ArticleBioinformatics (Oxford, England)2022
TogoID: an exploratory ID converter to bridge biological datasets.
Article in Bioinformatics (Oxford, England), 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- TogoMCP: natural language querying of life-science knowledge graphs via schema-guided LLMs and the Model Context Protocol.Database : the journal of biological databases and curation · 2026Article
- Assembly and reasoning over semantic mappings at scale for biomedical data integration.Bioinformatics (Oxford, England) · 2025Article
- Risk Prediction of RNA Off-Targets of CRISPR Base Editors in Tissue-Specific Transcriptomes Using Language Models.International journal of molecular sciences · 2025Article
- Expanding the concept of ID conversion in TogoID by introducing multi-semantic and label features.Journal of biomedical semantics · 2025Article
- Functional implications of glycans and their curation: insights from the workshop held at the 16th Annual International Biocuration Conference in Padua, Italy.Database : the journal of biological databases and curation · 2024Article
- An architecture for collaboration in systems biology at the age of the Metaverse.NPJ systems biology and applications · 2024Article
- PhyloSophos: a high-throughput scientific name mapping algorithm augmented with explicit consideration of taxonomic science, and its application on natural product (NP) occurrence database processing.BMC bioinformatics · 2023Article
- Advancing reuse of genetic parts: progress and remaining challenges.Nature communications · 2023Article
- MantaID: a machine learning-based tool to automate the identification of biological database IDs.Database : the journal of biological databases and curation · 2023Article
- Prediction and curation of missing biomedical identifier mappings with Biomappings.Bioinformatics (Oxford, England) · 2023Article
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Authors and funding
11 authors.
Funding
Abstract
motivationUnderstanding life cannot be accomplished without making full use of biological data, which are scattered across databases of diverse categories in life sciences. To connect such data seamlessly, identifier (ID) conversion plays a key role. However, existing ID conversion services have disadvantages, such as covering only a limited range of biological categories of databases, not keeping up with the updates of the original databases and outputs being hard to interpret in the context of biological relations, especially when converting IDs in multiple steps.
resultsTogoID is an ID conversion service implementing unique features with an intuitive web interface and an application programming interface (API) for programmatic access. TogoID currently supports 65 datasets covering various biological categories. TogoID users can perform exploratory multistep conversions to find a path among IDs. To guide the interpretation of biological meanings in the conversions, we crafted an ontology that defines the semantics of the dataset relations. AVAILABILITY AND IMPLEMENTATION: The TogoID service is freely available on the TogoID website (https://togoid.dbcls.jp/) and the API is also provided to allow programmatic access. To encourage developers to add new dataset pairs, the system stores the configurations of pairs at the GitHub repository (https://github.com/togoid/togoid-config) and accepts the request of additional pairs. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.