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OpenTreeOfLife / reference-taxonomy

Open Tree Reference Taxonomy (OTT) tools
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Documentation of what flags mean #129

Closed josephwb closed 8 years ago

josephwb commented 9 years ago

Little to no information exists as to what the different OTT flags mean. The wiki page points to taxomachine code, but little information exists there.

Came up because a paleo person was trying to understand "extinct_direct" vs. "extinct_inherited".

josephwb commented 9 years ago

Can we make this a priority? I don't believe there even exists a complete list of flags. We need this for moving forward with the next synthesis.

jar398 commented 9 years ago

Please review https://github.com/OpenTreeOfLife/reference-taxonomy/wiki/Taxon-flags

josephwb commented 9 years ago

Much better!

"merged" probably needs a bit of extra information. "unplaced" is a bit of a head-scratcher. so, do we not want to include them? may be good species (or whatever), just of unknown placement. i guess the same goes for "incertae sedis": there are certainly real bird species without known taxonomic/phylogenetic relationships.

jar398 commented 9 years ago

On Wed, Aug 12, 2015 at 12:27 PM, Joseph W. Brown notifications@github.com wrote:

Much better!

"merged" probably needs a bit of extra information.

will get on it.

"unplaced" is a bit of a head-scratcher. so, do we not want to include them? may be good species (or whatever), just of unknown placement. i guess the same goes for "incertae sedis": there are certainly real bird species without known taxonomic/phylogenetic relationships.

I've been saying this for years now. Stephen has always said they couldn't be included, but I never understood why.

— Reply to this email directly or view it on GitHub https://github.com/OpenTreeOfLife/reference-taxonomy/issues/129#issuecomment-130362529 .