2023-03-18
This is PMA's DBGI daily open-notebook.
Today is 2023.03.18
Todo today
Have a look at the DBGI discussion forum
- https://github.com/orgs/digital-botanical-gardens-initiative/discussions
Doing
Interview to the selected projects' proposers
How did you get to know BiCIKL and this call?
[Max 100 words]
We have been following the work of Donat Agosti (http://plazi.org/) since some time with a lot of interest and have been aware of the BiCICKL project mostly through internet and social media.
Why did you apply here, to address what challenge/need?
[Max 100 words]
In the last years we established LOTUS, an open electronic ressource documenting the biological occurrences of natural products (https://doi.org/10.7554/eLife.70780). More recently, we launched the Digital Botanical Gardens Initiative (DBGI https://www.dbgi.org/). This Open Science project aims to establish workflows for the characterization of the global chemodiversity. In this context we describe novel chemical information (structures, occurrences, biological activities etc.). For this we depend on the access to previous knowledge on natural products chemistry. If some is shared in LOTUS, much of it remains locked in the existing corpus of publications. The extraction of this existing knowledge is the challenge to address.
How BiCIKL would help to address your need or challenge?
[Max 100 words]
In the frame of BiCICKL, the Swiss Institute of Bioinformatics Literature Services (SIBiLS) and Plazi's TreatmentBank service teamed to propose eBioDiv (https://ebiodiv.org/) a service for Swiss biodiversity scientists to access and disseminate their research data about species in legacy and prospective publications. Building on this experience, we will complement the pre-existing toolbox to mine the literature and extract natural products occurrences related information (chemical structures, biological organisms and their links). These objects will be associated to relevant identifiers and will then be shared in the Wikidata knowledge base were LOTUS lives.
Who will benefit from your project? (Target stakeholders)
[Max 100 words]
As daily user of the LOTUS ressource we will evidently benefit from the expected increase in available information volume. However, the wide availability of the LOTUS ressource (through Wikidata or other ressources such as PubChem) ensures that this increase in information volume will benefit any researcher interested in the chemical description of living systems.
What will you consider as a success for your project?
[Max 100 words]
The establishment of a robust toolbox allowing the automated extraction and sharing of natural products from the existing literature corpus would be, in itself, a success. Obviously the associated improvement expected in terms of knowledge dissemination is also very much looked after ! On a broader perspective, we also expect that such project will raise attention of researchers and publishers, on possible best practices to be implemented when reporting research outcomes in the field of natural products chemistry (e.g. tabular files of SMILES, InChI and InChIKey encoded structures together with binomial denomination of taxa).
Please individuate what's your group of reference.
What can BiCIKL can do for your community/group (please indicate relevant Twitter accounts / #hashtag (Private) for the group)
[Max 100 words]
Not sure to understand "Please individuate what's your group of reference."
No Twitter account for these projects. However we have two Mastodon accounts for the DBGI and Earth Metabolome Initiatives.
- @dbgi (Private)@earthstream.social (Private)
- @earth_metabolome (Private)@earthstream.social (Private)
We also follow Open Notebook Science approach (https://en.wikipedia.org/wiki/Open-notebook_science) so our current research is observable at https://www.dbgi.org/dendron-dbgi/
Please write here a personal quote that resumes the project
Mining historical pharmacognosy and natural products chemistry literature for the future of chemodiversity description.
Paused
Done
Look into protocols.io https://www.protocols.io/file-manager/3F4ABBC4C59511EDAB840A58A9FEAC02