# Using gnparser to check scientificName entries **URL:** \ **Category:** Data Publishing\ **Created:** [September 12, 2023, 11:31pm UTC](https://discourse.gbif.org/t/using-gnparser-to-check-scientificname-entries/4145 "2023-09-12T23:31:03Z")\ **Posts on this page:** 3\ **Page:** 1

**Author:** ![datafixer](https://sea1.discourse-cdn.com/gbif1/user_avatar/discourse.gbif.org/datafixer/32/956_2.png) [@datafixer](https://discourse.gbif.org/u/datafixer)\ **Post date:** [September 12, 2023, 11:31pm UTC](https://discourse.gbif.org/t/using-gnparser-to-check-scientificname-entries/4145/1 "2023-09-12T23:31:03Z")

Data publishers sometimes forget that the Darwin Core term [_verbatimIdentification_](https://dwc.tdwg.org/terms/#dwc:verbatimIdentification) heads a field in which you can put “A string representing the taxonomic identification as it appeared in the original record”. That original string might or might not be a proper scientific name. It’s the identification on a specimen label and/or in a local database. The [_scientificName_](https://dwc.tdwg.org/terms/#dwc:scientificName) field, on the other hand, is strictly for proper scientific names. It isn’t the place for informal names (“lichen”, “Carabus sp. A”), qualified names (“Mus cf. musculus”, “Eucalyptus aff. amygdalina”), comments (“Indet”, “Not a fungus”) or nonsense (“???”). Checking a long list of scientific names by eye for formal correctness can be tedious, but there are excellent tools available for doing the job programmatically. GBIF’s online [species name matcher](https://www.gbif.org/tools/species-lookup) is a good one; it relies on GBIF’s backbone taxonomy for matching, fuzzy-matching and non-matching name strings. My personal favourite is [**gnparser**](https://github.com/gnames/gnparser/blob/master/README.md). Written by Dmitry Mozzherin and colleagues, it’s a phenomenally fast tool that not only breaks up scientific names into name, author and year (when given), but also rates the _quality_ of the name string, with well-defined [quality categories](https://github.com/gnames/gnparser/blob/master/quality.md). For example, “lichen” has quality 0 (_Parsing failed_), “Carabus sp. A” and “Eucalyptus aff. amygdalina” have quality 4 (_Name approximate_), and “Aartsenia candida (Møller, 1842)” will earn you a quality 1 (_Parsing finished without detecting any problems_). **gnparser** is available both as an [online service](https://parser.globalnames.org/) with a limit of 5000 names per batch, or as a downloadable command-line program with no upper limit. I use the CLI version, which is currently (2023-09-12) at version 1.7.4. I needed **gnparser** for a recent check of the [Mollusca dataset](https://www.gbif.org/dataset/d962a7dc-2183-4824-bb88-5e0ba14ec62d) shared with GBIF by Naturalis Biodiversity Center. The dataset (ca 730K records) is very messy, and the _scientificName_ field is really a _verbatimIdentification_ field. I also noticed an apparently high level of pseudo-duplication in _scientificName_. In other words, a single name might appear in several different formats. To shed more light on the pseudo-duplication problem I first did a [tally](https://www.datafix.com.au/cookbook/content1.html#1) of the unique name strings in _scientificName_. There were 52011 unique strings in 738016 records. I then used **grep** and regular expressions to separate out the invalid and badly formatted entries. I passed the apparently OK name strings to **gnparser** and looked for entries with a quality rating other than “1”. Where appropriate, I added these to my list of rejects. The final list had 1913 rejected strings. The “OK” list of tallied name strings (50099 unique strings from 730154 records) could be _not_ OK in a a variety of ways. Even though the _form_ of the string might be correct, the taxon names, authors and authorship years could be wrong, or misspelled in the case of taxon and author names. Nevertheless, I was interested in pseudo-duplication, errors or no, so I used some AWK voodoo to generate from the **gnparser** output a separated list of pseudo-duplicate sets. There were 3851 such sets, mostly pairs with or without authorship or subgenus: ``` Lambis scorpius [7 records] Lambis scorpius (Linnaeus, 1758) [76] Melampus (Detracia) monile (Bruguière, 1789) [2 records] Melampus monile (Bruguière, 1789) [68] ``` There were also numerous sets with authorship with or without parentheses: ``` Leptothyra laeta (Montrouzier, 1863) [11 records; correct] Leptothyra laeta Montrouzier, 1863 [1; incorrect] ``` Two of the sets had serious [incremental fill-down errors](https://www.datafix.com.au/BASHing/2021-05-26.html): ``` Conus coronatus Gmelin, 1791 [478 records; correct] Conus coronatus Gmelin, 1792 [1] Conus coronatus Gmelin, 1793 [1] Conus coronatus Gmelin, 1794 [1] Conus coronatus Gmelin, 1795 [1] Conus coronatus Gmelin, 1796 [1] Conus coronatus Gmelin, 1797 [1] Conus coronatus Gmelin, 1798 [1] Conus coronatus Gmelin, 1799 [1] Conus eburneus Hwass, 1792 [204 records; correct] Conus eburneus Hwass, 1793 [1] Conus eburneus Hwass, 1794 [1] Conus eburneus Hwass, 1795 [1] Conus eburneus Hwass, 1796 [1] Conus eburneus Hwass, 1797 [1] Conus eburneus Hwass in Bruguière, 1792 [2] ``` and one set had five versions of the same name: ``` Vitrea crystallina [93 records] Vitrea crystallina (Müller, 1774) [213] Vitrea crystallina (O.F. Müller, 1774) [1] Vitrea (Crystallus) crystallina [23] Vitrea (Crystallus) crystallina (Müller, 1774) [39] ``` The sets also revealed authorship and formatting errors, e.g. ``` Cheilea papyracea Adams [1 record] Cheilea papyracea (Linnaeus, 1758) [1] Cheilea papyracea (Reeve, 1858) [2; correct] Thalotia conica (Gray 1827) [1 record] Thalotia conica (Gray, 1827) [25; correct] Thalotia conica [33] ``` This set-building would not have been possible without the excellent **gnparser** , which I highly recommend for data publishers and data checkers! * * * _Robert Mesibov (“datafixer”); [robert.mesibov@gmail.com](mailto:robert.mesibov@gmail.com)_ ---

**Author:** ![jwaller](https://avatars.discourse-cdn.com/v4/letter/j/c6cbf5/32.png) [@jwaller](https://discourse.gbif.org/u/jwaller)\ **Post date:** [September 13, 2023, 12:03pm UTC](https://discourse.gbif.org/t/using-gnparser-to-check-scientificname-entries/4145/2 "2023-09-13T12:03:50Z")

You can also use this for name parsing in R `rgbif::name_parse("Aartsenia candida (Møller, 1842)")` ---

**Author:** ![system](https://global.discourse-cdn.com/gbif1/original/1X/d2525d53d815eb0c992cc44730ed8a6a1be1dbb5.png) [@system](https://discourse.gbif.org/u/system)\ **Post date:** [October 13, 2023, 10:04pm UTC](https://discourse.gbif.org/t/using-gnparser-to-check-scientificname-entries/4145/3 "2023-10-13T22:04:22Z")

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