===== Taxonomy =====

==== Taxon search ====

Choose **Taxonomy** in the main **Menu** to open the **List Species** window:

{{ https://docs.google.com/drawings/d/1lH34WA01pcvliRDLKMCut24hwWEWziumOQYhyvN4sYI/pub?w=203&h=211&.png?203x211 | nomenclature 1}}


{{ https://docs.google.com/drawings/d/1XRO5xFJI0XR9v4hjBVYaTK8ORjq0DXYfGa_mkZCrUg8/pub?w=960&h=720&.png?700x800 | nomenclature 2}}

The **List Species** window is used to search for taxa. You can search for a given **Family**, a **Genus** or **Species** by using the corresponding fields, whilst for other taxonomic levels (e. g. tribe, subspecies) the relevant category needs to be selected from the drop-down list under **Rank**. You can also limit the search results to accepted names, synonyms, illegitimate names and a variety of other taxonomic status with the drop-down list under **Status**.\\ \\ 
By combining search terms with wildcards, it is possible to generate taxon lists. For instance, to search for all species of Jurinea, type Jurinea in **Genus** and the wildcard % in **Species** or, alternatively, choose “everything” in **Status**. Note that by just leaving **Species** and **Status** blank, only the entry containing genus //Jurinea// will be returned in the search. To search for all accepted names by Boissier at the species level in the genus //Carduus//, type //Carduus// in **Genus**, the wildcard % in **Species**, select acc. in **Status**, species in **Rank** and type Boiss. in **Author**. 

{{ https://docs.google.com/drawings/d/1E0cpTuGJ1BXaWx1MbHOX8vtPDh6syb-MjSUsUgnCcUg/pub?w=960&h=720&.png?700x800 | nomenclature 3}}

Further combinations are possible. For instance, you can search for all //Carduus// species starting or ending in “s” by typing s% or %s, in **Species**.\\
> Note: Searches producing more than 1000 hits cannot be displayed.

----

==== Editing an existing taxon ====

By clicking a taxon in a search the **edit Species** window is accessed. Here the different attributes of the selected taxon (status, literature citation, synonyms, etc.) can be entered or modified. In the following section we will review the possibilities of **edit Species** using //Pinus abies// L. as an example.\\

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By clicking //Pinus abies// in the **list Species** search page, we access the **edit Species** window for that entry. \\ 

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After a brief look at the Plant List, we discover that //Pinus abies// L. is a synonym of //Picea abies// (L.) H. Karst., so some editing is needed. To enter the editing mode, press the **Edit** button at the bottom of the page. As a result, the **taxonID** field is displayed in light green. \\ 

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Click the drop-down list **tax. Status** and select **syn**. \\ 

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Input //Picea abies// (L.) H. Karst. in the field **accepted Taxon**. This field is auto-completing and typing “pic ab” automatically displays the option //Picea abies// (L.) H. Karst. on your screen. You just need to click it to fill in the box. If no suggestions are displayed, the taxon is not yet in the database and you will need to enter it (see next section). \\ 

{{ https://docs.google.com/drawings/d/1_7RHI_LO5RA1GafKb6GOfOb9xwgHpFhcqg01qyV7RSM/pub?w=960&h=720&.png?960x720 | nomenclature 8}}

Now you need to input the reference for the **accepted taxon**. Click **accepted Taxon** and the window **list Synonyms** will open. \\ 

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Click **add new Line** and the window **edit Synonymy** opens. \\ 

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Input the available information. In field **acc. taxon** type //Picea abies// and in **source**, select **service** and then the name of the online database where you checked, for instance **The Plant List (K and MO)** and the date in **Ref Date**. \\

> Note: The Plant List is a compilation of several data sets, such as [[http://www.ildis.org/|ILDIS]] (Leguminosae), [[http://apps.kew.org/wcsp/prepareChecklist.do?checklist=selected_families%40%40183020720131112020/|WCSP]] (World Checklist of Selected Plant Species), [[http://compositae.landcareresearch.co.nz/|TICA]] (Global Compositae Checklist) or [[http://www.tropicos.org//|TROPICOS]]. The source of any entered taxon is given in The Plant List. Usually such taxonomic data lists should be entered in the field **source (service)** but you should check if the status is still correct (e.g. search for a taxon of Leguminosae in ILDIS). In special cases, status information is given in The Plant List before the original data set is officially online (e.g. “WCSP (in review)”). As a result, you will not find such a taxon name in WSCP and this taxon should be linked to The Plant List in the field **source**. Additionally the short information “WCSP (in review)” can be copied in the field **annotations**. \\ 

Alternatively, you can use **person**, if the synonymy is unpublished and for instance provided by a reviser on a herbarium label. If a **literature** reference is available, then select literature and type the name of the author and also e.g. the year to reduce the provided list of references. If you cannot find your reference among them, you will need to input the reference (see the Literature section for further details). \\ 

{{ https://docs.google.com/drawings/d/1PG_M1O9qLQymgt70vx0phv8DJP11KBYO9urDU-P0z4M/pub?w=960&h=720&.png?960x720 | nomenclature 11}}

Once finished, click the button Update to save changes. \\
> Note: You can add multiple synonymys to show the revision history of the taxa, making sure the most recent one is selected in the **edit Species** window. \\

=== Adding a literature reference ===


Back in the **edit Species** page you can add literature references by clicking **edit Index** which opens the **list Index** window. \\

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Then click **add new Line** (for further details refer to [[documentation:input:literature|Literature]]). \\
> Note: In some cases it might be necessary to enter two literature references. \\ Example 1: A name is validly published on a herbarium label (see "schedae-publications" in [[documentation:input:literature|structure of literature]]) and later published in a journal; add both the label and the journal, as journals tend to be more widely accessible than the label. \\ Example 2: A name is published in 2 different publications and it is impossible to know which came first i.e. both were published the same year but the month is not specified. If the 2 articles are found in the same journal, assume that the one that comes first is published earlier. \\

=== Adding the type and protologue information ===

Back to the **edit Species** window, it is also possible to include types and protologues. Clicking **edit Type**, opens the window **list Type**. \\ 

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By clicking add **new Line** you open the **edit Type** window, which should be filled in with the information extracted from the original publication (protologue). The field **annotations** should contain the //indicatio locotypica//. Use quotation marks for the original text of the protologue. You can use square brackets to add relevant information (like [nom. nud.]; or to add the collector, collection date etc. if it is not mentioned in the protologue but elsewhere in the text) or to omit irrelevant parts (for instance morphological descriptions [...]). \\ 

{{ https://docs.google.com/drawings/d/1YYrzIH1SThpT7sPQmOvd7GnOyBxkp9x_PN-_zZt9GEE/pub?w=767&h=718&.png?767x718 | nomenclature 14}}

You can check the changes in the **edit Species** form, after clicking **Reload**. \\ 

{{ https://docs.google.com/drawings/d/10xRHJw1K3SWOUzKlXCwhOs-KXOIU8yLD3VkphgGKFNg/pub?w=960&h=720&.png?960x720 | nomenclature 15}}

=== Linking a register with its basionym ===

Combinations and new names should always be linked with their basionyms. In the preceding example, //Picea abies// (L.) H. Karst. needs to be linked to its basionym, //Pinus abies// L. To access the **edit Species** form of //Picea abies//, click the **Link** button under its name in accepted Taxon. You can access the **edit Species** form of any taxon by filling the desired name in the **accepted Taxon** or **Basionym** fields (making sure you are not in editing mode). This will display a drop-down list where you can select the targeted name. Then by clicking **enter** on your keyboard the **Link** button will appear below the field. Click on it and the desired **edit Species** window will open. \\ 

{{ https://docs.google.com/drawings/d/1oJC0xOyZiVhJEcLVlWtFqiAqC1ooccug_jL1Xz3Qnyo/pub?w=960&h=720&.png?960x720 | nomenclature 16}}

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Now enter the editing mode and type the basionym name //Pinus abies// L. in the field **basionym**. \\ 

=== Homotypic (nomenclatural) and heterotypic (taxonomic) synonyms ===

In order to check if the synonyms are correctly linked enter e. g. //Ranunculus ficaria// subsp. //bulbifer// (Marsden-J.) Lawalrée Willd. It is synonym of the accepted name //Ficaria verna// Huds. Now click on **list synonyms** and this window will open, where all the linked synonyms are listed below the accepted name: heterotypic synonyms – preceded by "=" – and homotypic ones – preceded by "≡". 

{{ https://docs.google.com/drawings/d/1E0xCkto1bsMOgcL8DDCGDeJfl4lkBG7XrgHivBWQIoU/pub?w=874&h=715&.png?874x715 | nomenclature 18}}

**__Recommendation:__** \\ \\ 

=== Adding annotation labels ===

If your specimen is the type for a later synonymized name, and the accepted name does not appear on the herbarium sheet, you will need to add an annotation label. Here you should include: (1) the information source (e.g. "fide TROPICOS" or "fide R. Govaerts & al. 2008. World checklist of Myrtaceae"); (2) the accepted name (e.g. ≡ //Picea abies// or = //Picea abies//, depending on whether the names are homotypic or heterotypic synonyms, respectively); and (3) the name and affiliation of the reviser, and the revision date (e. g. "annot. P. Escobar García (W) 2013-06"). \\
> Note: Only add an annotation label for information that is completely different to that given on the herbarium sheet such as: type status, basionym, accepted name, author(s). If there is only a slight divergence i.e. a missing "ex …" in the authorship there is no need for a new label).


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==== Entering new taxa from scratch ====


Before entering a new species, make sure the name is not yet in the database. Please note that there may already be homonyms with different authors in the database! \\ \\
We will use the name //Phonus rhiphaeus// (Font Quer & Pau) G. López as an example. \\
From the main **list Species** window click on **new entry**, to open a blank data entry form. Check to see if the name has already been entered by typing it in the fields **accepted Taxon** or **Basionym**. A drop-down list will appear showing the most similar names to your input, in alphabetical order. \\ 

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As you can see, //Phonus rhiphaeus// is not yet in the database. Start by typing //Phonus// in the field **Genus**, and selecting the appropriate name from the drop-down list. \\ 

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=== Adding a new epithet ===

Then type **rhiphaeus** in the **Species** field. As you can see from the drop-down list, the epithet //rhiphaeus// is not yet in the database. \\ 

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To enter a new epithet, click on the **Species** field and the window **edit Epithet** will open. Type the new epithet and click **Insert**. Now you can select your new epithet from the drop-down list in the **Species** field. Please be very careful with the spelling and always check new epithets in a standard work. Take care not to introduce blank spaces after the last letter if you copy and paste! \\ 

{{ https://docs.google.com/drawings/d/1fpG8vaHyCXG4fwLgsiDT28mwx10Ha69M1l9o-FodsXM/pub?w=960&h=720&.png?960x720 | nomenclature 22}}


=== Adding a new author ===

Start typing the author "Font Quer &..."; the desired combination (Font Quer & Pau) G. López does not appear in the drop-down list so you need to input the new author combination in the database. \\ 

{{ https://docs.google.com/drawings/d/1mgRCapHfYlM-eTlGx5aiL7juhwsh9UJ_Gy0_uUM3qj0/pub?w=960&h=720&.png?960x720 | nomenclature 23}}

To add a new authorship click on the field **Author** to open th **edit Author** window. Type the new authorship in **Author** and click **Insert**. Now you can select it from the drop-down list. Abbreviations of author names generally follow Brummit & Powell (1992), and are available at the online database ipni.org. Note that only the clickable, underlined author names follow the standardized form. You can include them in our database after adding blank spaces after the initials (e. g. „B.Bremer“ should become „B. Bremer“). Before entering a new complex authorship check separately for the correct standard form of each author’s name. The field **Author** can be filled either with a complex authorship or a single author’s name. In the latter case, you have to fill the **Brummit** field with the complete name and further relevant information such as dates of birth and death. \\ 

{{ https://docs.google.com/drawings/d/1HPHpaWx4JNPdtgC9QjT-5hQCS0UR8thMtpIzRSy-E9U/pub?w=960&h=720&.png?960x720 | nomenclature 24}}

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Finish by adding other information, such as the **Basionym**, **accepted Taxon**, etc. Link the names to their basionyms as explained[[documentation:input:taxonomy:#Linking a register with its basionym | here]].

{{ https://docs.google.com/drawings/d/1UoDtHCMWwYWCp8Wi86Ij2IW5FFM6-iPEAKQGsbIjH5k/pub?w=960&h=720&.png?960x720 | nomenclature 26}}

If your specimen does not include the accepted name on the herbarium sheet, you will need to add it on a label. (see [[documentation:input:taxonomy:#Adding annotations in new herbarium tags|Taxonomy - Adding Annotations]]). \\ 

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==== New entries by copying and editing an existing one ====

New entries can also be added by copying an existing one and then editing it. This option is useful when entering homonyms or infraspecific taxa that share some fields with entries already present in the database. In the following example we will input the name //Eurybia rudis// Benth. var. //arguta// Benth. using the existing entry //Eurybia rudis// Benth. as a template. \\ 

First, enter the //Pinus abies// L. **edit Species** form by searching in **list Species** or as already explained in the previous section. \\ 

{{ https://docs.google.com/drawings/d/1H5psrRWfh5X8ZSwYXm6i_ruIAR6FrxRcFP7O8g_8KzM/pub?w=904&h=714&.png?904x714 | nomenclature 27}}

Then click **New & Copy** at the bottom of the **edit Species** form. Edit the required fields, in our case **Author** and **accepted Taxon**. \\ 

{{ https://docs.google.com/drawings/d/1aDjGC_E9JlrJeK3kq2xt3m-LvI4badIW5TqEq82JcUk/pub?w=960&h=720&.png?960x720 | nomenclature 28}}

Click **Insert**. \\

> Note: New epithets and author’s names can only be added in blank fields, as existing ones cannot be overwritten. If you need to add a new epithet or author’s name, you can do it using any empty field of the infraspecific ranks. \\ 

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==== Entering infraspecific taxa ====

Follow the previous steps and continue adding the relevant information in the suitable fields (Subspecies, Variety etc.). \\ 

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==== Entering genera ====

Start by selecting **Taxonomy** in the main menu and then clicking **new entry** in the **list Species** form. \\ 

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This opens a new **edit Species** form. \\ 

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Make sure that the genus is not yet entered in the database, paying special attention to the existence of possible orthographic variants. Write the new genus (e. g. //Razafimandimbisonia//) in the **Genus** field and a drop-down list will display the genera already present in the database with their corresponding authors, families and identity numbers. Please note the possible existence of homonymous genera in the database. Always ay attention the author and family! \\ 

In our example //Razafimandimbisonia// is not yet entered in the database. \\ 

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Open the **edit Genera** window by clicking **Genus** in the new **edit Species** window. \\ 

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Start by entering //Razafimandimbisonia// in the **Genus** field (there is no drop-down list here), then the author in the **Author** field. Choose family using the **Family** field. Check always for the genus name in Index Nominum Genericorum [[http://botany.si.edu/ing/|ING]]. If the genus you want to enter is not there this should be noted in the **Remarks** field. Add a type species if known.

Click **Insert** when you are ready, making sure that everything is correct as the fields will no longer be editable after. The **edit Genera** window will close. \\ 

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Now back in the **edit Species** form enter the author(s) in the **Author** field and choose genus in Rank. Then press the **Insert** button. \\ 

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==== Entering hybrids ====

There are two possibilities for entering hybrids. \\

=== Entering hybrid formulas (e.g. Potamogeton berchtoldii x obtusifolius) ===

Open a new **edit Species** form, enter the genus name (for example //Potamogeton//) and choose **Genus** in the **Rank** field. Then choose **x** in the **tax. Status** field. Then click **Insert**. This makes the field **tax. Status** change into **parents**. By clicking on the **parents** button, you can enter the parental species. Save changes by clicking **Insert** when finished. The hybrid formula will appear on top line of the **edit Species** page, besides the taxonID and change the **Rank** field to **species**. \\ 

{{ https://docs.google.com/drawings/d/1mKnebC_PfsEVNxTf_YjH_ksUzJF9GBp0ZxBWXNywt6Y/pub?w=856&h=675&.png?856x675 | nomenclature 35 "Because **** you thats why":oP }} 

Hybrid formulas appear only as a genus name in the drop-down lists of the **accepted Taxon** or **Basionym** fields (each with its own ID number). To search for hybrid formulas go to the **list Species** form, input the relevant genus name and select **x** in **Status**. \\ 

{{ https://docs.google.com/drawings/d/1YbKkbBMiB5JHEIhF9I7l7TZ2zNks7uNrS1KZ-6oPn2A/pub?w=959&h=607&.png?959x607 | nomenclature 36}}


=== Entering hybrid taxa ===

Enter the epithet in the corresponding rank (Species, Subspecies, Variety etc.) and proceed as explained above. \\ 

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==== Typification ====

Information regarding types and typification should be entered in the database at two levels: **Specimens** and **Taxonomy**. In the **edit Specimens** form the **T** field allows you to choose the kind of type from a drop-down list (holo-, isolecto-, syn-, etc.). The field **typified by** should be filled in with the information available on the researcher who typified the voucher. Enter the researcher´s name, their herbarium or institutional acronym in brackets [e.g. (M) for Munich] and the date of the typification [e.g. S. Zarre (M) 1994]. \\ 

{{ https://docs.google.com/drawings/d/1tnFDzmYLqAJg4Jb0A27ijqYl6AusdJc9_uP8qqQg1s8/pub?w=735&h=719&.png?735x719 | nomenclature 37}}

Clicking on **T** opens the **list Specimens Types** window. Here, you should enter the names a given specimen is the type for. Click **add new line** to start inputting information and a second window **edit Specimens Types** will open. Enter the basionym in **taxon** (here only basionyms are correct), the kind of type in **type**, the reviser with institution acronym in **typified by** and date if available in **date**. Any further information can be added in **annotations** [e. g. information about lectotypification (please add the reference), divergent opinions about the typifications, etc.]. Click **Insert** to save and close the **list Specimens Types** window. \\ 

{{ https://docs.google.com/drawings/d/1SVs82k9rwEwiW2fIcN-xEvQHXBvXWGNwMzL347x2HbM/pub?w=959&h=561&.png?959x561 | nomenclature 38}}

Note that a given specimen can be the type of more than one name, or that different revisers may hold conflicting or complementary opinions. In this case, use **add new line** to enter further typifications as explained before. If a certain species is type for a genus, you need to add this information to the type specimen. \\ 

{{ https://docs.google.com/drawings/d/1lZP26cha3mMqhQTxD4aPrsz6lgku7VGIFZX6tmaBKH4/pub?w=955&h=317&.png?955x317 | nomenclature 39}}

Above the **Genus** field there is the **type specimens** button, which allows you to check the typification entries for the relevant taxon. This opens the **list Specimens** window, which displays the typified name (basionym) on the top with all the entered specimens listed under their accepted names. The **specimens** button takes you to the main **list Specimens** window where you will see all the specimens entered under the name, including those that are not types for that name. The number in brackets next to each button indicates the number of entries in each case.\\ 

{{ https://docs.google.com/drawings/d/1vanQeZs59TeF2ufNqWKPNm6t5J2A-DpAdDR1pghoBXs/pub?w=960&h=720&.png?960x720 | nomenclature 40}}

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==== Useful taxonomic and bibliographic links ====

=== Taxonomy === 

  * [[http://www.anbg.gov.au/cgi-bin/apni|APNI]]: The Australian Plant Name Index of Australian Plant Census (CHAH).
  * [[http://ww2.bgbm.org/EuroPlusMed/query.asp|Euro+Med]]: Taxonomic and floristic information from the Flora Europaea and Med-Checklist areas.
  * [[http://http://www.ildis.org/|ILDIS]]: The International Legume Database & Information Service.
  * [[http://botany.si.edu/ing/|ING]]: The Index Nominum Genericorum, a compilation of generic names published for organisms.
  * [[http://www.ipni.org/ipni/plantnamesearchpage.do|IPNI]]: The International Plant Names Index, a database of names and associated basic bibliographical details.
  * [[http://www.theplantlist.org/|The Plant List]]: Kew’s working list of all known vascular plants.
  * [[http://http://compositae.landcareresearch.co.nz/|TICA]]: The Global Compositae Checklist.
  * [[http://www.tropicos.org/|TROPICOS]]: Missouri Botanical Garden’s database of nomenclature, bibliography and specimens.
  * [[http://apps.kew.org/wcsp/home.do|WCSP]]: The World Checklist of Selected Plant Families.

=== Literature online ===

  * [[http://www.biodiversitylibrary.org/|BHL]]: The Biodiversity Heritage Library.
  * [[http://bibdigital.rjb.csic.es/ing/index.php|Biblioteca digital]]: The digital library of the Madrid Botanical Garden.
  * [[http://gallica.bnf.fr/?lang=DE|GALLICA]]: The digital library of the Bibliothèque Nationale de France.
  * [[http://archive.org/details/texts|Internet Archive]]: A non-profit organisation providing a vast permanant digital library.
  * [[http://www.digitale-sammlungen.de/|MDZ]]: The digital library of the Bavarian State Library.

=== Further useful links ===

  * [[https://docs.google.com/document/d/1TA-RqL0BEIw6unIVRFbyCx9_CHBc4wy5NGX1HFQCPEo/edit?usp=sharing|Summary of important nomenclatural dates]]. 
  * [[https://docs.google.com/document/d/1TA-RqL0BEIw6unIVRFbyCx9_CHBc4wy5NGX1HFQCPEo/edit?pli=1|Glossary of important nomenclatural terms]].
  * [[http://www.iapt-taxon.org/nomen/main.php| The Melbourne Code]]: The International Code of Nomenclature for algae, fungi, and plants. 
  * [[http://www.iapt-taxon.org/icbn/main.htm| The Appendix III (NOMINA GENERICA CONSERVANDA ET REJICIENDA) of Vienna Code]].

Pedro's diagram (Google docs) [[https://docs.google.com/drawings/d/1e3ps2m_nZvAe0oa9B_q1ydXrm60WyNJnasCQm7XwnX4/edit?usp=sharing|type categories]]. \\ 

Karen´s diagram (Google docs)[[https://docs.google.com/drawings/d/1oWqASw_DmBt3zcUisGl2gPVRhErh1l_WzAeJ4_nkH1s/edit?usp=sharing|specimen typification]]. \\ 

Name categories diagram (Google docs) [[https://docs.google.com/drawings/d/10VtnxORj0ALVmSeHMnXPsJYS2abbSCPf2i8a4vkesRQ/edit?usp=sharing|Name categories diagram]]. \\ 

Captures of name categories diagram (Google docs) [[https://docs.google.com/document/d/1lvuavOx3jp_3oux9wQeKNtHFAPxAuaYejUD3kfCHfxg/edit?usp=sharing|Captures of name categories diagram]]. \\ \\ 


=== Important modifications ===

__**Case 1**__ \\ 

Dealing with a lectotypified taxon consisting of several syntypes which are recently linked to different accepted taxa, you may have problems to print labels for the syntypes. The accepted taxon on the printed labels will always be that of the lectotypified specimen independent of the syntypes. \\ 
In such a case you have to temporarily change the accepted taxon on the **edit species** page in **accepted taxon** to the name which you need to appear on the label. After saving your changes, you can print the labels.
Remember to change the accepted taxon back to that of the lectotypified syntype.
### mit Beispiel und vermutlich auch screenshots ######


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