BASE Core specification Biomaterials

Biomaterials

1. There are 4 types of biomaterials:
   • biosources (e.g. cell lines, patients)
   • samples (e.g. tumor samples or treated cell lines)
   • extracts
   • labeled extracts
2. Biosource, sample and extract is the parent type of sample, extract and labeled extract, respectively.
3. 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.
4. [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.
5. [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.
6. 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.
7. 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.
8. There are different labels (dyes), and each labeled extract is associated with one label.
9. [NOTE] Sample tissues (a BASE 1 concept) are implemented as annotations.
10. [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).
11. 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.
12. 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.
13. With each biomaterial creation should be associated a protocol.