# Data Model

Each sequencing run produces log files, instrument health data, run metrics, base call information (\*.bcl files), and other data. BaseSpace Sequence Hub demultiplexes base call information to create the FASTQ files used in secondary analysis.

![Data Model](https://330234082-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fg3bE5PSqw4Kkyc9yUsgB%2Fuploads%2Fgit-blob-c9097defc251f40a9955b9a02377688dc46df234%2Fdata-model-biosamples-samples.png?alt=media)

### Common Terms

* **Biosamples** represent the source biological sample being sequenced. They are associated with data aggregated from multiple sequencing runs according the sample name provided in the samplesheet of each run.
* **Samples** represent a set of FASTQ files from a single sequencing run, according to the sample name provided in the samplesheet.
* **Libraries** are produced when a biosample is prepped with a library prep kit.
* **Pools** are an aliquot of one or more libraries, pooled together in order to be placed in a flowcell lane.
* **Datasets** are sets of files produced by a Basespace application. Some views will refer to them as "Other Datasets" to distinguish them from Datasets containing FASTQ files. These were formerly referred to as "App Results."
* **FASTQ Datasets** are a set of FASTQ files produced by FASTQ-Generation or BclConvert apps. Given their proment place in the Basespace data model, they're often treated as a distinct type from "Other Datasets," which aids in data management tasks like filtering & sorting.
* **Projects** are the containers for datasets and dataset files, which can include FASTQ, BAM, and VCF files. Projects can be associated with runs, analyses, and other entities in BaseSpace Sequence Hub. If a given project contains FASTQ files, it will also be associated with one or more Samples & Biosamples.

### Analyzing FASTQ Data

![Analayzing FASTQ Data with Biosample or Sample inputs](https://330234082-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fg3bE5PSqw4Kkyc9yUsgB%2Fuploads%2Fgit-blob-b1d1dfe6cf3e1a35c11dcfa46de87038b41e4947%2Fbiosample-sample-app-launch-colors.png?alt=media)

* Basespace apps that analyze FASTQ files can accept either Biosamples or Samples in the input form, and the system will utilize the proper set of FASTQ files in each situation.
* Basespace users can select their preferred input at the top of the form, and Basespace will load the correct controls into the form:

![Use the radio buttons to reload the form with preferred input types](https://330234082-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fg3bE5PSqw4Kkyc9yUsgB%2Fuploads%2Fgit-blob-f4fcdd32c725149502a82bd24e6207bee52d364d%2Fapp-launch-form.png?alt=media)

### More on Biosamples

{% hint style="info" %}
Runs and Projects are compatible with both Biosamples and Samples to offer maximum flexibility to all types of users
{% endhint %}

* *A run's **Biosamples** tab will list all of the Biosamples that this run contributed yield to:*

![Run-Biosamples List](https://330234082-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fg3bE5PSqw4Kkyc9yUsgB%2Fuploads%2Fgit-blob-3f4f8f7dc741254f7127d278d05d6954591a9fb3%2Frun-details-biosamples.png?alt=media)

* *A project's **Biosamples** tab will list all of the Biosamples associated with FASTQ Datasets that live this this project:*

![Project-Biosamples List](https://330234082-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fg3bE5PSqw4Kkyc9yUsgB%2Fuploads%2Fgit-blob-e6389b8a6db2253867f67d8abbc3258c95a448ef%2Fproj-details-biosamples.png?alt=media)

{% hint style="success" %}
Because BaseSpace Sequence Hub tracks data for the biosample, you can easily aggregate data from a biosample that has been sequenced as part of multiple libraries or pools.
{% endhint %}

### What Happened to the Classic Data Model?

Basespace still has full support for classic data types like Samples (see term definitions above for more info). You can continue to use Samples and the associated set of features if that model is a good fit for your lab's needs, like launching an app with input FASTQ files from a single run.

* *A run's **Samples** tab will continue to list the samples containing FASTQ files produced from that run's sequencing data:*

![Run-Samples List](https://330234082-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fg3bE5PSqw4Kkyc9yUsgB%2Fuploads%2Fgit-blob-3a5e04fcbbf2bb8cdcc564c2328958e7cfd5e51f%2Frun-details-samples.png?alt=media)

* *A project's **Samples** tab will continue to list the samples associated with FASTQ files that live in that project:*

![Project-Samples List](https://330234082-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2Fg3bE5PSqw4Kkyc9yUsgB%2Fuploads%2Fgit-blob-a91525078c3e187ce799beada0cccf71729a5a1f%2Fproj-details-samples.png?alt=media)


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