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ParasiteTracker / other-projects-modeling-biotic-interactions

A place to link, explore, document and make lists of other projects that are already modeling biotic interactions.
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Arctos now linked to Globi. Thread includes descriptions of data and biotic interaction fields #3

Open seltmann opened 5 years ago

seltmann commented 5 years ago

http://arctos.database.museum/guid/MSB:Para:27069

https://www.globalbioticinteractions.org/2019/07/10/associating-with-natural-history-collections/

seltmann commented 5 years ago

@jhpoelen can you provide me with an example of a file from Arctos that Globi is using? Or a list of fields and format being provided to Globi? Is it a DwC file? I am asking because @neilcobb is considering adding fields to Symbiota and we need concrete examples of things that already work.

seltmann commented 5 years ago

Examples from the Arctos DwC Archive file/s from MSB Parasite Collection (Arctos) - Version 32.29 Resource: Division of Parasites, Museum of Southwestern Biology (http://arctos.database.museum/SpecimenSearch.cfm) Example database record (http://arctos.database.museum/guid/MSB:Para)

Darwin Core Archive: http://ipt.vertnet.org:8080/ipt/resource?r=msb_para

This is a list of fields that seem important in understanding biotic interactions, with examples of data and format from the DwC-Archive file

field name: organismID http://arctos.database.museum/guid/MSB:Para:20033 http://arctos.database.museum/guid/MSB:Para:25319 http://arctos.database.museum/guid/MSB:Para:2405 http://arctos.database.museum/guid/MSB:Para:2508 http://arctos.database.museum/guid/MSB:Para:1760

field name: dynamicProperties age class=adult ; experimental=no ; location in host=intestine ; verbatim host ID=Histrionicus histrionicus

A full list of all data included in dynamicProperties is here: dynamic-properties.txt

Relationships found in the dynamic properties are: age class experimental sex location in host verbatim host ID verbatim host sex

field name: associatedMedia http://arctos.database.museum/MediaSearch.cfm?collection_object_id=21336140 http://arctos.database.museum/MediaSearch.cfm?collection_object_id=21909334 http://arctos.database.museum/MediaSearch.cfm?collection_object_id=21909526 http://arctos.database.museum/MediaSearch.cfm?collection_object_id=21909528 http://arctos.database.museum/MediaSearch.cfm?collection_object_id=21909530

field name: associatedSequences http://www.ncbi.nlm.nih.gov/nuccore/ EU394169; http://www.ncbi.nlm.nih.gov/nuccore/EU394134 http://www.ncbi.nlm.nih.gov/nuccore/ KP721422; http://www.ncbi.nlm.nih.gov/nuccore/KP721404 http://www.ncbi.nlm.nih.gov/nuccore/ KP734312.1

field name: associatedTaxa Other host value ABJ1185 This parasite has been entered twice into the database. This is reflected in the "same individual as" relationship This species was coeinfected with Paragordius obamai Vial contains also the host tissue

These are all the values stored in the associatedTaxa field

field name: habitat marine Narrow-leaf cottonwood riparian, pinyon-juniper puddle on a dirt road salt pond small farm pond stream

field name: associatedOccurrences (host of) MSB:Para http://arctos.database.museum/guid/MSB:Para:40; (host of) MSB:Para http://arctos.database.museum/guid/MSB:Para:41 (parasite of) UAM:Mamm http://arctos.database.museum/guid/UAM:Mamm:83861; (same individual as) UAM:Ento http://arctos.database.museum/guid/UAM:Ento:276889 (parasite of) MVZ:Mamm http://arctos.database.museum/guid/MVZ:Mamm:225318

Relationship information is shared through associatedOccurrences. Relationships indicated in associatedOccurrences are: collected with host of offspring of parasite of parent of same individual as same lot as sibling of

lifeStage adult adult; adult adult; egg(s) adult; immature adult; larva cyst(s) egg(s) immature juvenile larva larva, nymph larva, nymph; larva larva; adult larva; larva, nymph mature mature; immature tetrathyridia

establishmentMeans captive unknown wild caught

seltmann commented 5 years ago

Data in Globi is linked through Arctos records based on an interaction between two organisms as supported by Arctos. The links are not for individual records. An example link from the Arctos record http://arctos.database.museum/guid/MSB:Para:27070 to GloBI

Screen Shot 2019-08-28 at 1 43 15 PM

jhpoelen commented 5 years ago

@seltmann GloBI does keep pointers to individual records, only the web UI also shows other records that support/describe the same interaction. So, for every single Arctos records association there exists a single interaction record in GloBI.

jhpoelen commented 5 years ago

See for example https://github.com/jhpoelen/eol-globi-data/issues/134#issuecomment-508321721 .

jhpoelen commented 5 years ago

@seltmann please let me know if you have any remaining questions.

seltmann commented 4 years ago

http://arctos.database.museum/info/ctDocumentation.cfm?table=CTID_REFERENCES