This is the help file for Bibi, the BibTeX Manager, version 2.0 beta
As of version 2.0, you need Java 1.5 to run Bibi.
For more information or for bug reports, don't hesitate to contact Ute Platzer at ute @ ujap.de
$Date: 2006/07/30 19:28:45 $
Bibi is a tool for editing and managing BibTeX files. Apart from simply editing a file in a graphical user interface, Bibi offers lots of other possibilities!
For each file, an editor window is displayed which contains a list of all entries and an editor for the selected entry (type of entry, Key, plus a table with the fields),
PubMed is a Web-based retrieval system for literature references in the area of medicine, biology, and life sciences in general. It can be found at this URL: http://www.ncbi.nlm.nih.goc/pubmed. Bibi can parse the entries, so you can paste text directly from the web page into Bibi.
The format of a Pubmed Record is this:
Authors (without dots inside). Title (without dots). Journal title. Year month; volume(number): page-page. [optional a note.] [PMID: optional]
Example:
Mutai H, Heller S. Vertebrate and invertebrate TRPV-like mechanoreceptors. Cell Calcium. 2003 Mar;33(5-6):471-8. Review. PMID: 12765692
This is the "Summary" format. In the future, Bibi will offer a parser for the "Abstract" format, as well.
The resulting Bibtex entry looks like this:
author: Mutai, H. and Heller, S. title: Vertebrate and invertebrate TRPV-like mechanoreceptors. journal: Cell Calcium year: 2003 month: March volume: 33 number: 5--6 pages: 471--478 note: Review. pmid: 12765692
You can define pieces of text which Bibi will look for in a PubMed record and will automatically replace by other text, e.g. to convert some specific strings in the title of articles to TeX macros. To do this, you create a macro definition file the location of which you specify in the preferences (File Menu - Preferences). The file is plain text: the first line specifies the text to search, and the second line specifies by what it shall be replaced.
Example macro definition file:
invertebrate \invert -like --like
This macro definitions applied to the above entry produce:
author: Mutai, H. and Heller, S. title: Vertebrate and \invert TRPV--like mechanoreceptors. journal: Cell Calcium year: 2003 month: March volume: 33 number: 5--6 pages: 471--478 note: Review. pmid: 12765692
Changes are highlighted. The replacements are performed in the order given in the file and they are case-sensitive. To convert "vertebrate" to "\vert" and "invertebrate" to "\invert" independent of the case, you need the following file:
invertebrate \invert Invertebrate \invert vertebrate \vert Vertebrate \vert
Don't put the vertrebrate-replacement before the invertebrate, or you'll get something like "in\vert"!
You can use this replacement to get rid of dots within the title if they occur in a specific context, e.g. if you often parse PubMed records that contain "C. elegans" in the title, you can use a macro definition like tis:
C. elegans C elegansand you will no longer get a parse error everytime.
To make sure your bibtex file conforms to bibtex syntax, and can also be understood by the Bibi tool, use the menuitem "Tools -> Check file".This invokes a procedure that checks especially the format of the author names (see authors), but also makes sure the page numbers are separated by -- this looks nicer in LaTeX output.
There is a feature to automatically generate keys for all entries, or for those which don't have a key, or for the selected entry. The key is generated from the author names and the year and has the form Author_year if there's only one author, or FirstAuthor_et_al_year if there are multiple authors. To avoid duplicate keys, a, b, c are appended for the second, third, forth article with the same first author and year. The key generation will only work correctly if the author names are in the correct form (see authors).
The string with the author/editor names should be in the following format
Lastname, Firstname and Anothername, F.M. and Smith Jun., Fred L.
The other format also understood by Bibtex is this
Firstname Lastname and F. M. Anothername and Fred L. Smith Jun.
However, this is ambiguous because it is not clear where the first names end and the last names start. This format is not supported by all functions of Bibi (e.g., xml file generation, and automatic key generation).
The format in which PubMed delivers the authors is
Lastname F, Anothername FM, Smith Jun FL.
If you use the "New Entry ... from Pubmed" feature, this is converted automatically to the "Bibi-accepted" format.
You can search a bibtex file for a specific text. This can be done via the "Find" menu item in the "Edit" menu, or by clicking on the binoculars. Searching gives you a subset of all entries that match your query. The result is only a view, not a copy of the original, so if you modify some entries in the result, the originals will also be modified! If you really want a copy, save the result in a new file, close it and re-load it.
You can search either all fields or one specific field, e.g. if you're looking for an author name, select "author" in the "Field to search" combo box in the "Find" dialog. You can also enter a new field name if you need to, e.g. if you have a field named "foo" in some of your entries... If you regularly want to search for the field "foo" you may want to add it to the combo box. This can be done by specifying a file in the File → Preferences that contains the names of all search fields for the combo box. An example file is contained in the data/ directory of your Bibi distribution: data/bibi-search.dat -- you may want to simply extend that (but you must still specify it in the preferences). The file is plain text and contains one field name per line, empty lines are ignored.
Bibi can export any BibTeX file as an XML file. The XML file has exactly the syntax expected by the (Bib)XML→HTML transforming XSL stylesheet provided at http://www.authopilot.com/xml/. This stylesheet can be used with xsltproc or Saxon (there's one for each transformer) to generate a set of HTML pages. I'll just explain two things about this here. For more information, esp. on the names of special fields in the BibTeX entries, please refer to the authopilot website.
You can assign categories to your entries so that several web pages will be generated, one for each category. To do this, add fields named catid1, catid2, ... to your entry and enter the specific caategroy as the field value.
Example: If catid1 = animal and catid2 = cat or dog, you'll have html pages like this:
Animal
Cat ref1
ref2
Dog ref3
ref4
ref5
Create an extra field called "pdf" and specify the filename of the corresponding pdf document. There will be a link to this location on the web page.