A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records
A high-precision rule-based extraction system for expanding geospatial metadata in GenBank records
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DOI：
10.1093/jamia/ocv172
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发表时间：
2016-09-01
影响因子：
6.4
通讯作者：
Gonzalez, Graciela
中科院分区：
文献类型：
--
作者：
Tahsin, Tasnia;Weissenbacher, Davy;Gonzalez, Graciela
目的GenBank中反映病毒序列感染宿主位置（LOIH）的元数据往往缺乏特异性。这项工作旨在通过从相关全文文章中提取更具体的地理信息，并使用来自外部地理数据库的知识将其映射到纬度/经度，从而增强该元数据。我们开发了一个基于规则的信息提取框架，用于将GenBank记录与LOIH的经纬度联系起来。我们的系统首先从GenBank记录中提取现有的地理空间元数据，并试图通过从相关全文PubMed Central文章的文本和表格中寻找额外的相关地理信息来改进它。根据从这些来源吸收的数据，最后提取出记录的位置，然后消除歧义并将其映射到各自的地理坐标。我们在包含5728条甲型流感病毒GenBank记录的人工注释数据集上评估了我们的方法。结果我们发现我们的系统将GenBank记录与其LOIH的经纬度联系起来的精度、召回率和f-measure分别为0.832、0.967和0.894。我们的系统在将GenBank记录与LOIH的地理坐标联系起来方面具有很高的准确性。然而，它可以通过扩展我们的地理空间数据数据库，结合拼写校正和增强用于提取的规则来进一步改进。结论基于记录元数据和从相关全文文章中提取的信息，我们的系统可以很好地将甲型流感病毒的GenBank记录与其LOIH的地理坐标链接起来。
Objective The metadata reflecting the location of the infected host (LOIH) of virus sequences in GenBank often lacks specificity. This work seeks to enhance this metadata by extracting more specific geographic information from related full-text articles and mapping them to their latitude/longitudes using knowledge derived from external geographical databases.Materials and Methods We developed a rule-based information extraction framework for linking GenBank records to the latitude/longitudes of the LOIH. Our system first extracts existing geospatial metadata from GenBank records and attempts to improve it by seeking additional, relevant geographic information from text and tables in related full-text PubMed Central articles. The final extracted locations of the records, based on data assimilated from these sources, are then disambiguated and mapped to their respective geo-coordinates. We evaluated our approach on a manually annotated dataset comprising of 5728 GenBank records for the influenza A virus.Results We found the precision, recall, and f-measure of our system for linking GenBank records to the latitude/longitudes of their LOIH to be 0.832, 0.967, and 0.894, respectively. Discussion Our system had a high level of accuracy for linking GenBank records to the geo-coordinates of the LOIH. However, it can be further improved by expanding our database of geospatial data, incorporating spell correction, and enhancing the rules used for extraction.Conclusion Our system performs reasonably well for linking GenBank records for the influenza A virus to the geo-coordinates of their LOIH based on record metadata and information extracted from related full-text articles.