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BibGene

BibGene is a BibTeX-compatible Macintosh application for maintaining databases of references to scientific papers. BibGene was designed with two purposes:

Ä To maintain BibTeX information in a cross-linked object-oriented format which makes it easier to detect and correct common mistakes such as multiple spellings of an author¼s or journal¼s name.

Ä To provide a way to store information that does not fit well into the BibTeX framework, such as citations from one paper to another, pointers to online preprints, and author addresses.

BibGene is freeware, and may be freely distributed and included on CD-ROMs.


Release Notes

The main new feature in BibGene 1.1 is an Eprint card, for maintaining information about electronic preprints on archives such as the one at xxx.lanl.gov. Adding an Eprint card to a document causes an „eprint=...¾ line to be added to each BibTeX record for the document, and also (if the Eprint archive is set) creates another record of type „@misc¾ for the eprint itself. BibGene 1.2 adds a „Find Unlinked¾ command, which opens all cards that neither link to nor are linked from any other card. Both versions also include many bugfixes and smaller improvements to BibTeX import/export and report generation.


Using BibGene

To load a BibTeX file into BibGene, drag it onto the BibGene application. You may also use BibGene¼s Open command (cmd-L), or select it in the dialog that BibGene starts up with, if you uncheck the box marked „Show Only BibGene Files¾. Use the Export command (cmd-E) to save the database as a BibTeX file. BibGene¼s Save command (cmd-S) instead creates a file in BibGene¼s own internal format.

As its icon indicates, BibGene displays information in cards, each of which is divided into three panes. The top pane, the fields, contains structured information such as the names of other cards. The second pane, the links, lists other cards containing this card¼s name in their fields. The third pane, the text contains free-form text. To change the information in a BibGene database, simply select a field or text pane and type the new value you wish to place there. You can not type into the links pane; instead, it is updated automatically when other cards are changed.

BibGene¼s database engine and user interface are taken from Gene, a popular shareware program for maintaining family history information. For more detailed information on how to use BibGene, and on how BibGene files are formatted, see the Gene User Guide and Technical Notes, available from the Gene home page. We list here some quick tips on usage that might not otherwise be obvious:

Ä To change e.g. the spelling of a the title of a paper, you need only change the Title field in the Document card; all other cards referring to that paper will be automatically updated. Do not attempt to change the spelling by retyping the name in the Publication card, because that will create a new Document card without deleting the old Document or updating other publications that refer to it. The same applies to any other situation in which some fields refer to the names of other fields: always change the name on the original card, not the fields that refer to it on other cards.

Ä The most convenient way to add cards that relate to existing parts of your database is with the Templates submenu of the Cards menu. The commands in this submenu create new cards with some values already filled in, based on the existing card you are currently viewing. Many templates have keyboard shortcuts. For instance, to create a new paper by an author already in your database, open the author¼s card and type cmd-D.

Ä You can search for any substring of a name of a card (such as an author¼s name or document title) by typing the substring into the list of card names obtained by the List Cards command in the Cards menu. The same search feature also works for on-screen displays of reports.

Ä You can produce BibTeX files for a subset of your database by using the Report command (cmd-R). Open the card for an author or location you wish to select the papers of, and select the Preview BibTeX report, with output style Simple Text. BibGene will then output the BibTeX preview to a text file which can be used as input to BibTeX.

Ä If a field is restricted to a limited set of values (such as the BibTeX type field of a Publication card), you can click on the field name to produce a pop-up menu of those values. If a field contains the name of another card, clicking on the field name will instead open that other card.

Ä If a field is used for the name of another card (such as the Document field of a Publication card), you only need to type enough of the name to uniquely identify it, then press the tab key to complete the name.

Ä If you have typed some text into a field, but not yet typed return, you may cancel your changes with cmd-period.


BibGene¼s Cards and Fields

In order to use BibGene effectively, you need to know what information it expects to see in each of its types of cards, and how that information will be copied into the BibTeX files it produces. We list here each of BibGene¼s cards and the expected content of their fields. It is assumed that you already understand BibTeX format.

Author
The name and contact information for a person who wrote a paper. It has the following fields:

Ä Author. The author¼s name, also used as the name of the Author card. Accented characters should be typed with the option key as in any other Macintosh program; they will be translated to TeX when exported to BibTeX. Names may be either first-name-first (¾David Eppstein¾) or last-name-first (¾Eppstein, David¾). If the surname consists of multiple words, and the name is listed first-name-first, the words should be separated by option-spaces so that BibGene can know to alphabetize the name correctly. Modifiers such as „Jr.¾ may be placed after the name (e.g. „Kenneth E. Hoff III¾; do not use a comma). No two Author cards may have the same name in their Author fields.
Ä The Organization lists the university or research lab with which an author is associated. May be left blank; will not be exported to BibTeX.
Ä The Home Page and Email fields list electronic contact information for the author. May be left blank; will not be exported to BibTeX.



Citation
This card indicates that one paper cites another (e.g. as listed in Science Citation Index). It is not exported to BibTeX. It has the following fields:

Ä From. The title of the paper containing the citation. Must be the name of a
Document card.
Ä To. The title of the paper listed in the citation. Must be the name of a
Document card.
Ä Citing versions. A list of BibTeX tags separated by semicolons. Should refer to the paper whose title appears in the From field. May be left blank.
Ä Cited versions. A list of BibTeX tags separated by semicolons. Should refer to the paper whose title appears in the To field. May be left blank.
Ä Date. The date of first publication of the citing paper. Used to sort citations in the links pane and in the Count Citations report.



Document
This card lists the title and authors of a paper. A single paper may occur in multiple publication records, e.g. if it has technical report, conference, and journal versions. A Document card has the following fields:

Ä Title. The title of the paper. It should be capitalized exactly the way you want it to appear in the bibliography; BibGene exports it surrounded by extra brackets to preserve the capitalization. This is used as the name of the Document card, so no two cards may have the same title, even though it is possible for two actual papers to have the same title. If you need to refer to two different papers with the same title, you can avoid name conflicts by modifying the title in this card, without changing the way it appears in the bibliography, e.g. by replacing spaces by option-spaces, or by adding extra curly brackets around some characters.
Ä Authors. A list of author names, separated by semicolons. Each name must be listed in a separate Author card.
Ä Keywords. A list of keywords or key phrases, separated by semicolons. Optional. Each keyword must be listed in a separate Author card.

When exporting a BibTeX file, BibGene will look for a special Document card with the title „(preamble)¾. If found, the text pane of that card will be included in the BibTeX file before any publication records.



Eprint
This card lists information about the inclusion of a paper in an online preprint archive such as xxx.lanl.gov. Its fields are the archive¼s identifier for the paper, the title of the paper, the archive name, and the date of electronic publication. If an eprint card exists for a paper, a line eprint={identifier} will be included in any BibTeX entry for that paper; in addition, Gene will create a BibTeX entry for the eprint itself, using the identifier as the BibTeX tag.



Keyword
A word or phrase occurring in the Keywords field of a Document card. Its one field contains the keyword or key phrase, and is used as the name of the Keyword card; no two cards can have the same name.



Location
A journal, proceedings title, series of books, or other collection in which references might be published. Location cards can also be used to set type=... and howpublished=... fields in BibTeX entries. A location card has the following fields:

Ä Location. The name of the journal, or title of the book or series. Also used as the name of the Location card; no two cards can have the same name.
Ä Type. Which BibTeX tag to use in referring to this location, e.g. booktitle=... or journal=.... This should always be set, but if it isn¼t, journal is assumed.
Ä Publisher. The company or institution which published the book or journal. If not blank, this must be the name of an Organization card.
Ä Series. If this location is a book or conference proceedings, this field can be used to list the book series in which it was published. It should be the name of another Location card.
Ä Number. The book¼s number in the series. Should be blank if the Series field is blank.
Ä Editor. The editor of the book. You can include this for journals too, but most bibliographic styles don¼t. Should be the name of an Author card.



Organization
A corporation, university department, or other publisher of books and papers. It has the following fields:

Ä The Organization field gives the name of the organization, and is also used as the name of the card. No two Organization cards can have the same name.
Ä The Address lists the city or other contact information of the organization. Note that, if an organization is used in a Publication card with an Org Type of address, the address should go in the Organization field, not here.
Ä The Home Page lists electronic contact information for the organization.



Pub Info
These cards are used to record BibTeX information that does not otherwise fit cleanly into BibGene¼s data model. A Pub Info card has the following fields:

Ä Document. The title of the document the information refers to.
Ä Version. If the information is valid only for one of the instances in which this document was published, this field should give the BibTeX tag of the appropriate publication record.
Ä BibTeX key. What keyword to use when listing this information. E.g. to produce a line „month={Spring/Summer}¾, this field should contain the word „month¾.

The text pane of this card is used as the data in the BibTeX line it produces. In the same example, the text should be „Spring/Summer¾.



Publication
These cards are the most important components of a BibGene file; each publication card corresponds to a BibTeX record. It has the following fields:

Ä The BibTeX tag is used as the record identifier in the BibTeX file, and as the name of the publication card. No two publication cards may have the same BibTeX tag.
Ä The BibTeX type gives the type of publication for this record, and must be one of the types predefined in BibTeX such as article or inproceedings.
Ä The Document gives the title of the paper, and must be the name of a Document card.
Ä The Location gives the place in which the paper was published (such as a journal, conference proceedings title, or book series) and must be the name of a Location card. The Location may be blank e.g. for a technical report or thesis.
Ä The Organization gives the name of a publisher, school, or other organization publishing the paper, and must be the name of an Organization card; it may be blank e.g. if the publisher is unknown or is listed in the location card.
Ä The Organization Type is used to determine which BibTeX tag to use when exporting the Organization; e.g. a university might be listed as school=... for a thesis but institution=... for a technical report. The Organization Type should be blank if the organization is blank.
Ä The Cross Ref lists the BibTeX tag of another publication entry giving further information about this publication. We do not recommend using this field in new databases but it is needed for importing old cross-referenced BibTeX files.
Ä The Volume is the volume of the journal or multi-volume book in which the paper was published.
Ä The Number is the issue number of the journal, or series number of the book in which the paper was published.
Ä The Pages gives the page numbers of the paper in its publication location. Some BibTeX users also use this field to denote the total number of pages in a book.
Ä The Date gives the date of publication. Note that unlike BibTeX we do not split the date into separate month and year fields. The date must fit a fixed format in which certain date values such as „Spring/Summer 1998¾ can not be represented; if you need to use such dates, the year should be placed in this field and the month should be in a separate Pub Info card.

If the text pane of a publication card is non-empty, it is exported to a note line in the BibTeX file.



Review
This is a special kind of Publication card used to record publications that review other publications (for instance, in journals such as Math. Reviews). It has the following fields:

Ä Document. The title of the paper under review.
Ä Version. The BibTeX tag of the particular publication of the paper used in this review.
Ä Reviewer. The name of the author of the review, if the review was signed. Should be the name of an Author card, or multiple names separated by semicolons.
Ä Location. The name of the journal in which the reviews were published.
Ä Volume, Number, Pages, Date. Same as for publication cards. However a review might have a number within an issue of a review journal; if so, that should go in the Number field. For instance reviews in
Math. Reviews should be listed with a Volume like „91a¾ and a Number like „68125¾.

When exporting to BibTeX, BibGene will make up a BibTeX tag for the review based on the location, volume, and number.



URL
The online location of a paper. It has the following fields:

Ä Document. The title of the paper that is available online.
Ä Version. If the online preprint reproduces some particular print publication, this field should give the BibTeX tag of the corresponding publication record.
Ä URL. The Uniform Resource Locator specifying how to retrieve the paper from the internet. Also used as the name of the URL card. No two URL cards can have the same name.
Ä Last modified. Optional. Date at which the most recent update to this preprint was made.
Ä Last visited. Optional. Date at which the BibGene user most recently verified that the URL was still valid.