Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
Thanks Peter,
I’ve moved that onto the issue here, and tried to change formatting: https://github.com/tdwg/hc/issues/3
Can you please verify that the largest nested concept is 3 deep (I assumed “-“ meant nesting)? Are there definitions for these concepts please?
Thanks, Tim
From: tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org on behalf of "Brenton, Peter (NCMI, Black Mountain)" Peter.Brenton@csiro.au Reply to: The Humboldt Core Task Group discussion tdwg-humboldt@lists.tdwg.org Date: Wednesday, 16 December 2020 at 15.09 To: "tdwg-humboldt@lists.tdwg.org" tdwg-humboldt@lists.tdwg.org Subject: [tdwg-humboldt] Survey types used in BioCollect platform so far
Great meeting everyone,
Here is our current list of survey types:
Air quality - Fixed sensor,Air quality - Mobile sensor,Bat survey - Echolocation recorder,Bat survey - Harp trapping,Beach profile survey - Emery method,Beach profile survey - Optical method,Bird survey - Distance sample (along transect),Bird survey - Fixed-area,Bird survey - Fixed-time,Bird survey - Fixed-time & Fixed-area,Bird survey - Mist netting,Fauna survey - 2-Ha track plot method,Fauna survey - Active search,Fauna survey - Aerial distance sampler method,Fauna survey - Cage trapping,Fauna survey - Call playback,Fauna survey - Camera trapping,Fauna survey - Elliot trapping,Fauna survey - Funnel trapping,Fauna survey - Hair tubes,Fauna survey - Nest box monitoring,Fauna survey - Pitfall trapping,Fauna survey - Scat survey,Fauna survey - Spotlight search,Fauna survey - Strip transect aerial survey,Fauna survey - Turtle trapping,Fish survey - Electrofishing,Fish survey - Set net/trap,Fish survey - Sweep netting,Insect survey - Black light,Insect survey - Malaise trap,Insect survey - Baited trap,Insect survey - Glue trap,Insect survey - Sweep netting,Plant propagation - Systematic seed propagation batch testing with different techniques,Vegetation condition assessment - Biocondition (QLD),Vegetation condition assessment - BioMetric (NSW),Vegetation condition assessment - Bushland Condition (SA),Vegetation condition assessment - Expert elicitation,Vegetation condition assessment - Habitat Hectares (VIC),Vegetation condition assessment - LEBRA,Vegetation condition assessment - TasVeg (TAS),Vegetation condition assessment - Post fire - Simple Photo Protocol,Vegetation survey - General transect & plot,Vegetation survey - Intensive inventory,Vegetation survey - Step point method,Water quality - Standardised physical/chemical attribute measurements,Water quality - Macroinvertebrate survey - SIGNAL2 method,Water quality - Macroinvertebrate survey - ALT method,Riparian condition assessment - Rapid Appraisal of Riparian Condition (RARC)
[cid:image001.png@01D6D3C7.EF4EA670] Peter Brenton Manager, Applications Atlas of Living Australia National Collections & Marine Infrastructure, CSIRO Clunies Ross Street, Acton ACT 2601 | GPO Box 1700, Canberra ACT 2601 E peter.brenton@csiro.au | T +61 2 6246 5813 | M +61 436 630 766 www.ala.org.au<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.ala.org.au> | www.csiro.au/Research/Collections<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.csiro.au/Research/Collections>
Check out our BioCollect tool at http://www.ala.org.au/biocollect/
CSIRO acknowledges the Traditional Owners of the lands that we live and work on across Australia and pays its respect to Elders past and present.
PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.
NW Tim, thanks for doing that.
There’s a few things to unpack with this current list so I’ll try to itemise and structure for legibility:
1. I think that the concept of having a higher level methodType category and then a way to break these down into nested sub-categories is the best way to organise what is a very large and disparate set of methods to make them searchable and re-usable 2. Whilst the implementation approach that I’ve used seems to work pretty well, the methodType list that I’ve provided is really only a start and already has some obvious issues with it (eg. Mixing specific methods with higher level methodType categories, being Australian centric, etc.). Having said that, I think it is a reasonable starting point to work with and the work that Rob Stevenson has been doing to corral published methods should help a lot to improve on the current list. In my mind, this piece should be a separate task for the TG to tackle in parallel with the broader job around use case testing and terms mapping to existing datasets. 3. The “-“ separator is effectively a way of building a nested structure into a flat list of terms. This works for us because it is indexable, parsable, and easy to work with in the interface, much more so than a relational nested structure. I haven’t found a need to go more than 3 levels deep with the hierarchy that I’ve used and I think that more than 3 levels would start to become a bit unwieldy. 4. There are many ways to categorise these things into a hierarchical structure. I chose one that seemed to make sense and work for us. This is basically a top-level thematic or major taxon category, with a second-level category that represents a particular method or grouping of methods in which data from different variants of a given methodType could be reasonably aggregated and interpreted in the same way, even if some degree of calibration/modulation is required to do so. I’ve left the specifics of a particular application of a method to be articulated by description/publication. Such specifics might include variations such as trap dimensions, length of transect, trap placement density, baits used, etc. 5. I don’t actually have definitions for the different methodType concepts documented, but I can draft up my definitions for them and we can discuss/agree/adjust as a group.
BTW, some other useful resources that are worth knowing about are from the ALA’s sister NCRIS facility the Terrestrial Ecosystem Research Network (TERN) in Australia:
* https://www.tern.org.au/integrating-plot-based-ecological-data-in-australia-... * https://ternaustralia.github.io/ontology_tern-plot/ * https://ternaus.atlassian.net/wiki/spaces/CDI/pages/694321185/Overview+of+Al... – Note that CORVEG is the database of the Queensland Herbarium which stores one of the major datasets comprising the BioCondition vegetation condition assessment methodology (https://www.qld.gov.au/environment/plants-animals/biodiversity/biocondition). The ALA (represented by me) is currently working with the method owner in the expectation that ALA’s BioCollect tool will be used as the principal field data collection facility for BioCondition data by most users of the methodology across Queensland, including state and local government actors, natural resource managers, consultant ecologists, etc.
I hope this helps,
[cid:image001.png@01D6D490.89D8E340] Peter Brenton Manager, Applications Atlas of Living Australia National Collections & Marine Infrastructure, CSIRO Clunies Ross Street, Acton ACT 2601 | GPO Box 1700, Canberra ACT 2601 E peter.brenton@csiro.au | T +61 2 6246 5813 | M +61 436 630 766 www.ala.org.au<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.ala.org.au> | www.csiro.au/Research/Collections<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.csiro.au/Research/Collections>
Check out our BioCollect tool at http://www.ala.org.au/biocollect/
CSIRO acknowledges the Traditional Owners of the lands that we live and work on across Australia and pays its respect to Elders past and present.
PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.
From: tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org On Behalf Of Tim Robertson Sent: Thursday, 17 December 2020 2:25 AM To: The Humboldt Core Task Group discussion tdwg-humboldt@lists.tdwg.org Subject: Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
Thanks Peter,
I’ve moved that onto the issue here, and tried to change formatting: https://github.com/tdwg/hc/issues/3
Can you please verify that the largest nested concept is 3 deep (I assumed “-“ meant nesting)? Are there definitions for these concepts please?
Thanks, Tim
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> on behalf of "Brenton, Peter (NCMI, Black Mountain)" <Peter.Brenton@csiro.aumailto:Peter.Brenton@csiro.au> Reply to: The Humboldt Core Task Group discussion <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Date: Wednesday, 16 December 2020 at 15.09 To: "tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org" <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Subject: [tdwg-humboldt] Survey types used in BioCollect platform so far
Great meeting everyone,
Here is our current list of survey types:
Air quality - Fixed sensor,Air quality - Mobile sensor,Bat survey - Echolocation recorder,Bat survey - Harp trapping,Beach profile survey - Emery method,Beach profile survey - Optical method,Bird survey - Distance sample (along transect),Bird survey - Fixed-area,Bird survey - Fixed-time,Bird survey - Fixed-time & Fixed-area,Bird survey - Mist netting,Fauna survey - 2-Ha track plot method,Fauna survey - Active search,Fauna survey - Aerial distance sampler method,Fauna survey - Cage trapping,Fauna survey - Call playback,Fauna survey - Camera trapping,Fauna survey - Elliot trapping,Fauna survey - Funnel trapping,Fauna survey - Hair tubes,Fauna survey - Nest box monitoring,Fauna survey - Pitfall trapping,Fauna survey - Scat survey,Fauna survey - Spotlight search,Fauna survey - Strip transect aerial survey,Fauna survey - Turtle trapping,Fish survey - Electrofishing,Fish survey - Set net/trap,Fish survey - Sweep netting,Insect survey - Black light,Insect survey - Malaise trap,Insect survey - Baited trap,Insect survey - Glue trap,Insect survey - Sweep netting,Plant propagation - Systematic seed propagation batch testing with different techniques,Vegetation condition assessment - Biocondition (QLD),Vegetation condition assessment - BioMetric (NSW),Vegetation condition assessment - Bushland Condition (SA),Vegetation condition assessment - Expert elicitation,Vegetation condition assessment - Habitat Hectares (VIC),Vegetation condition assessment - LEBRA,Vegetation condition assessment - TasVeg (TAS),Vegetation condition assessment - Post fire - Simple Photo Protocol,Vegetation survey - General transect & plot,Vegetation survey - Intensive inventory,Vegetation survey - Step point method,Water quality - Standardised physical/chemical attribute measurements,Water quality - Macroinvertebrate survey - SIGNAL2 method,Water quality - Macroinvertebrate survey - ALT method,Riparian condition assessment - Rapid Appraisal of Riparian Condition (RARC)
[cid:image002.png@01D6D490.89D8E340] Peter Brenton Manager, Applications Atlas of Living Australia National Collections & Marine Infrastructure, CSIRO Clunies Ross Street, Acton ACT 2601 | GPO Box 1700, Canberra ACT 2601 E peter.brenton@csiro.aumailto:peter.brenton@csiro.au | T +61 2 6246 5813 | M +61 436 630 766 www.ala.org.au<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.ala.org.au> | www.csiro.au/Research/Collections<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.csiro.au/Research/Collections>
Check out our BioCollect tool at http://www.ala.org.au/biocollect/
CSIRO acknowledges the Traditional Owners of the lands that we live and work on across Australia and pays its respect to Elders past and present.
PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.
Hi everyone,
As I started thinking about Tim’s questions and what I’ve done so far in this space, I began to unpack it a bit more to put some more structured thought into it. Clearly what I’ve done so far has many gaps and deficiencies, but it is a useful starting point (for me at least).
Anyway, I have begun to reorganise and define my methods list in a more structured way in this Google doc (https://docs.google.com/spreadsheets/d/1ojS1gRk5MJZ5OWYuaXaGt0oFn3J-JPvpHT-0...). This is proving to be quite an interesting process, but before I go too far with it, I’d appreciate the group’s thoughts on this as an approach to progressing the “methods” part of the work, in particular any thoughts on categorisations and nesting. Rob Stevenson, would this sort of structure work for you in parsing methods out of your literature reviews?
Thanks all,
Peter Brenton
From: tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org On Behalf Of Brenton, Peter (NCMI, Black Mountain) Sent: Thursday, 17 December 2020 4:21 PM To: The Humboldt Core Task Group discussion tdwg-humboldt@lists.tdwg.org Subject: [ExternalEmail] Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
NW Tim, thanks for doing that.
There’s a few things to unpack with this current list so I’ll try to itemise and structure for legibility:
1. I think that the concept of having a higher level methodType category and then a way to break these down into nested sub-categories is the best way to organise what is a very large and disparate set of methods to make them searchable and re-usable 2. Whilst the implementation approach that I’ve used seems to work pretty well, the methodType list that I’ve provided is really only a start and already has some obvious issues with it (eg. Mixing specific methods with higher level methodType categories, being Australian centric, etc.). Having said that, I think it is a reasonable starting point to work with and the work that Rob Stevenson has been doing to corral published methods should help a lot to improve on the current list. In my mind, this piece should be a separate task for the TG to tackle in parallel with the broader job around use case testing and terms mapping to existing datasets. 3. The “-“ separator is effectively a way of building a nested structure into a flat list of terms. This works for us because it is indexable, parsable, and easy to work with in the interface, much more so than a relational nested structure. I haven’t found a need to go more than 3 levels deep with the hierarchy that I’ve used and I think that more than 3 levels would start to become a bit unwieldy. 4. There are many ways to categorise these things into a hierarchical structure. I chose one that seemed to make sense and work for us. This is basically a top-level thematic or major taxon category, with a second-level category that represents a particular method or grouping of methods in which data from different variants of a given methodType could be reasonably aggregated and interpreted in the same way, even if some degree of calibration/modulation is required to do so. I’ve left the specifics of a particular application of a method to be articulated by description/publication. Such specifics might include variations such as trap dimensions, length of transect, trap placement density, baits used, etc. 5. I don’t actually have definitions for the different methodType concepts documented, but I can draft up my definitions for them and we can discuss/agree/adjust as a group.
BTW, some other useful resources that are worth knowing about are from the ALA’s sister NCRIS facility the Terrestrial Ecosystem Research Network (TERN) in Australia:
* https://www.tern.org.au/integrating-plot-based-ecological-data-in-australia-... * https://ternaustralia.github.io/ontology_tern-plot/ * https://ternaus.atlassian.net/wiki/spaces/CDI/pages/694321185/Overview+of+Al... – Note that CORVEG is the database of the Queensland Herbarium which stores one of the major datasets comprising the BioCondition vegetation condition assessment methodology (https://www.qld.gov.au/environment/plants-animals/biodiversity/biocondition). The ALA (represented by me) is currently working with the method owner in the expectation that ALA’s BioCollect tool will be used as the principal field data collection facility for BioCondition data by most users of the methodology across Queensland, including state and local government actors, natural resource managers, consultant ecologists, etc.
I hope this helps,
[cid:image003.png@01D6D7A7.460B8A40] Peter Brenton Manager, Applications Atlas of Living Australia National Collections & Marine Infrastructure, CSIRO Clunies Ross Street, Acton ACT 2601 | GPO Box 1700, Canberra ACT 2601 E peter.brenton@csiro.aumailto:peter.brenton@csiro.au | T +61 2 6246 5813 | M +61 436 630 766 www.ala.org.au<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.ala.org.au> | www.csiro.au/Research/Collections<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.csiro.au/Research/Collections>
Check out our BioCollect tool at http://www.ala.org.au/biocollect/
CSIRO acknowledges the Traditional Owners of the lands that we live and work on across Australia and pays its respect to Elders past and present.
PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> On Behalf Of Tim Robertson Sent: Thursday, 17 December 2020 2:25 AM To: The Humboldt Core Task Group discussion <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Subject: Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
Thanks Peter,
I’ve moved that onto the issue here, and tried to change formatting: https://github.com/tdwg/hc/issues/3
Can you please verify that the largest nested concept is 3 deep (I assumed “-“ meant nesting)? Are there definitions for these concepts please?
Thanks, Tim
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> on behalf of "Brenton, Peter (NCMI, Black Mountain)" <Peter.Brenton@csiro.aumailto:Peter.Brenton@csiro.au> Reply to: The Humboldt Core Task Group discussion <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Date: Wednesday, 16 December 2020 at 15.09 To: "tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org" <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Subject: [tdwg-humboldt] Survey types used in BioCollect platform so far
Great meeting everyone,
Here is our current list of survey types:
Air quality - Fixed sensor,Air quality - Mobile sensor,Bat survey - Echolocation recorder,Bat survey - Harp trapping,Beach profile survey - Emery method,Beach profile survey - Optical method,Bird survey - Distance sample (along transect),Bird survey - Fixed-area,Bird survey - Fixed-time,Bird survey - Fixed-time & Fixed-area,Bird survey - Mist netting,Fauna survey - 2-Ha track plot method,Fauna survey - Active search,Fauna survey - Aerial distance sampler method,Fauna survey - Cage trapping,Fauna survey - Call playback,Fauna survey - Camera trapping,Fauna survey - Elliot trapping,Fauna survey - Funnel trapping,Fauna survey - Hair tubes,Fauna survey - Nest box monitoring,Fauna survey - Pitfall trapping,Fauna survey - Scat survey,Fauna survey - Spotlight search,Fauna survey - Strip transect aerial survey,Fauna survey - Turtle trapping,Fish survey - Electrofishing,Fish survey - Set net/trap,Fish survey - Sweep netting,Insect survey - Black light,Insect survey - Malaise trap,Insect survey - Baited trap,Insect survey - Glue trap,Insect survey - Sweep netting,Plant propagation - Systematic seed propagation batch testing with different techniques,Vegetation condition assessment - Biocondition (QLD),Vegetation condition assessment - BioMetric (NSW),Vegetation condition assessment - Bushland Condition (SA),Vegetation condition assessment - Expert elicitation,Vegetation condition assessment - Habitat Hectares (VIC),Vegetation condition assessment - LEBRA,Vegetation condition assessment - TasVeg (TAS),Vegetation condition assessment - Post fire - Simple Photo Protocol,Vegetation survey - General transect & plot,Vegetation survey - Intensive inventory,Vegetation survey - Step point method,Water quality - Standardised physical/chemical attribute measurements,Water quality - Macroinvertebrate survey - SIGNAL2 method,Water quality - Macroinvertebrate survey - ALT method,Riparian condition assessment - Rapid Appraisal of Riparian Condition (RARC)
[cid:image005.png@01D6D7A7.460B8A40] Peter Brenton Manager, Applications Atlas of Living Australia National Collections & Marine Infrastructure, CSIRO Clunies Ross Street, Acton ACT 2601 | GPO Box 1700, Canberra ACT 2601 E peter.brenton@csiro.aumailto:peter.brenton@csiro.au | T +61 2 6246 5813 | M +61 436 630 766 www.ala.org.au<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.ala.org.au> | www.csiro.au/Research/Collections<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.csiro.au/Research/Collections>
Check out our BioCollect tool at http://www.ala.org.au/biocollect/
CSIRO acknowledges the Traditional Owners of the lands that we live and work on across Australia and pays its respect to Elders past and present.
PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.
Thanks Peter
I’m obviously not equipped to comment on the domain aspects, but the structure is certainly helpful. It is easy to imagine how this could help in application development / data workflows.
Thinking ahead, there are a few columns encoding different fields into text that might need parsing. E.g. “Marine invertebrates” which captures a taxon/habitat combination and “area/duration” combining location and time elements. In the future, we might consider the merits of splitting into taxonomicScope, temporalScope, geographicScope, sampling target, habitat etc to help application development – in particular extracting the taxa will help. Alternatively, this could be achieved with addition columns keeping the more familiar “combined text” for the reader. This doesn’t need to happen now.
Nesting seems sensible to me as it helps orient a reader in a list that might get long plus gives the opportunity for people to get really specific if they need to.
Best wishes, Tim (I’ve also reworded the mailing list to avoid “The Humbodlt Core Task Group discussion” which was configured wrongly)
From: tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org on behalf of "Brenton, Peter (NCMI, Black Mountain)" Peter.Brenton@csiro.au Reply to: The Humboldt Core Task Group discussion tdwg-humboldt@lists.tdwg.org Date: Tuesday, 22 December 2020 at 09.27 To: The Humboldt Core Task Group discussion tdwg-humboldt@lists.tdwg.org Subject: Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
Hi everyone,
As I started thinking about Tim’s questions and what I’ve done so far in this space, I began to unpack it a bit more to put some more structured thought into it. Clearly what I’ve done so far has many gaps and deficiencies, but it is a useful starting point (for me at least).
Anyway, I have begun to reorganise and define my methods list in a more structured way in this Google doc (https://docs.google.com/spreadsheets/d/1ojS1gRk5MJZ5OWYuaXaGt0oFn3J-JPvpHT-0...). This is proving to be quite an interesting process, but before I go too far with it, I’d appreciate the group’s thoughts on this as an approach to progressing the “methods” part of the work, in particular any thoughts on categorisations and nesting. Rob Stevenson, would this sort of structure work for you in parsing methods out of your literature reviews?
Thanks all,
Peter Brenton
From: tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org On Behalf Of Brenton, Peter (NCMI, Black Mountain) Sent: Thursday, 17 December 2020 4:21 PM To: The Humboldt Core Task Group discussion tdwg-humboldt@lists.tdwg.org Subject: [ExternalEmail] Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
NW Tim, thanks for doing that.
There’s a few things to unpack with this current list so I’ll try to itemise and structure for legibility:
1. I think that the concept of having a higher level methodType category and then a way to break these down into nested sub-categories is the best way to organise what is a very large and disparate set of methods to make them searchable and re-usable 2. Whilst the implementation approach that I’ve used seems to work pretty well, the methodType list that I’ve provided is really only a start and already has some obvious issues with it (eg. Mixing specific methods with higher level methodType categories, being Australian centric, etc.). Having said that, I think it is a reasonable starting point to work with and the work that Rob Stevenson has been doing to corral published methods should help a lot to improve on the current list. In my mind, this piece should be a separate task for the TG to tackle in parallel with the broader job around use case testing and terms mapping to existing datasets. 3. The “-“ separator is effectively a way of building a nested structure into a flat list of terms. This works for us because it is indexable, parsable, and easy to work with in the interface, much more so than a relational nested structure. I haven’t found a need to go more than 3 levels deep with the hierarchy that I’ve used and I think that more than 3 levels would start to become a bit unwieldy. 4. There are many ways to categorise these things into a hierarchical structure. I chose one that seemed to make sense and work for us. This is basically a top-level thematic or major taxon category, with a second-level category that represents a particular method or grouping of methods in which data from different variants of a given methodType could be reasonably aggregated and interpreted in the same way, even if some degree of calibration/modulation is required to do so. I’ve left the specifics of a particular application of a method to be articulated by description/publication. Such specifics might include variations such as trap dimensions, length of transect, trap placement density, baits used, etc. 5. I don’t actually have definitions for the different methodType concepts documented, but I can draft up my definitions for them and we can discuss/agree/adjust as a group.
BTW, some other useful resources that are worth knowing about are from the ALA’s sister NCRIS facility the Terrestrial Ecosystem Research Network (TERN) in Australia:
* https://www.tern.org.au/integrating-plot-based-ecological-data-in-australia-... * https://ternaustralia.github.io/ontology_tern-plot/ * https://ternaus.atlassian.net/wiki/spaces/CDI/pages/694321185/Overview+of+Al... – Note that CORVEG is the database of the Queensland Herbarium which stores one of the major datasets comprising the BioCondition vegetation condition assessment methodology (https://www.qld.gov.au/environment/plants-animals/biodiversity/biocondition). The ALA (represented by me) is currently working with the method owner in the expectation that ALA’s BioCollect tool will be used as the principal field data collection facility for BioCondition data by most users of the methodology across Queensland, including state and local government actors, natural resource managers, consultant ecologists, etc.
I hope this helps,
[cid:image001.png@01D6D849.4ED03B10] Peter Brenton Manager, Applications Atlas of Living Australia National Collections & Marine Infrastructure, CSIRO Clunies Ross Street, Acton ACT 2601 | GPO Box 1700, Canberra ACT 2601 E peter.brenton@csiro.aumailto:peter.brenton@csiro.au | T +61 2 6246 5813 | M +61 436 630 766 www.ala.org.au<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.ala.org.au> | www.csiro.au/Research/Collections<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.csiro.au/Research/Collections>
Check out our BioCollect tool at http://www.ala.org.au/biocollect/
CSIRO acknowledges the Traditional Owners of the lands that we live and work on across Australia and pays its respect to Elders past and present.
PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> On Behalf Of Tim Robertson Sent: Thursday, 17 December 2020 2:25 AM To: The Humboldt Core Task Group discussion <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Subject: Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
Thanks Peter,
I’ve moved that onto the issue here, and tried to change formatting: https://github.com/tdwg/hc/issues/3
Can you please verify that the largest nested concept is 3 deep (I assumed “-“ meant nesting)? Are there definitions for these concepts please?
Thanks, Tim
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> on behalf of "Brenton, Peter (NCMI, Black Mountain)" <Peter.Brenton@csiro.aumailto:Peter.Brenton@csiro.au> Reply to: The Humboldt Core Task Group discussion <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Date: Wednesday, 16 December 2020 at 15.09 To: "tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org" <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Subject: [tdwg-humboldt] Survey types used in BioCollect platform so far
Great meeting everyone,
Here is our current list of survey types:
Air quality - Fixed sensor,Air quality - Mobile sensor,Bat survey - Echolocation recorder,Bat survey - Harp trapping,Beach profile survey - Emery method,Beach profile survey - Optical method,Bird survey - Distance sample (along transect),Bird survey - Fixed-area,Bird survey - Fixed-time,Bird survey - Fixed-time & Fixed-area,Bird survey - Mist netting,Fauna survey - 2-Ha track plot method,Fauna survey - Active search,Fauna survey - Aerial distance sampler method,Fauna survey - Cage trapping,Fauna survey - Call playback,Fauna survey - Camera trapping,Fauna survey - Elliot trapping,Fauna survey - Funnel trapping,Fauna survey - Hair tubes,Fauna survey - Nest box monitoring,Fauna survey - Pitfall trapping,Fauna survey - Scat survey,Fauna survey - Spotlight search,Fauna survey - Strip transect aerial survey,Fauna survey - Turtle trapping,Fish survey - Electrofishing,Fish survey - Set net/trap,Fish survey - Sweep netting,Insect survey - Black light,Insect survey - Malaise trap,Insect survey - Baited trap,Insect survey - Glue trap,Insect survey - Sweep netting,Plant propagation - Systematic seed propagation batch testing with different techniques,Vegetation condition assessment - Biocondition (QLD),Vegetation condition assessment - BioMetric (NSW),Vegetation condition assessment - Bushland Condition (SA),Vegetation condition assessment - Expert elicitation,Vegetation condition assessment - Habitat Hectares (VIC),Vegetation condition assessment - LEBRA,Vegetation condition assessment - TasVeg (TAS),Vegetation condition assessment - Post fire - Simple Photo Protocol,Vegetation survey - General transect & plot,Vegetation survey - Intensive inventory,Vegetation survey - Step point method,Water quality - Standardised physical/chemical attribute measurements,Water quality - Macroinvertebrate survey - SIGNAL2 method,Water quality - Macroinvertebrate survey - ALT method,Riparian condition assessment - Rapid Appraisal of Riparian Condition (RARC)
[cid:image002.png@01D6D849.4ED03B10] Peter Brenton Manager, Applications Atlas of Living Australia National Collections & Marine Infrastructure, CSIRO Clunies Ross Street, Acton ACT 2601 | GPO Box 1700, Canberra ACT 2601 E peter.brenton@csiro.aumailto:peter.brenton@csiro.au | T +61 2 6246 5813 | M +61 436 630 766 www.ala.org.au<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.ala.org.au> | www.csiro.au/Research/Collections<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.csiro.au/Research/Collections>
Check out our BioCollect tool at http://www.ala.org.au/biocollect/
CSIRO acknowledges the Traditional Owners of the lands that we live and work on across Australia and pays its respect to Elders past and present.
PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.
Hello all,
Just to let you know that Rob Stevenson, cc and I we just had a call on extracting methods categories from the books and possible main categories (around geometry, time, tech and target). Apparently Rob did not receive today’s messages below, would be nice to add Rob manually, if possible?
Thanks, Dmitry
From: tdwg-humboldt tdwg-humboldt-bounces@lists.tdwg.org On Behalf Of Tim Robertson Sent: 22 December, 2020 10:01 To: The Humboldt Core Task Group discussion tdwg-humboldt@lists.tdwg.org Subject: Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
Thanks Peter
I’m obviously not equipped to comment on the domain aspects, but the structure is certainly helpful. It is easy to imagine how this could help in application development / data workflows.
Thinking ahead, there are a few columns encoding different fields into text that might need parsing. E.g. “Marine invertebrates” which captures a taxon/habitat combination and “area/duration” combining location and time elements. In the future, we might consider the merits of splitting into taxonomicScope, temporalScope, geographicScope, sampling target, habitat etc to help application development – in particular extracting the taxa will help. Alternatively, this could be achieved with addition columns keeping the more familiar “combined text” for the reader. This doesn’t need to happen now.
Nesting seems sensible to me as it helps orient a reader in a list that might get long plus gives the opportunity for people to get really specific if they need to.
Best wishes, Tim (I’ve also reworded the mailing list to avoid “The Humbodlt Core Task Group discussion” which was configured wrongly)
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> on behalf of "Brenton, Peter (NCMI, Black Mountain)" <Peter.Brenton@csiro.aumailto:Peter.Brenton@csiro.au> Reply to: The Humboldt Core Task Group discussion <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Date: Tuesday, 22 December 2020 at 09.27 To: The Humboldt Core Task Group discussion <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Subject: Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
Hi everyone,
As I started thinking about Tim’s questions and what I’ve done so far in this space, I began to unpack it a bit more to put some more structured thought into it. Clearly what I’ve done so far has many gaps and deficiencies, but it is a useful starting point (for me at least).
Anyway, I have begun to reorganise and define my methods list in a more structured way in this Google doc (https://docs.google.com/spreadsheets/d/1ojS1gRk5MJZ5OWYuaXaGt0oFn3J-JPvpHT-0...). This is proving to be quite an interesting process, but before I go too far with it, I’d appreciate the group’s thoughts on this as an approach to progressing the “methods” part of the work, in particular any thoughts on categorisations and nesting. Rob Stevenson, would this sort of structure work for you in parsing methods out of your literature reviews?
Thanks all,
Peter Brenton
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> On Behalf Of Brenton, Peter (NCMI, Black Mountain) Sent: Thursday, 17 December 2020 4:21 PM To: The Humboldt Core Task Group discussion <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Subject: [ExternalEmail] Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
NW Tim, thanks for doing that.
There’s a few things to unpack with this current list so I’ll try to itemise and structure for legibility:
1. I think that the concept of having a higher level methodType category and then a way to break these down into nested sub-categories is the best way to organise what is a very large and disparate set of methods to make them searchable and re-usable 2. Whilst the implementation approach that I’ve used seems to work pretty well, the methodType list that I’ve provided is really only a start and already has some obvious issues with it (eg. Mixing specific methods with higher level methodType categories, being Australian centric, etc.). Having said that, I think it is a reasonable starting point to work with and the work that Rob Stevenson has been doing to corral published methods should help a lot to improve on the current list. In my mind, this piece should be a separate task for the TG to tackle in parallel with the broader job around use case testing and terms mapping to existing datasets. 3. The “-“ separator is effectively a way of building a nested structure into a flat list of terms. This works for us because it is indexable, parsable, and easy to work with in the interface, much more so than a relational nested structure. I haven’t found a need to go more than 3 levels deep with the hierarchy that I’ve used and I think that more than 3 levels would start to become a bit unwieldy. 4. There are many ways to categorise these things into a hierarchical structure. I chose one that seemed to make sense and work for us. This is basically a top-level thematic or major taxon category, with a second-level category that represents a particular method or grouping of methods in which data from different variants of a given methodType could be reasonably aggregated and interpreted in the same way, even if some degree of calibration/modulation is required to do so. I’ve left the specifics of a particular application of a method to be articulated by description/publication. Such specifics might include variations such as trap dimensions, length of transect, trap placement density, baits used, etc. 5. I don’t actually have definitions for the different methodType concepts documented, but I can draft up my definitions for them and we can discuss/agree/adjust as a group.
BTW, some other useful resources that are worth knowing about are from the ALA’s sister NCRIS facility the Terrestrial Ecosystem Research Network (TERN) in Australia:
* https://www.tern.org.au/integrating-plot-based-ecological-data-in-australia-... * https://ternaustralia.github.io/ontology_tern-plot/ * https://ternaus.atlassian.net/wiki/spaces/CDI/pages/694321185/Overview+of+Al... – Note that CORVEG is the database of the Queensland Herbarium which stores one of the major datasets comprising the BioCondition vegetation condition assessment methodology (https://www.qld.gov.au/environment/plants-animals/biodiversity/biocondition). The ALA (represented by me) is currently working with the method owner in the expectation that ALA’s BioCollect tool will be used as the principal field data collection facility for BioCondition data by most users of the methodology across Queensland, including state and local government actors, natural resource managers, consultant ecologists, etc.
I hope this helps,
[cid:image001.png@01D6D849.4ED03B10] Peter Brenton Manager, Applications Atlas of Living Australia National Collections & Marine Infrastructure, CSIRO Clunies Ross Street, Acton ACT 2601 | GPO Box 1700, Canberra ACT 2601 E peter.brenton@csiro.aumailto:peter.brenton@csiro.au | T +61 2 6246 5813 | M +61 436 630 766 www.ala.org.au<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.ala.org.au> | www.csiro.au/Research/Collections<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.csiro.au/Research/Collections>
Check out our BioCollect tool at http://www.ala.org.au/biocollect/
CSIRO acknowledges the Traditional Owners of the lands that we live and work on across Australia and pays its respect to Elders past and present.
PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> On Behalf Of Tim Robertson Sent: Thursday, 17 December 2020 2:25 AM To: The Humboldt Core Task Group discussion <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Subject: Re: [tdwg-humboldt] Survey types used in BioCollect platform so far
Thanks Peter,
I’ve moved that onto the issue here, and tried to change formatting: https://github.com/tdwg/hc/issues/3
Can you please verify that the largest nested concept is 3 deep (I assumed “-“ meant nesting)? Are there definitions for these concepts please?
Thanks, Tim
From: tdwg-humboldt <tdwg-humboldt-bounces@lists.tdwg.orgmailto:tdwg-humboldt-bounces@lists.tdwg.org> on behalf of "Brenton, Peter (NCMI, Black Mountain)" <Peter.Brenton@csiro.aumailto:Peter.Brenton@csiro.au> Reply to: The Humboldt Core Task Group discussion <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Date: Wednesday, 16 December 2020 at 15.09 To: "tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org" <tdwg-humboldt@lists.tdwg.orgmailto:tdwg-humboldt@lists.tdwg.org> Subject: [tdwg-humboldt] Survey types used in BioCollect platform so far
Great meeting everyone,
Here is our current list of survey types:
Air quality - Fixed sensor,Air quality - Mobile sensor,Bat survey - Echolocation recorder,Bat survey - Harp trapping,Beach profile survey - Emery method,Beach profile survey - Optical method,Bird survey - Distance sample (along transect),Bird survey - Fixed-area,Bird survey - Fixed-time,Bird survey - Fixed-time & Fixed-area,Bird survey - Mist netting,Fauna survey - 2-Ha track plot method,Fauna survey - Active search,Fauna survey - Aerial distance sampler method,Fauna survey - Cage trapping,Fauna survey - Call playback,Fauna survey - Camera trapping,Fauna survey - Elliot trapping,Fauna survey - Funnel trapping,Fauna survey - Hair tubes,Fauna survey - Nest box monitoring,Fauna survey - Pitfall trapping,Fauna survey - Scat survey,Fauna survey - Spotlight search,Fauna survey - Strip transect aerial survey,Fauna survey - Turtle trapping,Fish survey - Electrofishing,Fish survey - Set net/trap,Fish survey - Sweep netting,Insect survey - Black light,Insect survey - Malaise trap,Insect survey - Baited trap,Insect survey - Glue trap,Insect survey - Sweep netting,Plant propagation - Systematic seed propagation batch testing with different techniques,Vegetation condition assessment - Biocondition (QLD),Vegetation condition assessment - BioMetric (NSW),Vegetation condition assessment - Bushland Condition (SA),Vegetation condition assessment - Expert elicitation,Vegetation condition assessment - Habitat Hectares (VIC),Vegetation condition assessment - LEBRA,Vegetation condition assessment - TasVeg (TAS),Vegetation condition assessment - Post fire - Simple Photo Protocol,Vegetation survey - General transect & plot,Vegetation survey - Intensive inventory,Vegetation survey - Step point method,Water quality - Standardised physical/chemical attribute measurements,Water quality - Macroinvertebrate survey - SIGNAL2 method,Water quality - Macroinvertebrate survey - ALT method,Riparian condition assessment - Rapid Appraisal of Riparian Condition (RARC)
[cid:image002.png@01D6D849.4ED03B10] Peter Brenton Manager, Applications Atlas of Living Australia National Collections & Marine Infrastructure, CSIRO Clunies Ross Street, Acton ACT 2601 | GPO Box 1700, Canberra ACT 2601 E peter.brenton@csiro.aumailto:peter.brenton@csiro.au | T +61 2 6246 5813 | M +61 436 630 766 www.ala.org.au<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.ala.org.au> | www.csiro.au/Research/Collections<../../../Local/Microsoft/Windows/Temporary%20Internet%20Files/Content.Outlook/JCZSR1WG/www.csiro.au/Research/Collections>
Check out our BioCollect tool at http://www.ala.org.au/biocollect/
CSIRO acknowledges the Traditional Owners of the lands that we live and work on across Australia and pays its respect to Elders past and present.
PLEASE NOTE The information contained in this email may be confidential or privileged. Any unauthorised use or disclosure is prohibited. If you have received this email in error, please delete it immediately and notify the sender by return email. Thank you. To the extent permitted by law, CSIRO does not represent, warrant and/or guarantee that the integrity of this communication has been maintained or that the communication is free of errors, virus, interception or interference. Please consider the environment before printing this email.
participants (3)
-
Brenton, Peter (NCMI, Black Mountain) -
Dmitry Schigel -
Tim Robertson