3.4 notes

Author: mtholder

doc/ott3.4.md

@@ -0,0 +1,153 @@
+# Open Tree of Life reference taxonomy version 3.2
+
+Version 3.3 draft 1 was generated on 01 June, 2021.
+
+## Download
+
+[Download](http://files.opentreeoflife.org/ott/ott3.4/ott3.4.tgz)
+
+## Major changes since OTT 3.2
+
+* Incorporated https://github.com/OpenTreeOfLife/edOTTs 
+  up to commit [5bff4bc32a91a7c6e0541d94b71a0a9ae2fdda02](https://github.com/OpenTreeOfLife/edOTTs/commit/5bff4bc32a91a7c6e0541d94b71a0a9ae2fdda02)
+
+## Statistics
+
+* OTT identifiers ('taxa'): 4,528,224 
+* Visible: 3,943,215 
+* Synonyms: 2,225,600
+       
+  
+## Contents of download
+
+All files use UTF-8 character encoding.  For documentation about file formats, see [the documentation in the reference taxonomy
+wiki](https://github.com/OpenTreeOfLife/reference-taxonomy/wiki/Interim-taxonomy-file-format),
+on github.
+
+**taxonomy.tsv**: The file that contains the taxonomy.
+
+**synonyms.tsv**: The list of synonyms.
+
+**forwards.tsv**: Aliases ('forwarding pointers') - a list of OTT ids that are
+  retired and should be replaced by new ones (usually due to
+  'lumping')
+
+**version.txt**: The version of OTT.
+
+
+
+## Build script
+
+    otc-taxonomy-patcher \
+      --demand-all-applied \
+      --edits /work/opentree/edOTTs/edott-000009.json \
+      --edits /work/opentree/edOTTs/edott-000010.json \
+      /work/opentree/ott/ott3.3 \
+      --write-taxonomy /work/opentree/ott/ott3.4 2>&1 | tee patch.log
+
+with otcetera commit [2cacc9004b4a781d3c937f16278584f943d638ce](https://github.com/OpenTreeOfLife/otcetera/commit/2cacc9004b4a781d3c937f16278584f943d638ce)
+
+## Sources
+
+Any errors in OTT
+should be assumed to have been introduced by the Open Tree of Life 
+project until confirmed as originating in the source taxonomy.
+
+Download locations are for the particular versions used to construct
+OTT 3.0.  For new work, current versions of these sources should be
+retrieved.
+
+1.  Curated additions from the Open Tree amendments-1 repository as processed into https://github.com/OpenTreeOfLife/edOTTs 
+  up to commit [5bff4bc32a91a7c6e0541d94b71a0a9ae2fdda02](https://github.com/OpenTreeOfLife/edOTTs/commit/5bff4bc32a91a7c6e0541d94b71a0a9ae2fdda02) These taxa are added during OTU mapping using the curator application.
+
+1.  Taxonomy from: 
+    DS Hibbett, M Binder, JF Bischoff, M Blackwell, et al. 
+    A higher-level phylogenetic classification of the <i>Fungi</i>.
+    [Mycological Research</i> <b>111</b>(5):509-547, 2007](http://dx.doi.org/10.1016/j.mycres.2007.03.004).
+    Newick string with revisions
+    archived at [http://figshare.com/articles/Fungal\_Classification\_2015/1465038](http://figshare.com/articles/Fungal_Classification_2015/1465038).
+    <br />
+    Download location: [https://github.com/OpenTreeOfLife/reference-taxonomy/tree/ott2.10draft11/feed/h2007](https://github.com/OpenTreeOfLife/reference-taxonomy/tree/ott2.10draft11/feed/h2007)
+
+1.  Taxonomy from: SILVA 16S ribosomal RNA database, version 115.
+    See: Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, Peplies J,
+    Gl&ouml;ckner FO (2013) The SILVA ribosomal RNA gene database project:
+    improved data processing and web-based tools. 
+    [Nucleic Acids Research</i> 41 (D1): D590-D596](http://dx.doi.org/10.1093/nar/gks1219).
+    Web site: [http://www.arb-silva.de/](http://www.arb-silva.de/).
+    <br />
+    Download location: [ftp://ftp.arb-silva.de/release\_115/Exports/tax\_ranks\_ssu\_115.csv](ftp://ftp.arb-silva.de/release_115/Exports/tax_ranks_ssu_115.csv).
+
+1.  Index Fungorum.
+    Download location: derived from database query result files provided by Paul
+    Kirk, 7 April 2014 (personal communication).
+    Web site: [http://www.indexfungorum.org/](http://www.indexfungorum.org/).
+    <br />
+    Download location (converted to OTT format): [http://files.opentreeoflife.org/fung/fung-9/fung-9-ot.tgz](http://files.opentreeoflife.org/fung/fung-9/fung-9-ot.tgz).
+
+1.  Taxonomy from:
+    Sch&auml;ferhoff, B., Fleischmann, A., Fischer, E., Albach, D. C., Borsch,
+    T., Heubl, G., and M&uuml;ller, K. F. (2010). Towards resolving Lamiales
+    relationships: insights from rapidly evolving chloroplast
+    sequences. 
+    [<i>BMC evolutionary biology</i> 10(1), 352.](http://dx.doi.org/10.1186/1471-2148-10-352).
+    Manually transcribed from the paper and converted to OTT format.
+    <br />
+    Download location: [http://purl.org/opentree/ott/ott2.8/inputs/lamiales-20140118.tsv](http://purl.org/opentree/ott/ott2.8/inputs/lamiales-20140118.tsv)
+
+1.  [World Register of Marine Species (WoRMS)](http://www.marinespecies.org/aphia.php) - harvested from web site using web API over several days ending around 1 October 2015.
+    Download location: [http://files.opentreeoflife.org/worms/worms-1/worms-1-ot.tgz](http://files.opentreeoflife.org/worms/worms-1/worms-1-ot.tgz)
+
+1.  NCBI Taxonomy, from the 
+    [US National Center on Biotechnology Information](http://www.ncbi.nlm.nih.gov/).
+    Web site: [http://www.ncbi.nlm.nih.gov/Taxonomy/](http://www.ncbi.nlm.nih.gov/Taxonomy/).
+    <br />
+    We used a version dated 16 September, 2019.
+    Archived location: [http://files.opentreeoflife.org/ncbi/ncbi-20190916/ncbi-20190916.tgz](http://files.opentreeoflife.org/ncbi/ncbi-20190916/ncbi-20190916.tgz).
+    <br />
+    Current version download location:
+    [ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz](ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/taxdump.tar.gz)
+
+1.  GBIF Backbone Taxonomy, from the 
+    [Global Biodiversity Information facility](http://www.gbif.org/).
+    <br />
+    We used a version dated 2019-09-16.
+    Download location: [http://files.opentreeoflife.org/gbif/gbif-20190916/gbif-20190916.zip](http://files.opentreeoflife.org/gbif/gbif-20190916/gbif-20190916.zip).
+    <br />
+    Current version download location (unverified):
+    [http://rs.gbif.org/datasets/backbone/backbone-current.zip](http://rs.gbif.org/datasets/backbone/backbone-current.zip).
+
+1.  [Interim Register of Marine and Nonmarine Genera (IRMNG)](http://irmng.org/).
+    <br />
+    We used a version dated 2014-01-31.  Download location:
+    [http://purl.org/opentree/ott/ott2.8/inputs/IRMNG\_DWC-2014-01-30.zip](http://purl.org/opentree/ott/ott2.8/inputs/IRMNG_DWC-2014-01-30.zip).
+ 
+1.  Taxon identifiers are carried over from [OTT 3.1](http://files.opentreeoflife.org/ott/ott3.1/) when possible
+ 
+It has been requested that we relay the following statement:
+
+> REUSE OF IRMNG CONTENT:
+> IRMNG (the Interim Register of Marine and Nonmarine Genera) is assembled, with permission, from a range of third party data sources, certain of which permit data reuse only under specific conditions. In particular, for data originating from the Catalogue of Life (CoL), please refer to the relevant terms and conditions for reuse of CoL data as available at [http://www.catalogueoflife.org/content/terms-use](http://www.catalogueoflife.org/content/terms-use), and for data originating from the World Register of Marine Species (WoRMS) refer the paragraph "Terms of Use and Citation" at [http://www.marinespecies.org/about.php](http://www.marinespecies.org/about.php). The compilers of IRMNG accept no liability for any reuse of IRMNG content by downstream users which may be construed by the original data providers to violate their publicly available conditions of use.
+
+The Open Tree Taxonomy does not reproduce its sources in their
+entirety or in their original form of expression, but only uses
+limited information expressed in them. See "[Scientific names of
+organisms: attribution, rights, and licensing](http://dx.doi.org/10.1186/1756-0500-7-79)" ([http://dx.doi.org/10.1186/1756-0500-7-79](http://dx.doi.org/10.1186/1756-0500-7-79))
+regarding use of taxonomic information and attribution.
+
+## Priority
+
+Where taxonomies conflict regarding taxon relationships, they are
+resolved in favor of the higher priority taxonomy.  The priority
+ordering is as given above, with the following exceptions:
+
+The non-Fungi content of Index Fungorum is separated from the Fungi
+content and given a priority lower than NCBI and GBIF.
+
+The non-Malacostraca, non-Ctenophora content of WoRMS is separated from the
+Malacostraca and Ctenophora content and given a priority lower than NCBI but higher
+than GBIF.
+
+## Previous versions
+
+See <a href="http://files.opentreeoflife.org/ott/">http://files.opentreeoflife.org/ott/</a>