Taxon Editor

In this module you can browse, add or edit the taxa in your project. For fresh projects it is advised to first enter the taxonomic ranks that you want to include. You find this option at the bottom of this page.

All taxa included in the project will be listed as an automatically generated interactive tree. You can find an existing taxon name by typing in the text box on top of this page or use the tree. The names in blue have underlying taxa, click the name to unfold them. Clicking the arrow at the right of a name opens the taxon page where you can edit.

Before applying for your own site you can experiment with all the available functions of this module in the LNG Sandboxes: http://linnaeus.naturalis.nl/wiki/Sandboxes

New taxon concept

On this page you can add a new taxon (lower or higher taxa). Enter a rank, parent, name and other relevant information.
When adding an underlying taxon to an existing taxon (e.g. a subspecies) the parent is already defined. After finishing click "save".

When you get the warning “Combination of name, rank and parent already exists (deleted taxon). Concept not saved.” you can click “Show taxon”. It can be the taxon is present in the database as a ‘deleted taxon’. You cannot overwrite this taxon but you can undo the deletion and then edit it afterwards.

Edit taxon concept

From this page you can edit or delete a taxon. Click "edit" next to the term you want to edit. At the bottom of the page you see a list of other options and sections of the taxon concept. Click on the name of the section you want to examine or edit.

To delete a taxon concept click “mark taxon as deleted”. This deletes the concept card from the project; it will no longer be part of the taxonomic tree or visible in the view mode (front end).
But this doesn’t remove the concept entirely from the database. It will still be visible in the back-end in the list of deleted taxon concepts. To go to this list click “taxon concepts marked as deleted” under “tasks” at the Taxon editor starting page. By clicking a name in the list you go to the editing page of the deleted taxon. From here you can undo the deletion by clicking “undo deletion” below “CONCEPT IS MARKED AS DELETED”.

Edit scientific name

On this page you can edit or delete the scientific names of a taxon concept (e.g. valid name, synonym etc). You can change or specify the concept type and rank. Click “save” before leaving this page.
To delete a name click “delete”. Deleting a valid name doesn’t mean the taxon concept is removed from your project or the taxonomic tree. To do so go back to “Edit taxon concept” and click “mark taxon as deleted”.

Add scientific name
You can add a scientific name for a taxon concept (e.g. a synonym, basionym, homonym). You can specify the concept type and rank.

Edit common name

On this page you can edit or delete a common name of a taxon concept. You can specify the language for the common name and the type (alternative or preferred name). The preferred name in the default language of the project will appear in front of the concept name in the taxonomic tree.

Add common name
On this page you can add a common name. When you add a new common name you have to specify the language for the new name. You also can specify the type (alternative or preferred name). The preferred name in the default language of the project will appear in front of the concept name in the taxonomic tree.

Edit taxon passport

On this page you can edit different sections (tabs) of the description page of a taxon by clicking on the name of the section you want to edit. First click the name of the section you want to edit, e.g. Description, to open it. Then click "edit" at the bottom of the text to open the editor. Clicking on the arrow opens the specific section (tab) in the view-mode.

You also see the following sections listed:
< Key links >
< Literature >
< Media >
< Presence status >

These sections you cannot edit from here. In the view mode these sections will be presented as a tab once they contain data.
< Key links > are added in the Single acces key module. These are link(s) to specific steps in the single acces key, used to jump to the startpoint in the key for the identification of members of a specific (higher) taxon group, like family or genus
< Literature > references are added in the literature section of the Taxon editor module or in the Literature module
< Media > media is added in the media section of the Taxon editor module
< Presence status > is NSR only.

Internal links
You can add links to other sections of your project. To do so, copy the link adres where you want to link to.
For media first go to the Media module. Click “browse media for this project” and choose list-view. Copy the url adres of the media item you want to link.
Then type and select the word(s) you want to be clickable (become the actual link) and click the chain-symbol in the upper centre of the editing-box. Paste the URL you want to link to.
After pasting the URL go to the second tab (Target) and choose a target from the pop-up:
Frame – media opens in new tab
Popup window – media opens in pop-up window. You can choose the size of the pop-up by filling in “Width” and “Height”
New window– media opens in new tab
Topmost window– media opens in same tab
Same window– media opens in same tab
Parent window– media opens in same tab

Click "ok" to save the link.

Edit taxon passport meta-data

On this page you can link an author, organisation or publication to a taxon. Clicking "add author" or "add organisation" opens a list from which you choose the name that you want to add. Clicking "add reference" opens a search window. Enter text to find the relevant publication and select the publication found. This adds the publication to the taxon passport.

Taxon images

Only available in NSR project

Media

You can link media to a taxon concept. Click "upload media" to upload new media, click "attach media" to attach media already present in the project.

After uploading/attaching media to your taxon concept, additional options appear. In the caption text-field you can enter information (text) for the media file (e.g. female, juvenile, enlarged, etc.). In the view mode of the species-section this text will be visible below the media file.
The order in which the media is shown here will be the order in which it will appear in the view mode. To change the order click the ↑ and ↓ arrows.
When you check "is overview image" the related image will appear in the view mode on the upper right hand corner of the description page of the taxon. It will be scaled to 241 (width) x 281 (hight) pixels. When you choose an image with different dimensions it will be scaled, any remaining space will be filled with grey. After finishing click "save" to save your edits.

To detach a media-item from a taxon concept click "detach".

Media meta-data

The overall metadata are the metadata directly related to the media, unrelated to the modules it is connected to (e.g. title, location, photographer and tags).
To replace the media file or to edit the overall metadata of a media file click "edit" on the right-hand side of ‘Metadata’. This will open the Media module where you can edit the overall metadata of the media file.

On this page you also see the option 'replace with'. Be aware that replacing a media file here means the media file is replaced with the new one everywhere in the project where it is linked. When you want to replace a media file only in specific modules then go to this module and detach the media file there. After detaching you can then upload and link a new media file for the specific module.

Media meta-data bulk

Only available for NSR project!
Enter raw meta-data (TAB separated, like copy/pasted excel cells) in the area below.
Columns containing the file name and the NSR ID are mandatory, as is at least one column with meta-data. Images should be specified with their file name only, not full paths. The system will assume that they reside at http://images.naturalis.nl/original/; if they do not (yet) exist there, a warning is generated, but the data is saved nonetheless. Dates in meta-data should be in the format DD-MM-YYYY.

Taxon literature

On this page you can link a literature reference to a taxon. Click "add reference" and type text in the pop-up to find the reference you want to link. Clicking the name of the reference will link it directly. To unlink a reference click the x behind its name. This will unlink the reference without further warning. Click "save" before leaving the page.

Rename taxon concept directly

On this page the taxon concept can be renamed directly, without checks. Use this only in exceptional cases in which there is a discrepancy between the concept name and the valid name. For instance if in imported data the concept name is different from the valid name. In these cases there is the option "Rename taxon concept directly" renaming without all the automatic effects involved in changing the valid name.

Adjusting the name of the taxon concept doesn't affect the name in the taxonomic tree or classification. It only affects the name of the concept and species card in the view-mode.

The proper/standard way to adjust the name of a concept is by changing the valid name that involves all the automatic effects as renaming and valid name to synonym-actions. Please note: underlying precondition is that concept name = valid name

add traits:

When there are trait groups defined in your project this option will appear on the bottom of each taxon concept card. (You can add a new trait group in the Trait module.) Clicking a trait group listed under "add traits" brings you to the taxon trait date page in the Trait module. Clicking "save" links the trait group to the taxon concept.

Taxa marked as deleted

This page shows a log list with all the removed taxon concepts. These taxa concepts are no longer part of the project: they are not part of the taxonomic tree or visible in the view mode (front end).
But they are not entirely removed from the database. By clicking a name in the list you go to the editing page of the deleted taxon. From here you can undo the deletion by clicking “undo deletion” below “CONCEPT IS MARKED AS DELETED”.

Update index table

On this page you can update an index table. This functionality updates the extra index table which holds the parent-child relations of the taxon concepts. Basically the table is updated automatically but in case that, for instance, the count of underlying taxa in the taxonomic tree doesn't match with the actual count, then you should update this by hand. Take in account that updating can take about a minute.

Orphaned taxa

This page shows an automatic generated list of the taxa that have no parent in your project.

Taxon file upload


Taxon passport content upload


Define categories

Each taxon page consists of one or more categories. In the view mode, these categories are presented as tabs in the taxon page. Some of these categories - printed in red - are created automatically, others are defined by the Lead Expert (with a limit of 50 categories). The category overview contains the following columns:
Grip-icon which you can use to drag and drop categories to a different position. The positions determine the order in which the tabs are presented in the view mode. Be sure to click "save" after changing the order of categories.
The system name. If there is no translation available, this is the name that is presented in the view mode.
Translation(s). The category name in your project language(s). If empty, the system name will be displayed in the view mode.
Show when empty. When set to "no", the tab is hidden if no data is available for that tab for the taxon you are looking at in view mode.
Start order. This determines the order in which the system looks for the first non-empty tab to open, the first time in a session a user accesses a taxon page.
Delete / suppress. Link to delete a regular category, or suppress an automatic category (automatic categories cannot be deleted).
Attributes. Special attributes, like external references or hidden tabs. These can only be edited by the system administrator.

If you have made changes, make sure to click "save" before leaving the page.

To add a new category enter the name in the text-field behind 'Add a new category:' at the bottom of the page. Click "add" to save the new category.

Category

On this page you can edit attributes of a category. This functionality is for system administrators only!

Taxonomic ranks

On this page you can define which taxonomic ranks can be used in the project. Currently selected ranks are shown on the right. To remove a rank from the selection, double click its name. The uppermost rank, regio, is mandatory and cannot be deleted.
On the left you see all the possible ranks you can add. Click the rank to add the rank to the selection.

By clicking “Select all the ranks used in Catalogue Of Life, marked in blue in the list below” all these ranks will be added to the project. This option is only available if there are no ranks specified yet.

In addition, you can specify where the distinction between the modules "higher taxa" and "species" will be. You can move the line by clicking the ↑ and ↓ arrows. The setting is saved when you click "save selected ranks".
Be advised that this division is different from the one that defines which taxa can be the end-point of your keys. That division is defined in the Single-access key and Multi-entry key modules.

Click "save selected ranks" to save your edits.

Once you have saved the selection, you can specify the correct label of each rank in the language or languages defined in your project. To do so click “change the ranks' names and provide translations”.

Taxonomic ranks: labels

On this page you can specify the correct label of each rank in the language or languages defined in your project.
On the left hand side, the labels in the default language are displayed; on the right hand side, the labels in the other languages. These are shown one language at a time; you can switch between languages by clicking its name at the top of the column. The current active language is shown underlined.
Names you enter are automatically saved when you leave the input field.

Define sections



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