Wednesday, March 20, 2013

BioNames update - matching taxon names to classifications

On eof the things BioNames will need to do is match taxon names to classifications. For example, if I want to display a taxonomic hierarchy for the user to browse through the names, then I need a map between the taxon names that I've collected and one or more classifications. The approach I'm taking is to match strings, wherever possible using both the name and taxon authority. In many cases this is straightforward, especially if there is only one taxon with a name. But often we have cases where the same name has been used more than once for different taxa. For example, here is what ION has for the name "Nystactes".
Nystactes Bohlke2735131
Nystactes Gloger 18274888093
Nystactes Kaup 18294888094

If I want to map these names to GBIF then these are corresponding taxa with the name "Nystactes":
Nystactes Böhlke, 19572403398
Nystactes Gloger, 18272475109
Nystactes Kaup, 18293239722

Clearly the names are almost identical, but there are enough little differences (presence or absence of comma, "o" versus "ö") to make things interesting. To make the mapping I construct a bipartite graph where the nodes are taxon names, divided into two sets based on which database they came from. I then connect the nodes of the graph by edges, weighted by how similar the names are. For example, here is the graph for "Nystactes" (displayed using Google images:

I then compute the maximum weighted bipartite matching using a C++ program I wrote. This matching corresponds to the solid lines in the graph above.

In this way we can make a sensible guess as to how names in the two databases relate to one another.