Direct patch from Curator

[hdliv]

When OTUs don't map...in microbial studies many times due to strains... Can we create a direct patching system or 'ADD to OTT' so that we can directly map them? Another study where everything has binomial species plus strain plus GB#.

[josephwb]

My concern: while this may be useful, it also has the potential for abuse (i.e. tree contributors insisting on the existence of taxa no one else recognizes). JTB.

On 29 June 2014 16:46, Dail Laughinghouse notifications@github.com wrote:

When OTUs don't map...in microbial studies many times due to strains... Can we create a direct patching system or 'ADD to OTT' so that we can directly map them? Another study where everything has binomial species plus strain plus GB#.

[image: screen shot 2014-06-29 at 4 43 12 pm] https://cloud.githubusercontent.com/assets/6361361/3424399/6311b32e-ffce-11e3-9439-761428c7ec21.png

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/opentree/issues/343.

[hdliv]

This is useful until we get more microbes in. We can think about turning it off afterwards, but we need to find a way to add.

Another study needs to be added...

[kcranston]

What is the provenance for these names? Or, a broader question - what should we require in terms of provenance beyond a simple assertion by a curator that the names exist? All of the names in OTT have a link from nodes in the tree browser to more information about the source of the name. What would we use in this case?

[kcranston]

Also, note that we would need to know the placement of these taxa in OTT (the parent node). Otherwise, we have no way to link these tree with OTT or other trees.

[hdliv]

My understanding was that Strains have the parent node as the species epithet, so the parent node would be the binomial species in that case. And provenance would be the DOI of the paper. since these are the same that the patch requires.

[jar398]

We've been talking about this idea for a long time. There are two issues here.

One is whether this is a desirable feature. I sort of like it but there are arguments both ways. I would prefer for there to be consensus before going forward with it.

The other issue is programmer resources. We're stretched thin. This would be a major project with many parts, and would compete with all the other things we're looking at, including the SILVA update and Genbank strain processing, and the many things we need to do to help make the system scale up, such as quality control and conflict visualization. If you want to get involved I'd be happy to talk about it.

Not saying no, just saying why it's not an immediate yes.

On Mon, Jun 30, 2014 at 4:25 PM, Dail Laughinghouse < notifications@github.com> wrote:

Strains have the parent node as the species, so the parent node would be the binomial species in that case. And provenance would be the DOI of the paper. since these are the same that the patch requires.

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/opentree/issues/343#issuecomment-47582041 .

[hdliv]

@jar398 We understand the programmer issues. I made this suggestion since I had thought this would be an easier way both for the curators and later the community to add tips which are not in OTT. This way one would not have to go out and create a patch for each study. As to SILVA...please see the e-mail I sent you about the issue with the stability of the tips which all of us had talked about in Virginia. Let us know what we can do to help.

[kcranston]

We now have a "Adding new taxa" feature in the curator app. Only took two years... ;)