BROKE-WEST dataset mapped to ratified Humboldt terms + Questions
Hi all,
I have finally mapped the BROKE-WEST dataset to the ratified Humboldt terms. I mapped it in a different way after chatting with John last year. I am trying to explore if using combinations of target scope per row in Humboldt table will make more sense instead of using pipe separated values (see below):
[Screenshot 2024-05-14 at 14.17.42.png]
I don’t know if I am understanding things well.
I feel it is a little confusing - each row in the Humboldt extension file seems to be conflating the Scopes and Event. For example the value of hasNonTargetTaxa for each row above has to check whether Taxon in Occurrences exist in ALL targetTaxonomicScope where eventID == “BROKE_WEST_RMT_001” (multiple records in Humboldt table) …
I also have multiple questions when performing this mapping which I documented in the Rmarkdown herehttps://raw.githack.com/biodiversity-aq/humboldt-for-eco-survey-data/main/src/create-humboldt-ext.html. Overall, I find it very challenging and complicated (took me 2 full days with the help of chatgpt) to write the code to fill in the boolean values (is___, has____) …
I would love a third pair of eyes to help me to look at this. Is anyone willing to look at my work with me please? I am fine with walking you through at our usual meeting times.
GitHub repo: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data This is the only script that I worked on these two weeks: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/sr... Humboldt Extension generated by the script: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/ou...
@John, I saw that the new data modelhttps://docs.google.com/document/d/1eGD69E-KzqdOcjh637iPrp1gv_J55CM2VPAjD1PSu_w/edit?usp=sharing is updated - is there some instructions available somewhere where I can test the Publishing and Conceptual model please? Thank you so much!!
Cheers Ming
https://www.naturalsciences.be[clip_image002.png] Yi-Ming Gan
Institute of Natural Sciences Operational Directorate Natural Environment
Data manager - Antarctic Biodiversity Portal
T +32 (0)2 627 42 77
Rue Vautier 29 Brussels 1000 Belgium
Hi all,
I wanted to send this again because I did not get the opportunity to ask my questions nor did I get any answers (except the GitHub issuehttps://github.com/tdwg/hc/issues/103) and I have put in ample amount of time in this. My questions here maybe relevant for the publishing guide that Kate is working on. OBIS underwent some restructuring earlier this year and there is an opportunity for me to present this to the OBIS Data Coordination Group in the future.
I understand the importance of the paper. However, to be fair, I sent this email since mid may … can I at least have a meeting to ask these questions please? Thank you.
Sincerely Ming
Begin forwarded message:
From: Yi-Ming Gan ymgan@naturalsciences.be Subject: BROKE-WEST dataset mapped to ratified Humboldt terms + Questions Date: 14 May 2024 at 15:45:55 CEST To: Humboldt Core TG tdwg-humboldt@lists.tdwg.org
Hi all,
I have finally mapped the BROKE-WEST dataset to the ratified Humboldt terms. I mapped it in a different way after chatting with John last year. I am trying to explore if using combinations of target scope per row in Humboldt table will make more sense instead of using pipe separated values (see below):
[Screenshot 2024-05-14 at 14.17.42.png]
I don’t know if I am understanding things well.
I feel it is a little confusing - each row in the Humboldt extension file seems to be conflating the Scopes and Event. For example the value of hasNonTargetTaxa for each row above has to check whether Taxon in Occurrences exist in ALL targetTaxonomicScope where eventID == “BROKE_WEST_RMT_001” (multiple records in Humboldt table) …
I also have multiple questions when performing this mapping which I documented in the Rmarkdown herehttps://raw.githack.com/biodiversity-aq/humboldt-for-eco-survey-data/main/src/create-humboldt-ext.html. Overall, I find it very challenging and complicated (took me 2 full days with the help of chatgpt) to write the code to fill in the boolean values (is___, has____) …
I would love a third pair of eyes to help me to look at this. Is anyone willing to look at my work with me please? I am fine with walking you through at our usual meeting times.
GitHub repo: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data This is the only script that I worked on these two weeks: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/sr... Humboldt Extension generated by the script: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/ou...
@John, I saw that the new data modelhttps://docs.google.com/document/d/1eGD69E-KzqdOcjh637iPrp1gv_J55CM2VPAjD1PSu_w/edit?usp=sharing is updated - is there some instructions available somewhere where I can test the Publishing and Conceptual model please? Thank you so much!!
Cheers Ming
https://www.naturalsciences.be/[clip_image002.png] Yi-Ming Gan
Institute of Natural Sciences Operational Directorate Natural Environment
Data manager - Antarctic Biodiversity Portal
T +32 (0)2 627 42 77
Rue Vautier 29 Brussels 1000 Belgium
Hi Ming, Sorry for the lack of response. I am just getting back to Humboldt things this week. Would you like to meet tomorrow (maybe 4pm) or on Monday (in e afternoon) to discuss this. I may need an intro to the issue. Cheers,
Yani
On Wed, Jul 10, 2024 at 2:58 PM Yi Ming Gan ymgan@naturalsciences.be wrote:
Hi all,
I wanted to send this again because I did not get the opportunity to ask my questions nor did I get any answers (except the GitHub issue https://github.com/tdwg/hc/issues/103) and I have put in ample amount of time in this. My questions here maybe relevant for the publishing guide that Kate is working on. OBIS underwent some restructuring earlier this year and there is an opportunity for me to present this to the OBIS Data Coordination Group in the future.
I understand the importance of the paper. However, to be fair, I sent this email since *mid may* … can I at least have a meeting to ask these questions please? Thank you.
Sincerely Ming
Begin forwarded message:
*From: *Yi-Ming Gan ymgan@naturalsciences.be *Subject: **BROKE-WEST dataset mapped to ratified Humboldt terms + Questions* *Date: *14 May 2024 at 15:45:55 CEST *To: *Humboldt Core TG tdwg-humboldt@lists.tdwg.org
Hi all,
I have finally mapped the BROKE-WEST dataset to the ratified Humboldt terms. I mapped it in a different way after chatting with John last year. I am trying to explore if using combinations of target scope per row in Humboldt table will make more sense instead of using pipe separated values (see below):
[image: Screenshot 2024-05-14 at 14.17.42.png]
I don’t know if I am understanding things well.
I feel it is a little confusing - each row in the Humboldt extension file seems to be conflating the Scopes and Event. For example the value of hasNonTargetTaxa for each row above has to check whether Taxon in Occurrences exist in ALL targetTaxonomicScope where eventID == “BROKE_WEST_RMT_001” (multiple records in Humboldt table) …
I also have multiple questions when performing this mapping which I documented in the Rmarkdown here https://raw.githack.com/biodiversity-aq/humboldt-for-eco-survey-data/main/src/create-humboldt-ext.html . Overall, I find it very challenging and complicated (took me 2 full days with the help of chatgpt) to write the code to fill in the boolean values (is___, has____) …
I would love a third pair of eyes to help me to look at this. Is anyone willing to look at my work with me please? I am fine with walking you through at our usual meeting times.
GitHub repo: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data This is the only script that I worked on these two weeks: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/sr...
Humboldt Extension generated by the script: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/ou...
@John, I saw that the new data model https://docs.google.com/document/d/1eGD69E-KzqdOcjh637iPrp1gv_J55CM2VPAjD1PSu_w/edit?usp=sharing is updated - is there some instructions available somewhere where I can test the Publishing and Conceptual model please? Thank you so much!!
Cheers Ming
https://www.naturalsciences.be/[image: clip_image002.png]
*Yi-Ming Gan Institute of Natural Sciences* Operational Directorate Natural Environment
Data manager - Antarctic Biodiversity Portal
T +32 (0)2 627 42 77
Rue Vautier 29 Brussels 1000 Belgium
tdwg-humboldt mailing list -- tdwg-humboldt@lists.tdwg.org To unsubscribe send an email to tdwg-humboldt-leave@lists.tdwg.org
Hi Yani,
Thank you so much! Yes today at 4pm works for me, I appreciate it!
Cheers Ming
On 11 Jul 2024, at 20:49, Yanina Sica yanina.sica@gmail.com wrote:
Hi Ming, Sorry for the lack of response. I am just getting back to Humboldt things this week. Would you like to meet tomorrow (maybe 4pm) or on Monday (in e afternoon) to discuss this. I may need an intro to the issue. Cheers,
Yani
On Wed, Jul 10, 2024 at 2:58 PM Yi Ming Gan <ymgan@naturalsciences.bemailto:ymgan@naturalsciences.be> wrote: Hi all,
I wanted to send this again because I did not get the opportunity to ask my questions nor did I get any answers (except the GitHub issuehttps://github.com/tdwg/hc/issues/103) and I have put in ample amount of time in this. My questions here maybe relevant for the publishing guide that Kate is working on. OBIS underwent some restructuring earlier this year and there is an opportunity for me to present this to the OBIS Data Coordination Group in the future.
I understand the importance of the paper. However, to be fair, I sent this email since mid may … can I at least have a meeting to ask these questions please? Thank you.
Sincerely Ming
Begin forwarded message:
From: Yi-Ming Gan <ymgan@naturalsciences.bemailto:ymgan@naturalsciences.be> Subject: BROKE-WEST dataset mapped to ratified Humboldt terms + Questions Date: 14 May 2024 at 15:45:55 CEST To: Humboldt Core TG <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org>
Hi all,
I have finally mapped the BROKE-WEST dataset to the ratified Humboldt terms. I mapped it in a different way after chatting with John last year. I am trying to explore if using combinations of target scope per row in Humboldt table will make more sense instead of using pipe separated values (see below):
<Screenshot 2024-05-14 at 14.17.42.png>
I don’t know if I am understanding things well.
I feel it is a little confusing - each row in the Humboldt extension file seems to be conflating the Scopes and Event. For example the value of hasNonTargetTaxa for each row above has to check whether Taxon in Occurrences exist in ALL targetTaxonomicScope where eventID == “BROKE_WEST_RMT_001” (multiple records in Humboldt table) …
I also have multiple questions when performing this mapping which I documented in the Rmarkdown herehttps://raw.githack.com/biodiversity-aq/humboldt-for-eco-survey-data/main/src/create-humboldt-ext.html. Overall, I find it very challenging and complicated (took me 2 full days with the help of chatgpt) to write the code to fill in the boolean values (is___, has____) …
I would love a third pair of eyes to help me to look at this. Is anyone willing to look at my work with me please? I am fine with walking you through at our usual meeting times.
GitHub repo: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data This is the only script that I worked on these two weeks: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/sr... Humboldt Extension generated by the script: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/ou...
@John, I saw that the new data modelhttps://docs.google.com/document/d/1eGD69E-KzqdOcjh637iPrp1gv_J55CM2VPAjD1PSu_w/edit?usp=sharing is updated - is there some instructions available somewhere where I can test the Publishing and Conceptual model please? Thank you so much!!
Cheers Ming
https://www.naturalsciences.be/<clip_image002.png> Yi-Ming Gan
Institute of Natural Sciences Operational Directorate Natural Environment
Data manager - Antarctic Biodiversity Portal
T +32 (0)2 627 42 77
Rue Vautier 29 Brussels 1000 Belgium
_______________________________________________ tdwg-humboldt mailing list -- tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org To unsubscribe send an email to tdwg-humboldt-leave@lists.tdwg.orgmailto:tdwg-humboldt-leave@lists.tdwg.org _______________________________________________ tdwg-humboldt mailing list -- tdwg-humboldt@lists.tdwg.org To unsubscribe send an email to tdwg-humboldt-leave@lists.tdwg.org
Has 4pm already passed for you two? I'm in a BCON meeting for an hour and a half longer, but interested in the discussion.
On Fri, Jul 12, 2024 at 2:35 AM Yi Ming Gan ymgan@naturalsciences.be wrote:
Hi Yani,
Thank you so much! Yes today at 4pm works for me, I appreciate it!
Cheers Ming
On 11 Jul 2024, at 20:49, Yanina Sica yanina.sica@gmail.com wrote:
Hi Ming, Sorry for the lack of response. I am just getting back to Humboldt things this week. Would you like to meet tomorrow (maybe 4pm) or on Monday (in e afternoon) to discuss this. I may need an intro to the issue. Cheers,
Yani
On Wed, Jul 10, 2024 at 2:58 PM Yi Ming Gan ymgan@naturalsciences.be wrote:
Hi all,
I wanted to send this again because I did not get the opportunity to ask my questions nor did I get any answers (except the GitHub issue https://github.com/tdwg/hc/issues/103) and I have put in ample amount of time in this. My questions here maybe relevant for the publishing guide that Kate is working on. OBIS underwent some restructuring earlier this year and there is an opportunity for me to present this to the OBIS Data Coordination Group in the future.
I understand the importance of the paper. However, to be fair, I sent this email since *mid may* … can I at least have a meeting to ask these questions please? Thank you.
Sincerely Ming
Begin forwarded message:
*From: *Yi-Ming Gan ymgan@naturalsciences.be *Subject: **BROKE-WEST dataset mapped to ratified Humboldt terms + Questions* *Date: *14 May 2024 at 15:45:55 CEST *To: *Humboldt Core TG tdwg-humboldt@lists.tdwg.org
Hi all,
I have finally mapped the BROKE-WEST dataset to the ratified Humboldt terms. I mapped it in a different way after chatting with John last year. I am trying to explore if using combinations of target scope per row in Humboldt table will make more sense instead of using pipe separated values (see below):
<Screenshot 2024-05-14 at 14.17.42.png>
I don’t know if I am understanding things well.
I feel it is a little confusing - each row in the Humboldt extension file seems to be conflating the Scopes and Event. For example the value of hasNonTargetTaxa for each row above has to check whether Taxon in Occurrences exist in ALL targetTaxonomicScope where eventID == “BROKE_WEST_RMT_001” (multiple records in Humboldt table) …
I also have multiple questions when performing this mapping which I documented in the Rmarkdown here https://raw.githack.com/biodiversity-aq/humboldt-for-eco-survey-data/main/src/create-humboldt-ext.html . Overall, I find it very challenging and complicated (took me 2 full days with the help of chatgpt) to write the code to fill in the boolean values (is___, has____) …
I would love a third pair of eyes to help me to look at this. Is anyone willing to look at my work with me please? I am fine with walking you through at our usual meeting times.
GitHub repo: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data This is the only script that I worked on these two weeks: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/sr...
Humboldt Extension generated by the script: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/ou...
@John, I saw that the new data model https://docs.google.com/document/d/1eGD69E-KzqdOcjh637iPrp1gv_J55CM2VPAjD1PSu_w/edit?usp=sharing is updated - is there some instructions available somewhere where I can test the Publishing and Conceptual model please? Thank you so much!!
Cheers Ming
https://www.naturalsciences.be/<clip_image002.png>
*Yi-Ming Gan Institute of Natural Sciences* Operational Directorate Natural Environment
Data manager - Antarctic Biodiversity Portal
T +32 (0)2 627 42 77
Rue Vautier 29 Brussels 1000 Belgium
tdwg-humboldt mailing list -- tdwg-humboldt@lists.tdwg.org To unsubscribe send an email to tdwg-humboldt-leave@lists.tdwg.org
tdwg-humboldt mailing list -- tdwg-humboldt@lists.tdwg.org To unsubscribe send an email to tdwg-humboldt-leave@lists.tdwg.org
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Sorry John, we already met. But we put our thoughts in the GitHub issue https://github.com/tdwg/hc/issues/103! Happy to talk more about this, maybe we can dedicate a couple of minutes to this next Wednesday. Cheers, Yani
On Fri, Jul 12, 2024 at 5:27 PM John Wieczorek gtuco.btuco@gmail.com wrote:
Has 4pm already passed for you two? I'm in a BCON meeting for an hour and a half longer, but interested in the discussion.
On Fri, Jul 12, 2024 at 2:35 AM Yi Ming Gan ymgan@naturalsciences.be wrote:
Hi Yani,
Thank you so much! Yes today at 4pm works for me, I appreciate it!
Cheers Ming
On 11 Jul 2024, at 20:49, Yanina Sica yanina.sica@gmail.com wrote:
Hi Ming, Sorry for the lack of response. I am just getting back to Humboldt things this week. Would you like to meet tomorrow (maybe 4pm) or on Monday (in e afternoon) to discuss this. I may need an intro to the issue. Cheers,
Yani
On Wed, Jul 10, 2024 at 2:58 PM Yi Ming Gan ymgan@naturalsciences.be wrote:
Hi all,
I wanted to send this again because I did not get the opportunity to ask my questions nor did I get any answers (except the GitHub issue https://github.com/tdwg/hc/issues/103) and I have put in ample amount of time in this. My questions here maybe relevant for the publishing guide that Kate is working on. OBIS underwent some restructuring earlier this year and there is an opportunity for me to present this to the OBIS Data Coordination Group in the future.
I understand the importance of the paper. However, to be fair, I sent this email since *mid may* … can I at least have a meeting to ask these questions please? Thank you.
Sincerely Ming
Begin forwarded message:
*From: *Yi-Ming Gan ymgan@naturalsciences.be *Subject: **BROKE-WEST dataset mapped to ratified Humboldt terms + Questions* *Date: *14 May 2024 at 15:45:55 CEST *To: *Humboldt Core TG tdwg-humboldt@lists.tdwg.org
Hi all,
I have finally mapped the BROKE-WEST dataset to the ratified Humboldt terms. I mapped it in a different way after chatting with John last year. I am trying to explore if using combinations of target scope per row in Humboldt table will make more sense instead of using pipe separated values (see below):
<Screenshot 2024-05-14 at 14.17.42.png>
I don’t know if I am understanding things well.
I feel it is a little confusing - each row in the Humboldt extension file seems to be conflating the Scopes and Event. For example the value of hasNonTargetTaxa for each row above has to check whether Taxon in Occurrences exist in ALL targetTaxonomicScope where eventID == “BROKE_WEST_RMT_001” (multiple records in Humboldt table) …
I also have multiple questions when performing this mapping which I documented in the Rmarkdown here https://raw.githack.com/biodiversity-aq/humboldt-for-eco-survey-data/main/src/create-humboldt-ext.html . Overall, I find it very challenging and complicated (took me 2 full days with the help of chatgpt) to write the code to fill in the boolean values (is___, has____) …
I would love a third pair of eyes to help me to look at this. Is anyone willing to look at my work with me please? I am fine with walking you through at our usual meeting times.
GitHub repo: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data This is the only script that I worked on these two weeks: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/sr...
Humboldt Extension generated by the script: https://github.com/biodiversity-aq/humboldt-for-eco-survey-data/blob/main/ou...
@John, I saw that the new data model https://docs.google.com/document/d/1eGD69E-KzqdOcjh637iPrp1gv_J55CM2VPAjD1PSu_w/edit?usp=sharing is updated - is there some instructions available somewhere where I can test the Publishing and Conceptual model please? Thank you so much!!
Cheers Ming
https://www.naturalsciences.be/<clip_image002.png>
*Yi-Ming Gan Institute of Natural Sciences* Operational Directorate Natural Environment
Data manager - Antarctic Biodiversity Portal
T +32 (0)2 627 42 77
Rue Vautier 29 Brussels 1000 Belgium
tdwg-humboldt mailing list -- tdwg-humboldt@lists.tdwg.org To unsubscribe send an email to tdwg-humboldt-leave@lists.tdwg.org
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participants (3)
-
John Wieczorek -
Yanina Sica -
Yi Ming Gan