Priority additions to NexSON vocabulary

[pmidford]

Opening this to solicit high priority additions to the NexSON vocabulary, particularly things that phylografter should be writing but isn't currently and that should be captured in the document store.

I'll start with Cody's changes
add:
ot:specifiedRoot
ot:branchLengthTimeUnit

change name (parsers should continue to recognize old vocabulary until??)
ot:ottolName -> ot:ottTaxonName
ot:treebaseOtulid -> ot:treebaseOTUId
ot:ottolid -> ot:ottId
ot:isLeaf -> ot:isOTU
ot:years -> ot:time

From Oct 9 call
ot:curatedType (tree) - phylografter's type column - frequently contains inference method, but also other free text.

Please comment to add to this list. The current NexSON vocabulary is defined at http://opentree.wikispaces.com/NexSON. The google doc (contact me if you need the link for this) lists what's available in phylografter that we could write to a NexSON file.

[pmidford]

Issue 88 resolved all of these except ot:ottTaxonName, which was actually new and I accidentally attached to otu rather than node. I will removed the misplacement, but defer adding ot:ottTaxonName to nodes.

[mtholder]

Hi Peter, It looks to me as if all nodes (at least for study 9) are being flagged with the "isLeaf" annotation (regardless of whether or not they are leaves). I'm not sure it this is a bug in logic in the code or a legacy error caused by an error in updating the db at some point in the past). I am basing this on running a GET on http://www.reelab.net/phylografter/study/export_gzipNexSON.json/9 and finding 504 of the isLeaf of the annotations and 504 nodes. I'm not sure how many other studies are affected.

[pmidford]

I'm looking at it now.

On Oct 26, 2013, at 8:27 PM, "Mark T. Holder" notifications@github.com wrote:

Hi Peter, It looks to me as if all nodes (at least for study 9) are being flagged with the "isLeaf" annotation (regardless of whether or not they are leaves). I'm not sure it this is a bug in logic in the code or a legacy error caused by an error in updating the db at some point in the past). I am basing this on running a GET on http://www.reelab.net/phylografter/study/export_gzipNexSON.json/9 and finding 504 of the isLeaf of the annotations and 504 nodes. I'm not sure how many other studies are affected.

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[pmidford]

Fixed. Merge (#93) and server update waiting for Rick.

On Oct 26, 2013, at 8:45 PM, Peter Midford peter.midford@gmail.com wrote:

I'm looking at it now.

On Oct 26, 2013, at 8:27 PM, "Mark T. Holder" notifications@github.com wrote:

Hi Peter, It looks to me as if all nodes (at least for study 9) are being flagged with the "isLeaf" annotation (regardless of whether or not they are leaves). I'm not sure it this is a bug in logic in the code or a legacy error caused by an error in updating the db at some point in the past). I am basing this on running a GET on http://www.reelab.net/phylografter/study/export_gzipNexSON.json/9 and finding 504 of the isLeaf of the annotations and 504 nodes. I'm not sure how many other studies are affected.

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Reply to this email directly or view it on GitHub.