The DataPLANT Ontology Service Landscape

In the dynamic field of life sciences, managing and interpreting datasets is important. The DataPLANT data annotation concept integrates the ISA standard with the semantic capabilities of Swate, a metadata annotation tool, and the terminology service offered by DataPLANT. This synergistic approach tackles the challenge of harmonizing diverse data sources, allowing researchers to seamlessly collaborate, share, and analyze data while promoting reproducibility and interoperability. The ISA data model, established for capturing and representing metadata, provides a structured and adaptable framework for detailing experimental design and context. Swate, operating as a spreadsheet-based tool, streamlines metadata annotation by leveraging the ISA-Tab format alongside ontology term search through a terminology service. This streamlined process not only enhances the precision and efficiency of metadata annotation but also ensures standardization. To achieve this, Swate integrates a collection of established ontologies (SwateDB) connected to the tool and updated via Swobup, an automatic process handler. Swobup detects updates to ontology source files in a Git repository, seamlessly applying changes to SwateDB, which are instantly visible in Swate. With Git, changes in ontology source files are tracked, ensuring data integrity and version control. Moreover, DataPLANT curates the DataPLANT biology ontology (DPBO), facilitating metadata annotation with new terms as needed. Our approach demonstrates the efficient utilization of standards like ISA in combination with ontologies across all life science domains for spreadsheet-based (meta)data annotation.