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From Bibus

Bibus main interface

The main interface of Bibus should be intuitive for anybody used to a mail reader. On the left is a tree with keys. Each key is associated with a list of references. When the key is selected, the references associated with this key are listed in the listView located on the top panel of the right side of the window. When a reference is selected in this list, this reference is shown at the bottom right of the window. In the figure above, the key selected is 'References', the reference selected is 'Alvarez2001' and this reference is displayed with its abstract etc.. at the bottom right.

In the status bar, the following information is displayed from left to right: help messages | number of references in the selected key : number of selected references | style selected.

Key tree

The keys are ordered in a non rooted tree. There are eight main categories named 'All my references', 'References', 'Tagged', 'Queries', 'PubMed search', 'Import buffer', 'cited' and 'non classified'. You cannot modify or add any key at this level. Let first describe these main categories:

• All my references displays all references included in the references key
• References. It is where you can classify your references. You can add subkeys, modify their names, move them using drag&drop, tag etc... To do that you can either use the popup menu that appears when you right click on the keys or the third menu 'Reference'. The preferred way is to right click on the key since there are more choices than in the menu and only the available choices will be displayed.
• 'Tagged' This category allows quick organization of your references. When you go through your reference, you may sometimes need to 'tag' a reference to remember it. In such a case, just select the reference and hit the 't' key (or Ctrl + T) and the reference will be copied under the key 'tagged'.

Queries. We will see later how to define queries. You can see them as 'live search'. You can define a search and save it. When you click on this query, Bibus looks in the database and show the references that fulfill the search. If you change the database, the search will be automatically updated. In fact a query is simply an SQL query.

• 'PubMed search' When you do a PubMed search, the result is available here.
• 'Import buffer'. When you import a file (Medline or EndNote/Refer), the result is available here.

Cited. If the connection with OOo is active, all the citations cited in the current OOo document are displayed under this key.

• 'non classified' displays all the refs in the database which are not in "All".

Reference list

Here are displayed all the references associated with the currently selected key. Again, you can manipulate them by right clicking on them or by using the menu 'Reference'. An important way to manipulate the references is by using drag & drop. For instance in the figure above, I would like to associated the selected reference(s) (Alvarez2001) with the key 'References/hake' because it is related to this fish. I can drag & drop it on the key References/Hake. If you now select this key, you will see that the dropped reference is there. If you need to unfold a key for dropping the reference, you can move the cursor (during the drag & drop) over the (+) before the key name. It is important to understand what happens when you do that: You don't really move the reference. In fact you just create a link between the reference and the key. You can see that as a shortcut under windows or a symbolic link under linux. You can drag from any key but you can only drop to the key 'References' and its children simply because it does not make sense to drag on the other keys since their content is defined by Bibus. By default, drag & drop is equivalent to Cut/Paste, but in some cases (when the reference cannot be deleted from the source) it is Copy/Paste. In fact when the source is References and its children it is a Cut/Paste, and otherwise Copy/Paste. As usual, you can force Copy/Paste by holding down the Ctrl key when dragging. Because we are just creating links it is very economic in term of disk usage. So, don't hesitate to associate a reference with several keys. Since it is a link, if you modify the reference under any of the keys, you will also modify the reference in the other places (in 'All my references' and in the other keys) not only for yourself but also for the other users of the database. By right-clicking on a reference, you can either:

• tag the reference
• edit the reference
• create a new reference
• delete the reference

Editing/Creating a reference

Reference editor

To edit (create) a reference, select Edit (New) in the popup menu or in the menu 'Reference'. You can also double click on the selected reference(s). You will get a reference editor that allow you to modify and see all the fields. There are three tabs.

• Main Fields should normally be filled since they correspond to fields needed by most styles.
• Supplementary Fields may be partially filled and correspond to less frequently used values for the current reference type (for instance, the issue Number for an article.
• Other Fields are the other possible fields.

There is a Choice at the top for the reference type. By default it is ARTICLE. If you change this type, you will notice that the fields change. This is because the Required fields (Main) fields for a BOOK are different than the fields required for an ARTICLE or an URL. If the default values for Main/Supplementary/other fields don't suit your needs, you can change them in the "Preferences" under the "Editor" tab. When you edit a reference by default you cannot change the Identifier field. This is because changing this field may be dangerous if the edited reference is used in one of your article. Bibus won't be able to find the reference to format your article in OpenOffice.org. You can however change the identifier by first checking the "Edit identifier" check box.

URL field - opening an URL

If your navigator is correctly configured, you can use the URL field to put a link either to a website or to a "locale" copy of the paper. If you have on your disk (or somewhere else) a pdf version of the following paper: Marx.pdf located in /home/toto/pdf/ put, in the URL field

file:///home/toto/pdf/Marx.pdf

When you select 'openURL', the webbrowser will be called and will open your pdf viewer to handle the document.

Alternatively, you can specify a default directory for your pdf in Edit->Preferences->Paths. Set $FILE to

.../WorkDir/PaperCollection

both on your linux and Windows computers. Now use

file:///$FILE/paper01.pdf (it seems that file:///$FILE\paper01.pdf also works on windows)

If you use bibus to select the pdf file, it will automatically replace "WorkDir/PaperCollection" with $FILE.

Tips when entering the information

• Enter author names as Lastname, F M (separating authors with a semi-colon and initials with a space). Do not add other punctuation such as periods. e.g. Bloggs, Joe Someone; Smith, S D. A practical solution is to use shortcuts.
• If desired the full first and middle names can be entered.
• Theoretically, journals titles and names should be entered in full with the correct capitalisation (e.g. not full caps). However, to benefit of the abbreviations facility, journals should be written in the Pubmed form (this behaviour may change in the future, see this topic [1]). The list of abbreviations may be find in Edit->Preference->Journal. A handy solution is to use shortcuts.

About deleting a reference

When a reference is selected, you can "delete" it by right clicking and choosing "delete" in the menu (or in the third main menu). The reference is moved in the non-classified category. Click on Edit->Clean database to definitively remove references.

Creating and using shortcuts

The reference editor window contains a menu bar. When you first start Bibus, this menubar contains three elements (Authors, Journal and Divers). If you click in one of these categories the menu will look like this:

To insert any of the menu item in a field, just locate your cursor at the correct position in the correct field then choose the menu item. For instance, you can insert "FEBS Lett" with a single click in the corresponding menu item in the Journal field. This can save you a lot of typing (and errors).

To save a shortcut, you can either:

• Select some text in a fields and choose "Capture selection". The current selection will then appear at the bottom of the menu.
• Select "Edit shortcuts ...". In the window that appear you can edit any shortcut, sort them and capture them from the database. This last option is explained below.

Capturing shortcuts from the database. Instead of entering each shortcut by hand, you can decide that you want to capture all the author names present in the database and put them in your shortcut list called journal. Here is how to do that:

• Click on the Author menu
• Select "Edit Shortcut"
• Click the "Capture ..." button
• Select "Author" in the menuChoice
• Check "using separator" and select ";"
• Click OK
• All the authors available in the database will now appear in the Shortcut window. You can sort them in ascending or descending order
• Close the Preference editor by clicking OK

You can create new shorcut in the Edition->Preferences->Shortcut window, by clicking on "New". Then you can capture the selection as explained above.

Sharing References

• References can be shared between people using Bibus and EndNote. You can export or import by using the "Refer" filter Importing_Endnote_7_into_Bibus_with_Fedora_6_and_Bibus_1.3.
• For those on Bibus, a shared mysql database has been setup on the network to allow everyone in the organisation to share their reference lists. References in your private tree will need to be moved or copied to the shared tree (tab). This can be done by dragging and dropping the citations between trees. Or by using the Edit->Cut/Copy and Paste menu items. Note that if you drag the items they will be removed from your personal tree. If you want them to remain in your personal tree, use copy instead.
• References will have to be exported from your local EndNote or Bibus and imported into the network database for all to be able to access them.

Interacting with a wordprocessor

Bibus can interact with either openoffice or Microsoft word. The methods are very similar therefore we will only present the interaction with openoffice.

Make openoffice writer listen

Have a look at the First connection wizard tutorial after bibus installation.

Inserting a citation

Select your citation(s) and insert them directly at the cursor location. Further explanation shouldn't be necessary: just give it a try. Bibus always enters the citation into the “current” word or openoffice document.

Therefore when using Bibus, it is better to have only one document open to avoid citations being placed in the wrong documents.

Formatting the bibliography

Once you have some citations and have saved your document, you can see what the result would look like by “finalising” the document. This option is available in the “MS Word” or “OpenOffice” menu item. This will generate a new document which will be the final output. You can also use "Format bibliography" (format the bibliography but not the citations). The citation style can be configured to almost anything and any styles used out there. This may take some time to get it to suit your style, but once it's done it should make life easier. Styles can be shared between users Styles repository.

Styles

Using styles

In the OpenOffice.org/Formatting sub menu, there is a list of available styles. There are also options for creating, editing or loading styles from disk, and a link to the Styles repository. The currently active style is displayed at the right of the status bar of the Main Window. The list of styles is divided in two parts.

• The first displayed styles are the default styles seen by all the users of Bibus. Those styles are located in the Format/Styles/ directory in the Bibus installation directory. If you create a style and want to make it available to all the users, just drop it in this directory (if you have write permission) and it will appear in the menu of Bibus (after restart). You cannot edit those styles. If you choose Edit, Bibus will do a copy of it in order to allow editing.
• The second part of the list, after the separator under linux or just the end of the list under Windows, contains your personal styles. You are the only user with those styles in your menu (actually another user can share them if he has read access to them and load them using the load item). You can freely Edit those styles.

Creating a style

Creating or editing a new style is very easy. When you select New the following 'Style editor' will pop up.

Style informations

You start with a style corresponding to the 'default' style of the style menu. This is a fairly reasonable style and most of the time you just have to modify few settings. In this first Tab "Style information", You can put any relevant informations concerning this style. It is a good idea to give an e-mail address where users can contact you and of course for which journal the style is intended.

Bibliographic index

The second Tab controls how the index is formated. The choices are easy to understand and correspond to the available choices in OpenOffice.org.

Fields formatting

This Tab controls the filters that are applied to the record fields before insertion in OpenOffice.org. On the left, there is a list of all the available reference types that OpenOffice.org knows about. The main type is of course ARTICLE and it is why we use it as the default type. If you click on any other type, for instance BOOK, you will see that all the choices are dimmed and that the first RadioBox says that for BOOK you must 'Format fields as in ARTICLE'. Therefore when you want to define a new style, in most of the case you just have to format ARTICLE even the fields which are not relevant for an ARTICLE like 'Booktitle' or 'Editors'.

The most important part of this dialog is how authors and editors must be formatted. To help you, there is a preview that shows the result of your choices as you type. You can abbreviate the author list, if needed (For instance PNAS requires the listing of only the first 10 authors). If you choose 6 for instance, authors 1 to 6 will be listed and the 7th and followings will be replaced by 'et al.' (or something else). You can use 'singular | plural' forms. In the displayed example, you can see that Bibus will add, after the editor list, either (Ed.) or (Eds.) depending on the number of editors. Choosing 'As in database' means that you don't want Bibus to format this field. The field will be directly copied from the database to OpenOffice.org. At the top there is a checkbox 'use current language for month'. If you check it, month will use your current language, otherwise it will be in English. The month in the database must be either in you current language or in English in order for Bibus to recognize it.

Journal abbreviation field enables to select an abbreviation for journal titles. The list of abbreviations may be find in Edit->Preference->Journal.

Fields ordering

The last Tab controls how the fields are ordered and formatted. For instance you may want to format references as: Authors. Title. Journal (Year) Volume: pages. This can be done in this Tab. To help you, there is a preview that shows the result of your choices as you type. Till now you can't format a part of a fields (for example italicizing scientific species name), however you can find some workaround in the Community portal.

Citation

In this tab, you can define the formatting of the citations in the text. This tab is a bit special because it contains features not supported by OpenOffice.org. The configuration option in this tab are used by the 'OpenOffice.org/Finalize' menu. Because it is a one-way formatting and because it is not possible to go back to the cancel these formatting, Bibus will use these setting on a copy of your current document.

Here is a short description:

Top: You can define here, the style of the citation and the way citations are sorted when citations are fused.

Depending on the settings in the 'Bibliographic Index' tab, you will be also able to define either the formatting of the numbering or author-date:

For author-date, you must first define the template (for instance 'Author', 'Year'), then how Bibus should try to solve the duplicates. There are 3 possibilities:

• Bibus can add a letter after the year. This method will always generate unique citation markers.
• You can choose to add authors or to add their firstname. In some case this may not be possible to solve all the duplicates. Bibus will warn you if there are still some duplicates and you will have to edit them by hand.
• You can add a field. For instance, in APA style, you usually add the 'title' of the book after the author. Again, in some rare cases, it may not be enough to solve some duplicates. Again, Bibus will warn you if it is the case.

Please also have a look at the Community portal and to the forums if you have any problem Further formatting Read the OpenOffice.org help to understand how styles works in OpenOffice.org. Bibus uses paragraph and character styles to format the bibliography and the citations. You can thus re-format easily the citations and/or the Bibliography. Citation After using the Finalize function, the citations uses the character style 'bibus_citation_base'. For instance, you can choose a yellow background for this style and all the text citations will be easy to localize in you text. Bibliography The Bibliography title uses the paragraph style "Bibliography title" The Bibliography uses the paragraph style "Bibliography 1" The References use the character style "bibus_base"