释放PubMed中央补充数据文件的潜力
Julien Gobeill1,2, Déborah Caucheteur1,2, Alexandre Flament1,2
1SIB Text Mining Group, Swiss Institute of Bioinformatics, Geneva 1206, Switzerland.
Bioinformatics advances
|August 27, 2025
概括
补充数据文件包含了标准搜索遗漏的关键生物信息. 提取这些数据显著改善了对生物实体和数据库的文献搜索,增强了生物修复工作.
科学领域:
- 生物信息学
- 数据科学
- 生物科学
背景情况:
- 生物治疗依赖于对生物实体的文献搜索.
- 标准搜索引擎 (例如,MEDLINE,PubMed Central) 在补充文件中错过了数据.
- 这限制了科学文献的完整性.
研究的目的:
- 通过从补充文件中提取数据来弥补文献索引的差距.
- 评估生物治疗的补充数据所获得的信息.
- 使用此增强数据集评估全球核心生物数据资源 (GCBR) 的可搜索性.
主要方法:
- 在两年内从85%的补充数据文件中系统地提取文本.
- 创建了一个可搜索的3500万份文件.
- 搜索全球核心生物数据资源 (GCBR) 的名称和加入号码.
主要成果:
- 补充文件为资源名称提供6%的回忆增长.
- 97%的已识别的加入号码仅在补充文件中发现.
- 加入号码在补充文件中的公布越来越多,主要是以Excel格式.
结论:
- 补充数据文件对于全面的文献搜索和生物库存至关重要.
- 埃克塞尔文件的普及阻碍了机器可读性和互操作性.
- 需要采用替代数据发布方法来提高数据的可访问性和可重复使用性.
更多相关视频
09:20Cloud-Based Phrase Mining and Analysis of User-Defined Phrase-Category Association in Biomedical Publications
Published on: February 23, 2019
8.8K
05:47Evidence-based Knowledge Synthesis and Hypothesis Validation: Navigating Biomedical Knowledge Bases via Explainable AI and Agentic Systems
Published on: June 13, 2025
575
相关概念视频
01:57Gene Families
9.1K
Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
Occasionally these regions can be adapted to take on new roles within the organism, becoming novel genes...
9.1K
02:46Chi-square Analysis
38.7K
The chi-square test is a statistical hypothesis test. It is used to check whether there is a significant difference between an expected value and an observed value. In the context of genetics, it enables us to either accept or reject a hypothesis, based on how much the observed values deviate from the expected values.
The chi-square test was developed by Pearson in 1990.
The first step of performing a Chi-square analysis is to establish a null hypothesis, which assumes that there is no real...
The chi-square test was developed by Pearson in 1990.
The first step of performing a Chi-square analysis is to establish a null hypothesis, which assumes that there is no real...
38.7K
02:21Globular and Fibrous Proteins
44.4K
Many proteins can be classified into two distinct subtypes - globular or fibrous. These two types differ in their shapes and solubilities.
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
Globular proteins are also known as spheroproteins and typically are approximately round in shape. They contain a mix of amino acid types and contain differing sequences in their primary structures. Globular proteins have many different functions, such as enzymes, cellular messengers, and molecular transporters. These roles often require the proteins to be...
44.4K
02:10Additional Subnuclear Structures
4.7K
The eukaryotic nucleus is a double membrane-bound organelle that contains nearly all of the cell’s genetic material in the form of chromosomes. It is rightly called the “brain” of the cell as it shoulders the responsibility of responding to various physiological processes, stress, altered metabolic conditions, and other cellular signals.
The nucleus contains many membrane-less subnuclear organelles or nuclear bodies, such as nucleoli, Cajal bodies, speckles,...
The nucleus contains many membrane-less subnuclear organelles or nuclear bodies, such as nucleoli, Cajal bodies, speckles,...
4.7K
01:15Western Blotting
17.6K
Western blotting is an analytical technique for protein identification. It has various applications in immunology and medicine, including detecting diseases like bovine spongiform encephalopathy, mad cow disease, and human and feline immunodeficiency virus from biological samples.
The technique begins with separating proteins from the sample using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), followed by protein transfer, immunoblotting, and finally, protein detection.
The technique begins with separating proteins from the sample using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE), followed by protein transfer, immunoblotting, and finally, protein detection.
17.6K
01:12Analysis of Population Pharmacokinetic Data
382
Analysis of population pharmacokinetic data involves studying the behavior of drugs within diverse populations to understand their pharmacokinetic parameters. Traditional pharmacokinetic methods typically involve collecting samples from a few individuals and estimating these parameters. While these methods are commonly used, they have limitations in capturing the variability in drug response among individuals or heterogeneous populations. Population pharmacokinetics is employed to address these...
382