Within the definition of a Sample Type, you can indicate one or more columns that will generate a parentage relationship with the samples being created. The parent(s) can exist in the same or different Sample Type than the one you are creating. Adding a parent and providing a File Import Column Name (aka a "Parent Alias") in the definition of a Sample Type creates the linkage to parent samples during import. You can opt to make this relationship Required if desired. Note that the column alias/import column name is not actually added to the Sample Type, instead the system pulls data from it to determine parentage relationships.
For example, if you have a group of "Vial" samples like the following, where v1 has two 'children', v1.1 and v1.2:
| SampleID | MyParent |
|---|---|
| v1 | |
| v1.1 | v1 |
| v1.2 | v1 |
...you could indicate the parent column name "MyParent" as part of the definition of this Sample Type, so that these relationships would be represented in lineage immediately upon import.
You will see the Parent Import Alias(es) listed on the overview tab for the Sample Type.
Within the definition of a Sample Type, you can indicate one or more columns that will indicate a Source of the samples being created. Adding a source of a given type in the definition of a Sample Type creates the linkage to sources during import, rather than requiring sources be added later.
As for sample parents, you'll select the type, give a File Import Column Name (a "Source Alias"), and can optionally check the Required box if you want every sample to have a source of this type. You can include multiple source aliases as needed. When you use an import template or add samples manually in a grid, columns for all source aliases will be included.
You will see the Source Import Aliases listed on the overview tab for the Sample Type.
Learn more about sources in this section:
When creating samples, you can include parent/source information based on the Lineage Settings in the sample type, i.e. for any parents or sources included. When you use a template to import from file columns for all parent/source lineage relationships will be included. As shown below, the "MyParent" column contains the parent identifier.
If you add samples manually in a grid, a parent of the selected type will included by default, though the "File Import Column Name" you gave will not be shown in the UI. Instead it will be named for the selected sample type plus the word "Parents", i.e. "Vial Parents".
The system will capture and generate lineage for the parent(s) of the samples you have created. Learn more about using the Lineage tab in sample details below.
If you want to require that all samples of a given type have a given type of parent or source entity, use the checkbox in the Sample Type definition:
When you add new samples, this column will be required. Note that if you are using a grid method, you won't see the "MyParent" column name, you'll see the type of the parent that must be provided.
Once you have created the parent samples in the system and want to create new samples with specific parents (i.e. aliquot, pool, or derive new samples), you can do so from the Samples grid or by importing from a file referencing the parent sample IDs.
Within the application, you can create new samples from any grid of parent samples. Note that if you select more than 1000 rows, the option to create samples with those parents is disabled.
Learn more about providing the required information to Finish Creating the selected type of child sample in this topic:
If you have already created the Sources in the system and want to create new samples from specific sources, you can do so from the Sources grid.
After creating the parent samples, you can create new derivatives, pooled samples, and aliquots by importing from a file, referencing the parent samples you already created. Obtain the expected import format template, then populate it to indicate the relationships.
You can also update existing samples with parent and source relationships, or merge both existing and new samples using the Edit > Update from File option.
Learn more about the specific fields to populate in this topic: Aliquots, Derivatives, and Sample Pooling
You can include fields from ancestor samples and sources in customized grid views. Any user can make their own named custom views, selectively sharing them with the rest of the team, and administrators can customize the default view everyone sees.
For example, if you had a "PBMC" sample type and wanted to include in the grid both the "Draw Date" field from the parent "Blood" sample type AND the "Strain" field from a "Mouse" source, you would add the following:
| Sample Type: PBMC | |||
|---|---|---|---|
| Parent Type | Parent Field | Label | Position |
| Blood (a Sample Type) | Draw Date | Blood Draw Date | right of Processing Operator |
| Mice (a Source Type) | Strain | Mouse Strain | right of Blood Draw Date |
The selection of the Mouse Strain field would look like this, with Ancestor and Mice nodes expanded:
Save the updated grid view, and you can then filter, sort, and search based on that parent metadata. Shown below, we're showing only samples that come from "BALB/c" mice.
Up to 20 levels of ancestor can be traversed and displayed in a grid.
Lineage across multiple sample types in one tabbed grid can be viewed using the Ancestor node on the All Samples tab. Note that when viewing some grids, such as picklists, the Ancestor node will be under the Sample ID instead of at the top level in the customizer.
Viewing any sample detail page, you will see a tab for Lineage in the header bar. For example:
The lineage graph lets you explore a visual representation of the parentage of samples.
Note that only five generations will display on the lineage graph. To see additional generations, walk the tree up or down to see more levels in either direction.
You can switch to the grid view of the lineage by clicking the green Go To Lineage Grid button.
When lineage is complex, different "generations" are shown horizontally aligned.
The lineage grid can be especially helpful when viewing lengthy lineages or derivation histories. By default, the children of the currently selected sample, aka the "seed", are shown.
If this sample has parents, the Show Parents button will be enabled and you can click it to see them. If the sample has children that are not shown, the Show Children button will be enabled and you can click it to see them.
Entries in the Names column are clickable and connect to the overview page for the sample.
The Distance column specifies the number of generations between each row and the selected seed sample.
Use the arrow buttons in the Change Seed column to change the focus of the grid, expanding and collapsing lineage hierarchies to focus on a different seed.
In situations where sample names are only strings of digits, you may see unexpected lineage results if those "number-names" overlap with row numbers of other samples. In such a situation, when there is ambiguity between sample name and row ID, the system will presume that the user intends to use the value as the name.
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