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OpenTreeOfLife / phylografter

web2py app for tree store and grafting
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node with otu ids that are not valid #102

Closed mtholder closed 10 years ago

mtholder commented 10 years ago

There are several cases, summarized at http://phylo.bio.ku.edu/tmp/nodes_with_invalid_otu_ids.txt

zbolander commented 10 years ago

I'll re-upload re-map the studies and see if that helps. A lot of the earlier phylografter uploads had problems of various sorts.

Bryan

On Sat, Feb 8, 2014 at 1:15 AM, Mark T. Holder notifications@github.comwrote:

There are several cases, summarized at http://phylo.bio.ku.edu/tmp/nodes_with_invalid_otu_ids.txt

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/phylografter/issues/102 .

mtholder commented 10 years ago

Hi Bryan, if the remapping is time-consuming and these studies are not needed, we could just delete them. i don't know how important those studies are. the list came from a script run over every study in the entire corpus.

jar398 commented 10 years ago

Along these lines, although I think not the same problem:

When the taxonomy gets updated some of the OTT ids become deprecated, for a variety of reasons that I won't go into here. In some but not all cases a replacement id is stored in a column of the file deprecated.tsv in the taxonomy dump. I had anticipated that most problems would be fixed through some automatic process such as use of the deprecated.tsv files and application of the TNRS. These fixes would be applied in the curation interface, in treemachine, or in both. Treemachine applies the TNRS I believe in this situation. Re-entering the study is probably the wrong approach in general as the issue applies to all studies and doing manual remapping does not scale.

On Sat, Feb 8, 2014 at 1:15 AM, Mark T. Holder notifications@github.comwrote:

There are several cases, summarized at http://phylo.bio.ku.edu/tmp/nodes_with_invalid_otu_ids.txt

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/phylografter/issues/102 .

rhr commented 10 years ago

Let's hold off deleting stuff until I have a chance to look at those studies in particular and do some database curation.

On Sat, Feb 8, 2014 at 7:38 AM, Mark T. Holder notifications@github.comwrote:

Hi Bryan, if the remapping is time-consuming and these studies are not needed, we could just delete them. i don't know how important those studies are. the list came from a script run over every study in the entire corpus.

Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/phylografter/issues/102#issuecomment-34544106 .

rhr commented 10 years ago

I think the update to ott 2.4 will fix this.