposition Gateway allows BioAssay depositors to use spreadsheet files to upload assay description information. Note that this is independent of the CSV file which is accepted to upload BioAssay data. By using CSV files to upload assay description information, one can conveniently prepare an upload inside popular spreadsheet programs without the need to convert to other file formats. There is, however, a requirement that the description information be organized in specific ways so that our system can recognize and better validate it. The principal way this is done is through standard header tags that must be used at the top of each column.

The following is a listing of the accepted CSV file formats, including header requirements and appropriate value tags.
CSV File Types
  1. General Description Items
  2. Result Definitions (TIDs)
  3. Target Definitions
  4. XRefs (Cross References to Other Databases)
  5. Categorized Comments
  6. Panel Assay Information
§Header tag must be in the first column and is mandatory.
*Header tag is mandatory.

1. General Description Items Top of Page
This CSV file defines individual items in the description such as the Name and External RegId of the assay.
Example Usage:
CSV Assay Description General Example
Headers:
  • DESCR_TAG§
  • DESCR_VALUE*
Accepted DESCR_TAGs:
  • PUBCHEM_EXT_DATASOURCE_REGID
  • PUBCHEM_ASSAY_NAME
  • PUBCHEM_ASSAY_DESCRIPTION
  • PUBCHEM_ASSAY_PROTOCOL
  • PUBCHEM_ASSAY_COMMENTS
  • PUBCHEM_GRANT_NUMBER
  • PUBCHEM_HOLD_UNTIL_DATE
    • Accepted format of values for this tag: YYYY/MM/DD, like 2000/12/31. An alternative form of YYYY-MM-DD is also accepted.

  • PUBCHEM_PROJECT_CATEGORY
    • Accepted values for this tag: NIH_MLSCN, NIH_MLPCN,NIH_MLSCN_ASSAY_PROVIDER, NIH_MLPCN_ASSAY_PROVIDER, JOURNAL_ARTICLE, ASSAY_VENDOR, LITERATURE_EXTRACTED, LITERATURE_AUTHOR, LITERATURE_PUBLISHER, RNAI_GLOBAL_INITIATIVE, OTHER

  • PUBCHEM_ACTIVITY_OUTCOME_METHOD
    • Accepted values for this tag: OTHER, PRIMARY_SCREENING, CONFIRMATORY, SUMMARY

  • PUBCHEM_SUBSTANCE_TYPE
    • Accepted values for this tag: SMALL_MOLECULE, NUCLEOTIDE
  • PUBCHEM_ASSAY_PANEL_NAME
  • PUBCHEM_ASSAY_PANEL_DESCRIPTION
2. Result Definitions (TIDs) Top of Page This CSV file defines the result definitions (TIDs) for which you will be providing data (in a later step of the submission process). The format of this file has changed to make it more convenient, but the previous format is still accepted.
Example Usage:
CSV Assay Description Results Example
Column Headers:
  • PUBCHEM_RESULT_TAG§
  • Submitter-defined Result Names (1 per column)*
Row Headers (optional, starting from Row 2):
  • RESULT_TYPE*
    • Accepted values for this tag: FLOAT, INTEGER, BOOLEAN, STRING, PUBCHEM_NCBI_PUBMED_ID, PUBCHEM_NCBI_MMDB_ID, PUBCHEM_EXT_URL, PUBCHEM_NCBI_PROTEIN_GI, PUBCHEM_NCBI_NUCLEOTIDE_GI, PUBCHEM_NCBI_TAXONOMY_ID, PUBCHEM_NCBI_OMIM_ID, PUBCHEM_NCBI_GENE_ID, PUBCHEM_NCBI_PROBE_ID, PUBCHEM_AID, PUBCHEM_SID, PUBCHEM_CID, TARGET_NCBI_PROTEIN_GI, TARGET_NCBI_BIOSYSTEMS_ID, TARGET_NAME, TARGET_DESCRIPTION, TARGET_NCBI_TAXONOMY_ID, TARGET_NCBI_GENE_ID, TARGET_NCBI_DNA_GI, TARGET_NCBI_RNA_GI

  • RESULT_DESCR
  • RESULT_UNIT
    • Accepted values for this tag: PPT, PPM, PPB, MILLIMOLAR, MICROMOLAR, NANOMOLAR, PICOMOLAR, FEMTOMOLAR, MILLIGR_PER_ML, MICROGR_PER_ML, NANOGR_PER_ML, PICOGR_PER_ML, FEMTOGR_PER_ML, MOLAR, PERCENT, RATIO, SECONDS, RECIPROCAL_SECONDS, MINUTES, RECIPROCAL_MINUTES, DAYS, RECIPROCAL_DAYS, ML_MIN_KG, L_KG, HR_NG_ML, CM_SEC, MG_KG, OTHER, NONE, UNSPECIFIED

  • RESULT_ATTR_CONC_MICROMOL
  • RESULT_CONC_RESPONSE_SERIES_ID
  • RESULT_IS_ACTIVE_CONCENTRATION
    • Use 1 for true or leave blank otherwise.

3. Target Definitions Top of Page This CSV file defines one or more targets of the BioAssay.
Example Usage:
CSV Assay Description Target Example
Headers:
  • TARGET_TYPE§
  • TARGET_ID*
  • TARGET_DESCRIPTION
  • TARGET_COMMENT
  • TARGET_NAME
Accepted TARGET_TYPEs:
  • PUBCHEM_NCBI_PROTEIN_GI
  • PUBCHEM_NCBI_DNA_GI
  • PUBCHEM_NCBI_RNA_GI
  • PUBCHEM_NCBI_GENE_ID
  • PUBCHEM_NCBI_BIOSYSTEMS_ID
4. XRefs (Cross References to Other Databases) Top of Page This CSV file provides XRefs, cross references to relevant information in other databases. One example would be PubChem AIDs of other related BioAssays.
Example Usage:
CSV Assay Description XRefs Example
Headers:
  • XREF_TYPE§
  • XREF_VALUE*
  • XREF_ANNOTATION
  • XREF_TYPE_QUALIFIER (Accepted Value: PRIMARY_CITATION)
    Use this only for PubMed-Id type to indicate it is a primary citation directly relevant to the assay.
Accepted XREF_TYPEs:
  • PUBCHEM_AID
  • PUBCHEM_EXT_DATASOURCE_REGID
  • PUBCHEM_NCBI_PUBMED_ID
  • PUBCHEM_NCBI_MESH_TERM
  • PUBCHEM_GENBANK_GENERIC_ID
  • PUBCHEM_NCBI_MMDB_ID
  • PUBCHEM_SID
  • PUBCHEM_CID
  • PUBCHEM_EXT_DATASOURCE_URL
  • PUBCHEM_EXT_SUBSTANCE_URL
  • PUBCHEM_EXT_ASSAY_URL
  • PUBCHEM_NCBI_PROTEIN_GI
  • PUBCHEM_NCBI_NUCLEOTIDE_GI
  • PUBCHEM_NCBI_TAXONOMY_ID
  • PUBCHEM_NCBI_OMIM_ID
  • PUBCHEM_NCBI_GENE_ID
  • PUBCHEM_NCBI_BIOSYSTEMS_ID
  • PUBCHEM_REGNUM
5. Categorized Comments Top of Page Currently, the mechanism for adding/modifying Categorized Comments is via the Load from CSV link on the Assay Description form or via the Upload Description File page. The Categorized Comments CSV file allows for the definition of user-defined TAG-VALUE pairs which are stored in the assay record as comments. All such comments will be searchable in PubChem and provide a convenient placeholder for user-defined ontologies or other definitions outside the scope of the PubChem specification.
Example Usage:
CSV Assay Description Categorized Comments Example
Headers:
  • CAT_COMMENT_TAG§
  • CAT_COMMENT_VALUE*
6. Panel Assay Information Top of Page This CSV file defines the Panel Member information for a Panel Assay. Note that this CSV file is currently input via the separate, dedicated Panel Components Upload dialog.
Headers:
  • PANEL_ID§
  • PANEL_NAME
  • PANEL_DESCRIPTION
  • PANEL_PROTOCOL
  • PANEL_COMMENT
  • PANEL_TARGET_NAME
  • PANEL_TARGET_ID
  • PANEL_TARGET_TYPE
  • PANEL_ACT_OUTCOME_METHOD
  • PANEL_TID_NAMES_REGULAR
  • PANEL_TAXONOMY
  • PANEL_GENE
  • PANEL_TID_NAMES_OUTCOME
  • PANEL_TID_NAMES_SCORE
  • PANEL_TID_NAMES_AC
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