NTR: DNA processed specimen

[Dalalghamdi]

DNA processed specimen Label: DNA processed specimen Definition: A processed specimen which is the output of preparing a DNA sample for further analysis Definition source: derived from NCI Thesaurus Parent class: processed specimen (OBI:0000953)

[DanBerrios]

@Dalalghamdi Can you give examples of DNA processed specimen, to give us an idea of the nature and use of it. Is it a result of something that happens before, during or after DNA extraction?

[Dalalghamdi]

Hi @DanBerrios A DNA processed specimen is a result of a planned process that happens after DNA extraction. For example: target region enrichment assay is a planned process that has "DNA extract" as specified input, and "DNA processed specimen" as specified output Thanks

[bpeters42]

Thanks! Is it true that you only want specimens that still contain DNA? In that case we would keep the axiom that DNA molecules are contained in the specimen. You could envision a process that completely destroys the content (e.g. if it is sent through a MS/MS spectrometer).

In which case we could simply define it as: "A processed specimen that contains DNA molecules".

[Dalalghamdi]

@bpeters42 Yes, I need a term that describes a specimen that still contains DNA; My goal here is to differentiate between planned processes' input and outputs. I agree that we should keep that axiom

[bpeters42]

Thanks for the reply, that makes perfect sense. I suspect that we could get similar terms in the future, and it would be nice to have a set design pattern, so I apologize if I ask you more questions than necessary for the particular term requested. Let me explain:

• we currently have a standard way to describe specimens derived from specific anatomical entities, e.g. 'blood specimen', 'urine specimen', 'liver specimen' etc. Many of those contain DNA, which could be extracted, enriched etc.

• the 'DNA processed specimen' you request could be derived from such samples

• Could we more generally refer to 'DNA containing specimen' as a type of 'X containing specimen' where X is what the subject of interest is. And the specimen collection or processing is done in a way that does not destroy the X?

I hope this is making sense.

• Bjoern

I

On Mon, Apr 11, 2022 at 10:33 AM Dalia Alghamdi @.***> wrote:

@bpeters42 https://github.com/bpeters42 Yes, I need a term that describes a specimen that still contains DNA; My goal here is to differentiate between planned processes' input and outputs. I agree that we should keep that axiom

— Reply to this email directly, view it on GitHub https://github.com/obi-ontology/obi/issues/1512#issuecomment-1095336999, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJX2IWDVCQFEJE7V6O373LVERO7DANCNFSM5Q4Z5S5A . You are receiving this because you were mentioned.Message ID: @.***>

-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[DanBerrios]

OBI has "nucleic acid extraction" (process http://purl.obolibrary.org/obo/OBI_0666667) that outputs "nucleic acid". That output thing was intended to be this concept of DNA processed specimen and is often called a DNA extract or nucleic acid extract.

has_specified_output some nucleic acid

the output is currently "nucleic acid" which is the component of interest of the extract (in this case) but not the entire extract itself. Is our axiom on nucleic acid extraction wrong, @bpeters42 ? Should it instead be http://purl.obolibrary.org/obo/OBI_0001010 "nucleic acid extract". I think so....

[DanBerrios]

See PR 1677

[Dalalghamdi]

Dear @DanBerrios my apologies for the delay. my intention for DNA processed specimen was to label DNA specimens that has been processed (e.g. specimen that went through library prep process). So here, the "nucleic acid extract" would be the input of library prep process and "DNA processed specimen" would be the output of the process.

[DanBerrios]

@Dalalghamdi OBI currently has various library objects that are output of library prep process: http://purl.obolibrary.org/obo/OBI_0000711 Granted, libraries are processed DNA specimens.... Do you feel we need the more general class "processed DNA specimen" above the various kinds of libraries?