[tdwg-humboldt] meeting this week

John Wieczorek tuco at berkeley.edu
Tue Jul 25 10:02:17 UTC 2023 

Welcome back, Kate!

On Tue, Jul 25, 2023 at 6:46 AM Kate Ingenloff <kathryn.ingenloff at gmail.com>
wrote:

> 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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>> tdwg-humboldt at lists.tdwg.org
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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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