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nvs-vocabs / P01

Repository to manage issues related to the BODC P01 Vocabulary
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Request for Abundance of protistan plankton per unit volume of the water body by optical microscopy #66

Closed jdelbel closed 1 year ago

jdelbel commented 3 years ago

Abundance of protistan plankton per unit volume of the water body by optical microscopy

Related to: http://vocab.nerc.ac.uk/collection/P01/current/PU00M00Z/ (Abundance of phytoplankton per unit volume of the water body by optical microscopy)

The majority of the species in the data I am working to submit to OBIS are autotrophic, but mixotrophic and heterotrophic species were also observed and enumerated. I suspect this is common for phytoplankton microscopy data and I propose a more encompassing term.

gwemon commented 3 years ago

Hello @jdelbel Are the species you mention named in the Occurrence record? If so then the OBIS protocol is to use http://vocab.nerc.ac.uk/collection/P01/current/SDBIOL01/ for the abundance in the ExtendedMeasurementOrFact Extension.

jdelbel commented 3 years ago

Hi Gwen,

Thank you for your response.

Yes, the species are mentioned in the Occurrence extension. I saw and considered that concept, but it does not include "by optical microscopy", which I suspect is an important addition. Is there a similar term that includes this?

Justin

On Tue, 27 Apr 2021 at 10:58, Gwen Moncoiffé @.***> wrote:

Hello @jdelbel https://github.com/jdelbel Are the species you mention named in the Occurrence record? If so then the OBIS protocol is to use http://vocab.nerc.ac.uk/collection/P01/current/SDBIOL01/ for the abundance in the ExtendedMeasurementOrFact Extension.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nvs-vocabs/P01/issues/66#issuecomment-827800834, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPW44XS7UXMLNGJZ6NJ34LTK33MZANCNFSM42DDIZ3Q .

-- Justin Del Bel Belluz, MSc. Research Technician - Bio-Optical Oceanography Hakai Institute 100 - 1002 Wharf Street Victoria, BC Canada V8W 1T4 www.hakai.org

gwemon commented 3 years ago

Hi Justin, it is my understanding that in the DWC-A format, the methodology should be captured separately from the P01 code. I will direct your query to the OBIS Vocab management group where somebody should be able to advise on the best way to capture that information using a controlled vocabulary like e.g. http://vocab.nerc.ac.uk/collection/S04/current/S0423/

jdelbel commented 3 years ago

Thanks Gwen. Yes, That would be great. I'm curious as to where this would go (eventCore or emof). I will send a message out to the SMBD group as well.

Much appreciated.

On Wed, 28 Apr 2021 at 23:29, Gwen Moncoiffé @.***> wrote:

Hi Justin, it is my understanding that in the DWC-A format, the methodology should be captured separately from the P01 code. I will direct your query to the OBIS Vocab management group where somebody should be able to advise on the best way to capture that information using a controlled vocabulary like e.g. http://vocab.nerc.ac.uk/collection/S04/current/S0423/

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nvs-vocabs/P01/issues/66#issuecomment-828973667, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPW44SFJQSYRQUGQVY4N5TTLD4ETANCNFSM42DDIZ3Q .

-- Justin Del Bel Belluz, MSc. Research Technician - Bio-Optical Oceanography Hakai Institute 100 - 1002 Wharf Street Victoria, BC Canada V8W 1T4 www.hakai.org

pieterprovoost commented 3 years ago

I think it would be best to specify "optical microscopy" in a MeasurementOrFact record linked to the Event. There's http://vocab.nerc.ac.uk/collection/L05/current/LAB05/ "optical microscope", so it could look like this:

term value
measurementType sampling instrument name
measurementTypeID http://vocab.nerc.ac.uk/collection/Q01/current/Q0100002/
measurementValue optical microscope
measurementValueID http://vocab.nerc.ac.uk/collection/L05/current/LAB05/

I'm just not entirely convinced that "sampling instrument" is apprpropriate, maybe there's a better term for that. I'll check with our nodes.

I also recommend populating samplingProtocol in the event core.

jdelbel commented 3 years ago

Hi Pieter,

Thank you for your email.

Currently, I have:

measurementType: abundance measurementTypeID: http://vocab.nerc.ac.uk/collection/P01/current/SDBIOL01/ measurementunit: number per litre measurementUnitID: http://vocab.nerc.ac.uk/collection/P06/current/UCPL/

I think this works, but I need to figure out where to put: http://vocab.nerc.ac.uk/collection/S04/current/S0423/

My colleague, Tim van der Stamp, suggested either,

measurementMethod: http://vocab.nerc.ac.uk/collection/S04/current/S0423/

and/or

samplingProtocol: http://vocab.nerc.ac.uk/collection/S04/current/S0423/

Any thoughts? Would this work?

Originally I had:

measurementType: abundance of phytoplankton measurementTypeID: http://vocab.nerc.ac.uk/collection/P01/current/PU00M00Z/

This was nice because it encompassed everything, but while my data is focused on phytoplankton, non-autotrophic species were also enumerated and recorded in the occurrence extension. This was my original thinking of a new term "abundance of protistan plankton per unit of the water body by optical microscopy"

Thank you for your time and help.

Justin

On Fri, 30 Apr 2021 at 07:42, Pieter Provoost @.***> wrote:

I think it would be best to specify "optical microscopy" in a MeasurementOrFact record linked to the Event. There's http://vocab.nerc.ac.uk/collection/L05/current/LAB05/ "optical microscope", so it could look like this: term value measurementType sampling instrument name measurementTypeID http://vocab.nerc.ac.uk/collection/Q01/current/Q0100002/ measurementValue optical microscope measurementValueID http://vocab.nerc.ac.uk/collection/L05/current/LAB05/

I'm just not entirely convinced that "sampling instrument" is apprpropriate, maybe there's a better term for that. I'll check with our nodes.

I also recommend populating samplingProtocol in the event core.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nvs-vocabs/P01/issues/66#issuecomment-830142843, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPW44WRIDM5UHJXM3XSQFLTLK6WXANCNFSM42DDIZ3Q .

-- Justin Del Bel Belluz, MSc. Research Technician - Bio-Optical Oceanography Hakai Institute 100 - 1002 Wharf Street Victoria, BC Canada V8W 1T4 www.hakai.org

pieterprovoost commented 3 years ago

@jdelbel I think measurementMethod is a good choice. In addition you could add the term to samplingProtocol, unless you have a link/DOI pointing to a more detailed protocol which also covers sampling methods for example.

jdelbel commented 3 years ago

Thanks Pieter. Sounds good.

On Wed, 5 May 2021 at 03:30, Pieter Provoost @.***> wrote:

@jdelbel https://github.com/jdelbel I think measurementMethod is a good choice. In addition you could add the term to samplingProtocol, unless you have a link to a more detailed protocol which also covers sampling methods.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/nvs-vocabs/P01/issues/66#issuecomment-832584035, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJPW44SUH54GE63GF254FDTTMEM3XANCNFSM42DDIZ3Q .

-- Justin Del Bel Belluz, MSc. Research Technician - Bio-Optical Oceanography Hakai Institute 100 - 1002 Wharf Street Victoria, BC Canada V8W 1T4 www.hakai.org

gwemon commented 1 year ago

I am closing this ticket @jdelbel as I think this issue is now resolved. Kind regards.