- tdwg-humboldt - lists.tdwg.org

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

Meeting today?
by Kate Ingenloff 28 Dec '22

28 Dec '22

Hi HC team, are we meeting today? Hope everyone is having a lovely holiday season. ------------------------------ Kate Ingenloff, PhD Pronouns: she/her(s) (+45) 51 44 13 23 "When one tugs at a single thread in nature, he finds it attached to the rest of the world." ~John Muir

1 0

Humboldt Task Group Meeting Wed 16 November 2022, 08:00 EST
by Sica, Yanina 29 Nov '22

29 Nov '22

Hi all! Hope everybody is well! I am very sorry, but I will not be able to lead the meeting tomorrow. I encourage you to meet and finish discussing what we learnt during the testing phase (see these slides<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> for reference). Specifically, we should discuss if we want to incorporate two terms: * isInventoryComplete (if user reported every species observed) * speciesCount (if user wants to report the total species observed) If so, we need proposed term names, descriptions and examples. We also need to start preparing for the next steps. Steve, is there a document that we should start completing for the public review? Very sorry for the short notice, but I will need to make a last-minute trip tomorrow morning. Zoom link: https://yale.zoom.us/j/97318391101 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 5

TDWG Working Sessions next week
by Sica, Yanina 04 Nov '22

04 Nov '22

Hi all, As you know, next week we will have an open session to discuss the Humboldt Extension status with everybody who is interested. The time is the same BUT we will not be using the usual link, you need to register here<https://www.tdwg.org/conferences/2022/working-sessions/> and you will receive an email with the link. Last Wednesday we agreed that we will mainly discuss how people describe the methods they used, the sampling effort involved in their surveys, and the concept of completeness. I started some slides <https://docs.google.com/presentation/d/1Ie1cHPNd58HYE3LUK-qT9sQZPlt8ggrMuAN…> based on the TDWG presentation, please add/edit them! See you next week, cheers! 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.

1 0

FW: Editor's choice: A protocol for reproducible functional diversity analyses https://t.co/KB9E6yDiLS #openscience #reproducibility #standradprotocol #RStats #shinyApp
by Dmitry Schigel 04 Nov '22

04 Nov '22

Not sure if this came across, I sense HC like thinking – to read for me, maybe you, too? DS From: Dmitry Schigel <schigel(a)gmail.com> Sent: 01 November 2022 19:20 To: Dmitry Schigel <dschigel(a)gbif.org> Subject: Editor's choice: A protocol for reproducible functional diversity analyses https://t.co/KB9E6yDiLS #openscience #reproducibility #standradprotocol #RStats #shinyApp EcographyJourna (@Ecography) Tweeted: Editor's choice: A protocol for reproducible functional diversity analyses https://t.co/KB9E6yDiLS #openscience #reproducibility #standradprotocol #RStats #shinyApp https://twitter.com/ecographyjourna/status/1587395036961980416?s=51&t=J9Web…

1 0

TDWG 2022 presentation
by Sica, Yanina 04 Nov '22

04 Nov '22

Hi all! Hope everybody is well and healthy. I heard you had a great meeting this week, hopefully it was a useful discussion for the Field Museum folks! TDWG 2022 is next week! There are still a couple of things that we should finish before the symposium: * update the TG webpage<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.tdwg.…> to include our new members * Review documentation/user guide<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> to share broadly * Finish the presentation<https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.goog…> slides. In particular, the dataset examples and the key feedback gathered. If you have any example dataset you would like to include, please add it to the slides. (Kate, I was thinking we could potentially include a screen shot of the MOL dataset that you loaded using HE). Also, there is a specific slide about issues/complications based on our discussions, I would really appreciate if you can help me with that one! Thank you again and see you soon (online or in Sofia!) Have a great conference!! 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 4