A major challenge in the use of ontologies is that the formal terminology used in the ontology hierarchy does not always match the "layman” language commonly used by practitioners. This causes two problems: (1) in biocuration, text strings are often significantly different from their corresponding ontology terms; and (2) ontology terms do not always match the common terminology.
Tools to address (1) include ZOOMA and OntoString developed at EMBL-EBI for the Human Cell Atlas Data Coordination Platform and EOSCLife. However, (2) is less well explored. Some ontologies are beginning to provide “layperson” synonyms for terms. However, this approach is not standardised, and lacks support in ontology tooling such as the Ontology Lookup Service (OLS). We will therefore explore how this functionality can be implemented, so that users can choose between formal and informal language when browsing an ontology.
Secondly, we will explore how this approach can be used by the microbial biotechnology ELIXIR community to make their applications more user friendly and FAIR compliant. FAIR data standards and ontologies are critical for the FAIR compliance and usability of biological design knowledge. Semantically well-defined data models are available; e.g. SBOL and SyBiOnt. However, these efforts have not primarily taken the needs of the tool user into account. Their vocabulary is therefore in many cases significantly different from terms used by experimentalists, impeding biocuration and adoption of FAIR principles.
We will therefore construct a presentation layer vocabulary for non-developer users of FAIR synthetic biology tools and repositories, with BioHackathon participants and the wider community. We will incorporate this vocabulary into existing FAIR workflows to make them more accessible to end-users while retaining their underlying ontological representation.
Compute Platform, Data Platform, Interoperability Platform, Microbial Biotechnology, Tools Platform
Project Number: 14
[email protected], [email protected]
The first draft of an application ontology for synthetic biology/biotechnology - completion by first month after the Biohackathon Support for alternate terminologies implemented in OLS code - By the end of the biohackathon A microbial biotechnology white paper - submitted as an ELIXIR F1000 within 3 months of the event A project homepage and contributors network - Established at the Biohackathon An SBOL SEP standard update proposal - 6 months after the event
Java developers to contribute to OLS code. Researchers in the synthetic biology and biotechnology domain. Especially ontology builders, tool builders. We will also need experimental scientists - these will be invited if the project is successful. We would also like to work closely with the RDMKit project as joint work already carried out at the previous BioHackathon is very relevant.
Number of expected hacking days: 4