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Add interpretation for DWC term - preparations #474
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We don't yet interpret the DWC
VertNet's query "is there tissue that can be used for DNA sequencing" is then an OR-query on |
Implementation in #477:
This is only setting interpreted dwc:preparations if verbatim dwc:preparations matches one of the VertNet tissue types ("tiss", "blood" etc). We don't need that filter -- people might want to search for other preparations. We should split the value on Later, we can interpret the values ("tiss" → "tissue" etc), but that requires a vocabulary first. |
I don't understand if this signifies that tissues will be fully detected or
not. For example, if preparations contains, "piel | cranio | riñon" and a
preparations vocabulary says that "riñon" is "liver", that will be great,
but how will the fact that this signifies a viable tissue be accomplished.
It will require the other vocabulary that says which standardized
preparation clauses constitute tissues and then either add that to the list
or use a different "hasTissue" index in the way we did. Just trying to
confirm that the "hasTissue" concept will remain functional under the
proposed scenario.
…On Thu, Feb 11, 2021 at 4:39 PM Matt Blissett ***@***.***> wrote:
Implementation in #477 <#477>:
hasTissue: es term preparation exists (Parse field DwcTerm.preparation ->
if hasTissue -> add original value into index/hdfs)
This is only setting interpreted dwc:preparations if verbatim
dwc:preparations matches one of the VertNet tissue types ("tiss", "blood"
etc).
We don't need that filter -- people might want to search for other
preparations. We should split the value on | etc, and store them in an
array.
Later, we can interpret the values ("tiss" → "tissue" etc), but that
requires a vocabulary first.
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My recommendation would be to start with adding As a second, future step I propose we consider the VertNet wish for |
My approximate view is that hasTissue/hasPreparations is less important than stillExistsInSomePhysicalFormThatCouldInPrincipleBeExaminedOrStudiedOrSequencedEtc. In other words - is there a specimen or some part of a specimen that remains and can be studied? Not sure if that helps in any way ... |
Whereas I understand and applaud the broader vision, the need to be able to
determine which specimens have viable tissues arose from a concrete need
within the community actually sharing their data. We implemented it as an
elegant and simple solution to a request to create a Tissues portal. For
these reasons is was and remains an important capability of the VertNet
portal that we would really like to replicate if we are going to abandon
that for a hosted portal.
…On Mon, Feb 15, 2021 at 2:02 AM Donald Hobern ***@***.***> wrote:
My approximate view is that hasTissue/hasPreparations is less important
than
stillExistsInSomePhysicalFormThatCouldInPrincipleBeExaminedOrStudiedOrSequencedEtc.
In other words - is there a specimen or some part of a specimen that
remains and can be studied?
Not sure if that helps in any way ...
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As part of the VertNet feature we need to interpret preparation field, add it into index and hdfs schemas.
Use VertNet feature branch
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