Difference between revisions of "Use Cases Enviro"

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(Created page with "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...")
 
 
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<div id="wikinote">'''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.</div>
 
<div id="wikinote">'''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.</div>
  
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=eDNA from eSample=
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=Background=
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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.
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=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.
 
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
 
Stable test example: http://sandbox.ggbn.org/ggbn_sandbox/search/record?unitID=DB+e200000&collectioncode=DNA+Bank&institutioncode=B
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The raw ABCD file can be retrieved by clicking on the links to the left.
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Search for eSamples is now working.
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Search for eDNA is also working. This is provided as preparationType, so now one can search for all preparation types (also leaf, muscle, gDNA etc.)
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Krona file is now embedded and displayed in the tab "Visualization" right to “Taxon List”.
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==Suggestion List==
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[[File:SuggestionList Enviro.jpg|thumb|600px|Search for "Achnanthidium" finds genomic and environmental samples]] 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.
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'''Next:'''
 
'''Next:'''
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* Include the Krona example: http://www.ggbn.org/ggbn_portal/documents/krona.html
 
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** 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
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* Improve the portal search
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* Krona file currently provided as sequencing-reference, term does not fit very well yet
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** scientific name in the hitlist makes no sense
 
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** search for ALL names not yet working
 
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** search for eDNA not yet working
 
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** search for eSamples not yet working
 
  
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=gDNA, culture, specimen, eSample from abiotic environment, eDNA=
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=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.
 
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.
  
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Real example: http://sandbox.ggbn.org/ggbn_sandbox/search/record?unitID=DB+8219_D03_030&collectioncode=DNA+Bank&institutioncode=B
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Real example (work in progress): http://sandbox.ggbn.org/ggbn_sandbox/search/record?unitID=DB+8219_D03_030&collectioncode=DNA+Bank&institutioncode=B
  
 
=eSample from biotic environment=
 
=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.
 
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.
  
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Real example: http://localhost/ggbn_sandbox/search/record?unitID=AA1BN60&collectioncode=Birds&institutioncode=USNM
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Real example: http://sandbox.ggbn.org/ggbn_sandbox/search/record?unitID=AE4SG27&collectioncode=Mammals&institutioncode=USNM
  
 
=eDNA or eSample from ancient material=
 
=eDNA or eSample from ancient material=
 
Coming soon.
 
Coming soon.
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'''Back to [[Use Case Collection]]'''

Latest revision as of 14:07, 8 June 2018

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.

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.

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

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

Suggestion List

Search for "Achnanthidium" finds genomic and environmental samples
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 (work in progress): 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=AE4SG27&collectioncode=Mammals&institutioncode=USNM

eDNA or eSample from ancient material

Coming soon.


Back to Use Case Collection

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