Enhancing bio.tools by Semantic Literature Mining

Mining mentions of software tools in scientific literature is important for resource discovery and analysis in bioinformatics. Despite advancements in deep-learning-based natural language processing techniques, accurately identifying software mentions remains challenging due to naming ambiguities, inconsistent citation practices, and homonyms. In this study, we developed methods to enhance the bio.tools registry through integration with Europe PMC. We systematically explored three distinct article-tool relationships: direct associations, citations of associated articles, and textual mentions without explicit citations. A hybrid approach combining rule-based heuristics and machine learning was evaluated at a F1-score of 74.4% in contextual software mention disambiguation tasks. We further demonstrated the potential for mining software co-mentions and co-citations from EuropePMC, constructing interactive networks in Cytoscape to visualize relationships between tools. Leveraging bio.tools metadata significantly improved disambiguation accuracy, including for tools with generic names. In the future, we will expand annotated datasets, handle software synonyms, and make bio.tools software mentions retrievable through the Europe PMC Annotations API to enrich bio.tools with usage data, making software more findable, including for recommendation systems

Mitochondrial DNA single nucleotide polymorphism associated with weight estimated breeding values in Nelore cattle (Bos indicus)

We sampled 119 Nelore cattle (Bos indicus), 69 harboring B. indicus mtDNA plus 50 carrying Bos taurus mtDNA, to estimate the frequencies of putative mtDNA single nucleotide polymorphisms (SNPs) and investigate their association with Nelore weight and scrotal circumference estimated breeding values (EBVs). The PCR restriction fragment length polymorphism (PCR-RFLP) method was used to detect polymorphisms in the mitochondrial asparagine, cysteine, glycine, leucine and proline transporter RNA (tRNA) genes (tRNAasn, tRNAcys, tRNAgly, tRNAleu and tRNApro). The 50 cattle carrying B. taurus mtDNA were monomorphic for all the tRNA gene SNPs analyzed, suggesting that they are specific to mtDNA from B. indicus cattle. No tRNAcys or tRNAgly polymorphisms were detected in any of the cattle but we did detect polymorphic SNPs in the tRNAasn, tRNAleu and tRNApro genes in the cattle harboring B. indicus mtDNA, with the same allele observed in the B. taurus sequence being present in the following percentage of cattle harboring B. indicus mtDNA: 72.46% for tRNAasn, 95.23% for tRNAleu and 90.62% for tRNApro. Analyses of variance using the tRNAasn SNP as the independent variable and EBVs as the dependent variable showed that the G -> T SNP was significantly associated (p < 0.05) with maternal EBVs for weight at 120 and 210 days (p < 0.05) and animal's EBVs for weight at 210, 365 and 455 days. There was no association of the tRNAasn SNP with the scrotal circumference EBVs. These results confirm that mtDNA can affect weight and that mtDNA polymorphisms can be a source of genetic variation for quantitative traits