Skip to content

Commit

Permalink
πŸ“ Document samples and specimens
Browse files Browse the repository at this point in the history
πŸ”₯ Remove test text
  • Loading branch information
chris-s-friedman committed May 29, 2024
1 parent 2b5ee89 commit 18250dd
Showing 1 changed file with 21 additions and 11 deletions.
32 changes: 21 additions & 11 deletions docs/source/design/concepts/samples_and_specimens.rst
Original file line number Diff line number Diff line change
@@ -1,12 +1,13 @@
=====================
.. _samples_and_specimens:

========================
Samples and Biospecimens
=====================
========================

Although similarly named, samples and biospecimens refer to different things:

- A **sample** is a physical piece of tissue, blood, or other material taken
from a patient.
- A **biospecimen** is a part of that sample, e.g. an aliquot of a sample.
* A **sample** is a physical piece of tissue, blood, or other material taken from a patient.
* A **biospecimen** is a part of that sample, e.g. an aliquot of a sample.

While samples and biospecimens are distinct concepts, they share much in common.
In fact, when the ingest library was first written, its primary target API,
Expand All @@ -20,11 +21,20 @@ biospecimens.

A sample has qualities:

* A sample may have ino
* A sample may have information about itself, such as the type of tissue it is, the type of tumor it comes from, when the sample was collected from the participant, its volume, etc.
* A sample may have information about shipping, such as the date it was shipped


As discussed above, a biospecimen is a child class of sample, so biospecimens
may have all of the same qualities of a sample*. In addition:

A biospecimen takes on
This
is the smallest unit that a piece of biological material can take, as
represented in the ingest library.
* a biospecimen may have information about its concentration
* a biospecimen may have information about its analyte type (e.g. DNA vs RNA)
* a biospecimen may have information about the consent under which it was collected.

Some
Biospecimen is designed as a child class of sample to provide for
backwards-compatibility with older ingest packages that existed before the
sample concept. Moving forward, it is advised to use the sample class when
extracting information that is most related to the sample and use biospecimen
only when extracting information that is specific to the biospecimen
(such as concentration, analyte, and consent information).

0 comments on commit 18250dd

Please sign in to comment.