ArticleIEEE/ACM transactions on computational biology and bioinformatics
RLIMS-P 2.0: A Generalizable Rule-Based Information Extraction System for Literature Mining of Protein Phosphorylation Information.
Article in IEEE/ACM transactions on computational biology and bioinformatics. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed.
- From prior knowledge to data-informed models: a review of Boolean network inference.Briefings in bioinformatics · 2026Review
- GenPTM: A Generalizable Framework for Protein Post-Translational Modification Information Extraction from the Scientific Literature.Research square · 2026Article
- GlyGen: a knowledgebase linking glycan data with protein and gene data to reveal novel biological connections.Research square · 2026Article
- Integrating text mining and knowledge graph to enhance biopharmaceutical process optimization.PloS one · 2026Article
- GlycoSiteMiner: an ML/AI-assisted literature mining-based pipeline for extracting glycosylation sites from PubMed abstracts.Glycobiology · 2025Article
- Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity.Database : the journal of biological databases and curation · 2025Article
- Automated assembly of molecular mechanisms at scale from text mining and curated databases.Molecular systems biology · 2023Article
- KSFinder-a knowledge graph model for link prediction of novel phosphorylated substrates of kinases.PeerJ · 2023Article
- Identification of Novel Kinases of Tau Using Fluorescence Complementation Mass Spectrometry (FCMS).Molecular & cellular proteomics : MCP · 2022Article
- Expanding a database-derived biomedical knowledge graph via multi-relation extraction from biomedical abstracts.BioData mining · 2022Article
- Large-scale protein-protein post-translational modification extraction with distant supervision and confidence calibrated BioBERT.BMC bioinformatics · 2022Article
- A Text Mining and Machine Learning Protocol for Extracting Posttranslational Modifications of Proteins from PubMed: A Special Focus on Glycosylation, Acetylation, Methylation, Hydroxylation, and Ubiquitination.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Text Mining and Machine Learning Protocol for Extracting Human-Related Protein Phosphorylation Information from PubMed.Methods in molecular biology (Clifton, N.J.) · 2022Article
- ANDDigest: a new web-based module of ANDSystem for the search of knowledge in the scientific literature.BMC bioinformatics · 2020Article
- Article
- RESTful API for iPTMnet: a resource for protein post-translational modification network discovery.Database : the journal of biological databases and curation · 2020Article
- Constructing knowledge graphs and their biomedical applications.Computational and structural biotechnology journal · 2020Review
- Identification of conclusive association entities in biomedical articles.Journal of biomedical semantics · 2019Article
- iPTMnet: an integrated resource for protein post-translational modification network discovery.Nucleic acids research · 2018Article
- iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature.Database : the journal of biological databases and curation · 2018Article
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Authors and funding
6 authors.
Funding
Abstract
We introduce RLIMS-P version 2.0, an enhanced rule-based information extraction (IE) system for mining kinase, substrate, and phosphorylation site information from scientific literature. Consisting of natural language processing and IE modules, the system has integrated several new features, including the capability of processing full-text articles and generalizability towards different post-translational modifications (PTMs). To evaluate the system, sets of abstracts and full-text articles, containing a variety of textual expressions, were annotated. On the abstract corpus, the system achieved F-scores of 0.91, 0.92, and 0.95 for kinases, substrates, and sites, respectively. The corresponding scores on the full-text corpus were 0.88, 0.91, and 0.92. It was additionally evaluated on the corpus of the 2013 BioNLP-ST GE task, and achieved an F-score of 0.87 for the phosphorylation core task, improving upon the results previously reported on the corpus. Full-scale processing of all abstracts in MEDLINE and all articles in PubMed Central Open Access Subset has demonstrated scalability for mining rich information in literature, enabling its adoption for biocuration and for knowledge discovery. The new system is generalizable and it will be adapted to tackle other major PTM types. RLIMS-P 2.0 online system is available online (http://proteininformationresource.org/rlimsp/) and the developed corpora are available from iProLINK (http://proteininformationresource.org/iprolink/).
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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.