search

OpenTreeOfLife / treemachine

Source tree graph database
Other
16 stars 6 forks source link

Many "isolated" taxa in treemachine (bad Lucene index?) #36

Closed jimallman closed 10 years ago

jimallman commented 11 years ago

There are currently lots of taxa that appear alone in argus -- no ancestors or descendant nodes, just one lonely dot. For example, search for Hominidae.

Most nodes close to the root (life) node are intact, eg, http://dev.opentreeoflife.org/opentree/otol.draft.22@3103299/Metazoa-Monosiga-ovata

...but treemachine fails when retrieving a subtree for Chordata: http://dev.opentreeoflife.org/opentree/otol.draft.22@417744/Chordata

The error message describes a Lucene error, where multiple items are found in the index where one is expected.

It appears that all descendants nodes (within the clade Chordata) are isolated, eg: http://dev.opentreeoflife.org/opentree/argus/ottol@947318/Craniata

blackrim commented 11 years ago

Yeah, the synthesis does not require all traces be present yet. That is what i am implementing now so i will close this once that is done. Stephen On Jun 15, 2013 12:08 PM, "Jim Allman" notifications@github.com wrote:

There are currently lots of taxa that appear alone in argus -- no ancestors or descendant nodes, just one lonely dot. For example, search for Hominidae.

Most nodes close to the root (life) node are intact, eg,

http://dev.opentreeoflife.org/opentree/otol.draft.22@3103299/Metazoa-Monosiga-ovata

...but treemachine fails when retrieving a subtree for Chordata: http://dev.opentreeoflife.org/opentree/otol.draft.22@417744/Chordata

The error message describes a Lucene error, where multiple items are found in the index where one is expected.

It appears that all descendants nodes (within the clade Chordata) are isolated, eg: http://dev.opentreeoflife.org/opentree/argus/ottol@947318/Craniata

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/treemachine/issues/36 .

chinchliff commented 10 years ago

@blackrim, Is this done?

chinchliff commented 10 years ago

This seems to be obsolete, perhaps interceding changes to taxonomy, etc. have solved the problem. Closing this issue for now.

jar398 commented 10 years ago

Typically these are taxa whose monophyly is denied by some source tree. We talked about this today (at the May 2014 F2F) and the agreed plan was to provide a treemachine service that lists the conflicting trees for such a taxon, and display this information in the UI when someone looks up one of these taxa in the TNRS completion box.

jar398 commented 10 years ago

Superseded by #98