ArticleDatabase : the journal of biological databases and curation2019
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language.
Article in Database : the journal of biological databases and curation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
What it found
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Who cites it
17 citing papers in PubMed.
- Applying prior knowledge of regulatory signaling to investigate macrophage cAMP dynamics during Mycobacterium tuberculosis infection.Scientific reports · 2026Article
- GPU-accelerated modeling of biological regulatory networks.Scientific reports · 2026Article
- VIOLIN: A modular framework for scalable reconciliation of heterogeneous interaction graphs.bioRxiv : the preprint server for biology · 2026Article
- Neuro-psycho MMSig: multimodal mechanism enrichment platform for neuropsychiatric disorders.Frontiers in bioinformatics · 2026Article
- SHACLens: a visualization workflow for SHACL violation exploration in knowledge graphs.Frontiers in bioinformatics · 2026Article
- MRAgent: an LLM-based automated agent for causal knowledge discovery in disease via Mendelian randomization.Briefings in bioinformatics · 2025Article
- BioKGrapher: Initial evaluation of automated knowledge graph construction from biomedical literature.Computational and structural biotechnology journal · 2024Article
- Automated assembly of molecular mechanisms at scale from text mining and curated databases.Molecular systems biology · 2023Article
- Nanopublication-based semantic publishing and reviewing: a field study with formalization papers.PeerJ. Computer science · 2023Article
- Exploring the Complex Network of Heme-Triggered Effects on the Blood Coagulation System.Journal of clinical medicine · 2022Article
- New reasons for biologists to write with a formal language.Database : the journal of biological databases and curation · 2022Article
- Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms' representation.BioData mining · 2021Article
- The role of metadata in reproducible computational research.Patterns (New York, N.Y.) · 2021Review
- Leveraging Structured Biological Knowledge for Counterfactual Inference: A Case Study of Viral Pathogenesis.IEEE transactions on big data · 2021Article
- The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases.Nucleic acids research · 2021Article
- Design and Use of Semantic Resources: Findings from the Section on Knowledge Representation and Management of the 2020 International Medical Informatics Association Yearbook.Yearbook of medical informatics · 2020Review
- Constructing knowledge graphs and their biomedical applications.Computational and structural biotechnology journal · 2020Review
Corrections and comments
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Authors and funding
11 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The rapid accumulation of new biomedical literature not only causes curated knowledge graphs (KGs) to become outdated and incomplete, but also makes manual curation an impractical and unsustainable solution. Automated or semi-automated workflows are necessary to assist in prioritizing and curating the literature to update and enrich KGs. We have developed two workflows: one for re-curating a given KG to assure its syntactic and semantic quality and another for rationally enriching it by manually revising automatically extracted relations for nodes with low information density. We applied these workflows to the KGs encoded in Biological Expression Language from the NeuroMMSig database using content that was pre-extracted from MEDLINE abstracts and PubMed Central full-text articles using text mining output integrated by INDRA. We have made this workflow freely available at https://github.com/bel-enrichment/bel-enrichment.
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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.