Nomenclature

Collectively gather all your relevant nomenclature information in one place in TW. Nomenclatural data are separated from but connected to the biological taxonomically-related information about such topics as host information, genetic/genomic or other biological associations data about a given biological taxon.

Nomenclature Quick Start

TW provides a suite of common tasks help you to manage your nomenclatural and related data. This section assumes you have some familiarity with the TW user interface conventions and introduces new user interface features where needed. Next, please familiarize yourself with the kinds of tasks TW offers related to Nomenclature.

Nomenclature, not biology!

  • A reminder, if you want to record information about biology (hosts, parasites, distribution, etc.) that doesn't belong in the nomenclature section, you will use the OTU radial icon or OTU nav icon to access and record those data from a nomenclatural context.
Legend: Navigate from Browse Nomenclature to the OTU for a given taxon. Biologically related information about a taxon goes into the Operational Taxonomic Unit (OTU) task
Legend: In the Browse OTU task, enter biologically-related information.

Finding Nomenclature Tasks

  • Navigate to the Tasks list
  • Use the left side bar filter to Select Nomenclature
    • The result is a list of task cards, each one related in some way to capturing, using, filtering, editing, and publishing nomenclatural data.
Legend: Color-coded Nomenclature tasks. Yellow tasks are more or less stable and useful, some changes anticipated but basic functionality will remain the same. If green, they likely won't change. Red indicates experimental status -- they work, but might not last or may radically change.

Browse nomenclature, New taxon name, and New combination are useful tasks to add, view, and modify existing classification. Browse nomenclature provides a convenient way of navigating from one Taxon Name to another. It also gives you an option to quickly jump to the Edit Task.

Hotkeys

Legend: Finding keyboard shortcuts associated with the Browse Nomenclature user interface
  • Mac computers use ctrl as triggering key, PCs use alt.

Example: From the New/Edit taxon name task there are different extensive keyboard shortcut options:

  • ctrl+s Save taxon name changes
  • ctrl+n Create a new taxon name
  • ctrl+p Create a new taxon name with the same parent
  • ctrl+d Create a child of this taxon name
  • ctrl+l Clone this taxon name
  • ctrl+e Go to comprehensive specimen digitization
  • ctrl+p Create a new taxon name with the same parent
  • ctrl+m Go to new type material
  • ctrl+c Go to comprehensive specimen digitization
  • ctrl+b Go to browse nomenclature
  • ctrl+o Go to browse otus

Additionally, on any Browse/Show page you can:

  • ctrl+p - automatically pin and default that name to the pinboard
  • ctrl+g - pop-up a quick navigation modal that lets you navigate to the defaulted records
Troubleshooting

If you are using Firefox on Windows or Linux, the alt key is bound to the Firefox browser menu system which conflicts with the TaxonWorks hotkeys. If you do not ever use the alt keys to access Firefox browser menus, you can disable it by navigating to about:config and editing these keys:

ui.key.menuAccessKeyFocuses = false
ui.key.menuAccessKey = 0

Understanding the data model

Extensive information exists about the TaxonWorks data model. Information is presented in text and searchable graphic formats.

Legend: Visualizing TaxonName relationships in TW

Curating data

Basic information

All Taxon Names are stored as uninomials (called Protonyms) in TaxonWorks. A hierarchical nomenclature is entered by you and is customizable to provide the maximum level of flexibility for classifications. Three fields are required to create a Taxon Name record in the database: Name, Parent, and Taxonomic rank using the New taxon name task.

  • Select the New taxon name task.
  • Enter the desired Name
  • Start typing to select the Parent from a drop-down that will appear
  • Select the Rank
    • Note that TW software smart logic guesses at the Rank so please check.
  • Click Create to save.
    • The Parent is any valid taxon of a rank higher than a new one. This section is the only section of the form which requires the use of the Save button (after Create step). All other sections of the New Taxon name form use autosave mode.
    • After you click Create the task name changes to Edit taxon name.
Three fields required to create a New taxon name

Once you have entered the required fields for New taxon name and clicked Create more fields become available for you to populate with data for adding Author, Status, Relationship, Synonymy, Type, Original Combination, Subsequent Combination, Classification, Gender, and Etymlogy. Please review the next screenshot for what this looks like in the UI. Below this screenshot after the Conceptual Approach section, you will find a brief description of each of these sections followed by detailed explanations and examples.

All fields in the New taxon name task

About Root

The highest rank taxon in a given hierarchy is Root. This is a default Taxon and can not be modified, it is created when the project is first initiated. The first taxon attached to the Root requires selection of the Code of Nomenclature (ICZN, ICN, ICNP, ICTV). This selection is required to enforce validation rules specific to this particular Code of Nomenclature. All taxa below this taxon do not require selection of the Code, it will be inherited from the parent. The same database may contain taxa covered by different Codes of Nomenclature.

Illustrating the concept of Root in TaxonWorks

See this next screenshot to show how you can have other taxa at the Root as needed, that reference a different Code of Nomenclature.

Showing several taxa that cross kingdoms and Codes of Nomenclature at the level of root

Conceptual approach

To understand nomenclature in TaxonWorks it's important to understand that the basic idea is to accumulate/add new facts rather than update, change, or delete existing records. This is incredibly liberating in many ways, as the system will resolve the current status by inferring across the facts that you have added. As an example, rather than think "how do I change this name to invalid", think "how do I add the fact that so-and-so stated this name is invalid". The name was valid in the past, now we add a fact to indicate somebody more recently thinks it's invalid. The system will look at the years the facts were applied and then summarize the facts as we presently see them. This also lets the complete nomenclatural history, in all its gory detail, be recorded.

Authorship

In the Author section of Edit taxon name you have three optional ways to pick from to record authorship. This information sets the original authorship of the name (as opposed to a subsequent citation).

Three ways to add original authorship via Source, Verbatim, or Person

The Source option works if you have added the relevant Source (e. g. publication) for this particular Taxon name to TaxonWorks.

Add original authorship via Source
  • Click Source
  • Type just a few characters in the search box to find the correct source. A drop-down appears with your search results. Select the relevant publication.
    • Source author and Source year of that publication will be used for the taxon name Author.
    • Note you can pin this source if you know you'll immediately be adding more names with the same Author.
  • Results for this example above would be Suricata Desmarest, 1804.
Add original authorship via Verbatim
  • Click Verbatim
  • Enter the Verbatim author and Verbatim year directly.
Add original authorship via Person
  • Click Person
  • Search (enter only a few letters)
  • Click to select the desired Person
    • This example shows Desmarest was found by Search and then selected.
    • If you pick an incorrect Person then Click on the trash can to remove and search to pick a different person.
    • If you have more than one Author, then pick the others here as well.

If authorship is provided by you in more than one way it is prioritized and works as follows:

  • From the Verbatim Author and Verbatim Year fields
  • From the Person (TaxonNameAuthor) assigned as an author of the taxon name
  • From the Source author and source year fields
  • From the Person assigned as an author of the Source (SourceAuthor) assigned as the original citation

The preferred priority for your workflow is:

  • Assign an original citation (Source in Author section) that has People assigned as authors to that Source entry.
  • Override the authorship in the Source if needed by assigning one or more People from that source as authors in the Person section (for example when doing Smith in Jones & Smith).
  • Use Verbatim Author and year, if original source and People roles are not provided.

Keep in mind.

TaxonWorks is about creating the links between concepts (e.g. things like People, Collection Objects, Names, OTUs). How those concepts are visualized is a big can of worms. You can assign alternate values to People's names (e.g. abbreviations, alternate spellings) if you want to reflect how an author's name is spelled in different contexts.

ICZN

Parentheses around author/year
  • The preferred mechanism to rendering parentheses around an author/year (indicating current placement is different than original) is to assign the original Genus in the Original Combination (see below). This will automatically render the name correctly.
Use Original Combination in Edit taxon name to render parentheses
  • If you do not know the original combination, or you wish to "force" the use of parentheses you must use the Verbatim Author option.
    • Place the parentheses around the author there: (Smith). The code will automatically include the year in rendering out the name as needed.
Year of publication (availability) versus stated year

The year a name becomes available defines its priority for nomenclatural purposes. It may differ from the year printed on the matter which is made available. The year of publication can be inferred from the Source you linked to the name as an original combination, or explicitly noted in the Edit taxon name task in the Author > Verbatim > Verbatim year section.

From the Source hub task

  • Type a few characters to find your Source and select it.
  • Click the Edit (pencil) icon to edit the year (month, day) as follows
    • If you only have reference to a single value, it goes in year (month, day)
    • If you have reference to two year values, the actual year of publication goes in year, and the stated year of publication goes in stated_year.
    • If you have month or day publication, they go in month or day.
    • The value provided in Edit taxon name > Author > Verbatim > verbatim_year is always assumed to be the actual year of publication.

We assume that if two dates are known then the user will create and reference a Source to record those values, i.e. there is no mechanism to provide and differentiate the two types of year directly with the name itself.

Nomenclatural Status

This section of Edit taxon name relates to nomenclatural statuses, which are applicable to the taxon itself and does not require any knowledge of related taxa (e.g., Nomen nudum, Non binomial). Note that valid is the default Status so that you do not usually have to select Valid (except in certain circumstances, see below).

In Edit taxon name: Three ways to assign Status to a taxon name
  • Multiple Statuses could/can be assigned to the same taxon
  • Most common status are listed directly in the Common section for you to pick from.
  • The Advanced option allows you to search for a specific status.
  • All available statuses are listed in Show all section in a pop-up for you to scroll down and click to select. The statuses which are not applicable to a current taxon are greyed out.
Using Show all to select a Status for a taxon

Keep in mind.

  1. All names by default are valid names, i.e. a valid status should not be assigned to all the names in the database. Use of the Valid status is reserved for special cases, for example when the taxon has a nomenclatural history of being treated as a synonym, and later was treated as a valid name again, in order to preserve a historical record of synonymy, and override it, a status valid could be added to the taxon, the citation on the status will indicate the source where the validity of taxon was confirmed.
  2. Status Homonym could be added to the taxon to indicate invalid status in cases where the senior homonym is not known, but this should be avoided -- the better way to record homonymy is to create a relationship (see below).

Example 1: Nomen nudum

After you select a Common status, e. g. Nomen nudum
  • Select Status = Nomen nudum option under Common.
  • Note your choice is automatically saved after you selected it.

Relationship

In this sense, a Relationship references a nomenclatural status (or more than one status) based on the connection to other taxon names.

These nomenclatural relationships are the statuses which require record of two Taxon Names. For example, Aus is a synonym of Bus. In this relationship we can specify a status for each of those two names:

  • Aus is a Junior synonym
  • Bus is a Senior synonym

Keep in mind.

For a given invalid name, navigate to Edit taxon name > Relationship for that invalid name. In the Relationship section, you will do two things: search for and select the related name, then you declare the relationship status picking from the options provided (as described above).

Here's a quick example of what it looks like when you have completed the above process. In this example, we started by using the Browse Nomenclature task to search for and find the Nomenclatural record for the invalid name Thysanidae Peck, 1951. Then, we clicked the to get to Edit taxon name and go to the Relationship section. We searched for the (valid) name Signiphoridae Howard, 1894 and picked it. We then selected one of the default statuses: Subjective synonym of. Our choice was saved automatically.

What we see after we declared the Subjective synonym status relationship
  1. Always start with the invalid name and add relationships that reference the valid (or senior) name
  2. Use Browse nomenclature to find the invalid name, then Edit the Relationship for that name.
  3. Check the soft validation messages, they will let you know what may be improved or added.
  4. When adding a relationship, select one that is as specific as possible, subjective synonym is better than just synonym, primary homonym is better than just homonym.
Note the Soft validation help in the right margin

Example 1: Synonymy

  • Although each relationship could be read in either direction (Aus is junior synonym of Bus, Bus is senior synonym of Aus) only one way recording of the information is supported in TaxonWorks at the moment. The relationship should always start from invalid name. In our example, it is Aus, so the editing should start on the Edit taxon name Page for Aus. Then, to build a new relationship, search for the second (related) name, in our example it is Bus, and then select the status for this relationship, which is objective synonym in this case.
  • Once the relationship is created a citation could be added to this relationship to indicate the Source, where this synonymy was first proposed.
  • In cases of competing synonymy, where in one source Aus is recorded as synonym of Bus, and in the next publication it is a synonym of Cus, both synonym relationships should be created in the database, if the citations are provided, the latest citation will be used to position the taxon in the classification.
  • In cases where the name was reported as a synonym by mistake and was revalidated in a later publication, the relationship should not be deleted, a valid status could be added to the taxon to overwrite the synonymy (see above)

Example 2: Homonomy

If we know that Aus aus is a homonym of Bus aus, and that Aus bus is a replacement name, then we have to express two "facts", i.e. relationship between taxa, in this case 1) A. aus is a synonym of B. aus, 2) A. aus is replaced by A. bus. Both of those statemens are invalidating statements, so both of them start with the taxonomic page for A. aus

The basic steps:

  1. Ensure all 3 protonyms exist in the database (aus, aus, bus)
  2. Navigate to the invalid name Aus aus
  3. Create the first relationship: Select the senior homonym name Bus aus and a homonym relationship (be specific: primary homonym or secondary homonym)
  4. Create the second relationship: Select the valid name (replacement name) Aus bus and add a synonym relationship (replaced by or subjective synonym of, the second option is true when the substitute name was selected from one of the junior synonyms)

Example 3: Misapplication

If we know that Aus aus Author2 is a misidentification of Aus aus Author1, and that Aus bus is a correct name, then we have to express two "facts", i.e. relationship between taxa, in this case 1) A. aus Author 2 is a misidentification of A. aus Author 1, 2) A. aus is invalid name for A. bus. Both of those statements are invalidating statements, so both of them start with the taxonomic page for A. aus

The basic steps:

  1. Ensure all 3 protonyms exist in the database (aus, aus, bus). An additional protonym should be created in the database for 'Aus aus Author2' different from the correctly applied name 'Aus aus Author1'
  2. Navigate to the invalid name Aus aus Author2
  3. Create the first relationship: Select the correctly applied name name Aus aus Author1 and a misapplication relationship
  4. Create the second relationship: Select the valid name Aus bus and add non specific invalid, linked to relationship (do not use synonym relationships, since misapplication is not an avaliable name)

Misspelling

Create the misspelling relationship the same way as misapplication, but only a single relationship needed to link with correctly spelled protonym.

Original combinations

The original combination is required to keep track of the taxon history, properly handle parentheses in the author string, and also to validate homonymy between taxa. There are two ways to enter the original combination in TaxonWorks.

Citing the original combination

To cite usage of the original combination cite the taxon name (Protonym) itself. This is because you are citing the fact that a) there is some name that b) came into existence in some first use, i.e. the definition of a Protonym.

Method 1 (original combination different from the current combination)

  1. To properly handle taxonomy, always enter taxon name (basic information) in the original form (e.g. species was described as Aus albus Author, now it is Ba alba (Author), the name of the taxon should stay as albus, the form transition will be handled by the genus gender and the species part of speech.
  2. To build an original combination, first move the name of the taxon to the nomenclatural rank level, at which it was originally described.
    • This is important, because a species could be originally described at the subspecies level.
  3. Select the original genus and if needed the original subgenus, assuming those taxa are already in the database.
    • If they are not, open a separate browser tab and enter missing names in the classification.
  4. The rank of each name can be adjusted, the name can be dragged up or down.
Entering misspelled names

Hint: if the original name has an incorrect spelling which had to be corrected (e.g. mülleri or albi-lineata), or the original genus was misspelled, two protonyms have to be stored in the database. The first one with the correct spelling and the second one with the original spelling. The second protonym should be linked to the first one with the Incorrect original spelling relationship. This relationship also overrrides the restriction on the Taxon Name spelling.

You will sometimes discover you cannot create a taxon with a misspelling. The soft validation software steps in. To enter a misspelled name in TaxonWorks:

  • Enter the correct spelling for the TaxonName
  • Click Save to save this Taxon
  • Add misspelling or incorrect original spelling in Relationship
  • Then change the Taxon name spelling to the misspelled form and
  • Click Save again.

Method 2 (when the original combination is the same as the current combination)

  • Click the button Set as current

Type metadata

Genus and Family group names

Data can be added directly in the Type section of these tasks

  • New type specimen or via
  • New taxon name

Find the New type specimen task via the New taxon name task Type section or directly from the tasks tab (filter by Nomenclature on the left to quickly find the New type specimen task).

Species group names

See also the basic article parsing exercise for a walk through that addresses many of these issues in a more contextual framework.

Manage Biocuration Groups and the Classes associated with each of the groups

Adding Groups and Classes can be done independently. You can then assign classes to a given group (e. g. class Female or Male get added to group Sex). Classes do not have to be part of a group. Adding Groups and Classes work the same way. Classes, once added, can be associated with any given group created. Note the "plus" sign in the above screenshot which gives you a list of your classes you can add to that group.

Manage Biocuration Groups using the Manage Controlled Vocabulary task
  • To add a biocuration group
    • Select Biocuration Group from the menu bar.
    • Give your biocuration group a Name
    • Next, write a definition for this group so that others may apply it correctly for your project. Note that definitions must be at least 20 characters.
    • Then, select a color to apply to this group label for ease of use / finding in the user interface.
    • If one exists, enter a URL here to a known standard term / ontology entry for this group concept.
      • Example, for group = Sex there is a term in the Darwin Core Standard (DwC) (from Biodiversity Information Standards TDWG) for Sex. You would get this URL http://rs.tdwg.org/dwc/terms/sex from the DwC Terms List from tdwg.org and enter it in the URL field for this term. This ensures the data get mapped / associated with the intended concept on export.
    • Lastly, click Create.
Manage Biocuration Classes using the Manage Controlled Vocabulary task
  • To add a biocuration class
    • Select Biocuration Class from the menu bar.
    • Give your biocuration class a Name.
    • Next, write a definition for this class so that others may apply it correctly for your project. Note that definitions must be at least 20 characters.
    • Then, select a color to apply to this class label for ease of use / finding in the user interface.
    • If one exists, enter a URL here to a known standard term / ontology entry for this group concept.
      • Example, for class = Female there is a standard term and definition in the Phenotype and Trait Ontology (PATO). You can search PATO for female and you will get this URL http://purl.obolibrary.org/obo/PATO_0000383 to enter in the URL field for this term. This ensures the data get mapped / associated with the intended concept on export.
    • Lastly, click Create.

Now you can navigate to the New type specimen task

  • Select the type (e.g. holotype, paratype, etc.), this unlocks the Collection object section of the form (see screen shot next).
New Type Specimen Task options
  • If the type designator is not the same as either the 1) the original citation on the species Protonym or 2) the original citation on the type material record then select the type designator if known. The designator will be inferred from the aforementioned citations otherwise.
  • At present, if you have created a Collecting event, find it by id (the current search is a stub, and very crude), otherwise add verbatim data to the Buffered sections.
    • Buffered data persist with the Collection object, to be transcribed into Collecting events, determinations records, etc. some time downstream in the digitization process.
  • Select the Biocuration classes you want by clicking on a green button (remember green in TaxonWorks means create a record).
    • This creates a record indicating that the collection object is that class. The button will turn red (remember red in TaxonWorks means destroy a record). Clicking a red button will remove that classification from the object.
  • Select a repository
  • Click create. Your record will be added to the right side of the form, you will see it highlighted by type in a light green. That means the form on the left can be used to edit that record.
  • Click New type to add another record (e.g. paratype).
New Type Specimen task showing Buffered, Repository, and Biocurations sections

Family group names

Several categories for the family group name exist:

  • original family group name form;
  • incorrect original family group name form;
  • subsequent family group name form;
  • misspelling. All of them could be added to the database as individual Protonym linked to the correct family group name form (valid or synonym) with a single Taxon Name Relationship, for example Aini is family group name original form of Ainae.

To simplify the work with family family group names, two sections were added at the botom of Edit task. For each name (valid or synonym), an Original form could be added as well as multiple Subsequen name forms (with citations to the works where those forms were introduced). The two section should simplify working with history of a family-group name, and keeping track of spelling changes and/or historical changes of the taxon rank. It is recommended to track changes of a family-group name at the lovest coordinate rank taxon. For example, if you have a family, subfamily, and tribe based on the same genus name, all history should be added to the protonym at the tribe level (regardless at what level the name was treated in the literature historically).

Example

For tribe Cicadini in the Edit TaxonName the following could be reported: Original form: CicadinaSubsequent forms: CicadiniCicadinaeCicadidae

Citations

Incertae sedis

Incertae sedis implies a relationship between two protonyms. Any time something you want to express references two protonyms you must use a Taxon Name Relationship to express this data.

  • For the name in question select the parent under which it should be placed,
  • then select the relationship.

Misidentifications

Misidentifications are a tricky gray area. Remember that we only care about the nomenclatural consequences of the use of the names in question. Taxon Identifications are linkages of OTUs to Collection objects, this is the preferred mechanism for linking one or more identifications to a collection object.

A question from a user reflects the trickiness:

  1. Imagine there is a genus Aus, with type species Aus bus. Then someone describes a new species Aus cus, which subsequent authors don't even consider to be in the same superfamily. So I cannot enter Aus twice because the second one is a misidentification but no one knows for sure what it is.

This is just an original genus. This is the same genus in both species. The genus cannot be misidentified. This is just a position of the species in classification, regardless where it was originally described or subsequently placed.

The proper way to handle this is to use a single Aus, which is placed in the correct family. In both species Aus is the Original genus, in Aus bus, this is also a Parent taxon. In case of Aus cus, if the current genus is not assigned, the superfamily is the parent taxon. An incertae sedis relationship should connect Aus cus and the superfamily.

  1. Species misidentification/misapplication.

Misapplication itself does not make an available name. But this a common practice to include misapplication in the list of historical usages of the taxon names, especially in the cases where a new name is proposed as a "replacement" for a previously misidentified species. Remember, that nomen novum cannot be proposed for misapplication, since it requires a previously available name, but invalid because of homonymy.

To record this in TaxonWorks, a new Protonym for a misapplied name should be created in the database. This Protonym should be linked to two other Taxon Names with two Taxon Name Relationships. The first relationship is to an available name with the same spelling (it could be a valid name or a synonym). The relationship type is Misapplication. The second relationship Invalidating relationship should link this TaxonName to the correct name for this taxon. Remember, the Synonym relationship is not applicable here, since it assumes that both names are available name, and in this example Misapplication is not an available name. Follow the soft validation messages for other essential information for the Protonym in the database.

An example: The name Aus aus Author 1, is a misapplication for Aus bus, and Aus aus Author 2 is a completely different species.

After the Protonym for the first name is created two relationships will be added in the database:

  • Aus aus Author 1 Misapplication, linked to Aus aus Author 2
  • Aus aus Author 1 Invalid, linked to Aus bus

Once the misapplication is created, an OTU could be linked to the TaxonName, which could be used, for example, for taxon determination.

Nomenclature Senarios (aka How-To)

Add new taxon name

For this task, be sure you have put the source in the Pinboard and selected it as the default, as this will save a lot of time during the process. Note also, that TW is smart, and as soon as you enter the name, it checks to see if it already has it (see example below).

UCD Specific Note: UCD@TW has been previously populated with the data from John Noyes’ UCD, so inside the UCD@TW database you will not have to create a root for the taxonomic name tree (that is, there should always be a parent taxon). First, fill out the name of the highest-level taxon that you are creating, and indicate its parent taxon. For example, if you are creating a new genus with 2 new species, first create the genus, and then create the two new species. If one of the two new species is type-species for the genus, you can come back to the genus name and add the type-species later.

To manually create a new taxon name (e.g. species / genus / family):

  • Select the New Taxon Name card from the Hub.
Finding the New Taxon Name task card
  • In the New Taxon Name form add the new name and select the parent.
    • Entering a string in the Parent field gives you a list of possible matching names to pick from.
    • The new Name field works similarly to help you avoid adding the same name twice (think about collaborations).
Partial view of the New Taxon Name task
Adding new name and selecting the parent in New Taxon Name task
  • Based on the rank of the parent, TW will then ask you to select the precise taxonomic rank of the new name (see below). If everything is correct, hit Create. Once you do this, the rest of the fields related to a new name will appear (see below).
Check rank of name to be added is correct and click create
The entire New Taxon Name form options now appear
  • Now you provide the Source (publication) and authors. If you have pinned the source, the pinboard icon will be blue and you can click it to automatically fill in the source details.
  • Then choose Person, and enter enough letters to bring up each author (they should be in the database if they were entered with the source).
    • If the authors of the Source are the same as the authors of the new name, you can click the button to the right Clone from source.
    • If multiple persons pop up that appear to be the same (for example A. Dal Molin and Ana Dal Molin), you can use the Uniquify People task to resolve and merge them (see Scenario: Resolving redundant person name strings, and matching author names with and without diacritical marks).
    • If an author name is not found, you can enter it and add it by clicking the green Add New button. This will add the author to the names table.

In most cases, for new taxa, you can skip over the Status and Relationship fields.

  • However, if the taxon is a fossil, you should check Fossil in the Status field. The name will now appear with a little cross symbol to the left. There are special rules in ICZN and TW for fossil taxa.

Notes for Status and Relationship fields.

  • To pick a Status for a name, you note Common ones are listed by default for you to pick from.

    • Pick from the Common list OR
    • Click Advanced to search for a Status not in the Common list and pick it OR
    • Click Show all to get a scrollable list of all Status options possible for the given code (e.g. ICN vs ICZN options will differ) to pick from.

  • To declare a Relationship

    • First go to the Edit Taxon Name record with the lesser status (e.g. the Synonym name)
    • From there, in the Relationship field, search for the name with the higher status (e.g. accepted or valid name).
    • Select the desired name
    • You then get to select the Status of the Relationship for the two names.
    • The result always in TaxonWorks is that you read the result as the lesser status name has Relationship (what ever you selected) to the higher status name. (Not in the other direction).
The Status and Relationship fields in Add/Edit new taxon name task
The scrollable Status list resulting when you click Show All

The Type form is next, which opens up a new form to capture details on the type. We prefer to complete the rest of the New Taxon Name form first, and then do the Type.

  • For new species, the Original Combination will be the same as used in the paper, so Set as Current.

  • Finally you can specify the gender and form of the new name. For species-level names there are four possibilities:

    1. Adjective. Most species epithets are probably treated as adjectives, for example, Signiphora flavella meaning a yellow species. These will change their ending if moved to a genus with a different gender. Names with the suffix “-ensis” (usually referring to a place), change the ending only if put in combination with a genus name that is neuter, in which case it becomes “-ense”.
    2. Noun in Apposition. These don’t change gender when transferred to other genera with a different gender. An example might be a name like Aphelinus mali, named after the common host, the woolly apple aphid. An arbitrary combination of letters is treated as a noun.
    3. Noun in genitive case. These are commonly patronyms, ending in “-i” for males and “-ae” for females.
    4. Participle. A participle is an adjectival form of a verb. These are treated as adjectives, and they must agree in gender with the genus name.

  • There is a text field to capture the Etymology, in most cases you can simply paste this text from the publication.

  • Be sure to Save all the information (green Save button at upper right) before moving to the Type screen. (UCD prefers to enter Type information last, after everything else on this page has been saved).

In most cases, the Quick type screen will provide all the details you need to enter information on the type, and this is what we show below. However, if you have other information to add for the type, such as Lat/Long data, you will need to use the Comprehensive form.

In Edit Taxon Name task add type information using Quick or Comprehensive options
The Quick New Type Specimen form
The Comprehensive form to add many type specimen details

  • First, pick the nature of the type (for most new species this will be a holotype), provide the source (click blue pin button if source is the default), and the page number(s) on which the type is designated. The rest of the information on the type is filled in with the screen below.

    1. In most cases, the type will be a new specimen, not already in TW as an existing Collection Object. If so, click New.
    2. Paste the label data for the type into Buffered Collecting event. This is a verbatim text field.
    3. In most cases, you can ignore Buffered determinations, and Buffered other labels.
    4. Total is number of specimens (one for a holotype).
    5. Designate the preparation type (pin, slide-mount, there are several choices).
    6. The Repository is the institution where the type is deposited. Hopefully the repository will be in the TW table, otherwise you may need to create it using the Repositories card in the Data portfolio.
    7. Collection Event refers to a specimen already in the TW database, which in most cases will not be the case if you are curating a new species description.
    8. In Biocurations, indicate whether the type is an adult or immature, and a male or female.
Adding more Type information
  1. Finally, you enter the Identifier for the type, which consists of two parts. Note that this may be different from the repository (a single institution may have several collections, each with a different “namespace”). Think of the namespace as the part of a specimen ID number that does not change for each specimen, for example, TAMU in TAMU x01234567. If the namespace is not in the database, you may need to create it, but since these are shared across projects, there is a good chance it will be there. (See the Glossary for more details)
  • Click to open the Radial Annotator.
  • Select the Identifiers option.
  • For Identifier group, select Local.
  • Next Search for the Namespace of the collection in which the type is deposited.
  • Once you have selected the namespace, paste in the type or specimen number (only) in the Identifier field.
  • Click the green Create button.
Open the Radial Annotator to add a specimen Identifier in TaxonWorks
Adding the specimen Identifierinformation

If you wish to add paratypes (optional), you essentially follow the same process for each one.

For many contemporary taxa, there may also be a ZooBank number associated with the species. The correct way to enter this is to:

  • Scroll to the top of the Edit Type Specimen page (or Edit taxon name page) and click the Radial Annotator to the right of the blue species name.
    • In this case, the Identifier will be Global.
    • Pick Lsid, and enter the ZooBank accession number in the Identifier box. Note that some publications will provide the link to ZooBank which is not accepted by TW, but not the actual Lsid. In this case, navigate to ZooBank to get the valid Lsid, which will have the following format:

urn:lsid:zoobank.org:act:5EB72879-1E9C-4A89-BCD8-FF37534B7172

If the paper does not list an Lsid for the new species, it might be worth a try to find it on the Zoobank.org web site.

  • Be sure to click the green Create button at the bottom of the screen before leaving!

You show now add any additional information about the new species (or genus) in the publication following the process described next.

If you are creating a new genus-level or family-level name, the process is similar, but in many ways more simple because the type will be a species name or a genus name, respectively. If the type-species or type-genus name is also new, probably the easiest path would be to create the family-level or genus-level name first, then create the name of the type-species or type-genus, and then return to the new genus-level or family-level name and indicate the type. If you enter an existing name in the New Taxon Name task and select it (assuming it is found), TW will take you to the Edit Taxon Name screen where you can enter the type information.

After you click Create and Save you should be returned to the Browse Nomenclature page:

[INSERT SCREENSHOT HERE]

If you have entered all the information correctly, it should be shown here. Note that the Validation form can serve as a checklist. In this case, we have neglected to enter several items, indicated here. To fix these, the easiest way is hit the Navigate Radial button (3 at upper right) and from here choose Edit. We think the easiest way to proceed from here is to hit the Browse OTUs button (1 at top of screen). This takes you to the summary form for the OTU that you have just created. Note that there is a similar icon on the Browse OTUs page, which will take you back to Browse Nomenclature page. This is an easy way to move back and forth between these two important screens.

Add / amend type information for a new taxon

For many older species group names, there will be no information on the type in TW. If you wish to add this information, you will want to have the original description handy, and pin it to the Pinboard. The easiest way to proceed is to use the New type specimen task. You can then follow the steps above for designating a type for a new species.

HINT: The New type specimen task is also used to add or modify information on types already in the system.

New synonymy or removal from synonymy (stat. rev.)

  • Find the junior synonym name using the Browse Nomenclature task.
  • Click the Edit icon to navigate to the Edit taxon name page.
  • Enter the senior synonym in the Relationship box. A list of candidate names will come up.
  • Select the correct one and Set to Parent.
    • A list of choices for the synonym relationship will include Subjective synonym, Objective synonym, subsequent Misspelling, and Homonym of.
  • Note that you must also tag this nomenclatural act (new synonymy) to a citation and page number.
    • Click the Radial Annotator icon to the right in the Relationship box, and choose Citations.
    • Enter the Source (use the blue pin key!) and page number(s).
    • If this is the first time the synonymy has been proposed, check the Is Original box.

Example of Synonymization of subgenera

Problem: Eremidium had five subgenera that became synonyms. Current state of modified data: Eremidium (Eremidium) has almost all citations, 4 synonyms and 22 species whereas Eremidium has 28 species (the species of the synonyms were moved under the genus). What would be the easiest way to end up with Eremidium without subgenus and all the 50 species?

The method is to delete the genus and elevate subgenus to the genus level using the following steps. In this way you will preserve most of the data.

  • Rename the genus to something recognizable, e.g. "Eremidiumdelete"
  • Go to the subgenus and change parent and rank to "Eremidium"
  • Synonymize all subgenera to "Eremidium" (previous subgenus)
  • Apply all soft validation fixes
  • Follow the procedure to delete the duplicate e.g. "Eremidiumdelelete".
  • If species remain under Eremidiumdelete, make Eremidiumdelete genus a syn of Eremidium and transfer all the species as suggested. Then delete synonym relationship.
  • Now the children of Eremidiumdelete need to run the soft validation fix to change the parent.

Transfer species to new parent or not

If the junior synonym is a genus name, you must then decide if you want to transfer some or all of the species to the new parent.

  • Once you have made the synonymy, TW will present a table called Manage Synonyms. This shows the current parent, and by default, the new parent. You can change the latter to cover cases in which a genus is being split up and the species are being moved to different genera.
    • You can select species individually, or select All of them.
    • At the bottom of the screen click the green Move button. TW will ask you if you are sure you want to do this!

HINT a la UCD@TW: It is the consenus of UCD@TW curators that if a genus is synonymized under another genus, and the author(s) of the paper do not explicitly treat generic placement of the species formerly contained in it, that all species are considered to belong to the senior synonym, by default.

Remove name from synonomy

  1. To do this, find the junior synonym and move to the Edit taxon name page as above.
  2. Scroll down to Status and click the Show All button to the right. This brings up a list of all possibilities.
  3. Choose Valid (nested under Available), and then be sure to
  4. enter the Source citation and pagination as above, but this time use the Radial annotator in the right lower corner of the Status box.

HINT: Note well, after a name has been removed from synonymy using the Valid Status, if that name is moved into synonymy again, first complete the steps to create the new synonymy, then delete the Valid status. This last step is required to show the name in its new, synonymized state.

New combination

In an older version of TW, your strategy depended upon whether the combination is really new (that is, the species has previously been placed in that genus), or whether the combination had been used before. Scenarios 1 and 2 below cover those cases, respectively. Both procedures still work, but as of November 2021, there is new functionality on the Edit Taxon Name page that allows you to handle either case. This is shown as option 3 below. Option 3 is probably the easiest, most preferred way to handle all new combinations now.

For New Combinations.

  • Open the New Combination task, and type in the new combination. TW will bring up a list of candidate genera and candidate species.
    • If you enter a trinomial (for assigning to a subgenus, TW will show 3 sets of names. Pick the correct genus name and species name
    • Click the pinboard icon to paste in the citation, add the page number, and hit Create.
  • Once you have created the new combination, be sure to click the green button to move the species to the new genus.
    • (The only time you would not want to move the species to this genus is if you were entering a historical combination, and the species is not currently classified in that genus). It’s as simple as that!

Combinations used before.

  • Navigate to the Edit Taxon name page for the species.
  • Change the parent to the current genus (the revived combination).
  • Then move to the Radial annotator to the right of the species name shown in blue at the top right of the screen.
    • Choose citation and enter the source and page number for the paper in which the former combination was revived.

Option 3 (either use case above)

  • Navigate to the Edit Taxon Name page for the species in its existing combination.
  • Change the parent to the genus in which it has now been placed.
  • Scroll down to the Subsequent combination box. Click Set as current, or drag down the old combination to the species line and enter the genus for the new combination on the genus line.
  • Enter the source and page number of the paper in which the transfer was published and click Create.

The new combination will be added to the chronological list at the bottom of the box, and it should show in the historical list when you return to the name in Browse Nomenclature.

If the gender of species is incorrect following the new combination, you may need to change the Gender and form of the species name, and/or the gender of the genus (on the Edit taxon name forms for the species name and genus respectively). This correction can also be made using Click to edit verbatim (use sparingly).

Revised family placement for a genus or genus placement for a species

If someone has published a new family-level placement for a genus, recording this is a two step process.

  • Navigate to the Edit taxon name form for the genus.
  • First, change the Parent at the top of the Edit taxon name form to the new family-level taxon.
    • If the family name has not been used at this hierarchical level before, you many need to create the protonym for it first.
  • Second, you must record the source of this change. Scroll to the bottom of the Edit taxon name screen and find the Classification box. Search for the new family-level taxon and Set to Parent.
  • In the Radial annotator that now appears, choose Citation and enter the source and page number where the revised placement was published.

If you are moving a subfamily, tribe or subtribe to a new family, the process is the same, but you would work from the Edit taxon name screen for the appropriate family-level taxon.

To move a species to a different genus or subgenus, use the New Combination task Scenario . If you are moving a subfamily, tribe or subtribe to a different family level taxon, but the categorical level of the taxon you are moving does not change, follow the same procedure.

However, if you are changing the categorical level of a family-group name, the process is more complicated, and you will need to refer to Scenario: Changing rank of a family-level taxon.

Designate nomen nudum or numen dubium

  • To designate a name as a _nomen nudum_, _nomen dubium_ or as unavailable, navigate to the Status field in the Edit Taxon Name form.
    • The default for this field is valid. Four common choices are shown: Unavailable, Nomen Nudum, Nomen Dubium, and Fossil.
    • Click the All button here brings up a comprehensive list of other possibilities. For unavailable names you should probably look at the entire list and designate the reason the name is not available.
    • Be sure to enter the source and page number for the paper that published this information.

Homonyms and replacement names

The most common scenario will be that someone has discovered a junior homonym and provided a replacement name. Here are the steps you would follow. First be sure the source is the default in your pinboard.

  • First create the replacement name using the New Taxon Name task, as described above, entering all information on the authors, citation, etc.
  • Two relationships need to be created:
  • Then move to the junior homonym (Browse Nomenclature, click the green Edit button at top right corner).
    • In the Relationships field, enter the senior homonym.
    • You will be given a list of choices, choose Homonym of.
  • Now designate the replacement name. In the Relationships field, enter the replacement name.
    • HINT: Replaced By does not appear in the short list of choices, so either search for it (easiest) or find it in the table of All choices.
    • Enter the citation and page number where the replacement name was published.

Resolving redundant person name strings, and matching author names with and without diacritical marks

Often when you enter a person's name string in a search field, such as for authors of a source or taxon, multiple entries will pop up that appear to be the same person, such as A. Dal Molin and Ana Dal Molin. The Uniquify People task provides tools to resolve and merge these.

  • Find one instance of the person in the Select Person field, and
  • Load another instance (probably with different abbreviations of names) in the Match People field. The task will show you information about each person, such as representative publications.
  • If you are sure that they are the same people, you can merge them by clicking the Merge People button.

Diacritical marks (e.g. umlauts, tildas) on author names pose special problems, as the search engines may not find them. For example, if the author name is Ferrière and you enter Ferriere (without the diacritical mark), the search engine will not find it. The best way to resolve this is to treat Ferriere as an alternate spelling of the name Fèrriere. To accomplish this:

  • Go to the People data card, and pull up the name.
  • In the Radial annotator at the top of the screen, choose Alternate Values
  • Then click the Alternate Spelling tab.
  • Select whether it is the first or last name, enter the alternate spelling, and click Create. Once this is done, the search engine will find the person using either spelling of the name.

Recording subsequent misspelling of a name

  • First, you need to create the misspelled name using the New Taxon Name task. Do not give it an author.
  • Scroll down to the Relationship field
  • Search for the correctly spelled name
  • Set the correctly spelled name as the Parent, and
  • Choose the Misspelling Of button.
  • Enter the citation (source) for the misspelled name and the page number in the Radial Annotator on the right of the Relationship field.

Changing rank of a family-level taxon

This is a multi-step process. You may need to raise or lower the rank of a family-level taxon. The process is the same. Here's an example: let’s assume that we wish to raise the categorical level of the taxon Coccophaginae to family level, Coccophagidae. Here are the steps to follow.

  1. Check to see if Coccophagidae has been used at the family level before (use Browse Nomenclature). If it has, you can skip step 2 below, because the taxon name Coccophagidae already exists in the system.

  2. If the taxon at the family-level (Coccophagidae here) does not exist, navigate to the taxon name Coccophaginae (Browse Nomenclature) and move to the Edit Taxon Name screen to create the name Coccophagidae.

  • The best way to do this is to Clone the subfamily level name (green button in upper right), as this will retain the author and date, type genus, and other historical information.
  • Select all the boxes to retain all historical information and type CLONE in the box. This will active the green Clone button. Note that you are creating a taxon name here, not an OTU, which is a separate issue.
  1. You are now on the Edit taxon name page for the cloned name.
  • Change the family ending suffix to “idae”, or Coccophagidae.
  • Now change the parent. In this case, it will now be Chalcidoidea.
  • Then Show all ranks, and pick Family.
  1. To record who made the change in categorical level:
  • Scroll down to the Classification field
  • Click Set to Parent (which will pick up Chalcidoidea from above), if the current classification is correct. Otherwise, type in the correct parent.
    • Below the field will be two choices, Incertae Sedis and Classified As. Pick Source Classified As.
  • Enter the source and page number for the publication in which the change was made (in this case, elevation of Coccophaginae to Coccophagidae).
  1. Now you need to make the appropriate changes to the nominate subfamily taxon, the subfamily Coccophaginae in this example.
  • Navigate to the Edit Taxon Name form for Coccophaginae.
  • Change the parent here to the new family-level name, in this case, Coccophagidae.
  1. Next, scroll down to the Relationships field.
  • Enter the new family-level name (Coccophagidae), and
  • show all possible choices (blue box to right).
    • Choose Family Group Name, Original Form Of from the menu of choices (it is below Usage which is below Unavailable or Invalid, linked to).
  • Enter the source and page number, as always.

  1. At this point, a Manage Synonymy screen will appear. This provides a dashboard for assigning the classification of all taxa subordinate to the family name (children, in other words).

  2. Below the Manage Synonymy screen you will find the Classification screen.

  • Type in new Parent (Coccophagidae in this example), and
  • Choose Source Classified As.
  • Enter the citation and page number for the appropriate publication.

Changing rank of a genus-level taxon or species-level taxon

Example: to elevate a subgenus to genus level:

  • First Navigate to the name of the subgenus and click on the Edit taxon name tool.
  • Change the parent as appropriate (family, subfamily, tribe etc.) and
  • Change the rank to genus.

Next, how to record the citation? Note well, classification relationships should be used only above the genus level.

For making any changes in rank at the genus level and below use the New Combination task: (explained in the New Combination Scenario). There is still a 2-part process required at the moment.

  1. Create the combination (using the New Combination task), e.g. Camptoptera (Eofoersteria), and add the citation for same there.
  2. Update the classification by changing the parent for the "now" subgenus. You will be required to manually select the rank, (e.g. subgenus)

One should be aware that UCD@NHM did not use subgeneric names, they were treated as synonyms of the parent genus. However, if species names were originally described in a subgenus, the original combination was recorded and will show in UCD@TW as a combination, as in the following example:

INSERT Screenshot

If you are working with a genus in which a subgeneric classification has been used, you have the following options:

  1. You can create all of the subgeneric names, or find them and treat them as valid children of the appropriate genus. Nominate subgeneric names can be created by cloning the genus name and changing rank (see examples for subfamilies above, section 4.14). Whether or not you want to take the time to do this is up to you and your colleagues, but the tools are there in UCD@TW and in TaxonWorks generally.

  2. You can continue to treat the subgenera as junior synonyms of the parent genus. However, if you curate a paper in which a species is originally described in a subgenus, you should be sure to enter both the Genus and Subgenus names in the Original Combination and Rank section of Edit Taxon Name.

  3. If you want to record historic subgeneric placement, use the New Combination task.

Species groups

These are used in many genera of chalcidoids as informal grouping of species without nomenclatural rank or status. UCD@TW provides the tools to treat these formally (as superspecies which is what the ICZN recommends) but it will not display them as such in Browse Nomenclature. However, the consensus in the UCD project seems to be that it is preferable to leave species groups as informal groupings without nomenclatural baggage. How then to indicate or record assignment to species groups? There are several options, each of which has strong and weak points. It is a "policy decision". You will have to decide which option works best for your group.

One.

  • Add the species group designation to the OTU name field using the edit OTU function. The OTU can remain linked to the original taxonomic name. It will display as follows, every time the OTU name is displayed:

INSERT screenshot

Two.

You will need to use a data attribute with the Predicate name species group and add the predicate as a default option to the OTU display.

  • First, create a new Predicate using the Manage Controlled Vocabulary task.
  • Provide a definition and choose a color.
  • Next, go to Project (upper right corner of any screen)
  • Choose Edit Preferences under Edit (upper left corner of screen)
  • Select OTU, scroll down toSpecies Group and select it.

Now the Predicate is created and will be available for any OTU and can be designated where needed.

  • Second, Browse to a particular OTU and choose Data Attributes in the Radial annotator.
  • Type species group in the Select a Predicate box, the name of the species group in the Value box, and click the green Create button.
  • If you want to associate this placement with a literature citation, enter it using the citations button to the right of the species group name at bottom of the screen.

Once you have completed Step One above, the Predicate will be available for any OTU, you can designate them using Step Two.

Three.

  • Create a Tag for each species group in Manage Controlled Vocabulary,
  • Apply the tag to the OTU using the Radial annotator. This will allow you to pull up all OTUs assigned to a particular species group in the Radial annotator.
  • Note well, however, the downside is that the tags will appear in the list for everyone in the project.

Four.

  • Create a matrix of OTUs for each species group.

About tribes and subtribes

Again, using the UCD@NHM Project as an example, they did not formally recognize taxonomic levels between genera and subfamilies. Names of tribes and subtribes were treated as junior synonyms of their respective families. However, tribal and subtribal classifications are currently used in many families of chalcidoids. If you wish to incorporate these into classifications in UCD@TW, steps to follow are describe below. First, you must determine if the tribal or subtribal form of the name is in UCD@TW, treated as a synonym of the subfamily. See the entire scenario next.

One.

  • To determine if the tribal or subtribal form of the name is in UCD@TW and treated as a synonym of the subfamily, go to Browse Nomenclature, search for the name, for example, Coccophagini.
    • Be sure that you do not have the redirect to valid name box checked!
    • If you get a result showing the tribe (or subtribe) name in a black box to the right of the subfamily name (see below), the tribal form is in TW treated as a synonym of the subfamily.

In most cases, if the tribe or subtribe name has been used in the literature, it will show up as a synonym of the nominate subfamily. If it does not, you will need to create it, so skip to section Five below.

  • Navigate to the name with the tribal name at right (not to the valid form of the subfamily name, which may come up without the tribe name in the black box). It will be shown as an invalid synonym of the subfamily.
  • Click the green Edit icon to move to the Edit Taxon Name form.
  • Show all ranks in the Basic Information form and pick tribe.
  • Then change the suffix from -inae to -ini and pick the appropriate parent.

Two.

  • Scroll down to Status, Show All, and select Valid.
  • Provide the citation and page number using the Radial annotator to the right.

Three.

  • If you wish to provide a citation for this usage of the name, scroll down to Classification, choose Set to Parent (in this case it would be Coccophagini)
  • Choose Source Classified As.

Four.

  • One more (obsure) task remains. Using the Navigate Radial icon to the right of the tribal name at the top of the page, choose Show
  • Then choose Edit in the menu bar at the top of the next screen. This takes you to an older version of the Edit Taxon Name form.
  • If a name appears in the Verbatim Name field at the bottom of the screen (like Coccophaginae ), deleteit and click the greenUpdate Taxon Name` button. This removes an artifact created when tribal or subtribal names were imported as synonyms from TW@NHM.

Continue from this point only if the tribal or subtribal form of the name did not show up as synonym when you searched for it in step One above. Most likely, in this case it has not been used at this hierachical level before. If it does not show up, create it using the following process.

Five.

  • Navigate to the taxon name at the subfamily level, for example, Coccophaginae (via Browse Nomenclature) and move to the Edit Taxon Name screen.
  • Create the name at the tribal or subtribal level, for example, Coccophagini. The best way to do this is to Clone the subfamily level name (see green button in upper right), as this will retain the author and date, type genus, and other historical information. Select all the boxes to retain all historical information and type CLONE in the box. This will active the green Clone button. Note that you are creating a taxon name here, not an OTU, which is a separate issue.

Six.

  • Navigate to the tribal (or subtribal) name in Browse Nomenclature and move to the Edit Taxon Name screen.
  • Pick the rank (tribe) and change the ending to -ini.
  • Change the parent. In this case, the parent of Coccophagini would be Coccophaginae.

Seven.

  • Under Classification, set to parent (Coccophaginae) and choose Source Classified As.
  • Use the Radial annotator to the right to enter a citation for the publication and page number of the paper in which the tribe was recognized or moved.

Eight.

  • The problem with this approach is that all of the children of Coccophaginae will have been transferred to Coccophagini. If some of these genera belong to another tribe, you will need to create any such tribe, using the steps above, and transfer the genera, one by one.

Taxon classified as Incertae Sedis

  • First navigate to the appropriate taxon name
  • Click the green Edit Taxon Name button.
  • Change the parent to the higher level taxon in which the taxon has been classified as Incertae Sedis.
  • Navigate down to the Classification field
  • Click Set to Parent, and choose Incertae Sedis.
  • Then record the source and page number in which the classification was made using the Radial annotator to the right.

Species name endings changing due to movement to another genus, or correction by publication

For some name:

A - start (origin)
B - current -> current classification
change the parent here -> everything looks more or less right
C - second move
preserve "b"

A - Protonym
B - Combination
C - Parent (Combination)

From a practical standpoint, when a name changes, use New Combination task. Why?

  1. It lets you create the new combination just by typing in the string
  2. Having that combination, even if its just a B, pre-adapts you for C's. This gives you the historical record.
  3. In the New Combination task, after the combination has been created, there is an option to easily move the name to the correct parent

Considerations vs. line endings.

  1. In the New combination task you will find/pick the species in its original latin form
  • If that name has gendered data with it
    • and the new genus has gendered data with it
      • Then conjugation of the species name will automatically be rendered correctly in the new combination, and in reference to the new Parent (after you do 3) above)
    • To pre-adapt your steps above being easy, follow best practices and add the gendered information at the time of entry of a Protonym.

Never just change parent, always go the Combination route. (i.e. 2) above).

Example use case of name ending corrected by subsequent publication:

  • Species published with incorrect ending
    • Name is always the original form, latinized, never changed
  • Author "corrects" the ending in a subsequent publication
    • Key information: in this case there is no second Protonym, the gender ending correction happens automagically
    • Key trick: to add a citation with this "fixed" data you must create a new Combination, and cite it. You must compose the combination with the same protonym that was "misspelled"
  • Key bits of making new combinations
    • Think about making your new combination by finding
      • Protonyms in the original combination
    • Remember if you type in a gendered ending, and no suggestions are found, you can always click to search directly by the original combination, or to track down the protonym in the taxon name autocomplete.
    • For all of the above to work, the Gender and form section of the Edit Taxon Name form on the original protonym must be filled in.

Species synonymized with two or more other species

  • A name is published.
  • A type series is used (i.e. there is no holotype)
  • The type series is found to represent two different species.
  • The author says "we're stating this is two different species, and synonymizing the original name under two other names, but not selecting a holotype. If a future worker selects a holotype, our actions here may need to be changed again" (alternatively, author may synonymize the species in partim).
    • Recommendation: Do nothing (do not post the two synonymies in TW) but add a citation and note, there are no governed consequences to manage.
    • If you did have specimen catalog numbers then you could create 2 OTUs, each with the same species name, pre-adapting the data to receive new names for the new names if they come out.
    • Recommendation 2: Use a Nomen Dubium status and attach a citation to this.

Junior synonym conserved by ICZN decision (i.e. senior synonym suppressed)

  • Start at the Edit Taxon Name form for the suppressed name (senior synonym).
  • Under the Relationship section type in the conserved name (junior synonym).
  • And using the Show all button, select suppressed under.
  • Cite this.
  • If the two names had already been synonymized in TaxonWorks, you will next have to go to the Edit Taxon Name form for the junior synonym.
  • Under the Status section, use the Show all button to find official list of specific names in zoology and select valid.
  • NB: use the Advanced button if for some reason the Show all button is grayed out.
  • Cite this.

Entering names with incorrect endings for their taxonomic level

One method:

  • Create name using correct ending, Save.
  • Designate as Not Latin under status.
  • Change the name ending to the form wanted, Save.

Second method:

  • Create name. Using navigation radial, go to Show.
  • Click on Edit
  • Scroll down to bottom of form to Verbatim field and type in name as it was originally published.
  • Click Update Taxon Name

Third method:

  • Create the name. Click on Edit to get to Edit taxon name form.
  • Click onClone.
  • Select Add invalid relationship.
  • Type clone and then click the Clone button.
  • Edit the Relationship field and select Family Group Name Form.

What about fossil taxa in TaxonWorks?

  • If the taxon is a fossil, you need to select Fossil in the Status field of the New (Edit) Taxon name task. The name will now appear with a little cross symbol to the left.

There are special rules in ICZN and TW for fossil taxa. From Article 1 of the ICZN Code "1.2.1. The scientific names of extant or extinct animals include names based on domesticated animals, names based on fossils that are substitutions (replacements, impressions, moulds and casts) for the actual remains of animals, names based on the fossilized work of organisms (ichnotaxa), and names established for collective groups (see, in particular, Articles 10.3, 13.3.2, 23.7, 42.2.1, 66.1, 67.14), as well as names proposed before 1931 based on the work of extant animals."

Note well that for simplicity in TW, the flag fossil = extinct is set to true by default. If the taxon name is based on a fossil remnant or cast or animal evidence trace, the organismal group may not be extinct. In this case, unselect the flag.

Can you describe how the authorship label for a name is determined?

Authorship of a name can asserted in 4(!) different ways. That seems confusing at first, but determining what gets shown is pretty straightforwrd.

The authorship label is determined by the FIRST option in the following list that is true. All other values are referenced only in validation reports.

  • If the verbatim name field is filled out, then it is used.
  • If People are assigned as TaxonName authors, then their family names are used.
  • If People are assigned to a Source as authors, and that Source is the original source for the taxon name, then their family group names are used.
  • If the author field of a Source is filled out, then that field is used.

There are a lot of options for assigning the authorship of a TaxonName, which is the preferred way?

The preferred mechanism is to link the TaxonName to a Source, and assign authors (People) to that source (third option in the list above). This is the most granular way of creating the data, and therefor it will ultimately give you the most flexibility in reporting and validating the data.

Do you have any instructions on how to change combinations or enter new synonymies in TW?

Please follow the instruction in the Nomenclature Basics.

How do I find out where types are deposited, do you not yet have this function in TW?

Specimen deposition could be assigned to Specimen. If you create the type specimen for the Taxon Name, there is a field for the type repository. To create the type specimen follow one of the links provided in the Edit Taxon Name task, either Quick or Comprehensive in the Type section. Quick type specimen task allow to copy the entire verbatim-label information. The Comprehensive collection object allow to provide more detailed information about the specimen.

How do I get to the place in TW where I can add a new basionym? I need to try it out and see what happens.

For ICN names, the basionym have to be creaed as a separate protonym and linked to current name with basionym TaxonNameRelationship For ICZN names, the original combination of protonym is an equivalent of basionym in botany.

How would I remove a name from synonymy?

You can symply delete the Synonym Taxon Name Relationship. But when the name has been historically treated as a synonym, and subsequently was restored, the best practice would be to preserve both treatments in the database. Keep the synonym Taxon Name Relationship with its original citation in the database. Add the nomenclatural Status Valid to the name. This status will overwrite the Taxon Name relationship. Please remember to add the citation to the status, to know where and when the name was reinstated.

What is the word form for "arbitrary combination of letters"?

The word form is "noun in apposition"; etymology "arbitrary combination of letters"

How to record in the database a situation when a taxon, species or genus, is moved from one family to another?

Edit TaxonName task has a special section for this, Classification. Select the family-group name, and the relationship Classified as. This could be used for original placement of the taxon, or for the subsequent classification. Once the Taxon Name Relationship is created, assigne the citation using the radial annotator.

How to record a nomen nudum that was "subsequently validated"?

ICZN does not provide a procedure to "validate" a nomen nudum. Once unavailable, the taxon name keeps this status. The taxon could be described in a subsequent publication by the same or a different author(s), with the same or a different spelling. Both names in TaxonWorks should be regarded as separate protonyms. Nomen nudum should be marked with one or several of the appropriate nomenclatural statuses: nomen nudum or, preferrably, a more specific one, for example nomen nudum: no description. Once the valid name is described and the second protonym is entered to the TaxonWorks database, the nomen nudum could be linked to the available name (valid or invalid) with a TaxonName Relationship "unavailable or invalid".

How to enter the author for misspelled name?

The name which is not spelled correctly, the original source, where the misspelling was introduced, is still required. The role is not require, because the author string is always generated from the correctly spelled protonym. Protonym of misspelled name is linked to the correctly spelled name with the Misspelling TaxonNameRelationship.

How can I record the history of the taxon which had several historical Incertae sedis placements?

The incertae sedis relationship always correspond to the current placement of the taxon. For example, a species assigned to the family, instead of proper genus as a parent. Normally, this will be marked as an invalid placement, the incertae sedis relationship helps to override the error. For historical placements, a different relationship should be used: source classified as.

In the Edit TaxonName scroll down to the Original form section and enter the original spelling of the name. Alternatively, another protonym with the original spelling should be created in the database. Clone button could be used to replicate all information from the current family-group name. This new taxon name should be linked to the original name using special Taxon Name Relationship Incorrect original spelling or Family group name original form. TW could be restrictive in the ending of the original name before you assigne the relationship, so it is recommended to save the Taxon Name with the proper ending, add the ralationship and return back to modify the Name to the original form. And save Taxon Name again. Assigning the relationship removes the restriction on the family-group name form and ending.

What protonyms do I need to create for each form of the family-group name?

Individual protonyms should be created for original and each subsequent form of the family group name. Each protonym should be linked to the current form with the "Family-group name form" or "Family-group name original form" relationships

To which ranked Protonym do I attach the type genus?

The type genus shoild be attached to any available family-group protonym.

Do I have to re-attach the type genus to each family group protonym?

If there are several coordinate names with the same type genus (for example, a family with nomynopypical subfamily), the same type could be automatically assigned from one to another through the Soft Validation fixes.

Do I have to create nominotypical subgenus or subspecies manually?

When a new subgenus or subspecies created and the parent taxon does not contain any other sub- taxa, you can see the soft validation message like this: "The parent species of this subspecies does not contain nominotypical subspecies". TaxonWorks can detect and created the nominotypical subgenus and subspecies automatically when running Soft validation fixes, but now it could only be done programmatically. Before the fix is implemented to the interface, it is advisable to created the missing subgenus or subspecies manually.

To which rank should I attach the type species in cases where nominotypical genera exist, genus, or subgenus? What if I have done the opposite?

The type species should be attached to each available protonym. If the type species is attached to either genus or subgenus, it could be automatically re-assigned to the other through Soft Validation Fixes.

Does the attachment of the type species differ if the nominotypical subgenus came with, or after the original description of the genus?

According to the ICZN Art. 43, a name established for a taxon at either rank in the genu-group is deemed to have been simultaneously established by the same author for a nominal taxon at the other rank in the group; both nominal taxa have the same type species, whether it was fixed originally or subsequently. Changes in the rank also do not affect the type genus designation.

I have a species which was originally described in genus which obviously lies outside the scope of my group. How can I use this genus in the original combination?

The genus name have to be entered into the classification before the use. It may have to Root assigned as the parent, or, preferrably, the basic classification (class, order, family) could be provided as well.

Do I have to create a nominotypical subspecies?

See the description above for the nominotypical subgenus.

Which ranked name should I attach the type material to, species, or subspecies?

The type material could be attached to the coordinate taxon of any rank (species, subspecies, superspecies). The Soft Validation Fix will help to re-attache the same specimen to different ranks. Multiple specimens should not be created.

When creating protonym, what names should I put in Original combination fields?

When selecting Original genus for a species, sometimes two options are available: a valid genus name and coordinate subgenus with the same name("Aus" and "Aus (Aus)"). In cases like this the preference should always be given to the lower coordinate taxon name ("Aus (Aus)"). If the genus name is selected instead, you will get a soft validation waring "Original Combination: Relationship should move from genus to subgenus". This is not a critical error. TaxonWorks can detect and automatically move the relationship from a genus to coordinate subgenus. But at the present implementation, it could only be done programmatically.

How do delete a duplicate Taxon Name?

  • In the future, we expect an interface to to merge two records. But it is not available at the moment
  • A taxon name could only be deleted if it does not have any associated record. All of those have to be deleted or reassigned before a TaxonName could be deleted. Suggestion, select one of two duplicate which has lower number of associated data (citations, relationships, otus, etc.)
    • First, rename a TaxonName so you can isolate it from the name, which stays in the database. for example, if you have species name 'aus', change the name to 'ausdelete', so you can use the filter functionality to quickly navigate to the name.
    • Delete associated OTU. In the Browse Nomenclature, check if the name has an OTU, if present you can see it in the summany at the top right. If you follow the link, you will get to the OTU page. before deleting OTU. You can check if it has any data using OTU Radial, for example distribution, if it does, you can reassing the OTU to another TaxonName in the Edit mode, just select the other of two duplicates. If the OTU does not have related date, it could be safly deleted.
    • On the duplicate TaxonName page go to Edit mode. In this interface, look at any Statuses, Relationships, Original or Subsequent combinations, Gender or Part of Speech, Type species, etc. If anything is present, it should be deleted, all of those will prevent TaxonName from being deleted. Once everething is cleared, try to use Delete button. The duplicate name may get deleted.
    • If the TaxonName is still not deletable, it means that still there are some related records, which need some resolution. One of the common problem could be that a genus name, for example, is used as a Original genus or a genus name in a subsequent combination. To see if this is the case, use the Radial Navigator button and Related sector. It can redirect you to the interface which shows all TaxonName relationships (original and subsequent combinations, where this name is used). You can change all of them one by one, selecting the appropriate taxon, but there is also a helper task: Merge Taxon Names which could help to move all relationships from one TaxonName to another. Select from Taxon Name and To Taxon Name. and Proceed.
    • You can use the Radial Navigator button and Related sector to verify that everything is moved. You can try to delete TaxonName again.
    • If TaxonName could not be deleted, check what else is present in Related, see if there are still some relationship left in the list, which need to be resolved manually. Potential problem may also come from the Collection Object where the name is used for the type specimen, holotype, for example, if present, reassigne to another name, once the Relatead is cleare, the TaxonName could be safely delete.
    • The things which could be deleted together with a TaxonName (they do not block deletion): authors, citations, data attributes, notes, tags, depictions, and other attributes, those if present will be deleted automatically together with TaxonName.
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Contributors: Dmitry Dmitriev, Debbie Paul, Heidi Hopkins, jlpereira, Geoff Ower, hhopkins77, Deborah Paul, Dmitry Dmitriev, José Luis Pereira