January 2023 - tdwg-humboldt

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.

4 3

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/

4 3

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

3 3

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%…>

1 0

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%…>

1 0

Humboldt Task Group Meeting Wed 18 January 2023, 08:00 EST
by ys628 18 Jan '23

18 Jan '23

Hi all, Hope everybody is well, it was great catching up last week! This week we will discuss: * Field Museum testing feedback (see these slides<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> for reference). * definitions and comments for potential new terms: * isInventoryComplete (?) (if user reported every species observed) * summary of meeting regarding absences and GBIF data model * start planning the “implementation experience report” Hope you can make it, see you later! 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.

4 3

Humboldt Task Group Meeting Wed 10 January 2023, 08:00 EST
by ys628 11 Jan '23

11 Jan '23

Hi all! Hope you had a great start of the year and enjoyed the holidays! First, I would like to apologize for dropping the ball in our task group. I went to Argentina to visit my family (and win the world cup!) and I started a new and exciting position at IPBES Technical Support Unit for Knowledge and Data in Senckenberg, Germany! Second, I would love to catch up on our latest discussions and plan our next steps, could we meet at our regular time this week? I propose the following agenda, but since I missed the last meetings maybe there are new or different topics we should cover as well, so feel free to edit! * summarize what we learnt during the testing phase (see these slides<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> for reference). * Write definitions and comments for potential new terms: * isInventoryComplete (?) (if user reported every species observed) * speciesCount (?) (if user wants to report the total species observed) * start writing 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.

5 5