University of Sofia (formely Faculty of Biology, SU)

[ManonGros]

University of Sofia

GRSciColl URL: https://www.gbif.org/grscicoll/institution/70b18cea-8fba-41ac-94e2-f04b9640a2a5 Code: BFUS Fuzzy name search in GBIF publisher: None

Number of linked occurrences: 304 (https://www.gbif.org/occurrence/search?advanced=1&institution_key=70b18cea-8fba-41ac-94e2-f04b9640a2a5) Publishing organizations for linked occurrences:

• https://www.gbif.org/publisher/315b3c03-4a0a-424e-83a5-d25aa748e666

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1. Find out if the information is complete and up to date:

• [x] Check the homepage if available or google the institution name in the country. Check if all collections for that institution are represented in GRSciColl.
• [x] Add missing collections/information to the institution on GRSciColl directly in the registry. If some collections are digitized, put the information in the GRSciColl Notes field.

2. Check if the data is also in GBIF:

• [x] If there are GBIF occurrence records linked, check from which dataset/publisher they come. Is the institution a registered publisher? Or do the records come from a third party publisher? Are all the collections in GRSciColl also in GBIF? (add comments to the issue)
• [x] If no record is linked to GRSciColl, look for the institution name on the GBIF list of publishers. Is there any corresponding publisher? Have they published any data? (add comments to the issue)
• [x] If data has been published on GBIF but isn’t linked to GRSciColl, notify Marie (tag ManonGros), she can link the data.
• [x] Translate outcome of your checks into labels. See guidelines here: https://github.com/gbif/collection-mobilization#readme

[spalp]

• Renamed the institution to 'Department of Zoology and Anthropology, Sofia University' to distinguish from the Department of Botany where the herbarium is located. Added BFUS as Institution code, and BF and SU as alternative codes found to be used in datasets published by Plazi (see below). Update (21.11.2023): Renamed to Sofia University after the suggestion of IG.
• Updated the link to the website, the physical adress, and the contacts
• Added the ROR ID of the university
• As of 05.10.2023 there are 304 GBIF occurrence records linked, published from a third party: Scratchpads, all of which are associated with the zoological collection (ALG) is I think only partially published via the dataset Ants of Bulgaria, which otherwise contain occurences not only from ALG | UPDATE (09.11.2023): Dataset deleted from GBIF by the request of the owner.
• From the webpage it is not clear if there are more collections but I expect that there should be more. Asked the relevant people (see below).
• Updated the name of the collection and updated the Collection code for the Zoological collection: https://registry.gbif.org/collection/7f10ed32-b003-4297-ab21-f85257e237d9 from ALG ( to BFUS used in the dataset Trechus (s. str.) “ subnotatus ” species group. ALG was left an alternative collection code for (31.10.2023), which is used in the dataset Ants of Bulgaria

[spalp]

Linking occurrences to the institution

Institution code: "BFUS", "BFSU", "SU", or "BF"

Step 1: Are there any occurrences in GBIF with these institution codes? Are all from this institution?

https://www.gbif.org/occurrence/charts?basis_of_record=MATERIAL_SAMPLE&basis_of_record=MATERIAL_CITATION&basis_of_record=PRESERVED_SPECIMEN&institution_code=BFUS&institution_code=BFSU&institution_code=SU&institution_code=BF Result (20.11.2023): 102 occurrences from 7 datasets. Occurrences with code SU (n = 60) are NOT from this institution.

Step 2: Are occurrences with these codes going to be linked automatically to the institution according to the Lookup API?

https://api.gbif.org/v1/grscicoll/lookup?institutionCode=BFUS --> YES (e.g. https://api.gbif.org/v1/grscicoll/lookup?institutionCode=BFUS&datasetKey=ee639eb0-bf6f-410b-a903-21665b3bdb85)

https://api.gbif.org/v1/grscicoll/lookup?institutionCode=BF --> YES (alternative)

https://api.gbif.org/v1/grscicoll/lookup?institutionCode=BFSU --> YES (alternative)

https://api.gbif.org/v1/grscicoll/lookup?institutionCode=SU --> No: good because currently, these occurrences are from this institution

NOTE: Currently not linked becayse MaterialCitation is not yet accepted.

Step 3: Occurrence mapping with an API

OccurrenceMapping API for the institution: https://api.gbif.org/v1/grscicoll/institution/70b18cea-8fba-41ac-94e2-f04b9640a2a5

NOTES: The manual mapping of occurrences with code SU from the dataset Ants of Bulgaria, because the latter is now deleted from GBIF.

[spalp]

The 121 occurrences (from the previous post) with the Institutional Code SU from the dataset The Ants of Bulgaria: https://www.gbif.org/occurrence/search?dataset_key=e08de352-9383-48b0-88ae-be15cce386c5&institution_code=SU are mapped to the Institution (31.10.2023) BUT are not yet linked with the collection.

According to the lookup API, it these cases could be linked: https://api.gbif.org/v1/grscicoll/lookup?institutionCode=SU&collectionCode=ALG&datasetKey=e08de352-9383-48b0-88ae-be15cce386c5

As we discussed, the problem might that I have first to indicate that records with institutionCode=SU from this dataset belong to the institution. See the APIs occurrenceMapping to the Institution : https://api.gbif.org/v1/grscicoll/institution/70b18cea-8fba-41ac-94e2-f04b9640a2a5

[spalp]

Linking occurrences to the collection

Collection codes: "BFUS", "BFSU", "SU", or "BF"

Step 1: Are there any occurrences in GBIF with these collection codes? Are all from this collection?

https://www.gbif.org/occurrence/charts?basis_of_record=MATERIAL_SAMPLE&basis_of_record=MATERIAL_CITATION&basis_of_record=PRESERVED_SPECIMEN&collection_code=SU Result (20.11.2023): 58 occurrences from 8 datasets. The occurrences with code SU are NOT from this institution.

https://www.gbif.org/occurrence/charts?basis_of_record=MATERIAL_SAMPLE&basis_of_record=MATERIAL_CITATION&basis_of_record=PRESERVED_SPECIMEN&collection_code=BFUS Result (20.11.2023): 19 occurrences from 1 dataset.

https://www.gbif.org/occurrence/charts?basis_of_record=MATERIAL_SAMPLE&basis_of_record=MATERIAL_CITATION&basis_of_record=PRESERVED_SPECIMEN&collection_code=BFSU&collection_code=BF Result (20.11.2023): 0 occurrences.

Step 2: Are occurrences with these codes going to be linked automatically to the collection according to the Lookup API?

https://api.gbif.org/v1/grscicoll/lookup?collectionCode=BFUS --> YES (e.g. https://api.gbif.org/v1/grscicoll/lookup?&collectionCode=BFUS&datasetKey=6e526631-5cf0-49cb-8f6c-ede87474b30d)

https://api.gbif.org/v1/grscicoll/lookup?collectionCode=BFSU --> No https://api.gbif.org/v1/grscicoll/lookup?collectionCode=BF --> No

Step 3: Manual mapping

As of 20.11.2023 no need to map anythig to the Zoological collection: https://registry.gbif.org/collection/7f10ed32-b003-4297-ab21-f85257e237d9

The available mappings could be checked here: https://api.gbif.org/v1/grscicoll/collection/7f10ed32-b003-4297-ab21-f85257e237d9/occurrenceMapping (NOTE: 98 is left in case, the dataset the Ants of Bulgaria is restored)

[spalp]

• Contacted the curator (Sivilov) to ask to update info about their collections and institution in GRSciColl. Sent a link to show the occurrence linked with their datasets and proposed to consider becoming a publisher.
• Contacted one of the Point of contacts (Ilia Gjonov) of the dataset The Ants of Bulgaria to ask whether he could update the InstitutionCode=SU to BFUS to solve the ambiguous match to the institution.

UPDATE (09.11.2023): The curator of the zoological collection expressed interest in becoming publisher, but request the dataset the Ants of Bulgaria to be removed (as it was the wish of the datset owner).

[spalp]

Changed to University of Sofia, as one of the collection managers insisted.

[spalp]

The following 4 occurences should be linked to herbarium SO. Can you help, @ManonGros ?

3 nucleotide sequences from specimens: SO-101206 | SO-105775 | SO105807, the first 2 are part of the INSDC sequences dataset, the third is from iBOL. 1 specimen from the Tropicos dataset: https://www.gbif.org/occurrence/search?dataset_key=e053ff53-c156-4e2e-b9b5-4462e9625424&catalog_number=100563227