Tuesday, November 27, 2012

Fuzzy matching taxonomic names using ngrams

Quick note to self about possible way to using fuzzy matching when searching for taxonomic names. Now that I'm using Cloudant to host CouchDB databases (e.g., see BioStor in the the cloud) I'd like to have a way to support fuzzy matching so that if I type in a name and misspelt it, there's a reasonable chance I will still find that name. This is the "did you mean?" feature beloved by Google users. There are various ways to tackle this problem, and Tony Rees' TAXAMATCH is perhaps the best known solution.

Cloudant supports Lucence for full text searching, but while this allows some possibility for approximate matching (by appending "~" to the search string) initial experiments suggested it wasn't going to be terribly useful. What does seem to work is to use ngrams. As a crude example, here is a CouchDN view that converts a string (in this case a taxon name) to a series of trigrams (three letter strings) then indexes their concatenation.

"_id": "_design/taxonname",
"language": "javascript",
"indexes": {
"all": {
"index": "function(doc) { if (doc.docType == 'taxonName') { var n = doc.nameComplete.length; var ngrams = []; for (var i=0; i < n-2;i++) { var ngram = doc.nameComplete.charAt(i) + doc.nameComplete.charAt(i+1) + doc.nameComplete.charAt(i+2); ngrams.push(ngram); } if (n > 2) { ngrams.push('$' + doc.nameComplete.charAt(0) + doc.nameComplete.charAt(1)); ngrams.push(doc.nameComplete.charAt(n-2) + doc.nameComplete.charAt(n-1) + '$'); } ngrams.sort(); index(\"default\", ngrams.join(' '), {\"store\": \"yes\"}); } }"

To search this view for a name I then generate trigrams for the query string (e.g., "Pomatomix" becomes "$Po Pom oma mat ato tom omi mix ix$" where "$" signals the start or end of the string) and search on that. For example, append this string to the URL of the CouchDB database to search for "Pomatomix":


Initial results are promising (searching on bigrams generated an alarming degree of matches that seemed rather dubious). I need to do some more work on this, but it might be a simple and quick way to support "did you mean?" for taxonomic names.