Open turbomam opened 2 weeks ago
sequencer roots:
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 |
OBI:0003683,Illumina HiSeq Instrument OBI:0003684,Illumina NextSeq Instrument OBI:0003685,Illumina NovaSeq Instrument
I will start with recent Illumina sequencers
see also