模式生物文献检索基准测试：以盘基网柄菌为例
Benchmarking Literature Retrieval for a Model Organism: A Dictyostelium Case Study
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中文总结 AI 辅助
针对模式生物盘基网柄菌，构建了基于策展查询的检索基准，并研究了重排序、基因感知扩展及全文检索对窄领域生物检索的改善作用。
中文摘要 AI 辅助
生物文献检索系统通常使用广泛的生物医学语料库和通用搜索任务进行开发和评估。然而，许多精选知识库在更狭窄的模式生物领域运作，这些领域的文献稀少且术语具有物种特异性。我们为盘基网柄菌（Dictyostelium）引入了来自dictyBase的检索基准，盘基网柄菌是细胞和发育生物学中的一种模式生物。该基准包含由策展人生成的、与PubMed索引文章相关联的生物查询，以及结构化的基因注释。利用这一基准，我们研究了窄领域生物检索中的三个因素：交叉编码器重排序、基因感知查询扩展，以及仅摘要检索与全文检索。我们报告称，重排序和基因感知查询扩展能选择性地改善检索效果：当模型非常适合生物证据匹配时，重排序最为有用，而策展注释通过减少词汇不匹配来帮助澄清紧凑的生物查询。当摘要遗漏支持性证据时，全文分块能显著提高检索性能，既增加候选召回率又提升排名靠前的性能，尽管这些情况比由摘要支持的查询更难。数据和代码可在该https URL公开获取，基准数据集还额外存档于Zenodo。
英文摘要
Biological literature retrieval systems are often developed and evaluated using broad biomedical corpora and general-purpose search tasks. However, many curated knowledge bases operate in narrower model-organism domains, where the literature is sparse and terminology is organism-specific. We introduce a retrieval benchmark from dictyBase for Dictyostelium, a model organism in cell and developmental biology. The benchmark consists of curator-generated biological queries linked to PubMed-indexed articles, together with structured gene annotations. Using this benchmark, we study three factors in niche biological retrieval: cross-encoder reranking, gene-aware query expansion, and abstract-only versus full-text retrieval. We report that reranking and gene-aware query expansion improve retrieval selectively: reranking is most useful when the model is well suited to biological evidence matching, whereas curated annotations help clarify compact biological queries by reducing vocabulary mismatch. Full-text chunks substantially improve retrieval when abstracts omit supporting evidence, increasing both candidate recall and top-rank performance, although these cases are harder than queries supported by abstracts. Data and code are publicly available at https://github.com/fulaibaowang/dictycite, and the benchmark dataset is additionally archived on Zenodo.
发表机构
- University of Ljubljana（卢布尔雅那大学）
- Baylor College of Medicine（贝勒医学院）
机构由 AI 辅助整理，请以论文原文为准。
