Assay and instrument data often includes a specimen id field, but not participant id or visit fields. In many cases, this is "by design", since it allows laboratories to work with research data in a de-identified form: the laboratory only knows the specimen id, but does not know the participant ids or visit ids directly.
But, when combining assay data with other sorts of data, how do you transform specimen ids into participant ids and visit ids?
When you upload many types of assay data, you can select a Participant/Visit Resolver, which defines how the assay data will be mapped to samples, specimens, participants, or other types of data. For most assay types, the ParticipantVisitResolver is a batch property. The batch property participant/visit resolver
, lets you declare how to map the collected instrument or specimen data back to participants and visits in order to integrate it with other datasets in your study.
This topic outlines some general principles and options available for data identifiers; specific options available vary based on the type of assay.
When uploading runs of instrument data, the operator selects from a set of options which may include:
- Sample information in the data file (may be blank).
- Participant id and visit id.
- Participant id and date.
- Participant id, visit id, and date.
- Specimen/sample id.
- Sample indices, which map to values in a different data source.
Mapping Sample Indices
The "Sample indices, which map to values in a different data source" option allows you to use an existing indexed list of participant, visit, date, and sample information for your data. At upload time, the user will enter a single index number for each specimen; the target data source will contain the required mapping values. The sample indices list must have your own specimen identifier as its primary key, and uses the values of the 'SpecimenID', 'ParticipantID', 'Date', and 'VisitID' columns.
You can specify a mapping either by pasting a TSV file or by selecting a specific folder, schema, and list. Either method can be used during each upload or specified as a default. To paste a TSV file containing the mapping, you can first click Download Template
to obtain a correctly typed template. After populating it with your data, cut and paste the entire spreadsheet (including column headers) into the box provided:
To specify an existing list, use the selection dialog pulldowns to choose the folder, schema, and specific query (list) containing your mapping:
Using Default Values
The operator may specify the mapping each time data is uploaded, but in some cases you may want to set automatic defaults. For example, you might always want to use a specific source list for the participant/visit identifier, such as a thaw list populated at the time samples are removed from the freezer for testing. The operator could specify the list at the time of each batch upload, but by including the default list as part of your assay design you can simplify upload and improve consistency.
- Select Manage Assay Design > Set Default Values > [design name] Batch Fields.
- Select Sample indices, which map to values in a different data source.
- Either paste the contents of a TSV file or select Use an existing list and select the Folder, Schema, and Query containing your list.
- Click Save Defaults.
- Click Save and Close.
You may also choose to include the list or other default value as part of the assay design directly