Open Tree Reference Taxonomy (OTT) tools
Python Java Roff Makefile Other
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new_taxa get a few more OTT ids Feb 20, 2017
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ott_id_list change Proximity heuristic from merge/noinfo to default noinfo/split (#… Feb 25, 2017
resources fix irmng date in 2.10 metadata Oct 18, 2016
service memory 7G instead of 14G Nov 6, 2016
t 3.0draft1 - smoothing out the writeup Feb 19, 2017
tax rename skel -> separation, and add Nematoda to it (Corymorpha) Feb 26, 2017
util change Proximity heuristic from merge/noinfo to default noinfo/split (#… Feb 25, 2017
ws-tests address issue #214 Oct 31, 2016
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CONTRIBUTORS smasher cleanups Jun 27, 2016
LICENSE fix #27, and a few other things Nov 17, 2015
Makefile finish up separation and Corymorpha changes Feb 26, 2017
README.md Update README.md Sep 23, 2016
TESTING.md minimal documentation May 13, 2016
adjustments.py finish up separation and Corymorpha changes Feb 26, 2017
amendments.py tweak amendments.py Feb 20, 2017
assemble_ott.py finish up separation and Corymorpha changes Feb 26, 2017
hom-report-script.py finish bringing changes over from registry branch Nov 17, 2015
ids_in_synthesis.tsv update ids lists, and count number of OTUs covered by NCBI Feb 19, 2017
ids_that_are_otus.tsv update ids lists, and count number of OTUs covered by NCBI Feb 19, 2017
inclusions.csv finish up separation and Corymorpha changes Feb 26, 2017
irmng_only_otus.csv remove huge additions file from source control; restore accidentally … Sep 11, 2016
legacy-forwards.tsv 2.9 draft 11 Oct 7, 2015
make-ott.py 3.0draft1 - smoothing out the writeup Feb 19, 2017
ncbi_ott_assignments.py fix gbif canonicalName extraction, and a few ** errors Nov 21, 2016
sources.txt Smasher version corresponding to OTT 2.1 - edit system, etc Jul 16, 2013

README.md

This repository contains the following:

  • taxa, Java classes for taxa and taxonomies
  • smasher, a Java program for combining taxonomies
  • jython and shell scripts for creating OTT, the Open Tree reference taxonomy

For Open Tree of Life documentation see the germinator repository's wiki.

How to use 'smasher'

See file doc/scripting.md for documentation on using the scripting features of smasher for building, subsetting, querying and other operations on taxonomies.

Taxonomies are represented as directories, see here.

To test to see whether you can run Smasher, do 'make aster'.

If you're puzzled by some decision the algorithm has made, it might be helpful to look at log.tsv and conflicts.tsv.

How to create a new version of OTT

See files in the doc/ directory for release notes for the taxonomy itself.

  • You may have to put certain source taxonomies such as Index Fungorum in place. Some of these are 'personal communication' so contact JAR to get ahold of them (until better arrangements are made).

  • Put previous version of OTT in tax/prev_ott/ . The taxonomy file name should be taxonomy.tsv, similarly synonyms.tsv and so on. (Around version 2.2 the file names changed from no extension to a .tsv extension.) The purpose of prev_ott is to get continuity of identifier assignments.

  • Edit definition of WHICH in Makefile to be new version number, e.g. WHICH=2.7.draft13

  • To refresh NCBI, rm -rf tax/ncbi. Similarly GBIF and Silva. (Note that GBIF is being updated very infrequently, so refreshing it is sort of a waste of time. Silva is updated every few months, I think.)

  • 'make ott'

  • Result will be in tax/ott/

  • Simple quality control check: do 'make short-list.tsv' - this will show you taxa have three properties: (1) are used in study OTUs, (2) are deprecated in this version of OTT 2.3, (3) have no replacement taxon id.