Talk:Pests-diseases-weeds

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Summary of changes since May 2010 (as of December 2011)

There have been several changes since May 2010 on the structure and organization of pages providing information on pests, diseases and weeds. Therefore, some of the explanations and examples given below in May 2010 are no longer valid. The following gives an update of development work as of December 2011:

Categories of pests, diseases and weeds

The previous system of "redirecting" category pages to normal pages caused problems with the literature database structure. The category pages (e.g. Category:Aphididae) are therefore now the main units and normal pages (e.g. Aphididae) are redirected to the category pages. Entering the normal pages is still useful because the names will appear in the search suggestions and users can find the category pages quickly without the prefix "Category".

Literature database queries for pests, diseases and weeds

Each page for a pest, disease or weed now contains a box on the top left side with links to literature database queries (using the Template:LiteratureDB). The literature lists are either displayed in separate pages under the namespace "Bibliography" (e.g. Bibliography:Acyrthosiphon pisum) or in "query pages" (e.g. click on "Recent publications" in the page Acyrthosiphon pisum (top left side). In the "query pages" the user can change the parameters and repeat the query with the "Run query" option at the bottom of the page. There are still 2 aspects of the literature queries which we will try to improve:

  • For common pests, diseases or weeds with many literature records it can take some time for the system to construct the list, e.g. Bibliography:Myzus persicae (crops).
  • In the query pages the back button of the browser does not work (for some browsers) once the user has used the "Run query" option.

Original content of May 2010

Content of email discussions on the subject "Pages for pests, diseases and weeds" initiated by the International Society for Pest Information (ISPI) on 26 May 2010:

Introduction

Pages for pests, diseases and weeds would basically follow the standard pattern for a Wikipedia page with sections, photos, links and references. Examples of pages which have already received some inputs are: Chrysomela lapponica, Drosophila suzukii and Oryctes rhinoceros nudivirus (entomopathogen). Our Pest Directory database has very little text about a given pest, disease or weed and contains mainly information on relevant literature, synonyms, vernacular names, as well as a taxonomic structure. The page Leptinotarsa decemlineata is a good example of the type of information we already have (and would import) for most pests, diseases, weeds and beneficials.

It would be useful to encourage users to follow a standard format for arranging elements like synonyms, vernacular names or taxonomic information. User can then find the information needed more easily. In addition, we need to arrange the pages on pests and diseases into a taxonomic structure. This will help finding a particular pest but is also necessary for our database features. We will introduce the taxonomic structure here and will cover other standard elements of our pest pages in a later email.

The MediaWiki "Category" concept:

Categories are the standard way of bringing wiki pages into a logical order. They also play an important role in wiki database functions (Semantic MediaWiki). Therefore, categories are the best system for a taxonomic structure. The name of a category page always has the prefix (namespace) "Category" followed by a colon, as an example see the page Category:Aphididae. It can be created and can contain text and images like a normal wiki page, such text is the top part of the page. In the bottom part it will have a list of subcategories and/or pages (ordered alphabetically), and at the very bottom it will show whether it is a subcategory of another category. In this case the category Aphididae is a subcategory of the category Aphidoidea. If you look at the script of this category page (click on the "edit" or "view form" tab at the top) you can see only the text for the top part and the line "Category:Sternorrhyncha" at the bottom. This line assigns the category Aphididae to the higher category Sternorrhyncha. The subcategories and pages under this category are not specified on this page. They are listed automatically by the system through the category assignments on the other pages (see for example the category assignment Category:Aphididae in the page Brevicoryne brassicae.

We can navigate through the taxonomic system by clicking on the subcategories, the "[+]" signs (of course, these work only if there are further subcategories), or the next higher category at the bottom. However, to find the category Aphididae with the search box, we have to type in "Category:Aphididae". In order to avoid this we can create a redirect page with the name "Aphididae". A redirect page is a unique type of wiki page which has only the line "#REDIRECT[[name of another page]]" which will bring the user to the specified page. For example, typing "Aphididae" into the search box brings you again to the category Aphididae, except for the line "Redirected from Aphididae" at the top. By clicking on "Aphididae" in this line, we come to the #REDIRECT page and see the line "#REDIRECT[[:Category:Aphididae]]" in the edit (or view source) mode. Note that we are using here a colon before the word "Category", otherwise the page "Category:Aphididae" will also list the page "Aphididae" which does not make sense because it would be a redirect to itself.

Thus, in our category tree for pests, diseases and weeds we need 2 pages for each taxonomic unit, a category page and a normal page which is a redirect page. Redirect pages are also very useful for entering synonyms and common names of pests and diseases into the system. By typing the word "Röhrenläuse" into the search box we are directed again to the category page Aphididae and the page "Röhrenläuse" is again a redirect page.

A proposed modified category system for pests, diseases and weeds:

The wiki category system, as described above, would work for our taxonomic classification of pests, diseases and weeds. However, it has some disadvantages:

  • It is not common in wikis to place a lot of text and images into a category page and it would take time for people to get used to this.
  • The normal features of a category page are not ideal. In the page Category:Pests-diseases-weeds it would be better to list from the start further subcategories (e.g. what we would see if we click on all the "[+]" signs). In the page Category:Aphididae it would be preferable to list also the species pages under genera like "Aphis (genus)" or "Myzus (genus)", and finally we would like more information on which higher categories exist.

In order to improve on these aspects, we propose the following modified category system, based on the ideas of Gregor Hagedorn. The modified system is illustrated in the page Hypocreales and in other pages on plant diseases. Here we use a normal page for entering text and images for the fungal order "Hypocreales" and provide taxonomic information with the help of the function "#categorytree". With this function we can include the pages (shown in italic) in addition to the subcategories, control how many levels of the category are displayed, and we can also display a tree structure for the higher taxonomic units (shown at the top right). The page Pests-diseases-weeds is an example how we can display larger taxonomic structures with the "#categorytree" function. It is not useful to display more than 3 lower taxonomic levels, because the structure would become too complex and the page too long.

In the modified category system the category pages still exist in the background and when creating a new taxonomic unit we still need to create a separate category page (except for the lowest taxonomic units which can be normal pages). However, the category pages will then be all redirect pages. If you look at the page "Category:Hypocreales" in the edit (or view source) mode, you will see 2 lines: "#REDIRECT[[Hypocreales]]" which redirects to the normal page "Hypocreales", and "[[Category:Sordariomycetes]]" which assigns the category Hypocreales to the next higher category Sordariomycetes. Amazingly this combination of a redirect and a category assignment works in the MediaWiki system and when clicking on any unit of the taxonomic tree (e.g. on "Ascomycota" in the top right corner of the Hypocreales page) we are redirected through the category page to the normal page Ascomycota. We are not certain yet if this modified taxonomic structure will allow us to use all Semantic MediaWiki database features, but we are optimistic.