This document covers the details of how biomaterials (samples
etc.) are handled by BASE.
- There are 4 types of biomaterials:
- biosources (e.g. cell lines, patients)
- samples (e.g. tumor samples or treated cell lines)
- labeled extracts
- Biosource, sample and extract is the parent type of
sample, extract and labeled extract, respectively.
- A non-biosource biomaterial may be created either from a single
biomaterial of its parent type, or from a set of biomaterials
of the same type as itself (pooling). It can also be created
without references to any other biomaterial.
- [IMPLEMENTATION NOTE] This is implemented as a parent
column in the sample
table, which references a biosource. If the value is NULL,
another table holds the set of samples used for pooling.
Ditto for extract and labeled extract.
- [IMPLEMENTATION NOTE] Of each type, there should
be one special biomaterial which
represents 'none', so that a graph of biomaterials always
can stretch all the way up to biosource. Such a graph must
always be a directed acyclic graph. The 'none' biomaterials
cannot be annotated or deleted, and must be readable by all.
- A biosource can only be created from scratch, with
no association to any kind of parent. Biomaterials of other
types can be created from scratch as well, and will then
reference the 'none' biomaterial of the parent type.
- A biomaterial can be dissociated from its parent(s). The core
will not take any responsibility for downstream data that may
depend on the original association, for example inherited annotations
and analysis results.
- There are different labels (dyes), and each labeled extract is
associated with one label.
- [NOTE] Sample tissues (a BASE 1 concept) are
implemented as annotations.
- [Possibly a client issue] When a biomaterial is created
from pooling, BASE may give it as secondary annotations those
annotations that are common to all the pooled biomaterials. Primary
annotations may be created from the consensus of parent annotations
(think goat + sheep -> mammal).
- With each biomaterial is optionally associated an original
quantity (with unit?) and a remaining quantity. When an extract is
created, its original (extracted) quantity is subtracted from its
parent sample's remaining quantity. In the case of pooling, the
amount used of each source biomaterial may be given.
- Changes to the original/remaining quantity should be logged and
sum up to the right amount. It should be possible to withdraw
material and leave a note about it.
- With each biomaterial creation should be associated a protocol.