Workbench

Take the effort out of tabular data curation

Organizations may face a variety of challenges when recording data, such as limited reusability due to idiomatic or historic nomenclature used by individuals or groups, siloed information hindering transparency and collaboration, and a time-consuming and error-prone process of integrating data from multiple sources.

Advanced curation management

SciBite has developed Workbench, a user-friendly visual tool for curating and editing term lists, personalized dictionaries, and semi-structured data sets to match your preferred terminology standard. Utilizing SciBite’s TERMite and VOCab technologies, Workbench helps organizations implement a FAIR approach to data management, which emphasizes making data Findable, Accessible, Interoperable, and Reusable.

Figure 1: Simple user interface and smart spreadsheet-like functionality for loading, semantically annotating, and cleaning tabular data

Figure 2: Workbench workflow. Workbench will tag columnar entities with your chosen vocabulary or ontology within a few clicks.

Simplifying the arduous task of data curation

Cleaning datasets by aligning them to ontologies can be arduous, often requiring specific expertise in both the subject domain and the available standards. Scientific data curators perform fundamental work within an organization, enabling much of the downstream data integration and analysis.

Workbench aims to support these scientists by streamlining the curation process through a simple and intuitive user interface. Workbench allows you to reuse and repeat previously seen curation, saving time and allowing teams to get more done.

Accurately curate complex data

Annotate data from selected columns with your chosen vocabulary or ontology, including SciBite’s VOCabs – a library of manually curated vocabularies enriched with >20 million synonyms. You can also upload your custom ontologies and use these for annotating your data.

Promoting replicability with Workbench’s annotation rules

Workbench utilizes SciBite’s award-winning Named Entity Recognition system, TERMite, that can be configured and fine-tuned to support fuzzy-matching and handle variations in spelling and typographic errors. For data riddled with internal codes or proprietary terms, you can use Workbench to map them to your chosen ontology terms or vocabulary with ‘annotation rules’, eliminating the error-prone and monotonous editing process. Workbench promotes replicability by storing these annotation rules, which can be re-run during subsequent data annotation tasks.

Build workflows with the API

Workbench comes with a powerful REST API that provides programmatic access to the same core functions from the user interface. The API can be used to integrate Workbench functionality into your custom data curation workflows.

Easy data sharing and export

Workbench has built-in sharing functionalities for collaborative curation projects. As a data owner, you can create a group where you can invite other colleagues to view or edit your annotations. Annotated data can be exported in Excel for use with many 3^rd party tools.

Workbench requirements

SciBite Workbench is a data curation and harmonization tool powered by SciBite’s core Semantic Technologies. SciBite Workbench provides a user-friendly interface for annotating semi-structured datasets with ontologies and VOCabs from SciBite’s TERMite Named Entity Recognition engine.

SciBite Workbench requires access to a TERMite server; if you already license TERMite and have access to a server, you can configure Workbench to use that server. If you don’t currently have access to TERMite, you can run Workbench with an embedded TERMite server.

Get in touch with the team to learn more or download the Workbench datasheet.

Download Workbench datasheet
Please get in touch with our experts for a demonstration.