In this webinar, Henirette Harmse, Software Engineer at the European Bioinformatics Institute (EBI) presents OLS, ZOOMA, and OxO– platforms developed by the ontology tools team at EBI. These services are used extensively by bioinformaticians, biocurators, and biological researchers both inside and outside of EBI. OLS enables searches across 260+ ontologies representing 6.5 million terms. Given a specific string of text, it is possible that multiple terms may be suitable to represent the string of text. ZOOMA can be used to guide curators in choosing the most suitable term representing the string of text. In the case where a curator already has a term, but this term is not from their preferred ontologies, OxO can be used to try and map the given term to a term in a preferred ontology. We will discuss these tools, how they are used, the benefits of using them, and some future considerations.

Tools presented

– OLS

– ZOOMA

– OxO

Speaker

Henirette Harmse, Software Engineer at the European Bioinformatics Institute

Timeline

00:01:00 – Presentation – Henriette Harmse

00:28:00 – Q&A 

• 00:28:20 – Could OxO help us map some of the agriculture-related ontologies we use with controlled vocabularies and data dictionaries and the ICASA variables used in crop modeling? – Medha Devare 
• 00:31:36 – Are those tools open-source? – Medha Devare 
• 00:32:22 – How do you choose the cross-reference database term which is to map in OxO when there are many PMID for example? – Magalie Weber
• 00:35:50 – Are there best practices or recommendations for mapping annotation properties for use in SSSOM? – Kai Blumberg
• 00:37:30 – What is the roadmap for the tools, especially for the OLS? any key new features on the horizon? what about timelines? – Erick Antezana
• 00:41:07 – Could you comment on how the Data Governance aspect is handled at the EBI while using these tools? – Erick Antezana
• 00:43:55 – What kind of automatic mappers are used in OxO and how is confidence determined? – Antonis Koukourikos