Automatic extraction of mutations from Medline and cross-validation with OMIM
Automatic extraction of mutations from Medline and cross-validation with OMIM
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DOI：
10.1093/nar/gkh162
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发表时间：
2004-01-01
影响因子：
14.9
通讯作者：
Kirsch, H
中科院分区：
文献类型：
--
作者：
Rebholz-Schuhmann, D;Marcel, S;Kirsch, H
突变帮助我们了解疾病的分子起源。因此，研究人员在公共数据库和科学文献中发布和寻找与疾病相关的突变，例如医学线。检索往往非常耗时且不完整。文献自动筛选更加高效。我们开发了提取方法（称为 MEMA），可以扫描 Medline 摘要中的突变。 MEMA 从 16 728 份摘要中鉴定出 24 351 个与 HUGO 基因名称相关的单突变。从 100 份摘要的样本中，我们估计突变基因对识别的召回率为 35%，精确度为 93%。仅突变检测的召回率>67%，准确率>96%。这表明我们的系统产生了可靠的数据。将来自 MEMA 的蛋白质序列突变 (PSM) 组成的子集与 OMIM 中的条目进行比较（分别为 20 503 个条目和 6699 个条目）。我们发现两个数据集有 1826 个 PSM 基因对相同（交叉验证）。这占 OMIM 中所有 PSM 基因对的 27%，占 OMIM 中同时出现在至少一篇 Medline 摘要中的 PSM 基因对的 91%。我们得出的结论是，Medline 涵盖了 OMIM 已知的大部分突变。另一大部分可能是通过诱变实验人工产生的突变。可通过 EBI 网页访问提取的突变基因对数据库（请参阅 http://www.ebi.ac.uk/rebholz/index.html）。
Mutations help us to understand the molecular origins of diseases. Researchers, therefore, both publish and seek disease-relevant mutations in public databases and in scientific literature, e.g. Medline. The retrieval tends to be time-consuming and incomplete. Automated screening of the literature is more efficient. We developed extraction methods (called MEMA) that scan Medline abstracts for mutations. MEMA identified 24 351 singleton mutations in conjunction with a HUGO gene name out of 16 728 abstracts. From a sample of 100 abstracts we estimated the recall for the identification of mutation-gene pairs to 35% at a precision of 93%. Recall for the mutation detection alone was >67% with a precision rate of >96%. This shows that our system produces reliable data. The subset consisting of protein sequence mutations (PSMs) from MEMA was compared to the entries in OMIM (20 503 entries versus 6699, respectively). We found 1826 PSM-gene pairs to be in common to both datasets (cross-validated). This is 27% of all PSM-gene pairs in OMIM and 91% of those pairs from OMIM which co-occur in at least one Medline abstract. We conclude that Medline covers a large portion of the mutations known to OMIM. Another large portion could be artificially produced mutations from mutagenesis experiments. Access to the database of extracted mutation-gene pairs is available through the web pages of the EBI (refer to http://www.ebi. ac.uk/rebholz/index.html).