Identification of highly related references about gene-disease association
1Department of Medical Informatics, Tzu Chi University, Hualien, Taiwan. rlliutcu@mail.tcu.edu.tw.
Insights
A new method, Conclusive, Rich, and Focused References (CRFref), effectively ranks biomedical literature relevant to specific gene-disease associations. This tool aids researchers and curators in efficiently identifying key information for gene-disease studies.
Area of Science:
- Biomedical Informatics
- Genetics
- Computational Biology
Background:
- Accurate curation of gene-disease associations requires thorough literature review.
- Efficient retrieval of relevant references is crucial for timely and complete data curation.
Purpose of the Study:
- To develop and evaluate a novel technique for ranking biomedical references based on their relevance to specific gene-disease pairs.
- To improve the identification of conclusive, rich, and focused literature for gene-disease association studies.
Main Methods:
- The Conclusive, Rich, and Focused References (CRFref) technique was developed.
- CRFref scores candidate references by integrating measures of conclusiveness, richness, and focus concerning a given gene-disease pair.
- Experiments involved over 100,000 references for more than 1,000 gene-disease pairs.
Main Results:
- CRFref significantly outperforms baseline methods in ranking relevant biomedical references.
- The technique successfully identifies literature highly pertinent to specific gene-disease associations.
- Expert curators' selected references for developing gene-disease association summaries were effectively prioritized by CRFref.
Conclusions:
- CRFref is an effective method for prioritizing literature related to gene-disease associations.
- The technique can enhance existing search engines and text mining systems focused on gene-disease studies.
- CRFref supports curators and researchers by improving the discoverability of essential biomedical references.
Background:
Curation of gene-disease associations published in literature should be based on careful and frequent survey of the references that are highly related to specific gene-disease associations. Retrieval of the references is thus essential for timely and complete curation.
Results:
We present a technique CRFref (Conclusive, Rich, and Focused References) that, given a gene-disease pair < g, d>, ranks high those biomedical references that are likely to provide conclusive, rich, and focused results about g and d. Such references are expected to be highly related to the association between g and d. CRFref ranks candidate references based on their scores. To estimate the score of a reference r, CRFref estimates and integrates three measures: degree of conclusiveness, degree of richness, and degree of focus of r with respect to < g, d>. To evaluate CRFref, experiments are conducted on over one hundred thousand references for over one thousand gene-disease pairs. Experimental results show that CRFref performs significantly better than several typical types of baselines in ranking high those references that expert curators select to develop the summaries for specific gene-disease associations.
Conclusion:
CRFref is a good technique to rank high those references that are highly related to specific gene-disease associations. It can be incorporated into existing search engines to prioritize biomedical references for curators and researchers, as well as those text mining systems that aim at the study of gene-disease associations.
Related Concept Videos
01:11Genome-wide Association Studies-GWAS
GWAS does not require the identification of the target gene involved in...
01:29Pharmacogenomics: Identification of New Drug Targets
01:11Genetic Lingo
01:43Incomplete Dominance
01:35Pedigree Analysis
02:46Genetic Screens
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which...