Converting comments in ISA-TAB files

[abiga...@gmail.com]

Hi ISA Team,

We are creating ISA-TAB files and using the isatab2json API (with use_new_parser=True) to convert them to JSON documents.  We are noticing that comments on our source data are not ending up in the converted JSON.  For example, if we add a comment for the ENCODE accession ID after "Source Name" in our study file (very similar to the use case described here in section 2.3) the comments are not represented in the final JSON document.  I could be missing something, but I don't see a place for comments in the schema files for material, source, or sample.

Do you have any suggestions for using comments on sources such that they appear in the converted JSON?

Thanks in advance for your help.

Abigail

[Philippe]

Hi Abigail

Thank you for reporting this. We'll investigate  (It seems to be an ommission).

In the meantime, for an attribute such as this one, you may wish to use a Characteristics.category "ENCODE accession ID" on the Source or any other material.

All the best

Philippe

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