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NEWS.md

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For 2.4.draft15 (2014-01-28):

  • Hibbett 2007 upper fungal taxonomy

  • Spreadsheet of assignments for Chromista and Protozoa (in progress)

  • "Deforestation" removes all but one tree

  • Improved rank merging

  • "major rank conflict" flagging is now restricted to IF and GBIF

  • IRMNG and extinct determinations

  • Fixed a bug in 'refinementp' that led to spurious taxon insertions

  • Diacritic normalization (normal form is without diacritics)

  • Scripting via jython

  • A suite of operators is now available for use from jython scripts

For 2.4.draft3 (2014-01-06):

  • Fixed a bug in synonym processing (it copied from source taxonomy to union taxonomy incorrectly)
  • Fixed some problems with SILVA synonyms file
  • Support for diacritics, folding together sibling taxa whose names differ only in diacritic marks
  • Beginnings of jython scripting support
  • The NCBI and GBIF subsets needed to build the 'model village' (Asterales) taxonomy
  • Updated NCBI of course

For 2.4.draft2 (2013-12-22):

The synonyms.tsv file now has four columns; 'type' column is new. Inspect the header row to figure out which get column(s) you need to look at. They may move in the future. Currently name, uid (= OTT id), type, and uniqueName.

New 'fold' patch command moves children of A to B and makes A a synonym for B. (could have been done with 'elide' I guess)

The model taxonomy ('aster') now includes synonyms.

'in-part', 'includes', 'type material', and 'authority' "synonyms" from NCBI are now discarded.

For 2.4.draft1 (2013-12-14):

Added Index Fungorum (generated by Peter M's script)

Stitched taxonomies together properly under Silva:

  • Added Chloroplastida as a synonym for Viridiplantae (that's what Silva calls it)
  • Added code-level taxa Fungi, Metazoa etc. as taxa in Silva to ensure correct placement
  • Added additional taxa to base of study 713 to force plants and bacteria to be disjoint

Sibling homonyms are smushed together, when encountered in Index Fungorum or GBIF.

Internal changes (not "user visible"):

  • Spelling variants file from Rick is now checked in
  • GBIF source taxonomy list checked in
  • Edits formerly in ott_edits.tsv have been moved out to misc_edits.tsv
  • Synonyms file now has four columns; 'type' column is new
  • Simplified the Makefile a bit
  • Added rules to make short-list.tsv, the list of most serious deprecations
  • New rule for aster-tarball
  • New '--select2' directive improving on '--select' (will switch over to new name later)
  • New '--sample' proportional sampling feature
  • Pull some collection modifications out of loop to avoid concurrent modification exceptions
  • Improve name lookup logic in patch system to reduce number of ambiguities
  • New "fold" command
  • Fix patch for Berendtia
  • Improve postmortem reports, e.g. for unresolved/ambiguous show the alternatives that were being considered
  • 'eschew-tattered' rule discourages matching to tattered nodes
  • Improvements to metadata handling