Use Cases Enviro

This page describes the progress of all use cases related to environmental DNA and environmental samples. For all use cases described below we are currently working on stable test examples, that one can follow. If already available we will use real examples to play with.

Note: Until further notice the real examples will look very different in the production portal and in the sandbox! All examples refer to the sandbox. The test examples are of course not included in the production portal.

eDNA from abiotic eSample

This is a simple parent-child relation. The difficult issue is the big amount of taxa resulting from BLAST/sequencing. They should be displayed without confusion. Also one should be able to search for all included taxa without confusion regarding the hitlist.

Stable test example: http://sandbox.ggbn.org/ggbn_sandbox/search/record?unitID=DB+e200000&collectioncode=DNA+Bank&institutioncode=B

Next:

• Include the Krona example: http://www.ggbn.org/ggbn_portal/documents/krona.html
  • Will place it in a separate tab right to “Taxon List”. How should I name the tab? Since others might use other graph tools than Krona it should be named generically.
• Add the Dryad resource for the raw data
• Add Loan information for the enviro sample
• Do the same thing with DwC-A
• Improve the portal search
  • scientific name in the hitlist makes no sense
  • search for ALL names not yet working
  • search for eDNA not yet working
  • search for eSamples not yet working

gDNA, culture, specimen, eSample from abiotic environment, eDNA

This is a complex parent-child relation. The gDNA points to the culture. The specimen also points to the culture. Both specimen and culture points to the eSample. In addition the eSample is the mother of hundreds of further cultures, specimens, gDNA samples and of course a eDNA sample.

Real example: http://sandbox.ggbn.org/ggbn_sandbox/search/record?unitID=DB+8219_D03_030&collectioncode=DNA+Bank&institutioncode=B

eSample from biotic environment

In comparison to the abiotic eSample this one has a main taxon, e.g. the animal or plant which serves as the environment. This makes a difference in search and display.

Real example: http://localhost/ggbn_sandbox/search/record?unitID=AA1BN60&collectioncode=Birds&institutioncode=USNM

eDNA or eSample from ancient material

Coming soon.