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when encountering occurrence id reference [United States National Parasite Collection 080155] look for match catalog number [USNPC # 080155]] #4

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jhpoelen opened this issue May 27, 2021 · 3 comments
Open

when encountering occurrence id reference [United States National Parasite Collection 080155] look for match catalog number [USNPC # 080155]] #4

jhpoelen opened this issue May 27, 2021 · 3 comments

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@jhpoelen
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jhpoelen commented May 27, 2021 •
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From #1 and

      1 found unresolved reference [United States National Parasite Collection 97980]
      1 found unresolved reference [United States National Parasite Collection 97644]
      1 found unresolved reference [United States National Parasite Collection 95442]
      1 found unresolved reference [United States National Parasite Collection 95441]
      1 found unresolved reference [United States National Parasite Collection 95440]
      1 found unresolved reference [United States National Parasite Collection 94980]
      1 found unresolved reference [United States National Parasite Collection 94139]
      1 found unresolved reference [United States National Parasite Collection 92705]
      1 found unresolved reference [United States National Parasite Collection 81320]
      1 found unresolved reference [United States National Parasite Collection 79658]
      1 found unresolved reference [United States National Parasite Collection 77654]
      1 found unresolved reference [United States National Parasite Collection 77651]
      1 found unresolved reference [United States National Parasite Collection 77650]
      1 found unresolved reference [United States National Parasite Collection 77649]
      1 found unresolved reference [United States National Parasite Collection 77648]
      1 found unresolved reference [United States National Parasite Collection 71848]
      1 found unresolved reference [United States National Parasite Collection 102989]
      1 found unresolved reference [United States National Parasite Collection 102929]
      1 found unresolved reference [United States National Parasite Collection 102907]
      1 found unresolved reference [United States National Parasite Collection 081321]
      1 found unresolved reference [United States National Parasite Collection 080545]
      1 found unresolved reference [United States National Parasite Collection 080544]
      1 found unresolved reference [United States National Parasite Collection 080158]
      1 found unresolved reference [United States National Parasite Collection 080157]
      1 found unresolved reference [United States National Parasite Collection 080156]
      1 found unresolved reference [United States National Parasite Collection 080155]
      1 found unresolved reference [United States National Parasite Collection 080154]
      1 found unresolved reference [United States National Parasite Collection 080023]
      1 found unresolved reference [United States National Parasite Collection 080022]
      1 found unresolved reference [United States National Parasite Collection 080021]
      1 found unresolved reference [United States National Parasite Collection 080019]

and from USNM, turns out that they collected the imported USNPC records with as record numbers with format USNPC # [some number]

For example, United States National Parasite Collection 080155 as mentioned in MSB-Para, has a matching record in http://n2t.net/ark:/65665/386ad940e-e24f-4c20-b874-2a94371fe10e via record number USNPC # 080155

suggest for GloBI to take this into account when linking records.

fyi @dustymc @campmlc

$ zipgrep "USNPC # 080155" 60c10aea7c4dfdfd81e078541a271ceb379ab8605af819f90cd6882e8712d12e 
occurrence.txt:http://n2t.net/ark:/65665/386ad940e-e24f-4c20-b874-2a94371fe10e	PhysicalObject		http://biocol.org/urn:lsid:biocol.org:col:34871	USNM	Invertebrate Zoology	NMNH Extant Biology	PreservedSpecimen	http://n2t.net/ark:/65665/386ad940e-e24f-4c20-b874-2a94371fe10e	1375515	{"hostGen":"Strix","hostSpec":"occidentalis caurina"}	USNPC # 080155	J. Reid	1			Slide62	62	1987	3	3						North America, United States, Oregon	North America		United States	Oregon																Hoberg, Eric P.; Wallner-Pendleton, E.; Hedstrom, O. R.			Centrorhynchus conspectus	Animalia, Acanthocephala, Palaeacanthocephala, Polymorphida, Centrorhynchidae	Animalia	Acanthocephala	Palaeacanthocephala	Polymorphida	Centrorhynchidae	Centrorhynchus		conspectus			Van Cleave & Pratt
jhpoelen pushed a commit to globalbioticinteractions/globalbioticinteractions that referenced this issue May 28, 2021
first pass at indexing custom US Parasite Collection catalogNumber ->…
0a9ec22 
… occurrenceId mapping; related to globalbioticinteractions/msb-para#4
@jhpoelen jhpoelen mentioned this issue May 28, 2021
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jhpoelen pushed a commit to globalbioticinteractions/globalbioticinteractions that referenced this issue Jun 2, 2021
add United States Parasite Collection mapping; globalbioticinteractio…
97d4e35 
…ns/msb-para#4
@jhpoelen
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note that various MSB Para records reference the US Parasite Collection records with a (same individual as) relation, technically not an interaction, so not yet indexed and resolved:

$ zipgrep "080155" datasets/local/0e7f50547be1add0b78c29f36a66e471ee04909a4775b31e0868d320a7877e15
occurrence.txt:http://arctos.database.museum/guid/MSB:Para:27648?seid=4144958	PhysicalObject	2021-03-26 11:01:32.394413	en		http://vertnet.org/resources/norms.html	http://arctos.database.museum/guid/MSB:Para:27648	MSB	27	MSB	Parasite specimens	PreservedSpecimen		age class=adult;verbatim host ID=Strix occidentalis caurina	http://arctos.database.museum/guid/MSB:Para:27648?seid=4144958	MSB:Para:27648		2426	Collector(s): Eric P. Hoberg	1		adult	wild caught	observation	collector number=2426		http://arctos.database.museum/guid/MSB:Para:27648	(parasite of) MSB:Host http://arctos.database.museum/guid/MSB:Host:22909; (same individual as) USNM: National Museum of Natural History 1375515; (same individual as) USNPC: United States National Parasite Collection 080155	[{"scientific_name":"Centrorhynchus conspectus","nature_of_id":"unknown","accepted_id_fg":1,"made_date":"1987-03-03","short_citation":null,"publication_id":null,"identification_remarks":"Van Cleave & Pratt, 1940; Former nature_of_id: legacy.","idby":"Eric P. Hoberg","concept_label":null}]		1987-03-03	1987-03-03	62	1987	03	03	3-III-87				North America, United States, Oregon	North America				United States	Oregon		Oregon	Oregon				Eric P. Hoberg								Eric P. Hoberg	1987-03-03 00:00:00		unverified									Eric P. Hoberg	1987-03-03		Van Cleave & Pratt, 1940; Former nature_of_id: legacy.	A	unknown		Centrorhynchus conspectus	Animalia, Acanthocephala, Palaeacanthocephala, Polymorphida, Centrorhynchidae, Centrorhynchus,	Animalia	Acanthocephala	Palaeacanthocephala	Polymorphida	Centrorhynchidae	Centrorhynchus	conspectus		species	ICZN

@jhpoelen
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jhpoelen commented Jun 23, 2021 •
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some other parasite references use the (collected with) relation (e.g., (collected with) USNPC: United States National Parasite Collection 102989). This relation is currently not interpreted as an interaction record.

$ zipgrep -o "\t.*USNPC.*\t" datasets/local/0e7f50547be1add0b78c29f36a66e471ee04909a4775b31e0868d320a7877e15 | grep "collected with" | head -n2 | tail -n1
occurrence.txt:	PhysicalObject	2021-03-26 11:01:32.394413	en		http://vertnet.org/resources/norms.htmlhttp://arctos.database.museum/guid/MSB:Para:5877	MSB	27	MSB	Parasite specimens	PreservedSpecimen	verbatim host ID=Alopex lagopus;verbatim host sex=female	http://arctos.database.museum/guid/MSB:Para:5877?seid=1873192	MSB:Para:5877		13802	Collector(s): Robert L. Rausch	1				whole organism (slide)	collector number=13802	http://arctos.database.museum/MediaSearch.cfm?collection_object_id=22532860			http://arctos.database.museum/guid/MSB:Para:5877	(collected with) USNPC:Para http://arctos.database.museum/guid/USNPC:Para:341; (collected with) USNPC: United States National Parasite Collection 102989; (parasite of) MSB:Host http://arctos.database.museum/guid/MSB:Host:2645; (parasite of) USNM: National Museum of Natural History 298475	[{"scientific_name":"Mesocestoides","nature_of_id":"unknown","accepted_id_fg":1,"made_date":"1954-08-27","short_citation":null,"publication_id":null,"identification_remarks":"R.L.Rausch verbatim ID = Mesocestoides; Former nature_of_id: legacy.","idby":"Robert L. Rausch","concept_label":null}]		1954-08-27	1954-08-27	239	1954	08	27	Aug 27 '54				North America, Bering Sea, United States, Alaska, Saint Matthew Island	North America	Bering Sea		Saint Matthew Island	United States	Alaska		Old quonset, SE valley, St. Matthew Island	Old Quonset, SE Valley, SMI					Mariel L. Campbell				60.3844540000	-172.6565890000		30926	Mariel L. Campbell	2012-10-04 00:00:00	GeoLocate	GeoLocate	unverified									Robert L. Rausch	1954-08-27		R.L.Rausch verbatim ID = Mesocestoides; Former nature_of_id: legacy.	A	unknown		Mesocestoides	Animalia, Platyhelminthes, Cestoda, Eucestoda, Cyclophyllidea, Mesocestoididae,	Animalia	PlatyhelminthesCestoda	Cyclophyllidea	Mesocestoididae	Mesocestoides			genus

@jhpoelen
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@campmlc should the arctos relation (collected with) be interpreted as co-occurs with or similar? If so, the (collected with) may indicate a likelihood of an interaction because two individuals were close to each other.

@jhpoelen jhpoelen mentioned this issue Nov 18, 2021
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