[tdwg-humboldt] meeting this week

Tue Jul 25 09:43:58 UTC 2023

Hi all!

I'm officially back from leave and will join the meeting on Wednesday. It
looks like I have a lot to catch up on! I'll try to have a thorough look at
the document by then, and look forward to helping however I can to continue
pushing Humboldt forward.

Cheers,
Kate

On Mon, Jul 17, 2023 at 3:56 AM John Wieczorek <tuco at berkeley.edu> wrote:

> 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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-- 
------------------------------
Kate Ingenloff, PhD
Pronouns: she/her(s)
(+45) 51 44 13 23

"When one tugs at a single thread in nature, he finds it attached to the
rest of the world." ~John Muir
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