annotation principle: use case from molecular biology

[Brilator]

Hey everyone,

this might also be a topic to discuss in the next DataSteward Circle.

Here's part of an example protocol from molecular biology (test restriction digest of plasmid DNA) for which I'm still unsure how to properly document this via ISA.
(Note, I left out the TSR TAN columns for readability).

A) row-wise

Input [Material]	Parameter [Concentration]	Unit	Parameter [Volume]	Unit	Output [Material]
Plasmid DNA	200	ng / µl	1	microliter	TestDigest01
Restriction Enzyme 1	100	ng / µl	1	microliter	TestDigest01
Restriction Enzyme 2	100	ng / µl	1	microliter	TestDigest01
Restriction Buffer	10	x	1	microliter	TestDigest01
ddH2O			6	microliter	TestDigest01

B) column-wise

Component [Plasmid DNA]	Parameter [Plasmid DNA concentration]	Unit	Parameter [Plasmid DNA volume]	Unit	Component [Restriction Enzyme 1]	Parameter [Restriction Enzyme 1 concentration]	Unit	Parameter [Restriction Enzyme 1 volume]	Unit	Component [Restriction Enzyme 2]	Parameter [Restriction Enzyme 2 concentration]	Unit	Parameter [Restriction Enzyme 2 volume]	Unit	Component [Restriction Buffer]	Parameter [Restriction Buffer concentration]	Unit	Parameter [Restriction Buffer volume]	Unit	ddH2O	Unit	Output [Material]
		ng / µl		microliter			ng / µl		microliter			ng / µl		microliter			ng / µl		microliter		microliter	TestDigest01

Option A is closer to what it looks like in user notes now. With the downside, that TestDigest02, TestDigest03, ... would have to be appended below. The Input [Material]s could reference to Output IDs of different tables (plasmid, enzymes, chemicals) with further metadata.

Option B is probably more ISA-like. It allows for more granularity (e.g. use of type specific units).

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🚀 Now the extra challenge: "Incubate at 37°C for 2 h and then analyze by gel electrophoresis."

In B, I could just keep going.
For A, I'd probably take my outputs through new processes: TestDigest01 -- [Incubation] -- [gel electrophoresis] --> image