Revision as of 15:18, 14 March 2017 (view source) WikiSysop (talk | contribs) (→‎eSample from biotic environment) ← Older edit		Revision as of 10:43, 15 March 2017 (view source) WikiSysop (talk | contribs) Newer edit →
Line 13:		Line 13:
	Search for eSamples is now working. Not yet working for different prepatationTypes (eDNA, aDNA, gDNA).		Search for eSamples is now working. Not yet working for different prepatationTypes (eDNA, aDNA, gDNA).
		+
		+	Search for eDNA is also working. This is provided as preparationType, so now one can search for all preparation types (also leaf, muscle etc.)
		+
		+	Krone file is now embedded and displayed in the tab "Visualization" right to “Taxon List”.
	==Suggestion List==		==Suggestion List==
Line 19:		Line 23:
	'''Next:'''		'''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 the Dryad resource for the raw data
	* Add Loan information for the enviro sample		* Add Loan information for the enviro sample
	* Do the same thing with DwC-A		* Do the same thing with DwC-A
−	* Improve the portal search	+	* Krona file currently provided as sequencing-reference, term does not fit very well yet
−	** search for eDNA not yet working	+
	=gDNA, culture, specimen, abiotic eSample, eDNA=		=gDNA, culture, specimen, abiotic eSample, eDNA=

---

Revision as of 10:43, 15 March 2017

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.

Background

Environmental sample data are causing trouble regarding proper mapping with ABCD and Darwin Core. The traditional way of a few identifications for a single specimen is not working here. Since the eDNA itself can be stored similar to gDNA, this topic is of interest for GGBN and we must find a solution. Currently a working mapping with ABCDGGBN_Enviro exist. As soon as this works as required, a solution for DwC-A will be created as well.

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 The raw ABCD file can be retrieved by clicking on the links to the left.

Search for eSamples is now working. Not yet working for different prepatationTypes (eDNA, aDNA, gDNA).

Search for eDNA is also working. This is provided as preparationType, so now one can search for all preparation types (also leaf, muscle etc.)

Krone file is now embedded and displayed in the tab "Visualization" right to “Taxon List”.

Suggestion List

Search results for a taxon that occurrs in an environmental sample should be clearly distinguished from genomic DNA samples. Solved by the following phrase: Mame 'xyz' appears in environmental sample(s) or eDNA. Search for all taxa occuring in the sample is solved. The proper display in the hitlist is not yet solved for biotic eSamples.

Next:

• Add the Dryad resource for the raw data
• Add Loan information for the enviro sample
• Do the same thing with DwC-A
• Krona file currently provided as sequencing-reference, term does not fit very well yet

gDNA, culture, specimen, abiotic eSample, 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://sandbox.ggbn.org/ggbn_sandbox/search/record?unitID=AA1BN60&collectioncode=Birds&institutioncode=USNM

eDNA or eSample from ancient material

Coming soon.