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Basic notes for version 2.8, and 2.6 converted to md
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‎doc/README.md‎

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# Release notes for versions of the Open Tree Reference Taxonomy (OTT)
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* [Version 2.8](ott2.8.md) 11 June 2014
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* Version 2.7 8 May 2014 (no release notes)
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* [Version 2.6](ott2.6.md) 11 April 2014
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* [Version 2.4 and earlier](https://github.com/OpenTreeOfLife/reference-taxonomy/wiki/Release-notes---deprecated)
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‎doc/ott2.6.md‎

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This is the Open Tree Taxonomy (OTT) version 2.6, created on 2014-04-11.
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# Open Tree of Life reference taxonomy version 2.6
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Version 2.6 was generated on 11 April 2014.
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The taxonomy was generated using the 'smasher' utility, commit
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f624223f31, which resides on github, here:
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https://github.com/OpenTreeOfLife/reference-taxonomy/commit/f624223f31767fa1787f3ba2ddad5daa56fd939b
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File in this package
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====================
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ott/taxonomy.tsv
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ott/synonyms.tsv
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The format of these files is described in doc/Interim-taxonomy-file-format.md
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https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/doc/Interim-taxonomy-file-format.md
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ott/hidden.tsv
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Report on 'hidden' taxa (incertae sedis and other suppressed taxa).
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Columns are OTT id, name, source taxonomy and id, containing major
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group, and flags (reasons for hiding).
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ott/used-but-hidden.tsv
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Subset of hidden.tsv for taxa that are referenced from source trees.
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Columns are as for hidden.tsv, with the addition of a column for
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Phylografter study number.
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ott/conflicts.tsv
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Report on taxa that are hidden because they are paraphyletic with
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respect to a higher priority taxon. Number at beginning is height
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in taxonomic tree of nearest common ancestor with priority taxon
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that 'steals' one or more children.
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ott/deprecated.tsv
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List all of taxa that have been deprecated since version 2.5.
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ott/log.tsv
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Additional debugging information related to deprecated taxa.
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Inputs required to create this version
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======================================
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The following information is current as of 2014-05-28.
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SILVA
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Retrieved from
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https://www.arb-silva.de/fileadmin/silva_databases/release_115/Exports/SSURef_NR99_115_tax_silva.fasta.tgz
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Last-modified date: 2013-09-07
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See: Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P,
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Peplies J, Glockner FO (2013) The SILVA ribosomal RNA gene
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database project: improved data processing and web-based tools.
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Nucleic Acids Research 41 (D1): D590-D596.
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http://dx.doi.org/10.1093/nar/gks1219
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Web site: https://www.arb-silva.de/
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Taxonomy from Hibbett et al 2007, with updates through 2014
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Retrieved from
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http://dx.doi.org/10.6084/m9.figshare.915439
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Last-modified date: 2014-03-10
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There is a copy in feed/h2007/ in the git repository.
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See: A higher-level phylogenetic classification of the Fungi.
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DS Hibbett, M Binder, JF Bischoff, M Blackwell, et al.
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Mycological Research 111(5):509-547, 2007.
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http://dx.doi.org/10.1016/j.mycres.2007.03.004
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Index Fungorum
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We received database table dumps from Paul Kirk in email in
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November-December 2013, and converted them to the interim taxonomy
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format using ad hoc scripts. The converted form is here:
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http://purl.org/opentree/ott2.6-inputs/tax/if/taxonomy.tsv
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http://purl.org/opentree/ott2.6-inputs/tax/if/synonyms.tsv
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Web site: http://www.indexfungorum.org/
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Lamiales taxonomy from Schaferhof et al 2010
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File prepared from figure by Open Tree of Life staff.
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There is a copy in tax/713/ in the git repository.
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See:
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Schaferhoff, B., Fleischmann, A., Fischer, E., Albach, D. C.,
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Borsch, T., Heubl, G., and Muller, K. F. (2010). Towards resolving
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Lamiales relationships: insights from rapidly evolving chloroplast
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sequences. BMC evolutionary biology 10(1), 352.
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http://dx.doi.org/10.1186/1471-2148-10-352
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NCBI Taxonomy
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Retrieved from ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz
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Last-modified date: 2014-01-06
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As far as we can tell, NCBI does not archive past versions of its
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taxonomy. We have captured the applicable version here:
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http://purl.org/opentree/ott2.6-inputs/feed/ncbi/taxdump.tar.gz
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Web site: https://www.ncbi.nlm.nih.gov/taxonomy
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GBIF backbone taxonomy
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Retrieved from http://ecat-dev.gbif.org/repository/export/checklist1.zip
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Last-modified date: 2013-07-02
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GBIF intends to reorganize their data archives and this file may
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move. We will make a best effort to maintain the following PURL:
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http://purl.org/opentree/gbif-backbone-2013-07-02.zip
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In case these links do not work, search gbif.org data sets and use the
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following file information for confirmation:
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Size: 323093992 bytes
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sha1sum: b7c7c19f1835af3f424ce4f2c086c692c1818b90
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Format: Zip file containing a Darwin Core Archive
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Contains file taxon.txt which has 4416348 lines
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Web site: http://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c
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IRMNG (Interim Register of Marine and Nonmarine Genera)
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Retrieved from http://www.cmar.csiro.au/datacentre/downloads/IRMNG_DWC.zip
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Last-modified date: 2014-01-12
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The file at that URI is replaced from time to time. A capture of
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the version used for OTT 2.6 is here:
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http://purl.org/opentree/ott2.6-inputs/feed/irmng/in/IRMNG_DWC.zip
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Web site: http://www.obis.org.au/irmng/
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OTT version 2.5
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The previous version of OTT is used only for the purpose of ensuring
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identifier choice consistency from one version of OTT to the next.
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http://purl.org/opentree/ott/ott2.5.tgz
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f624223f31, which resides on github, [here](https://github.com/OpenTreeOfLife/reference-taxonomy/commit/f624223f31767fa1787f3ba2ddad5daa56fd939b)
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## File in this package
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* ott/taxonomy.tsv, ott/synonyms.tsv
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The format of these files is described in [doc/Interim-taxonomy-file-format.md](doc/Interim-taxonomy-file-format.md)
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* ott/hidden.tsv
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Report on 'hidden' taxa (incertae sedis and other suppressed taxa).
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Columns are OTT id, name, source taxonomy and id, containing major
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group, and flags (reasons for hiding).
19+
20+
* ott/used-but-hidden.tsv
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Subset of hidden.tsv for taxa that are referenced from source trees.
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Columns are as for hidden.tsv, with the addition of a column for
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Phylografter study number.
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* ott/conflicts.tsv
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Report on taxa that are hidden because they are paraphyletic with
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respect to a higher priority taxon. Number at beginning is height
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in taxonomic tree of nearest common ancestor with priority taxon
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that 'steals' one or more children.
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* ott/deprecated.tsv
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List all of taxa that have been deprecated since version 2.5.
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* ott/log.tsv
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Additional debugging information related to deprecated taxa.
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## Inputs required to create this version
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* SILVA 115:
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Retrieved from
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[https://www.arb-silva.de/fileadmin/silva_databases/release\_115/Exports/SSURef\_NR99\_115\_tax\_silva.fasta.tgz](https://www.arb-silva.de/fileadmin/silva_databases/release_115/Exports/SSURef_NR99_115_tax_silva.fasta.tgz).
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Last-modified date: 2013-09-07.
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See: Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P,
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Peplies J, Glockner FO (2013) The SILVA ribosomal RNA gene
49+
database project: improved data processing and web-based tools.
50+
Nucleic Acids Research 41 (D1): D590-D596.
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[http://dx.doi.org/10.1093/nar/gks1219](http://dx.doi.org/10.1093/nar/gks1219).
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Web site: [https://www.arb-silva.de/](https://www.arb-silva.de/).
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* Taxonomy from Hibbett et al 2007, with updates through April 2014:
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Retrieved from
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[http://dx.doi.org/10.6084/m9.figshare.915439](http://dx.doi.org/10.6084/m9.figshare.915439)
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Last-modified date: 2014-03-10.
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There is a copy in feed/h2007/ in the git repository.
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See: A higher-level phylogenetic classification of the Fungi.
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DS Hibbett, M Binder, JF Bischoff, M Blackwell, et al.
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Mycological Research 111(5):509-547, 2007.
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[http://dx.doi.org/10.1016/j.mycres.2007.03.004](http://dx.doi.org/10.1016/j.mycres.2007.03.004)
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* Index Fungorum:
65+
We received database table dumps from Paul Kirk in email in
66+
November-December 2013, and converted them to the interim taxonomy
67+
format using ad hoc scripts. The converted form is here:
68+
[http://purl.org/opentree/ott2.6-inputs/tax/if/taxonomy.tsv](http://purl.org/opentree/ott2.6-inputs/tax/if/taxonomy.tsv) and
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[http://purl.org/opentree/ott2.6-inputs/tax/if/synonyms.tsv](http://purl.org/opentree/ott2.6-inputs/tax/if/synonyms.tsv).
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Web site: [http://www.indexfungorum.org/](http://www.indexfungorum.org/).
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* Lamiales taxonomy from Schaferhof et al 2010:
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File prepared from figure by Open Tree of Life staff.
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There is a copy in tax/713/ in the git repository.
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See:
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Schaferhoff, B., Fleischmann, A., Fischer, E., Albach, D. C.,
77+
Borsch, T., Heubl, G., and Muller, K. F. (2010). Towards resolving
78+
Lamiales relationships: insights from rapidly evolving chloroplast
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sequences. BMC evolutionary biology 10(1), 352.
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[http://dx.doi.org/10.1186/1471-2148-10-352](http://dx.doi.org/10.1186/1471-2148-10-352)
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* NCBI Taxonomy:
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Retrieved from [ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz](ftp://ftp.ncbi.nih.gov/pub/taxonomy/taxdump.tar.gz).
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Last-modified date: 2014-01-06.
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As far as we can tell, NCBI does not archive past versions of its
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taxonomy. We have captured the applicable version here:
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http://purl.org/opentree/ott2.6-inputs/feed/ncbi/taxdump.tar.gz .
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Web site: https://www.ncbi.nlm.nih.gov/taxonomy
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* GBIF backbone taxonomy:
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Retrieved from http://ecat-dev.gbif.org/repository/export/checklist1.zip .
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Last-modified date: 2013-07-02.
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GBIF intends to reorganize their data archives and this file may
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move. We will make a best effort to maintain the following PURL:
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http://purl.org/opentree/gbif-backbone-2013-07-02.zip .
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In case these links do not work, search gbif.org data sets and use the
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following file information for confirmation:
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Size: 323093992 bytes
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sha1sum: b7c7c19f1835af3f424ce4f2c086c692c1818b90
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Format: Zip file containing a Darwin Core Archive
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Contains file taxon.txt which has 4416348 lines
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Web site: http://www.gbif.org/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c
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* IRMNG (Interim Register of Marine and Nonmarine Genera):
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Retrieved from http://www.cmar.csiro.au/datacentre/downloads/IRMNG_DWC.zip .
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Last-modified date: 2014-01-12.
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The file at that URI is replaced from time to time. A capture of
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the version used for OTT 2.6 is here:
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http://purl.org/opentree/ott2.6-inputs/feed/irmng/in/IRMNG_DWC.zip .
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Web site: [http://www.obis.org.au/irmng/](http://www.obis.org.au/irmng/).
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* OTT version 2.5:
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The previous version of OTT is used only for the purpose of ensuring
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identifier choice consistency from one version of OTT to the next.
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http://purl.org/opentree/ott/ott2.5.tgz

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