taxonomy browser

[Karen Cranston]

We have just released a browser for OTT. This post contains links:

http://blog.opentreeoflife.org/2016/01/11/open-tree-taxonomy-browser/

This new tool should make it much simpler to see the structure of the taxonomy and understand how OTT influences the synthetic tree.

Cheers,

Karen

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@kcranstn
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[Tony Rees]

Hi all,

I took a look and it seems very well executed and the displayed information is useful (congrats to the developers).

Regards - Tony

Tony Rees, New South Wales, Australia

https://about.me/TonyRees

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[Tony Rees]

Although I did wonder about one thing - could not understand the default sort of the child txa for any node (or maybe there is none), e.g. for a part of the node = infrakingdom Stramenopiles https://tree.opentreeoflife.org/taxonomy/browse?id=266745 there is a portion of the displayed children like this: 

<snip>

• genus Pseudellipsoidion ncbi:1435009, irmng:1237458 sibling_higher
• species Rictus lutensis ncbi:743684, silva:GQ223284 sibling_higher
• species Giraudyopsis stellifera ncbi:45653, silva:U78034, worms:590471, gbif:2636886, irmng:11239375sibling_higher
• species Ochromonas villosa ncbi:1034829, silva:FR865768, gbif:3194611, irmng:10016273sibling_higher
• class Phaeothamniophyceae silva:AB365197/#4, ncbi:82162, worms:368667, irmng:1435sibling_higher
• class Chrysophyceae silva:M32704/#4, ncbi:2825, worms:146230, gbif:7073563, irmng:1377sibling_higher
• species Aurearena cruciata ncbi:479719, silva:AB365192, worms:590476, gbif:5824958, irmng:11751861sibling_higher
• species Aurearena sp. HSY-2011 ncbi:1104433 sibling_higher
• order Pinguiochrysidales silva:U40929/#4, ncbi:1004267, worms:345508, gbif:1316, irmng:11759sibling_higher
• order Synurales silva:M55285/#4, ncbi:420622, worms:345523, gbif:600, irmng:12612 sibling_higher

</snip>

Maybe would be good to sort first by rank, then alphabetically, or is there an implied nesting here? (I would think not...)

Regards - Tony

Tony Rees, New South Wales, Australia

https://about.me/TonyRees

[Jonathan A Rees]

Thanks for the comments. Yes, I admit that's confusing. The ranks shown are simply whatever was assigned by the source taxonomy. In a proper taxonomy all children of a given node are of the same rank, but not here. So in the example you show there is no implied hierarchy. Since the ranks have almost no semantics, I wonder if it would be better to not show ranks at all in the children list, and just show a taxon's source-taxonomy rank in the taxon data at the top of the its page. That's what NCBI does.

We've talked a bit about what the sort order ought to be. Looks like it's currently random; alphabetical would be better. Ideally the order would be user selectable, I suppose: alphabetical, by taxon size, by rank, by source taxonomy, and so on.

Jonathan

[Tony Rees]

Hi Jonathan,

To me it would make sense if the default sort were to be grouped by rank high-low, then alphabetical within ranks, since the higher ranks implies more taxonomic precision, while low ranked thingies tend to be a bit of a wastebasket for incertae sedis names etc. Then folk wishing to traverse a familiar taxonomy are most likely to find what they want (i.e. next level children) near the top. Just my 2 cents, of course...

I would not want to see the rank indicators dropped as these are very useful in deciding how to get around in a less familiar group, also in indicating how the various source taxonomies represent particular names.

Regards - Tony

Tony Rees, New South Wales, Australia

https://about.me/TonyRees