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Restore linkage of and search tools for reciprocal relationships between records #6249

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campmlc opened this issue May 5, 2023 · 20 comments
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Restore linkage of and search tools for reciprocal relationships between records #6249

campmlc opened this issue May 5, 2023 · 20 comments
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@ccicero @mkoo @dustymc @Jegelewicz @amgunderson @acdoll @jldunnum @gracz-UNL
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Function-Relationship Grant funded (Arctos member) This issue is related to an Arctos member grnat funded project. Grant funded (Arctos) This issue is related to an Arctos grant funded project Priority-High (Needed for work) High because this is causing a delay in important collection work..
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In next release

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@campmlc
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campmlc commented May 5, 2023 •
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Our original model developed a decade ago by @dustymc @campmlc and Gordon Jarrell to link host and parasite records in Arctos (NSF funded project for Rausch collection) included the following components:

  1. use of other identifiers with relationship other than self (code table controlled) to assert relationships between catalog records within and external to Arctos.
  2. Following the model originally developed for reciprocal relationships with GenBank, when these identifiers linked to another Arctos url, a notification would be sent to the contact agent for the relevant collection which provided a mechanism for review and approval, and creation of the reciprocal relationship in the host or parasite record.
  3. Pulling of not only the related identifier and asserted relationship, but also the currently accepted identification and collecting event information across collections and institutions, so that this information was visible in the catalog record page of each reciprocallly related record.
  4. The ability, as a result of the above, to view the host or parasite currently accepted identification, locality, geography, and date information from the related host or parasite record, to verify that these match, as they should.
  5. The creation of a host observation record in a specific Host portal set up explicitly to capture host data and create the reciprocal relationship when the host was either not collected or its disposition was unknown. Unlike use of a parasite attribute such as "verbatim host ID", this record was given a taxonomic identification and associated classification which could be updated with identification history and synonymy.
  6. Most importantly, and the point of all of the above: Enable complex searches of related records across taxon name and classification, including geography date and other collecting event information. While we could not search across all classification levels due to resource limitation, we did have the option of searching by identification, family, locality etc.
    See below.
    Screenshot 2023-05-05 08 00 53

In the conversion to PG and the subsequent UI change, we have lost the ability to do # 3, 4, and 6 above. I would like to explore what options we have for restoring this previously funded functionality, which is critically important for new initiatives. Thoughts?
@campmlc campmlc added Priority-High (Needed for work) High because this is causing a delay in important collection work.. Function-Relationship Grant funded (Arctos) This issue is related to an Arctos grant funded project Grant funded (Arctos member) This issue is related to an Arctos member grnat funded project. labels May 5, 2023
@dustymc
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dustymc commented May 5, 2023

Duplicate of #5135

@dustymc dustymc marked this as a duplicate of #5135 May 5, 2023
@campmlc
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campmlc commented May 5, 2023

Please leave this open, as it has explicit explanation and justification of what was done and is needed.

@campmlc campmlc mentioned this issue May 7, 2023
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@campmlc
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campmlc commented May 8, 2023

Find all Family Sciuridae from Alaska that have the relationship "host of" to Order Siphonaptera

@Jegelewicz
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Family and Order as asserted by the collection.

@campmlc
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campmlc commented May 8, 2023

Find all Muridae from Panama with Examined for "Virus:Orthohantavirus" and Detected: "Virus:Orthohantavirus"

@Jegelewicz
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What output is needed? Simple?

host GUID, host identification, host collection locality, parasite GUID, parasite identification, parasite collection locality

@dustymc
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dustymc commented May 8, 2023

Find all Muridae from Panama with Examined for "Virus:Orthohantavirus" and Detected: "Virus:Orthohantavirus"

https://arctos.database.museum/search.cfm?family=Muridae&attribute_type_1=detected&attribute_value_1=virus%3A%20Orthohantavirus&attribute_type_2=examined%20for&attribute_value_2=virus%3A%20Orthohantavirus&country=Panama

Find all Family Sciuridae from Alaska that have the relationship "host of" to Order Siphonaptera

This is greatly complicated by #6163, but here's a QnD approximation:

select a.guid,b.guid from flat a
inner join coll_obj_other_id_num on a.collection_object_id=coll_obj_other_id_num.collection_object_id
inner join flat b on coll_obj_other_id_num.other_id_type||':'||coll_obj_other_id_num.display_value=b.guid
where a.family='Sciuridae' and
a.state_prov='Alaska' and
coll_obj_other_id_num.id_references='host of' and
b.phylorder='Siphonaptera'
;

      guid       |      guid       
-----------------+-----------------
 UAM:Mamm:47277  | UAM:Ento:282060
 UAM:Mamm:41610  | UAM:Ento:280803
 UAM:Mamm:35157  | UAM:Ento:276944
 UAM:Mamm:38307  | UAM:Ento:278157
 UAM:Mamm:48320  | UAM:Ento:282514
 UAM:Mamm:48330  | UAM:Ento:282383
 UAM:Mamm:48426  | UAM:Ento:279584
 UAM:Mamm:70880  | UAM:Ento:280675
 UAM:Mamm:48431  | UAM:Ento:277273
 UAM:Mamm:48447  | UAM:Ento:281795
 UAM:Mamm:70918  | UAM:Ento:278825
 UAM:Mamm:51095  | UAM:Ento:279080
 UAM:Mamm:70850  | UAM:Ento:279787
 UAM:Mamm:70892  | UAM:Ento:276625
 UAM:Mamm:70929  | UAM:Ento:276440
 UAM:Mamm:70893  | UAM:Ento:280618
 UAM:Mamm:70943  | UAM:Ento:280049
 UAM:Mamm:70944  | UAM:Ento:280045
 UAM:Mamm:70953  | UAM:Ento:277940
 UAM:Mamm:70951  | UAM:Ento:277376
 UAM:Mamm:70982  | UAM:Ento:279989
 UAM:Mamm:71011  | UAM:Ento:281074
 UAM:Mamm:71011  | UAM:Ento:334630
 UAM:Mamm:71043  | UAM:Ento:278595
 UAM:Mamm:70993  | UAM:Ento:280269
 MSB:Mamm:193566 | MSB:Para:26151
 UAM:Mamm:71205  | UAM:Ento:279511
 UAM:Mamm:86397  | UAM:Ento:282422
 UAM:Mamm:71023  | UAM:Ento:277247
 UAM:Mamm:71025  | UAM:Ento:281866
 UAM:Mamm:93135  | MSB:Para:26445
 MSB:Mamm:136519 | MSB:Para:5967
 MSB:Mamm:192793 | MSB:Para:1412
 MSB:Mamm:192797 | MSB:Para:1624
 MSB:Mamm:198278 | MSB:Para:37250
 MSB:Mamm:192798 | MSB:Para:6094
 MSB:Mamm:192805 | MSB:Para:1756
 MSB:Mamm:193321 | MSB:Para:37179
 MSB:Mamm:193324 | MSB:Para:37317
 MSB:Mamm:198279 | MSB:Para:37266
 MSB:Mamm:198307 | MSB:Para:37003
 MSB:Mamm:198281 | MSB:Para:37255
 MSB:Mamm:198292 | MSB:Para:37260
 MSB:Mamm:198293 | MSB:Para:37267
 MSB:Mamm:198295 | MSB:Para:37269
 MSB:Mamm:198296 | MSB:Para:37257
 MSB:Mamm:198297 | MSB:Para:37268
 MSB:Mamm:198298 | MSB:Para:37253
 MSB:Mamm:198299 | MSB:Para:37275
 MSB:Mamm:198300 | MSB:Para:37273
 MSB:Mamm:232705 | MSB:Para:37065
 UAM:Mamm:111878 | UAM:Ento:279367
 UAM:Mamm:111879 | UAM:Ento:281583
 MSB:Host:715    | MSB:Para:795
 MSB:Mamm:233665 | MSB:Para:37041
 MSB:Mamm:247656 | MSB:Para:36964
 MSB:Host:1498   | MSB:Para:1756
 MSB:Host:7417   | MSB:Para:1624
 MSB:Host:4395   | MSB:Para:5967
 MSB:Host:6922   | MSB:Para:1412
 MSB:Host:10445  | MSB:Para:1460
 MSB:Host:8786   | MSB:Para:6094
 MSB:Host:11229  | MSB:Para:17807
 MSB:Host:10189  | MSB:Para:1757
 MSB:Host:10196  | MSB:Para:1765
 MSB:Host:10703  | MSB:Para:7541
 MSB:Host:16598  | MSB:Para:22159
 MSB:Host:14695  | MSB:Para:14819
 MSB:Host:14697  | MSB:Para:14830
 MSB:Host:19671  | MSB:Para:22160
 MSB:Host:16325  | MSB:Para:22155
 MSB:Host:16326  | MSB:Para:22156
 MSB:Host:19721  | MSB:Para:22115
 UAM:Mamm:127679 | UAM:Ento:443108
 UAM:Mamm:127641 | UAM:Ento:443356

@campmlc
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campmlc commented May 8, 2023 via email

@campmlc
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campmlc commented May 8, 2023 via email

@dustymc dustymc added this to the In next release milestone Aug 21, 2023
@dustymc dustymc closed this as completed Aug 22, 2023
@campmlc
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campmlc commented Aug 22, 2023

Just curious when next release will be?

@campmlc campmlc reopened this Sep 13, 2023
@campmlc campmlc mentioned this issue Sep 13, 2023
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@dustymc
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dustymc commented Sep 13, 2023

Why has this been reopened?

@campmlc
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campmlc commented Sep 13, 2023

I would like all these related issues to remain open until we can document in the context of each issue what solutions were implemented.
#5135

@Jegelewicz
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@campmlc I don't know what to document - and it would probably be better to open an issue in the documentation repo for that?

@campmlc
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campmlc commented Sep 13, 2023

@dustymc can you provide a description of what was done here related to last release?
And perhaps this can be moved to discussion as the overall issue isn't resolved?

@acdoll
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acdoll commented Sep 13, 2023

I believe this may have been closed because the new search interface does address your need for 6. the complex search, as demonstrated here (if you turn on all the search fields you'll see how):

https://arctos.database.museum/search.cfm?family=Muridae&attribute_type_1=detected&attribute_value_1=virus%3A%20Orthohantavirus&attribute_type_2=examined%20for&attribute_value_2=virus%3A%20Orthohantavirus&country=Panama

But that doesn't address your needs for 3. and 4. The host/parasite information (identification and collecting info) does not display on the respective parasite/host records. While that would make things easier, it is just one click away and reduces the amount of content on any particular page.

@Jegelewicz
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the host/parasite information (identification and collecting info) does not display on the respective parasite/host records

it does! Just mouse over the link to the related record

Screenshot 2023-09-13 17 05 25

@campmlc
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campmlc commented Sep 13, 2023

I just discovered this by accident yesterday, but that wasn't explained here, hence my request for a response to what solutions have been implemented. And I'm not sure anyone else would find this except by accident.
Can we get this info integrated into the table? It used to display under the equivalent of what is now the url. ?

the host/parasite information (identification and collecting info) does not display on the respective parasite/host records

it does! Just mouse over the link to the related record

@campmlc
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campmlc commented Sep 13, 2023

I believe this may have been closed because the new search interface does address your need for 6. the complex search, as demonstrated here (if you turn on all the search fields you'll see how):

https://arctos.database.museum/search.cfm?family=Muridae&attribute_type_1=detected&attribute_value_1=virus%3A%20Orthohantavirus&attribute_type_2=examined%20for&attribute_value_2=virus%3A%20Orthohantavirus&country=Panama

But that doesn't address your needs for 3. and 4. The host/parasite information (identification and collecting info) does not display on the respective parasite/host records. While that would make things easier, it is just one click away and reduces the amount of content on any particular page.

Having the related host or parasite info displayed on the same page allows for double checking for accuracy to make sure the right records were associated, which was hugely beneficial. It is also not obvious to a non-Arctos or even Arctos user that following the url would get you that info. For example, following a link to other external resources won't necessarily get you a taxon ID and collecting event information.

And #6 also is a request for being able to search on selected higher classification values, including backwards from the parasite record - e.g Find all Cestodes collected from Sciuridae. We had this functionality.

We are trying to see if we can develop a separate module for host/pathogen queries, but I have no idea if that will work broadly for other purposes or be supported in the long term. We previously had all these functions in Arctos. I would like to keep all these options in discussion, and would be happy to have committee or task force with other interested parties.

@acdoll
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acdoll commented Sep 14, 2023

it does! Just mouse over

Well, would you look at that! I'd swear that wasn't popping up yesterday, but maybe I was scrolling and clicking too fast.

@dustymc dustymc closed this as completed Sep 19, 2023
@campmlc
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campmlc commented Sep 19, 2023 •
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Again, this issue is not completed. There are multiple aspects that have not been addressed, and there needs to be more discussion. Happy to form a task group. But we by no means have restored the lost functionality as requested, and I don't think these concepts are being understood. We spent three years developing this model. Can we move this to a discussion so that it stops bothering @dusty?

@campmlc campmlc reopened this Sep 19, 2023
@dustymc dustymc closed this as completed Oct 17, 2023
@campmlc campmlc mentioned this issue May 6, 2024
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@acdoll acdoll

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@gracz-UNL gracz-UNL

Labels
Function-Relationship Grant funded (Arctos member) This issue is related to an Arctos member grnat funded project. Grant funded (Arctos) This issue is related to an Arctos grant funded project Priority-High (Needed for work) High because this is causing a delay in important collection work..
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@ccicero @mkoo @dustymc @Jegelewicz @amgunderson @acdoll @campmlc @jldunnum @gracz-UNL