first-meeting
Participants:
Pierre-Marie Allard, Patrick Ruch, Donat Agosti, Alexandre Flament, Adriano Rutz
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NB: The project is using an OpenNotebook Science (https://en.wikipedia.org/wiki/Open-notebook_science)
Project description
Agenda:
- project presentation,
- Todo
- [...]
- The Digital Botanical Gardens Initiative
- From earth metabolome to botanic species
- Mass spec is used to characterize fingerprints with localization
- All exposed with a RDF endpoints
- LOTUS provides the link between (natural) small molecules and their occurrence
- All data in LOTUS is also in Wikidata
- Global Metabolome Initiative
Challenge: Create a link between the treatments in TB, the material citation and the small molecules
Gap: some knowledge is still found only in PDF, here comes the TNA project !
Possible extension of the first tasks: A possible extension would be to move towards nano-publications
Key: the level of evidence (silver level of evidence → Evidence and Code Ontology ECO) for the inferred statements is relatively weak as it uses mass spectrometry
annotate articles in SIBiLS using an extended SIBiLS ontology
how to share the extracted knowledge: -talking nonopubs
get a list of journals (the most important ones) -Phytochemistry -Journal of Natural Products
small molecule names Who is providing the the list? Are there tools to recognize molecule names are tools available to discover names based on figure in the article?
1st step. Get the articles to find out what molecule classes are present in an article 2nd step.
get a get a vocabulary that includes all the methods, such as also HMBC
Questions:
PDF contents Annotation types New relationships Extend the SiBiLS ontology with small molecules possible? how to type the relation ship molecule - organism; eaten by, tested on, living in, from where do we get the dictionnary of small molecules: source could be pubchem can the provenance of users be monitored to give him project related access
Ex: of wd LOTUS entry https://www.wikidata.org/wiki/Q213511
Links: SIBiLS ontology: https://goldorak.hesge.ch/rdf4sibils/ontology/sibils-ontology.html SPARQL endpoint: https://goldorak.hesge.ch/sparql Example of SPARQL queries: https://goldorak.hesge.ch/rdf4sibils/sparql_examples.txt
https://doi.org/10.1016/j.phytochem.2020.112469
Example journals: https://www.sciencedirect.com/journal/phytochemistry https://pubs.acs.org/journal/jnprdf
PubChem RDF for compounds dictionary: https://ftp.ncbi.nlm.nih.gov/pubchem/RDF/
To Do:
- PM & Adriano provide a list of the articles
- PM & Adriano provide ca 20 articles where the elements are highlighted that need to be extracted
- DA get Journal of Natural Products and Phytochemistry articles
- DA talk to GS/CN to scrape
- PM & Adriano defines the annotation schema: molecules, taxon, predicate, methods, specimen, organs (PO), habitats/location
- PM & Adriano provides a list of vocabularies/ontologies for each entities
- PM & Adriano provide annotated articles
- PR/AF check how to hide access to closed access into SIBiLS
Next meeting / recurring meeting March 16, 2023, 2 - 3 pm
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