UniBioDicts: Unified access to Biological Dictionaries.

John Zobolas,Vasundra Touré,Martin Kuiper,Steven Vercruysse

doi:10.1093/bioinformatics/btaa1065

John Zobolas, Vasundra Touré + Show 2 more

Open Access

https://doi.org/10.1093/bioinformatics/btaa1065

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Abstract

SummaryWe present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools. The Unified Biological Dictionaries (UniBioDicts or UBDs) provide a single query-interface for accessing the online API services of leading biological data providers. Given a search string, UBDs return a list of matching term, identifier and metadata units from databases (e.g. UniProt), controlled vocabularies (e.g. PSI-MI) and ontologies (e.g. GO, via BioPortal). This functionality can be connected to input fields (user-interface components) that offer autocomplete lookup for these dictionaries. UBDs create a unified gateway for accessing life science concepts, helping curators find annotation terms across resources (based on descriptive metadata and unambiguous identifiers), and helping data users search and retrieve the right query terms.Availability and implementationThe UBDs are available through npm and the code is available in the GitHub organisation UniBioDicts (https://github.com/UniBioDicts) under the Affero GPL license.Supplementary information Supplementary data are available at Bioinformatics online.

Highlights

Summary: We present a set of software packages that provide uniform access to diverse biological vocabulary resources that are instrumental for current biocuration efforts and tools
UBDs return a list of matching term, identifier and metadata units from databases (e.g. UniProt), controlled vocabularies (e.g. PSI-MI) and ontologies (e.g. GO, via BioPortal)
UBDs create a unified gateway for accessing life science concepts, helping curators find annotation terms across resources, and helping data users search and retrieve the right query terms

Summary

Motivation

The plethora of ontology terms and biological entity identifiers (IDs) provides a vast resource for use in annotations (by curators) and in database queries (by life scientists and computers), but specifying and finding them requires extensive navigation through an intimidating number of web resources and look-up forms. The Visual Syntax Method (VSM) for example (Vercruysse and Kuiper, 2020), a technology that allows the flexible annotation of virtually any type of contextual information, can take advantage of unified access to such a large diversity of terms, e.g. in applications like causalBuilder (Toureet al., 2020). For these reasons, we set out to create a software suite that maps many of the diverse resources to a single data access and representation form

Implementation

Main methods and data-types

Additional features

Implemented UBDs

Potential users