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OpenTreeOfLife / opentree

Opentree browsing and curation web site. For overarching or cross-repo concerns, please see the 'germinator' repo.
http://tree.opentreeoflife.org/
BSD 2-Clause "Simplified" License
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It's probably time to rename 'webapp' to something more descriptive. #94

Closed jar398 closed 10 years ago

jar398 commented 10 years ago

especially now that there are multiple web apps.

jimallman commented 10 years ago

Agreed! As long as it's not opentree, since that's pretty overloaded as it is.

I keep thinking something along the lines of "tree explorer", since that's currently most of what we can do in this app. But you can also comment, moderate existing comments, and maybe do other things eventually.

chinchliff commented 10 years ago

I find the word "browse" to be better-understood than "explore". What the web app browses though, is not just any tree, but specifically the synthesized tree of life. That tree also does not have a name, but it should. I'll call it "synthtol" for convenience here, in which case a simple and clear name for the webapp might the "synthtol browser".

Clearly, "synthtol" is not a good name for that tree. What is?

On Wednesday, October 16, 2013, Jim Allman wrote:

Agreed! As long as it's not opentree, since that's pretty overloaded as it is.

I keep thinking something along the lines of "tree explorer", since that's currently most of what we can do in this app. But you can also comment, moderate existing comments, and maybe do other things eventually.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/opentree/issues/94#issuecomment-26459683 .

jimallman commented 10 years ago

We're still hoping for the ability to browse other trees, right? Source trees, at least.

jar398 commented 10 years ago

On Oct 17, 2013, at 1:50 PM, Jim Allman wrote:

We're still hoping for the ability to browse other trees, right? Source trees, at least.

I would think so... maybe taxonomies too... although there are some hurdles, such as lack of labels on internal nodes of source trees, which might make orientation a bit of a challenge.

We can probably stay with 'opentree' for a while, I just wanted it on the issues list - I just noticed it when setting up a web2py instance, and seeing that the directory name in the repo (webapp) didn't match the application name in web2py (opentree)... so it goes...

— Reply to this email directly or view it on GitHub.

jimallman commented 10 years ago

Clearly, "synthtol" is not a good name for that tree. What is?

I believe this is a very important question, quite apart from our immediate need for an app name. Important for public outreach and understanding, since the current synthesis tree (always a work in progress) is a likely focus of outside interest. Maybe Karl's group has worked on this?

In any case, here are some off-the-cuff notions to kick around:

josephwb commented 10 years ago

Yeah, "synthtol" is a little to close to "Synthehol" of Star Trek lore. JWB.

On 17 October 2013 14:00, Jim Allman notifications@github.com wrote:

Clearly, "synthtol" is not a good name for that tree. What is?

I believe this is a very important question, quite apart from our immediate need for an app name. Important for public outreach and understanding, since the current synthesis tree (always a work in progress) is a likely focus of outside interest. Maybe Karl's group has worked on this?

In any case, here are some off-the-cuff notions to kick around:

  • the Big Tree
  • Ubertree
  • concensus tree
  • AVAToL
  • TOL
  • AToL (assembled tree of life)
  • phylotree
  • phyloTOL
  • assembled tree
  • compromise tree
  • Open Tree of Life
  • synthetic tree
  • OToL synthesis tree
  • current synthesis tree
  • live synthesis tree

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/opentree/issues/94#issuecomment-26532328 .

chinchliff commented 10 years ago

I am not sure we want to use the same tool for browsing The Big Tree (arbitrary name choice for now) and source trees. The goals and features associated with these two activities seem very different to me, and I do not see why we would want to switch back and forth.

One thing I think we do want is the ability to display conflicting topologies in the browser webapp. So in a sense, that would be browsing source trees, but not individually. The node information, for instance, will include metadata for all overlapping trees in the synthesis tree. It seems like if we want to browse an individual source tree, that would be in the scope of the study editor, which, without credentials, I imagine would function as a study viewer instead.

On Thu, Oct 17, 2013 at 1:50 PM, Jim Allman notifications@github.comwrote:

We're still hoping for the ability to browse other trees, right? Source trees, at least.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/opentree/issues/94#issuecomment-26531538 .

chinchliff commented 10 years ago

There is an important consideration that I just remembered when mentioning browsing conflicts. The Big Tree browser is intended to browse the graph, not the tree. So now I have an idea for the name said "Big Tree", which we have previously used, and which I think is succinct, explicit, and unique to the scope of this project:

The graph of life.

On Thu, Oct 17, 2013 at 2:02 PM, Joseph W. Brown notifications@github.comwrote:

Yeah, "synthtol" is a little to close to "Synthehol" of Star Trek lore. JWB.

On 17 October 2013 14:00, Jim Allman notifications@github.com wrote:

Clearly, "synthtol" is not a good name for that tree. What is?

I believe this is a very important question, quite apart from our immediate need for an app name. Important for public outreach and understanding, since the current synthesis tree (always a work in progress) is a likely focus of outside interest. Maybe Karl's group has worked on this?

In any case, here are some off-the-cuff notions to kick around:

  • the Big Tree
  • Ubertree
  • concensus tree
  • AVAToL
  • TOL
  • AToL (assembled tree of life)
  • phylotree
  • phyloTOL
  • assembled tree
  • compromise tree
  • Open Tree of Life
  • synthetic tree
  • OToL synthesis tree
  • current synthesis tree
  • live synthesis tree

— Reply to this email directly or view it on GitHub< https://github.com/OpenTreeOfLife/opentree/issues/94#issuecomment-26532328>

.

— Reply to this email directly or view it on GitHubhttps://github.com/OpenTreeOfLife/opentree/issues/94#issuecomment-26532533 .

jimallman commented 10 years ago

graph of life

Interesting! And accurate, if slightly jargon-y for a general audience. But I suspect this meaning of "graph" is slowly entering the public consciousness in the same way that "network" has.

I like how it prompts a second look at the fixed notion of a "Tree of LIfe". That it has ambiguity, and areas of active discussion, and that the tree itself is always a work in progress. Nice.