ITIS Taxonomic Metadata Tool Use Guidelines

The prototype ITIS Taxonomic Metadata Tool generates reports and SGML output for a component of the FGDC Biological Data Profile (FGDC-STD.001.1-1999). It allows users to quickly obtain the taxonomic hierarchy in SGML form for an unlimited number of scientific names. The SGML output can then be imported into any metadata software or other applications.

To use the tool, follow these steps:

1. Step 1: Create a text document (file ending in .txt) with a list of scientific names only (without author, rank, etc.) with one name per line. It is also necessary to put a category heading titled “name” at the top of the page.
   At the ITIS webpage for the ITIS Taxonomic Metadata Tool, use the browse button to select the file, and then hit the “Upload File” button. A message appears indicating the file upload was successful. Press OK to return to the form. The file name should appear in the text block associated with the 3rd bullet. Hit the “Step 2” button to continue.
2. Step 2: If you want to be sure your file is being read properly, hit the “view data file” button and you can see whether your names are in the right category.
3. Step 3: Select your kingdom. Please note, you can only select one kingdom at a time. If your dataset has more than one kingdom, you can generate a report for each kingdom and append them in the SGML file. (See note below on “duplicate names” occurring in more than one kingdom.)
4. Step 4: Choose “Scientific Name (FGDC Biological Profile Report – Prototype)”
5. Step 5: Leave both boxes checked.
6. Hit the “Taxonomy Compare” button.
7. Your match/non-match report consists of five possible sections:
   1. Matches Between ITIS and Input Data – Valid/Accepted Names
      This shows valid scientific names in your data that were successfully matched in ITIS, and shows the corresponding valid/accepted names in ITIS that match invalid/not accepted names in your data.
   2. Matches Between ITIS and Input Data – Invalid/Not Accepted Names
      This shows scientific names in your data and in ITIS that are invalid/not accepted with their associated TSNs (Taxonomic Serial Numbers), and shows the corresponding valid/accepted names in ITIS for them. These invalid/not accepted names will be replaced by the accepted names in the SGML output.
   3. Non-matches from Input Data
      These are names that are not matched at all, either due to misspelling (a common problem) or another cause.
   4. Duplicates in Input Data
      This identifies scientific names that are listed more than once in your input file. (See notes below on duplicates.)
   5. Duplicates Existing in ITIS
      This identifies scientific names that are listed more than once in the ITIS database. You can click on the TSN links to the left to explore what the duplicates represent, then return to make your decision of which record to use in each case. Place a check in the “use” box once you’ve decided which scientific names to use. (See notes below on duplicates.)
      The report is your opportunity to check any problems with your data. You may have to go back and fix your initial file, and repeat the steps again.
8. When you are content with the report, hit the “FGDC Biological Profile SGML” button at the bottom of the page. You will be taken to another page that explains how to save your report.

Note on “Duplicates”:

"Duplicate" occurrences of the same scientific name (in ITIS or in other sources), generally speaking, can either represent the same taxon, or different taxa. ITIS contains some duplicates representing the same taxon, due to different practices of ITIS' predecessor database (National Oceanographic Data Center's "N.O.D.C. Code") or accidental introduction into ITIS.

ITIS' policy for "same taxon" duplicate name cases is to render one as an invalid/not accepted "database artifact" (reflected in unacceptability_reason and comment_detail), and to link it in to the non-artifact record (or next to it if the non-artifact is itself invalid/unaccepted for other reasons). For example, see Acirsa borealis (Lyell, 1841) (TSNs 72352 & 72354). Such cases are an ongoing cleanup effort in ITIS.

"Different taxon" duplicate cases ("homonymy," or the use of the same name to represent more than one taxon, simply put) can occur under several circumstances:

(a) The two names may be regulated by different "Nomenclatural Codes" (e.g., the International Code of Zoological Nomenclature, the International Code of Botanical Nomenclature, the International Code of Nomenclature of Bacteria, each of which regulates names at particular ranks in particular kingdoms), or not regulated by any such Code. Such cases are perfectly "legal" (though perhaps frowned upon). For example, Ficus Röding, 1798 (TSN 73159) is a valid mollusk genus, while Ficus L. (TSN 19081) is an accepted flowering plant (fig) genus. N.O.D.C. data practices resulted in two additional copies of each genus record (TSNs 73160 & 19082, respectively), which are both invalid/not accepted. In another example, Ctenophora is used as a valid animal phylum (comb jellies) and a valid genus of crane fly. The rank of phylum is not regulated by a Nomenclatural Code, so there is no requirement to address this homonymy. Note that cross-kingdom homonymies can result in multiple different metadata listings for your matching name, so take care in appending multiple-kingdom outputs into the same file.

(b) Where names are regulated by the same Code, such homonymy ought not occur, but sometimes it does, and sometimes the two names can both be seen as valid/accepted! When authors catch such cases they can resolve them with a replacement name, but sometimes this has not yet happened. For example, Dendrocerus australicus (Dodd, 1914) is applied to two valid taxa within the same insect genus (!!), and the homonymy has not yet been resolved in the literature: one was originally described in the genus Megaspilus, the other was originally described in the genus Lygocerus, and they were each moved into Dendrocerus... Both are considered valid taxa, but no replacement name has been designated to resolve the homonymy. Such cases are extremely rare within a particular taxonomic group, but become somewhat more common between groups (mollusks vs. birds, etc.) or in very large or little-known groups.