- tdwg-humboldt - lists.tdwg.org

Humboldt Task Group Meeting Wed 12 May 2021, 08:00 EST
by Yanina Sica 12 May '21

12 May '21

Hi all, As last week, tomorrow we will review Humbodlt terms related to temporal, spatial, and taxonomic scope and sampling methods. With those in mind we will then go back to the more complex terms (e.g. effort, completeness). For reference: - check the definitions of the original related terms in HC (see Vocabulary file <https://github.com/tdwg/hc/tree/main/vocabulary>) - revisit our discussion notes here <https://docs.google.com/document/d/10cvJl9nuVZIsfKJStA4DsqcNNfrtb8jfc-mUXck…> See you tomorrow! Yanina V. Sica, PhD Data Manager | Map of Life Yale University pronouns: she/her/hers

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Re: [tdwg-humboldt] tdwg-humboldt Digest, Vol 6, Issue 2
by Neil Cobb 11 May '21

11 May '21

John, Thanks, I either forgot about this pub/group or never knew about them. I will reach out to them, it would be great to have bee collaborators from Brazil as well as working on plant-pollinator interaction terms. Cheers, Neil Neil S. Cobb, Symbiota Collections of Arthropods Network (SCAN) <https://scan-bugs.org/portal/index.php> Biodiversity Outreach Network <https://www.bon-earth.org/> Northern Arizona University Flagstaff, AZ 86011 Neil.Cobb(a)nau.edu neilscobb(a)gmail.com (Mobile Office) 928-607-4075 Skype Name: neil_cobb Calendar: https://doodle.com/neilcobb Virtual Meeting: Contact for Zoom URL ORCID https://orcid.org/0000-0002-6155-9444 On Fri, May 7, 2021 at 5:00 AM <tdwg-humboldt-request(a)lists.tdwg.org> wrote: > Send tdwg-humboldt mailing list submissions to > tdwg-humboldt(a)lists.tdwg.org > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.tdwg.org/mailman/listinfo/tdwg-humboldt > or, via email, send a message with subject or body 'help' to > tdwg-humboldt-request(a)lists.tdwg.org > > You can reach the person managing the list at > tdwg-humboldt-owner(a)lists.tdwg.org > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of tdwg-humboldt digest..." > > > Today's Topics: > > 1. Re: Humboldt Core use cases (John Wieczorek) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 7 May 2021 00:37:13 -0300 > From: John Wieczorek <tuco(a)berkeley.edu> > To: Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> > Subject: Re: [tdwg-humboldt] Humboldt Core use cases > Message-ID: > < > CAHwKGGdoXZq7FvOnwFoq2HHYU289+mJ9VHwqOfjGf1zkii0mHQ(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi Neil, > > I think demonstrating a case for inventories with interactions would be > particularly compelling. Working with the Plant-Pollinator Interactions > Group in Brazil (https://github.com/BioComp-USP/rebipp-data-standard) has > shown that there are many core (pun partially intended) issues in common in > terms (another pun?) of shared hierarchical Event structuring. > > Cheers, > > John > > On Wed, Apr 28, 2021 at 4:09 AM Neil Stanley Cobb <Neil.Cobb(a)nau.edu> > wrote: > > > Hi, > > > > > > > > I have popped into a couple of working group meetings in the past three > > weeks. I am not sure I can attend meetings on a regular basis. My > primary > > interest is two-fold; 1) want to extend SCAN > > <https://scan-bugs.org/portal/index.php>?s ability to incorporate fields > > from arthropod projects that incorporate inventory/monitoring that DwC > does > > not provide. The biggest use case involves bee/pollinator data sets. We > are > > starting to incorporate files from ecological studies on > bees/pollinators. > > All of the cases so far would benefit from adopting a HC set of fields, > > however the form (e.g., DwC extensions). I am also interested in > monitoring > > projects and pitfall data (see below); and 2) I do want to provide > feedback > > to make HC as robust and effective as possible. > > > > > > > > *Bee/Pollinator Projects* > > > https://scan-bugs.org/portal/collections/misc/collprofiles.php?collid=275 > Drought > > and Habitat Fragmentation on Native Bee Assemblages > > > https://scan-bugs.org/portal/collections/misc/collprofiles.php?collid=270 > Plant?pollinator > > community assembly across wildfire gradients > > > https://scan-bugs.org/portal/collections/misc/collprofiles.php?collid=272 > > Predicting changes in bee assemblages following state transitions > > > https://scan-bugs.org/portal/collections/misc/collprofiles.php?collid=278 > > Maine State Museum - Brianne Du Clos Pollinator Study *Mosquito > > Monitoring (i.e., repeated measures)* > > > https://scan-bugs.org/portal/collections/misc/collprofiles.php?collid=181 > > VectorBase (Bioinformatics Resource for Invertebrate Vectors of Human > > Pathogens) Ground-Dwelling Arthropods (pitfalls) > > > > Scores of data in SCAN were generated from pitfall studies. Currently, > > there is no way to compare across datasets (i.e. define ?effort? so > numbers > > are expressed in common currency). Sand Brantley is the only publication > I > > know where effort was defined in order to compare spider assemblages from > > two separate elevation gradients (attached). We might be able to > > retroactively populate ?effort? metrics for over a million records and a > > standard to guide the process would be very helpful. > > > > > > > > > > > > Cheers, > > > > Neil > > > > > > > > > > > > > > > > Neil S. Cobb, > > > > Symbiota Collections of Arthropods Network (SCAN) > > <https://scan-bugs.org/portal/index.php> > > > > Biodiversity Outreach Network <https://www.bon-earth.org/> > > > > > > > > Northern Arizona University Flagstaff, AZ 86011 > > > > Neil.Cobb(a)nau.edu neilscobb(a)gmail.com > > > > > > (Mobile Office) 928-607-4075 > > > > Virtual Office: https://us02web.zoom.us/j/82515787249 > > > > ORCID https://orcid.org/0000-0002-6155-9444 > > > > > > > > Do you know where all 200,000 North American arthropod species live? > > > > > > > > > > _______________________________________________ > > tdwg-humboldt mailing list > > tdwg-humboldt(a)lists.tdwg.org > > http://lists.tdwg.org/mailman/listinfo/tdwg-humboldt > > >

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Humboldt Core use cases
by Neil Stanley Cobb 06 May '21

06 May '21

Hi, I have popped into a couple of working group meetings in the past three weeks. I am not sure I can attend meetings on a regular basis. My primary interest is two-fold; 1) want to extend SCAN<https://scan-bugs.org/portal/index.php>'s ability to incorporate fields from arthropod projects that incorporate inventory/monitoring that DwC does not provide. The biggest use case involves bee/pollinator data sets. We are starting to incorporate files from ecological studies on bees/pollinators. All of the cases so far would benefit from adopting a HC set of fields, however the form (e.g., DwC extensions). I am also interested in monitoring projects and pitfall data (see below); and 2) I do want to provide feedback to make HC as robust and effective as possible. Bee/Pollinator Projects https://scan-bugs.org/portal/collections/misc/collprofiles.php?collid=275 Drought and Habitat Fragmentation on Native Bee Assemblages https://scan-bugs.org/portal/collections/misc/collprofiles.php?collid=270 Plant-pollinator community assembly across wildfire gradients https://scan-bugs.org/portal/collections/misc/collprofiles.php?collid=272 Predicting changes in bee assemblages following state transitions https://scan-bugs.org/portal/collections/misc/collprofiles.php?collid=278 Maine State Museum - Brianne Du Clos Pollinator Study Mosquito Monitoring (i.e., repeated measures) https://scan-bugs.org/portal/collections/misc/collprofiles.php?collid=181 VectorBase (Bioinformatics Resource for Invertebrate Vectors of Human Pathogens) Ground-Dwelling Arthropods (pitfalls) Scores of data in SCAN were generated from pitfall studies. Currently, there is no way to compare across datasets (i.e. define "effort" so numbers are expressed in common currency). Sand Brantley is the only publication I know where effort was defined in order to compare spider assemblages from two separate elevation gradients (attached). We might be able to retroactively populate "effort" metrics for over a million records and a standard to guide the process would be very helpful. Cheers, Neil Neil S. Cobb, Symbiota Collections of Arthropods Network (SCAN)<https://scan-bugs.org/portal/index.php> Biodiversity Outreach Network<https://www.bon-earth.org/> Northern Arizona University Flagstaff, AZ 86011 Neil.Cobb(a)nau.edu<mailto:Neil.Cobb@nau.edu> neilscobb(a)gmail.com (Mobile Office) 928-607-4075 Virtual Office: https://us02web.zoom.us/j/82515787249 ORCID https://orcid.org/0000-0002-6155-9444 Do you know where all 200,000 North American arthropod species live?

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Humboldt Task Group Meeting Wed 5 May 2021, 08:00 EST
by Yanina Sica 04 May '21

04 May '21

Hi all, As per our discussion last week we will do a review of Humbodlt terms related to temporal, spatial, and taxonomic scope and sampling methods. With those in mind we will then go back to the more complex terms (e.g. effort, completeness). For reference: - check the definitions of the original related terms in HC (see Vocabulary file <https://github.com/tdwg/hc/tree/main/vocabulary>) - revisit our discussion notes here <https://docs.google.com/document/d/10cvJl9nuVZIsfKJStA4DsqcNNfrtb8jfc-mUXck…> See you tomorrow! Yanina V. Sica, PhD Data Manager | Map of Life Yale University pronouns: she/her/hers

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Humboldt Task Group Meeting Wed 28 April 2021, 08:00 EST
by Yanina Sica 27 Apr '21

27 Apr '21

Hi all, Thanks for a great meeting last week! We are very close to settling on 3 terms related to effort. In the spirit of keeping the conversation rolling, we are moving to terms related with completeness. For tomorrow: - Suggest *term name* and *definition* (with examples) for reporting *effort unit* - *Continue discussions on terms and definitions in the *Vocabulary file <https://github.com/tdwg/hc/tree/main/vocabulary> - LIST OF TERMS TO BE DISCUSSED NEXT WED: - *original_HC_label* - was taxonomic completeness reported? - if reported incomplete, was how incompleteness assessed? - how was completeness inferred? - inferred or reported taxonomic completeness , lower bound - inferred or reported taxonomic completeness, upper bound - number of separate sites (if time allows) - site nesting (if time allows) - site names (if time allows) - site details (if time allows) - For reference: - check the definitions of the original related terms in HC (see Vocabulary file <https://github.com/tdwg/hc/tree/main/vocabulary>) - revisit our discussion notes here <https://docs.google.com/document/d/10cvJl9nuVZIsfKJStA4DsqcNNfrtb8jfc-mUXck…> See you tomorrow! Cheers, Yani

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Humboldt Task Group Meeting Wed 21 April 2021, 08:00 EST
by Yanina Sica 19 Apr '21

19 Apr '21

Hi all, As discussed this week, we submitted a symposium for TDWG 2021! Thanks to everybody that collaborated! You can see the abstract here <https://docs.google.com/document/d/1ckx3qQz1LtNRazYV2sI-jCTI84yh8t_A2DWKBoP…> For next week: - *Humbodlt extension Documentation <https://docs.google.com/document/d/1ZglRfoQUGpsDm4t2M4B6Qif2IlbPvuBaRBeOi9x…>* - Thanks for sharing your availability. Unfortunately, I did not realize that today was potentially a good day to meet. - Can we try next week?* Erland is there any chance you can make it work Tuesday 20 or Thursday 22 at 10 am? * - For those of you still interested in working on HC Documentation, please complete your availability here <https://www.when2meet.com/?11625326-XZfAc> to schedule our first subgroup meeting and decide how we will organize this task - *Continue discussions on terms and definitions in the *Vocabulary file <https://github.com/tdwg/hc/tree/main/vocabulary> - LIST OF TERMS TO BE DISCUSSED NEXT WED: - *original_HC_label* - effort amount upper bound - effort upper bound unit - effort amount lower bound - effort lower bound unit - number of separate sites - site nesting - site names - site details - For reference: - check the definitions of the original related terms in HC (see Vocabulary file <https://github.com/tdwg/hc/tree/main/vocabulary>) - revisit our discussion notes here <https://docs.google.com/document/d/10cvJl9nuVZIsfKJStA4DsqcNNfrtb8jfc-mUXck…> Have a nice weekend and see you next Wed! Cheers, Yanina V. Sica, PhD Data Manager | Map of Life Yale University pronouns: she/her/hers <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> Virus-free. www.avast.com <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campai…> <#DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2>

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Humboldt Task Group Meeting Wed 14 April 2021, 08:00 EST
by Yanina Sica 13 Apr '21

13 Apr '21

Hi team! Great meeting last week, thank you all for the interesting discussions! We settled on *3 action items* for this week: - *Start a subgroup on Humbodlt extension Documentation <https://docs.google.com/document/d/1ZglRfoQUGpsDm4t2M4B6Qif2IlbPvuBaRBeOi9x…>* - For those of you interested in working on HC Documentation, please complete your availability here <https://www.when2meet.com/?11625326-XZfAc> to schedule our first subgroup meeting and decide how we will organize this task - *Propose a symposium at the next TDWG 2021 Virtual Annual Conference <https://www.tdwg.org/conferences/2021/> on inventory data sharing* - Paula worked on a first draft of the abstract here <https://docs.google.com/document/d/1ckx3qQz1LtNRazYV2sI-jCTI84yh8t_A2DWKBoP…> - Please review and comment - For those of you interested in giving talks in the symposium, could you provide a tentative title of the talk so that we can see which topics are missing? - Can you propose other people we can invite to give talks? - *Continue discussions on terms and definitions in the *Vocabulary file <https://github.com/tdwg/hc/tree/main/vocabulary> - LIST OF TERMS TO BE DISCUSSED NEXT WED: - *original_HC_label* - effort amount upper bound - effort upper bound unit - effort amount lower bound - effort lower bound unit - number of separate sites - site nesting - site names - site details - For reference: - check the definitions of the original related terms in HC (see Vocabulary file <https://github.com/tdwg/hc/tree/main/vocabulary>) - revisit our discussion notes here <https://docs.google.com/document/d/10cvJl9nuVZIsfKJStA4DsqcNNfrtb8jfc-mUXck…> See you on Wed! Cheers, Yanina V. Sica, PhD Data Manager | Map of Life Yale University pronouns: she/her/hers

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Humboldt Task Group Meeting Wed 7 April 2021, 08:00 EST
by Yanina Sica 06 Apr '21

06 Apr '21

Hi all, Just a reminder that we are meeting this Wed (April 7) 8 am EST to continue the process of reviewing each and every of the *original HC terms and definitions *here: https://yale.zoom.us/j/96750659891 <https://www.google.com/url?q=https://yale.zoom.us/j/96750659891&sa=D&source…> We made quite a lot of progress last meeting, so tomorrow we aim to finish discussion of terms related to *protocol and effort *(see list below). As John pointed out in an earlier email, please consider watching the repository for discussions regarding these and all terms ( https://github.com/tdwg/hc). For reference: - check the definitions of the original related terms in HC (see Vocabulary file <https://github.com/tdwg/hc/tree/main/vocabulary>) - revisit the definition of dwc:samplingProtocol <https://dwc.tdwg.org/terms/#dwc:samplingProtocol> - revisit our discussion notes here Thank you and see you on Wed! LIST OF TERMS TO BE DISCUSSED NEXT WED: original_HC_label protocol name protocol detail protocol citation protocol reference effort amount upper bound effort upper bound unit effort amount lower bound effort lower bound unit If time allows we can start discussing site description terms: original_HC_label number of separate sites site nesting site names site details Yanina V. Sica, PhD Data Manager | Map of Life Yale University pronouns: she/her/hers

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HC terms first round review ready
by Paula Zermoglio 04 Apr '21

04 Apr '21

Dear all, Hope you are well and happy. I have finally uploaded a vocabulary csv file <https://github.com/tdwg/hc/tree/main/vocabulary> to the HC repo, containing the results of the first review round on the HC terms. Yani, Kate and I have worked hard to go through all of the terms reviewing their definitions, comments and examples. As you’ll see in the file, for some terms we were able to reach consensus, for some others we decided to just leave it open for group review. However, we need all of you to review ALL the terms and check if the decisions we are proposing make sense. To help in understanding the vocabulary file and how we would proceed with this, I’ve built a wiki page in the repo: How to review the HC Vocabulary <https://github.com/tdwg/hc/wiki/How-to-review-the-HC-Vocabulary>. Please take a look at that page before starting your review (and of course please let me know if something seems unreasonable there). You will note that there are issues already posted in the repo, most of those are about particular terms or sets of terms, and are linked in the vocabulary file (see Wiki for details). PLEASE consider watching the repo <https://github.com/tdwg/hc>, this will help us get everyone on board and on track to speed up the review process. Enjoy! paula

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Humboldt Task Group Meeting Wed 31 March 2021, 0800 EST: homework!
by Yanina Sica 30 Mar '21

30 Mar '21

Hi all, As per our discussion at the last meeting, we have homework for next Wednesday! Propose a definition (include comments and examples if appropriate) for the following HC terms: - protocolName - The idea of this term would be to capture a -more or less- specific protocol, but without including specific details in textual form. As discussed in our last meeting this term could involve the concatenation of General Target Category + Method Approach + General Method Type + Specific Method Name from Survey Methods Definition <https://docs.google.com/spreadsheets/d/1ojS1gRk5MJZ5OWYuaXaGt0oFn3J-JPvpHT-…> (better known as “Peter’s spreadsheet” :) ). Consider if such a term would need an associated controlled vocabulary, and if so, whether we would attempt to provide one, point to existing one(s), or leave open for future work. - protocolDescription/protocolDetail - As discussed in our last meeting, this term would allow users to capture detailed information about the protocol, including any deviation from the published methodologies and unpublished protocols. - protocolReference - From our conversation in our last meeting, it was not clear if this should be retained separately or included in protocolDescription/protocolDetail. If you feel it should be a separate term, please provide definition, comments, examples. This term would refer to formatted references and URL or direct DOI links to the protocols used. For reference: - check the definitions of the original related terms in HC (see Vocabulary file <https://github.com/tdwg/hc/tree/main/vocabulary>: protocol name, protocol detail, protocol citation, protocol reference) - revisit the definition of dwc:samplingProtocol <https://dwc.tdwg.org/terms/#dwc:samplingProtocol> *Please send your proposed definitions to me or Paula by Tuesday* so we include them in a small presentation to improve our discussions. Thank you and see you on Wed! LIST OF TERMS TO BE DISCUSSED NEXT WED: original_HC_label protocol name protocol detail protocol citation protocol reference effort amount upper bound effort upper bound unit effort amount lower bound effort lower bound unit If time allows we can start discussing site description terms: number of separate sites site nesting site names site details Yanina V. Sica, PhD Data Manager | Map of Life Yale University pronouns: she/her/hers

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