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ArctosDB / arctos

Arctos is a museum collections management system
https://arctos.database.museum
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Request to add soil or environmental sample as a part name #2841

Closed mlbowser closed 4 years ago

mlbowser commented 4 years ago

Issue Documentation is http://handbook.arctosdb.org/how_to/How-to-Use-Issues-in-Arctos.html

Goal More truthfully reflect the nature of environmental samples, soil samples in this case.

Context I am dealing with soil samples for metabarcoding of soil fungi and soil bacteria (one sample of soil per site, one DNA extraction per sample, two amplifications/analyses for each extraction). I would like to be able to enter the soil samples into Arctos as specimens. Currently, the only options available in the code table (https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecimen_part_name) for Env collections are "DNA extraction" and "filter paper". I can make "DNA extraction" work in this case, referring to the extractions instead of the original material samples. I would rather use "soil" (specific) or "environmental sample" (general), which would be more appropriate for the original samples.

Also, what would the appropriate identification be for such samples? "Life" is available in Arctos' taxonomy, but this may not be the most appropriate for a sample that might not contain life (even though we are looking for it).

Table https://arctos.database.museum/info/ctDocumentation.cfm?table=ctspecimen_part_name

Value "soil" or "environmental sample"

Definition soil: upper layer of the earth's surface environmental sample: a sample from the environment (e.g., soil, water, air) that is not intentionally associated with any particular organism.

Collection type Env

Attribute data type categorical

Attribute value "soil" or "environmental sample"

Part tissue flag no? May or may not include tissue. It is not a pure tissue sample.

Priority low

Jegelewicz commented 4 years ago

We have the part "geosample" does this seem sufficient? I added it to Env collections. If that suits your needs, please just close this issue.

Jegelewicz commented 4 years ago

Also, what would the appropriate identification be for such samples? "Life" is available in Arctos' taxonomy, but this may not be the most appropriate for a sample that might not contain life (even though we are looking for it).

See #2842

mlbowser commented 4 years ago

Sure, "geosample" would suffice for this type of sample. I will use it. Thanks!