- tdwg-humboldt - lists.tdwg.org

Advancing the Humboldt manuscript - new figures and other additions
by Yanina Sica 19 Mar '25

19 Mar '25

Dear all, I am sorry for the delay after our meeting in February. I had to take some time off and could not dig into this until recently. After our meeting, there are a number of updates that I would like you to take a look at: - Figures 1 and 2 were updated following your suggestions - The methods section was considerably reduced - In results, the information classes were revisited and many changes were incorporated (now terms are grouped in 6 non formal classes that describe different aspects of the data collection process) - An Application section was incorporated listing the different data repositories that can make use of the Humboldt Extension, and the use cases. Due to lack of space the main content of this section was moved to supplementary material. You can find the MS here <https://docs.google.com/document/d/1I7RRu6mj7u53-zz6c_8ZIYqLsNMA0o6VwP3fuST…> . *I would really appreciate it if you could take a look at these sections as well as the Discussion and get your feedback by April 7th. My goal is by the end of April to have a decent final draft and start contacting the Editor of the Journal. * I hope you find this timeline reasonable, let me know otherwise.* If you all agree, I will set up a call on April 9th to discuss the status of the MS and your inputs.* *Thank you so much for all your support in this process!* Best, Yani

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Advancing the Humboldt manuscript - meeting Feb 5
by Yanina Sica 28 Jan '25

28 Jan '25

Hi all, Thank you so much to all who have contributed to the manuscript. *For the ones that are still interested in contributing, please remember you have time until Feb 3 (MS here <https://docs.google.com/document/d/1I7RRu6mj7u53-zz6c_8ZIYqLsNMA0o6VwP3fuST…>). *Ideally, I would have some time to go through your comments and consolidate them before our *meeting on Wednesday 5 at 12 UTC. * *If you have conflicts with the time of the meeting (I maintained the original meeting date and time), please let me know and I am more than happy to meet separately or coordinate differently.* The success of next week's meeting is highly dependent on your input so reading the current state of the manuscript would be beneficial. The proposed agenda for the meeting is below but it is quite flexible regarding new comments or insight collected during the upcoming week, so please share freely. *Proposed agenda (wed 5)* - Figures, particularly Fig 1 since the message is still not clear. - Structure of sections and content, in particular regarding how to handle the case studies. - Sections or categories in which the terms have been organized. Current classes are described in https://eco.tdwg.org/terms/. Some of them may not be intuitive and we might need to double-check these. - Next steps regarding journals and potentially approaching editors in advance - Consensus on repeated terms or concepts (data collection process, inventory types, etc) Thank you again, and see you next week! All the best, Yani

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Re: Humboldt Extension manuscript reloaded
by Yanina Sica 27 Jan '25

27 Jan '25

Wow! I love all this activity! Thank you all and particularly Wesley for your inputs!! Between Tuesday and Wednesday and I can definitely work on current comments. I will let you know when I finish so Rob and others can review. Thanks again! See you next week Yani On Mon 27. Jan 2025 at 22:10, Wesley M. Hochachka <wmh6(a)cornell.edu> wrote: > Hi everyone, > > That red ink would mostly be mine. I think that it's important that I > cause the visual chaos, because it is at least a visual indicator that I > have sometimes suggested substantial changes in wording (albeit not of > content...I hope). > I don't know Google Docs at all well, but does anyone else know whether > it's possible to visually merge suggested changes in the same way that a > Microsoft Word document can hide changes in track changes? > > By the way, I've gone through the text up to just before the Case > studies subsection of the Results. So, you should assume that I will *not > *be revisiting any of the text before the Case studies during the current > round of reviewing/editing. > > Wesley > > > > ******************* > Wesley Hochachka > Senior Research Associate > Cornell Lab of Ornithology > ph. (607) 254-2484 > ******************* > ------------------------------ > *From:* Robert Guralnick <robgur(a)gmail.com> > *Sent:* Monday, January 27, 2025 13:54 > *To:* Steven J Baskauf <steve.baskauf(a)gmail.com> > *Cc:* Yanina Sica <yanina.sica(a)gmail.com>; Humboldt Core TG < > tdwg-humboldt(a)lists.tdwg.org>; Wesley M. Hochachka <wmh6(a)cornell.edu>; > Walter Jetz <walter.jetz(a)yale.edu>; Peter Brenton <Peter.Brenton(a)csiro.au>; > Paula Zermoglio <pzermoglio(a)gmail.com> > *Subject:* Re: Humboldt Extension manuscript reloaded > > I'd love it if we could resolve a lot of comments and edits before the > next read through. I personally find it hard to sort through a paper that > has a lot of red ink on it and see the narrative structure and "flow". I > can take some responsibility to accept changes or let Yani jump in and help > with that as the lead author. Gonna wait before I do more here. > -r > > On Mon, Jan 27, 2025 at 1:51 PM Steven J Baskauf <steve.baskauf(a)gmail.com> > wrote: > > I have read through the manuscript and have made some somewhat cosmetic > changes. Thanks for all of your wordsmithing, Wesley! > > Steve > On 12/22/24 12:54 PM, Yanina Sica wrote: > > Dear Humboldties! > > It's been a few weeks of silence as I've been integrating all your > contributions to the manuscript. Knowing all of you, it is not surprising > to have received so many good and productive comments and contributions on > this, I appreciate you finding the time for this despite your busy > schedule. I really like working so collaboratively with you! > > As a token of appreciation, my Christmas present for you is an updated, > considerably improved version of the manuscript. You can find it here > <https://docs.google.com/document/d/1I7RRu6mj7u53-zz6c_8ZIYqLsNMA0o6VwP3fuST…>. > Discussion and figures still need a lot of work (probably other parts as > well), but at least we have a first complete draft of the manuscript. > > Special requests: > - is anybody interested in taking a creative take on Figure 1? I would be > happy to discuss my ideas which I was not able to communicate with current > figure proposals > - I would appreciate any general comment regarding the current > structure of sections and content, in particular regarding how to handle > the case studies. The manuscript is already quite long... > - editorial skills are needed, please edit freely! > - big-picture thinkers are also needed, take a stab! > > I was hoping to have your feedback by the last week of January, do you > think this is doable? If yes, I will organize a meeting in the first week > of February to discuss your feedback and start making decisions regarding > journals. > > I hope you have a great start of the new year, all the best in 2025! > > Cheers, > > Yani > > > > > > > Yani > > > > -- > >

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Re: Humboldt Extension manuscript reloaded
by Yanina Sica 09 Jan '25

09 Jan '25

Thank you so much Peter! I accepted most of your editorial changes and left some comments for everybody to see. What about the rest of the team, *do you think you will be able to review the draft by the end of January? * *I propose a meeting on Wed Feb 5 at 12:00 UTC to discuss progress and figures. * *Please let me know if you **agree with the plan or if you **need more time.* Hope you all started a great 2025!!! Best, Yani On Mon, Dec 23, 2024 at 2:14 AM Brenton, Peter (NCMI, Black Mountain) < Peter.Brenton(a)csiro.au> wrote: > Hi Yani and team, > > > > Sorry I have been offline for a long time. I took a large block of leave > and have been travelling. I am back now for a while and am still picking up > threads that I left loose before I finished. > > I’ve added some comments and suggested edits to the draft manuscript. It > is looking very good though, congratulation all. > > > > Anyway, have a great Christmas and new year break and see you in a few > weeks. > > > > Cheers, > > > > Peter > > > > *From:* Yanina Sica <yanina.sica(a)gmail.com> > *Sent:* Monday, 23 December 2024 4:55 AM > *To:* Humboldt Core TG <tdwg-humboldt(a)lists.tdwg.org>; Steven J Baskauf < > steve.baskauf(a)gmail.com>; Wesley M. Hochachka <wmh6(a)cornell.edu>; Robert > Guralnick <robgur(a)gmail.com>; Walter Jetz <walter.jetz(a)yale.edu>; > Brenton, Peter (NCMI, Black Mountain) <Peter.Brenton(a)csiro.au>; Paula > Zermoglio <pzermoglio(a)gmail.com> > *Subject:* Humboldt Extension manuscript reloaded > > > > Dear Humboldties! > > > > It's been a few weeks of silence as I've been integrating all your > contributions to the manuscript. Knowing all of you, it is not surprising > to have received so many good and productive comments and contributions on > this, I appreciate you finding the time for this despite your busy > schedule. I really like working so collaboratively with you! > > > > As a token of appreciation, my Christmas present for you is an updated, > considerably improved version of the manuscript. You can find it here > <https://docs.google.com/document/d/1I7RRu6mj7u53-zz6c_8ZIYqLsNMA0o6VwP3fuST…>. > Discussion and figures still need a lot of work (probably other parts as > well), but at least we have a first complete draft of the manuscript. > > > > Special requests: > > - is anybody interested in taking a creative take on Figure 1? I would be > happy to discuss my ideas which I was not able to communicate with current > figure proposals > > - I would appreciate any general comment regarding the current > structure of sections and content, in particular regarding how to handle > the case studies. The manuscript is already quite long... > > - editorial skills are needed, please edit freely! > > - big-picture thinkers are also needed, take a stab! > > > > I was hoping to have your feedback by the last week of January, do you > think this is doable? If yes, I will organize a meeting in the first week > of February to discuss your feedback and start making decisions regarding > journals. > > > > I hope you have a great start of the new year, all the best in 2025! > > > > Cheers, > > > > Yani > > > > > > > > > > > > > > Yani >

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Humboldt Extension manuscript reloaded
by Yanina Sica 22 Dec '24

22 Dec '24

Dear Humboldties! It's been a few weeks of silence as I've been integrating all your contributions to the manuscript. Knowing all of you, it is not surprising to have received so many good and productive comments and contributions on this, I appreciate you finding the time for this despite your busy schedule. I really like working so collaboratively with you! As a token of appreciation, my Christmas present for you is an updated, considerably improved version of the manuscript. You can find it here <https://docs.google.com/document/d/1I7RRu6mj7u53-zz6c_8ZIYqLsNMA0o6VwP3fuST…>. Discussion and figures still need a lot of work (probably other parts as well), but at least we have a first complete draft of the manuscript. Special requests: - is anybody interested in taking a creative take on Figure 1? I would be happy to discuss my ideas which I was not able to communicate with current figure proposals - I would appreciate any general comment regarding the current structure of sections and content, in particular regarding how to handle the case studies. The manuscript is already quite long... - editorial skills are needed, please edit freely! - big-picture thinkers are also needed, take a stab! I was hoping to have your feedback by the last week of January, do you think this is doable? If yes, I will organize a meeting in the first week of February to discuss your feedback and start making decisions regarding journals. I hope you have a great start of the new year, all the best in 2025! Cheers, Yani Yani

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Available to meet today?
by Yanina Sica 14 Nov '24

14 Nov '24

Hi all, Hope you are doing well! I have been advancing on the manuscript (thanks to everybody who contributed so far!) and I am struggling with the figures. *Would any of you be available to meet briefly today at our regular meeting time? (12 UTC here <https://yale.zoom.us/j/97318391101>)* *Please contribute to the HE manuscript if you are interested (MS here <https://docs.google.com/document/d/1I7RRu6mj7u53-zz6c_8ZIYqLsNMA0o6VwP3fuST…>, track your changes please!). Introduction, Methods and Results need to be revised and edited. Discussion still needs a lot of writing so you are welcome to include your ideas there!* Hope to see you later today or next week, Cheers, Yani

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no meeting for me - working on the MS
by Yanina Sica 02 Nov '24

02 Nov '24

Dear all, Last week we had a great meeting where we discussed the advances on the HE manuscript (here <https://docs.google.com/document/d/1I7RRu6mj7u53-zz6c_8ZIYqLsNMA0o6VwP3fuST…>). We are still working on this first draft, in particular, we are still drafting the discussion and the figures. I will start assigning some sections for you to review or write from scratch. *Please let me know if you do not feel comfortable with these assignments. * One key item that we discussed is that we would like to switch the terminology to 'surveys'. This would be the main way to refer to a sampling event. Although 'inventory' and 'sampling' will also be used along the text. Somewhere we will need to add a paragraph saying that we will use the terms interchangeably. I do not think we need to meet today, but the *link is open and feel free to use it to discuss any particular matter.* Thanks, John for those great visuals on the events, I encourage you to meet and keep discussing this topic. All the best, Yani

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Cardinality of the Humboldt Extension to Events
by John Wieczorek 09 Oct '24

09 Oct '24

Hi folks, In our meeting today everyone was kind enough to give me a couple of minutes to make a survey about how a Humboldt Extension record is expected to relate to an Event record. I think it is of extreme importance that users of the extension understand how this is supposed to work, and that our paper explains it. If done correctly, consumers of the data won't actually need to understand it, because the results will already be explicit and not possible (famous last words) to interpret incorrectly. I made a couple of graphics to help show how the extension records are supposed to relate to events, and how not. Thanks for requesting this, Anahita. [image: image.png] Figure 1. Humboldt Extension records contain metadata about Surveys. The combination of a Survey record with its Event counterpart effectively creates a Survey Event (an Event that also has Survey metadata) - you could combine the Event terms and Survey terms into a single row in a spreadsheet. A Survey Event can, but doesn't have to, have a parent Event. As usual, the parent Event (a project, in the example) has to encompass the Surveys and other Events that are its children, both temporally and spatially. This model describes the relationship as a one-to-(zero-or-one) between Event and Survey. [image: image.png] Figure 2. Diagram of a model with a one-to-many relationship between Event and Survey. Such a model would allow an Event record to have zero, one, or multiple Survey records. The spreadsheet shows an example that would be valid in this model, with one Project Event and its related Survey records. One would interpret the data in the spreadsheet to mean that the Project Event event1 has multiple Surveys. The issue is that a Survey record contains metadata about a Survey, not about a Project. Without the specific protocol, temporal and spatial context information the Event is supposed to provide, the Survey is effectively disabled. The lesson is that the Event structure is supposed to be entirely within the Event, using the parentEventID to create the hierarchy between Events of different types and scales, not the relationship to Surveys. Surveys are just one of the different types of Events, and those have the Humboldt Extension, while the other types of Events do not. The other types of Events might have their own distinct extensions (e.g., Occurrence Extension). For the sake of partial completeness, the same reasoning applies to Occurrences. Occurrences are Events too )"Occurrence Events". The occurrenceID needs to correspond to an eventID for the Event that gives the context and protocol for the Occurrence. Those Occurrences can be the result of a Survey, but a) they won't have a Humboldt Extension record attached to them and b) the Survey Event they are a result from would be given by the Occurrence Event's parentEventID. I hope that last paragraph doesn't confuse the issue I was trying to address about the Event/Survey relationship. It is just a parallel example and you can ignore it if it muddles rather than clarifies. Cheers, John

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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

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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

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