refdb handbook: covers version 0.9.4
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Chapter 7. Data input

Table of Contents
Writing RIS datasets
The Emacs RIS mode
Input filters
Writing risx datasets
Writing extended notes

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.

Writing RIS datasets

Overview

The RIS 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:

       (1)
TY  - BOOK                 (2) 
AU  - Hoenicka,M.          (3)
TI  - The refdb manual
PY  - 2001
ER  -                      (4)
(1)
This is the empty line generated by a linefeed character (0x0A) that precedes every RIS citation, even at the start of a RIS file.
(2)
This is the mandatory first tag, the type specifier. In this case, we're looking at a BOOK entry.
(3)
This and the following lines are the contents proper of the citation. All additional tags would go here as well
(4)
This is the mandatory last tag which closes the citation. Although invisible here, this tag also has a trailing space like all others.

RIS tags

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. 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 an offprint or a file containing 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 an URL pointing to a file. In the latter case, this field has to start with the string "PATH:" with no space between this and the path proper. Using this feature requires some thought and is therefore explained in a separate section.

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

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. M1 is a good place for type or genre information, whereas M3 is suitable to hold the medium.

Format: A string with up to 255 characters

Examples

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  -
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