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Knowledge-driven geospatial location resolution for phylogeographic models of virus migration.

Weissenbacher D, Tahsin T, Beard R, Figaro M, Rivera R, Scotch M, Gonzalez G - Bioinformatics (2015)

Bottom Line: For detecting and disambiguating locations, our system performed best using the metadata heuristic (0.54 Precision, 0.89 Recall and 0.68 F-score).Our error analysis showed that a noticeable increase in the accuracy of toponym resolution is possible by improving the geospatial location detection.By improving these fundamental automated tasks, our system can be a useful resource to phylogeographers that rely on geospatial metadata of GenBank sequences. .

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA.

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Overview of the toponym resolver pipeline
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btv259-F1: Overview of the toponym resolver pipeline

Mentions: In this section we present our toponym resolver for phylogeographic documents (Fig. 1). Our system is composed of two modules applied sequentially. The first module attempts to identify all names of places in a document. The second module addresses the disambiguation of each toponym identified by the first module; it takes as input all the names of places and assigns a unique pair of coordinates to each of them.


Knowledge-driven geospatial location resolution for phylogeographic models of virus migration.

Weissenbacher D, Tahsin T, Beard R, Figaro M, Rivera R, Scotch M, Gonzalez G - Bioinformatics (2015)

Overview of the toponym resolver pipeline
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4542781&req=5

btv259-F1: Overview of the toponym resolver pipeline
Mentions: In this section we present our toponym resolver for phylogeographic documents (Fig. 1). Our system is composed of two modules applied sequentially. The first module attempts to identify all names of places in a document. The second module addresses the disambiguation of each toponym identified by the first module; it takes as input all the names of places and assigns a unique pair of coordinates to each of them.

Bottom Line: For detecting and disambiguating locations, our system performed best using the metadata heuristic (0.54 Precision, 0.89 Recall and 0.68 F-score).Our error analysis showed that a noticeable increase in the accuracy of toponym resolution is possible by improving the geospatial location detection.By improving these fundamental automated tasks, our system can be a useful resource to phylogeographers that rely on geospatial metadata of GenBank sequences. .

View Article: PubMed Central - PubMed

Affiliation: Department of Biomedical Informatics, Arizona State University, Scottsdale, AZ 85259, USA and Center for Environmental Security, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5904, USA.

Show MeSH
Related in: MedlinePlus