Category talk:Publications

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Content of email discussions on the subject "Scientific publications" initiated by the International Society for Pest Information (ISPI) on 19 May 2010:


Every scientific publication would have a separate page. The current format is illustrated in the example page Biocontrol Science and Technology (2004) 14, 201-209. By clicking on the "view form" tab at the top (or the "edit with form" tab for users who have already logged-in) the structure of the data becomes visible. The meaning of most data elements is obvious from the description on the left side. Some additional notes:

  • For entering the title or abstract a few formatting tags are needed, like double apostrophes before and behind a word in italic, <br> for a new line, or <sub>...</sub> and <sup>...</sup> for subscripts and superscripts.
  • We have 2 boxes for authors names (the names are always separated by commas). The first (with the label "Author(s):") is the list of all authors as it appears in the publication. The second (labeled "Link(s) to author page(s):") are the names of authors who have been already entered into the ISPI database and provides links to these. Note that an author may be spelled "J. Smith" in the publication, but "John Smith" in our database or vice versa. The template processing this form (a template is a page causing formatting actions) will create links to the author pages after the abstract (coloured either red or blue, depending on whether a page for an author already exits). The author page may be a simple link to the ISPI database of scientists (e.g. Sherif A. Hassan), or may be a wiki page with details on the authors affiliation and publications (e.g. Olaf Zimmermann). For the latter case the authors should put these pages on their watch lists to be able to monitor any changes.
  • The form can be set in different ways in order to help data input. For example, when typing into the journal box the system displays those journals already entered and allows selecting one of them. In the case of "research topic", the input is restricted to a list of "allowed values". For some boxes (with italic descriptions) an input is required and the form will display a red warning and will not save unless they are filled in.
  • At the end of an abstract we would normally have a copyright statement as in the above example. ISPI has permission to publish abstracts for almost all articles in our database. Some journals (e.g. the Brazilian SciELO journals) are already published under the Creative Commons licence.
  • The data on journal, volume and page numbers is displayed in a separate box. Is this desirable or distractive (comments would be helpful)? When creating a new article page (use Special:AddData/Publication in journal for this) journal, volume and page numbers are used to automatically create the page name in the standard format. (However, if these data are changed again at a later stage the pagename does not change.)
Comment: I repeat my concern about including the issue in the page title. this will inevitably lead to duplicates like "Biocontrol Science and Technology (2004) 14, 201-209". Maybe this is minor because we might also get "Biocontrol Sci. Tech. (2004) 14 (2), 201-209". I propose: add an issue field in the form, which is shown, but not included in page title. Specify in usage rules that for the rare cases where the pagination restarts repeatedly in each issue, to add the issue number to the volume field. In my own experience such "wrong numbered" journals are very rare. (Gregor Hagedorn, 20 May 2010)
Note (6 June 2010): A new article is now created by following a link in the respective journal.


Dividing the publication into these different data elements has 2 purposes:

  1. To display the publication in a uniform format, e.g. it is desirable to have a fixed order and appearance of the title, author(s), journal details and the abstract. This is done by the template behind the form which, among others, can also produce effects like converting the DOI number into a hotlink connecting to the article webpage at the publishers website.
  2. To enter some of the article elements into a database structure. This is again done by the template running in the back. The database structure can then be used for displaying the publication on other pages (and in different formats). Here are few examples for how we can use the data entered into this form on other pages of our wiki:
    • The example page Ostrinia nubilalis has only 3 lines (click on the "edit" or "view source" tab to see the 3 lines). The first is a heading and the last an assignment to a category. The middle line uses the "Template:Citation" (and an additional template) to display the journal details, authors and the title for two article pages in the format "{{Citation|<page name of article page>}}".
    • On the page Environmental Entomology (2005) 34 (1) we are using a database query to automatically display all articles which have journal = "Environmental Entomology", publication year= "2005" and volume (issue) = "34 (1)". If a new article is entered for this journal, year and issue it will automatically be displayed in this list. However, please note that this may be delayed for a day or so (this is how the MediaWiki Parser Cache works). To get an instant update of this list we may need to open the page Environmental Entomology (2005) 34 (1) and click on the Refresh button. The Refresh button appears for logged-in user under the combo box after "View history".
    • The literature list at the bottom of the page Olaf Zimmermann is another example for a database query (all pages which have the data "Author Page=Olaf Zimmermann" are automatically listed).

Future developments/discussions

Classification/indexing of scientific publications

At the bottom part of the page Biocontrol Science and Technology (2004) 14, 201-209 we have database assignments classifying the article, for example which pest, disease, research topic, crop or country the publication deals with. This database structure is still preliminary (causing texts like "{{#set_internal: ..." below these data) and will be developed and discussed further in the future. We are hoping that with such data it will become possible to display, for example, literature for pests, diseases and weeds occurring on crop X in country Y or for given research topics. There are publications which have many such host-distribution records and we would also need an additional structure for such data. The table at the bottom of page Studies in Mycology (2010) 65, 1-60 gives an example of a possible alternate structure for these data. Here the content of each column can be sorted by clicking on the tiny box behind a header.

Publications outside journals (e.g. books, conferences)

The current form is restricted to journal articles and filling in the box for the journal is required. We might need a separate form for articles not published in journals. The current form might become too complex if we want to cover all types of publications.

Comment: I would prefer a single template, else a person entering data must make complex choices before entering into a form. A single template means a single form, inside of which help can be given. What if an extra field "book title" is presented, and either one or the other must be present? In the page creation, both could be placed at the same point (because never both may be present). (Gregor Hagedorn, 20 May 2010)

Namespace "Bibliography"

In the MediaWiki system a "namespace" is a prefix before the page name, e.g. for the page "Category:Coleoptera" the namespace is "Category". The namespace characterizes the type of page. There are other standard namespaces like "Help" or "Template". In the biowikifarm the additional namespace "Bibliography" has been created and all publication pages could be renamed under this namespace. There are different advantages and disadvantages for using the namespace "Bibliography" which should be discussed at a later stage. First we need to establish our database structures and database functions and see if they work with a different namespace.

Modifications and additions - status January 2011

In the 2nd half of 2010 a number of modifications and additions have been introduced to the system of entering and displaying publications. Detailed descriptions and guidance have been also provided under Help:Publications. The changes include:

Preliminary form for entering publications

A preliminary form is needed to ensure that each publication has a standard pagename and to check whether the article has been entered already. The standard pagename depends on the type of publication and a number of preliminary forms exist. Usually the pagename of an article is composed of the journal or series name, the publication year, the volume and the page numbers. However, different formats may become necessary. For example, an on-line journal may not have page numbers or a book chapter does not have a series name.

For entering a new publication the user starts on the page Category:Journals, selects the journal, series or the category books and then clicks on "Enter a new article". This calls up the preliminary form applicable to the given journal, series or book. Data like volume, page numbers, or, if necessary, authors and title are entered and the system then checks if the publication already exist. After clicking on the "Run query" button, the user is directed either to an existing publication page, or to the main form for entering the remaining data for a new article. This system is quite flexible and the user is not involved in decisions on which form to use. If a journal has not yet been entered into the system or in case of other problems, a general preliminary form can also be used, see Special:RunQuery/NewArticle7. While there are different preliminary forms, there is only one main form for all publications.

Modifications in the main publication form

A number of smaller modifications have been introduced to the main publication form. For example a number of checks of the data are now done by the system and error messages (e.g. if the first page is larger then the last page), warnings (e.g. if no research topic was provided) or other messages may be displayed automatically.

Other modifications related to the literature database

The namespace "Bibliography" has caused technical problems during filtering out and displaying publications. This namespace is, therefore, no longer envisaged as a format for all publication pages. However, it will be very useful as a standard format for displaying publication lists of specific pests, diseases and weeds, e.g. see Bibliography:Leptinotarsa decemlineata.

The main pests, diseases, weeds, the associated beneficials, crops and countries a publication covers are displayed under the section "Pest and/or beneficial records". These lists can be quite long, e.g. see the bottom part of the page Studies in Mycology (2010) 65, 1-60. However they are needed for generating publication lists on pests found on a given crop in a given country, the hosts of a beneficial organism, etc. There are 2 problems related to the pest and beneficial records which need further attention:

  • The names for pests, diseases, weeds, beneficials, crops and countries need to be in a standard format so that the user can enter the correct name without help.
  • Names which have have been already entered into these records might change in the future, e.g. if the name of a given pest, disease or weed changes, due to the results of new taxonomic studies. In such cases the page of the affected pest, disease or weed would be moved to a new pagename with the old name becoming a REDIRECT page. In the pest and beneficial records of the publications the old names will still produce functional blue links (through the REDIRECT pages). However, such outdated names are then not recognized in queries and the publication will be missing in relevant publication lists if the pest and beneficial records are not changed. Therefore, an efficient procedure will be needed for changing the name in all publication pages affected. There may be many.