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GenomicsStandardsConsortium / mixs

Minimum Information about any (X) Sequence” (MIxS) specification
https://w3id.org/mixs
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names that begin with numbers #92

Open wdduncan opened 4 years ago

wdduncan commented 4 years ago

In the future we might want to abstain from begining names with a number. E.g.: The structured comment names: 16s_recover, 16s_recover_software

Many programing languages do not permit variables or function names to begin with a number. For example in the NMDC project, we are using the structured comment names to link samples to database values. But when using 16s_recover, we have to prepend an underscore ("_16s_recover"). Not a big deal, but something that the community might want to be aware of, and consider when adding new items.

I can't recall if all database engines allow for column names to begin with numbers.

ramonawalls commented 3 years ago

AI: Go through all structure comment names and rename them.

cmungall commented 3 years ago

Do we really want to do this? Do we have a way of evaluating the cost of changes like this? Would any such changes propagate through INSDC?

wdduncan commented 3 years ago

We can use aliases.

ramonawalls commented 3 years ago

Need to check with INSDCs re. backward compatibility issues. We need to be cautious about changing these lables.

If we change IRIs, we can add an alt-label that groups who can't use numbers can use.

We need to supply the translation machinery. Perhaps we host the mappings.

We should reach out to other groups (like qiime) to see how they are handling it.

ramonawalls commented 3 years ago

Moving this issue to the main MIxS repo.

wdduncan commented 3 years ago

@only1chunts The (core) terms 16s_recover and 16s_recover_software may cause problems with databases that don't allow column/field names to begin with a numbers. Although changing the terms may cause problems for systems already implemented this term.

Also row 274 has this as the structured comment name: History of kidney disorders; can include multiple disorders. The terms should be chosen from the DO (Human Disease Ontology) at http://www.disease-ontology.org, kidney disease (https://disease-ontology.org/?id=DOID:557).

ramonawalls commented 3 years ago

We are not aware of this causing problems so far, so we will consider this further for MIxS7.

wdduncan commented 3 years ago

That is probably b/c people are doing work arounds :)

E.g., We prepend such terms with an underscore.