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Release notes
Jonathan A Rees edited this page Feb 6, 2014
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1 revision
Not yet released. Will feature Index Fungorum, the Hibbett 2007 Updated fungal taxonomy, extinct flags from IRMNG, and many small algorithmic improvements.
- Incorporates SILVA (minus plants, animals, fungi) and the taxonomy from study 713
- Incorporates patches from the Interim taxonomy patch feature
- More thorough synonym processing
- The deprecated.tsv file has a column providing a replacement ID for cases where a newly known synonym caused an ID to be deprecated
- Updated to latest version of NCBI taxonomy (GBIF hasn't released a new version yet)
- Updated to latest version of NCBI taxonomy and GBIF nub
- Includes all taxa from NCBI, with "dubious" ones (unclassified, virus, etc.) marked with a "D" flag in the last column
- Various improvements to the "unique names"
- Synonyms file now contains "unique names" of the form "Xyz (synonym for Pqr)"
- Now includes synonyms from GBIF (about 800,000 of them)
- Synonyms file now has a column-name header row, like the taxonomy file
- Some IRMNG homonyms which were previously suppressed have been recovered (those taxa that have children)
- Eliminated the "kill lists" of certain NCBI and GBIF taxa. This might introduce some problems, unclear
- Fixed Rhodophyta duplications, Ciliophora mapping error, and various other minor problems
- Removed dubious IRMNG genera from top level of Metazoa and Plantae
- Editing system implemented, and used to add a list of about 70 fungal species
OTT 2.0 employs a version of the GBIF taxonomy that was published in July 2012. The GBIF taxonomy was retrieved via this page.
This version is intended to supersede what I'll call "version 1.0" (the OTToL we've been using through March 2013, see here).
New features / changes since version 1.0:
- Use of synonyms from NCBI in resolving taxa from GBIF
- A more careful merging method, some errors fixed
- Update to more recent version of NCBI (previous was from approximately March 1)
- Inclusion of "unclassified" taxa from NCBI
- About 600,000 additional taxa from GBIF
- Ensures that a name occurring under disjoint nomenclatural authorities is considered homonymous
- The build process is repeatable with identifier semantics preserved across updates to the sources
- A full mapping from "preottol" is provided
OTT 2.0 is provided as a suite of files gathered into a compressed tarball; see http://dev.opentreeoflife.org/ott2.0/