[tdwg-humboldt] Humboldt next steps!

Wed Aug 2 10:16:03 UTC 2023

Hi all,

Thank you Debbie and John!

I am almost done with the mapping of the dataset with the updated list of terms, but I need a bit more time because it’s very difficult to populate certain fields (e.g. eco:isLifeStageScopeComplete) due to it being at the dwc:Event level (limitation of star schema). I am also writing script to infer non-detection for presence-only data using Humboldt Extension for this dataset. This is still work in progress. I have what I need and logic in mind, but my R is rusty. I am doing this because it is otherwise difficult for me to see how I should populate the fields (and what not to do) in order to be able to interpret the data (make inference of non-detection). 

With this exercise, I came to a conclusion that all of the Humboldt terms related to scope and completeness MUST be populated at the lowest level of dwc:Event in order to infer non-detection within a dataset. The results of the exercise and best practices, I believe, is secondary and not the most important for the ratification process, but I hope my conclusion above could help to shape the Hierarchical Events document <https://docs.google.com/document/d/1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE/edit?usp=sharing>.

Regarding the __ID fields that Debbie mentioned, I formatted the table with dwciri: prefix of the Humboldt terms “pretending” that this feature is available on IPT: https://github.com/gbif/ipt/issues/1947 
This is especially useful for the scope terms (eco:targetTaxonomicScope, eco:targetLifeStageScope) This leads to my question - how to deal with list/array value for terms like dwciri:samplingPerformedBy? I noted that Ben Norton worked on a white paper about complex values/arrays (https://github.com/gbif/ipt/issues/1947#issuecomment-1447101388), wonder if anyone knows what happened? 

Cheers
Ming

> On 31 Jul 2023, at 16:52, Paul, Deborah <dlpaul at illinois.edu> wrote:
> 
> Greetings John, et al.
> 
> Stepping in gently here (having not been at all these conversations). So please feel free to ignore this if just too off-basae.
> 
> I'm wondering why not add 
> 
> Identification,identifiedByID? to
> 
> Identification,identifiedBy
> Identification,identificationReferences
> 
> And coherently then, 
> 
> Sampling Effort,samplingPerformedByID
> to go with 
> Sampling Effort,samplingPerformedBy
> 
> Same for Sampling and Vouchers?
> 
> Material Collected,hasVouchers
> Material Collected,voucherInstitutions
> 
> Who vouchered? (recordedBy, recordedByID?)
> 
> And, for all of the above information outlined in the XML list of groups and related terms, where does the information go about who did this sampling, as part of what project? grant numbers? etc. The EML file? (Where's the metadata?). Thanks for clueing me in.
> 
> Exciting to see the work getting to the place where it can be implemented 🙂
> 
> Debbie
> From: tdwg-humboldt <tdwg-humboldt-bounces at lists.tdwg.org> on behalf of John Wieczorek <tuco at berkeley.edu>
> Sent: Monday, July 31, 2023 9:18 AM
> To: Humboldt Core TG <tdwg-humboldt at lists.tdwg.org>
> Cc: Wesley M. Hochachka <wmh6 at cornell.edu>; tdwg-humboldt <tdwg-humboldt-bounces at lists.tdwg.org>
> Subject: Re: [tdwg-humboldt] Humboldt next steps!
>  
> Hi folks,
> 
> I hope the listserv is working.
> 
> I have made the necessary edits to the eco: terms in preparation for a new extension XML file. I set up the script so that the extension XML can be generated from the term_versions.csv file (the canonical management file where the term versions are archived). The script allows the XML file to contain sections in which to group terms so that they can be seen and mapped together in the IPT. I have proposed some new group names and rearranged the terms in them in the hope that it might make the mapping process flow better in the IPT.  The names of the group, the order of groups and the order of terms within the groups can all be set easily in a configuration file separate from the term_versions.csv file. It would be nice if we could decide as a Task Group on these groupings and orders before making a release. It will help people assess the proposal too, I believe. The groupings and term order I propose follow:
> 
> group,term
> Site,siteCount
> Site,siteNestingDescription
> Site,verbatimSiteDescriptions
> Site,verbatimSiteNames
> Site,geospatialScopeAreaInSquareKilometers
> Site,totalAreaSampledInSquareKilometers
> Site,reportedWeather
> Site,reportedExtremeConditions
> 
> Habitat Scope,targetHabitatScope
> Habitat Scope,excludedHabitatScope
> 
> Temporal Scope,eventDuration
> Temporal Scope,eventDurationUnit
> 
> Taxonomic Scope,targetTaxonomicScope
> Taxonomic Scope,excludedTaxonomicScope
> Taxonomic Scope,taxonCompletenessReported
> Taxonomic Scope,taxonCompletenessProtocols
> Taxonomic Scope,isTaxonomicScopeComplete
> Taxonomic Scope,isAbsenceReported
> Taxonomic Scope,absentTaxa
> 
> Organismal Scope,targetLifeStageScope
> Organismal Scope,excludedLifeStageScope
> Organismal Scope,isLifeStageScopeComplete
> Organismal Scope,targetDegreeOfEstablishmentScope
> Organismal Scope,excludedDegreeOfEstablishmentScope
> Organismal Scope,isDegreeOfEstablishmentScopeComplete
> Organismal Scope,targetGrowthFormScope
> Organismal Scope,excludedGrowthFormScope
> Organismal Scope,isGrowthFormScopeComplete
> 
> Identification,identifiedBy
> Identification,identificationReferences
> 
> Methodology Description,compilationType
> Methodology Description,compilationSourceTypes
> Methodology Description,inventoryTypes
> Methodology Description,protocolNames
> Methodology Description,protocolDescription
> Methodology Description,protocolReferences
> Methodology Description,isAbundanceReported
> Methodology Description,isAbundanceCapReported
> Methodology Description,abundanceCap
> Methodology Description,isVegetationCoverReported
> Methodology Description,isLeastSpecificTargetCategoryQuantityInclusive
> 
> Material Collected,hasVouchers
> Material Collected,voucherInstitutions
> Material Collected,hasMaterialSamples
> Material Collected,materialSampleTypes
> 
> Sampling Effort,samplingPerformedBy
> Sampling Effort,isSamplingEffortReported
> Sampling Effort,samplingEffortProtocol
> Sampling Effort,samplingEffortValue
> Sampling Effort,samplingEffortUnit
> 
> The original groups and term order were:
> 
> General Dataset & Identification,samplingPerformedBy
> General Dataset & Identification,identificationReferences
> General Dataset & Identification,identifiedBy
> 
> Geospatial Scope & Habitat,geospatialScopeAreaInSquareKilometers
> Geospatial Scope & Habitat,totalAreaSampledInSquareKilometers
> Geospatial Scope & Habitat,siteNestingDescription
> Geospatial Scope & Habitat,siteCount
> Geospatial Scope & Habitat,verbatimSiteDescriptions
> Geospatial Scope & Habitat,verbatimSiteNames
> Geospatial Scope & Habitat,targetHabitatScope
> Geospatial Scope & Habitat,excludedHabitatScope
> Geospatial Scope & Habitat,reportedWeather
> Geospatial Scope & Habitat,reportedExtremeConditions
> 
> Temporal Scope,eventDuration
> Temporal Scope,eventDurationUnit
> 
> Taxonomic & organismal Scope,targetTaxonomicScope
> Taxonomic & organismal Scope,targetDegreeOfEstablishmentScope
> Taxonomic & organismal Scope,targetGrowthFormScope
> Taxonomic & organismal Scope,targetLifeStageScope
> Taxonomic & organismal Scope,excludedTaxonomicScope
> Taxonomic & organismal Scope,excludedDegreeOfEstablishmentScope
> Taxonomic & organismal Scope,excludedGrowthFormScope
> Taxonomic & organismal Scope,excludedLifeStageScope
> 
> Methodology Description,compilationType
> Methodology Description,compilationSourceTypes
> Methodology Description,inventoryTypes
> Methodology Description,protocolNames
> Methodology Description,protocolDescription
> Methodology Description,protocolReferences
> Methodology Description,isAbundanceReported
> Methodology Description,isAbundanceCapReported
> Methodology Description,abundanceCap
> Methodology Description,isVegetationCoverReported
> Methodology Description,hasVouchers
> Methodology Description,voucherInstitutions
> Methodology Description,hasMaterialSamples
> Methodology Description,materialSampleTypes
> Methodology Description,isLeastSpecificTargetCategoryQuantityInclusive
> 
> Completeness & Effort,isSamplingEffortReported
> Completeness & Effort,samplingEffortProtocol
> Completeness & Effort,samplingEffortValue
> Completeness & Effort,samplingEffortUnit
> Completeness & Effort,taxonCompletenessReported
> Completeness & Effort,taxonCompletenessProtocols
> Completeness & Effort,isTaxonomicScopeComplete
> Completeness & Effort,isDegreeOfEstablishmentScopeComplete
> Completeness & Effort,isGrowthFormScopeComplete
> Completeness & Effort,isLifeStageScopeComplete
> Completeness & Effort,isAbsenceReported
> Completeness & Effort,absentTaxa
> 
> On Wed, Jul 26, 2023 at 12:14 PM Yanina Sica <yanina.sica at gmail.com <mailto:yanina.sica at gmail.com>> wrote:
> Hi all, 
> 
> Sorry about the listserve errors, duplicate emails, and event cancellations..the universe conspired against us today. Despite this, we managed to meet today and had a very good and productive meeting.
> 
> We have resolved our latest doubts regarding the principles in the hierarchical doc and summarized our next steps:
> - John will finish some small edits to the list of terms and update the IPT
> - Ming will map again the BROKE-West campaign with the latest eco: terms and guiding principles
> - John and Ming will populate some good examples in the hierarchical document
> - Dmitry will try to track GBIF's attention (and funding?) to push the Humboldt User Guide to the next level and transform it into a nice format that allows easy updates.
> 
> I cleaned and edited some of the previous documents and organized the Drive.
> Ratification-related documents are in this folder <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdrive.google.com%2Fdrive%2Fu%2F0%2Ffolders%2F1XI1P07lgGRpVyTWiCiA7yJcs9tD_L0ma__%3B!!DZ3fjg!9NlelMrKXtJt5BQ5SUCGHKWBiJ0Ff1TaFNIAFrFx8Bxrtxv4FRdB1uV_3UbQ2bZpEyN83WO29Njc17xi3A%24&data=05%7C01%7Cymgan%40naturalsciences.be%7C046cb178708145433df908db91d5d5a0%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638264119824394428%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ayY7R36Axx5pRgyhzDNguR78AMYAcU%2F6aGSCX%2Ff4bfY%3D&reserved=0>:
> Implementation Experience Report for Humboldt extension for ecological inventories <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1RFdSHoyzWCQk9qO6uup4xQjWOMzPyBb-A0mcjj98hbk%2Fedit__%3B!!DZ3fjg!9NlelMrKXtJt5BQ5SUCGHKWBiJ0Ff1TaFNIAFrFx8Bxrtxv4FRdB1uV_3UbQ2bZpEyN83WO29NjmRefcVQ%24&data=05%7C01%7Cymgan%40naturalsciences.be%7C046cb178708145433df908db91d5d5a0%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638264119824394428%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=vJEsX0xvBFnvAz1mQZa4D11XZ4jJb9RDZaLoi6oub8w%3D&reserved=0>
> Hierarchical Events in Humboldt Extension for ecological inventories <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1r_XMEgB7p7OI7a5Ouq6G9oa7LmQFPcFhZZCLD9gWOIE%2Fedit__%3B!!DZ3fjg!9NlelMrKXtJt5BQ5SUCGHKWBiJ0Ff1TaFNIAFrFx8Bxrtxv4FRdB1uV_3UbQ2bZpEyN83WO29NjXWXu-hg%24&data=05%7C01%7Cymgan%40naturalsciences.be%7C046cb178708145433df908db91d5d5a0%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638264119824394428%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ANvYx2g4uMBhsLPy80kogWrAY1DP3XSD3G8lm2nnZAo%3D&reserved=0>
> isLeastSpecificTargetCategoryQuantityInclusive <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F11fPW4JibRWUnrtTOZwDkAcxo5d-lwnATXyh3xmO65rs%2Fedit*heading%3Dh.yntaurhtrzrq__%3BIw!!DZ3fjg!9NlelMrKXtJt5BQ5SUCGHKWBiJ0Ff1TaFNIAFrFx8Bxrtxv4FRdB1uV_3UbQ2bZpEyN83WO29NjOqe_TuQ%24&data=05%7C01%7Cymgan%40naturalsciences.be%7C046cb178708145433df908db91d5d5a0%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638264119824706964%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=PgwDZL1egy7bUNRso%2BiAzb5jmUqwoGdiv89xIGVx2Vo%3D&reserved=0>
> List of  <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d7VEDyqOg%2Fedit*gid%3D673949815__%3BIw!!DZ3fjg!9NlelMrKXtJt5BQ5SUCGHKWBiJ0Ff1TaFNIAFrFx8Bxrtxv4FRdB1uV_3UbQ2bZpEyN83WO29NiNRIOAnA%24&data=05%7C01%7Cymgan%40naturalsciences.be%7C046cb178708145433df908db91d5d5a0%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638264119824706964%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xONoakYhiM2GxRMu4FqlrmA9vSjqGEj6NE64qlnmcUk%3D&reserved=0>terms <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdocs.google.com%2Fspreadsheets%2Fd%2F1AbUUKDkgilbtHu9Dh_5V2dnOeQNbKBcRo4d7VEDyqOg%2Fedit*gid%3D673949815__%3BIw!!DZ3fjg!9NlelMrKXtJt5BQ5SUCGHKWBiJ0Ff1TaFNIAFrFx8Bxrtxv4FRdB1uV_3UbQ2bZpEyN83WO29NiNRIOAnA%24&data=05%7C01%7Cymgan%40naturalsciences.be%7C046cb178708145433df908db91d5d5a0%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638264119824706964%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=xONoakYhiM2GxRMu4FqlrmA9vSjqGEj6NE64qlnmcUk%3D&reserved=0> in Humboldt Extension for ecological inventories 
> Humboldt Extension for ecological inventories User Guide <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fdocs.google.com%2Fdocument%2Fd%2F1rX4m94rtZDR_8iIe3RvRnNYKDJcmSX3ii4S5hCznEA0%2Fedit*heading%3Dh.saw9z0q9awkb__%3BIw!!DZ3fjg!9NlelMrKXtJt5BQ5SUCGHKWBiJ0Ff1TaFNIAFrFx8Bxrtxv4FRdB1uV_3UbQ2bZpEyN83WO29Njun44waQ%24&data=05%7C01%7Cymgan%40naturalsciences.be%7C046cb178708145433df908db91d5d5a0%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638264119824706964%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=osNcWRIpn%2F4SRDVd36ULRtlmh2wdD1yp%2BPSo7qlAOqs%3D&reserved=0>
> Next week, we will take a look at the examples from Ming and John and, if we all agree, we could formally submit the extension!We are getting there!
> 
> Thank you all for your last efforts!
> 
> All the best!
> 
> PS: You should have received a calendar invite for next week. In case you did not, please let me know. You can also find the info below:
> 
> When to meet
> Wednesdays 8 am EST (see your time here <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps*3A*2F*2Fwww.timeanddate.com*2Fworldclock*2Fconverter.html*3Fiso*3D20230419T120000*26p1*3D1440*26p2*3D111*26p3*3D37*26p4*3D136*26p5*3D51*26p6*3D179*26p7*3D64*26p8*3D75*26p9*3D224*26p10*3D248*26p11*3D152%26data%3D05*7C01*7Cyanina.sica*40yale.edu*7Ce0fad83cfdf844fe35b308db8de9d6ef*7Cdd8cbebb21394df8b4114e3e87abeb5c*7C0*7C0*7C638259807737182622*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C%26sdata%3DPa2KOTIVkSGSb4KlJPbgvASnRByvTGRogGfhdgdK3q8*3D%26reserved%3D0__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!DZ3fjg!9NlelMrKXtJt5BQ5SUCGHKWBiJ0Ff1TaFNIAFrFx8Bxrtxv4FRdB1uV_3UbQ2bZpEyN83WO29NjJ0Ujeyg%24&data=05%7C01%7Cymgan%40naturalsciences.be%7C046cb178708145433df908db91d5d5a0%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638264119824706964%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=I%2BYzC7I5KU6PYhiS9MTJIvwJCX8fAJGQxBvWPdkkwlI%3D&reserved=0>)
> 
> Where to meet
> Zoom link: https://yale.zoom.us/j/97318391101 <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.com%2Fv3%2F__https%3A%2F%2Fnam12.safelinks.protection.outlook.com%2F%3Furl%3Dhttps*3A*2F*2Fwww.google.com*2Furl*3Fq*3Dhttps*3A*2F*2Fyale.zoom.us*2Fj*2F97318391101*26sa*3DD*26source*3Dcalendar*26usd*3D2*26usg*3DAOvVaw131_ZV9o-84ivZDjGbSTBJ%26data%3D05*7C01*7Cyanina.sica*40yale.edu*7Ce0fad83cfdf844fe35b308db8de9d6ef*7Cdd8cbebb21394df8b4114e3e87abeb5c*7C0*7C0*7C638259807737182622*7CUnknown*7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0*3D*7C3000*7C*7C*7C%26sdata%3DNMXtT5JqDpdqUWJbqlP7685a*2Fcai1IIIqyIQTyfgyOw*3D%26reserved%3D0__%3BJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUlJSUl!!DZ3fjg!9NlelMrKXtJt5BQ5SUCGHKWBiJ0Ff1TaFNIAFrFx8Bxrtxv4FRdB1uV_3UbQ2bZpEyN83WO29NjlodfK6g%24&data=05%7C01%7Cymgan%40naturalsciences.be%7C046cb178708145433df908db91d5d5a0%7C4da8d35db472419c9e15665786aadbfb%7C1%7C0%7C638264119824706964%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=LPGk1%2FrhA6g3pPK53oZsuyGVtWJEsV1zPnjSLO%2F1%2BVs%3D&reserved=0>
> 
> Yani
> 
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