Add ontologies relevant to N4M to the Knowledge Base --> Output from a ticket

[babs1984]

Ticket + Reply from November 2023

Dear Steffen,

Thank you for your request and your patience!

After reaching out to our expert on ontologies I can provide you the following information:

First, you are right, the main issue is to find suitable ontologies (in biodiversity) among the many that are developed, and I give below a couple of pointers.
Thanks for the suggestion to look at our neighboring NFDI for better explanations of ontologies in the Knowledge Base, we will work on that!

Below are a few resources to find ontologies from the general to the specific:
• OntoBee (more targeted to developers)
• NCBO BioPortal has mostly biomedical ontologies
• Ontology Lookup Service v4
• The OBO Foundry

But above all, a usable and reliable ontology
• has sound terms definitions that you agree with
• is actively developed and updated to reflect the scientific practices
• has a community space to exchange with the community (tickets, issues)
• has an adequate license and appropriate funding (for maintenance)

These opinioned criteria are modified from:

1. Malone, James, Robert Stevens, Simon Jupp, Tom Hancocks, Helen Parkinson, and Cath Brooksbank. 2016. “Ten Simple Rules for Selecting a Bio-Ontology.” PLOS Computational Biology 12 (2): e1004743. https://doi.org/10.1371/journal.pcbi.1004743.
2. Rocca-Serra, Philippe, Susanna-Assunta Sansone, Danielle Welter, and Alasdair J. G. Gray. 2023. “Selecting Terminologies and Ontologies.” https://w3id.org/faircookbook/FCB020.
   I hope this is helpful! Good luck with your writings and contact us again if you have further questions.

Please take two minutes to rate our service and give us feedback, so we can improve our service: Link.
Best regards,

Barbara Götz, Project Manager NFDI4Microbiota

The helpdesk team of the NFDI4Microbiota consortium
Contact: [email protected]
Web portal: www.nfdi4microbiota.de
Twitter: @nfdi4microbiota
Mastodon: nfdi.social/@NFDI4Microbiota
LinkedIn: linkedin.com/company/nfdi4microbiota/

Hi,
In a chapter on metabolomics in biodiversity, I would like to reference a recommendation on how to find suitable ontologies in biodiversity. In the NFDI4Biodiversity KB I only found EDAM in the glossary. If you have a resource somewhere else, I'd love a pointer. If not, wouldn't it be cool if there was a review and KB article, similar to https://www.nfdi4plants.de/nfdi4plants.knowledgebase/docs/implementation/OntologyServiceLandscape.html https://nfdi4plants.org/nfdi4plants.knowledgebase/docs/fundamentals/Ontologies.html https://knowledgebase.nfdi4chem.de/knowledge_base/docs/ontology/

Yours, Steffen

[cpauvert]

Thanks @babs1984 you can assign me here, I'll do it during the sprint. Best

[babs1984]

Thanks @cpauvert! Looking forward to the sprint :)