[tdwg-humboldt] meeting this week

Mon Jul 17 01:56:28 UTC 2023

Yes, that is correct, I should be able to be free the following week.

On Sun, Jul 16, 2023 at 10:54 PM Rob Stevenson <rdstevenson10 at gmail.com>
wrote:

> 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.*
>>>>>
>>>>> _______________________________________________
>>>>> tdwg-humboldt mailing list
>>>>> tdwg-humboldt at lists.tdwg.org
>>>>> https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
>>>>>
>>>>> _______________________________________________
>>>>> tdwg-humboldt mailing list
>>>>> tdwg-humboldt at lists.tdwg.org
>>>>> https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
>>>>>
>>>>
>>>>
>>>> --
>>>> 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
> _______________________________________________
> tdwg-humboldt mailing list
> tdwg-humboldt at lists.tdwg.org
> https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
>
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