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Expand description of tiss_cult_growth_med slot #2267

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pkalita-lbl opened this issue Nov 13, 2024 · 5 comments
Open

Expand description of tiss_cult_growth_med slot #2267

pkalita-lbl opened this issue Nov 13, 2024 · 5 comments
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@pkalita-lbl
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Currently the description of the tiss_cult_growth_med slot is a bit vague, and it is also not well aligned with the example shown. The description simply says:

Description of plant tissue culture growth media used

And the one example is a URL:

https://link.springer.com/content/pdf/10.1007/BF02796489.pdf

This caused confusion for a Field Notes user (microbiomedata/nmdc-field-notes#188) because they weren't sure what was really being asked of them.

I would suggest that:

  1. The description should be updated to indicate that either a textual description or a URL where a description of the method can be found.
  2. A second example should be added to illustrate an actual description (as opposed to a URL)
@turbomam
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turbomam commented Dec 19, 2024

I don't see why this slot would be limited to plant culture situations (as opposed to any other cell or tissue culture situation)

nmdc-schema also includes MIxS' plant_growth_med

@turbomam
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using https://portal.nersc.gov/project/m3408/biosamples_duckdb/ncbi_biosamples_2024-11-19T1545EST-pre-alpha.duckdb.gz

select
	a.content ,
	count(1)
from
	main.attributes a
where
	harmonized_name = 'tiss_cult_growth_med'
group by
	content
order by
	count(1) desc ;

@turbomam
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content count(1)
NA 706
not applicable 630
not collected 218
L1-Si medium 21
missing 7
Liquid enrichment cultures and cultivation assays were performed using either MME medium or MMV medium (with 1x vitamin solution) cultured with variable carbon sources. 3
DOI: 10.1079/IVP2006748 2
Not applicable 2
N/A 1
King's 1
root nodules, field growth 1
corn meal agar 1
Potato dextrose agar 1

@turbomam
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turbomam commented Dec 19, 2024

"DOI: 10.1079/IVP2006748" = https://link.springer.com/article/10.1079/IVP2006748

That's restricted-access but provides an abstract that can be summarized like this:

Murashige and Skoog (MS) medium, supplemented with 4.0 mg/l GA3, 0.2 mg/l NAA 0.2 mg/l 2,4-D, with 1.0 mg/l KT for starting suspension culture and 60-90 g/l sucrose for developing early cotyledonary-stage somatic embryos into whole plants.

@turbomam
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For the slot description, I recommend

A PubMed ID, DOI , URL or text snippet documenting the tissue culture medium used.

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