Generate Descriptions

Generate a description data document

This tool is used to generate a structured documentation of description data stored in the database. To use this tool, start a query for descriptions and choose Data ->  Generate document … from the menu. A window with will open as shown below.

You may select all entries by clicking the all button, deselect all entries by clicking the none button or toggle your selection by clicking the swap button. Choose among the provided options and click on the button Create … documentation to create a document in one of the available formats.

By default no descriptions will be exported that include any descriptor with data status “Data withheld”. This is indicated by the button in the upper right corner of the window. You may click on this button to include those descriptions. The button will change to and only the marked descriptor summary data will be excluded from the document. 

HTML

If you create a HTML documentation, a local file named <Database name>_Description.htm is generated in the application directory, that might be copied and edited for own purposes. If you select option Include descriptors, the used descriptors are included at the end of the documents and links to that empedded descriptors are set in the description section. Otherwise the links are set to the entries specified in the Descriptor file: text box. By clicking button Select colors you may open a dialog window where you can select the colors of different elements (see window below).

If all descriptions in the selection box belong to the same project and a descriptor tree is defined, the Descriptor tree: drop-down list is shown in the options (see image below left). If a descriptor tree is selected and the Structured output keeps activated, the description data are arranged according the selected descriptor trees. Additionally leading descriptor name parts are omitted, if they are contained in the descriptor tree hierachy. Therefore “literature references” becomes to “references” contained in node “Literature” as shown below. If the selected descriptor tree contains only a subset of descriptors, only this subset will be displayed in the output. 

If the Structured output option is deactivated, all descriptors will be included in the output in the standard sequence order. Leading name parts will be reduced if they are already contained in the tree hierarchy as described in the Editing the description - Continuous viewtab section. With check box Include data titles the output of the titles “State”, “Text” and “Sequence” in the descriptor data can be controlled. If you select Resolve scopes, for each scope that is linked to a database entry a table with the foreighn database values will be inserted. To check and adjust the module connections click on button . 

If in the datasets RTF-like formatting tags like \i or \sub{} are included, use option Accept RTF mark-ups as shown in the picture below. 

MediaWiki

If you create a MediaWiki documentation, you may copy the generated text from the output window and insert it in the MediaWiki page. With the Layout option you may determine if all data shall be included in a large table or if several tables with additional header lines shall be generated (see image below). 

If all descriptions in the selection box belong to the same project and a descriptor tree is defined, the Descriptor tree: drop-down list is shown in the options (see image below left). If a descriptor tree is selected and the Restricted option is activated, the description data are restricted to the descriptors contained in the selected descriptor tree. 

If the Restriced option is deactivated, all descriptor data will be included in the output in the standard sequence order. Only name parts of the descriptor tree hierarchy will be included in the descriptor names as described in the Editing the description - Descriptor viewtab section. 

Pensoft content

If you like to publish description data in some online media, e.g. the Pensoft “Biodiversity Data Journal”, the description data are expected in a dedicated Microsoft Excel format. A template fille as shown below, that includes several tables, is available. DiversityDescriptions allows generating tabulator separated files for tables “Taxa” and “SpeciesDescriptionMatrix” of that template. 

If all descriptions in the selection box belong to the same project and a descriptor tree is defined, the Descriptor tree: drop-down list is shown in the options (see image below). If a descriptor tree is selected, the description data are arranged with heading according the selected descriptor trees. Additionally leading descriptor name parts are omitted, if they are contained in the descriptor tree hierachy.

When Ignore data status ist selected, it will not be included in the “CharacterValue” column. Option Ignore RTF mark-ups will remove RTF-like formatting tags like \i or \sub{}. If option Ignore notes is de-selected, notes will be inserted in the “Remarks” column of the “SpeciesDescriptionMatrix”.

If you select Resolve scopes and a scope entry for a taxon name is linked to an entry in DiversityTaxonNames, the corresponding fields of the “Taxa” table will be filled with that data. To check and adjust the module connections click on button . If scope data for a geographic area is available, it will be inserted in the “Distribution” column of the “Taxa” table.  

The results are stored in local files named <Database name>_Taxa.txt and <Database name>_SpeciesDescriptionMatrix.txt. 

Generate Descriptors

Generate a descriptor data document

This tool is used to generate a structured documentation of descriptors stored in the database. To use this tool, start a query for descriptors and choose Data ->  Generate Document … from the menu. A window will open as shown below.

You may select all entries by clicking the all button, deselect all entries by clicking the none button or toggle your selection by clicking the swap button. Choose among the provided options and click on the button Create … documentation to create a document in one of the available formats.

HTML

If you create a HTML documentation, a local file named <Database name>_Descriptor.htm is generated in the application directory, that might be copied and edited for own purposes. By clicking button Select colors you may open a dialog window where you can select the colors of different elements (see window below).

If in the datasets RTF-like formatting tags like \i or \sub{} are included, use option Accept RTF mark-ups as shown in the picture below. 

MediaWiki

If you create a MediaWiki documentation, you may copy the generated text from the output window and insert it in the MediaWiki page. With the Layout option you may determine if all data shall be included in a large table or if several tables with additional header lines shall be generated (see image below). 

Generate Projects

Generate a project data document

This tool is used to generate a structured documentation of project related data stored in the database. To use this tool, start a query for projects and choose Data ->  Generate Document … from the menu. A window will open as shown below.

You may select all entries by clicking the all button, deselect all entries by clicking the none button or toggle your selection by clicking the swap button. Choose among the provided options and click on the button Create … documentation to create a document in one of the available formats.

HTML

If you create a HTML documentation, a local file named <Database name>_Project.htm is generated in the application directory, that might be copied and edited for own purposes. By clicking button Select colors you may open a dialog window where you can select the colors of different elements (see window below).

You have the choice to output additional information besides the basic project data by selection the options Include descriptor trees, Include descriptor data or Include applicabilities (see window below).

MediaWiki

If you create a MediaWiki documentation, you may copy the generated text from the output window and insert it in the MediaWiki page. With the Layout option you may determine if all data shall be included in a large table or if several tables with additional header lines shall be generated (see image below). 

If you specify values in text fields Replace: and by: you can perform text replacements for Descriptor or Categorical state names in the generated output. By specifying a Prefix: for a Semantic MediaWiki (see next section) you can generate lokal links to this kind of Wiki pages. Additionally, you may insert the absolute link adresses by entering the base Wiki address in the URI: filed.  

Semantic MediaWiki

If you create a Semantic MediaWiki documentation, the descriptors, categorical states, descriptor trees and descriptor applicability information are generated in a format that fits to terminology platforms as used e.g by TDWG. In this scheme the most important entities are “Concept” and “Collection”. Each “Concept” represents a single descriptor or categorical state value, which is shown on an own page. Each “Collection” represents a single descriptor tree or descriptor tree node, which is shown on an own page. The pages are named according the schema <prefix>:<entity label> [(<number>)], where the <number> parts may be optional, depending on the Naming: setting (see image below):

• If Opt. order (Optional order) is selected the <number> part is omitted if the name is unambigious. Otherwise it starts with 1 for the first duplicate and is increased for each subsequent one to avoid duplicate page names. 
• If Order is selected the <number> starts with 1 and is increased for each subsequent duplicate to guarantee unambigious page names.
• If Entity ID is selected the <number> contains the database internal ID of each entry to guarantee unambigious page names.

The Cardinality option includes information about multiple occurance and the mandatory property in the descriptor concepts. By selecting the Include trees option the descriptor trees and the tree structure will be included as collections where subordinated tree nodes are represented by concatenated node names, e.g. <prefix>:<Tree name>.<Node 1 name>.<Node 2 name>. If you specify values in text fields Replace: and by: you can perform text replacements for Descriptor or Categorical state names in the generated output.

If Generate: XML for Wiki import is selected, the output is generated in an XML format that may be imported to a semantic media wiki. To show all generated data, the two templates “dwb_Descriptor” and “dwb_CategoricalState” must be inserted in the wiki.

If Generate: XSD/XML document is selected, an XML schema (XSD) is generated in the main window. If schema generation was ended without problems, a selection list will be shown where description items for the XML document may be selected. For the selected descriptions an XML document structured according the XSD will be shown in a separate window. By default no descriptions will be exported that include any descriptor with data status “Data withheld”. This is indicated by the button in the upper right corner of the window. You may click on this button to include those descriptions. The button will change to and only the marked descriptor summary data will be excluded from the document.

Descriptor applicability

The descriptor applicability tree shows the selected projects and as subordinated nodes the categorical descriptors that control the applicability of dependent descriptors. Contained in the controlling descriptor are their categorical states and the dependent descriptors with the applicability rule “applicable-if” or “inapplicable-if” . The descriptor names are prefixed with their sequence number in square brackets, the states with the descriptor’s sequence number and their own.

If you create a applicability tree documentation, two local tabulator-separated text files are generated. The first file named <Database name>_ApplicabilityNodes.txt contains the node list with columns “Id”, “Label” and “Modularity class” (“Project”, “Descriptor” or “State”). The second file named <Database name>_ApplicabilityEdges.txt contains the edges list with columns “Source”, “Target” and “Label” (“Includes” for project-descriptor relations, “Contains” for descriptor-state relations or “Applicable” rsp. “Inapplicable” for state-descriptor relations). You may import those files to a graphic program like “Gephi”  to visualize the descriptor applicabilities. 

By selecting the option Convert to applicable rule or Convert to inapplicable rule the applicability settings stored in the database can be converted to the required complatible format (see image below).