Summary of meeting and next steps
Hi all,
We had a great discussion today, thanks for being so flexible and staying longer!
We arrived at the conclusion that we will include 'bycatch' terms. One of the main issues with these terms was that the scopes were unclear (species out of taxonomic scope vs species out of lifeStage, growthForm scopes, etc). It became apparent that we needed to differentiate those cases so we propose 4 terms, 3 terms related to Taxa out of scope and 1 term related to Organisms out of organismal scopes. See here https://docs.google.com/document/d/184BjPL-Kd9lv_x39sVGNxFKFlb4hY_Xsli5_dmnBMqs/edit the 4 terms and their definitions.* Please review the 'bycatch' terms and share your thoughts before Friday 18. *Unless any of you has a strong feeling against it, John will include these terms as part of the main vocabulary.
We ran out of time, and were not able to discuss the Hierarchical document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit#heading=h.a0hj80sigtm6. Ming, John, Ani and Kate will meet on Friday or Monday to finish it.* Please let me know if you would like to join our discussion.*
We reviewed the List of Authors https://github.com/tdwg/hc/blob/main/build/authors_configuration.yaml and there was no major opposition. Basically our criteria of inclusion was to include every Task Group member that joined a considerable number of meetings and discussions plus the 3 authors of the original publication. *Please let me know If you have any thoughts regarding the inclusion and order of authors or if we forgot somebody!*
We also assigned people (mostly Kate) responsible for:
- Reviewing isLeastSpecificTargetCategoryQuantityInclusive https://github.com/tdwg/hc/blob/main/docs/inclusive/index.md - Yani and John will review - Reviewing Implementation report https://docs.google.com/document/d/1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj98hbk/edit#heading=h.l89l0grun7cp, making sure latest advances are captured in the text (e.g. Bycatch or non-target species recorded section) - Kate will clean up the doc - Reviewing Landing Page https://github.com/tdwg/hc/blob/main/docs/index.md - Kate will write an abstract for this and the rest of the documents (e.g. https://tdwg.github.io/hc/list/) - Reviewing User Guide https://docs.google.com/document/d/1rX4m94rtZDR_8iIe3RvRnNYKDJcmSX3ii4S5hCznEA0/edit#heading=h.rr2lqlf80rn0 - Kate and Ani will revise and accept main changes
*We aim to have everything revised for Wednesday 23. So, now is the time to wear your editor's hat!!*
Really looking forward to our next meeting and submitting the extension!!
All the best
Yani
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Hi all,
I have finish converting the list of terms header document from static Markdown to a template (https://github.com/tdwg/hc/blob/main/build/termlist-header.md). So now all of the document metadata gets inserted from the same source as is used to generate the machine-readable metadata about the document.
The practical implication of this is that the List of Terms document (https://tdwg.github.io/hc/list/) now displays contributor names and affiliations. The name is hyperlinked to the ORCID record and the affiliation is linked to the Wikidata page for the institution (or the closest thing I could come up with that was in Wikidata).
So please check this out by clicking on your links.
Once the abstract is finished, I will add it to the general document metadata (https://github.com/tdwg/rs.tdwg.org/blob/eco/process/document_metadata_proce...) so that it will be picked up as machine readable in addition to being inserted in this doc.
There is still one thing missing from the List of Terms, and that is section 2, “Use of Terms”. Somebody needs to write something for that. For comparison, see some examples like the Chrono extension https://tdwg.github.io/chrono/list/ , the establishmentMeans vocab https://dwc.tdwg.org/em/, and the “categories of terms” section 1.2 for Audiovisual Core https://ac.tdwg.org/termlist/. Basically, we need to imagine that this page is the only thing that people could see about the terms. What would they need to know? It would be appropriate to tell them about the two other standards docs we are creating that explain how to use the terms.
Steve
-- Steven J. Baskauf, Ph.D. he/him/his Data Science and Data Curation Specialist / Librarian III Jean & Alexander Heard Libraries, Vanderbilt University Nashville, TN 37235, USA
Biodiversity Information Standards (TDWG) Executive Committee/Technical Architecture Group Chair https://baskauf.github.io/
Thank you, Steve, this is awesome!
I took a stab at the Abstract and the Use of Terms, please see below and edit freely:
Abstract "The Humboldt Extension for Ecological Inventories provides a standardized vocabulary to report key information about biodiversity inventories maximizing the usability and interoperability of these data. This vocabulary is employed along with the Darwin Core (DwC) terms, effectively broadening the scope of dwc:Event records by incorporating terms absent from the main DwC vocabulary. Terms included in the extension are defined such that they can accommodate hierarchical data structures allowing the representation of complex, highly nested survey designs. This document lists all terms currently used in the vocabulary providing comments and examples of their usage along with ancillary documents that provide guidance on the use and interpretation of terms and the data structure needed to accommodate dwc:Event hierarchies frequently observed in ecological inventories."
*Do we need to define ecological/biodiversity inventories here?*
Use of terms "The terms in this extension are meant to provide stable definitions that can be used in a variety of biodiversity inventory contexts but were envisioned principally to function together as an extension to Darwin Core. This vocabulary allows the reporting of detailed information about the inventory process such as i) a general description of the survey, ii) where an inventory takes place and the habitat characteristics and environmental conditions of survey sites, ii) when an inventory takes place, iii) the target taxonomic group, life stages, growth forms, and degrees of establishment of the organisms sampled, iv) the methodology implemented (inventory type performed, protocol(s) used, absence reported, material samples or vouchers collected, non-target taxa reported), and v) the completeness of the inventory and the sampling effort applied. This extension allows the representation of complex, highly nested survey designs, an ancillary document explaining how dwc:Event hierarchies for ecological inventories should be structured and providing guidance on the use of the terms in the context of parent and child dwc:Event(s) can be found [add link]. To assist in the interpretation of the term eco:isLeastSpecificTargetCategoryQuantityInclusive a detailed description of its use is provided [add link]"
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On Thu, Aug 24, 2023 at 3:44 PM Baskauf, Steven James < steve.baskauf@vanderbilt.edu> wrote:
Hi all,
I have finish converting the list of terms header document from static Markdown to a template ( https://github.com/tdwg/hc/blob/main/build/termlist-header.md). So now all of the document metadata gets inserted from the same source as is used to generate the machine-readable metadata about the document.
The practical implication of this is that the List of Terms document ( https://tdwg.github.io/hc/list/) now displays contributor names and affiliations. The name is hyperlinked to the ORCID record and the affiliation is linked to the Wikidata page for the institution (or the closest thing I could come up with that was in Wikidata).
So please check this out by clicking on your links.
Once the abstract is finished, I will add it to the general document metadata ( https://github.com/tdwg/rs.tdwg.org/blob/eco/process/document_metadata_proce...) so that it will be picked up as machine readable in addition to being inserted in this doc.
There is still one thing missing from the List of Terms, and that is section 2, “Use of Terms”. Somebody needs to write something for that. For comparison, see some examples like the Chrono extension https://tdwg.github.io/chrono/list/ , the establishmentMeans vocab https://dwc.tdwg.org/em/, and the “categories of terms” section 1.2 for Audiovisual Core https://ac.tdwg.org/termlist/. Basically, we need to imagine that this page is the only thing that people could see about the terms. What would they need to know? It would be appropriate to tell them about the two other standards docs we are creating that explain how to use the terms.
Steve
--
Steven J. Baskauf, Ph.D. he/him/his
Data Science and Data Curation Specialist / Librarian III
Jean & Alexander Heard Libraries, Vanderbilt University
Nashville, TN 37235, USA
Biodiversity Information Standards (TDWG) Executive Committee/Technical Architecture Group Chair
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
Fantastic progress! Thanks to everyone for moving the effort through the final steps.
Two suggestions for the abstract
"The Humboldt Extension for Ecological Inventories provides a standardized vocabulary to report key information about biodiversity inventories, checklists and surverys, maximizing the usability and interoperability of these data.
.....
Terms included in the extension are defined such that they can accommodate hierarchical data structures allowing the representation of complex, highly nested survey designs, permitting the computation of relative abundances of species.
Thanks, Rob
On Fri, Aug 25, 2023 at 5:10 AM Yanina Sica yanina.sica@gmail.com wrote:
Thank you, Steve, this is awesome!
I took a stab at the Abstract and the Use of Terms, please see below and edit freely:
Abstract "The Humboldt Extension for Ecological Inventories provides a standardized vocabulary to report key information about biodiversity inventories maximizing the usability and interoperability of these data. This vocabulary is employed along with the Darwin Core (DwC) terms, effectively broadening the scope of dwc:Event records by incorporating terms absent from the main DwC vocabulary. Terms included in the extension are defined such that they can accommodate hierarchical data structures allowing the representation of complex, highly nested survey designs. This document lists all terms currently used in the vocabulary providing comments and examples of their usage along with ancillary documents that provide guidance on the use and interpretation of terms and the data structure needed to accommodate dwc:Event hierarchies frequently observed in ecological inventories."
*Do we need to define ecological/biodiversity inventories here?*
Use of terms "The terms in this extension are meant to provide stable definitions that can be used in a variety of biodiversity inventory contexts but were envisioned principally to function together as an extension to Darwin Core. This vocabulary allows the reporting of detailed information about the inventory process such as i) a general description of the survey, ii) where an inventory takes place and the habitat characteristics and environmental conditions of survey sites, ii) when an inventory takes place, iii) the target taxonomic group, life stages, growth forms, and degrees of establishment of the organisms sampled, iv) the methodology implemented (inventory type performed, protocol(s) used, absence reported, material samples or vouchers collected, non-target taxa reported), and v) the completeness of the inventory and the sampling effort applied. This extension allows the representation of complex, highly nested survey designs, an ancillary document explaining how dwc:Event hierarchies for ecological inventories should be structured and providing guidance on the use of the terms in the context of parent and child dwc:Event(s) can be found [add link]. To assist in the interpretation of the term eco:isLeastSpecificTargetCategoryQuantityInclusive a detailed description of its use is provided [add link]"
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On Thu, Aug 24, 2023 at 3:44 PM Baskauf, Steven James < steve.baskauf@vanderbilt.edu> wrote:
Hi all,
I have finish converting the list of terms header document from static Markdown to a template ( https://github.com/tdwg/hc/blob/main/build/termlist-header.md). So now all of the document metadata gets inserted from the same source as is used to generate the machine-readable metadata about the document.
The practical implication of this is that the List of Terms document ( https://tdwg.github.io/hc/list/) now displays contributor names and affiliations. The name is hyperlinked to the ORCID record and the affiliation is linked to the Wikidata page for the institution (or the closest thing I could come up with that was in Wikidata).
So please check this out by clicking on your links.
Once the abstract is finished, I will add it to the general document metadata ( https://github.com/tdwg/rs.tdwg.org/blob/eco/process/document_metadata_proce...) so that it will be picked up as machine readable in addition to being inserted in this doc.
There is still one thing missing from the List of Terms, and that is section 2, “Use of Terms”. Somebody needs to write something for that. For comparison, see some examples like the Chrono extension https://tdwg.github.io/chrono/list/ , the establishmentMeans vocab https://dwc.tdwg.org/em/, and the “categories of terms” section 1.2 for Audiovisual Core https://ac.tdwg.org/termlist/. Basically, we need to imagine that this page is the only thing that people could see about the terms. What would they need to know? It would be appropriate to tell them about the two other standards docs we are creating that explain how to use the terms.
Steve
--
Steven J. Baskauf, Ph.D. he/him/his
Data Science and Data Curation Specialist / Librarian III
Jean & Alexander Heard Libraries, Vanderbilt University
Nashville, TN 37235, USA
Biodiversity Information Standards (TDWG) Executive Committee/Technical Architecture Group Chair
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
participants (3)
-
Baskauf, Steven James -
Rob Stevenson -
Yanina Sica