SynthesisGenome medicine2019
Text-mining clinically relevant cancer biomarkers for curation into the CIViC database.
Synthesis in Genome medicine, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers, 1 of them a synthesis that pooled it.
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
28 citing papers in PubMed, 1 synthesis or guideline pooled it, 45 citations in OpenAlex.
- Emerging biomarkers for non-invasive diagnosis and treatment of cancer: a systematic review.Frontiers in oncology · 2024Pooled it
- EDEL: enhancing dense retrievers for curation of biomedical knowledge bases.Bioinformatics (Oxford, England) · 2026Article
- Unsupervised Deep Representation Learning and Probabilistic Clustering for the Systems-Level Discovery of Germline Mutation Signatures in Pediatric Cancers.Biomedicines · 2026Article
- Artificial intelligence and multi-omics integration in liquid biopsy for genitourinary cancers: a systematic scoping review.International urology and nephrology · 2026Article
- CancerSubtypeXplore: A Modular Platform for Multiomics Cancer Subtype Prediction and Biomarker Consensus Discovery.Computational and structural biotechnology journal · 2026Article
- MarkerPredict: predicting clinically relevant predictive biomarkers with machine learning.NPJ systems biology and applications · 2025Article
- Evaluating Language Models for Biomedical Fact-Checking: A Benchmark Dataset for Cancer Variant Interpretation Verification.bioRxiv : the preprint server for biology · 2025Article
- miRNA centered regulatory networks identify FN1 and miR27b as metastatic drivers in HPV negative head and neck cancer.Scientific reports · 2025Article
- Decoding resistance to immune checkpoint inhibitors in non-small cell lung cancer: a comprehensive analysis of plasma proteomics and therapeutic implications.Journal for immunotherapy of cancer · 2025Article
- Clonal hematopoiesis in cardiovascular aging: Insights from the verona heart study.GeroScience · 2025Article
- Developing foundations for biomedical knowledgebases from literature using large language models - A systematic assessment.Computational and structural biotechnology journal · 2025Article
- Cancer-Alterome: a literature-mined resource for regulatory events caused by genetic alterations in cancer.Scientific data · 2024Article
- Analysis of the regulatory role of miR-34a-5p/PLCD3 in the progression of osteoarthritis.Functional & integrative genomics · 2023Article
- CIViCdb 2022: evolution of an open-access cancer variant interpretation knowledgebase.Nucleic acids research · 2023Article
- Findings from precision oncology in the clinic: rare, novel variants are a significant contributor to scaling molecular diagnostics.BMC medical genomics · 2022Article
- MarkerGenie: an NLP-enabled text-mining system for biomedical entity relation extraction.Bioinformatics advances · 2022Article
- Identifying and Validating Networks of Oncology Biomarkers Mined From the Scientific Literature.Cancer informatics · 2022Article
- Molecular-based precision oncology clinical decision making augmented by artificial intelligence.Emerging topics in life sciences · 2021Review
- Knowledge bases and software support for variant interpretation in precision oncology.Briefings in bioinformatics · 2021Article
- SicknessMiner: a deep-learning-driven text-mining tool to abridge disease-disease associations.BMC bioinformatics · 2021Article
Corrections and comments
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Authors and funding
10 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundPrecision oncology involves analysis of individual cancer samples to understand the genes and pathways involved in the development and progression of a cancer. To improve patient care, knowledge of diagnostic, prognostic, predisposing, and drug response markers is essential. Several knowledgebases have been created by different groups to collate evidence for these associations. These include the open-access Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase. These databases rely on time-consuming manual curation from skilled experts who read and interpret the relevant biomedical literature.
methodsTo aid in this curation and provide the greatest coverage for these databases, particularly CIViC, we propose the use of text mining approaches to extract these clinically relevant biomarkers from all available published literature. To this end, a group of cancer genomics experts annotated sentences that discussed biomarkers with their clinical associations and achieved good inter-annotator agreement. We then used a supervised learning approach to construct the CIViCmine knowledgebase.
resultsWe extracted 121,589 relevant sentences from PubMed abstracts and PubMed Central Open Access full-text papers. CIViCmine contains over 87,412 biomarkers associated with 8035 genes, 337 drugs, and 572 cancer types, representing 25,818 abstracts and 39,795 full-text publications.
conclusionsThrough integration with CIVIC, we provide a prioritized list of curatable clinically relevant cancer biomarkers as well as a resource that is valuable to other knowledgebases and precision cancer analysts in general. All data is publically available and distributed with a Creative Commons Zero license. The CIViCmine knowledgebase is available at http://bionlp.bcgsc.ca/civicmine/.
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.