report

Improve past knowledge exploitation

Improve past knowledge exploitation: extract pairs of chemical compound and taxon from literature not present in LOTUS and relevant to the DBGI (papers describing phytochemical investigation of plants of the Swiss Botanical Gardens, e.g. https://doi.org/10.1016/j.phytochem.2020.112469)

What was done on Plazi's side

About Plazi

Plazi GBIF publisher page https://www.gbif.org/publisher/7ce8aef0-9e92-11dc-8738-b8a03c50a862

Done for the BiCICKL TNA

Issues form 100 - 208
1400 left to process
900 papers in TreatmentBank

See : https://tb.plazi.org/GgServer/dioStats/stats?outputFields=bib.year+bib.source&groupingFields=bib.year+bib.source&FP-bib.source=Phytochemistry&format=HTML

Phytochemistry's Taxo Treatment extracted https://tb.plazi.org/GgServer/srsStats/stats?outputFields=doc.uuid+doc.articleUuid+bib.source+tax.name&groupingFields=doc.uuid+doc.articleUuid+bib.source+tax.name&FP-bib.source=Phytochemistry&format=html

Taxonomic Treatment example

(Alchornea rugosa (Lour.) Muell. Arg.)

HTML version https://tb.plazi.org/GgServer/html/9E75879AFFF7FF8F6952B0FFFF7AF9B6
Raw JATS (xml) https://tb.plazi.org/GgServer/xml/9E75879AFFF7FF8F6952B0FFFF7AF9B6

Overall stats at Plazi

https://tb.plazi.org/GgServer/pdsStats

What was done on SIBILS's side

Overview

https://docs.google.com/presentation/d/1h88KPF_-H-EazGKu3QQppY0rwXc1hlNtYkq5qhgpGpw/edit?usp=sharing

Examples

Example of a Phytochemistry paper treated by Plazi and SiBILS https://sibils.text-analytics.ch/search/?query=Unique%20guanidine-conjugated%20catechins%20from%20the%20leaves%20of%20Alchornea%20rugosa%20and%20their%20autophagy%20modulating%20activity#results-section

Ask Donat and Deborah if they are overlappings papers that would be in BIODIVERSITY PMC ? Apparently this example is online in MEDLINE and the MEDLINE papers do not seem to benefit from the same treatment within SIBILS. Ask Deborah what are the differences ?

Enhance future knowledge dissemination

Enhance future knowledge dissemination: explore publication solutions to efficiently disseminate knowledge acquired from metabolomics, that is, putative occurrences of chemical structures in biological matrices (simple RDF triples, Nanopublications (https://nanopub.org/) or similar).

What was done on KnowledgePixel's side

Ressources