[tdwg-humboldt] meeting this week

Thu Jul 13 09:29:14 UTC 2023

Dear Humboldt Core TG

Below are notes from Wednesday.  John, your asynchronous input would be
especially helpful because we know you will not be able to attend the next
meeting. If I have misinterpreted something or someone, please jump in and
make a correction.

Thanks
Rob

On Wednesday (2023/07/12), Steve, Peter, Zach, Wesley and I met and had
fruitful discussions about points 6 and 7 in section 3.3 of the Properties
of hierarchical Events in Humboldt Extension for ecological inventories
<https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit>.
These are points John wrote to give guidance for applying the Humboldt
Extension.

The discussion was around whether the phrasing was too prescriptive.
Wesley asked “Could we come up with counter examples?”. Wesley will write a
few sentences to encapsulate the issue. Peter felt the wording may not be
necessary.

Peter showed us several inventories from BioCollect and described how they
fit into the Humboldt extension model. The BioCollect model uses a survey
template that can be applied repeated to a collection event and allows many
kinds of observations and measurements to be made. The series of collection
events together make a dataset.  In Humboldt terms this dataset is a parent
Event. To facilitate reuse each survey template is made up of a variety of
observation and measurement protocols that can be bundled together as
needed to make different survey templates.

Zach described how the Field Museum’s Rapid Inventories in which teams of
biologists document biodiversity of different taxa ( plants, fishes,
amphibians, reptiles, birds, and mammals) using a variety of methods at one
site and within one timeframe
<https://www.rapidinventories.fieldmuseum.org/what-is-a-rapid-inventory>
are being represented as one Event at the highest level.

Tim added a comment to the document asking that we consider rewriting the
definition of

He said “I think this definition might be improved. An inventory is a
complete list of something, but the definition doesn't capture this, only
referring to the activities used in the methodology. Perhaps something like:

"An inventory dataset accounts for all targeted organisms and measurements
recorded while following a structured sampling protocol. Observations and
measurements are captured in one or more dwc:Events that MAY..."

This request is in line with our discussion on Wednesday.

Our discussion suggested it would be helpful to put in some kind of
clarifying statement about what the lowest level Event might contain. My
current understanding is that this lowest level might contain just a one
zero to represent the event that occurred but that no occurrence was found
or NA that a measurement was attempted but the measurement failed for some
reason. On the complexity end of the spectrum of what an event could
contain, Peter gave an example (see text at the bottom of the document) of
an event pointing to an array of observations and measurements based on a
survey template for Vegetation condition assessment.  In a flattened (2D)
database this would take 40 records (rows) to represent what was part of
the event. Peter gave a second example about birds in which he added a
screen shot from the BioCollect application. Here again multiple records
are needed to contain the information in a flatten form.

This brings up the point of discussion in the meeting. Peter said that each
event and each occurrence will have their own ids.  This would mean if one
flattered an event and selectively removed species occurrence records
containing the occurrence ID that they could be traced back to the event in
which the collection took place.

The group hopes that others who could not attend have insights into the
issues and the descriptions. We felt John's comments would be very
important because of his knowledge about the new GBIF model.

On Tue, Jul 11, 2023 at 4:06 PM Rob Stevenson <rdstevenson10 at gmail.com>
wrote:

> Dear All,
> I wrote up some ideas.  It proved more difficult than I thought and I am
> not sure I captured the issue at the core of the discussion -
> How to deal with the lowest level of the event hierarchy
>
> Below is the text but it is also at the bottom of our document here
>
> https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
>
>
>
> Currently the vast majority of records in the GBIF archive contain an
> observation of one or more individuals of a single taxon. Many additional
> fields in the record, based on the Darwin Core, provide context for the
> observation including the observation type, the time and place of
> observation, the observer, etc.  At the present time, however, the metadata
> do not provide context about whether or not an observation is part of a
> systematic set of observations, herein called a survey. A survey is an
> approach based on the idea of statistical sampling, whereby an observer is
> unable to measure an entire population but instead focuses on a subset of
> the population to make inferences about the entire population.
>
>
>
> The added scientific value of the survey framework, over just a collection
> of unrelate observations indicating present only, is that a scientist can
> make inferences about how common or rare a taxon might be (its status) and
> over time, measure trends. The basic idea of a survey is intuitive: the
> more you look, the more you will find. In the fisheries literature this
> idea is called “catch per unit effort”.
>
>
>
> The goal of the Humboldt extension is to accurately describe a survey and
> its often hierarchical nature. Whereas an observation record is
> characterized by general sense of the observation approach (Basis of
> Record), a time and a location, a survey has a much more detailed
> description of the observation technique(s), and also includes the number
> of sampling units employed, a time or time interval (start time and
> duration), and a measure of the spatial extent over which the survey was
> conducted.
>
>
>
> A sampling unit, the finest measurement resolution of a survey,
> encompasses a variety of ways of looking for species.  It might include:
>
>
>
> A physical sample such as a leaf or a water sample containing molecules of
> DNA
>
> One or several sweeps of a net containing a collection of insects
>
> Camera trap – collection of images of mammals
>
> Quadrat  – estimating the percentage of space or numbers of space
> occupying organisms such as plants or clams
>
> Bird checklist – list of species of birds observed from a fixed-point
>
>
>
> Special considerations arise at the sampling unit level. First a
> measurement can detect no individuals or space occupied. In these cases the
> data need to reflect this fact with recording  0 for the observation.
> Second a measurement might be more than just a number or percentage.  It
> might a be compound structure that includes the flowering stage of each
> plant in a quadrat or the length and body mass of each insect in the sweep
> net sample or the location of each bird along a transect.
>
>
>
>
>
> On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel <dschigel at gbif.org> wrote:
>
>> Stuck in a GBIF meeting, not joining today
>>
>> DS
>>
>>
>>
>> *From:* tdwg-humboldt <tdwg-humboldt-bounces at lists.tdwg.org> *On Behalf
>> Of *John Wieczorek
>> *Sent:* Tuesday, 4 July, 2023 21:30
>> *To:* Humboldt Core TG <tdwg-humboldt at lists.tdwg.org>
>> *Cc:* wmh6 at cornell.edu
>> *Subject:* Re: [tdwg-humboldt] meeting this week
>>
>>
>>
>> Hi folks,
>>
>>
>>
>> I am giving the second module of a course on georeferencing tomorrow
>> throughout the time of the Task Group call. I haven't mastered the two
>> places at once thing, unfortunately.
>>
>>
>>
>> Cheers,
>>
>>
>>
>> John
>>
>>
>>
>> On Tue, Jul 4, 2023 at 4:27 PM ys628 <yanina.sica at yale.edu> wrote:
>>
>> Hi all,
>>
>>
>>
>> Lets discuss the Hierarchical Document
>> <https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit>this
>> week!
>>
>>
>>
>> With the TDWG 2023 rush, people might not have had time to review or work
>> on it. If that is the case, we can have a rather short meeting to agree on
>> the next steps.
>>
>>
>>
>> See you!
>>
>>
>>
>> Yani
>>
>>
>> <https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit>
>>
>> Hierarchical Events in Humboldt Extension for ecological inventories
>> <https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit>
>>
>> Properties of hierarchical Events in Humboldt Extension for ecological
>> inventories Title: Properties of hierarchical Events in Humboldt Extension
>> for ecological inventories Date version issued: 2023-xx-xx Date created:
>> 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This
>> ...
>>
>> docs.google.com
>>
>>
>>
>>
>>
>> Yanina V. Sica, PhD
>>
>> Lead Data Team
>>
>> Map of Life <https://mol.org/> | Center for Biodiversity and Global
>> Change <https://bgc.yale.edu/>
>>
>> Yale University
>>
>> pronouns: she/her/hers
>>
>> *If you are receiving this email outside of your working hours, I am not
>> expecting you to read or respond.*
>>
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>>
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>>
>
>
> --
> Robert D Stevenson
> Associate Professor
> Department of Biology
> UMass Boston
>

-- 
Robert D Stevenson
Associate Professor
Department of Biology
UMass Boston
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