Open gbif-portal opened 3 years ago
Contact is silknets@vt.edu or via this GitHub account!
Hi there,
If you used occ_download(), you should be able to locate the relevant downloads and their DOIs in your account: https://www.gbif.org/user/download
If that isn't the case, or if you simply wish to combine downloads regardless of the way they were obtained, you can indeed create a derived dataset. You simply need to summarize the combined dataset by the column datasetKey. More information is available here: https://www.gbif.org/derived-dataset/about
Let me know if you have any questions!
Daniel, thank you for the reply.
I provided incorrect information above, which seems to be the issue's root cause. I used the occ_search() function to retrieve GBIF records, and not occ_download() as I previously stated. The latter appears to require a login through GBIF, which explains why I don't see the downloads in questions in my GBIF downloads records associated with my profile.
Does the occ_search() query generate any DOIs or datasetKeys that I could track down, or would this require the query to be re-run as an occ_download()?
Occ_search() does not generate DOIs. If you still have the original data saved, does it have the column datasetKey
?
I don't have the original data saved. I used occ_search(), then applied a series of filters to this data for each species before saving the CSV output. This output doesn't include datasetKey.
However, this data has retained the following columns if this is helpful: datasetName, occurrenceID, catalogNumber, institutionCode
Could you paste a couple of lines here?
Acantharchus pomotis_occurrence data.txt I couldn't upload the csv file, but here it is as a txt file. I'm also pasting the first 5 lines below:
<html xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">
occurrenceStatus | species | decimalLongitude | decimalLatitude | year | eventDate | issues | geodeticDatum | countryCode | country | datasetName | occurrenceID | catalogNumber | institutionCode | locality | decimalLongitude.1 | decimalLatitude.1 | optional -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- | -- PRESENT | Acantharchus pomotis | -79.1819 | 33.87465 | 2021 | 2021-03-23T09:07:32 | cdround,gass84 | WGS84 | US | United States of America | iNaturalist research-grade observations | https://www.inaturalist.org/observations/71874817 | 71874817 | iNaturalist | NA | -79.1819 | 33.87465 | TRUE PRESENT | Acantharchus pomotis | -83.6579 | 30.46513 | 2021 | 2021-04-01T17:31:28 | cdround,gass84 | WGS84 | US | United States of America | iNaturalist research-grade observations | https://www.inaturalist.org/observations/75680450 | 75680450 | iNaturalist | NA | -83.6579 | 30.46513 | TRUE PRESENT | Acantharchus pomotis | -82.4704 | 30.2839 | 2021 | 2021-04-26T17:20:00 | cdround,gass84 | WGS84 | US | United States of America | iNaturalist research-grade observations | https://www.inaturalist.org/observations/77743228 | 77743228 | iNaturalist | NA | -82.4704 | 30.2839 | TRUE PRESENT | Acantharchus pomotis | -82.3384 | 30.36415 | 2021 | 2021-05-24T15:09:59 | gass84 | WGS84 | US | United States of America | iNaturalist research-grade observations | https://www.inaturalist.org/observations/80203305 | 80203305 | iNaturalist | NA | -82.3384 | 30.36415 | TRUE PRESENT | Acantharchus pomotis | -82.2869 | 30.29865 | 2021 | 2021-05-24T15:05:14 | cdround,gass84 | WGS84 | US | United States of America | iNaturalist research-grade observations | https://www.inaturalist.org/observations/80203259 | 80203259 | iNaturalist | NA | -82.2869 | 30.29865 | TRUE
I used the rgbif occ_download() function for an ongoing research project. I did not, however, save the DOI for each individual download. My understanding is that I could combine the CSV output files to create a derived dataset with a single DOI (for each of citing - we have 139 species in the study). Is it possible to either a) track down those original DOIs associated with my downloads, or b) create a derived dataset without them? Any help would be much appreciated!
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