myrmoteras
commented
2 years ago to watch the Webhook at work: sort of “rare event” when all workt, listen to the part after 1:42 when this described below happened: https://drive.google.com/drive/folders/1oqt4irXl1_eMX6v-jFRitARpA-0ObZ4I
The presentation at https://doi.org/10.5281/zenodo.5504089
The figure cited therein: https://zenodo.org/record/5507005#.YUCVx7gzb8A
today we have had a little unexpected but incredibly exciting firework at the end of our Arcadia project. Alex and I have been invited to present to the Flemish Government the virtue of Zenodo as a potential repository for Flemish scientists and governmental agencies. This event coincided with getting our microservice in production at Zenodo, one more deliverable in our Arcadia project, and the end of the project itself.
https://twitter.com/myrmoteras/status/1436302301493399561
This service allows uploading a PDF to Zenodo which then is externally processed by TreatmentBank, extracting treatments and images, uploads them to Zenodo each as its own deposit and including the custom metadata we jointly implemented in Zenodo, annotates the metadata of the original deposit with all the related links, submits the article as a treatment article dataset to GBIF where it gets reused. The new GBIF identifier in return is written into the metadata of the original deposit.
In GBIF, for each of the taxa a webpage has been created including the figures that have been extracted and made reusable in BLR, as well as for all of the occurrences, each with a link back to TreatmentBank or BLR and with this adding two new species names to the GBIF taxonomic backbone.
The publication has been published yesterday, and today all the data is accessible.
The entire process worked fully automatically from the moment the article has been published in Zenodo. No human interference, passing our quality controls to avoid incomplete or erroneous deposits in Zenodo and GBIF. It took 8 minutes in total, based on 5 minutes waiting time to get all external links, and three minutes to get the GBIF data set ID back so it could be included in the metadata of the publication deposit, thus avoiding unnecessary traffic between TB and Zenodo.
This in itself is a feast, with all the data available and reused for human and machine consumption and in a stable repository. The real thrill is that we now have a way to include more taxonomic works, but even more, this service can, and I am sure, will be the service to start open up PDFs from many other domains, and thus a real step beyond the still prevailing PDF centric view in science.
It is also a challenge because we need now to work hard to create the templates needed to decode PDFs to make this all happen at scale. We have the the tool to create templates, another achievement in the three years of Arcadia funding.
This all is possible through an incredible teamwork, dedicated highly skilled and motivated colleagues who not give in, despite the COVID-19 pandemic that stopped us from meeting in person.
A very interesting future – a challenge and a future we take on, hopefully together.
Cheers and thanks again for your generous support which made this all possible
Donat ,and I assume, the entire team
Original article: https://doi.org/10.11646/zootaxa.5032.4.6
Zenodo article deposition: https://zenodo.org/record/5499090#.YTtdHJ0zb8A Zenodo figure deposition: https://zenodo.org/record/5500033#.YTtdMJ0zb8A Zenodo/BLR treatment deposition: https://doi.org/10.5281/zenodo.5500037 (see the custom metadata)
OpenAIRE article: https://explore.openaire.eu/search/publication?pid=10.11646/zootaxa.5032.4.6
OpenAIRE treatment: https://explore.openaire.eu/search/publication?pid=10.5281%2Fzenodo.5500037
OpenAIRE occurrence: https://explore.openaire.eu/search/publication?pid=10.11646%2Fzootaxa.5032.4.6
TreatmentBank article: https://treatment.plazi.org/GgServer/summary/C154DB54FFA9B65D2460FFED5F578933 TreatmentBank treatment (HTML): http://treatment.plazi.org/id/3D6DA32C-FFA1-B655-24F7-FDAA5C4F8EC3 TreatmentBank treatment (JSON): https://zenodo.org/record/5500037/export/json TreatmentBank stats: https://tb.plazi.org/GgServer/dioStats/stats?outputFields=doc.articleUuid+doc.doi+doc.zooBankId+doc.gbifId+doc.zenodoDepId+bib.source+cont.pageCount+cont.treatCount+cont.treatCountDoi+cont.treatCitCount+cont.matCitCount+cont.figCount+cont.figCountZen+cont.bibRefCount&groupingFields=doc.articleUuid+doc.doi+doc.zooBankId+doc.gbifId+doc.zenodoDepId+bib.source&FP-doc.articleUuid=C154DB54FFA9B65D2460FFED5F578933&format=JSON GBIF dataset ID: https://www.gbif.org/dataset/8f239084-30f3-4a6c-ba97-3eb65356beb5 GBIF occurrence data set: https://www.gbif.org/occurrence/search?dataset_key=8f239084-30f3-4a6c-ba97-3eb65356beb5 GBIF occurrence data set, holotypes only: https://www.gbif.org/occurrence/search?dataset_key=8f239084-30f3-4a6c-ba97-3eb65356beb5&type_status=HOLOTYPE GBIF species pages: https://www.gbif.org/species/search?dataset_key=8f239084-30f3-4a6c-ba97-3eb65356beb5&origin=SOURCE&status=ACCEPTED&advanced=1 ChecklistBank dataset: https://www.checklistbank.org/dataset/4311/about ChecklistBank import overview: https://www.checklistbank.org/dataset/4311/imports/18 ChecklistBank species: https://www.checklistbank.org/dataset/4311/taxon/3D6DA32CFFA3B65624F7FAF25DC889CA.taxon ChecklistBank species verbatim: https://www.checklistbank.org/dataset/4311/taxon/3D6DA32CFFA3B65624F7FAF25DC889CA.taxon SIBiLS (treatment): http://denver.hesge.ch:5601/s/ebiodiv/app/discover?#/?_g=(filters:!(),refreshInterval:(pause:!t,value:0),time:(from:now-15m,to:now))&_a=(columns:!(_source),filters:!(),index:'6edc0d90-6bf8-11ed-ad48-bdea25be5ce9',interval:auto,query:(language:kuery,query:'taxon_name_%20%20Hemacroneuria%20flavomarginata'),sort:!()) (id eBioDiv eBioDiv2022 just click on Kibana, then Discover then search for Hemacroneuria flavomarginata
BiodiversityPMC: https://sibils.text-analytics.ch/search/collections/plazi/3D6DA32CFFA1B65524F7FDAA5C4F8EC3
OpenBioDiv: https://openbiodiv.net/literature-exploration?q=8b651444-02b7-4dd6-aff4-b6accb55cd41&type=taxons§ions=nomenclature Synospecies / LINDAS: https://synospecies.plazi.org/#Hemacroneuria+mengyuanae Ocellus (images): https://ocellus.info/?page=1&size=30&resource=images&articleDOI=10.11646%2Fzootaxa.5032.4.6 OpenBioDiv taxonomic name: https://openbiodiv.net/8b651444-02b7-4dd6-aff4-b6accb55cd41?query=Hemacroneuria+mengyuanae&merge_with=8b651444-02b7-4dd6-aff4-b6accb55cd41https://openbiodiv.net/8b651444-02b7-4dd6-aff4-b6accb55cd41?query=Hemacroneuria+mengyuanae&merge_with=8b651444-02b7-4dd6-aff4-b6accb55cd41
Donat Agosti