Revision [673]

This is an old revision of TaxonEditor made by LngWikiAdmin on 2016-09-01 14:33:06.

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".

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 .

Edit scientific name

On this page you can edit the scientific names of a taxon concept (e.g. valid name, synonym etc). You can specify the concept type and rank.

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 a common name of a taxon concept.

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.

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, type and select the word(s) you want to be clickable (become the actual link). Then click the chain-symbol in the upper centre of the editing-box. Paste the URL you want to link to. Go to the second tab (Target) and choose a target from the pop-up. Click "ok" to save the link.
To link media in the text 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.

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 taxon 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.

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 taxon 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, with a maximum of 50. The categories, 'Classification', 'Names' and 'Media' are mandatory. In the view mode, these categories are presented as tabs in the taxon page. Below, you can specify the correct label of each category 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 are displayed.
You can drag and drop the different categories to put them in the right position. The order in which the categories are presented here are the order in which the tabs are presented on the taxon page in the view mode. You can specify if you want empty categories to be presented in the view mode, by checking "y" (yes) or "n" (no).
With 'start order' you can specify the tab in which the species section opens in the view mode. When this tab (no 1) is empty and you checked "n" for 'show when empty' the tab with start order no 2 will be the opening tab, etc.

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.

Click "save" before leaving the page.

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, Kingdom, 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.

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 distinction is defined in the "dichotomous key" module. However, that distinction must be on the same level as the one you define here, or below it. It can never be higher up in the rank hierarchy.

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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Linnaeus NG Wiki : TaxonEditor