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.
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.
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.
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.
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.
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.
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 3rd party tools.
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.
Interactive user interface for fast and simple curation of data with terminology standards
Reproducible annotations using VOCabs or public/private ontologies
Store annotations and share rules to reduce the time to curate new data
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The 6.5.2 release of SciBite’s VOCabs introduces a range of new VOCab packs as well as updates to existing vocabularies. In this blog series we’ll be introducing each of the new VOCabs: IDMP, a new Sequence Ontology VOCab as part of the Genotype-Phenotype VOCab pack and, first up, the new Emtree VOCab pack.Read
At SciBite, we are passionate about enabling organizations to make full use of their data to help them make evidence-based decisions, especially to help organizations overcome their healthcare digital transformation challenges. To support organizations on this journey, we offer a suite of products to help organizations adopt FAIR data standards.Read
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