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NTR: Illumina Genome Analyzer (general/parent term) #832

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jahilton opened this Issue Jun 5, 2017 · 6 comments

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jahilton commented Jun 5, 2017

In order to register a term that includes all of the Illumina Genome Analyzer versions, we first propose that OBI:0002128 be renamed to Illumina Genome Analyzer I. Then a new term as follows...

editor preferred term: Illumina Genome Analyzer
textual definition: One of the DNA sequencer models developed by Illumina (Solexa) surrounding the use of clonal arrays and massively parallel sequencing of short reads using solid phase sequencing by reversible terminators (subsequently referred to as sequencing by synthesis technology, or SBS).
definition source for the textual definition: https://www.illumina.com/technology/next-generation-sequencing/solexa-technology.html
logical definition: DNA sequencer --> Illumina Genome Analyzer --> Illumina Genome Analyzer I, Illumina Genome Analyzer

Please advise if you have a more preferred way to insert the new umbrella term.

@cstoeckert cstoeckert self-assigned this Jun 12, 2017

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DanBerrios Jun 12, 2017

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I think the term Genome Analyzer is too commercially-oriented (like "Kleenex"). No one refers to any DNA sequencing instruments as "genome analyzers" conceptually.

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DanBerrios commented Jun 12, 2017

I think the term Genome Analyzer is too commercially-oriented (like "Kleenex"). No one refers to any DNA sequencing instruments as "genome analyzers" conceptually.

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cstoeckert Jun 19, 2017

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I can see the case for relabeling as there is a Illumina Genome Analyzer II (http://purl.obolibrary.org/obo/OBI_0000703). However, it is unclear given that there is only an Illumina Genome Analyzer I and II that an ontology term is needed as a general term. We haven't done that for the HiSeqs.

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cstoeckert commented Jun 19, 2017

I can see the case for relabeling as there is a Illumina Genome Analyzer II (http://purl.obolibrary.org/obo/OBI_0000703). However, it is unclear given that there is only an Illumina Genome Analyzer I and II that an ontology term is needed as a general term. We haven't done that for the HiSeqs.

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DanBerrios Jun 19, 2017

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I see now..so the intent of these classes is in fact to capture (perhaps small) differences in models for these DNA Sequencers... and not just differences in manufacturers. So Genome Analyzer I,II may be appropriate.

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DanBerrios commented Jun 19, 2017

I see now..so the intent of these classes is in fact to capture (perhaps small) differences in models for these DNA Sequencers... and not just differences in manufacturers. So Genome Analyzer I,II may be appropriate.

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turbomam Apr 30, 2018

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Existing terms:

http://purl.obolibrary.org/obo/OBI_0000703 (OBI):
Illumina Genome Analyzer II in Ontobee: OBI

http://purl.obolibrary.org/obo/OBI_0002128 (OBI):
Illumina Genome Analyzer in Ontobee: OBI
definition includes characteristics that are specific to GA I

DNA sequencer
Term IRI: http://purl.obolibrary.org/obo/OBI_0400103

Just rename OBI_0002128 to "Illumina Genome Analyzer I"? and add Genome Analyzer II ?

We'll decide on the 14th

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turbomam commented Apr 30, 2018

Existing terms:

http://purl.obolibrary.org/obo/OBI_0000703 (OBI):
Illumina Genome Analyzer II in Ontobee: OBI

http://purl.obolibrary.org/obo/OBI_0002128 (OBI):
Illumina Genome Analyzer in Ontobee: OBI
definition includes characteristics that are specific to GA I

DNA sequencer
Term IRI: http://purl.obolibrary.org/obo/OBI_0400103

Just rename OBI_0002128 to "Illumina Genome Analyzer I"? and add Genome Analyzer II ?

We'll decide on the 14th

@turbomam turbomam self-assigned this Apr 30, 2018

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jahilton May 2, 2018

To our best recollection, we requested the parent 'Genome Analyzer' term between 'DNA sequencer' and the children GA terms to allow for ease of grouping the child terms with each other, but separate from the other sequencers.
We had a hierarchy similar to the AB SOLiD system (OBI_0000696) & child terms (OBI_0002007, OBI_0002024) in mind with this structure.

jahilton commented May 2, 2018

To our best recollection, we requested the parent 'Genome Analyzer' term between 'DNA sequencer' and the children GA terms to allow for ease of grouping the child terms with each other, but separate from the other sequencers.
We had a hierarchy similar to the AB SOLiD system (OBI_0000696) & child terms (OBI_0002007, OBI_0002024) in mind with this structure.

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turbomam May 14, 2018

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Added 'Illumina Genome Analyzer I' alternative term for http://purl.obolibrary.org/obo/OBI_0002128
Otherwise, made no changes to hierarchy

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turbomam commented May 14, 2018

Added 'Illumina Genome Analyzer I' alternative term for http://purl.obolibrary.org/obo/OBI_0002128
Otherwise, made no changes to hierarchy

@turbomam turbomam closed this May 14, 2018

turbomam added a commit that referenced this issue May 21, 2018

jamesaoverton added a commit that referenced this issue May 22, 2018

Merge pull request #933 from obi-ontology/mam20180521
- demoted gene knockdown assay equivalence axiom to subClassOf #931
- alternative 'Genome Analyzer I term' for Illumina Genome Analyzer #832
- adding 'assay' to hitology and histpathology terms #853
- adding isoform sequencing #878
- updating def source for human and mouse nCounter 'arrays' #831
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