[tdwg-humboldt] Humboldt Task Group Meeting Wed 11 April 2023, 08:00 EST/13:00 UTC

ys628 yanina.sica at yale.edu
Wed Apr 12 14:57:22 UTC 2023 

Hi all, thanks for a great meeting.

I just wanted to share a summary of the next steps because we are very close and we would need some help finishing up all the required documents.


  *   Implementation report (please review and add yourself as an author here<https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj98hbk/edit#heading=h.8dmewb9wxxbk>)
  *   List of terms (please review all eco: terms here<https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d7VEDyqOg/edit#gid=673949815>, tab: complete_term_list_from_JW)
  *   Additional document to better explain eco:isLeastSpecificTargetCategoryQuantityInclusive (please add content, examples, links to other terms, etc. to this <https://docs.google.com/document/d/11fPW4JibRWUnrtTOZwDkAcxo5d-lwnATXyh3xmO65rs/edit> document).
     *   This will be added as an official document to the list of terms. The idea here, is that all the comments and relations of other terms will be better captured in a separate document instead of making a terribly long Comments section.
  *   Humboldt Extension Documentation (please review here<https://docs.google.com/document/d/1rX4m94rtZDR_8iIe3RvRnNYKDJcmSX3ii4S5hCznEA0/edit?usp=sharing>)
     *   This will not be an official document but will probably need to be linked in our presentation. Basically, I took our testing guide and removed all the parts related to the testing. We will need to update this document and polish it.

Thanks!!


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.
________________________________
From: ys628 <yanina.sica at yale.edu>
Sent: Wednesday, April 12, 2023 7:21 AM
To: Humboldt Core TG <tdwg-humboldt at lists.tdwg.org>; wmh6 at cornell.edu <wmh6 at cornell.edu>
Subject: Re: Humboldt Task Group Meeting Wed 11 April 2023, 08:00 EST/13:00 UTC

Sorry, I messed up with the time as well, lol! It is at 12:00 UTC. I forgot to add the link that Steve suggested!

Also, below you can find Wesley's comment about the term. Not sure if you all got it..

Regarding absences, we can talk about it today, I saw the documents Abby shared and there are members of this group already participating in developing the definitions so I hoped they would be aligned but definitely worth discussing!

From Wesley: Hi Yani,

   You will be the only one in the Humboldt Extension group to see this, because I still have not gotten into the listserv group.

   I'll be at the meeting later today, where I assume that we will be discussion this term, it's definition and comments.  For now, I just want to mention that overall what you and John have done looks nice!  The only, relatively minor, suggestion that I have is regarding the comments, which I think would be more understandable if they were broken into two paragraphs, with the second paragraph starting with this phrase: "For example, suppose there are three records with..."
   The reason that I am suggesting this change is because I originally thought that the example was only describing the "false" category of records.  I made this assumption because "For example..." directly follows text that is explaining the interpretation of a "false" value.
   Perhaps my suggested new paragraph could even start with a slightly modified phase to make the purpose of the example clearer, something like this: "As an example of the difference between "true" and "false" values, suppose there are three records with..."

   Anyway, that's the only thing that I want to mention here, in case I forget to mention this during the meeting.

Wesley

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
________________________________
From: tdwg-humboldt <tdwg-humboldt-bounces at lists.tdwg.org> on behalf of ys628 <yanina.sica at yale.edu>
Sent: Tuesday, April 11, 2023 3:51:57 PM
To: Humboldt Core TG <tdwg-humboldt at lists.tdwg.org>; wmh6 at cornell.edu <wmh6 at cornell.edu>
Subject: Re: [tdwg-humboldt] Humboldt Task Group Meeting Wed 11 April 2023, 08:00 EST/13:00 UTC

Sorry, I messed up the dates.
Our next Humboldt Task Group Meeting is Wed 12 April 2023, 08:00 EST/13:00 UTC
Zoom link: https://yale.zoom.us/j/97318391101



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.
________________________________
From: ys628 <yanina.sica at yale.edu>
Sent: Tuesday, April 11, 2023 3:41 PM
To: Humboldt Core TG <tdwg-humboldt at lists.tdwg.org>; wmh6 at cornell.edu <wmh6 at cornell.edu>
Subject: Humboldt Task Group Meeting Wed 11 April 2023, 08:00 EST/13:00 UTC

Hi all,

Thank you so much Wesley for last week's summary and everybody for advancing with the report!

Here<https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj98hbk/edit#heading=h.8dmewb9wxxbk> is the latest version of the report.

John and I have also been discussing the term isLeastSpecificTargetCategoryQuantityInclusive. There was a confusion between the previous name (sumQuantities) and the current name (isLeastSpecificTargetCategoryQuantityInclusive) because when sumQuantities is TRUE then isLeastSpecificTargetCategoryQuantityInclusive is FALSE. For example, in eBird, where ebird_target_1 (H. rustica, did not include the subspecies), we have to add organismQuantity to get the total detected quantity for the Taxon (H rustica at the species level). Or the opposite, for OBIS, where bw_target_3 (E. antarctica without lifestage distinction) is inclusive of the more specific lifeStage targets (is already the sum of organismQuantity for lava and postmeta) so we cannot add organismQuantity to get the total detected quantity for the Taxon (E. antarctica without lifestage distinction). Now, this is resolved, please take a look at this new definition/comments:

     *   Term name: isLeastSpecificTargetCategoryQuantityInclusive
     *   Definition: The total detected quantity of Organisms for a Taxon in an Event is given explicitly in a single record (dwc:organismQuantity value) for that Taxon.
     *   Comments: "Recommended values are 'true' and 'false'. If 'true', the dwc:organismQuantity values for a Taxon in an Event is inclusive of all Organisms of the Taxon (including more specific scopes such as different life stages or lower taxonomic ranks) and the total detected quantity of Organisms for that Taxon in the Event cannot be determined by summing the dwc:organismQuantity values for the Taxon in the Event. Instead, the total detected quantity of Organisms for the Taxon in an Event would have to be reported in a single record for the Taxon in the Event that had no further specific scopes. In this case the sum of dwc:organismQuantity values for the reported subsets of the Taxon must not exceed the value of dwc:organismQuantity for the single record for the Taxon without subsets (i.e., the total).  If 'false', the dwc:organismQuantity values for a Taxon in an Event can be added to get the total detected quantity of Organisms for that Taxon in the Event. For example, suppose there are three records with dwc:organismQuantity for a Taxon for an Event. One record is for adults of the Taxon with dwc:organismQuantity = 1 and dwc:organismQuantityUnit = 'individuals', one record is for juveniles of the Taxon with dwc:organismQuantity = 2 and dwc:organismQuantityUnit = 'individuals', and one record is for the Taxon without specifying the lifeStage and with dwc:organismQuantity = 4 and dwc:organismQuantityUnit = 'individuals'. If isLeastSpecificTargetCategoryQuantityInclusive is 'true', the total number of individuals of the Taxon for the Event is 4 (the least specific Taxon record - the one with no more specific scopes - includes all individuals of the Taxon). This means there was 1 adult, 2 juveniles and 1 individual whose lifeStage was not recorded. If isLeastSpecificTargetCategoryQuantityInclusive is 'false', the total number of individuals of the Taxon for the Event is 7 (the least specific Taxon record - the one with no more specific scopes - does not include all individuals of the Taxon, rather, it is a separate category that must also be added to get the total). This means there was 1 adult, 2 juveniles and 4 individuals whose lifeStage was not recorded. This term is only relevant if dwc:organismQuantity is a number.
        *   We could point to the DwC definition of Taxon<http://rs.tdwg.org/dwc/terms/Taxon> == A group of organisms (sensu http://purl.obolibrary.org/obo/OBI_0100026) considered by taxonomists to form a homogeneous unit. Should we do this adding  dwc:Taxon? or since it is a class adding the nameSpace is not correct.
     *

Tomorrow, we can discuss this term, review the report and assign the next step (public review??)😁

All the best!

Yani



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.

________________________________
From: Wesley M. Hochachka <wmh6 at cornell.edu>
Sent: Wednesday, April 5, 2023 10:15 AM
To: ys628 <yanina.sica at yale.edu>; Humboldt Core TG <tdwg-humboldt at lists.tdwg.org>
Subject: Re: Humboldt Task Group: Please review implementation report

Hi Yani,

   First, while I am trying to send this message to the Humboldt Core group in TDWG, I suspect that it will bounce, so could you forward the contents of the message to the group?  Anyway...

   Ming, Zach, Steve and I met today, and here's a brief summary of what we discussed:

  *   regarding the term isLeastSpecificTargetCategoryQuantityInclusive, we agreed that we should keep this name, which is a clear description of the intend of the term even though it's long.  There did not seem to be an obvious way to substantially shorten the term and still maintain clarity of meaning.  If there are comments during public review, then we can always revisit the name, but for now it did not seem worth holding up the process of going to public review in order to try to find a better alternative to the current name.
  *   Also regarding this term, we discussed that its Definition and Comments need a little more work, mostly or entirely associated with the use of "Taxon", which currently is used in a way that means that organisms of different sexes or age classes below to different taxa.  I'll try to create time before next Wednesday to suggest changes to wording, and I believe that Ming will look at the Definition and Comments as well.
  *   We also discussed the Implementation Report, and none of us felt that there were any topics missing from the current version (thanks for all of the work that you put into the report!).
  *   Personally, I am still wondering whether I will suggest one or two additional minor changes.  You should assume that if I make any changes, then I will have made these changes before next Wednesday.  I don't want to get in the way of wrapping up work on the report.

There, I think that's a complete summary of our discussions today.  Let me know if you have any questions!

Wesley



*******************
Wesley Hochachka
Senior Research Associate
Cornell Lab of Ornithology
ph. (607) 254-2484
*******************

________________________________
From: ys628 <yanina.sica at yale.edu>
Sent: Monday, April 3, 2023 20:56
To: Humboldt Core TG <tdwg-humboldt at lists.tdwg.org>; Wesley M. Hochachka <wmh6 at cornell.edu>
Subject: Humboldt Task Group: Please review implementation report

Dear all,

We have made a lot of progress with the Implementation report.  Please have a look and edit here<https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj98hbk/edit#heading=h.u3r7un3jbl3s>.

I would like to thank Wesley, Ming, Zach and Steve for pushing this forward! I really appreciate it!

Here is a brief description of the document, the goal is to convince TDWG people that this extension is useful an that it would work!
- Authors will include the people writing the report and participating in the testing (we may even publish this as a paper in BISS)
- Introduction and background will be the basis of the Feature report as it already includes the rationale behind building this extension. This means that this Implementation report will include the information needed in the Feature report. For more info on TDWG required documents see here: http://rs.tdwg.org/vms/doc/specification/#421-feature-report<https://www.google.com/url?q=http://rs.tdwg.org/vms/doc/specification/%23421-feature-report&sa=D&source=docs&ust=1680098196850728&usg=AOvVaw3MkAtmG8IRHVETy2hJFn4L>
- Development of the vocabulary includes some description of what is considered an inventory, a basic description of the terms, and a link to the final table with the terms
- Use cases will include a description of the datasets and how the mapping was done
- Lessons learned will include all the challenges identified during the mapping and testing that were addressed using the Humboldt extension
- Unresolved issues/remaining challenges will include all the challenges identified during the mapping and testing that were NOT addressed using the Humboldt extension
- Conclusions will be some sort of summary stating that we are ready to go to public review

I will not be able to join our next meeting, but it would be great if you can meet and discuss how the document is looking otherwise please take the time to review the document. The sooner we finish this the faster we can start the public review.

We also need to review the documentation and the list of terms<https://docs.google.com/spreadsheets/d/1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d7VEDyqOg/edit#gid=697606170> that will accompany the implementation report. I would also ask you to discuss line 41 of that sheet.


Hope everybody is good and we got this!

All the best!



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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