Changing Staining

[koellerMC]

https://github.com/imi-bigpicture/metadata-schema/blob/bd3d42840d5718531312ddd41d032125976e7a6b/src/BP.staining.xsd#L1

[koellerMC]

Ok now after working a bit I have come up with the following schema idea:

• The Staining Entity is reference-able (from a given Slide Entity).

• Stains within the Stain Set are not own reference-able Entities.

Pro:

• No new Entity is introduced in the Schema Contra:
• Reuse of Stains within different Stainings not possible.

However, I think this is not a big problem as:

• one will most likely define an Staining on its own
• there will only be a limited number of Stainings per data set
• Stains only exist within a given Staining, thereby defining them explicitly for each Staining might even be better, as no changes to other Stainings get propageted when changing a given Stain

Furthermore, I think the best way would be to make a bucked called Procedure Information: here normal BP AttributeType go in. We change the name of Staining Name to Staining Procedure Name in the MSMdad.

There are two modes: High-Level If people want to be high level, they just fill out the Procedure Information wit:

• Staining Procedure Name
• Staining Method.
• Nothing else. This can only be done with chemical stains. all other stains are forbidden there.

Granular In the more granular case you provide multiple stains in the stain set. A stain is just a BP Object. For any stain one must provide the following MSMdad attributes:

• Staining Compound
• Staining Method. If it is a targeted stain (i.e. immunogenic or iSH in the staining method, the staining compound is either: antibody (for immunogenic) or Double-stranded DNA, Singel stranded DNA, RNA, Synthetic oligonucleotide (for iSH). In the case of chemical stain the concrete compound must be listed.

For targeted stains (i.e. immunogenic or iSH) the following additional MSMdad Attributes must be used:

• Staining Target
• Staining Reporter Type
• Staining Reporter.

Thereby, we do not make a complicated stain object. We can reuse MSMdad Attributes efficiently. Only downside, that there has to be some checking that is conditional. Most likely not possible with the checklists. However, for maintenance purposes I think this might be the best as the XSDs don't have to be changes in future. Only the checks.