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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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MUSIT identificationQualifier #1

Closed dagendresen closed 3 years ago

dagendresen commented 3 years ago

MUSIT has moved the identificationQualifier "aff." and "cf." out of the scientificName and added a new column to the data-views (and data dump-files) IDENTIFICATIONPRECISION (with values "1" and "null").

This type of information is important for the ongoing red-listing work coordinated by NBIC.

Action: add IPT mapping for musit:IDENTIFICATIONPRECISION to dwc: dwc:identificationVerificationStatus Todo: map must:"identification-qualifier" to dwc:identificationQualifier if made available.

dagendresen commented 3 years ago

identificationQualifier

Identifier | http://rs.tdwg.org/dwc/terms/identificationQualifier Definition | A brief phrase or a standard term ("cf.", "aff.") to express the determiner's doubts about the Identification. Examples | aff. agrifolia var. oxyadenia (for Quercus aff. agrifolia var. oxyadenia with accompanying values Quercus in genus, agrifolia in specificEpithet, oxyadenia in infraspecificEpithet, and var. in taxonRank. cf. var. oxyadenia for Quercus agrifolia cf. var. oxyadenia with accompanying values Quercus in genus, agrifolia in specificEpithet, oxyadenia in infraspecificEpithet, and var. in taxonRank.

identificationVerificationStatus

Identifier | http://rs.tdwg.org/dwc/terms/identificationVerificationStatus Definition | A categorical indicator of the extent to which the taxonomic identification has been verified to be correct. Comments | Recommended best practice is to use a controlled vocabulary such as that used in HISPID and ABCD. Examples | 0 ("unverified" in HISPID/ABCD).

HISPID

See also HISPID for more information on proposed controlled vocabulary (for identificationVerfificationStatus, but not for identificationQualifier): https://github.com/hiscom/hispid/blob/master/vocabulary/identification_qualifier.xml https://github.com/hiscom/hispid/blob/master/vocabulary/identification_verification_status.xml https://github.com/hiscom/hispid/issues/16 https://github.com/hiscom/hispid/issues/115

dwc:Identification

This information was added to IPT using the data model for the Occurrence core. It would also be useful to add the identification history - if MUSIT can deliver this type of information. https://rs.gbif.org/extension/dwc/identification.xml https://rs.gbif.org/core/dwc_occurrence_2020-07-15.xml

dagendresen commented 3 years ago

I have now mapped musit:IDENTIFICATIONPRECISION to dwc: dwc:identificationVerificationStatus for these datasets

Museum Vascular Mycology Bryophyte Lichen
Bergen (bg) bg_vascular bg_fungi bg_bryophytes bg_lichens
Kristiansand (kmn) kmn_vascular
Oslo (o) o_vascular o_fungi o_bryophytes o_lichens
Stavanger (svg) svg_vascular
Trondheim (trh) trh_v trh_f trh_b trh_lichens
Tromsø (trom) trom_vascular trom_fungi trom_bryophytes trom_lichens
dagendresen commented 3 years ago

Some examples of records pubished with identificationVerificationStatus = 1 BG -- https://www.gbif.org/occurrence/1144026242 BG -- https://www.gbif.org/occurrence/1144026245 O -- https://www.gbif.org/occurrence/1702431950 O -- https://www.gbif.org/occurrence/1702431960 TRH -- https://www.gbif.org/occurrence/1701257242 TRH -- https://www.gbif.org/occurrence/1701242426 TROM -- https://www.gbif.org/occurrence/1323692704 TROM -- https://www.gbif.org/occurrence/1323692707

dagendresen commented 3 years ago

Added also mapping musit:IDENTIFICATIONPRECISION --> dwc:identificationQualifier for the ADB Red Listing work. However, we probably need a confirmation from MUSIT/museums about the intended meaning of the musit:IDENTIFICATIONPRECISION descriptor...

dagendresen commented 3 years ago

Good overview of open nomenclature qualifiers from: Sigovini, M., Keppel, E., and Tagliapietra, D. (2016). Open nomenclature in the biodiversity era. Methods Ecol. Evol. 7, 1217–1225. doi: 10.1111/2041-210X.12594

rukayaj commented 3 years ago

Is there anything left that we still need to do for this task?

dagendresen commented 3 years ago

I believe that the current mapping of identificationQualifier with values provided = "1" is not correct.

identificationVerfificationStatus = if the identification has been verified identificationQualifier = what type of doubt in identification

However, ADB wants to get it this way for the current ongoing Red List work... so let us keep it like this for now.

The best would be for MUSIT to provide the actual identificationQualifier strings ;-) Interpretation of the MUSIT provided information depends a lot on how the users of MUSIT intend their "1"s to be interpreted. Jenny Smedmark was interested in a meeting about this and more. I will contribute to a MUSIT meeting on 15 March - where this might come up.

dagendresen commented 3 years ago

On another side topic. I found while updating the IPT-mapping across ALL the MUSIT herbaria that identifying each and all herbaria was not so easy. I suggest making a table along the lines of the one I included above for MUSIT collections in the Wiki? With hyperlinks to the IPT admin for the datasets...?