The Alltrope Foundation is a major collaboration bringing data standards to the vast amount of laboratory data generated within Life Science research. Participants from across pharmaceutical and the laboratory instrumentation and informatics sectors have collaborated to generate an end-to-end solution for data capture, storage and analysis. Very early in the project the participants highlighted the need for meta-data standards to ensure consistency and reproducibility both within and across experiments. The Allotrope ontologies are the foundation of these standards, covering a range of concepts including the “equipment, processes, materials, and results” around laboratory experiments.
At SciBite we’re strong advocates for the power of open ontologies, and believe that community-based standards are a key pillar in effective data management. We were asked recently if our next-generation ontology management tool CENtree could be used to manage the Allotrope ontologies, and how this would work in practice. The answer to that question is a pretty straight forward “yes”! As the Allotrope ontologies are available in the industry-standard OWL format, they load into CENtree using the standard import tool. Read more about the latest version of CENtree.
With a few clicks, we’re now browsing the Allotrope ontologies.
We can also go and add new concepts or synonyms into the ontology. Let’s say we wanted to add a new synonym to the entry for Molecular Absorption Spectrophotometry. Opening up the editor panel presents us with the standard text entry box – but CENtree applies intelligent suggestions to make us aware of any terms that are already in the ontology elsewhere, helping to prevent duplication or assigning terms to the wrong class.
Another common scenario is the need to add a concept we need to use that’s not in the originating ontology. All standards and organic and must evolve with the constant change in science and technology. As you might expect, this is another simple operation, just clicking on the “+” button to add a new concept (in this case we’re adding Dielectric Spectroscopy to our ontology).
CENtree grabs the definition of this from certain key resources, here we’re using the Wikipedia definition, automatically obtained by CENtree during the editing process. We can of course add synonyms, relationships and any other properties as we go.
At any point, this ontology can be published and used within our applications. CENtree has a set of APIs for application integration. For instance, an application designed to make use of these data standards can create “smart” data capture forms with type-ahead boxes driven by the ontology. This helps to ensure users apply the correct terminology while helping them enter data quickly, a win-win scenario.
While that’s fulfilled our basic needs, uploading and adding to the Allotrope ontologies, it’s not the end of the story. As I mentioned at the very start of this article, SciBite is a huge supporter of open ontologies and the community-driven standards these provide. It’s here we see perhaps the most important feature of CENtree – its ability to help users contribute back. If we’ve added new concepts, definitions or synonyms then it’s likely others can benefit from these. A quick jump to the administration console takes us to the “Edits” listing, showing all the changes we’ve made to the ontology since it was imported. Read our use case on how Ontologies and Machine Learning work together.
This simple list hides a very powerful capability. Firstly, it is possible to export our modified ontology and provide this information back to the Allotrope foundation, such that they may consider incorporation of our changes into the official public release. This simple operation enables organisations to contribute back to any public body, reinforcing the standard for all.
However, the more complex issue is that it’s likely that the Allotrope foundation themselves will be also changing the ontology. If we’ve also modified our own internal copy of this, how do we bring in the latest updates in the public copy without losing our own internal changes? This is a major issue preventing the adoption of open ontologies more broadly across the enterprise.
Fortunately, CENtree is specifically designed to address this key concern. Within the tool we can upload the latest public ontology and ‘re-apply’ our edits, to create an up-to-date ontology merging internal and external changes. During this process CENtree will highlight any conflicts between the two, automatically resolving those with no negative consequences and guiding the user to resolve any that are in conflict. This unique capability makes embedding open standards in day-to-day data management a reality for many of our customers.
We think the work of organisations like Allotrope is critical to data stewardship and forms the foundation of applications such as AI/Deep Learning and Knowledge Graphs. Read our blog on Knowledge Graphs and using Semantic Enrichment to connect the dots. Ontologies are at the heart of this and applications like CENtree help keep those ontologies in step with both current business processes and external development in a simple, powerful system.
To learn more watch our webinar on scaling the data mountain with Ontologies, Deep Learning & FAIR or get in touch with the team to discuss our ontology management technology further.
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Public ontologies are essential for applying FAIR principles to data but are not built for use in named entity recognition pipelines. At SciBite, we build on the public ontologies to create VOCabs optimized for NER. In this blog, discover how we create a SciBite VOCab from a Public Ontology.Read
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