Source to Source or Sample to Sample processes?

[Bob MacCallum]

Hi all,

It's been a while, and I see since I was last here, ISA-JSON is a thing - yay!

I have a question I will phrase in ISA-Tab (though both apply).

Is it possible to process a Source node into another Source node, (or Sample into Sample?)

e.g.

Source Name   Protocol Ref    Source Name

cage1         PICK_ONE        mouse7

 

The old PDF specs almost say this is possible (e.g. with <Node> Name ... <Node> Name), the newer ones aren't so clear to me.

It looks like this should be possible, especially in ISA-JSON.  I just wondered if the DAG should have only one "level" of Source and Sample each?

many thanks,

Bob

[Philippe]

Hi Bob!

It's been a while indeed but really nice to hear from you :)

The python implementation is stricter than what the first version of the specifications  allowed and what the ISAcreator could right.

So even though I have not tested the situations you describe, I have some reservations about the isa python parsers would support it.

One thing is known is that the ISA-JSON serialization allows more complex representations than the ISA-Tab one. (e.g. Samples deriving from Sample).

Your requests for `ISA Source` deriving from another `ISA Source` isn't allows by the ISA JSON schema. I will however double check the behaviour of the ISA-API.

Happy to discuss further the use cases.

Many thanks!

Phil

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[Bob MacCallum]

Hi Philippe,

Good to hear from you too.

Aha yes, I see in the python API, there is no possibility of outputting a Source node.

No worries, I think our use case can also be Source->Sample->Sample (instead of Source->Source->Sample).  It would be good to keep within the specs as much as possible ;-)

I'll let you know if I have any further questions.

best regards,
Bob