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Please submit your helpdesk request here (or send an email to helpdesk@gbif.no). We will also use this repo for documentation of node helpdesk cases.
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Bulk collections dataset from NHM #117

Closed rukayaj closed 1 year ago

rukayaj commented 1 year ago

The collection consists mostly of bulk-samples - so this makes some of the datafields more challenging - e.g. when there are more than one taxa in one sample. The collection is registered in GRSciColl; "Collection for bulk- and project material".

The database for the collection is so far only an excel-sheet, e.g:

catalogNumber institutionCode collectionCode kingdom Phylum class order infraorder family genus specificEpithet identificationRemarks verbatimIdentification PreservedSpecimen recordedBy identifiedBy continent country stateProvince county locality verbatimLocality decimalLongitude decimalLatitude eventDate verbatimEventDate materialSampleID
658 NHMO BULK Animalia Arthropoda Thecostraca Balanomorpha Balanidae Balanus Bulk of organisms preserved in ethanol Immanuel Vigeland Singapore? 67a. Asbest plate. After 9. 02/07/1965 http://purl.org/nhmuio/id/A57D28C3-6082-12A2-9F86-111061A7032E
659 NHMO BULK Animalia Annelida Polychaeta Bulk of organisms preserved in ethanol Immanuel Vigeland Singapore? Bulk-sample collected from SFI (Skipsteknisk forskningsinstitutt) test raft 1965 http://purl.org/nhmuio/id/A5A01A14-6082-12A2-99F2-1211FB479C61
660 NHMO BULK Animalia Evertebrata Bulk of organisms preserved in ethanol E. Hansen, D. Distad Norwegian expedition. 17.2.193, 1928. Slepetrekk. (191). No '59. 1928 http://purl.org/nhmuio/id/A5C02535-6082-12A2-93A0-1BD8B33D7549
661 NHMO BULK Animalia Evertebrata Bulk of organisms preserved in ethanol Immanuel Vigeland Norwegia expeditioin Port Lockeroy http://purl.org/nhmuio/id/A5E894C6-6082-12A2-9936-1622532FF4B8
662 NHMO BULK Animalia Evertebrata Bulk of organisms preserved in ethanol Immanuel Vigeland 71 2 S, 12 W 71gr 2 S, 12 gr W (?) des. 191. http://purl.org/nhmuio/id/A6FFAA16-6082-12A2-94D2-15B739D14C6C
663 NHMO BULK Animalia Evertebrata Bulk of organisms preserved in ethanol Immanuel Vigeland 71 2 S, 12 16 W S.B. 71gr 2 CxL 12 gr 16min (hovedetikett). Kapt Ring. 16/12/1928 17.2.193, 16.12.1928 http://purl.org/nhmuio/id/A73F9947-6082-12A2-9394-1A6D53AC25AA
664 NHMO BULK Animalia Evertebrata Bulk of organisms preserved in ethanol Immanuel Vigeland Port Lockeroy http://purl.org/nhmuio/id/A7687E08-6082-12A2-9B91-184EB26BBB38
665 NHMO BULK Animalia Evertebrata Serupoedlaria. Bicillarina. Bulk of organisms preserved in ethanol Immanuel Vigeland Spitzbergen expedition? http://purl.org/nhmuio/id/A777E759-6082-12A2-9E42-14E767A2CE66
666 NHMO BULK Animalia Bryozoa Gymnomaelata Cheilostomata Mucronellidae Porella sacata Bulk of organisms preserved in ethanol Immanuel Vigeland http://purl.org/nhmuio/id/A7A3642B-6082-12A2-983A-1FC0D13A6272
667 NHMO BULK Animalia Bryozoa 1. Electra pilosa var. Detata. 2. Electra pilosa var. Verticillata. 3. Saropocallaria reptans. 4. Cellaporella haline. 5. Alcyoridium hirsutum. 6. Flustrallidra hispida. Organism or bulk of organisms preserved dry Immanuel Vigeland Immanuel Vigeland Sweden Bohuslän 1941 http://purl.org/nhmuio/id/A9669802-6082-12A2-93A4-112FD2AEF462
668 NHMO BULK Animalia Bryozoa Valkeria uva Organism or bulk of organisms preserved dry Immanuel Vigeland F. Borg Halland, Vaderø 199? http://purl.org/nhmuio/id/AA2E7BEA-6082-12A2-9D2F-1B21D4B513DD
gunnhilm commented 1 year ago

I was hoping that we could keep each entry as one record, even though there are several taxa, and mention them by the highest common level, e.g. "Bryozoa" for sample 667. There are several taxa in many of the samples, maybe in most of them, but its just for some that I have made a note about which they are. Generally we haven't recorded (or do not know) what the taxa are. Is this feasible, within GBIFs framework, to register bulks like this, with only the highest common taxonomic level mentioned? We can of course delete this kind of information from the verbatimIdentification-field. It is more "additional arbitrary information", not recorded in a systematic fashion, and I guess there is no dwc-field for that.

dagendresen commented 1 year ago

I agree entirely that dwc:MaterialSample entries (including notably the environment samples for eDNA) would often be bulk samples composed of multiple taxa, or even no taxa at all! I hope the new GBIF data model under development and enabling the move away from the Occurrence model straight-jacket will enable better representation of such bulk samples -- soonish!

dagendresen commented 1 year ago

And if a bulk sample includes a mixture of organisms from multiple kingdoms, I think that the super-class biota is completely legitimate to use https://www.catalogueoflife.org/data/taxon/5T6MX https://www.gbif.org/species/170809336

rukayaj commented 1 year ago

Thanks dag! Ok that sounds like a good move then, we keep 1 row per bulk sample, as you've got it currently, and use biota or whatever higher taxonomic level.

rukayaj commented 1 year ago

@gunnhilm I've made a dataset on the IPT for this - https://ipt.gbif.no/manage/resource.do?r=uio-nhm-bulk, I'll send you user credentials in an email.

rukayaj commented 1 year ago

Published https://www.gbif.org/dataset/a6e3fb90-33f7-446b-82d8-5eef4480f5f1