How to use the TNRS

To view a quick summary of instructions, click here: Quick Guide.

Settings

Prior to submitting a list, there are settings that can be adjusted. To change your settings, click Change Settings located at the lower right hand corner of the Current Settings box.

• Processing mode gives the option to only return results of the GNI parser or to perform a full name resolution. Parsed elements will return the name elements as determined by parsing the full name.
• Unchecking the Constrain best match by higher taxonomy box will return names with the best spelling match. It is possible that a name that is not within the same taxonomy group of the name submitted will return a higher score due to the algorithm used to apply the score. In this case, you will be shown a warning flag stating that there is a name with a lower score that is more taxonomically correct.

If you choose to constrain results, check the box. The returned results will be filtered to display the the most closely related taxonomic match. If there are better scoring names found, you will receive a warning flag.

For example, if you submit a genus+species with the genus name spelled correctly but the species name spelled incorrectly, the application may match a name that is a closer edit distance for the overall name. In this case, it is possible that genus+species will be returned with a higher score that is not the intended species. If you know that the genus or a higher taxon submitted is correct, you can use this option to filter the best match to be constrained by that higher taxon.

• A match accuracy setting of 1.00 will limit results to exact matches only.

Note: Changing the match accuracy of the TNRS will change the sensitivity of the fuzzy matching algorithm.

Enter or upload names for resolution

There are two ways to use this application: enter names directly or upload a list.

Enter names directly

1. Enter up to 5000 names in the Enter List tab, one name per line regardless of the file extension. You may type the names in the box or cut and paste from a text editor.
2. As an option, you may include the family name in front of the scientific name, separated by a space. Family name is NOT required. This option is provided to support ecological data where some taxa are identified only to family, followed by a morphospecies identifier (for example, Lauraceae sp.3). However, if you include family you may improve your matches by preventing fuzzy matching to similar names in different families.
3. Click the Go button to begin or Clear to start over.
4. Wait while the list is processed. Results appear when complete in a table immediately below the tabbed input box.
5. Proceed to Inspect results to continue.

Upload a list

1. Upload a list of names separated by commas in the Upload and Submit List tab, with or without authority. The list must use either windows encoding (WINDOWS-1254 or ISO-8859-1), UTF-8, or UTF-16 format and contain either LF or CRLF line separators; most files created using standard text editors will fit these requirements, but if you are unsure or have problems, please contact us at support@iplantcollaborative.org.

Note: If you upload your list in UTF-16 format, you may include special characters. However, if you manually enter your list, you may not include special characters as they can not be translated. If you manually enter your list with special characters, you may receive an inaccurate match score.

2. Because processing long lists takes time, you must enter an email address to receive a notification when the list is successfully submitted and another when it is completely processed. The second email will include a Submission Key to be used to retrieve your results in the Retrieve Results tab. The Name and Institution fields are optional.
3. Click the Submit List button to begin.
4. When the list is processed, enter your email address and Submission key in Retrieve Results. Click the Retrieve button.
5. Results appear in a table immediately below the tabbed input box.
6. A new feature for v2.0 is the ability to upload a list with a unique identifier for each name. The identifier must be in the 1st column of the list.
7. Proceed to Inspect results to continue.

Inspect results

The TNRS matching and name selection algorithms are still under development and may not always return the desired match. We strongly recommend users carefully examine any result with Overall Score less than 100%, or with more than one Name Matched (as indicated by the “+X more” link after the Name Matched; see step 2 below). The TNRS provides links to the original source of each name to help you with this research.

Results screen

Your results will appear in the following window:

• If the TNRS application finds only one match for a submitted name, that match is displayed in the results.
• If the TNRS application finds more than one near match for a submitted name, it will choose a single best match and display it in the list. You may select an alternate match if you prefer. Click the (+X more) link to view and select from multiple options when they exist.
  
  Select the preferred term from the popup list and click the Apply selected button or click Cancel to retain the current selection.
• If the TNRS finds multiple equally-good matches and cannot select a single best name, or if there are other issues with the results requiring inspection by the user, it will display a red warning flag:
  
  
  
  
• Mouse-over the flag to see the reason the name being flagged; click on the flag for a more detailed explanation.



Currently, the TNRS issues the following four warning flags:

1. Ambiguous Match

Names flagged as an "Ambiguous match" by the TNRS returned multiple best results with identical match scores and acceptance status, and therefore must be reviewed by the user to determine which is preferred.

2. Partial Match

Names flagged as a "Partial Match" by the TNRS matched only to a higher taxon than the one submitted by the user. For example, if you submitted a species name, but the TNRS matched only the genus, the result would be flagged as a partial match.


3. No Accepted Name

Names flagged with "No Accepted Name" by the TNRS returned a name flagged as synonymy, but no accepted names were provided by the taxonomic source.

4. Taxonomic Match

Names flagged as "Taxonomic Match" by the TNRS are constrained to the best match within the higher taxa submitted, even though a closer spelling match is available outside that higher taxon. These results only occur when Taxonomic Filtering is set to on. For example, if you submit "Steccherinaceae Irpex" (a fungus not in the TNRS database), and have Taxonomic Filtering Off, the TNRS will return "Aquifolicaceae Ilex" as the closest match. However, if you turn Taxonomic Filtering On, the TNRS will return "No suitable matches found" and flag the result as "Taxonomic Match.



• Click a matched name to open the Tropicos database page for the item.
  

• Click an accepted name to open the Tropicos database page for the item. Accepted names only appear for synonyms.
  
• Taxonomic Status tells you whether the matched name is also the accepted name (Accepted), or whether the matched name is a synonym of a different accepted name (Synonym). In some cases, there is either insufficient information to determine the status of the name, or the Computed Acceptance algorithm is unable to choose a single best name from among alternative conflicting accepted names (No opinion).
• Click Details to view a popup with more information about a matched name.
• Click Download results located at the top left corner of the results window to download a CSV file.

Download results

After clicking Download results, you will have the option to download in a Simple or Detailed format.

Note:

• Files are downloaded with Unix-like new line characters. This is usually not an issue with newer text editors and spreadsheets, but rarely results will appear to all be in a single line when using other applications.
• If your browser is set to prompt you for download information, be sure to select 'all files' as the download type to ensure proper retrieval of your data.

The following tables list the fields displayed within each download format and the definition for that field.

Simple download

The Simple download contains the general information displayed on the results screen.

Name_submitted	Name entered by the user.
Name_matched	Scientific name with the highest match score. May be an exact match or a fuzzy match. This score does not include the author score.
Author_matched	Stantard authority of the name with the highest match score name.
Overall_score	Score assigned by the TNRS to indicate overall similarity between the submitted name and the name returned by the TNRS. This score incorporates the author score as well.
Taxonomic_status	see Taxonomic Status
Accepted_name	Accepted name for the nameMatched, according to the taxonomic source used. If the nameMatched is accepted, this name will be the same as the nameMatched. If the nameMatched is a synonym, this name will be different.
Accepted_author	Standard authority of the accepted name.
Accepted_family	The accepted familial classification of the accepted name for the name matched by the TNRS.
Warnings	see warning flags.

Detailed download

The Detailed download contains detailed information of results and specifications of how the names are parsed and matched. It includes the fields found in Simple download as well as the following fields:

Name_matched_rank	The lowest taxonomic rank for the name matched.
Name_score	Overall score for the name matched based on the TNRS ranking algorithm.
Name_matched_author	Standard authority for the matched name.
Name_matched_url	Web link, if any, for the matched name.
Author_score	Score assigned by the TNRS to indicate the level of similarity to the author submitted, if any. This field will be blank if the user did not submit an author along with the name.
Family_matched	The closest matching family in the TNRS database to the family submitted. This field will be blank if you did not submit a family, or the family could not be matched.
Family_score	Score assigned by the TNRS to indicate the level of similarity to the family submitted, if any.
Genus_matched	The closest matching genus in the TNRS database to the genus submitted. This field will be blank if the genus submitted could not be matched.
Genus_score	Score assigned by the TNRS to indicate the level of similarity to the genus submitted.
Specific_epithet_matched	The specific epithet of closest matching species in the TNRS database to the species submitted. This field will be blank if the species submitted could not be matched.
Specific_epithet_score	Score assigned by the TNRS to indicate the level of similarity to the species submitted.
Infraspecific_rank	If an infraspecific taxon was submitted (subspecies, variety, etc.), this field provides the standardized rank abbreviation for that taxon (subspecies, variety, etc.).
Infraspecific_epithet_matched	The infraspecific epithet of closet matching subspecies or variety in the TNRS database to the subspecies or variety submitted. This field will be blank if no infraspecific taxon was submitted, or if the subspecies or variety could not be matched.
Infraspecific_epithet_score	Score assigned by the TNRS to indicate the level of similarity to the infraspecific taxon submitted.
Infraspecific_rank_2	If a quadrinomal taxon name was submitted (for example "Poa annua var. purpurea forma minima"), this field provides the standardized rank abbreviation for that taxon (in the preceding example, "fo.").
Infraspecific_epithet2_matched	The final epithet of closest matching quadrinomial infraspecific taxon in the TNRS database to the quadrinomial infraspecific taxon (for example, "Poa annua var. purpurea forma minima"). This field will be blank if a quadrinomial was not submitted or if the final epithet could not be matched.
Infraspecific_epithet_2_score	Score assigned by the TNRS to indicate the level of similarity to the lower infraspecific taxon (quadrinomial) submitted. This field will be blank if a quadrinomial was not submitted, or if the final epithet of the quadrinomial could not be matched.
Annotations	Any standardized botanical annotations of uncertainty embedded within the name, such as "cf." or "aff.", are removed and stored here.
Unmatched_terms	The complete trailing portion of the name not matched by the TNRS, minus any annotations.
Accepted_name	The accepted (correct) scientific name of the name matched by the TNRS, according to the taxonomic source used. If the name matched is an accepted name, or if the TNRS indicated "No opinion" for the name matched, then acceptedName will be the same as nameMatched. If nameMatched is a synonymy, then acceptedName will be different.
Accepted_name_url	Web link, if any, for the accepted name.
Accepted_species	The genus+species portion only of the acceptedName. If the rank of the acceptedName is species, then acceptedSpecies will be the same as acceptedName. If the rank of the acceptedName is higher than species (for example, if the acceptedName is a genus), then this field will be blank.
Selected	denotes the best match according to either taxonomic or maximum score