Taxomachine- problems with neo4j instance

[anatshafir1]

Dear Developers,
I am trying to install the standalone version of taxomachine for name resolutions purposes.
I followed the instructions until the point where the database should be moved into a neo4j instance that has a taxomachine plugin. After reading additionally the installation guidance for the taxomachine server, I understood that I should probably find and unpack some version of neo4j between 1.9 and 2. I found a community version 1.9.5 of neo4j from the following link: https://files.opentreeoflife.org/neo4j/ , however I was unable to unpack the tar.gz file.
Can you please let me know where else I can find a compatible version (or maybe I just misunderstood the instructions)?
Thank you very much!
Anat.

[bredelings]

Hi Anat,

We are not using taxomachine any more. We have reimplemented its functionality in C++ in otcetera (https://github.com/OpenTreeOfLife/otcetera) in the program otc-tol-ws (an acronym for otcetera-treeoflife-webservices).

It should be possible for you to compile otcetera and run otc-tol-ws. However, you might be the first person to try it, so the documentation may be lacking.

-BenRI

[anatshafir1]

Thank you very much for your quick response! I went over the documentation of otcetera, though I couldn't understand whether the program can serve my purposes for name resolution. Is it possible, using this program, to find resolved names (that match the names in the database) for a list of taxa or a phylogenetic tree? Thank you!

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On Tue, May 24, 2022 at 1:54 PM Benjamin Redelings ***@***.***> wrote: Hi Anat, We are not using taxomachine any more. We have reimplemented its functionality in C++ in otcetera ( https://github.com/OpenTreeOfLife/otcetera) in the program otc-tol-ws (an acronym for otcetera-treeoflife-webservices). It should be possible for you to compile otcetera and run otc-tol-ws. However, you might be the first person to try it, so the documentation may be lacking. -BenRI — Reply to this email directly, view it on GitHub <#160 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFTD57MJ22G43CJMOR54OGDVLSYNDANCNFSM5WY3SCXQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>

[bredelings]

I should first check -- is there a reason why you want to run your own server, instead of querying the existing server api.opentreeoflife.org?
See: https://github.com/OpenTreeOfLife/germinator/wiki/TNRS-API-v3
You can query the server directly using curl. You can also use the R package rotl or the python package opentree.

Assuming that you really want your own server, the answer is "yes", otcetera implements the TNRS api. This api was formerly provided by taxomachine.

[bredelings]

We also have a bulk name-mapping tool here that might fit your needs better than rotl or python-opentree: https://tree.opentreeoflife.org/curator/tnrs/

[anatshafir1]

Thank you very much for all the suggestions! I think I will try using rotl.

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On Tue, May 24, 2022 at 6:19 PM Benjamin Redelings ***@***.***> wrote: We also have a bulk name-mapping tool here that might fit your needs better than rotl or python-opentree: https://tree.opentreeoflife.org/curator/tnrs/ — Reply to this email directly, view it on GitHub <#160 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFTD57PLQ3FWJBPUU3OQI4LVLTXQJANCNFSM5WY3SCXQ> . You are receiving this because you authored the thread.Message ID: ***@***.***>