https://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362001-04-09T22:58:42ZEcoinformatics RedmineMorpho - Bug #165: taxonomic search facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/165?journal_id=5672001-04-09T22:58:42ZMatt Jonesjones@nceas.ucsb.edu
<ul></ul><p>Just handle taxonomic searches under this bug.</p> Morpho - Bug #165: taxonomic search facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/165?journal_id=5682001-04-11T18:32:04ZMatt Jonesjones@nceas.ucsb.edu
<ul></ul><p>Reassigned to jones.</p> Morpho - Bug #165: taxonomic search facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/165?journal_id=5692001-06-01T01:58:42ZMatt Jonesjones@nceas.ucsb.edu
<ul></ul><p>Basic taxonomic string matching implemented in the QueryDialog class. Need to<br />do term expansion and synonym lookup using ITIS (probably ITIS Canada because of<br />its XML interface).</p> Morpho - Bug #165: taxonomic search facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/165?journal_id=5702001-06-05T21:49:00ZMatt Jonesjones@nceas.ucsb.edu
<ul></ul><p>Created the "itislib" module, which contains a Java library for doing ITIS<br />searches. itislib allows one to search for taxa, determine the parent of a<br />taxon, determine the children of a taxon, and determine any synonyms for a taxon<br />name. Some issues remain with the delivery of synonym data for "not accepted" <br />taxa according to the ITIS classification.</p> Morpho - Bug #165: taxonomic search facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/165?journal_id=5712001-07-12T17:24:31ZMatt Jonesjones@nceas.ucsb.edu
<ul></ul><p>Considering blankman's comments on name expansion. I agree that expanding names<br />will be prohibitively costly at search time. Consider incorporating name<br />expansion into insert phase for Metacat. Still plan on doing ITIS synonym<br />lookup at search time. Reworded summary.</p> Morpho - Bug #165: taxonomic search facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/165?journal_id=5722001-07-12T17:37:25ZMatt Jonesjones@nceas.ucsb.edu
<ul></ul><p>Most features are complete, lowering priority for synonym lookup feature that<br />remains.</p> Morpho - Bug #165: taxonomic search facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/165?journal_id=5732001-09-06T21:29:13ZMatt Jonesjones@nceas.ucsb.edu
<ul></ul><p>Added support for looking up taxonomic synonyms using the ITIS system. This uses<br />the separate itislib library for doing the taxonomic query. Had to modify the<br />QueryDialog to support generting the proper XML query and repopulating it using<br />the new structure that supports synonyms. Now, taxon queries take one of two<br />basic forms:</p>
<p>No synonyms: <br /> QueryGroup(QueryGroup(QueryGroup(QueryTerm,QueryTerm)))<br />With synonyms: <br /> QueryGroup(QueryGroup(QueryGroup(QueryGroup(QueryTerm,QueryTerm))))</p>
<p>These are each handled in the QueryDialog methods for building and repopulating<br />taxon queries.</p>
<p>At this point in time, decided not to utilize the taxon expansion features that<br />are available in itislib because of the added cost to querying for groups that<br />have many subtaxa. For example, if someone queries on a genus that has a<br />thousand species, an expanded query would have a thousand additioanl terms to<br />match against. This is too high of a cost, and so I omitted this feature.</p>
<p>However, we could probably acheive the same effect by including the parent taxa<br />in the metadata either 1) when the metadata is created look it up in ITIS using<br />Morpho/itislib, or 2) when it is submitted to Metacat, generate a separate taxon<br />index in Metacat by looking up the taxa's parents in ITIS. In either case, the<br />query will still be fast. The cost of course is timeliness of the info -- as<br />the taxon names change or are added, the metadata will drift out of date, or be<br />incomplete.</p> Morpho - Bug #165: taxonomic search facilityhttps://projects.ecoinformatics.org/ecoinfo/issues/165?journal_id=5742013-03-27T21:13:30ZRedmine Admin
<ul></ul><p>Original Bugzilla ID was 165</p>