biodiversity-specimen-data / specimen-data-use-case Goto Github PK

Dear @biodiversity-specimen-data/maintainers,

I have developed, and would like to contribute, a solution to the Report metrics for collections within an institution use case. Is there any sort of review process for proposed solutions? I have already had @ekrimmel look at my solution via iDigBio Slack. I have both Rmd and rendered HTML files ready to upload, assuming you grant me push access. I am also willing to help you maintain the repository.

Thanks,

David Jennings

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?

What would you like to be able to do?
Find all specimen records mobilized to iDigBio via a Symbiota portal.

What problems are you having?

Do you have any ideas for technical solutions?
See Cat's solution: https://gist.github.com/CatChapman/65f212e87cda8e066279b7f1e3724feb