- tdwg-humboldt - lists.tdwg.org

Re: [tdwg-humboldt] Humboldt Extension namespace abbreviation
by Baskauf, Steven James 15 Feb '23

15 Feb '23

Hi all, LOV is back up again: https://lov.linkeddata.es/ I checked the vocabs https://lov.linkeddata.es/dataset/lov/vocabs for “eco”, “env”, and “ecoenv” and did not see any usage. However, I also checked dwc and ac and they don’t come up either (not sure why, I think I submitted them long ago). So that doesn’t mean for sure that they aren’t being used. 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/ From: "Wesley M. Hochachka" <wmh6(a)cornell.edu> Date: Wednesday, February 15, 2023 at 9:27 AM To: Steve Baskauf <steve.baskauf(a)vanderbilt.edu>, Yanina Sica <yanina.sica(a)gmail.com>, "tuco(a)berkeley.edu" <tuco(a)berkeley.edu>, Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> Subject: Re: [tdwg-humboldt] Humboldt Extension namespace abbreviation HI all, I'm slightly more inclined toward "ecoinv", because "eco" by itself feels to me like it is too generic. Darwin Core, for example, also contains ecological data, and "ecology" and "ecological" have all sorts of meanings even in English, and the meanings are even more diverse when one starts to look at other languages (e.g. "öko", the German-language equivalent to "eco" refers to organic food). Of source, "eco" is still a clearer descriptor of a type of information content than "Darwin", which in addition to being a surname is a surname associated with evolutionary more than ecological phenomena. Anyway, either "eco" or "ecoinv" feel appropriate to me, and thinking laterally from the name "Humboldt" was a great idea. Wesley ******************* Wesley Hochachka Senior Research Associate Cornell Lab of Ornithology ph. (607) 254-2484 ******************* ________________________________ From: Baskauf, Steven James <steve.baskauf(a)vanderbilt.edu> Sent: Wednesday, February 15, 2023 10:02 To: Yanina Sica <yanina.sica(a)gmail.com>; tuco(a)berkeley.edu <tuco(a)berkeley.edu>; Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> Cc: Wesley M. Hochachka <wmh6(a)cornell.edu> Subject: Re: [tdwg-humboldt] Humboldt Extension namespace abbreviation I think shorter is better, although ecoinv: isn’t that long. The Linked Open Vocabularies https://lov.linkeddata.es/dataset/lov<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flov.linke…> website, where I normally go to see what abbreviations people are using seems to be down. I don’t know if that is temporary or permanent. I’ll try check the various suggestions later. I agree with John that if eco: isn’t used, we should jump on it. It is simple and memorable. 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/ From: Yanina Sica <yanina.sica(a)gmail.com> Date: Wednesday, February 15, 2023 at 8:59 AM To: "tuco(a)berkeley.edu" <tuco(a)berkeley.edu>, Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> Cc: Steve Baskauf <steve.baskauf(a)vanderbilt.edu>, "wmh6(a)cornell.edu" <wmh6(a)cornell.edu> Subject: Re: [tdwg-humboldt] Humboldt Extension namespace abbreviation Great suggestion! I agree and am very supportive of the change in namespace removing Humboldt. Is a combination of your suggestions too much? ecoInv maybe? Yani On Wed, Feb 15, 2023 at 9:48 AM John Wieczorek <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>> wrote: I really like your idea. Solves all kinds of issues. I'll be surprised if "eco:" isn't already in common use, but if it isn't, we should jump on it. On Wed, Feb 15, 2023 at 11:44 AM Baskauf, Steven James <steve.baskauf(a)vanderbilt.edu<mailto:steve.baskauf@vanderbilt.edu>> wrote: Hi all, This is a follow-up to the brief discussion at the end of our meeting today. I had an idea in the shower (where I frequently have creative thoughts – must be something about being more relaxed) about what to use as a short abbreviation for Humboldt extension IRIs. As an official name for Humboldt, we call it the “Humboldt Extension for Ecological Inventories” or something like that. That already has the benefit of telling people what it’s about. Then for the abbreviation we either use “eco” or “inv” as the abbreviation instead of “humboldt” or “hmbldt”. That would make the IRIs either http://rs.tdwg.org/eco/term/foo<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Frs.tdwg.or…> or http://rs.tdwg.org/inv/term/foo<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Frs.tdwg.or…> which would be abbreviated as “eco:foo” or “inv:foo” respectively, following the established patterns we already are using in TDWG. This would have the added benefit of not confusing anybody if we suddenly discover that Humboldt was an evil space alien or something and decide we don’t want to name the extension after him anymore. Yes, I know that sounds weird, but Audubon Core is rebranding as Audiovisual Core and fortunately we can still use “ac:” without confusing anybody. This solution would also dodge that potential future problem. I haven’t checked to see if “eco” or “inv” are already being used by any well-known vocabularies, but I’ll do that if this idea gets any traction. Thoughts? -- 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/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbaskauf.g…> From: tdwg-humboldt <tdwg-humboldt-bounces(a)lists.tdwg.org<mailto:tdwg-humboldt-bounces@lists.tdwg.org>> on behalf of ys628 <yanina.sica(a)yale.edu<mailto:yanina.sica@yale.edu>> Reply-To: Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org<mailto:tdwg-humboldt@lists.tdwg.org>> Date: Tuesday, February 14, 2023 at 1:55 PM To: Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org<mailto:tdwg-humboldt@lists.tdwg.org>>, "wmh6(a)cornell.edu<mailto:wmh6@cornell.edu>" <wmh6(a)cornell.edu<mailto:wmh6@cornell.edu>> Subject: [tdwg-humboldt] Humboldt Task Group Meeting Wed 15 February 2023, 08:00 EST/13:00 UTC Hi valentines! I hope everybody is great. Let meet tomorrow and discuss the following items: * review taxonomic scope related terms (see slide 13 and 14 here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) * discuss the need for isReportedAbundanceAdditive (?) (slide 15 here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) --> john is still thinking about this * discuss the need for IdentificationConfidence (slide 15 here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) * start writing the implementation report!! See you soon! Zoom link: https://yale.zoom.us/j/97318391101<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.googl…> Yani Yanina V. Sica, PhD Lead Data Team Map of Life<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmol.org%2…> | Center for Biodiversity and Global Change<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbgc.yale.…> 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(a)lists.tdwg.org<mailto:tdwg-humboldt@lists.tdwg.org> https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.tdw…>

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Re: [tdwg-humboldt] Humboldt Extension namespace abbreviation
by Baskauf, Steven James 15 Feb '23

15 Feb '23

Forwarding Wesley’s message, which bounced from the HCTG email list. -- 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/ From: "Wesley M. Hochachka" <wmh6(a)cornell.edu> Date: Wednesday, February 15, 2023 at 9:27 AM To: Steve Baskauf <steve.baskauf(a)vanderbilt.edu>, Yanina Sica <yanina.sica(a)gmail.com>, "tuco(a)berkeley.edu" <tuco(a)berkeley.edu>, Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> Subject: Re: [tdwg-humboldt] Humboldt Extension namespace abbreviation HI all, I'm slightly more inclined toward "ecoinv", because "eco" by itself feels to me like it is too generic. Darwin Core, for example, also contains ecological data, and "ecology" and "ecological" have all sorts of meanings even in English, and the meanings are even more diverse when one starts to look at other languages (e.g. "öko", the German-language equivalent to "eco" refers to organic food). Of source, "eco" is still a clearer descriptor of a type of information content than "Darwin", which in addition to being a surname is a surname associated with evolutionary more than ecological phenomena. Anyway, either "eco" or "ecoinv" feel appropriate to me, and thinking laterally from the name "Humboldt" was a great idea. Wesley ******************* Wesley Hochachka Senior Research Associate Cornell Lab of Ornithology ph. (607) 254-2484 ******************* ________________________________ From: Baskauf, Steven James <steve.baskauf(a)vanderbilt.edu> Sent: Wednesday, February 15, 2023 10:02 To: Yanina Sica <yanina.sica(a)gmail.com>; tuco(a)berkeley.edu <tuco(a)berkeley.edu>; Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> Cc: Wesley M. Hochachka <wmh6(a)cornell.edu> Subject: Re: [tdwg-humboldt] Humboldt Extension namespace abbreviation I think shorter is better, although ecoinv: isn’t that long. The Linked Open Vocabularies https://lov.linkeddata.es/dataset/lov<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flov.linke…> website, where I normally go to see what abbreviations people are using seems to be down. I don’t know if that is temporary or permanent. I’ll try check the various suggestions later. I agree with John that if eco: isn’t used, we should jump on it. It is simple and memorable. 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/ From: Yanina Sica <yanina.sica(a)gmail.com> Date: Wednesday, February 15, 2023 at 8:59 AM To: "tuco(a)berkeley.edu" <tuco(a)berkeley.edu>, Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org> Cc: Steve Baskauf <steve.baskauf(a)vanderbilt.edu>, "wmh6(a)cornell.edu" <wmh6(a)cornell.edu> Subject: Re: [tdwg-humboldt] Humboldt Extension namespace abbreviation Great suggestion! I agree and am very supportive of the change in namespace removing Humboldt. Is a combination of your suggestions too much? ecoInv maybe? Yani On Wed, Feb 15, 2023 at 9:48 AM John Wieczorek <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>> wrote: I really like your idea. Solves all kinds of issues. I'll be surprised if "eco:" isn't already in common use, but if it isn't, we should jump on it. On Wed, Feb 15, 2023 at 11:44 AM Baskauf, Steven James <steve.baskauf(a)vanderbilt.edu<mailto:steve.baskauf@vanderbilt.edu>> wrote: Hi all, This is a follow-up to the brief discussion at the end of our meeting today. I had an idea in the shower (where I frequently have creative thoughts – must be something about being more relaxed) about what to use as a short abbreviation for Humboldt extension IRIs. As an official name for Humboldt, we call it the “Humboldt Extension for Ecological Inventories” or something like that. That already has the benefit of telling people what it’s about. Then for the abbreviation we either use “eco” or “inv” as the abbreviation instead of “humboldt” or “hmbldt”. That would make the IRIs either http://rs.tdwg.org/eco/term/foo<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Frs.tdwg.or…> or http://rs.tdwg.org/inv/term/foo<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2Frs.tdwg.or…> which would be abbreviated as “eco:foo” or “inv:foo” respectively, following the established patterns we already are using in TDWG. This would have the added benefit of not confusing anybody if we suddenly discover that Humboldt was an evil space alien or something and decide we don’t want to name the extension after him anymore. Yes, I know that sounds weird, but Audubon Core is rebranding as Audiovisual Core and fortunately we can still use “ac:” without confusing anybody. This solution would also dodge that potential future problem. I haven’t checked to see if “eco” or “inv” are already being used by any well-known vocabularies, but I’ll do that if this idea gets any traction. Thoughts? -- 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/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbaskauf.g…> From: tdwg-humboldt <tdwg-humboldt-bounces(a)lists.tdwg.org<mailto:tdwg-humboldt-bounces@lists.tdwg.org>> on behalf of ys628 <yanina.sica(a)yale.edu<mailto:yanina.sica@yale.edu>> Reply-To: Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org<mailto:tdwg-humboldt@lists.tdwg.org>> Date: Tuesday, February 14, 2023 at 1:55 PM To: Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org<mailto:tdwg-humboldt@lists.tdwg.org>>, "wmh6(a)cornell.edu<mailto:wmh6@cornell.edu>" <wmh6(a)cornell.edu<mailto:wmh6@cornell.edu>> Subject: [tdwg-humboldt] Humboldt Task Group Meeting Wed 15 February 2023, 08:00 EST/13:00 UTC Hi valentines! I hope everybody is great. Let meet tomorrow and discuss the following items: * review taxonomic scope related terms (see slide 13 and 14 here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) * discuss the need for isReportedAbundanceAdditive (?) (slide 15 here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) --> john is still thinking about this * discuss the need for IdentificationConfidence (slide 15 here<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) * start writing the implementation report!! See you soon! Zoom link: https://yale.zoom.us/j/97318391101<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.googl…> Yani Yanina V. Sica, PhD Lead Data Team Map of Life<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmol.org%2…> | Center for Biodiversity and Global Change<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbgc.yale.…> 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(a)lists.tdwg.org<mailto:tdwg-humboldt@lists.tdwg.org> https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.tdw…>

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Humboldt Task Group Meeting Wed 15 February 2023, 08:00 EST/13:00 UTC
by Yanina Sica 15 Feb '23

15 Feb '23

[sorry if you receive this message twice!] Hi valentines! I hope everybody is great. Let meet tomorrow and discuss the following items: - review *taxonomic scope related terms* (see slide 13 and 14 here <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> ) - *discuss the need for isReportedAbundanceAdditive (?) (slide 15 here <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) --> john is still thinking about this* - *discuss the need for IdentificationConfidence (slide 15 here <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) * - *start writing the implementation report!!* See you soon! Zoom link: https://yale.zoom.us/j/97318391101 <https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.googl…> Yani

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Humboldt Task Group Meeting Wed 15 February 2023, 08:00 EST/13:00 UTC
by ys628 14 Feb '23

14 Feb '23

Hi valentines! I hope everybody is great. Let meet tomorrow and discuss the following items: * review taxonomic scope related terms (see slide 13 and 14 here<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) * discuss the need for isReportedAbundanceAdditive (?) (slide 15 here<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) --> john is still thinking about this * discuss the need for IdentificationConfidence (slide 15 here<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>) * start writing the implementation report!! See you soon! Zoom link: https://yale.zoom.us/j/97318391101<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.googl…> 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.

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Humboldt Task Group Meeting Wed 8 February 2023, 08:00 EST/13:00 UTC
by ys628 07 Feb '23

07 Feb '23

Hi team, Hope you are all good! We have been having some great discussions lately and hopefully we will have another good one tomorrow. Peter Desmet has contacted us (thanks Steve for making the link!). He has been coordinating the development of the Camera Trap Data Package (Camtrap DP) and would like to discuss with us some terms that overlap with their use case. This relates a lot to the mapping exercise we did with the Wildlife Insights data (see slide 2 here <https://docs.google.com/presentation/d/18n83tttDvWDLI5UM30LIsfqrbpH5nbyrwIK…> to find the feedback we received). Peter will join us tomorrow to review some terms (see in agenda below) and hopefully discuss the transition from https://tdwg.github.io/hc/terms/<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftdwg.gith…> to the new TDWG design, see e.g. https://dwc.tdwg.org/<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdwc.tdwg.…> If it is ok with you, we can push the discussion regarding the addition of new terms (see slide 8 and 9 here<https://docs.google.com/presentation/d/18n83tttDvWDLI5UM30LIsfqrbpH5nbyrwIK…>) for the following week. Proposed agenda for this week's meeting: * Brief into to Camtrap DP (Peter Desmet) * Discuss Camtrap DP that may overlap with HE: * samplingPerformedBy ---> Would this apply to the person who setup the camera (but didn't take the actual photos)? * Geospatial Scope & Habitat ---> Geospatial scope is recorded in Camtrap DP, but as a geojson object. It does not specify the totalAreaSampledInSquareKilometer, siteCount, reportedWeather, etc. * verbatimSiteNames ---> location name is recorded, but there is no property listing all verbatimSiteNames . * habitat can be recorded, but there is no Camtrap DP property for the habitatScope. * eventDuration + eventDurationUnit ---> Temporal scope as well as deployment duration is recorded in Camtrap DP, but as a start-end date(time). * targetTaxonomicScope ---> Taxonomic scope in Camtrap DP records the observed species, not the target/excluded species, but see #41<https://github.com/tdwg/camtrap-dp/issues/41#issuecomment-1358149379> (comment) * targetLifestageScope, targetDegreeOfEstablishmentScope, targetGrowthFormScope are not recorded. * isAbundanceReported ---> Abundance is often reported, but not the fact whether or not that is the case (isAbundanceReported) * Methodology + Completeness & Effort ---> to be discussed * Transition from https://tdwg.github.io/hc/terms/<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftdwg.gith…> to the new TDWG design, see e.g. https://dwc.tdwg.org/<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdwc.tdwg.…> (Peter Desmet) * If time allows, review taxonomic scope related terms (see slide 8 and 9 here<https://docs.google.com/presentation/d/18n83tttDvWDLI5UM30LIsfqrbpH5nbyrwIK…>) See you soon! Zoom link: https://yale.zoom.us/j/97318391101<https://www.google.com/url?q=https://yale.zoom.us/j/97318391101&sa=D&source…> 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.

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Humboldt Task Group Meeting Wed 1 February 2023, 08:00 EST
by ys628 01 Feb '23

01 Feb '23

Hi all! Let's meet tomorrow and revise: * Definition and comments for isInventoryComplete (?) (see these slides<https://docs.google.com/presentation/d/18n83tttDvWDLI5UM30LIsfqrbpH5nbyrwIK…> for reference) * eventType term proposal<https://github.com/tdwg/dwc/issues/408> and how it relates to hc::inventoryTypes * start planning for the “implementation experience report” Zoom link: https://yale.zoom.us/j/97318391101<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fyale.zoom…> Hope you are all well, Saludos! 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.

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eventType
by Tim Robertson 30 Jan '23

30 Jan '23

Hi all, I hope you are all well. I’d like to draw your attention to the proposal to add eventType to Darwin Core [1]. As GBIF look to diversify our data model [2,3], we have identified the need for this term to be able to qualify what kind of events we’re arranging in the hierarchy. We know others have identified this need as well. Since GBIF are working with the ALA to bring Sampling Event search and download to GBIF and the ALA, we have added eventType for use in the TEST IPTs already [e.g. 4] in a GBIF(!) namespace, allowing this work to progress. eventType will likely capture a broad range of values to distinguish between things like visiting events, gathering events, material extraction events etc. It will take time to establish, but we imagine a hierarchical controlled vocabulary might be achievable, with an upper taxonomy that provides the anchoring points for communities to hang more specialist eventTypes from. This might be of use for those creating test datasets to showcase Humboldt as well. Thanks, Tim [1] https://github.com/tdwg/dwc/issues/408 [2] https://www.gbif.org/event/33MQ8ZI9xuC98AekewiMr8/gbif-community-webinar-di… [3] http://lists.tdwg.org/pipermail/tdwg-content/2021-December/003811.html [4] https://ipt.gbif.org/

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Use case representing absences and the Humboldt Extension
by Yi Ming Gan 27 Jan '23

27 Jan '23

Hi all (absence use case working group + Humboldt working group), John has developed the Broke west trawl dataset mini use case into a full use case representing absences and the Humboldt Extension and can be found ready for review at https://docs.google.com/document/d/1DgYrSlCCcvs4x59J8Koty6TTovRKtQhAYe8ItE0… Thank you so much John for working on this! YAYYYY!! Please feel free to review this! I will make time after tomorrow to have a closer look at this as well! Thank you all! Cheers Ming

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Re: [tdwg-humboldt] [EXTERNAL] Absence Use Case Meetings Summary (2022-01-11 meeting)
by Yi Ming Gan 18 Jan '23

18 Jan '23

Yes, thanks Abby!! Yani and John clarified that in our weekly meeting just now. I should have sent the mail after the meeting 😂 On 18 Jan 2023, at 15:56, Benson, Abigail L <albenson(a)usgs.gov> wrote: Thanks Ming for making these connections! A note that we have decided to hold off on adding Peter's use case for the time being because we wanted to work with John before things get too hectic for him with the collections effort that will take his focus soon. I'm hopeful that the trawl mini use case and the eBird mini use case provide a wide enough range in absences that the solution for these will accommodate other absence use cases. ________________________________ From: Yi Ming Gan <ymgan(a)naturalsciences.be<mailto:ymgan@naturalsciences.be>> Sent: Wednesday, January 18, 2023 5:59 AM To: tdwg-humboldt(a)lists.tdwg.org<mailto:tdwg-humboldt@lists.tdwg.org> <tdwg-humboldt(a)lists.tdwg.org<mailto:tdwg-humboldt@lists.tdwg.org>> Cc: Benson, Abigail L <albenson(a)usgs.gov<mailto:albenson@usgs.gov>> Subject: [EXTERNAL] Absence Use Case Meetings Summary (2022-01-11 meeting) This email has been received from outside of DOI - Use caution before clicking on links, opening attachments, or responding. Hi all, I just wanted to forward the updates to everyone (especially for Kate and Peter Brenton) to keep you all posted about the updates for the absence use case. Peter - Your datasets from ALA for the Humboldt use case for the new data model were mentioned in the meeting. Yani is looking into adding that for the absence use case? Related to this, I also wanted to bring up a previous email thread that I had with John Wieczorek to keep challenges to be solved in separate use cases. I was asking if it is possible to use the same dataset for combined use cases (community measurements + absence), this is his reply which makes lots of sense: " From our (GBIF's use case) perspective, keeping the challenges that are to be solved in separate use cases will make for easier review, not only by us, but by others interested in the proposed solutions. For that reason I would keep an absence use case distinct from a community measurements use case, though both of them can use the same underlying dataset as the example. It sounds like there will be many variations on the absence challenge, and it might end up that putting several of those together in a single use case might eventually be of benefit (how to deal with every kind of absence), but for now I would like to identify the distinct variations and solve each of them. Does that make sense to you all who have the more intimate knowledge? " Other than that, it was also acknowledged that taxonomic knowledge changes over time and it is a challenges for any taxonomic data. You can follow the discussions in the google doc here<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>. I hope this is sufficient to keeping everyone updated. Cheers Ming Begin forwarded message: From: John Wieczorek <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>> Subject: Re: Absence Use Case Meetings Summary Date: 12 January 2023 at 21:28:36 CET To: "Benson, Abigail L" <albenson(a)usgs.gov<mailto:albenson@usgs.gov>> Cc: Yi Ming Gan <ymgan(a)naturalsciences.be<mailto:ymgan@naturalsciences.be>>, Anton Van de Putte <avandeputte(a)naturalsciences.be<mailto:avandeputte@naturalsciences.be>>, Wesley Hochachka <wmh6(a)cornell.edu<mailto:wmh6@cornell.edu>>, "debora.arlt(a)slu.se<mailto:debora.arlt@slu.se>" <debora.arlt(a)slu.se<mailto:debora.arlt@slu.se>>, Tim Robertson <trobertson(a)gbif.org<mailto:trobertson@gbif.org>>, Yanina Sica <yanina.sica(a)yale.edu<mailto:yanina.sica@yale.edu>>, Rob Stevenson <rdstevenson10(a)gmail.com<mailto:rdstevenson10@gmail.com>>, Ruben Perez <ruben.perez(a)vliz.be<mailto:ruben.perez@vliz.be>>, "Provoost, Pieter" <p.provoost(a)unesco.org<mailto:p.provoost@unesco.org>> Reply-To: tuco(a)berkeley.edu<mailto:tuco@berkeley.edu> Thank you for the summary, Abby, and sorry to everyone for not making the meetings yesterday. But this will not work for something like eBird where a matrix would still be too unwieldy so we will still need a way to report taxon lists for events or datasets. The Humboldt extensiontargetTaxonomicScope<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftdwg.gith…> could be the answer for this. One concern I had from yesterday is providing these lists pipe delimited in that field but the new model should give us the ability to make terms expandable (John do I have that correct?). Yes, that is correct. By expandable we mean that there could be many different targetTaxonomicScope entries for an Event, each with one Taxon rather than only one targetTaxonomicScope entry for an Event with a list in a single |-delimited string, Cheers, John From: "Benson, Abigail L" <albenson(a)usgs.gov<mailto:albenson@usgs.gov>> Subject: Absence Use Case Meetings Summary Date: 12 January 2023 at 20:58:46 CET To: Yi Ming Gan <ymgan(a)naturalsciences.be<mailto:ymgan@naturalsciences.be>>, Anton Van de Putte <avandeputte(a)naturalsciences.be<mailto:avandeputte@naturalsciences.be>>, Wesley Hochachka <wmh6(a)cornell.edu<mailto:wmh6@cornell.edu>>, "debora.arlt(a)slu.se<mailto:debora.arlt@slu.se>" <debora.arlt(a)slu.se<mailto:debora.arlt@slu.se>>, Tim Robertson <trobertson(a)gbif.org<mailto:trobertson@gbif.org>>, John Wieczorek <tuco(a)berkeley.edu<mailto:tuco@berkeley.edu>>, Yanina Sica <yanina.sica(a)yale.edu<mailto:yanina.sica@yale.edu>>, Rob Stevenson <rdstevenson10(a)gmail.com<mailto:rdstevenson10@gmail.com>>, "'Ruben Perez'" <ruben.perez(a)vliz.be<mailto:ruben.perez@vliz.be>>, "Provoost, Pieter" <p.provoost(a)unesco.org<mailto:p.provoost@unesco.org>> Hi All, Thank you for the time yesterday and today to continue working through this topic. Yesterday we reviewed the mini use cases we have so far and agreed that a similarity is the need to infer absences to reduce data size and a major difference was the need to document life stage / sex absences. We determined that while changing taxonomy is an issue that needs to be considered, it's bigger than the absence use case can address. Also there is no need to determine a priori the taxon list. It was great to get an overview of the progress to date for the Humboldt extension- thanks Yani! I met with John today and have a few updates to share with you all from that meeting. 1. Occurrence as an event has been added to the unified model<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>. I don't think that affects what we are doing with this use case because we would prefer absences are inferred rather than making them explicit but it's good to know that we have the option of continuing to use occurrenceStatus if needed. 2. A species site matrix data format is being considered for inclusion in the new data model. This would probably simplify our ability to report the sampling event type of data that we are usually working with where taxa are provided as column headers. 3. But this will not work for something like eBird where a matrix would still be too unwieldy so we will still need a way to report taxon lists for events or datasets. The Humboldt extension targetTaxonomicScope<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftdwg.gith…> could be the answer for this. One concern I had from yesterday is providing these lists pipe delimited in that field but the new model should give us the ability to make terms expandable (John do I have that correct?). 4. One use case we should keep in mind for the true absence concept are folks that may want to report that something is not in a geographic area yet, e.g. an invasive species is not on a particular island yet. The plan going forward: 1. It would still be good to develop definitions for the concepts we have identified related to absences and share that out to the community for feedback. We should continue to work on this over the next month or two. 2. John will take the two mini-use cases we have (BROKE-west trawl and eBird) and work them up. Hopefully this will be ready for us to review before the end of the month I believe. But if not it may not be ready until sometime closer to May or June I'm guessing. Hopefully that gives some sense of where we are headed. I'll schedule a meeting for us soon to work on developing the definitions for the concepts. Thank you! Abby ------------ Abby Benson (she/her) Biologist U.S. Geological Survey Science Analytics and Synthesis Lakewood, CO 303.202.4087 ORCID: orcid.org/0000-0002-4391-107X<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Forcid.org%…>

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Absence Use Case Meetings Summary (2022-01-11 meeting)
by Yi Ming Gan 18 Jan '23

18 Jan '23

Hi all, I just wanted to forward the updates to everyone (especially for Kate and Peter Brenton) to keep you all posted about the updates for the absence use case. Peter - Your datasets from ALA for the Humboldt use case for the new data model were mentioned in the meeting. Yani is looking into adding that for the absence use case? Related to this, I also wanted to bring up a previous email thread that I had with John Wieczorek to keep challenges to be solved in separate use cases. I was asking if it is possible to use the same dataset for combined use cases (community measurements + absence), this is his reply which makes lots of sense: " >From our (GBIF's use case) perspective, keeping the challenges that are to be solved in separate use cases will make for easier review, not only by us, but by others interested in the proposed solutions. For that reason I would keep an absence use case distinct from a community measurements use case, though both of them can use the same underlying dataset as the example. It sounds like there will be many variations on the absence challenge, and it might end up that putting several of those together in a single use case might eventually be of benefit (how to deal with every kind of absence), but for now I would like to identify the distinct variations and solve each of them. Does that make sense to you all who have the more intimate knowledge? " Other than that, it was also acknowledged that taxonomic knowledge changes over time and it is a challenges for any taxonomic data. You can follow the discussions in the google doc here<https://docs.google.com/document/d/1xQGLHQW3hlMapT5utYi6kWXE7XbFjAGvoWI_V5I…>. I hope this is sufficient to keeping everyone updated. Cheers Ming Begin forwarded message: From: John Wieczorek <tuco(a)berkeley.edu> Subject: Re: Absence Use Case Meetings Summary Date: 12 January 2023 at 21:28:36 CET To: "Benson, Abigail L" <albenson(a)usgs.gov> Cc: Yi Ming Gan <ymgan(a)naturalsciences.be>, Anton Van de Putte <avandeputte(a)naturalsciences.be>, Wesley Hochachka <wmh6(a)cornell.edu>, "debora.arlt(a)slu.se" <debora.arlt(a)slu.se>, Tim Robertson <trobertson(a)gbif.org>, Yanina Sica <yanina.sica(a)yale.edu>, Rob Stevenson <rdstevenson10(a)gmail.com>, Ruben Perez <ruben.perez(a)vliz.be>, "Provoost, Pieter" <p.provoost(a)unesco.org> Reply-To: tuco(a)berkeley.edu Thank you for the summary, Abby, and sorry to everyone for not making the meetings yesterday. But this will not work for something like eBird where a matrix would still be too unwieldy so we will still need a way to report taxon lists for events or datasets. The Humboldt extensiontargetTaxonomicScope<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftdwg.gith…> could be the answer for this. One concern I had from yesterday is providing these lists pipe delimited in that field but the new model should give us the ability to make terms expandable (John do I have that correct?). Yes, that is correct. By expandable we mean that there could be many different targetTaxonomicScope entries for an Event, each with one Taxon rather than only one targetTaxonomicScope entry for an Event with a list in a single |-delimited string, Cheers, John From: "Benson, Abigail L" <albenson(a)usgs.gov> Subject: Absence Use Case Meetings Summary Date: 12 January 2023 at 20:58:46 CET To: Yi Ming Gan <ymgan(a)naturalsciences.be>, Anton Van de Putte <avandeputte(a)naturalsciences.be>, Wesley Hochachka <wmh6(a)cornell.edu>, "debora.arlt(a)slu.se" <debora.arlt(a)slu.se>, Tim Robertson <trobertson(a)gbif.org>, John Wieczorek <tuco(a)berkeley.edu>, Yanina Sica <yanina.sica(a)yale.edu>, Rob Stevenson <rdstevenson10(a)gmail.com>, "'Ruben Perez'" <ruben.perez(a)vliz.be>, "Provoost, Pieter" <p.provoost(a)unesco.org> Hi All, Thank you for the time yesterday and today to continue working through this topic. Yesterday we reviewed the mini use cases we have so far and agreed that a similarity is the need to infer absences to reduce data size and a major difference was the need to document life stage / sex absences. We determined that while changing taxonomy is an issue that needs to be considered, it's bigger than the absence use case can address. Also there is no need to determine a priori the taxon list. It was great to get an overview of the progress to date for the Humboldt extension- thanks Yani! I met with John today and have a few updates to share with you all from that meeting. 1. Occurrence as an event has been added to the unified model<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…>. I don't think that affects what we are doing with this use case because we would prefer absences are inferred rather than making them explicit but it's good to know that we have the option of continuing to use occurrenceStatus if needed. 2. A species site matrix data format is being considered for inclusion in the new data model. This would probably simplify our ability to report the sampling event type of data that we are usually working with where taxa are provided as column headers. 3. But this will not work for something like eBird where a matrix would still be too unwieldy so we will still need a way to report taxon lists for events or datasets. The Humboldt extension targetTaxonomicScope<https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Ftdwg.gith…> could be the answer for this. One concern I had from yesterday is providing these lists pipe delimited in that field but the new model should give us the ability to make terms expandable (John do I have that correct?). 4. One use case we should keep in mind for the true absence concept are folks that may want to report that something is not in a geographic area yet, e.g. an invasive species is not on a particular island yet. The plan going forward: 1. It would still be good to develop definitions for the concepts we have identified related to absences and share that out to the community for feedback. We should continue to work on this over the next month or two. 2. John will take the two mini-use cases we have (BROKE-west trawl and eBird) and work them up. Hopefully this will be ready for us to review before the end of the month I believe. But if not it may not be ready until sometime closer to May or June I'm guessing. Hopefully that gives some sense of where we are headed. I'll schedule a meeting for us soon to work on developing the definitions for the concepts. Thank you! Abby ------------ Abby Benson (she/her) Biologist U.S. Geological Survey Science Analytics and Synthesis Lakewood, CO 303.202.4087 ORCID: orcid.org/0000-0002-4391-107X<https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Forcid.org%…>

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