#1825 define and subclass Illumina sequencer serieses

[turbomam]

closes

• Add grouping classes for series of DNA sequencers #1825

@jamesaoverton some multi-quotes got messed up in this PR too. If you can show me how to fix one, then I can do the rest.

cc @aclum

[turbomam]

and

java -jar build/robot.jar --prefix "REO: http://purl.obolibrary.org/obo/REO_" merge \
--input src/ontology/obi-edit.owl \
template \
--template src/ontology/templates/devices.tsv \
annotate \
--ontology-iri "http://purl.obolibrary.org/obo/obi/dev/modules/devices.owl" \
--output src/ontology/modules/devices.owl

MANCHESTER PARSE ERROR the expression ('has part' some container) at row 3, column 17 in table "src/ontology/templates/devices.tsv" cannot be parsed: encountered 'container', but expected one of:
	Class name
	( ... )
	{ ... }
	Self

[jamesaoverton]

All of the dark green quotation marks in the diff have been added by your editor, and are changing the semantics of the table. There's no point in debugging the ROBOT command until they're removed.

On the last PR, I used a text editor to manually remove them. People usually use Excel for editing these tables. I like https://www.visidata.org/. I haven't used LibreOffice in many years, so I don't know how it behaves.

[turbomam]

thanks. I get the sense that the ROBOT template error might be resolved when I fix the quotations marks

[turbomam]

Thanks @jamesaoverton @mgiglio99 @sebastianduesing

I think I have implemented all of the suggestions from today's meeting

[jamesaoverton]

OBI is strict about lowercase labels, so I changed "Series Instrument" to "series instrument" throughout. Is that ok with you @turbomam?

If so, I'll update the devices.owl and then merge this.

[turbomam]

OBI is strict about lowercase labels, so I changed "Series Instrument" to "series instrument" throughout. Is that ok with you @turbomam?

If so, I'll update the devices.owl and then merge this.

Yes! Thank you.

[jamesaoverton]

Discussed on the OBI call 2024-10-21. We will release #1827, then merge this and make a new release candidate.