[tdwg-humboldt] meeting this week

Sun Jul 16 17:34:07 UTC 2023

I'm sharing some comments inline. These are accompanied by comments and
suggestions in the Event Hierarchy document.

On Thu, Jul 13, 2023 at 6:29 AM Rob Stevenson <rdstevenson10 at gmail.com>
wrote:

> 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.
>

Just to clarify, this doesn't present any problems to what we have defined
in the Event Hierarchies document, correct?

> 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.
>
>
Again, just to clarify, this doesn't present any problems to what we have
defined in the Event Hierarchies document, correct?

> 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..."
>
>
I commented in the text that it doesn't seem to me that completeness is a
requirement, but that the rest seems reasonable.

> 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.
>

This is a good idea to be clarified with examples, as long as it is not
proscriptive. I think the most common lowest-level Events would actually be
Occurrences, at least in the Unified Model, where Occurrences are one type
of Event.

> 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.
>

Is that supposed to be "they could not be traced"? I;m sorry I could not
make it to the meeting. I am having a hard time understanding the issue.

> 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.
>

I hope the comments I made cover this, but I suspect it might require more
interactive discussion to unravel completely.

>
> 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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