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The Ontology for Biomedical Investigations
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NTR: 10X Chromium Library Construction Platform #850

Open carrieadavis opened 7 years ago

carrieadavis commented 7 years ago

Project: ENCODE

So - libraries for next-generation sequencing used to all be made by hand. However, we are starting to see the emergence of platforms (machines) which do the library construction in an automated fashion. It would be useful to register these devices with OBI terms, similar to this OBI: http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0002012 (only I would put these under the class hierarchy of: Measurement Device -> Automated Library Construction.

NTR: "10X Genomics Chromium"

Editor preferred term: "10X Genomics Chromium"

Alternative terms: 10X Genomics Chromium Controller

Textual definition: The 10x Chromium System utilizes GemCode Technology for massively-parallel partitioning of high molecular weight DNA fragments (HMW-gDNA) or of whole single-cells into micelles, along with an adapter molecule and a barcode sequence. Within each micelle the gel bead dissolves, delivering reagents that barcode smaller fragments of genomic DNA or single-cell derived messenger RNA within the micelle. Each of the smaller fragments retain the barcode sequence which is used to identify its parent micelle, which map to the genomic HMW-gDNA molecule or to the single cell transcriptome from which they are originally derived. After amplification, the emulsion is broken and the fragments are pooled, where it undergoes a standard library preparation.

Definition source for the textual definition: https://www.10xgenomics.com/news/10x-genomics-new-chromium-system-enables-full-access-to-critical-molecular-and-cellular-information/

Logical definition (or parent term):

Example of usage: The library was prepared using the 10X Chromium platform and sequenced on the Illumina HiSeq 2500.

Term editor: Carrie A Davis

mkuhring commented 5 years ago

Second that. These platforms should be described with controlled vocabulary as they are more and more used, for instance in combination with single cell sequencing (which unfortunately is also missing in OBI #995 and #864 so far). What is holding the implementation of this term back?

turbomam commented 4 years ago

I dredged this up from the past. I'm glad to create it now if you still want it.

bonitalam commented 4 years ago

This is not high priority for ENCODE.