Table of Contents
This chapter explains the ways how you can generate reference and extended note data suitable for RefDB databases. We'll cover manual generation of RIS files and automatic conversion of other bibliographic data with the help of input filters. You'll learn about writing risx documents, a new XML data format designed to simplify funneling XML or SGML bibliographic data into RefDB. risx is the preferable format to fully utilize RefDB's capabilities. Finally we'll cover writing extended notes that allow to append additional information to objects in your database or to categorize references in a very flexible way.
To actually import the resulting RIS datasets into the RefDB database, use the addref command of the refdbc command line client, as explained in the next chapter.
The Reference Manager Manual contains sort of a specification of the RIS data format. This format is a tagged file format with the following general rules:
A file can hold one or more references
Each reference starts with a newline. This also means that every RIS file starts with an empty line.
There can be only one tag per line.
The tag must be at the very beginning of the line.
The tags consist of two capital letters denoting the type, followed by two spaces, a dash, and another space.
The first tag of each reference is the Type tag (TY - )
The last tag of each reference is the End tag (ER - )
The sequence of all other elements is arbitrary.
Note
There is one exception: In the case of multiple authors, editors, or series editors, the sequence of these authors is significant. E.g. the first AU tag will be used as the first author, the last one as the last author.
Therefore a minimal RIS file may look like this:
TY - BOOK
AU - Hoenicka,M.
TI - The RefDB manual PY - 2001 ER -
| | This is the empty line generated by a linefeed character (0x0A) that precedes every RIS citation, even at the start of a RIS file. |
| | This is the mandatory first tag, the type specifier. In this case, we're looking at a BOOK entry. |
| | This and the following lines are the contents proper of the citation. All additional tags would go here as well |
 | This is the mandatory last tag which closes the citation. Although invisible here, this tag also has a trailing space like all others. |
The RIS specification has no built-in means to specify the character encoding of the data. Commercial applications usually expect the data to be supplied in a particular encoding (e.g. Reference Manager uses the Windows ANSI character set). RefDB does not have this limitation, you are free to use any encoding available on your platform (except UTF-16 and UTF-32). However, you should be aware that this may cause an interchange issue if you plan to use these data in a commercial reference management program. In any case, as the datasets do not specify their encoding, you have to use -E option of the getref command if your input data use an encoding different from the default (UTF-8).
The following list shows all available tags and their use.
Note
Please keep in mind that a full tag consists of the letters mentioned below followed by two spaces, a dash, and another space. E.g. the first tag below would be written as “TY - ” in a RIS file.
- TY
This tag specifies the type of the reference and must be the first tag of each RIS dataset, preceeded by a newline.
Format: This can be any of the following strings:
ABST (abstract reference)
ADVS (audiovisual material)
ART (art work)
BILL (bill/resolution)
BOOK (whole book reference)
CASE (case)
CHAP (book chapter reference)
COMP (computer program)
CONF (conference proceeding)
CTLG (catalog)
DATA (data file)
ELEC (electronic citation)
GEN (generic)
HEAR (hearing)
ICOMM (internet communication)
INPR (in press reference)
JFULL (journal/periodical - full)
JOUR (journal/periodical reference)
MAP (map)
MGZN (magazine article)
MPCT (motion picture)
MUSIC (music score)
NEWS (newspaper)
PAMP (pamphlet)
PAT (patent)
PCOMM (personal communication)
RPRT (report)
SER (serial - book, monograph)
SLIDE (slide)
SOUND (sound recording)
STAT (statute)
THES (thesis/dissertation)
UNBILL (unenacted bill/resolution)
UNPB (unpublished work reference)
VIDEO (video recording)
- ER
This empty tag denotes the end of the reference. It must be the last tag of each RIS dataset.
- ID
This tag is used to uniquely identify the reference in the database. The value is either the unique ID that RefDB generates when a reference is imported into a database, or a unique citation key. The latter can be supplied by the user. If no citation key is specified when adding a reference, RefDB will automatically generate a unique citation key, based on the name of the first author and the publication year. RefDB will create an unique ID value for internal use regardless of whether a citation key is provided or not.
Note
ID values are always numerical (e.g. "11"), whereas citation keys are alphanumerical (e.g. "Miller1999").
While you are free to choose any reasonable citation key (as long as it is unique within the database), you should not attempt to create a ID value manually. It is ignored when adding the dataset, but it may overwrite an existing entry if you update a reference. Along the same line, you should leave the ID tag alone if you retrieve a dataset from the database and plan to update it. The citation key in the retrieved data set is essential to match the modified data with the copy in the database.
ID Format: Integer >0.
Citation key Format: A string with up to 255 characters. You should use 7-bit ASCII characters only to avoid character encoding issues. If you want to work with SGML documents, the citation keys should be all uppercase.
- TI
This is the title of a publication. For BOOK and UNPB references this is the same as the BT tag.
Format: A string with unlimited length.
- T2
This is the secondary title of a publication, e.g. the book title for a CHAP reference.
Format: A string with unlimited length.
- T3
This is the tertiary title of a publication, e.g. the series title for a CHAP reference.
Format: A string with unlimited length.
- AU
Synonym: A1. This is the name of one author of the reference. If a reference has multiple authors, each author is specified with an AU tag on a separate line. The number of authors per RIS dataset is not limited. The sequence of the authors in the authorlist will be determined from the sequence as they appear in the RIS dataset.
Format: A string with up to 255 characters in the form: Lastname[,(F.|First)[(M.|Middle)...][,Suffix]]. First and middle names can either be abbreviated or spelled out. Use periods to separate initials, and spaces to separate spelled-out first or middle names. Lastname can be a corporate name. Some examples for valid entries:
King,B.B.
Benberg,Steven C.
Mellencamp,John Cougar,Jr.
Van Zandt,Steven
- A2
Synonym: ED. This is the name of an editor of the reference, e.g. an editor of the book in which a CHAP reference was published. The same formatting requirements as for AU apply.
- A3
This is the name of a series editor of the reference, e.g. an editor of a series of books in one of which a CHAP reference was published. The same formatting requirements as for AU apply.
- PY
Synonym: Y1. This is the primary publication date.
Format: A string with the format “YYYY/MM/DD/otherinfo”, where YYYY denotes the four-digit year, MM and DD denote the two-digit month and day, respectively, and otherinfo denotes any other information with up to 255 characters. If any of these parts is not available, it can be left out, but the slashes must be present. E.g. “1999///Christmas edition” is a valid string.
- Y2
This is the secondary publication date.
Format: A string with the format “YYYY/MM/DD/otherinfo”, where YYYY denotes the four-digit year, MM and DD denote the two-digit month and day, respectively, and otherinfo denotes any other information with up to 255 characters. If any of these parts is not available, it can be left out, but the slashes must be present. E.g. “1999///Christmas edition” is a valid string.
- N1
The notes. This can be any form of additional information, like pointers to corrections or editorials, or just personal notes about the contents of the reference.
Format: A string with unlimited length
- N2
Synonym: AB. The abstract of a reference.
Format: A string with unlimited length
- KW
A keyword. If a publication has multiple keywords, each goes on a separate line preceeded with this tag. Keywords are crucial to find references in larger databases.
Format: A string with up to 255 characters
- RP
The reprint status of a reference. This can be any of the following strings:
IN FILE
NOT IN FILE
ON REQUEST MM/DD/YY
- AV
The availability information. This is a hint where you can find a physical copy or offprint of the reference.
Format: A string with up to 255 characters. This can either be a plain-text description like "methods folder, second drawer from top in the green cabinet on the yellow hallway", or a call number.
- SP
The start page of the reference
Format: A string with up to 255 characters
- EP
The end page of the reference
Format: A string with up to 255 characters
- JO
The abbreviated name of a journal or periodical.
Format: A string with up to 255 characters. The components should be separated by a single space without a period after abbreviated words. If you use periods, these should not be followed by spaces.
- JF
The full name of a journal or periodical.
Format: A string with up to 255 characters
- J1
The abbreviated name of a journal or periodical (user abbreviation 1).
Format: A string with up to 255 characters
- J2
The abbreviated name of a journal or periodical (user abbreviation 2).
Format: A string with up to 255 characters
- VL
The volume of the journal/periodical.
Format: A string with up to 255 characters
- IS
The issue of the journal/periodical
Format: A string with up to 255 characters
- CY
City of publication of a book.
Format: A string with up to 255 characters
- PB
Name of the publisher or the publishing company.
Format: A string with up to 255 characters
- SN
The ISBN or ISSN number.
Format: A string with up to 255 characters
- AD
The contact address, usually the any combination of postal or email address and the phone or fax number of the corresponding author.
Format: A string of unlimited length
- UR
The URL of an online version of the reference.
Format: A string with up to 255 characters
- L1 through L4
These fields hold the URLs of an offprint (e.g. a PDF or Postscript copy), of the fulltext (often available as HTML in addition to PDF), of a related resource, and of an image, respectively. Multiple entries of each type per reference are allowed. In contrast to the UR field above, these fields hold information which is stored for each user separately.
The L1 field is meant to store the location of local offprints. It is most common to use the "file://" protocol and specify a full path (starting with another slash on Unix systems) or a relative path. In the latter case the path is expanded with the pdfroot setting before it is displayed to the user. Using this feature requires some thought and is therefore explained in a separate section.
Format: A string with up to 255 characters
- U1 through U5
The user-defined fields 1 through 5. These fields are not intended to be filled with random bits of information. Each database should have a set of rules what information is to be stored in these fields.
A possible use for these fields is some relevance indicator (e.g. “#” means low, “#####” means high relevance).
You may also use one of these fields to create the equivalents of “folders” that some other reference databases praise as the panacea to organize your references. Just assign the same value to one of these fields for all references that belong to the same folder. Retrieve them by specifying this value in addition to your other search criteria.
Format: A string with up to 255 characters
- M1 through M3
The miscellaneous fields 1 through 3. These fields are used by various reference types to deal with additional information that doesn't fit anywhere else, and the usage differs from one type to another. An important information among the data contained here is the digital object identifier. Please refer to the Reference Manager Manual for the nasty details of these fields.
Format: A string with up to 255 characters
The following listing shows a few examples of valid RIS datasets. See also the example RIS file in the /usr/local/share/refdb/examples directory.
Note
Long entries like abstracts were divided into several lines using slashes. This is to make it more human-readable for this manual and should not be used in real data.
TY - JOUR T1 - T-lymphocytes from normal human peritoneum are phenotypically / different from their counterparts in peripheral blood and CD3- lymphocyte / subsets contain mRNA for the recombination activating gene RAG-1 A1 - Hartmann,J. A1 - Maassen,V. A1 - Rieber,P. A1 - Fricke,H. Y1 - 1995/// KW - Peritoneum KW - T cell KW - T lymphocyte KW - lymphocyte KW - immunology KW - CD3 KW - human KW - Adult KW - blood RP - IN FILE SP - 2626 EP - 2631 JF - European Journal of Immunology JA - Eur.J.Immunol. VL - 25 N2 - These findings are compatible with the hypothesis that the adult / human peritoneum provides a microenvirinment capable of supporting a / thymus-independent differentiation of T lymphocytes. ER - TY - BOOK T1 - Porphyrins and metalloporphyrins A1 - Smith,K.M. Y1 - 1975/// KW - Porphyrins KW - Metalloporphyrins KW - Spectrophotometry [methods] KW - spectroscopy RP - NOT IN FILE CY - Amsterdam PB - Elsevier Scientific Publishing Company ER - TY - CHAP T1 - Physiological studies of the natriuretic peptide family A1 - Lewicki,J.A. A1 - Protter,A.A. Y1 - 1995/// N1 - Atrial Natriuretic Peptide Cardiac synthesis and secretion of / ANP Regulation of ANP Gene Expression Regulation of ANP Release / ANP Receptors Biologic Actions of ANP Brain Natriuretic Peptide (BNP) / BNP Structure Biosynthesis of BNP Biological Actions of BNP C-Type / Natriuretic Peptide (CNP) Biologic Actions of CNP Modulators of / Natriuretic Peptide Clearance Effects of Clearance Receptor Blockers / Effects of Neutral Endopeptidase Inhibitors Role of the Natriuretic / Peitedes in Physiology and Disease Hypertension Congestive Heart / Failure Supraventricular Tachyarrhythmias Acute Renal Dysfunction KW - natriuretic KW - ANF KW - ANP KW - receptors KW - BNP KW - CNP KW - hypertension KW - congestive heart failure KW - review KW - cardiac KW - regulation KW - gene expression KW - expression KW - brain KW - structure KW - biosynthesis KW - receptor KW - inhibitor KW - physiology KW - renal KW - study KW - Peptides KW - atrial natriuretic peptide KW - MODULATOR KW - secretion KW - Gene Expression Regulation RP - IN FILE SP - 1029 EP - 1053 VL - 2 T2 - Hypertension: Pathophysiology, Diagnosis, and Management A2 - Laragh,J.H. A2 - Brenner,B.M. IS - 61 CY - New York PB - Raven Press, Ltd. ER -