New Term Request - Ion Torrent Ion Proton

obi-bot commented 9 years ago

editor preferred term: Ion Torrent Ion Proton alternative terms: Ion Torrent Proton, Ion Proton System, Ion Proton textual definition: Ion Torrent Ion Proton is a semiconductor sequencing technology manufactured by Life Technologies. Built for speed, the machine provides sequencing run times 2-4 hours on the Ion PI Chip converting DNA to variants in a single day.
definition source for the textual definition: http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-proton-system-for-next-generation-sequencing.html logical definition (or parent term): DNA Sequencer --> next generation sequencing --> Ion Torrent term editor: Sagar Jain, Richard Scheuermann, Jim Kent

Reported by: sbjain

Original Ticket: obi/obi-terms/756

obi-bot commented 9 years ago

summary: New Term Request --> New Term Request - Ion Torrent Ion Proton

Original comment by: bpeters42

obi-bot commented 9 years ago

1) We would like to avoid 'next generation sequencing' as there are already multiple generations out, and what 'next' is changes over time. 2) We would like to avoid marketing statements in the definition like 'built for speed' - as it implies other sequencer are not 'built for speed'. 3) It is hard to distinguish between the different instruments in the definitions, but that is what is needed. For example, the Proton is distinguished from the PGM in that the proton only deals with a single chip type (PI) while the PGM does multiple chip types. https://www.biotech.wisc.edu/services/dnaseq/sequencing/Ion_Torrent_PGM

Here is a revised textual definition textual definition: A DNA sequencer that is manufactured by Life Technologies and based on semiconductor sequencing technology that utilizes a 'PI' chip type that generates 60-80 million reads.

Please update the other definitions along these lines.

Original comment by: bpeters42

obi-bot commented 9 years ago

Yes, please include this under DNA Sequencer.
Yes, lets eliminate these marketing points.
Yes, please update the definition for Ion Proton to:

A DNA sequencer that is manufactured by Life Technologies and based on semiconductor sequencing technology that utilizes a 'PI' chip type that generates 60-80 million reads.

Original comment by: sbjain

obi-bot commented 9 years ago

Revised definition for Ion Torrent Ion Proton:

A DNA sequencer that is manufactured by Life Technologies for Exome sequencing, transcriptome sequencing, and copy number analysis. The semiconductor sequencing technology utilizes a 'PI' chip type that generates 60-80 million reads, with a read length of up to 200 base pairs.

Original comment by: sbjain

obi-bot commented 9 years ago

That's a better definition. I like the machine used for 'Exome sequencing, transcriptome sequencing, and copy number analysis.' We should add these relations into OBI.

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On Sun, May 10, 2015 at 11:38 PM, Sagar jainwave@users.sf.net wrote:

Revised definition for Ion Torrent Ion Proton:

A DNA sequencer that is manufactured by Life Technologies for Exome sequencing, transcriptome sequencing, and copy number analysis. The semiconductor sequencing technology utilizes a 'PI' chip type that generates 60-80 million reads, with a read length of up to 200 base pairs.

[obi-terms:#756] http://sourceforge.net/p/obi/obi-terms/756 New Term Request - Ion Torrent Ion Proton*

Status: open Group: instruments Labels: Ion Proton System Ion Torrent Ion Proton Ion Torrent Proton Ion Proton Created: Fri Apr 03, 2015 02:39 AM UTC by Sagar Last Updated: Mon Apr 20, 2015 06:42 AM UTC Owner: James A. Overton

editor preferred term: Ion Torrent Ion Proton alternative terms: Ion Torrent Proton, Ion Proton System, Ion Proton textual definition: Ion Torrent Ion Proton is a semiconductor sequencing technology manufactured by Life Technologies. Built for speed, the machine provides sequencing run times 2-4 hours on the Ion PI Chip converting DNA to variants in a single day. definition source for the textual definition: http://www.lifetechnologies.com/us/en/home/life-science/sequencing/next-generation-sequencing/ion-torrent-next-generation-sequencing-workflow/ion-torrent-next-generation-sequencing-run-sequence/ion-proton-system-for-next-generation-sequencing.html logical definition (or parent term): DNA Sequencer --> next generation sequencing --> Ion Torrent term editor: Sagar Jain, Richard Scheuermann, Jim Kent

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Original comment by: linyumichigan

obi-bot commented 8 years ago

assigned_to: James A. Overton --> Sagar

Original comment by: jamesaoverton

obi-ontology / obi

New Term Request - Ion Torrent Ion Proton #739

A DNA sequencer that is manufactured by Life Technologies for Exome sequencing, transcriptome sequencing, and copy number analysis. The semiconductor sequencing technology utilizes a 'PI' chip type that generates 60-80 million reads, with a read length of up to 200 base pairs.