Xper2 – Use FAQ

General presentation of Xper2

What does the Xper2 interface look like?

What do the Xper2 menus look like?

Four principal choices are available in Xper2  toolbar

« File »

« Open a base »: Open an existing KB

« New base »: Create a new KB

« Import -> XPER Original Format »:import a KB in XPER format

« Export -> XPER Original Format »: export a KB in XPER format

« Save »:  Save a KB

« Save as… »: Save a KB with another name

« Close the base »: Close the current KB

« Quit »: Close the current KB and quit Xper2

« Edit »

« Edit by descriptors » : Display the edition module of the descriptive system

« Edit by item » : Display the edition module of the KB

« Identification » : Display the CAI module

« Tools »

« Control the base -> Control everything » : check the integrity of the data

« Properties » : Display the properties of the KB

« Help »

« About… » : Display the About… window with the version of the program and the address of the LIS

N.B., At start, only the menus « File » and « Help » are accessible. The « Edit » menu is available in the complete version of Xper2.

How to create a new Knowledge Base (KB)?

In order to create a new KB, click on  « New base » in the menu « File ». A window will invite you to enter the name of the KB. Once entered, the Edition by descriptors module will automatically be opened. (cf. Edition of descriptors)

N.B. You can only create new KBs on the complete version of  Xper2!

How to open an existing KB?

Click on « Open an existing base » in the menu menu « File ». You will be invited to browse your hard disk in order to select the KB in a «xpd» format.

Is it possible to open several KB at the same time?

No, it is not. Xper2 can only work if a single instance of a KB. This means that you cannot open or create a KB if tjere is one already open.

How to save a KB?

If it is a new one, « Save » and « Save as » does the same. You will be invited to browse your hard disk and choose a file name. The extension (xpd) is automatically created. If you base exists already, « Save » will save your base on the same file. « Save as » will allow you to save your base under another file name.

Note, If you close your base or the software by mistake, a textbox will invite you to save your base.

Which files are created when saving a KB?

When a KB is saved in Xper2 format, 4 files are created:

• « xpd » : the descriptive system + the list of individuals (format xml)
• « xpg » : the groups of variables (text format) – deprecated
• « xpr » : relationships among variables (text format)
• « xpw » : weight (texte format) – not used for the moment
• « xpx » : item x descriptors matrix (text format)

The folder « images » is created if it does not already exist. It is used to stock the images illustrating your KB.

N.B. when you create a KB, save it before adding imagesin order to have the « images » folder created. Otherwise, you may find some problems concerning image management.

What files are created when exporting to XPER format?

Exporting to XPER format will create 8 files:

• « xpi » : the list of the names of individuals (text format)
• « xpg » : the groups of variables (text format)
• « xpm » : the list of states (text format)
• « xpp » : the KB parameters (text format)
• « xpr » : the relationships among variables (text format)
• « xpv » : the list of variables (text format)
• « xpw » : weighting scheme (text format)
• « xpx » : the individuals x variables matrix (text format)

Is it possible to import a base written in a different format?

XPER² can import KBs written in the old XPER format, in CSV (example here) and in SDD.

Is it possible to export my knowledge base in different format?

XPER² can export KBs written in the XPER format,in CSV, SDD, HTML and NEXUS format.

How to share KBs?

Given the fact that a KB is made up of several files (cf. Which files are created when saving a KB?) and a set of images, it is advised to put all the files together into a zip file in order to abtain a single file. This solution allows you to easily email your KB while keeping a total file compatibility.

Which are the properties of a KB?

in order to access the informations of a KB, click on « Properties » of the menu « Tools ».
N.B. Dates are written after the first saving of the KB.

How to rename a KB?

Open « Properties » window (cf. Which are the properties of a KB?), and edit the field « Name ». Save your changes clicking « Submit ».

N.B. the properties file is updated when the  KB is saved frome the menu « File ».

How to edit the description of a KB?

Open the « Properties » window (cf. Which are the properties of a KB?), and edit the « Knowledge base description » field. Save your changes clicking « Submit ».

N.B. the properties file is updated when the  KB is saved frome the menu « File ».

How to edit the names of the author of a KB?

Open the « Properties » window (cf. Which are the properties of a KB?), and edit the « Knowledge base description » field.
In order to add an author, click on  N.B. the properties file is updated when the  KB is saéved frome the menu « File ».

What is the terminology used in Xper2?

Xper2 uses the usual terms applied in life sciences. Obviously, this jargon is not suited for all the possibles applications of Xper2. Note that the terminology used by XPER has been updated in Xper2. Please refer to the following correpondence table:

How to know the version of Xper2?

OPen the « About… » window from the « Help » menu. On the title bar of the window you can see the name of the module (Xper2, Xper2-itemEdition, Xper2-Identification) and its version (e.g. 1.3)

How to check the integrity of the data of a KB?

On the « Tools » menu, select « Check base ».

How are checked the data?

There are three levels of control that allow you to know if your descriptive system is correctly defined (no unused descriptors, always used,…) and if your data is correctly entered (no doubles,…):

1-  descriptor control: it checks if descriptors are correctly described, i.e. there is not a misuse of child descriptor
How does the image manager work?

Note : It is possible to have two images with the same name. The solution is to rename them before their integration in the KB.

How to open the image manager ?

To open the image manager, click on the button

How to add an image ?

To open an image, select the object in the list, then open the image manager (cf. How to open the image manager?). Click on the button Note : It is possible that the image does not appear automatically in the visualization zone. (cf. Why nothing appears when I add an image?)

How to remove an image?

Select an object of the list, then open the image manager (cf. How to open the image manager ?). Select the image in the list, visualize it to check it and click on the button Note : Only the link between the image and the object will be removed, the image itself won’t be physically removed from the folder « images » of your KBd.

How to visualize the images ?

There are two ways :

1- With the image manager :

Select an object in the list, then open the image manager (cf. How to open the image manager ?).
Select on of the image in the list to visualize a thumbnails in the right part. Double-click on the element of the list to edit the image in real size.

2- With the “Image” tab of the “Information” zone :

Select an object of the list then right click on the “Image” tab of the « Information » zone.
The images will appear as thumbnails if avalaible.
Double-click one of them to visualize them in real size.

What are the supported formats ?

The supported formats are : JPEG, GIF and PNG.
We recommand the use the PNG format, which is a free format with a very good quality/size ratio. The images should be in RGB mode and not CMYK.

Why nothing appears when I add an image ?

The image might not appear automatically in the “Images” tab.
This is due to a lack of refreshment of the interface.
To check the presence of an image, click on another object of the list before coming back to thecright object.

How to create thumbnails ?

It is possible to create all the thumbnails in case of problems (corrupted thumbnail, not updated…). To do so, just go to the « Tools » menu then select “Update the thumbnails”.

How does the editor work ?

How to open the editor?

To open the editor, click on the button

How to add a definition to an object?

Select the object to define in the list and open the editor. (cf. How to open the editor ?). Enter the definition in the text zone and click on the button Note : May be a refreshment problem ! (cf. Why nothing appears when I add a definition ?)

How to modify a definition ?

Select the object you want to change the definition and open the editor. (cf. How to open the editor ?). Edit the definition and click on the button

Why nothing appears when I add a definition?

The definition might not appear automatically in the “Definition” tab.
That might be due to a refreshment problem of the interface.
To check if the definition is present, click on another object of the list before coming back to the current object.

Why the loading of my KB take so much time ?

The KB might be long to get loaded. That might be due to the creation of the thumbnails of delocated images (images added via URL). It is possible to desactivate the creation of thumbnail when launching Xper² by modifying directly the file « .preferencexper » located in the folder of the current user (C:\Documents and Settings\Users for windows) : change the line “thumbnailGeneration = true” by “thumbnailGeneration = false”.

descriptor edition

What is the edition module for?

The descriptor edition module lets you define and enter the descriptive system of a KB:
– Define descriptors,
– Edit the descriptor-states,
– Nest descriptors within descriptors, defining the exclusion criteria,
– Create groups,
– Group the descriptors according to the group they belong to.

What does the interface of Edition of the descriptors look like?

What is the process of edition of the descriptors?

Editing a descriptive system starts with the creation and the edition of descriptors (cf. How to create a new descriptor?) and their states, before nesting hierarchical descriptors (cf. Why structure the descriptors with a hierarchy?) and with the possibly to group them (cf. Why grouping the descriptors?).

How to create a new descriptor?

On the « descriptors » window, right click and choose « New ». Enter the name of the descriptor and save. The newly created descriptor appears on the top of the list and two states « State 1 » and « State 2 » are automatically created. You are invited to modify their name and, if needed, add other states.

If the descriptor is numerical, no states can be added but you can change the measurement unit.

N.B. A descriptor is unique. You cannot give the same name to two different charatcers.

How to modify the name of a descriptor?

Select the descriptor on the  « descriptors » window, right click on it and select « Rename ». Modify the name and validate.

How to remove a descriptor?

Select the descriptor on the « descriptors » window, right click and select « Delete ». A confirmation window will ask you to confirm.

N.B. Trying to remove a parent descriptor will give you the choice between removing only the parent descriptor or deleting the parent descriptor and its children. If you choose to remove only the parent descriptor, the children will be transferred to the next node of the hierarchy.

How to create a new state?

Select the descriptor  to which you want to add a state and right click on the « States » window, then select « New ». Enter the name of the state and confirm. You cannot have two identical descriptors.

How to modify the name of a state?

Select the descriptor-state that you want to modify on the « States » window, right click and select « Rename ». Modify the descriptor-state name and confirm it.

How to remove a state?

Select the descriptor-state that you want to modify on the « States » window, right click and select « Delete ».

A descriptor must have, at least, two states. The upper limit is 63 different states per descriptor.

Why grouping the descriptors?

The rationale of grouping is to be able to assemble a set of descriptors in a common entity. For instance, in a botanical KB it could be interesting to group the descriptors “colour of the bark”, “appearence of the bark”, “diameter of the trunk” into a group “Trunk”.

N.B. A descriptor may belong to several groups.

How to create a new group of descriptors?

Right click on the window « Groups » and select « New ». Enter the name of the group and confirm it. It is not possible two give the same name to different groups.

Attention, in order to right click on the « Groups » window, a descriptor must already have been selected.

How to modify the name of a group?

Select the group, right click and select  « Rename ». Enter the name of the group and confirm it. It is not possible to give the same name to different groups.

How to remove a group?

Select the group, right click and select « Delete ».

How to add a descriptor to a group?

Two possibilities are available in the Edition module:
1- Select the descriptor on the « descriptors » window, then right click and select « Add to a group ». Choose the group from the scrolling list and confirm it.
2- Select the descriptor, then right click on the « Groups » window and select « Add to an existing group ». Choose the group from the scrolling list and confirm it.

N.B. The groups to which the descriptor belongs are displayed in black. Otherwise they are displayed in gray colour.

How to remove a descriptor from a group?

Two possibilities are available in the Edition module:
1- Select the descriptor from the « descriptors », then right click on « Remove from a group ». Choose the group from the scrolling list and confirm it.
2- Select the descriptor, then right click ont he  « Groups » window, select « Remove a descriptor from a group ». Choose the group from the scrolling list and confirm it.

Why structuring the descriptors with a hierarchy?

The notion of hierarchy highlights the fact that other descriptors are applicable only if a descriptor “parent” is described.

N.B. A descriptor can have only one parent. However, a parent can have several children.

N.B : a numerical descriptor can’t have a child descriptor.

How to add a child descriptor to another descriptor?

Two possibilities:
1- Select the charatcer you want to mark as a child from the list and drag it to its parent. When the icon of the parent changes N.B.: when you select the child descriptor, the descriptor-states of the parent can be previewed in the conditions of inapplicability window. The inaplicability conditions are the states of the parent descriptor that will forbid, if checked, the edition of each particular child descriptor.

(cf. How to edit the conditions of inapplicability?)

How to add a parent descriptor to another descriptor?

Adding a parent descriptor to another descriptor follows the same process as adding a child descriptor. (cf. How to add a parent descriptor to another descriptor?)

N.B.: it is better to declare the parent descriptors first.

How to remove a child descriptor?

The process depend if you would like to:
– Remove a descriptor that is the child of another one. In this case, select the descriptor, right click and choose « Delete ». (cf.)
– Modify the relationship of the child descriptor: select the descriptor and drag and drop it to the right side of the list. The descriptor is moved to the root of the list. When the icon

How to remove a parent descriptor?

The process depend if you would like to:
– Remove a descriptor that is the parent of another one. In this case, select the descriptor, right click and choose « Delete ». (cf.)
– Modify the link of the relationship of the parent descriptor in order to release the relationship: in this case release one by one all the child descriptors before moving the descriptor.

How to edit the conditions of inapplicability of the states?

Editing the conditions of inapplicability is to the same thing as choosing the descriptor-states that will make the edition of the child descriptor impossible (for logical reasons in general). Select the child descriptor and check all the states that are displayed on the window « Conditions of inapplicability ».

N.B.: the conditions of inapplicability displayed are those of the parent descriptor!

Is it possible to sort the descriptors?

Yes. Four different sortings are available:
1- Sorting by group N.B.: Sorting by group and alphabetically do not allow the edition of the descriptors. To return to the “normal” list you have to sort by parent/child dependency.

Edition of Items

What is the item Edition module for?

The item edition module allows:
– Entering the definitions and images of the descriptors
– Entering the definitions and images of the descriptors-states,
– Adding and removing item,
– Entering the comments and images for item

What does the item Edition Module interface look like?

The image below represents the main window of the item edition module:

How to enter the data for a item?

Three steps are required in order to enter a item:
1- Create the item if it does not exist (cf. How to create a new item?)
2- Edition of the item: informations and images (cf. How to add an image?)
3- Edition of the descriptor-states for all the descriptors of the KB (cf. How to edit the descriptor-states of a item ?)

How to create a new item?

In order to add a new item, right click on the « item » region on the left and click on « New ». You will be invited to enter the name of the new item.

Note, Each item as to be unique, hence, it is not possible to have twice a same name.

How to modify the name of a item?

Select the item, right click then left click on « Rename ». You will be invited to enter a new name.

N.B.: Two item cannot have the same name.

How to remove a item?

To remove a item and its description, right click on the item, then left click on « Delete ». Confirm the deletion.

N.B.: The images concerning the removed item will not be automatically deleted.

Is it possible to sort the items?

Yes, it is possible to sort them alphabetically. Click on

How to select several item?

There are two possibilities:
– While keeping the « Ctrl » key pressed select the item from the list by left clicking on them.
– Left click on the first item you want to select, then, while keeping the « Shift » key pressed select the last one you want to select. All items between both will be selected

Is it possible to remove several item at once?

Yes, it is. Select several items from the list (cf. How to select several item?), right click and select « Delete ». Confirm for each of the selected items.

How to edit the states of a categorical descriptor for an item ?

Select an item in the list then select a categorical descriptor in the descriptors list. The states of the descriptors are displayed on the right.
Deselect the states that are not applicable to the selected item. A descriptor may have several states (therefore, selected).

Note : Edit the parent descriptors first in norder to exclude directly the non applicable children descriptors.

How to edit the values for a numerical descriptor for an item?

Select an item in the list then select a numerical descriptor in the list. Some textboxes will be displayed on the right. Then simply fill out the fields and press the record button (top right) to save them..

Possible values:
– Min : minimum value observed (extreme value)
– Max : maximum value observed (extreme value)
– UmethLower : lower value of the normal distribution
– UmethUpper : higher value of the normal distribution
– Mean : mean
– SD : standard deviation
– Sample : sample size

During identification the range used will be primarily [min, max] if exist, then [UmethLower, UmethUpper] and [Mean – 2SD, Mean + 2SD].

In the case of a unique value (ex : the number of legs) you must enter the same value for the min and max.

Is it possible to simultaneously edit the descriptor-states of several item?

Yes, it is. Select several item from the list (cf. How to select several item?), right click and select the descriptors you want to edit. Check the states that are common to the selected item. This method allows you to  speed up the edition of quite similar item.

Is it possible to compare the descriptor-states of several item?

Yes it is. Select the item from the list (cf. How to select several item?). Then select the descriptors you’d like to compare.
In the « States » zone, on the right, are displayed the selected descriptor-states.
The states displayed in black, either checked or not, are the descriptor-states common to all the items.
The states displayed in grey, either checked or not, are the descriptor-states common to some of the items.

Example :

Is it possible to sort the descriptors?

Yes, it is possible to sort them alphabetically. Click on  What is the interest for the tab “Comments” on the right of “States”?

The tab “Comments” is useful to add detail on the duo Item-Descriptor.

For example, for a numerical descriptor, it’s important to keep the list of the specimens of the sample.

How to select all the states of a descriptor?

Click on the button

How to deselect all the states of a descriptor?

Click on the button

Why can’t I add a state for a descriptor?

Apparently, it means that the descriptor cannot be entered. You did not select the right state (inapplicable one) of the parent descriptor that allows you to enter the states of the children. To solve it, go back to the parent descriptor and select a different state, or modify the conditions of inapplicability (descriptors edition mode).

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<xper targetNamespace="http://lis.snv.jussieu.fr/xper/XML xper.xsd" 
	xml="http://www.w3.org/XML/1998/namespace" xpdversion="0.95" 
     xper="http://lis.snv.jussieu.fr/xper/XML/Schema">
<informations>
<firstedition date=""/>
<lastedition date=""/>
<authors/>
</informations>
<base lang="">
<name></name>
<statistics nbind="" nbmod="" nbvar=""/>
<description/>
<variables>
<variable homology="" id="" nbmodes="">
<name></name>
<description/>
<images/>
<modes>
<mode id="">
<name/>
<description/>
<images>
<image url=""/>
</images>
</mode>
</modes>
</variable>
</variables>
<individuals>
<individual id="">
<name></name>
<description></description>
<images>
<image url=""/>
</images>
<description_list>
<desc_element unknown="" var_ref="">
<comment/>
</desc_element>
</description_list>
</individuals>
<groups>
<group id="">
<name/>
<description/>
<groupvar>1/2/</groupvar>
</group>
</groups>
</base>
</xper>

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