- tdwg-humboldt - lists.tdwg.org

advances on the HE manuscript
by Yanina Sica 09 Oct '24

09 Oct '24

Dear all, Thank you so much to everybody who has provided content to the first draft. I have advanced quite a lot consolidating your contributions but there is still more to be done. You can take a look here <https://docs.google.com/document/d/1I7RRu6mj7u53-zz6c_8ZIYqLsNMA0o6VwP3fuST…> . It would be great if we can meet today at our usual place and time (Wednesday at 12:00 UTC, https://yale.zoom.us/j/97318391101) to discuss potential figures, what is missing and timelines. Thanks again! Yani PS: Sorry Steve, I did not realize you were not receiving our emails anymore. I added your new email here

1 0

Updates on humboldt dissemination - meeting today?
by Yanina Sica 02 Oct '24

02 Oct '24

Dear all, I have 1 bad news and 1 good news...I'll start with the bad one which has implications in today's meeting. Sadly, I did not do my homework and I was not able to condense and harmonize everybody's contribution to the manuscript. In that sense, *I would suggest skipping the meeting today and pushing it to next week where I could provide a summary* of what is done and have a better understanding of what is missing. The good news is that I will be* attending COP 16 and will be presenting the Humboldt Extension (and DwC) as a tool to implement FAIR principles in data flows to calculate biodiversity indicators.* We organized a session with colleagues from GEOBON that are involved in the development of the EBV framework. I think this is a very good opportunity to present our work as part of a comprehensive ecosystem of interlinked tools designed to streamline and enhance data processes for parties to report to the Convention of Biological Diversity. I may reach out later on regarding input for the presentation. The session is called *Advancing NBSAP* Reporting Using GEO BON's EBV Data Ecosystem: Live Demonstration and Training* to be held on October 21st at 3 pm at the GEO – GEO BON Pavillion (*NBSAPs are the national reports that countries have to present to the CBD) Please share your thoughts and if you want to meet today, the link is available for everybody. Cheers, Yani

2 1

Will miss the meeting today
by Yanina Sica 25 Sep '24

25 Sep '24

Dear all, I am sorry for the short notice but I will not be able to join the Humboldt meeting today. The link and time will be available for anybody who wants to join to discuss any topics. I noticed a lot of activity in the manuscript, thank you all for your input. I will try to harmonize all your contributions for next week so we can already have a first draft and identify missing topics or sections. Thanks and sorry again, Yani

2 1

Humboldt Extension manuscript
by Yanina Sica 29 Jul '24

29 Jul '24

Hi all, We advanced quite a lot with the manuscript outline, thank you all! You can find the outline as well as journal alternatives and key messages here <https://docs.google.com/document/d/171Blq1BDza_psrIQtBH-USIBzRuJAz-KQ4vS-xY…> Ideally tomorrow we can assign people responsible for different sections. I sent the invite again but in case it does not work, we are meeting on *Wednesday 24th at 12:00 UTC* in this link: https://yale.zoom.us/j/97318391101 Thank you! Yani <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>

2 2

BROKE-WEST dataset mapped to ratified Humboldt terms + Questions
by Yi Ming Gan 12 Jul '24

12 Jul '24

Hi all, I have finally mapped the BROKE-WEST dataset to the ratified Humboldt terms. I mapped it in a different way after chatting with John last year. I am trying to explore if using combinations of target scope per row in Humboldt table will make more sense instead of using pipe separated values (see below): [Screenshot 2024-05-14 at 14.17.42.png] I don’t know if I am understanding things well. I feel it is a little confusing - each row in the Humboldt extension file seems to be conflating the Scopes and Event. For example the value of hasNonTargetTaxa for each row above has to check whether Taxon in Occurrences exist in ALL targetTaxonomicScope where eventID == “BROKE_WEST_RMT_001” (multiple records in Humboldt table) … I also have multiple questions when performing this mapping which I documented in the Rmarkdown here<https://raw.githack.com/biodiversity-aq/humboldt-for-eco-survey-data/main/s…>. Overall, I find it very challenging and complicated (took me 2 full days with the help of chatgpt) to write the code to fill in the boolean values (is___, has____) … I would love a third pair of eyes to help me to look at this. Is anyone willing to look at my work with me please? I am fine with walking you through at our usual meeting times. GitHub repo: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data This is the only script that I worked on these two weeks: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/s… Humboldt Extension generated by the script: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/o… @John, I saw that the new data model<https://docs.google.com/document/d/1eGD69E-KzqdOcjh637iPrp1gv_J55CM2VPAjD1P…> is updated - is there some instructions available somewhere where I can test the Publishing and Conceptual model please? Thank you so much!! Cheers Ming <https://www.naturalsciences.be>[clip_image002.png] Yi-Ming Gan Institute of Natural Sciences Operational Directorate Natural Environment Data manager - Antarctic Biodiversity Portal T +32 (0)2 627 42 77 Rue Vautier 29 Brussels 1000 Belgium

3 5

Humboldt Extension manuscript
by Yanina Sica 11 Jul '24

11 Jul '24

Hi all, Thanks for a very nice meeting last week. It was great to catch up with you after quite a few months! During the meeting we discussed (and agreed on) what are the key messages we wanted to include in this paper (you can revise them here <https://docs.google.com/document/d/171Blq1BDza_psrIQtBH-USIBzRuJAz-KQ4vS-xY…>). With these messages in mind, we expanded on an *outline for the manuscript (see here <https://docs.google.com/document/d/171Blq1BDza_psrIQtBH-USIBzRuJAz-KQ4vS-xY…>). *We will discuss this outline next Wednesday 17th at 12:00 UTC. If you already feel inspired, you can start writing paragraphs or proposing figures in the corresponding sections of the outline! Next meeting: *Zoom link: https://yale.zoom.us/j/97318391101 <https://yale.zoom.us/j/97318391101>* *Wednesday 17th July at 12:00 UTC.* *Special thanks to Kate that got us together again to advance with the manuscript!!* All the best! Yani

1 0

Humboldt workshop at ESA 2024: a few vacant slots
by Dmitry Schigel 09 Jul '24

09 Jul '24

Hello all, As many of you know, 2+ years of work on Humboldt extension to Darwin Core standard have culminated with TDWG ratification of the extension. The ESA2024 conference is one (of hopefully many) engagement event where we will be connecting ecologists holding survey & monitoring with the opportunities offered by the deeper data standardization. There are still a few (of total 20) slots available to ESA delegates to claim - are you in touch with anyone attending ESA through a GBIF Node, through your personal or organizational network? If yes, you might like to inform them on this opportunity. My colleague Kate Ingenloff, cc, will lead the show: https://events.rdmobile.com/Sessions/Details/2318662 (Never mind the fee mentioned there by ESA, GBIF will cover these). Lots of North Am ecologists call ESA annual meetings their main conference, and data standards awareness at ESA is very high already. Please let your ESA people know about this opportunity. You can also promote the event more broadly in: X https://x.com/GBIF/status/1810694151647772742 Fb https://www.facebook.com/gbifnews/posts/pfbid02sqWmyVaLr4Chp93ov5tp6jB8BcFg… In https://www.linkedin.com/posts/gbif_esa2024-humboldt-activity-7216437747375…<https://www.linkedin.com/posts/gbif_esa2024-humboldt-activity-7216437747375…> Best regards and thanks in advance, Dmitry Dmitry Schigel, PhD Scientific officer GBIF | Global Biodiversity Information Facility Secretariat Universitetsparken 15 DK-2100 Copenhagen Ø DENMARK Office +45 35 32 14 85 Mobile +45 30 45 02 25 E-mail dschigel(a)gbif.org<mailto:dschigel@gbif.org> Zoom https://ucph-ku.zoom.us/my/dschigel<http://pta-smg2.csir.co.za:32224/?dmVyPTEuMDAxJiYzMjZjOWE1ZGUyNGEyNzM2ND02M…> Web www.gbif.org<http://pta-smg2.csir.co.za:32224/?dmVyPTEuMDAxJiYzNTc1YzA1OGFiNGE2NTM4MT02M…> [cid:image001.png@01DAD245.10DB39F0]

1 0

Humboldt extension manuscript
by Kate Ingenloff 08 Jul '24

08 Jul '24

Hi all! It's been a minute since the days of weekly meetings, but now that we're into the second half of the year I thought it might be time to revisit the Humboldt extension manuscrip <https://docs.google.com/document/d/171Blq1BDza_psrIQtBH-USIBzRuJAz-KQ4vS-xY…>t. We haven't made much progress since the Task Group disbanded, and I know everyone is busy with other commitments, but I think it would be nice if we could have a working draft ready to submit for review before the end of the year (and a solid working draft by TDWG would be amazing). Does that sound feasible to everyone? For anyone interested in taking part in the writing, I'm happy to organize a quick zoom planning session to get back into the groove of things -- just give me an idea of your availability for the near future. A simple agenda could include: - confirming our target journal (Ecography) so as to be able to research and follow author guidelines from the start - identify references for citation - draft a working outline with figure concepts - assign sections to people for initial drafting On a totally different topic, I did not forget that I was working on a GBIF version of the Humboldt guide. Over the recent months, that concept has morphed into a more general guide for mapping survey and monitoring data as DwC Event core including use of the Humboldt extension. The aim is to have it general enough that ecologists and data publishers outside the DwC and GBIF community can easily understand why and what to do in standardizing their data with DwC. it's still in progress, but I will share it later this summer for comments. I hope everyone is doing well! Hope to hear from you soon. Best, Kate -- ------------------------------ 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

7 8

Humboldt Extension enabled in production at GBIF
by John Wieczorek 17 Apr '24

17 Apr '24

Dear all, Today GBIF made the changes necessary to enable the addition of the Humboldt Extension in Darwin Core archives published via production versions of the IPT. This milestone is monumental. Humboldt is only the second ever ratified Darwin Core extension after ChronometricAge, and now has the full body of documentation and capacity to publish data. What remains for future work is the development of Events in general and Inventories in particular in the GBIF data ingestion pipeline. But the development today provides good incentive to start to invest in those additions. I have asked Tim if he can initiate the process for the release of a news item on gbif.org. That might result in a request for input from this group. I think it would also be good to ask for a news item for TDWG, and to provide a suggestion for what that might look like. I am super content with what has been accomplished. Cheers, John

6 7

no meeting today
by Yanina Sica 11 Apr '24

11 Apr '24

Dear task group, Since we are in Easter week and many people are home with kids or preparing for some days off I suggest we cancel today's meeting. On our table there are still some things to do but we can discuss them over email: - External communication and socialization: - make progress on the paper - oververview can be found here: https://docs.google.com/document/d/171Blq1BDza_psrIQtBH-USIBzRuJAz-KQ4vS-xY… - advance on documentation, - Kate, would you like to share your advances? - Any ideas for TDWG 2024? other conferences? News on ESA? BES? - advance on sharing the promised datasets to finish the Task Group - Wesley and Zach already shared their datasets as csv with great documentation - Ani, any news on your dataset? - John, is it possible to have the GBIF IPT updated with eco: terms so we can share these datasets using it? Hope everybody is doing great! All the best! Yani <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>

4 6