How to install and use this tool.

[aminards]

I don't see any information on how to install and use this tool.
Do you have instructions for this?
I am curious, how does this automatically gather the information?

[turbomam]

Good question! The main branch of this repo contains version 6 of the MIxS standard expressed in the LinkML language, but that conversion was performed with a one-off approach. We are currently developing a more sustainable conversion of the MIxS specification, as TSV files, into the LinkML syntax.

Any LinkML model can be used to validate and convert the model itself or data that is intended to be model compliant. Several file formats are supported including YAML, TSV, CSV, OWL/RDF/TTL, JSON and JSON schema, and even SQLite databases. There is sample Python code and a sample Makefile in the main branch of this repo, but the examples will be much better once https://github.com/GenomicsStandardsConsortium/mixs/tree/issue-551-tested-schemasheets is merged in. Most of the use cases for these resources requires some understanding of LinkML

Eventually, there will be a MIxS Python package at the PyPI website.

Independent of that, the BBOP group at the Lawrence Berkeley National Laboratory has developed tools for converting the contents of the web-hosted, XML-based NCBI Biosample collection into a SQLite relational database. The structure of that database isn't tightly aligned with the MIxS schema yet.

Can you say more about how you would like to computationally use the MIxS standard or the Biosample SQLite database?

@cmungall @ramonawalls @lschriml @only1chunts would you like to add anything to this?

[ramonawalls]

Great answer, @turbomam . @aminards there are also several other organizations that support use of MIxS standards for data collection. If we know more about your use case, we may be able to point you at a community that is similar.

[turbomam]

see also

• https://github.com/GenomicsStandardsConsortium/mixs/issues/630