Load Biosamples

The biosample importer allows you to specify an analysis: for this pipeline, we won’t.

Load the samples

The Biosample loader is provided by the tripal_biomaterial module (distributed with the tripal_analysis_expression module), and is located at admin/tripal/loaders/chado_biosample_loader. Biosamples can be loaded as either an xml file, or a set of csv/tsv files. xml is preffered, and can be optained from NCBI. csv/tsv format requires that the first line is the column names for the biosample properties.

Select the organism. Note that loading biomaterials from multiple species at a time is not supported. Split up your files to load one organism at a time.

After your file is uploaded, press the Check Biomaterials button to access the CVTERM FIELD CONFIGURATION section. The section will list each property associated with your biosamples. If a term exists in the CVterm database matching the property, it will appear in this section. For every biosample property, associate the property with a CVterm. In a perfect world, all terms will map to an established CV (sequence ontology, plant trait ontology, etc). If no term is listed, or if the only terms listed are biomaterial_property terms, you should

  • Load appropriate CVterms for each property. You can load an entire CV, or individual CVterms using the CVterm loader located at admin/tripal/loaders/chado_cvterms.
  • Rename the properties in your source file so that they match existing CVterms. You can look up available CVterms at admin/tripal/loaders/chado_cvterms.
  • Re-upload the biosample file, and rerun Check Biomaterials.
  • Repeat this process until you have suitable CVterms associated with all biosample properties.

New feature: the above process can now also be applied to the property values. Please see the github documentation for more information.

That said, you can import your biosamples without assigning CVterms. In this case, the generic biomaterial_property CV will be used.

After clicking Submit, you will need to run the job for the samples to be processed.

Publish the biosamples

Once the samples are loaded, they must be published to appear as entities. To do so, go to Content -> Tripal Content -> Publish Tripal Content and select the Biological Sample content type.

Once published, the biomaterial data can be located through the menu under Content > Tripal Content. Filter results by Type > Biological Sample.

Below is an example of successfully uploaded biomaterial data.