Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis
Yalbi Itzel Balderas-Martínez1,2, Fabio Rinaldi3,4, Gabriela Contreras4
1Facultad de Ciencias, Departamento Biología Celular, Universidad Nacional Autónoma de México, Ciudad Universitaria, Circuito Exterior s/n, Coyoacán, CP 04510, Ciudad de México, CDMX, México.
Abstract:
MicroRNAs (miRNAs) are small and non-coding RNA molecules that inhibit gene expression posttranscriptionally. They play important roles in several biological processes, and in recent years there has been an interest in studying how they are related to the pathogenesis of diseases. Although there are already some databases that contain information for miRNAs and their relation with illnesses, their curation represents a significant challenge due to the amount of information that is being generated every day. In particular, respiratory diseases are poorly documented in databases, despite the fact that they are of increasing concern regarding morbidity, mortality and economic impacts. In this work, we present the results that we obtained in the BioCreative Interactive Track (IAT), using a semiautomatic approach for improving biocuration of miRNAs related to diseases. Our procedures will be useful to complement databases that contain this type of information. We adapted the OntoGene text mining pipeline and the ODIN curation system in a full-text corpus of scientific publications concerning one specific respiratory disease: idiopathic pulmonary fibrosis, the most common and aggressive of the idiopathic interstitial cases of pneumonia. We curated 823 miRNA text snippets and found a total of 246 miRNAs related to this disease based on our semiautomatic approach with the system OntoGene/ODIN. The biocuration throughput improved by a factor of 12 compared with traditional manual biocuration. A significant advantage of our semiautomatic pipeline is that it can be applied to obtain the miRNAs of all the respiratory diseases and offers the possibility to be used for other illnesses.
Database Url:
http://odin.ccg.unam.mx/ODIN/bc2015-miRNA/.
Insights
This study introduces a semiautomatic method to improve the curation of microRNAs (miRNAs) linked to diseases, significantly boosting efficiency for respiratory conditions like idiopathic pulmonary fibrosis.
Area of Science:
- Biomedical Informatics
- Molecular Biology
- Computational Biology
Background:
- MicroRNAs (miRNAs) are key regulators of gene expression with roles in disease pathogenesis.
- Existing miRNA-disease databases face curation challenges due to rapidly growing literature.
- Respiratory diseases, particularly idiopathic pulmonary fibrosis, are underrepresented in current miRNA databases.
Purpose of the Study:
- To develop and evaluate a semiautomatic approach for enhancing the biocuration of miRNAs associated with diseases.
- To improve the documentation of miRNAs in respiratory diseases, addressing a gap in existing databases.
- To assess the efficiency of the proposed semiautomatic pipeline compared to manual curation.
Main Methods:
- Adapted the OntoGene text mining pipeline and the ODIN curation system.
- Applied the system to a full-text corpus of publications on idiopathic pulmonary fibrosis.
- Utilized a semiautomatic approach for identifying and curating miRNA-disease relationships.
Main Results:
- Successfully curated 823 miRNA text snippets, identifying 246 miRNAs related to idiopathic pulmonary fibrosis.
- Achieved a 12-fold improvement in biocuration throughput compared to traditional manual methods.
- Demonstrated the pipeline's potential for broader application to other respiratory diseases and illnesses.
Conclusions:
- The semiautomatic OntoGene/ODIN pipeline significantly enhances the efficiency of miRNA biocuration for diseases.
- This approach addresses the underrepresentation of respiratory diseases in miRNA-disease databases.
- The methodology is adaptable for curating miRNA information across various diseases, offering a scalable solution.
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