ITIS Taxonomic Metadata Tool Use Guidelines
The ITIS Taxonomic Name Compare Tool can generate reports and SGML
output for a component of the FGDC Biological Data Profile (FGDC-STD.001.1-1999).
This 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 metadata software or other applications.
To use the tool, follow these steps:
- Create a text document (file ending in .txt) with a list
of scientific names only (without author, rank, etc.). This file should begin with
the word "name", followed by one scientific name
per line. You can only put names from one kingdom in each file.
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 regarding duplicate names occurring in more than
- Go to the ITIS Taxon Compare page and click on
the browse button. Select the file you just created, then click
the "Upload File" button. A message appears indicating
the file upload was successful.
- Click OK to return to the previous page. The file name
will now appear in the "File Name" text block.
- Verify the file name matches the file you want to compare against.
- If you have multiple columns in your text file (i.e. name, author, etc.), select
the character you're using to separate the columns. You may use the pipe ( | ), tab,
or the number sign ( # ).
- Click the "Next" button to continue.
- The next page begins with a "View Data File" button. You can
click this to see a formatted version of your data file and ensure it is
being parsed correctly by the tool. Click the "Back to Option Selection"
button to return from this page.
- Select the kingdom contained in your file.
- In the next section, choose the "Scientific Name" selection
- In the Display options section, leave both boxes checked.
- Click the "FGDC Compare" button to start the comparison with ITIS. Note
that the time to finish this comparison will vary depending on how many names are
listed in your text file.
- The next page contains your match/non-match report, consisting of five possible sections:
- Matches Between ITIS and Input File – 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.
- Matches Between ITIS and Input File – Invalid/Not Accepted
This shows scientific names in your data and in ITIS that are invalid/not
accepted, with their associated TSNs (Taxonomic Serial Numbers).
It also shows the corresponding valid/accepted names in ITIS for these names.
These invalid/not accepted names will be replaced by the accepted
names in the SGML output.
- Non-matches from Input File
These are names that are not matched at all, either due to misspelling
(a common problem) or another cause.
- Duplicates in Input File
This identifies scientific names that are listed more than once
in your input file.
- 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 explore what the duplicates represent, then make the
decision of which record to use for each case. Select the
checkbox in the "Use" column once you've decided which scientific
names to use (See notes below on duplicates).
This report is your opportunity to check for any problems with your data.
You may need to make changes to your text file, then repeat the compare
steps to create a report you are satisfied is correct.
- Use the "Generate SGML" section to create an SGML export file when you are satisfied
with the report content.
Click the "Download" button to immediately download the generated
SGML file to your computer.
Click the "View" button to see the generated SGML output. Note that
the view page also has a "Download" button.
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
The 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) can occur under several circumstances:
- 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 created two additional copies of each genus record, and ITIS inherited those names (TSNs 73160 & 19082 respectively) and made them invalid - unavailable, database artifact; and not accepted - database artifact, respectively.
In another example, Ctenophora is used as a valid animal phylum for comb jellies (Ctenophora Eschscholtz, 1829, TSN 53856) and a valid
genus of crane fly (Ctenophora Meigen, 1803, TSN 118845). 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.
- 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: TSN 611215 was originally described in the genus Lygocerus, and TSN 611214 was originally described in the genus Megaspilus. The homonym has not yet been resolved in the literature. They became secondary homonyms when the species were 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 lesser-known groups.