ArticleISRN bioinformatics2012
Chemical Entity Recognition and Resolution to ChEBI.
Article in ISRN bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed.
- Genome-wide transcriptomics revealed carbon source-mediated gamma-aminobutyric acid (GABA) production in a probiotic,Heliyon · 2025Article
- Chemical entity normalization for successful translational development of Alzheimer's disease and dementia therapeutics.Journal of biomedical semantics · 2024Article
- Enhancing Genome-Scale Model by Integrative Exometabolome and Transcriptome: Unveiling Carbon Assimilation towards Sphingolipid Biosynthetic Capability ofJournal of fungi (Basel, Switzerland) · 2022Article
- Probing Genome-Scale Model Reveals Metabolic Capability and Essential Nutrients for Growth of ProbioticBiology · 2022Article
- NLM-Chem, a new resource for chemical entity recognition in PubMed full text literature.Scientific data · 2021Article
- Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning.Database : the journal of biological databases and curation · 2016Article
- The CHEMDNER corpus of chemicals and drugs and its annotation principles.Journal of cheminformatics · 2015Article
- Optimising chemical named entity recognition with pre-processing analytics, knowledge-rich features and heuristics.Journal of cheminformatics · 2015Article
- Article
- Chemical named entities recognition: a review on approaches and applications.Journal of cheminformatics · 2014Review
- A rule-based ontological framework for the classification of molecules.Journal of biomedical semantics · 2014Article
- Enhancement of chemical entity identification in text using semantic similarity validation.PloS one · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Chemical entities are ubiquitous through the biomedical literature and the development of text-mining systems that can efficiently identify those entities are required. Due to the lack of available corpora and data resources, the community has focused its efforts in the development of gene and protein named entity recognition systems, but with the release of ChEBI and the availability of an annotated corpus, this task can be addressed. We developed a machine-learning-based method for chemical entity recognition and a lexical-similarity-based method for chemical entity resolution and compared them with Whatizit, a popular-dictionary-based method. Our methods outperformed the dictionary-based method in all tasks, yielding an improvement in F-measure of 20% for the entity recognition task, 2-5% for the entity-resolution task, and 15% for combined entity recognition and resolution tasks.
Identifiers
What OpenQuestion holds
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.