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. Setting a parent alias in the definition of a Sample Type creates the linkage to parent samples during import, but note that the column aliased 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 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 alias "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 Aliases listed on the overview tab for the Sample Type.
When importing samples of this type, include parent information in one of the aliased columns. As shown below, the "MyParent" column contains the parent identifier.
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.
Within the definition of a Sample Type, you can indicate one or more columns that will indicate a Source of the samples being created. Setting a source alias in the definition of a Sample Type creates the linkage to sources during import, rather than requiring sources be added later.
You will see the Source Import Aliases listed on the overview tab for the Sample Type.
Give the name of the source alias column and select the source type from the dropdown, as for parent samples. You can include multiple source aliases as needed.
Learn more about sources in this section:
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, 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 | Draw Date | Blood Draw Date | right of Processing Operator |
Mice | Strain | Mouse Strain | right of Blood Draw Date |
You could then filter, sort, and search based on that parent metadata. Shown below, we're showing only samples that come from "BALB/c" mice.
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.
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.