characteristics for dataFiles in ISA-JSON

[rafael buono]

In the ISA-JSON schemas, one can add characteristics referencing to a characteristic category declaration to Source, Sample, and otherMaterials. How can one add characteristics to data files in dataFiles?

For example, one would like to add a field stating the file type of the referenced file (e.g. fastq). How is this currently handled?

Best,

Rafael

[Philippe]

Hi Rafael

With the  current ISA model and ISA API , 'Characteristics' can not be used to annotate Data File nodes.

'ISA.Characteristics' solely applies to Material Nodes (as you pointed out).

We recommend using 'ISA.Comment' instead, this is currently used to cater for the kind of situation you are describing.

It could be useful to collect the set of attributes for Files (e.g. file format, file size, file compression, checksum, checksum type, etc..), some of which are already available from controlled terminologies.

Hope this helps

best wishes

Philippe

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[rafael buono]

Thanks Philippe!

With Comments being used in multiple places in an ISAjson, it might get a bit tricky to make sure that the correct comment goes to the correct entry in the correct node.

Are there plans to expand the dataFiles to also accept characteristics described in the characteristic category? As you exemplified, there are a few characteristics of files that are important to collect.

Best,

Rafael

[Philippe]

Hi Rafael

With Comments being used in multiple places in an ISAjson, it might get a bit tricky to make sure that the correct comment goes to the correct entry in the correct node.

It wouldn't be very different had there been an ISA.Characteristics property on the ISA DataFile object.

In fact, it should be easier / more  straightforward if the ISA object you want to annotate is of the type Commentable. (e.g. Material or File)

I currently use  ISA.Comments on Data File myself.

Regarding your second question (allowing 'characteristics' on 'DataFiles'), we have currently no plans to do so as it would imply extensive work + testing.

Sorry if this this is not necessarily the answer you wanted to hear :)

One more things: thanks for logging issue 421, should be fixed shortly.

All the best

Philippe

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[rafael buono]

Hi Philippe,

thank you for the answer, even if not exactly what I wanted to hear. Haha.

What I mean with making sure that the correct comments go with the correct entry is that by just tagging an attribute as a "comment" it is not sufficient to know where it should go. While tagging something a "parameter value" is sufficient to identify a value as pertaining to a protocol. With comments, they might belong to one of many objects. That complicates things if one is trying to built an ISAjson file outside of the ISA API or ISA creator.

With characteristics one can just list them at "characteristicCategories" and reference to the correct characteristic inside the correct material item (source, sample, or othermaterial).

Under the current situation, we might need to create a way to tag a comment as a "datafile_comment". Something we were trying to avoid.

Best,

Rafael