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IRMNG export in Darwin Core Archive (DwC-A)

The link below provide access to the latest data dumps of IRMNG from kingdom down to genus in Darwin Core Archive (DwC-A) format. Please note that, so far as the compilers are aware, no restrictions on re-use for any purpose apply to IRMNG data to genus level. IRMNG data to species level (see below) incorporates some content from the Catalogue of Life, the World Register of Marine Species (WoRMS) and other providers and may be subject to their respective terms of use, for more information refer (e.g.) http://www.catalogueoflife.org/content/terms-use and http://www.marinespecies.org/about.php. Note that the data dumps below represent "snapshots" of the database at the cited date and that "live" data on the IRMNG site may continue to evolve as new records are added, gaps filled, and errors rectified where detected. The individual taxon pages on the IRMNG site also contain some additional content (information fields), especially in the area of references, not representable in the data dump.

Due to the variant nature of sources used to compile IRMNG, errors and inconsistencies may occasionally be present (especially at species level which have received less scrutiny than genera at this time); if you find such errors we would be happy to hear from you so that they can be rectified as resources are available.

IRMNG higher taxonomy for extant taxa is intended to eventually follow Ruggiero et al., "A higher level classification of all living organisms", PLoS One 10(4):e0119248, but has not yet been upgraded for all groups.

Where appropriate, IRMNG numeric identifiers (example, genus Sykidion E.P. Wright, 1881 has the IRMNG ID: 1344254) can be embedded in web documents as links of the format http://irmng.org/aphia.php?p=taxdetails&id=1344254 , which will then link back to the latest version of the record in question on the IRMNG website.

If you require a dump of IRMNG to species rather than genus level please contact info@irmng.org

If you find IRMNG content of value for your work we would appreciate an acknowledgement on your web page or printed work. A suggested form of citation of IRMNG is as follows: Rees, T. (compiler) (2019). The Interim Register of Marine and Nonmarine Genera. Available from http://www.irmng.org at VLIZ. Accessed 2019-01-19

Additional details on the IRMNG database and its present content may be found in a paper by T. Rees et al. entitled "IRMNG 2006–2016: 10 years of a global taxonomic database" published in the journal "Biodiversity Informatics" in mid-2017 and available at https://journals.ku.edu/jbi/article/view/6522.

Downloads

Dowloads are available at http://www.irmng.org/export

The latest version is always available in the root directory and it's name will not change.

Download notes

IRMNG data are available for download in the Darwin Core Archive (DwCA) format which is described more fully elsewhere on the web, e.g. see https://github.com/gbif/ipt/wiki/DwCAHowToGuide. The data are in tab-delimited format with no text qualifiers, and after unzipping are provided as .txt files that also can be opened as .csv if desired (simply rename e.g. taxon.txt to taxon.csv, reference.txt to reference.csv, speciesprofile.txt to speciesprofile.csv, ignoring any associated warnings).

As per those examples, the main data content is contained in three files: taxon names, IDs and associated basic information are in "taxon.txt", references are in "reference.txt", and habitat and extant/fossil status are in "speciesprofile.txt" (which contains values for the flags isMarine, isFreshwater, isTerrestrial, isExtinct). Data are encoded in the UTF-8 character set which is required to hold the full range of diacritical marks in use for taxon authority name in particular.

Note, the IRMNG DwCA "taxon" table can be opened in a text editor, but is likely too large (e.g. >500k rows as at March 2018) to be opened completely in MS Excel. If you import it to a database program e.g. MS Access it will be easier to manage and also rapid to review, sort/filter by any desired field or value, etc. The method below has been developed using MS Access on a Windows PC but other options are of course available.

Importing IRMNG data to MS Access using the "taxon.txt" table as an example

  1. Download the desired file from http://www.irmng.org/export/ - latest will always be named "IRMNG_genera_DwCA.zip", or you can browse the archives as desired to find this or older versions of the download as needed.

  2. As desired, rename the file from default (IRMNG_genera_DwCA.zip) to a preferred unique form e.g. IRMNG_genera_DwCA_2018-03-20.zip (or select that named file from the archive - latest will be the same as the current one) and unzip to a desired local directory (e.g. create the new directory /IRMNG_genera_DwCA_2018-03-20)

  3. Rename the file taxon.txt to taxon.csv (??possibly not needed, but doing this enables the file (or leading portion) to also be opened in Excel for inspection as desired)

  4. Open MS Access and create a new blank Access DB with a preferred location and name (e.g. IRMNG_genera_DwCA_2018-03-20.accdb)

  5. From the "External data" tab, select import > text file and then the option "import the source data into a new table in the current database"

  6. Browse to find "taxon.csv" as the data source in the relevant local directory, then use the following settings for import:

    • data format is delimited, delimiter = tab
    • data has header row ("First row contains field names"), text qualifier: {none}
    • via "Advanced" settings:
      • set encoding to UTF-8
      • change the default date format to date order = YMD, delimiter = "-", leading zeros = yes
      • change namePublishedIn field type to "long text" from the default which is "short text", otherwise this field will not load properly (** note, this is different from the field namePublishedInID which is OK to be short text)
    • set taxonID to Indexed = "Yes (no duplicates)"
    • deselect default option "Let Access add primary key", instead use "Choose my own primary key" with selection = "taxonID"

  7. Choose a table name (the default "Taxon" is fine) and press "Finish" to do the import; you can save these import steps if desired to re-run in the future.

Note, the IRMNG genera file as at 2018-03-20 contains 515797 rows, of which 488546 have taxonRank = Genus and the remainder are higher taxa. The file contains both presently "accepted" and "unaccepted" records. This version of the file is 231 MB as an unzipped text/csv file and occupies 510 MB when converted to a MS Access table.

Hopefully, the above steps should result in a correctly imported file with no errors. If the latter exist (will be placed in a separate "paste errors" table), review and use for any troubleshooting as needed, then delete that table before trying again, otherwise you will not easily see if any new errors have been created in a subsequent run.

If you want the references and species profile data as supplementary tables, use similar settings to import these files as well.

Please note that the web version of IRMNG may contain additional information on any taxon (for example notes fields) as well as child records (species) for genera which are not included in the download file. (Species data in IRMNG are not maintained as currently as genus records and may be out-of-date and/or contain errors not yet rectified, also some originate from systems that do not permit unrestricted onward distribution at this time). In addition, new content may have been added to the master version of IRMNG on the web which post-dates any specific data dump, but will be picked up next time an export file is created, typically once or twice per year.

IRMNG Release Notes

March 2018 version

  • Higher taxonomic categories of land plants extensively revised in accordance with the treatment of Ruggiero et al., 2015 for extant forms, together with an analogous treatment for extinct forms, in particular:
    • classes Anthoceratopsida (hornworts) and Hepaticopsida (liverworts) now raised to separate phyla (Anthocerotophyta, Marchantiophyta), no longer within Bryophyta
    • phylum Tracheophyta created for all vascular plants, with new subphyla Lycopodiophytina, Polypodiophytina and Spermatophytina for lycopods, ferns (including horsetails), and seed plants, respectively
    • Equisetopsida (horsetails) no longer a separate class or phylum, now a subclass (Equisetidae) within ferns
    • class Lycopsida (lycopods) no longer in ferns but within its own subphylum, also changed name (now Lycopodiopsida)
    • former phyla Gymnosperophyta and Magnoliophyta are now superclasses (Gymnospermae, Angiospermae) within subphylum Spermatophytina of phylum Tracheophyta, phylum Pteridophyta is now a subphylum (Polypodiophytina)
    • Welwitschiales and Ephedrales are now combined with Gnetales (treatment of Ruggiero et al.), although other sources maintain these as distinct
  • treatment of extinct plant groups revised for better alignment with recent systems, in particular that of Novikoff & Barabasz-Krasny, 2015 for families/classes/orders, while remaining congruent with the treatment of extant forms as above; new families and classes created as required (work is ongoing)
  • numerous fossil plant genera not previously allocated to family (also without accepted/synonym status yet held) now upgraded in those respect (work is ongoing)
  • treatment of extant ferns largely upgraded based on the most recent work (e.g. PPG 1, 2016) including generic reallocations and several families split or combined
  • c. 1,650 new genera of extant flowering plants + ferns added, based on additions to IPNI (International Plant Name Index) for the period 2010-2017, plus a small number of extinct forms where not previously held
  • other errors and inconsistencies rectified where apparent (mainly concerning changes from "accepted" to "unaccepted" status for certain batches of genera, also incorrect "rank" indications for certain higher taxa as contained in the previous download file)

December 2017 version

  • Inspected c.500 families previously unplaced to order, upgraded the taxonomic placement of the majority of these as data available
  • Added correct status, synonyms for 350+ rejected plant genus names previously listed as "accepted"
  • Reviewed 300+ duplicated names in Protozoa and Chromista, updated status and synonymy as needed
  • Added some fossil flags to a subset of Diptera species and genera incorrectly listed as extant (from Catalogue of Life 2006)
  • Added some>100 new references, others deduplicated and consolidated
  • Added some newly published orders and other higher taxa as needed
  • Added a small number of additional genus names
  • Revised the higher taxonomy of non-Chromist algal groups (reds, greens, glaucophytes, euglenoids) to follow Ruggiero et al., 2015, in the main
  • Reviewed habitat flags for all genera of extant fishes, 2,600 genera updated
  • A range of ad hoc corrections to attributes for individual taxon names as discovered since the April 2017 release.

April 2017 version

This is the first IRMNG release sourced from its new (2016) location (www.irmng.org) for any queries please contact the database management team via info@irmng.org.

Principal changes since January 2014 version:
  • Around 17,500 additional genus names have been added (including new animal names to around mid 2014, sourced from BioNames/ION database, plus update from WoRMS, October 2016)
  • Extant/fossil status has been added for around 16,000 genus names where not previously held
  • Kingdoms Protozoa and Chromista have been added for consistency with the 2015 higher classification of Ruggiero et al., PLoS One 10(4):e0119248, previous members of kingdom Protista distributed accordingly
  • The status of all metazoan and protist (Protozoa + Chromista) phyla has been checked and amended as needed, also protist classes
  • Intermediate ranks have been added between kingdom and class for all protists as per the treatment of Ruggiero et al., existing names have been re-ranked as required (e.g. Foraminifera is now a subphylum)
  • Phylum Charophyta has been introduced for Charophytes and related classes (previously in phylum Chlorophyta)
  • (Subphylum) name Urochordata is now used in place of Tunicata
  • Subphyla have been introduced for phyla Arthropoda and Chordata for the first time
  • Angiosperm orders, families and some genera have been rearranged as per the treatment of APG IV, 2016 (Bot. J. Linn. Soc. 181: 1-20)
  • A small number of ad hoc fixes have been made to individual taxon and authority names as discovered by or reported to IRMNG editors.

In the accompanying web version to this release, references are gradually being added as full citations, in place of the abbreviated versions previously used.

Note, with the exception of a small number of ad hoc corrections as above, plus the removal of some names (principally errors) now deleted from WoRMS, the species component of IRMNG is not greatly changed since the previous (2014) release.