Revision [432]

This is an old revision of TaxonEditor made by LngWikiAdmin on 2016-06-30 09:53:32.

Taxon Editor

This is the starting page from which you can add a name for a taxon (species or higher taxa) by clicking "new taxon concept". For fresh projects it is advised to first enter the Taxonomic ranks that you want to include in the project. New names need to be linked to a parent taxon. All taxa will be listed as an interactive tree. To edit an existing taxon name you can "Type to find" or use the tree. Clicking the name unfolds underlying taxa, clicking the arrow opens the taxon page where you can edit.

Index

This page shows an automatically generated list of taxa included in this project under Taxonomic tree: all species and other taxa described in the taxon editor. The blue names have underlying taxa, click the name to unfold them. To jump to the page of a taxon click on the arrow behind its name.

New taxon concept

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

Edit taxon concept

This is the starting page to edit or delete a taxon. Click "edit" next to the field you want to edit. At the bottom of the page you see a list of other 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 name of a taxon concept. You can specify the concept type and rank and add a literature reference.

New scientific name
You can add a scientific name for a taxon concept. e.g. a synonym, basionym, homonym etc. You can specify the concept type and rank and add a literature reference.

Edit common name

On this page you can edit a common name of a taxon concept.

New common name
When you add a new common name you have to specify the language for the new name.

Rename taxon concept directly

On this page the taxon concept can be renamed directly, without checks. Perform this only in exceptional cases in which there is a discrepancy between the concept name and the valid name. Like when in imported data the concept name is different then the valid name. For this cases there is this option "Rename taxon concept directly" 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/usual way to adjust the name of a concept is through the valid name with all the automatic effects like renaming and valid name to synonym-actions. But: underlying precondition is that concept name = valid name

Edit common name directly

Taxon images

Only available in NSR project

Edit taxon passport

On this page you can edit the different sections of the description page of a taxon by clicking on the name of the section you want to edit. Clicking on the arrow opens the specific section in the view-mode.

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.

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-item (for example: female, juvenile, enlarged, etc.). In the view mode of the species-section this text will be visible below the media-item.
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 the check-box "is overview image" the related image will appear in the view mode on the right hand side 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, the 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".

For replacing or editing the overall metadata of a media-item click "edit" on the right-hand side of the word ‘Metadata’. This will open the section where you can edit the overall metadata of the media-item:

Media meta-data

The overall metadata are the metadata directly related to the media, independent of the modules it is related to (like title, location, photographer and tags).

Media meta-data bulk

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.

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.

Taxonomic ranks

On this page you can define which taxonomic ranks can be used in the project. Click the arrow next to a rank to add that rank to the selection used in this project. Currently selected ranks are shown on the right. To remove a rank from the selection, double click it in the list on the right. The uppermost rank, regio, is mandatory and cannot be deleted.

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. After you have made the appropriate selection, click the save-button. 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”.

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.

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.
Text you enter is automatically saved when you leave the input field.

Define sections

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.

Activity log

This page shows a log of all the edits.

External ID resolver

On this page you can paste a list of ID's. To do so paste the list - one on each line - in the section. Click "search" (only for taxa!). Hundred or less codes are displayed in the screen directly and are downloadable as txt-file by clicking on "download results as text-file". Batches of more then 100 codes are only downloadable and thus are not displayed.
This functionality only works from code to name, not the other way around.

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Linnaeus NG Wiki : TaxonEditor