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Annotations

Annotations help users search for and find data, and they are a powerful tool used to systematically group and/or describe things in Synapse.

Annotations are stored as key-value pairs in Synapse, where the key defines a particular aspect of your data, for example (species, assay, fileFormat) and the value defines a variable that belongs to that category (mouse, RNAseq, .bam). You can use annotations to add additional information about a project, file, folder, table, or view.

Annotations can be based on an existing ontology or controlled vocabulary, or can be created as needed and modified later as your metadata evolves.

Note: You may optionally follow the Uploading data in bulk tutorial instead. The bulk tutorial may fit your needs better as it limits the amount of code that you are required to write and maintain.

Tutorial Purpose

In this tutorial you will:

  1. Add several annotations to stored files
  2. Upload 2 new files and set the annotations at the same time

Prerequisites

  • Make sure that you have completed the File tutorial or have at least 1 file in your Synapse project.

1. Add several annotations to stored files

First let's retrieve all of the Synapse IDs we are going to use

{!docs/tutorials/python/tutorial_scripts/annotation.py!lines=5-23}

Next let's define the annotations I want to set

{!docs/tutorials/python/tutorial_scripts/annotation.py!lines=25-31}

Finally we'll loop over all of the files and set their annotations

{!docs/tutorials/python/tutorial_scripts/annotation.py!lines=33-51}
You'll see that each file now has a number of annotations: 
Batch 1 Folder ID: syn53205629
Got the annotations for File: SRR12345678_R1.fastq.gz, ID: syn53205687, Annotations: {}
Set the annotations for File: SRR12345678_R1.fastq.gz, ID: syn53205687, Annotations: {'assay': ['SCRNA-seq'], 'species': ['Homo sapiens'], 'dataType': ['geneExpression'], 'fileFormat': ['fastq']}
Got the annotations for File: SRR12345678_R2.fastq.gz, ID: syn53205688, Annotations: {}
Set the annotations for File: SRR12345678_R2.fastq.gz, ID: syn53205688, Annotations: {'assay': ['SCRNA-seq'], 'species': ['Homo sapiens'], 'dataType': ['geneExpression'], 'fileFormat': ['fastq']}

2. Upload 2 new files and set the annotations at the same time

Assuming we have a few new files we want to upload we'll follow a similar pattern defined in the File tutorial, except now we'll specify the annotations attribute before uploading the file to Synapse.

In order for the following script to work please replace the files with ones that already exist on your local machine.

{!docs/tutorials/python/tutorial_scripts/annotation.py!lines=53-78}
You'll notice the output looks like: ``` Stored file: SRR92345678_R1.fastq.gz, ID: syn53206218, Annotations: { "assay": [ "SCRNA-seq" ], "dataType": [ "geneExpression" ], "fileFormat": [ "fastq" ], "species": [ "Homo sapiens" ] } Stored file: SRR92345678_R2.fastq.gz, ID: syn53206219, Annotations: { "assay": [ "SCRNA-seq" ], "dataType": [ "geneExpression" ], "fileFormat": [ "fastq" ], "species": [ "Homo sapiens" ] } ```

Results

Now that you have annotated your files you'll be able to inspect this on the individual files in the synapse web UI. It should look similar to:

annotation

Source code for this tutorial

Click to show me 
{!docs/tutorials/python/tutorial_scripts/annotation.py!}

References used in this tutorial

  • [Annotations][synapseclient.Annotations]
  • [File][file-reference-sync]
  • [syn.login][synapseclient.Synapse.login]
  • [syn.findEntityId][synapseclient.Synapse.findEntityId]
  • [syn.getChildren][synapseclient.Synapse.getChildren]
  • [syn.get_annotations][synapseclient.Synapse.get_annotations]
  • [syn.set_annotations][synapseclient.Synapse.set_annotations]
  • [syn.store][synapseclient.Synapse.store]