Find specimens with cryo-preserved tissue

[ekrimmel]

What would you like to be able to do?
From Deb: Hi All, getting close to a possible useful search to investigate if we have specimens -- for which there could be cryo-preserved tissue for study. These three genera in the query are ones of interest for corona virus at the moment. BUT, it's not yet really known what the vector/s is/are. And so these are only preliminary -- and could help researchers find tissue samples of interest. Next, we need to add to the query, or use R likely better, to look at what's in dwc:preparations (because "alcohol" isn't going to be what's needed by the researchers).

https://search.idigbio.org/v2/search/records/?rq={"genus":["manis","rhinolophus","paguma"],"data.dwc:preparations":{"type":"exists"}}

returns 14570 records.

A more fine-grained approach would include these species: Manis culionensis, M. pentadactyla M. javanica Manis crassicaudata. Paguma larvata, and the Genus Rhinolophus.

We would need to look in the dwc:preparations and possibly other fields for anything indicating cryopreserved tissue exists.

What problems are you having?
Need to figure out how to filter data in dwc:preparations.

Do you have any ideas for technical solutions?

[ekrimmel]

My initial start:

#load libraries
library(ridigbio)
library(tidyverse)

#search for records within genera of interest
records <- idig_search(rq = list(genus = c("manis","rhinolophus","paguma")),
                       fields = c("uuid", "recordset", "institutioncode", "data.dwc:preparations"))

#list distinct values for preparation field
distinctPrep <- records %>% 
  group_by(`data.dwc:preparations`) %>% 
  tally() %>% 
  arrange(desc(n))

#save as csv
write_csv(distinctPrep, "distinctPrep.csv")

[ekrimmel]

see draft use case: find-tissue-samples.md

[ekrimmel]

see also draft .Rmd in solution directory