Create python module for manipulating xlsx/tsvs and generating rdf

[cmungall]

Regardless of whether the nature of the rdf representation (#9) we will need a toolkit for doing conversion.

I would nominate python, and we can use @wdduncan's code as the starting point:

https://github.com/GenomicsStandardsConsortium/mixs-rdf/blob/master/notebooks/common-mixs-package-terms.ipynb

If we go with a native tsv representation (#10) I imagine we will retain something pretty similar to the existing column headings in the excel

The library would generate rdf (and possibly shex, as per comments in #9, also json-schema for the json-ld representation), we can play around with different representations. There are some decisions that can be made independent of properties vs classes, I suggest the following mappings:

• MIXS IDs would become the URIs (see #8)
• Package item -> rdfs:label
• Environmental package -> skos:inScheme
• Definition -> skos:definition

I suggest URIs for each of the packages too (could use skos:scheme here)

[wdduncan]

Writing the python code to convert a TSV should be pretty straightforward. We can put code in a docker container if we want to run it as a service.
Another option would be using robot template. It depends on how much custom control we need. Robot might not elegantly handle all our needs.

[johanneswerner]

The link of the notebook does not seem valid anymore, I assume it is in the common-mixs-package-terms folder of https://github.com/GenomicsStandardsConsortium/mixs-rdf/tree/master/src/notebooks.

[wdduncan]

@johanneswerner Yes. That is the notebook.
We are also working on a more general metadata converter for MIxS. See here:
https://github.com/microbiomedata/metadata_converter

And specifically in the Makefile around here: https://github.com/microbiomedata/metadata_converter/blob/5d5c52c9cda8d1023d977ce4b805a597e079a599/Makefile#L23

[jdeck88]

+1 for python and +1 for docker

On Tue, Feb 16, 2021 at 12:31 PM Bill Duncan notifications@github.com wrote:

@johanneswerner Yes. That is the notebook. We are also working on a more general metadata converter for MIxS. See here: https://github.com/microbiomedata/metadata_converter

And specifically in the Makefile around here: https://github.com/microbiomedata/metadata_converter/blob/5d5c52c9cda8d1023d977ce4b805a597e079a599/Makefile#L23

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[ramonawalls]

Is there code to do this already with linkml?

[ramonawalls]

See also https://github.com/linkml https://pypi.org/project/linkml/