[tdwg-humboldt] meeting this week

Mon Jul 17 01:54:39 UTC 2023

Hi John

Thanks for your comments. We want the document to align with the
unified model

 I think we understand the importance of not being proscriptive.  That was
not our intent .

Your comment "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. "  was helpful for me.  Let's see if others respond.

Having a zoom discussion may turn out to be the best way to make sure we
all get to a common understanding..

Based on your previous email, you will be teaching at our scheduled meeting
time this week but free the following week.  Is that correct?

Thanks again for your help and insights

Rob

On Sun, Jul 16, 2023 at 1:34 PM John Wieczorek <tuco at berkeley.edu> wrote:

> 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
>>
>

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