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Merge pull request #1828 from obi-ontology/1825-add-grouping-classes-…
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…for-series-of-dna-sequencers

#1825 define and subclass Illumina sequencer serieses
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@jamesaoverton
jamesaoverton authored Oct 22, 2024
2 parents 32e262e + 77dd03e commit 26c29ce
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139 changes: 117 additions & 22 deletions src/ontology/modules/devices.owl
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<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002000">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000703"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
<owl:hasValue rdf:resource="http://purl.obolibrary.org/obo/OBI_0000759"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>Gravina, Michael T., Jenny H. Lin, and Stuart S. Levine. &quot;Lane-by-lane sequencing using Illumina&apos;s Genome Analyzer II.&quot; BioTechniques 54.5 (2013): 265-269. PMID: 23662897</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIx is the most widely adopted next-generation sequencing platform and proven and published across the broadest range of research applications.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng, Alan Ruttenberg</obo:IAO_0000117>
<obo:IAO_0000118>Genome Analyzer IIx</obo:IAO_0000118>
<obo:IAO_0000118>Illumina GA IIx</obo:IAO_0000118>
<obo:IAO_0000118>Illumina Genome Analyzer IIx</obo:IAO_0000118>
<obo:IAO_0000119>ENCODE group</obo:IAO_0000119>
<rdfs:label>Genome Analyzer IIx</rdfs:label>
<rdfs:label>Illumina Genome Analyzer IIx</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0002001 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002001">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003683"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand All @@ -6395,7 +6401,7 @@
<!-- http://purl.obolibrary.org/obo/OBI_0002002 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002002">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003683"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand Down Expand Up @@ -6427,9 +6433,9 @@
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000120"/>
<obo:IAO_0000115 xml:lang="en">A DNA sequencer which is manufactured by the Illumina corporation. Built upon sequencing by synthesis technology, the machine provides an end-to-end solution (cluster generation, amplification, sequencing, and data analysis) in a single machine.</obo:IAO_0000115>
<obo:IAO_0000117>PERSON: Venkat Malladi, Chris Stoeckert, Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000118>Illumina MiSeq</obo:IAO_0000118>
<obo:IAO_0000118>MiSeq</obo:IAO_0000118>
<obo:IAO_0000119>http://res.illumina.com/documents/products/datasheets/datasheet_miseq.pdf</obo:IAO_0000119>
<rdfs:label>MiSeq</rdfs:label>
<rdfs:label>Illumina MiSeq</rdfs:label>
</owl:Class>


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<!-- http://purl.obolibrary.org/obo/OBI_0002021 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002021">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003684"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand All @@ -6637,17 +6643,17 @@
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">A DNA sequencer which is a desktop sequencer ideal for smaller-scale studies manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology.</obo:IAO_0000115>
<obo:IAO_0000117>Person: Venkat Malladi, Chris Stoeckert, Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000118>Illumina NextSeq 500</obo:IAO_0000118>
<obo:IAO_0000118>NextSeq 500</obo:IAO_0000118>
<obo:IAO_0000119>http://systems.illumina.com/systems/nextseq-sequencer.html</obo:IAO_0000119>
<rdfs:label>NextSeq 500</rdfs:label>
<rdfs:label>Illumina NextSeq 500</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0002022 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002022">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003683"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand Down Expand Up @@ -6750,12 +6756,18 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002027">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0000703"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
<owl:hasValue rdf:resource="http://purl.obolibrary.org/obo/OBI_0000759"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000115 xml:lang="en">An Illumina Genome Analyzer II which is manufactured by the Illumina corporation. It supports sequencing of single, long or short insert paired end clone libraries relying on sequencing by synthesis technology. The Genome Analyzer IIe makes industry-leading next-generation sequencing technology accessible to more laboratories.</obo:IAO_0000115>
<obo:IAO_0000117>Person: Venkat Malladi, Chris Stoeckert, Jie Zheng</obo:IAO_0000117>
<obo:IAO_0000118>Genome Analyzer IIe</obo:IAO_0000118>
<obo:IAO_0000118>Illumina GA IIe</obo:IAO_0000118>
<obo:IAO_0000118>Illumina Genome Analyzer IIe</obo:IAO_0000118>
<obo:IAO_0000119>http://res.illumina.com/documents/products/datasheets/datasheet_genome_analyzer_iie.pdf</obo:IAO_0000119>
<rdfs:label>Genome Analyzer IIe</rdfs:label>
<rdfs:label>Illumina Genome Analyzer IIe</rdfs:label>
</owl:Class>


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<!-- http://purl.obolibrary.org/obo/OBI_0002048 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002048">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003683"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand All @@ -6813,7 +6825,7 @@
<!-- http://purl.obolibrary.org/obo/OBI_0002049 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002049">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003683"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand Down Expand Up @@ -6913,6 +6925,12 @@

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002128">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
<owl:hasValue rdf:resource="http://purl.obolibrary.org/obo/OBI_0000759"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111>Illumina Genome Analyzer</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A DNA sequencer manufactured by Solexa as one of its first sequencer lines, launched in 2006, and capable of sequencing 1 gigabase (Gb) of data in a single run.</obo:IAO_0000115>
Expand All @@ -6927,7 +6945,13 @@
<!-- http://purl.obolibrary.org/obo/OBI_0002129 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002129">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003683"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
<owl:hasValue rdf:resource="http://purl.obolibrary.org/obo/OBI_0000759"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000111>Illumina HiSeq X Ten</obo:IAO_0000111>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000125"/>
<obo:IAO_0000115 xml:lang="en">A DNA sequencer that consists of a set of 10 HiSeq X Sequencing Systems.</obo:IAO_0000115>
Expand Down Expand Up @@ -7097,7 +7121,7 @@
<!-- http://purl.obolibrary.org/obo/OBI_0002630 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0002630">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003685"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand Down Expand Up @@ -8446,7 +8470,7 @@
<!-- http://purl.obolibrary.org/obo/OBI_0003386 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003386">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003683"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand All @@ -8470,7 +8494,7 @@
<!-- http://purl.obolibrary.org/obo/OBI_0003387 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003387">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003684"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand All @@ -8485,7 +8509,7 @@
<obo:IAO_0000119>https://www.illumina.com/systems/sequencing-platforms/nextseq.html</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1546</obo:IAO_0000233>
<obo:IAO_0000234>gEAR</obo:IAO_0000234>
<rdfs:label>NextSeq 550</rdfs:label>
<rdfs:label>Illumina NextSeq 550</rdfs:label>
</owl:Class>


Expand Down Expand Up @@ -9126,7 +9150,7 @@
<!-- http://purl.obolibrary.org/obo/OBI_0003606 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003606">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003684"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand Down Expand Up @@ -9161,7 +9185,7 @@
<!-- http://purl.obolibrary.org/obo/OBI_0003663 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003663">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003685"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand All @@ -9184,7 +9208,7 @@
<!-- http://purl.obolibrary.org/obo/OBI_0003664 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003664">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0003685"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
Expand All @@ -9204,6 +9228,77 @@



<!-- http://purl.obolibrary.org/obo/OBI_0003683 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003683">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
<owl:hasValue rdf:resource="http://purl.obolibrary.org/obo/OBI_0000759"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>https://www.illumina.com/content/dam/illumina-support/documents//products/datasheets/datasheet_hiseq_systems.pdf</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word HiSeq.</obo:IAO_0000115>
<obo:IAO_0000116>This class represents a series of instruments with various model names. There are several models in this series, including one that was simply called “HiSeq” as the model name. GENEPIO:0100110 ‘Illumina HiSeq’ may refer to a model, not the series. OBI may not have classes for all of the instruments in this series.</obo:IAO_0000116>
<obo:IAO_0000117>PERSON: Mark Andrew Miller</obo:IAO_0000117>
<obo:IAO_0000118>HiSeq series</obo:IAO_0000118>
<obo:IAO_0000119>PERSON: Mark Andrew Miller</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1825</obo:IAO_0000233>
<obo:IAO_0000234>Alicia Clum</obo:IAO_0000234>
<rdfs:label>Illumina HiSeq Series Instrument</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003684 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003684">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
<owl:hasValue rdf:resource="http://purl.obolibrary.org/obo/OBI_0000759"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000112>https://www.cd-genomics.com/blog/nextseq/</obo:IAO_0000112>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NextSeq.</obo:IAO_0000115>
<obo:IAO_0000116>This class represents a series of instruments with various model names. There are several models in this series. OBI may not have classes for all of the instruments in this series. It is unclear whether GENEPIO:0100126 ’Illumina NextSeq’ refers to the series or a model.</obo:IAO_0000116>
<obo:IAO_0000117>PERSON: Mark Andrew Miller</obo:IAO_0000117>
<obo:IAO_0000118>NextSeq series</obo:IAO_0000118>
<obo:IAO_0000119>PERSON: Mark Andrew Miller</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1825</obo:IAO_0000233>
<obo:IAO_0000234>Alicia Clum</obo:IAO_0000234>
<rdfs:label>Illumina NextSeq Series Instrument</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0003685 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0003685">
<rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/OBI_0400103"/>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/OBI_0000304"/>
<owl:hasValue rdf:resource="http://purl.obolibrary.org/obo/OBI_0000759"/>
</owl:Restriction>
</rdfs:subClassOf>
<obo:IAO_0000114 rdf:resource="http://purl.obolibrary.org/obo/IAO_0000123"/>
<obo:IAO_0000115 xml:lang="en">A DNA Sequencer manufactured and/or marketed by Illumina and branded with the word NovaSeq.</obo:IAO_0000115>
<obo:IAO_0000116>This class represents a series of instruments with various model names. There are several models in this series. OBI may not have classes for all of the instruments in this series. It is unclear whether GENEPIO:0100122 ‘Illumina NovaSeq’ refers to the series or to a model.</obo:IAO_0000116>
<obo:IAO_0000117>PERSON: Mark Andrew Miller</obo:IAO_0000117>
<obo:IAO_0000118>NovaSeq series</obo:IAO_0000118>
<obo:IAO_0000119>PERSON: Mark Andrew Miller</obo:IAO_0000119>
<obo:IAO_0000233>https://github.com/obi-ontology/obi/issues/1825</obo:IAO_0000233>
<obo:IAO_0000234>Alicia Clum</obo:IAO_0000234>
<rdfs:label>Illumina NovaSeq Series Instrument</rdfs:label>
</owl:Class>



<!-- http://purl.obolibrary.org/obo/OBI_0302886 -->

<owl:Class rdf:about="http://purl.obolibrary.org/obo/OBI_0302886"/>
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