Add grouping classes for series of DNA sequencers

[turbomam]

I will start with recent Illumina sequencers

see also

• Representing specific flow cells for DNA sequencers #1820

[turbomam]

sequencer roots:

• OBI:0400103 'DNA sequencer'
• GENEPIO:0001921 'sequencing instrument model'
• EFO:0003739 'sequencer'

[turbomam]

I created dumps for the three ontologies with OAK commands like

runoak --input sqlite:obo:efo info --output-type tsv .desc//p=i 'sequencer' > efo-sequencers.tsv

then used ChatGPT 4o to align them, then reviewed them manually

Harmonized Label	OBI CURIe	OBI Label	GENEPIO CURIe	GENEPIO Label	EFO CURIe	EFO Label	notes
Illumina Genome Analyzer	OBI:0002128	Illumina Genome Analyzer	GENEPIO:0100106	Illumina Genome Analyzer	EFO:0004200	Illumina Genome Analyzer
Illumina Genome Analyzer II	OBI:0000703	Illumina Genome Analyzer II			EFO:0004201	Illumina Genome Analyzer II
Illumina Genome Analyzer IIe	OBI:0002027	Genome Analyzer Iie
Illumina Genome Analyzer IIx	OBI:0002000	Genome Analyzer IIx			EFO:0004202	Illumina Genome Analyzer IIx
Illumina HiScanSQ			GENEPIO:0100109	Illumina HiScanSQ
Illumina HiSeq			GENEPIO:0100110	Illumina HiSeq
Illumina HiSeq 1000	OBI:0002022	Illumina HiSeq 1000			EFO:0004204	Illumina HiSeq 1000
Illumina HiSeq 1500	OBI:0003386	Illumina HiSeq 1500	GENEPIO:0100115	Illumina HiSeq 1500	EFO:0011027	Illumina HiSeq 1500
Illumina HiSeq 2000	OBI:0002001	Illumina HiSeq 2000			EFO:0004203	Illumina HiSeq 2000
Illumina HiSeq 2500	OBI:0002002	Illumina HiSeq 2500			EFO:0008565	Illumina HiSeq 2500
Illumina HiSeq 3000	OBI:0002048	Illumina HiSeq 3000			EFO:0008564	Illumina HiSeq 3000
Illumina HiSeq 4000	OBI:0002049	Illumina HiSeq 4000			EFO:0008563	Illumina HiSeq 4000
Illumina HiSeq X			GENEPIO:0100111	Illumina HiSeq X	EFO:0008567	Illumina HiSeq X
Illumina HiSeq X Five			GENEPIO:0100112	Illumina HiSeq X Five
Illumina HiSeq X Ten	OBI:0002129	Illumina HiSeq X Ten	GENEPIO:0100113	Illumina HiSeq X Ten
Illumina iSeq			GENEPIO:0100120	Illumina iSeq
Illumina iSeq 100			GENEPIO:0100121	Illumina iSeq 100	EFO:0008635	Illumina iSeq 100
Illumina MiniSeq	OBI:0003114	Illumina MiniSeq	GENEPIO:0100124	Illumina MiniSeq	EFO:0008636	Illumina MiniSeq
Illumina MiSeq	OBI:0002003	MiSeq			EFO:0004205	Illumina MiSeq
Illumina NextSeq			GENEPIO:0100126	Illumina NextSeq			ChatGPT says this is only a series, and was never used as the name of an instrument
Illumina NextSeq 1000	OBI:0003606	Illumina NextSeq 1000	GENEPIO:0004432	Illumina NextSeq 1000	EFO:0010962	Illumina NextSeq 1000
Illumina NextSeq 2000			GENEPIO:0100129	Illumina NextSeq 2000	EFO:0010963	Illumina NextSeq 2000
Illumina NextSeq 500	OBI:0002021	NextSeq 500			EFO:0009173	Illumina NextSeq 500
Illumina NextSeq 550	OBI:0003387	NextSeq 550	GENEPIO:0100128	Illumina NextSeq 550	EFO:0008566	Illumina NextSeq 550
Illumina NovaSeq			GENEPIO:0100122	Illumina NovaSeq			ChatGPT says this is only a series, and was never used as the name of an instrument
Illumina NovaSeq 5000							not modeled in OBI, GENEPIO or EFO?!
Illumina NovaSeq 6000	OBI:0002630	Illumina NovaSeq 6000	GENEPIO:0100123	Illumina NovaSeq 6000	EFO:0008637	Illumina NovaSeq 6000
Illumina NovaSeq X					EFO:0022840	Illumina NovaSeq X
Illumina NovaSeq X Plus					EFO:0022841	Illumina NovaSeq X Plus

[turbomam]

OBI:0003683,Illumina HiSeq Instrument
OBI:0003684,Illumina NextSeq Instrument
OBI:0003685,Illumina NovaSeq Instrument