ReviewGenome biology2008
Linking genes to literature: text mining, information extraction, and retrieval applications for biology.
Review in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 83 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
83 citing papers in PubMed, 235 citations in OpenAlex.
- Word embeddings as autonomous predictors in materials design-the effect of inherent variability on information transfer.Journal of cheminformatics · 2026Article
- RECODE - Relational Ecological COrpus for Data Extraction.Biodiversity data journal · 2026Article
- A curation system of rice trait ontology with reliable interoperation by LLM and PubAnnotation.Genomics & informatics · 2025Article
- Large Language Model-Enhanced Drug Repositioning Knowledge Extraction via Long Chain-of-Thought: Development and Evaluation Study.JMIR medical informatics · 2025Article
- The influence of prompt engineering on large language models for protein-protein interaction identification in biomedical literature.Scientific reports · 2025Article
- An Accurate and Efficient Approach to Knowledge Extraction from Scientific Publications Using Structured Ontology Models, Graph Neural Networks, and Large Language Models.International journal of molecular sciences · 2024Article
- Comparative Efficacy of Metformin and Glimepiride in Modulating Pharmacological Network to Increase BDNF Levels and Benefit Type 2 Diabetes-Related Cognitive Impairment.Biomedicines · 2023Article
- PMIDigest: Interactive Review of Large Collections of PubMed Entries to Distill Relevant Information.Genes · 2023Article
- Early Deregulation of Cholangiocyte NR0B2 During Primary Sclerosing Cholangitis.Gastro hep advances · 2023Article
- WINNER: A network biology tool for biomolecular characterization and prioritization.Frontiers in big data · 2022Article
- A Second Look at FAIR in Proteomic Investigations.Journal of proteome research · 2021Article
- UniProt-Related Documents (UniReD): assisting wet lab biologists in their quest on finding novel counterparts in a protein network.NAR genomics and bioinformatics · 2020Article
- Text-mining in cancer research may help identify effective treatments.Translational lung cancer research · 2019Article
- Lipid Related Genes Altered in NASH Connect Inflammation in Liver Pathogenesis Progression to HCC: A Canonical Pathway.International journal of molecular sciences · 2019Article
- ProtFus: A Comprehensive Method Characterizing Protein-Protein Interactions of Fusion Proteins.PLoS computational biology · 2019Article
- Linking Bisphenol S to Adverse Outcome Pathways Using a Combined Text Mining and Systems Biology Approach.Environmental health perspectives · 2019Article
- Semi-automated fact-checking of nucleotide sequence reagents in biomedical research publications: The Seek & Blastn tool.PloS one · 2019Article
- An Ontology-Based Knowledge Methodology in the Medical Domain in the Latin America: the Study Case of Republic of Panama.Acta informatica medica : AIM : journal of the Society for Medical Informatics of Bosnia & Herzegovina : casopis Drustva za medicinsku informatiku BiH · 2018Article
- Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.BMC bioinformatics · 2018Article
- A comprehensive and quantitative comparison of text-mining in 15 million full-text articles versus their corresponding abstracts.PLoS computational biology · 2018Article
23 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Efficient access to information contained in online scientific literature collections is essential for life science research, playing a crucial role from the initial stage of experiment planning to the final interpretation and communication of the results. The biological literature also constitutes the main information source for manual literature curation used by expert-curated databases. Following the increasing popularity of web-based applications for analyzing biological data, new text-mining and information extraction strategies are being implemented. These systems exploit existing regularities in natural language to extract biologically relevant information from electronic texts automatically. The aim of the BioCreative challenge is to promote the development of such tools and to provide insight into their performance. This review presents a general introduction to the main characteristics and applications of currently available text-mining systems for life sciences in terms of the following: the type of biological information demands being addressed; the level of information granularity of both user queries and results; and the features and methods commonly exploited by these applications. The current trend in biomedical text mining points toward an increasing diversification in terms of application types and techniques, together with integration of domain-specific resources such as ontologies. Additional descriptions of some of the systems discussed here are available on the internet http://zope.bioinfo.cnio.es/bionlp_tools/.
Indexed as
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.