link from biodiversityPMC to zenodo BLR via zenodo deposition ID

[myrmoteras]

Service

Biodiversity PMC

Contact Details

[email protected]

Is your feature request related to a problem?

linking from biodiversityPMC to BLR/Zenodo, as discussed with Patrick

in this case, the external link uses the DOI of the article which should be the DOI of the treatment, or if pointing to the article it should use the Zenodo deposition ID which is also in the metadata provided by Plazi's XML.

If the original DOI is used then a firewall is hit.

All the treatments are open access - and most recently, when using a zenodo deposition ID then the user could become part of the Zenodo community and have access to the otherwise closed access publication

Example: https://sibils.text-analytics.ch/search/?query=what%20is%20the%20length%20of%20%22Guibemantis%20ambakoana%22%3F#

• DOI for treatment https://doi.org/10.5281/zenodo.10471789
• Zenodo deposition number for article: https://zenodo.org/records/10469003

Describe the solution you'd like

see above

Additional context

No response

[emilie19]

@myrmoteras: It seems that we do not have this information in the documents we are receiving from PLAZI.

[myrmoteras]

@emilie19 do you have an example of a JATS that you use from us? Talking to Guido, in the MODS header this information ought to be. Let's find out

[jgobeill]

03B3990EC5234645FF2CF9F8FD68FE9C.zip

Here is the XML that was deposited in the SIBiLS FTP for this treatment.

There is a zenodo-doi (10.11646/zootaxa.5397.4.1), which is not 10.5281/zenodo.10471789. This one links to mapress.com.

And there is no mention to the Zenodo deposition record (10469003).

If we had one of them, we should be able to correctly link to Zenodo.

I've tried to find a manual strategy for retrieving this Zenodo URL , via Google or Zenodo, but I can't manage it. If you have this information, could you include it in the XML treatments records deposited in SIBiLS FTP ?

Or maybe this is just a matter of Zenodo DOI corrupted for this file ?

[myrmoteras]

I see

<uri content-type="zenodo-doi">10.11646/zootaxa.5397.4.1</uri>
<uri content-type="treatment-bank-uri">http://treatment.plazi.org/id/03B3990EC5234645FF2CF9F8FD68FE9C</uri>
<article-title>Unexpected diversity and co-occurrence of phytotelmic frogs (Guibemantis) around Andasibe, one of the most intensively surveyed amphibian hotspots of Madagascar, and descriptions of three new species</article-title>
<pub-id pub-id-type="doi">10.11646/zootaxa.5397.4.1</pub-id>

in this case
<uri content-type="zenodo-doi">10.11646/zootaxa.5397.4.1</uri>

should be

<uri content-type="zenodo-doi">10.11646/zootaxa.5397.4.1</uri>

I will talk to Guido to change. Alternatively you can get it from here our stats: https://tb.plazi.org/GgServer/srsStats/stats?outputFields=doc.uuid+lnk.doi+lnk.zenodoDepId+lnk.gbifTaxonId+lnk.clbTaxonId+lnk.sibIlsUrl&groupingFields=doc.uuid+lnk.doi+lnk.zenodoDepId+lnk.gbifTaxonId+lnk.clbTaxonId+lnk.sibIlsUrl&FP-doc.uuid=03B3990EC5234645FF2CF9F8FD68FE9C&format=JSON

[myrmoteras]

Hi Guido
When upload our XML to SIBiLS, we provide a wrong DOI in the metadata for the treatment. Currentyl in the place of the treatment DOI we provide the DOI of the article.
Here is an example
SIBiLS

Zip treatment example
the

<uri content-type="zenodo-doi">10.11646/zootaxa.5397.4.1</uri>
<uri content-type="treatment-bank-uri">[http://treatment.plazi.org/id/03B3990EC5234645FF2CF9F8FD68FE9C</uri](http://treatment.plazi.org/id/03B3990EC5234645FF2CF9F8FD68FE9C%3c/uri)>
<article-title>Unexpected diversity and co-occurrence of phytotelmic frogs (Guibemantis) around Andasibe, one of the most intensively surveyed amphibian hotspots of Madagascar, and descriptions of three new species</article-title>
<pub-id pub-id-type="doi">10.11646/zootaxa.5397.4.1</pub-id>

<uri content-type="zenodo-doi">10.11646/zootaxa.5397.4.1</uri>
should be
<uri content-type="zenodo-doi">10.11646/zootaxa.5397.4.1</uri>
That is the zenodo doi of the treatment.

Thanks for looking into this

Donat

[myrmoteras]

plazi/ggxml2taxpub#71