This vignette use case will combine concepts from Annotations and QueriesAnnotating Data With Metadata, /wiki/spaces/DOCS/pages/2011070739, Uploading and Downloading Data in BulkOrganizing Data Into Projects, Files, and Folders. You will learn how to:
Create a manifest
Upload 100 files
Edit annotations on these files using the Synapse programmatic clients
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To batch upload files, create a tab-delimited manifest which contains, at minimum, the columns path and parent. You can also add additional annotations as columns in your manifest. For example, your manifest might have the following headers: path, parent, specimenID, assay, species, platform, sex, and fileFormat. See Creating a Manifest in Uploading and Downloading Data in Bulk for additional details.
path: the local path to your file
parent: the Synapse ID (in the format syn123456) of the folder or project where your files will be uploaded
specimenID: the unique identifier for each of your specimens
assay: the technology used to generate the data in this file (for example, RNASeq, ChIPSeq, wholeGenomeSeq)
species: the species of your sample (for example, Mouse, Rat, Human, Triceratops)
platform: the hardware used to generate the data (for example, HiSeq2500, Affy6.0, HoodDNASequencer)
sex: a label assigned at birth based on biological attributes (for example, male or female)
fileFormat: is the type of file (e.g. fastq, R script)
path | parent | specimenID | assay | species | platform | sex | fileFormat |
|---|---|---|---|---|---|---|---|
/local/path/to/velociraptor_b.fastq | syn123 | blue_1 | wholeGenomeSeq | Velociraptor mongoliensis | HoodDNASequencer | female | fastq |
/local/path/to/velociraptor_d.fastq | syn123 | delta_1 | wholeGenomeSeq | Velociraptor mongoliensis | HoodDNASequencer | female | fastq |
Save this file in a tab-delimited format called velociraptor_manifest.tsv.
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