meeting this week
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit this week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani [https://lh3.googleusercontent.com/docs/ADP-6oHMdd4mw25hw7lvSXn4ZCiwspb9cc28U...]https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit Hierarchical Events in Humboldt Extension for ecological inventorieshttps://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ... docs.google.com
Yanina V. Sica, PhD Lead Data Team Map of Lifehttps://mol.org/ | Center for Biodiversity and Global Changehttps://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.
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 yanina.sica@yale.edu wrote:
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/editthis week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit Hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ... docs.google.com
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.* _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
Stuck in a GBIF meeting, not joining today DS
From: tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org On Behalf Of John Wieczorek Sent: Tuesday, 4 July, 2023 21:30 To: Humboldt Core TG tdwg-humboldt@lists.tdwg.org Cc: wmh6@cornell.edu Subject: Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 <yanina.sica@yale.edumailto:yanina.sica@yale.edu> wrote: Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit this week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani [https://lh3.googleusercontent.com/docs/ADP-6oHMdd4mw25hw7lvSXn4ZCiwspb9cc28U...]https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit Hierarchical Events in Humboldt Extension for ecological inventorieshttps://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ... docs.google.comhttp://docs.google.com
Yanina V. Sica, PhD Lead Data Team Map of Lifehttps://mol.org/ | Center for Biodiversity and Global Changehttps://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. _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW...
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA
One or several sweeps of a net containing a collection of insects
Camera trap – collection of images of mammals
Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams
Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel dschigel@gbif.org wrote:
Stuck in a GBIF meeting, not joining today
DS
*From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org *On Behalf Of *John Wieczorek *Sent:* Tuesday, 4 July, 2023 21:30 *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org *Cc:* wmh6@cornell.edu *Subject:* Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 yanina.sica@yale.edu wrote:
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/editthis week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ...
docs.google.com
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.*
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
Thank you so much Rob!
I am still unsure if I will be able to join this week's meeting (I am attending a workshop). But it would be great if you can discuss Rob's additional text and some of the doubts we had on principle 3 (i added comments to the text). Hopefully, John can join and is able to provide some context.
Thanks again and i hope to see you later today!
Yanina V. Sica, PhD Lead Data Team Map of Lifehttps://mol.org/ | Center for Biodiversity and Global Changehttps://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 ________________________________ From: tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org on behalf of Rob Stevenson rdstevenson10@gmail.com Sent: Tuesday, July 11, 2023 10:06:18 PM To: Humboldt Core TG tdwg-humboldt@lists.tdwg.org Cc: tuco@berkeley.edu tuco@berkeley.edu; wmh6@cornell.edu wmh6@cornell.edu Subject: Re: [tdwg-humboldt] meeting this week
Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW...
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA
One or several sweeps of a net containing a collection of insects
Camera trap – collection of images of mammals
Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams
Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel <dschigel@gbif.orgmailto:dschigel@gbif.org> wrote:
Stuck in a GBIF meeting, not joining today
DS
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> On Behalf Of John Wieczorek Sent: Tuesday, 4 July, 2023 21:30 To: Humboldt Core TG <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Cc: wmh6@cornell.edumailto:wmh6@cornell.edu Subject: Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 <yanina.sica@yale.edumailto:yanina.sica@yale.edu> wrote:
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit this week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
[https://lh3.googleusercontent.com/docs/ADP-6oHMdd4mw25hw7lvSXn4ZCiwspb9cc28U...]https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Hierarchical Events in Humboldt Extension for ecological inventorieshttps://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ...
docs.google.comhttp://docs.google.com/
Yanina V. Sica, PhD
Lead Data Team
Map of Lifehttps://mol.org/ | Center for Biodiversity and Global Changehttps://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.
_______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
_______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
Thank you Rob and hi all!! I won’t be able to make it again for the meeting today as I need to rush some works, but I made the event-parentEvent figure as promised.
Cheers Ming
On 12 Jul 2023, at 09:45, ys628 yanina.sica@yale.edu wrote:
Thank you so much Rob!
I am still unsure if I will be able to join this week's meeting (I am attending a workshop). But it would be great if you can discuss Rob's additional text and some of the doubts we had on principle 3 (i added comments to the text). Hopefully, John can join and is able to provide some context.
Thanks again and i hope to see you later today!
Yanina V. Sica, PhD Lead Data Team Map of Life https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmol.org%2F&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=H8c6bTvQBWqGQs65ExLWsdaAwkcq74LDXn4YMo%2BRUDE%3D&reserved=0 | Center for Biodiversity and Global Change https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbgc.yale.edu%2F&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=G0D%2FYgJL3dmx%2FV4JonvLvOMU6aADl40LLlx9RDaNJ%2F8%3D&reserved=0 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 From: tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org on behalf of Rob Stevenson rdstevenson10@gmail.com Sent: Tuesday, July 11, 2023 10:06:18 PM To: Humboldt Core TG tdwg-humboldt@lists.tdwg.org Cc: tuco@berkeley.edu tuco@berkeley.edu; wmh6@cornell.edu wmh6@cornell.edu Subject: Re: [tdwg-humboldt] meeting this week
Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW... https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE%2Fedit&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BFDfyxcwh4pppa%2BhgdOChIq%2BISumDpDMjmAKCKRaXM0%3D&reserved=0
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA One or several sweeps of a net containing a collection of insects Camera trap – collection of images of mammals Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel <dschigel@gbif.org mailto:dschigel@gbif.org> wrote: Stuck in a GBIF meeting, not joining today
DS
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.org mailto:tdwg-humboldt-bounces@lists.tdwg.org> On Behalf Of John Wieczorek Sent: Tuesday, 4 July, 2023 21:30 To: Humboldt Core TG <tdwg-humboldt@lists.tdwg.org mailto:tdwg-humboldt@lists.tdwg.org> Cc: wmh6@cornell.edu mailto:wmh6@cornell.edu Subject: Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 <yanina.sica@yale.edu mailto:yanina.sica@yale.edu> wrote:
Hi all,
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE%2Fedit&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BFDfyxcwh4pppa%2BhgdOChIq%2BISumDpDMjmAKCKRaXM0%3D&reserved=0 Hierarchical Events in Humboldt Extension for ecological inventories https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE%2Fedit&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BFDfyxcwh4pppa%2BhgdOChIq%2BISumDpDMjmAKCKRaXM0%3D&reserved=0 Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tdwg.org%2Fstandards%2F450&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Fc8PdmckoqEMfPnzugmWe6ujeC25kdlM9yFZjqgGiM4%3D&reserved=0 This ...
Yanina V. Sica, PhD
Lead Data Team
Map of Life https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmol.org%2F&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=H8c6bTvQBWqGQs65ExLWsdaAwkcq74LDXn4YMo%2BRUDE%3D&reserved=0 | Center for Biodiversity and Global Change https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbgc.yale.edu%2F&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=G0D%2FYgJL3dmx%2FV4JonvLvOMU6aADl40LLlx9RDaNJ%2F8%3D&reserved=0 Yale University
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tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org mailto:tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.tdwg.org%2Fmailman%2Flistinfo%2Ftdwg-humboldt&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tnkNeQFaBR8zczkBIpVxSQ9%2B86UB0rB7AOLFSoQN34Q%3D&reserved=0_______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org mailto:tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.tdwg.org%2Fmailman%2Flistinfo%2Ftdwg-humboldt&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tnkNeQFaBR8zczkBIpVxSQ9%2B86UB0rB7AOLFSoQN34Q%3D&reserved=0
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
Dear all,
I managed to double-book myself, and won't be able to make the meeting today. Apologies!
Ani
On 12/07/2023 10:44, Yi Ming Gan wrote:
Thank you Rob and hi all!! I won’t be able to make it again for the meeting today as I need to rush some works, but I made the event-parentEvent figure as promised.
Cheers Ming
On 12 Jul 2023, at 09:45, ys628 yanina.sica@yale.edu wrote:
Thank you so much Rob!
I am still unsure if I will be able to join this week's meeting (I am attending a workshop). But it would be great if you can discuss Rob's additional text and some of the doubts we had on principle 3 (i added comments to the text). Hopefully, John can join and is able to provide some context.
Thanks again and i hope to see you later today!
Yanina V. Sica, PhD Lead Data Team Map of Life https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmol.org%2F&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=H8c6bTvQBWqGQs65ExLWsdaAwkcq74LDXn4YMo%2BRUDE%3D&reserved=0| Center for Biodiversity and Global Change https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbgc.yale.edu%2F&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=G0D%2FYgJL3dmx%2FV4JonvLvOMU6aADl40LLlx9RDaNJ%2F8%3D&reserved=0 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
*From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org on behalf of Rob Stevenson rdstevenson10@gmail.com *Sent:* Tuesday, July 11, 2023 10:06:18 PM *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org *Cc:* tuco@berkeley.edu tuco@berkeley.edu; wmh6@cornell.edu wmh6@cornell.edu *Subject:* Re: [tdwg-humboldt] meeting this week Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW... https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE%2Fedit&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BFDfyxcwh4pppa%2BhgdOChIq%2BISumDpDMjmAKCKRaXM0%3D&reserved=0
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA One or several sweeps of a net containing a collection of insects Camera trap – collection of images of mammals Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel dschigel@gbif.org wrote:
Stuck in a GBIF meeting, not joining today DS *From:* tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.org> *On Behalf Of *John Wieczorek *Sent:* Tuesday, 4 July, 2023 21:30 *To:* Humboldt Core TG <tdwg-humboldt@lists.tdwg.org> *Cc:* wmh6@cornell.edu *Subject:* Re: [tdwg-humboldt] meeting this week Hi folks, I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately. Cheers, John On Tue, Jul 4, 2023 at 4:27 PM ys628 <yanina.sica@yale.edu> wrote: Hi all, Lets discuss theHierarchical Document <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE%2Fedit&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BFDfyxcwh4pppa%2BhgdOChIq%2BISumDpDMjmAKCKRaXM0%3D&reserved=0>this week! With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps. See you! Yani <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE%2Fedit&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BFDfyxcwh4pppa%2BhgdOChIq%2BISumDpDMjmAKCKRaXM0%3D&reserved=0> Hierarchical Events in Humboldt Extension for ecological inventories <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE%2Fedit&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=BFDfyxcwh4pppa%2BhgdOChIq%2BISumDpDMjmAKCKRaXM0%3D&reserved=0> Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.tdwg.org%2Fstandards%2F450&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=Fc8PdmckoqEMfPnzugmWe6ujeC25kdlM9yFZjqgGiM4%3D&reserved=0> This ... docs.google.com <https://eur02.safelinks.protection.outlook.com/?url=http%3A%2F%2Fdocs.google.com%2F&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ws5H0h0uK2tw2JNeKEgAaP1Z05ErW9yaMeryDWGLSa8%3D&reserved=0> Yanina V. Sica, PhD Lead Data Team Map of Life <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmol.org%2F&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=H8c6bTvQBWqGQs65ExLWsdaAwkcq74LDXn4YMo%2BRUDE%3D&reserved=0> | Center for Biodiversity and Global Change <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbgc.yale.edu%2F&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=G0D%2FYgJL3dmx%2FV4JonvLvOMU6aADl40LLlx9RDaNJ%2F8%3D&reserved=0> 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@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.tdwg.org%2Fmailman%2Flistinfo%2Ftdwg-humboldt&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tnkNeQFaBR8zczkBIpVxSQ9%2B86UB0rB7AOLFSoQN34Q%3D&reserved=0> _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.tdwg.org%2Fmailman%2Flistinfo%2Ftdwg-humboldt&data=05%7C01%7Cymgan%40naturalsciences.be%7C5ed5a47179824c52af6008db82ac05b9%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638247447573583653%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=tnkNeQFaBR8zczkBIpVxSQ9%2B86UB0rB7AOLFSoQN34Q%3D&reserved=0>-- Robert D Stevenson Associate Professor Department of Biology UMass Boston _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
------------------------------------------------------------------------
Dr Anahita JN Kazem
Data Steward & Biodiversity Informatics Scientist
Data & Code Unit (iBID / iBON) German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig |www.idiv.de
Department of Informatics Friedrich-Schiller-University Jena
anahita.kazem@idiv.de | Puschstraße 4 | D-04103 Leipzig | Germany
Hi all,
Sorry, I have been very late on doing my bit for this too. I am hoping to get something together before our meeting tonight though.
Peter
From: tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org On Behalf Of ys628 Sent: Wednesday, 12 July 2023 5:46 PM To: Humboldt Core TG tdwg-humboldt@lists.tdwg.org Cc: tuco@berkeley.edu; wmh6@cornell.edu Subject: Re: [tdwg-humboldt] meeting this week
Thank you so much Rob!
I am still unsure if I will be able to join this week's meeting (I am attending a workshop). But it would be great if you can discuss Rob's additional text and some of the doubts we had on principle 3 (i added comments to the text). Hopefully, John can join and is able to provide some context.
Thanks again and i hope to see you later today!
Yanina V. Sica, PhD Lead Data Team Map of Lifehttps://mol.org/ | Center for Biodiversity and Global Changehttps://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 ________________________________ From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> on behalf of Rob Stevenson <rdstevenson10@gmail.commailto:rdstevenson10@gmail.com> Sent: Tuesday, July 11, 2023 10:06:18 PM To: Humboldt Core TG <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Cc: tuco@berkeley.edumailto:tuco@berkeley.edu <tuco@berkeley.edumailto:tuco@berkeley.edu>; wmh6@cornell.edumailto:wmh6@cornell.edu <wmh6@cornell.edumailto:wmh6@cornell.edu> Subject: Re: [tdwg-humboldt] meeting this week
Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW...
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA
One or several sweeps of a net containing a collection of insects
Camera trap – collection of images of mammals
Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams
Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel <dschigel@gbif.orgmailto:dschigel@gbif.org> wrote:
Stuck in a GBIF meeting, not joining today
DS
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> On Behalf Of John Wieczorek Sent: Tuesday, 4 July, 2023 21:30 To: Humboldt Core TG <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Cc: wmh6@cornell.edumailto:wmh6@cornell.edu Subject: Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 <yanina.sica@yale.edumailto:yanina.sica@yale.edu> wrote:
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit this week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
[https://lh3.googleusercontent.com/docs/ADP-6oHMdd4mw25hw7lvSXn4ZCiwspb9cc28U...]https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Hierarchical Events in Humboldt Extension for ecological inventorieshttps://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ...
docs.google.comhttp://docs.google.com/
Yanina V. Sica, PhD
Lead Data Team
Map of Lifehttps://mol.org/ | Center for Biodiversity and Global Changehttps://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.
_______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
Hi folks,
This is the second week of three giving a georeferencing workshop that surrounds the time of the Humboldt meeting, so I will not be able to attend again. Sorry.
John
On Wed, Jul 12, 2023 at 5:45 AM Brenton, Peter (NCMI, Black Mountain) < Peter.Brenton@csiro.au> wrote:
Hi all,
Sorry, I have been very late on doing my bit for this too. I am hoping to get something together before our meeting tonight though.
Peter
*From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org *On Behalf Of *ys628 *Sent:* Wednesday, 12 July 2023 5:46 PM *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org *Cc:* tuco@berkeley.edu; wmh6@cornell.edu *Subject:* Re: [tdwg-humboldt] meeting this week
Thank you so much Rob!
I am still unsure if I will be able to join this week's meeting (I am attending a workshop). But it would be great if you can discuss Rob's additional text and some of the doubts we had on principle 3 (i added comments to the text). Hopefully, John can join and is able to provide some context.
Thanks again and i hope to see you later today!
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*
*From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org on behalf of Rob Stevenson rdstevenson10@gmail.com *Sent:* Tuesday, July 11, 2023 10:06:18 PM *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org *Cc:* tuco@berkeley.edu tuco@berkeley.edu; wmh6@cornell.edu < wmh6@cornell.edu> *Subject:* Re: [tdwg-humboldt] meeting this week
Dear All,
I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion -
How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW...
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA
One or several sweeps of a net containing a collection of insects
Camera trap – collection of images of mammals
Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams
Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel dschigel@gbif.org wrote:
Stuck in a GBIF meeting, not joining today
DS
*From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org *On Behalf Of *John Wieczorek *Sent:* Tuesday, 4 July, 2023 21:30 *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org *Cc:* wmh6@cornell.edu *Subject:* Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 yanina.sica@yale.edu wrote:
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/editthis week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ...
docs.google.com
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.*
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
--
Robert D Stevenson Associate Professor
Department of Biology UMass Boston
Dear Humboldt Core TG
Below are notes from Wednesday. John, your asynchronous input would be especially helpful because we know you will not be able to attend the next meeting. If I have misinterpreted something or someone, please jump in and make a correction.
Thanks Rob
On Wednesday (2023/07/12), Steve, Peter, Zach, Wesley and I met and had fruitful discussions about points 6 and 7 in section 3.3 of the Properties of hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit. These are points John wrote to give guidance for applying the Humboldt Extension.
The discussion was around whether the phrasing was too prescriptive. Wesley asked “Could we come up with counter examples?”. Wesley will write a few sentences to encapsulate the issue. Peter felt the wording may not be necessary.
Peter showed us several inventories from BioCollect and described how they fit into the Humboldt extension model. The BioCollect model uses a survey template that can be applied repeated to a collection event and allows many kinds of observations and measurements to be made. The series of collection events together make a dataset. In Humboldt terms this dataset is a parent Event. To facilitate reuse each survey template is made up of a variety of observation and measurement protocols that can be bundled together as needed to make different survey templates.
Zach described how the Field Museum’s Rapid Inventories in which teams of biologists document biodiversity of different taxa ( plants, fishes, amphibians, reptiles, birds, and mammals) using a variety of methods at one site and within one timeframe https://www.rapidinventories.fieldmuseum.org/what-is-a-rapid-inventory are being represented as one Event at the highest level.
Tim added a comment to the document asking that we consider rewriting the definition of
He said “I think this definition might be improved. An inventory is a complete list of something, but the definition doesn't capture this, only referring to the activities used in the methodology. Perhaps something like:
"An inventory dataset accounts for all targeted organisms and measurements recorded while following a structured sampling protocol. Observations and measurements are captured in one or more dwc:Events that MAY..."
This request is in line with our discussion on Wednesday.
Our discussion suggested it would be helpful to put in some kind of clarifying statement about what the lowest level Event might contain. My current understanding is that this lowest level might contain just a one zero to represent the event that occurred but that no occurrence was found or NA that a measurement was attempted but the measurement failed for some reason. On the complexity end of the spectrum of what an event could contain, Peter gave an example (see text at the bottom of the document) of an event pointing to an array of observations and measurements based on a survey template for Vegetation condition assessment. In a flattened (2D) database this would take 40 records (rows) to represent what was part of the event. Peter gave a second example about birds in which he added a screen shot from the BioCollect application. Here again multiple records are needed to contain the information in a flatten form.
This brings up the point of discussion in the meeting. Peter said that each event and each occurrence will have their own ids. This would mean if one flattered an event and selectively removed species occurrence records containing the occurrence ID that they could be traced back to the event in which the collection took place.
The group hopes that others who could not attend have insights into the issues and the descriptions. We felt John's comments would be very important because of his knowledge about the new GBIF model.
On Tue, Jul 11, 2023 at 4:06 PM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW...
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA
One or several sweeps of a net containing a collection of insects
Camera trap – collection of images of mammals
Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams
Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel dschigel@gbif.org wrote:
Stuck in a GBIF meeting, not joining today
DS
*From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org *On Behalf Of *John Wieczorek *Sent:* Tuesday, 4 July, 2023 21:30 *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org *Cc:* wmh6@cornell.edu *Subject:* Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 yanina.sica@yale.edu wrote:
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/editthis week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ...
docs.google.com
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.*
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
I'm sharing some comments inline. These are accompanied by comments and suggestions in the Event Hierarchy document.
On Thu, Jul 13, 2023 at 6:29 AM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear Humboldt Core TG
Below are notes from Wednesday. John, your asynchronous input would be especially helpful because we know you will not be able to attend the next meeting. If I have misinterpreted something or someone, please jump in and make a correction.
Thanks Rob
On Wednesday (2023/07/12), Steve, Peter, Zach, Wesley and I met and had fruitful discussions about points 6 and 7 in section 3.3 of the Properties of hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit. These are points John wrote to give guidance for applying the Humboldt Extension.
The discussion was around whether the phrasing was too prescriptive. Wesley asked “Could we come up with counter examples?”. Wesley will write a few sentences to encapsulate the issue. Peter felt the wording may not be necessary.
Peter showed us several inventories from BioCollect and described how they fit into the Humboldt extension model. The BioCollect model uses a survey template that can be applied repeated to a collection event and allows many kinds of observations and measurements to be made. The series of collection events together make a dataset. In Humboldt terms this dataset is a parent Event. To facilitate reuse each survey template is made up of a variety of observation and measurement protocols that can be bundled together as needed to make different survey templates.
Just to clarify, this doesn't present any problems to what we have defined in the Event Hierarchies document, correct?
Zach described how the Field Museum’s Rapid Inventories in which teams of biologists document biodiversity of different taxa ( plants, fishes, amphibians, reptiles, birds, and mammals) using a variety of methods at one site and within one timeframe https://www.rapidinventories.fieldmuseum.org/what-is-a-rapid-inventory are being represented as one Event at the highest level.
Again, just to clarify, this doesn't present any problems to what we have defined in the Event Hierarchies document, correct?
Tim added a comment to the document asking that we consider rewriting the definition of
He said “I think this definition might be improved. An inventory is a complete list of something, but the definition doesn't capture this, only referring to the activities used in the methodology. Perhaps something like:
"An inventory dataset accounts for all targeted organisms and measurements recorded while following a structured sampling protocol. Observations and measurements are captured in one or more dwc:Events that MAY..."
I commented in the text that it doesn't seem to me that completeness is a requirement, but that the rest seems reasonable.
This request is in line with our discussion on Wednesday.
Our discussion suggested it would be helpful to put in some kind of clarifying statement about what the lowest level Event might contain.
This is a good idea to be clarified with examples, as long as it is not proscriptive. I think the most common lowest-level Events would actually be Occurrences, at least in the Unified Model, where Occurrences are one type of Event.
My current understanding is that this lowest level might contain just a one zero to represent the event that occurred but that no occurrence was found or NA that a measurement was attempted but the measurement failed for some reason. On the complexity end of the spectrum of what an event could contain, Peter gave an example (see text at the bottom of the document) of an event pointing to an array of observations and measurements based on a survey template for Vegetation condition assessment. In a flattened (2D) database this would take 40 records (rows) to represent what was part of the event. Peter gave a second example about birds in which he added a screen shot from the BioCollect application. Here again multiple records are needed to contain the information in a flatten form.
This brings up the point of discussion in the meeting. Peter said that each event and each occurrence will have their own ids. This would mean if one flattered an event and selectively removed species occurrence records containing the occurrence ID that they could be traced back to the event in which the collection took place.
Is that supposed to be "they could not be traced"? I;m sorry I could not make it to the meeting. I am having a hard time understanding the issue.
The group hopes that others who could not attend have insights into the issues and the descriptions. We felt John's comments would be very important because of his knowledge about the new GBIF model.
I hope the comments I made cover this, but I suspect it might require more interactive discussion to unravel completely.
On Tue, Jul 11, 2023 at 4:06 PM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW...
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA
One or several sweeps of a net containing a collection of insects
Camera trap – collection of images of mammals
Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams
Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel dschigel@gbif.org wrote:
Stuck in a GBIF meeting, not joining today
DS
*From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org *On Behalf Of *John Wieczorek *Sent:* Tuesday, 4 July, 2023 21:30 *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org *Cc:* wmh6@cornell.edu *Subject:* Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 yanina.sica@yale.edu wrote:
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/editthis week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ...
docs.google.com
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.*
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
Hi John
Thanks for your comments. We want the document to align with the unified model
I think we understand the importance of not being proscriptive. That was not our intent .
Your comment "I think the most common lowest-level Events would actually be Occurrences, at least in the Unified Model, where Occurrences are one type of Event. " was helpful for me. Let's see if others respond.
Having a zoom discussion may turn out to be the best way to make sure we all get to a common understanding..
Based on your previous email, you will be teaching at our scheduled meeting time this week but free the following week. Is that correct?
Thanks again for your help and insights
Rob
On Sun, Jul 16, 2023 at 1:34 PM John Wieczorek tuco@berkeley.edu wrote:
I'm sharing some comments inline. These are accompanied by comments and suggestions in the Event Hierarchy document.
On Thu, Jul 13, 2023 at 6:29 AM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear Humboldt Core TG
Below are notes from Wednesday. John, your asynchronous input would be especially helpful because we know you will not be able to attend the next meeting. If I have misinterpreted something or someone, please jump in and make a correction.
Thanks Rob
On Wednesday (2023/07/12), Steve, Peter, Zach, Wesley and I met and had fruitful discussions about points 6 and 7 in section 3.3 of the Properties of hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit. These are points John wrote to give guidance for applying the Humboldt Extension.
The discussion was around whether the phrasing was too prescriptive. Wesley asked “Could we come up with counter examples?”. Wesley will write a few sentences to encapsulate the issue. Peter felt the wording may not be necessary.
Peter showed us several inventories from BioCollect and described how they fit into the Humboldt extension model. The BioCollect model uses a survey template that can be applied repeated to a collection event and allows many kinds of observations and measurements to be made. The series of collection events together make a dataset. In Humboldt terms this dataset is a parent Event. To facilitate reuse each survey template is made up of a variety of observation and measurement protocols that can be bundled together as needed to make different survey templates.
Just to clarify, this doesn't present any problems to what we have defined in the Event Hierarchies document, correct?
Zach described how the Field Museum’s Rapid Inventories in which teams of biologists document biodiversity of different taxa ( plants, fishes, amphibians, reptiles, birds, and mammals) using a variety of methods at one site and within one timeframe https://www.rapidinventories.fieldmuseum.org/what-is-a-rapid-inventory are being represented as one Event at the highest level.
Again, just to clarify, this doesn't present any problems to what we have defined in the Event Hierarchies document, correct?
Tim added a comment to the document asking that we consider rewriting the definition of
He said “I think this definition might be improved. An inventory is a complete list of something, but the definition doesn't capture this, only referring to the activities used in the methodology. Perhaps something like:
"An inventory dataset accounts for all targeted organisms and measurements recorded while following a structured sampling protocol. Observations and measurements are captured in one or more dwc:Events that MAY..."
I commented in the text that it doesn't seem to me that completeness is a requirement, but that the rest seems reasonable.
This request is in line with our discussion on Wednesday.
Our discussion suggested it would be helpful to put in some kind of clarifying statement about what the lowest level Event might contain.
This is a good idea to be clarified with examples, as long as it is not proscriptive. I think the most common lowest-level Events would actually be Occurrences, at least in the Unified Model, where Occurrences are one type of Event.
My current understanding is that this lowest level might contain just a one zero to represent the event that occurred but that no occurrence was found or NA that a measurement was attempted but the measurement failed for some reason. On the complexity end of the spectrum of what an event could contain, Peter gave an example (see text at the bottom of the document) of an event pointing to an array of observations and measurements based on a survey template for Vegetation condition assessment. In a flattened (2D) database this would take 40 records (rows) to represent what was part of the event. Peter gave a second example about birds in which he added a screen shot from the BioCollect application. Here again multiple records are needed to contain the information in a flatten form.
This brings up the point of discussion in the meeting. Peter said that each event and each occurrence will have their own ids. This would mean if one flattered an event and selectively removed species occurrence records containing the occurrence ID that they could be traced back to the event in which the collection took place.
Is that supposed to be "they could not be traced"? I;m sorry I could not make it to the meeting. I am having a hard time understanding the issue.
The group hopes that others who could not attend have insights into the issues and the descriptions. We felt John's comments would be very important because of his knowledge about the new GBIF model.
I hope the comments I made cover this, but I suspect it might require more interactive discussion to unravel completely.
On Tue, Jul 11, 2023 at 4:06 PM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW...
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA
One or several sweeps of a net containing a collection of insects
Camera trap – collection of images of mammals
Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams
Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel dschigel@gbif.org wrote:
Stuck in a GBIF meeting, not joining today
DS
*From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org *On Behalf Of *John Wieczorek *Sent:* Tuesday, 4 July, 2023 21:30 *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org *Cc:* wmh6@cornell.edu *Subject:* Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 yanina.sica@yale.edu wrote:
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/editthis week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ...
docs.google.com
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.*
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
Yes, that is correct, I should be able to be free the following week.
On Sun, Jul 16, 2023 at 10:54 PM Rob Stevenson rdstevenson10@gmail.com wrote:
Hi John
Thanks for your comments. We want the document to align with the unified model
I think we understand the importance of not being proscriptive. That was not our intent .
Your comment "I think the most common lowest-level Events would actually be Occurrences, at least in the Unified Model, where Occurrences are one type of Event. " was helpful for me. Let's see if others respond.
Having a zoom discussion may turn out to be the best way to make sure we all get to a common understanding..
Based on your previous email, you will be teaching at our scheduled meeting time this week but free the following week. Is that correct?
Thanks again for your help and insights
Rob
On Sun, Jul 16, 2023 at 1:34 PM John Wieczorek tuco@berkeley.edu wrote:
I'm sharing some comments inline. These are accompanied by comments and suggestions in the Event Hierarchy document.
On Thu, Jul 13, 2023 at 6:29 AM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear Humboldt Core TG
Below are notes from Wednesday. John, your asynchronous input would be especially helpful because we know you will not be able to attend the next meeting. If I have misinterpreted something or someone, please jump in and make a correction.
Thanks Rob
On Wednesday (2023/07/12), Steve, Peter, Zach, Wesley and I met and had fruitful discussions about points 6 and 7 in section 3.3 of the Properties of hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit. These are points John wrote to give guidance for applying the Humboldt Extension.
The discussion was around whether the phrasing was too prescriptive. Wesley asked “Could we come up with counter examples?”. Wesley will write a few sentences to encapsulate the issue. Peter felt the wording may not be necessary.
Peter showed us several inventories from BioCollect and described how they fit into the Humboldt extension model. The BioCollect model uses a survey template that can be applied repeated to a collection event and allows many kinds of observations and measurements to be made. The series of collection events together make a dataset. In Humboldt terms this dataset is a parent Event. To facilitate reuse each survey template is made up of a variety of observation and measurement protocols that can be bundled together as needed to make different survey templates.
Just to clarify, this doesn't present any problems to what we have defined in the Event Hierarchies document, correct?
Zach described how the Field Museum’s Rapid Inventories in which teams of biologists document biodiversity of different taxa ( plants, fishes, amphibians, reptiles, birds, and mammals) using a variety of methods at one site and within one timeframe https://www.rapidinventories.fieldmuseum.org/what-is-a-rapid-inventory are being represented as one Event at the highest level.
Again, just to clarify, this doesn't present any problems to what we have defined in the Event Hierarchies document, correct?
Tim added a comment to the document asking that we consider rewriting the definition of
He said “I think this definition might be improved. An inventory is a complete list of something, but the definition doesn't capture this, only referring to the activities used in the methodology. Perhaps something like:
"An inventory dataset accounts for all targeted organisms and measurements recorded while following a structured sampling protocol. Observations and measurements are captured in one or more dwc:Events that MAY..."
I commented in the text that it doesn't seem to me that completeness is a requirement, but that the rest seems reasonable.
This request is in line with our discussion on Wednesday.
Our discussion suggested it would be helpful to put in some kind of clarifying statement about what the lowest level Event might contain.
This is a good idea to be clarified with examples, as long as it is not proscriptive. I think the most common lowest-level Events would actually be Occurrences, at least in the Unified Model, where Occurrences are one type of Event.
My current understanding is that this lowest level might contain just a one zero to represent the event that occurred but that no occurrence was found or NA that a measurement was attempted but the measurement failed for some reason. On the complexity end of the spectrum of what an event could contain, Peter gave an example (see text at the bottom of the document) of an event pointing to an array of observations and measurements based on a survey template for Vegetation condition assessment. In a flattened (2D) database this would take 40 records (rows) to represent what was part of the event. Peter gave a second example about birds in which he added a screen shot from the BioCollect application. Here again multiple records are needed to contain the information in a flatten form.
This brings up the point of discussion in the meeting. Peter said that each event and each occurrence will have their own ids. This would mean if one flattered an event and selectively removed species occurrence records containing the occurrence ID that they could be traced back to the event in which the collection took place.
Is that supposed to be "they could not be traced"? I;m sorry I could not make it to the meeting. I am having a hard time understanding the issue.
The group hopes that others who could not attend have insights into the issues and the descriptions. We felt John's comments would be very important because of his knowledge about the new GBIF model.
I hope the comments I made cover this, but I suspect it might require more interactive discussion to unravel completely.
On Tue, Jul 11, 2023 at 4:06 PM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW...
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA
One or several sweeps of a net containing a collection of insects
Camera trap – collection of images of mammals
Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams
Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel dschigel@gbif.org wrote:
Stuck in a GBIF meeting, not joining today
DS
*From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org *On Behalf Of *John Wieczorek *Sent:* Tuesday, 4 July, 2023 21:30 *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org *Cc:* wmh6@cornell.edu *Subject:* Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 yanina.sica@yale.edu wrote:
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/editthis week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ...
docs.google.com
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.*
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
Hi all!
I'm officially back from leave and will join the meeting on Wednesday. It looks like I have a lot to catch up on! I'll try to have a thorough look at the document by then, and look forward to helping however I can to continue pushing Humboldt forward.
Cheers, Kate
On Mon, Jul 17, 2023 at 3:56 AM John Wieczorek tuco@berkeley.edu wrote:
Yes, that is correct, I should be able to be free the following week.
On Sun, Jul 16, 2023 at 10:54 PM Rob Stevenson rdstevenson10@gmail.com wrote:
Hi John
Thanks for your comments. We want the document to align with the unified model
I think we understand the importance of not being proscriptive. That was not our intent .
Your comment "I think the most common lowest-level Events would actually be Occurrences, at least in the Unified Model, where Occurrences are one type of Event. " was helpful for me. Let's see if others respond.
Having a zoom discussion may turn out to be the best way to make sure we all get to a common understanding..
Based on your previous email, you will be teaching at our scheduled meeting time this week but free the following week. Is that correct?
Thanks again for your help and insights
Rob
On Sun, Jul 16, 2023 at 1:34 PM John Wieczorek tuco@berkeley.edu wrote:
I'm sharing some comments inline. These are accompanied by comments and suggestions in the Event Hierarchy document.
On Thu, Jul 13, 2023 at 6:29 AM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear Humboldt Core TG
Below are notes from Wednesday. John, your asynchronous input would be especially helpful because we know you will not be able to attend the next meeting. If I have misinterpreted something or someone, please jump in and make a correction.
Thanks Rob
On Wednesday (2023/07/12), Steve, Peter, Zach, Wesley and I met and had fruitful discussions about points 6 and 7 in section 3.3 of the Properties of hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit. These are points John wrote to give guidance for applying the Humboldt Extension.
The discussion was around whether the phrasing was too prescriptive. Wesley asked “Could we come up with counter examples?”. Wesley will write a few sentences to encapsulate the issue. Peter felt the wording may not be necessary.
Peter showed us several inventories from BioCollect and described how they fit into the Humboldt extension model. The BioCollect model uses a survey template that can be applied repeated to a collection event and allows many kinds of observations and measurements to be made. The series of collection events together make a dataset. In Humboldt terms this dataset is a parent Event. To facilitate reuse each survey template is made up of a variety of observation and measurement protocols that can be bundled together as needed to make different survey templates.
Just to clarify, this doesn't present any problems to what we have defined in the Event Hierarchies document, correct?
Zach described how the Field Museum’s Rapid Inventories in which teams of biologists document biodiversity of different taxa ( plants, fishes, amphibians, reptiles, birds, and mammals) using a variety of methods at one site and within one timeframe https://www.rapidinventories.fieldmuseum.org/what-is-a-rapid-inventory are being represented as one Event at the highest level.
Again, just to clarify, this doesn't present any problems to what we have defined in the Event Hierarchies document, correct?
Tim added a comment to the document asking that we consider rewriting the definition of
He said “I think this definition might be improved. An inventory is a complete list of something, but the definition doesn't capture this, only referring to the activities used in the methodology. Perhaps something like:
"An inventory dataset accounts for all targeted organisms and measurements recorded while following a structured sampling protocol. Observations and measurements are captured in one or more dwc:Events that MAY..."
I commented in the text that it doesn't seem to me that completeness is a requirement, but that the rest seems reasonable.
This request is in line with our discussion on Wednesday.
Our discussion suggested it would be helpful to put in some kind of clarifying statement about what the lowest level Event might contain.
This is a good idea to be clarified with examples, as long as it is not proscriptive. I think the most common lowest-level Events would actually be Occurrences, at least in the Unified Model, where Occurrences are one type of Event.
My current understanding is that this lowest level might contain just a one zero to represent the event that occurred but that no occurrence was found or NA that a measurement was attempted but the measurement failed for some reason. On the complexity end of the spectrum of what an event could contain, Peter gave an example (see text at the bottom of the document) of an event pointing to an array of observations and measurements based on a survey template for Vegetation condition assessment. In a flattened (2D) database this would take 40 records (rows) to represent what was part of the event. Peter gave a second example about birds in which he added a screen shot from the BioCollect application. Here again multiple records are needed to contain the information in a flatten form.
This brings up the point of discussion in the meeting. Peter said that each event and each occurrence will have their own ids. This would mean if one flattered an event and selectively removed species occurrence records containing the occurrence ID that they could be traced back to the event in which the collection took place.
Is that supposed to be "they could not be traced"? I;m sorry I could not make it to the meeting. I am having a hard time understanding the issue.
The group hopes that others who could not attend have insights into the issues and the descriptions. We felt John's comments would be very important because of his knowledge about the new GBIF model.
I hope the comments I made cover this, but I suspect it might require more interactive discussion to unravel completely.
On Tue, Jul 11, 2023 at 4:06 PM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW...
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA
One or several sweeps of a net containing a collection of insects
Camera trap – collection of images of mammals
Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams
Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel dschigel@gbif.org wrote:
Stuck in a GBIF meeting, not joining today
DS
*From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org *On Behalf Of *John Wieczorek *Sent:* Tuesday, 4 July, 2023 21:30 *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org *Cc:* wmh6@cornell.edu *Subject:* Re: [tdwg-humboldt] meeting this week
Hi folks,
I am giving the second module of a course on georeferencing tomorrow throughout the time of the Task Group call. I haven't mastered the two places at once thing, unfortunately.
Cheers,
John
On Tue, Jul 4, 2023 at 4:27 PM ys628 yanina.sica@yale.edu wrote:
Hi all,
Lets discuss the Hierarchical Document https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/editthis week!
With the TDWG 2023 rush, people might not have had time to review or work on it. If that is the case, we can have a rather short meeting to agree on the next steps.
See you!
Yani
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit
Properties of hierarchical Events in Humboldt Extension for ecological inventories Title: Properties of hierarchical Events in Humboldt Extension for ecological inventories Date version issued: 2023-xx-xx Date created: 2023-xx-xx Part of TDWG Standard: http://www.tdwg.org/standards/450 This ...
docs.google.com
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.*
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston _______________________________________________ tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
tdwg-humboldt mailing list tdwg-humboldt@lists.tdwg.org https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt
Welcome back, Kate!
On Tue, Jul 25, 2023 at 6:46 AM Kate Ingenloff kathryn.ingenloff@gmail.com wrote:
Hi all!
I'm officially back from leave and will join the meeting on Wednesday. It looks like I have a lot to catch up on! I'll try to have a thorough look at the document by then, and look forward to helping however I can to continue pushing Humboldt forward.
Cheers, Kate
On Mon, Jul 17, 2023 at 3:56 AM John Wieczorek tuco@berkeley.edu wrote:
Yes, that is correct, I should be able to be free the following week.
On Sun, Jul 16, 2023 at 10:54 PM Rob Stevenson rdstevenson10@gmail.com wrote:
Hi John
Thanks for your comments. We want the document to align with the unified model
I think we understand the importance of not being proscriptive. That was not our intent .
Your comment "I think the most common lowest-level Events would actually be Occurrences, at least in the Unified Model, where Occurrences are one type of Event. " was helpful for me. Let's see if others respond.
Having a zoom discussion may turn out to be the best way to make sure we all get to a common understanding..
Based on your previous email, you will be teaching at our scheduled meeting time this week but free the following week. Is that correct?
Thanks again for your help and insights
Rob
On Sun, Jul 16, 2023 at 1:34 PM John Wieczorek tuco@berkeley.edu wrote:
I'm sharing some comments inline. These are accompanied by comments and suggestions in the Event Hierarchy document.
On Thu, Jul 13, 2023 at 6:29 AM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear Humboldt Core TG
Below are notes from Wednesday. John, your asynchronous input would be especially helpful because we know you will not be able to attend the next meeting. If I have misinterpreted something or someone, please jump in and make a correction.
Thanks Rob
On Wednesday (2023/07/12), Steve, Peter, Zach, Wesley and I met and had fruitful discussions about points 6 and 7 in section 3.3 of the Properties of hierarchical Events in Humboldt Extension for ecological inventories https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit. These are points John wrote to give guidance for applying the Humboldt Extension.
The discussion was around whether the phrasing was too prescriptive. Wesley asked “Could we come up with counter examples?”. Wesley will write a few sentences to encapsulate the issue. Peter felt the wording may not be necessary.
Peter showed us several inventories from BioCollect and described how they fit into the Humboldt extension model. The BioCollect model uses a survey template that can be applied repeated to a collection event and allows many kinds of observations and measurements to be made. The series of collection events together make a dataset. In Humboldt terms this dataset is a parent Event. To facilitate reuse each survey template is made up of a variety of observation and measurement protocols that can be bundled together as needed to make different survey templates.
Just to clarify, this doesn't present any problems to what we have defined in the Event Hierarchies document, correct?
Zach described how the Field Museum’s Rapid Inventories in which teams of biologists document biodiversity of different taxa ( plants, fishes, amphibians, reptiles, birds, and mammals) using a variety of methods at one site and within one timeframe https://www.rapidinventories.fieldmuseum.org/what-is-a-rapid-inventory are being represented as one Event at the highest level.
Again, just to clarify, this doesn't present any problems to what we have defined in the Event Hierarchies document, correct?
Tim added a comment to the document asking that we consider rewriting the definition of
He said “I think this definition might be improved. An inventory is a complete list of something, but the definition doesn't capture this, only referring to the activities used in the methodology. Perhaps something like:
"An inventory dataset accounts for all targeted organisms and measurements recorded while following a structured sampling protocol. Observations and measurements are captured in one or more dwc:Events that MAY..."
I commented in the text that it doesn't seem to me that completeness is a requirement, but that the rest seems reasonable.
This request is in line with our discussion on Wednesday.
Our discussion suggested it would be helpful to put in some kind of clarifying statement about what the lowest level Event might contain.
This is a good idea to be clarified with examples, as long as it is not proscriptive. I think the most common lowest-level Events would actually be Occurrences, at least in the Unified Model, where Occurrences are one type of Event.
My current understanding is that this lowest level might contain just a one zero to represent the event that occurred but that no occurrence was found or NA that a measurement was attempted but the measurement failed for some reason. On the complexity end of the spectrum of what an event could contain, Peter gave an example (see text at the bottom of the document) of an event pointing to an array of observations and measurements based on a survey template for Vegetation condition assessment. In a flattened (2D) database this would take 40 records (rows) to represent what was part of the event. Peter gave a second example about birds in which he added a screen shot from the BioCollect application. Here again multiple records are needed to contain the information in a flatten form.
This brings up the point of discussion in the meeting. Peter said that each event and each occurrence will have their own ids. This would mean if one flattered an event and selectively removed species occurrence records containing the occurrence ID that they could be traced back to the event in which the collection took place.
Is that supposed to be "they could not be traced"? I;m sorry I could not make it to the meeting. I am having a hard time understanding the issue.
The group hopes that others who could not attend have insights into the issues and the descriptions. We felt John's comments would be very important because of his knowledge about the new GBIF model.
I hope the comments I made cover this, but I suspect it might require more interactive discussion to unravel completely.
On Tue, Jul 11, 2023 at 4:06 PM Rob Stevenson rdstevenson10@gmail.com wrote:
Dear All, I wrote up some ideas. It proved more difficult than I thought and I am not sure I captured the issue at the core of the discussion - How to deal with the lowest level of the event hierarchy
Below is the text but it is also at the bottom of our document here
https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gW...
Currently the vast majority of records in the GBIF archive contain an observation of one or more individuals of a single taxon. Many additional fields in the record, based on the Darwin Core, provide context for the observation including the observation type, the time and place of observation, the observer, etc. At the present time, however, the metadata do not provide context about whether or not an observation is part of a systematic set of observations, herein called a survey. A survey is an approach based on the idea of statistical sampling, whereby an observer is unable to measure an entire population but instead focuses on a subset of the population to make inferences about the entire population.
The added scientific value of the survey framework, over just a collection of unrelate observations indicating present only, is that a scientist can make inferences about how common or rare a taxon might be (its status) and over time, measure trends. The basic idea of a survey is intuitive: the more you look, the more you will find. In the fisheries literature this idea is called “catch per unit effort”.
The goal of the Humboldt extension is to accurately describe a survey and its often hierarchical nature. Whereas an observation record is characterized by general sense of the observation approach (Basis of Record), a time and a location, a survey has a much more detailed description of the observation technique(s), and also includes the number of sampling units employed, a time or time interval (start time and duration), and a measure of the spatial extent over which the survey was conducted.
A sampling unit, the finest measurement resolution of a survey, encompasses a variety of ways of looking for species. It might include:
A physical sample such as a leaf or a water sample containing molecules of DNA
One or several sweeps of a net containing a collection of insects
Camera trap – collection of images of mammals
Quadrat – estimating the percentage of space or numbers of space occupying organisms such as plants or clams
Bird checklist – list of species of birds observed from a fixed-point
Special considerations arise at the sampling unit level. First a measurement can detect no individuals or space occupied. In these cases the data need to reflect this fact with recording 0 for the observation. Second a measurement might be more than just a number or percentage. It might a be compound structure that includes the flowering stage of each plant in a quadrat or the length and body mass of each insect in the sweep net sample or the location of each bird along a transect.
On Wed, Jul 5, 2023 at 8:08 AM Dmitry Schigel dschigel@gbif.org wrote:
> Stuck in a GBIF meeting, not joining today > > DS > > > > *From:* tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org *On > Behalf Of *John Wieczorek > *Sent:* Tuesday, 4 July, 2023 21:30 > *To:* Humboldt Core TG tdwg-humboldt@lists.tdwg.org > *Cc:* wmh6@cornell.edu > *Subject:* Re: [tdwg-humboldt] meeting this week > > > > Hi folks, > > > > I am giving the second module of a course on georeferencing tomorrow > throughout the time of the Task Group call. I haven't mastered the two > places at once thing, unfortunately. > > > > Cheers, > > > > John > > > > On Tue, Jul 4, 2023 at 4:27 PM ys628 yanina.sica@yale.edu wrote: > > Hi all, > > > > Lets discuss the Hierarchical Document > https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/editthis > week! > > > > With the TDWG 2023 rush, people might not have had time to review or > work on it. If that is the case, we can have a rather short meeting to > agree on the next steps. > > > > See you! > > > > Yani > > > https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit > > Hierarchical Events in Humboldt Extension for ecological inventories > https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit > > Properties of hierarchical Events in Humboldt Extension for > ecological inventories Title: Properties of hierarchical Events in Humboldt > Extension for ecological inventories Date version issued: 2023-xx-xx Date > created: 2023-xx-xx Part of TDWG Standard: > http://www.tdwg.org/standards/450 This ... > > docs.google.com > > > > > > 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.* > > _______________________________________________ > tdwg-humboldt mailing list > tdwg-humboldt@lists.tdwg.org > https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt > > _______________________________________________ > tdwg-humboldt mailing list > tdwg-humboldt@lists.tdwg.org > https://lists.tdwg.org/mailman/listinfo/tdwg-humboldt >
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
-- Robert D Stevenson Associate Professor Department of Biology UMass Boston
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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
participants (8)
-
Anahita Kazem -
Brenton, Peter (NCMI, Black Mountain) -
Dmitry Schigel -
John Wieczorek -
Kate Ingenloff -
Rob Stevenson -
Yi Ming Gan -
ys628