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Minor refinements about software and cvterms #55

Merged
merged 6 commits into from
Sep 14, 2024
Merged

Minor refinements about software and cvterms #55

merged 6 commits into from
Sep 14, 2024

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ypriverol
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@ypriverol ypriverol commented Sep 12, 2024

This PR includes the following modelling:

  • How do I capture CV terms in all the parquet list structures as struct (aka record in Avro)?

@lazear in https://github.com/lazear/mz_parquet captures the CVterms for each spectrum, as Cvterm Accession and name. This approach is good but for data science I don't see people querying by CVTerms. I would love to extend that approach and use the following:

  • name: Name in the ontology (required). This will enable us to search in the ontologies easily.

  • value: Some of the ontology terms, for example, MS level, need a value, you can use MS level 2, Then this is optional because in the majority of the cases will be null.

  • Capture the software provider at the project level.

  • Some minor changes to the schema double -> float32

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@ypriverol ypriverol merged commit d28b5af into main Sep 14, 2024
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@lazear
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lazear commented Sep 15, 2024

The recent version of mzparquet I've been using is in long format (each ion is it's own row) with no CV terms. Just purely a mz/intensity/isolation window/etc storage format with no/little metadata

@ypriverol
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Can you do a PR to the current dev of quantms.io with your current version of mzparquet, in that way you will be a leading contributor ;)

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3 participants