The study
The FAIRsharing team was pleased to learn how the authors in “Combining knowledge graphs and LLMs for hazardous chemical information management and reuse” (2024 International Conference on Bioinformatics and Biomedicine (BIBM)) used FAIRsharing.org to find and analyse the FAIRness of chemical databases. In this paper, Da Silviera et al. performed analyses on the attributes of hazardous chemical databases and evaluated their compliance with the FAIR principles.
In the first part of their analysis, they needed metadata from hazardous chemical data sources that follow international standards. They used two repositories to obtain information about these databases: PubChem and FAIRsharing.org, preferring “to use the url published in the FAIRsharing”. In their assessment, this information is passed as input to FAIR analysis tools.
They also recommend the use of FAIRsharing as the reference repository of information to improve interoperability: “To tackle interoperability issues, metadata with a minimal set of standardized information should be made available by all data providers in a common metadata registry (e.g., FAIRsharing.org) with persistent identifiers linking back to the data repositories. “
Curators from registries like FAIRsharing are not always able to discover comprehensive information about a resource, and consequently record metadata may be incomplete when the information is not easily discoverable in a resource’s documentation: “Despite the valuable efforts of the community to describe and publish metadata on FAIRsharing, often using standards like Dublin Core, much important information is still missing. For instance, license information was frequently absent from the selected metadata. Consequently, the FAIRsharing community proposes minimal descriptions of data, with the expectation that publishers will maintain and complete this data.” Ideally, each record in FAIRsharing should have comprehensive and complete metadata, but such information is not always findable. As a manually-curated registry, FAIRsharing is always working towards comprehensive coverage of research standards, databases and policies.
As part of our ongoing efforts to increase coverage, we used this paper as the base of further curation within Chemistry.
Our updates
Despite the steady increase in chemistry database records in FAIRsharing (there are currently more than 150 active or in development Chemistry records in FAIRsharing), the number of research databases is vast and always growing. Fully curating database records can often be quite complicated. Based on the paper, we took two main actions with the help of three Community Champions who specialise in Chemistry (Christian Bonatto Minella, Kay Burrows, and Yojana Gadiya):
- Adding missing databases. The authors studied ten Chemistry databases, and three of them were missing in FAIRsharing. These have now been added to our registry.
- Reviewing the existing database records used in the study and updating their curation focusing on licenses and links to standards (e.g. persistent identifiers)
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We wish to thank the authors for using FAIRsharing and for the positive comments that they made about our registry.
For us, this work is a magnificent example of how FAIRsharing data can be used by researchers to investigate data sources from a specific discipline.
| NAME | FAIRsharing link |
|---|---|
| ECHA REACH registered substance factsheets | https://doi.org/10.25504/FAIRsharing.ab25e3 |
| ECHA Classification and Labelling (C&L) Inventory | https://doi.org/10.25504/FAIRsharing.4782f1 |
| ECHA database for information on Substances of Concern In articles as such or in complex objects (Products) (SCIP) | https://fairsharing.org/6136 |
| European Commission’s Cosmetic ingredient database (Cosing) | https://fairsharing.org/6238 |
| Joint Research Centre’s Information platform for chemical monitoring (IPChem) | https://doi.org/10.25504/FAIRsharing.667115 |
| ChemSpider (Royal Society of Chemistry) | https://doi.org/10.25504/FAIRsharing.96f3gm |
| EPA ChemView | https://fairsharing.org/6221 |
| Comparative Toxicogenomics Database (CTD) | https://doi.org/10.25504/FAIRsharing.h3tjtr |
| EPA CompTox Chemicals Dashboard | https://doi.org/10.25504/FAIRsharing.tfj7gt |
| Toxin and Toxin Target Database (Toxic Exposome Database, T3DB) | https://doi.org/10.25504/FAIRsharing.psn0h2 |