Upload BioAssays

Format Bioactivity Data

If you have only a few records to upload, use our web form to fill in your information.

 

To submit many test results, it is most convenient to prepare a file for upload. You can do this with a standard spreadsheet file, like CSV (though we also accept an XML format based on our data specification):

  • First row contains PubChem-standard or your custom tags defining each column
  • Each subsequent row defines one tested substance result

 

Make Sure Your Spreadsheet Includes Some Key Columns

 

Define Tested Substances

When reporting bioactivity results, you will likely have one intial column containing an identifier for the substance that you are testing. That is a good start, but we need your substance identifier to refer to an actual substance record in PubChem, typically one that you have uploaded. If your tested substances are chemicals, you might have the structure for them (e.g. a SMILES string) and perhaps a common name for the molecules. If your substances are siRNAs, for example, you might have a Gene identifier for each.

 

First create a substance submission as you must have a unique identifier for each tested substance. Typically, the easiest way to do this is to extract a couple of relevant columns from your bioactivity spreadsheet and create a second substance spreadsheet containing only data defining the molecules, not the test results.

 

Make Expert Judgment Inactive/Active For Each Result

After the column with your unique substance identifiers, you must create a second column with a summarized, expert determination of whether the tests you performed for that substance were inactive (1) or active (2) using those numerical codes. This can be defined however you think is appropriate, but please clearly state in the Comments section of the assay description exactly how you made this judgment call.

 

Create Active Concentration Column

In many assay experiments there will be a single numerical data point for the response measured from the test, such as an AC50, IC50. This is often the data on which the inactive/active outcome determination is made.

 

Describe Experiment So That Users Can Find It

As important as it is to record the bioactivity results you measured, it is essential to include a clear description of your experiment with keywords and links to relevant literature, gene and protein resources.

 

Name your assay and write up a concise summary including keywords for search

 

Unique Identifier

Create an identifier unique to your PubChem Bioassay collection. It should be a short alpha-numeric string that is meaningful mainly to you and easy to reproduce (i.e. does not contain spaces and other characters susceptible to "typo" errors). You can use this identifier in the future to make updates or to revoke your assay.

 

Name Using Keywords

Create a moderately-short phrase of keywords to describe and to distinguish your assay experiment from other experiments.

 

Description, Protocol And Comments

Arrange a description of your assay experiment in these fields as appropriate so that a lay-user can understand what you did. Make sure to include a clear statement of how you determined outcome inactive/active values.

 

Categorized Comments

Associate tag/value pairs with your experiment if, for example, you wish to include ontology terms and their corresponding values.

 

Link To Target Sequence, Literature And Other Databases

 

Target Molecule

For assays testing chemicals interacting with a target such as an enzyme inhibitor, please specify the sequence identifier. For a chemical assay, the target is typically a protein, but it can also be a gene or nucleotide.

 

Cell-based assays can skip this field.

 

If you have more than a couple of targets, such as an RNAi assay, list them instead as a separate column in the Assay Data.

 

Cross References To Literature and Other Databases

Link your assay to related database records such as a published paper listed in PubMed or a particular tested species listed in NCBI Taxonomy.

 

Set Options Like Group Related Assays And Hold-Until Date

 

Assay Group For Multiple Targets or Experiments

Typically, one PubChem BioAssay record reports on one experiment performed on one target. If you performed the same experiment against multiple targets or conducted follow-up counter screens, etc., you will likely have the need to create multiple PubChem BioAssay records. In this case, they can all be tied together by using the same unique identifier in this field for all of the BioAssay records.  This group label will not display on the public page, but simply connects logically-related assays.

 

Set the Assay Group label under the Options tab.

 

Hold-Until Date

Optional hold-until date to delay public access of assay data in PubChem. During this on-hold period, you can share restricted access with others by generating a private URL via your PubChem Upload account.

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