Provided by: refdb-clients_1.0.2-3ubuntu1_amd64 
NAME
med2ris - converts Medline/Pubmed bibliographic data to the RIS format
SYNOPSIS
med2ris [-e logdest] [-f from-encoding] [-h] [-i] [-l loglevel] [-L logfile] [-o file] [-O file] [-q]
[-t to-encoding] [-T type] [-y path]
DESCRIPTION
med2ris converts Pubmed reference data into RIS data. The converter understands both the tagged Pubmed
format (which superficially resembles RIS) and the XML format according to the PubMedArticle DTD[1]. In
most cases med2ris is able to automatically detect the input data type.
OPTIONS
-e log-destination
log-destination can have the values 0, 1, or 2, or the equivalent strings stderr, syslog, or file,
respectively. This value specifies where the log information goes to. 0 (zero) means the messages
are sent to stderr. They are immediately available on the screen but they may interfere with command
output. 1 will send the output to the syslog facility. Keep in mind that syslog must be configured
to accept log messages from user programs, see the syslog(8) man page for further information.
Unix-like systems usually save these messages in /var/log/user.log. 2 will send the messages to a
custom log file which can be specified with the -L option.
-f from-encoding
Select the input character encoding. Supported encodings are platform-dependent and can usually be
found in iconv_open(3). If no encodings are specified, ISO-8859-1 aka Latin-1 is assumed.
-h
Displays help and usage screen, then exits.
-i
Output additional information about unknown or unused tags. Mainly useful to debug the conversion if
the input format has changed.
-l log-level
Specify the priority up to which events are logged. This is either a number between 0 and 7 or one of
the strings emerg, alert, crit, err, warning, notice, info, debug, respectively (see also Log level
definitions). -1 disables logging completely. A low log level like 0 means that only the most
critical messages are logged. A higher log level means that less critical events are logged as well.
7 will include debug messages. The latter can be verbose and abundant, so you want to avoid this log
level unless you need to track down problems.
-L log-file
Specify the full path to a log file that will receive the log messages. Typically this would be
/var/log/refdba.
-o file
Send output to file. If file exists, its contents will be overwritten.
-O file
Send output to file. If file exists, the output will be appended.
-q
Start without reading the configuration files. The client will use the compile-time defaults for all
values that you do not set with command-line switches.
-t to-encoding
Select the output character encoding. Supported encodings are platform-dependent and can usually be
found in iconv_open(3). If no encodings are specified, ISO-8859-1 aka Latin-1 is assumed.
-T type
Overrides the automatic type detection. Allowed values for type are "tag" and "xml" for the tagged
Pubmed format and the XML Pubmed format, respectively.
-y confdir
Specify the directory where the global configuration files are Note: By default, all RefDB
applications look for their configuration files in a directory that is specified during the configure
step when building the package. That is, you don't need the -y option unless you use precompiled
binaries in unusual locations, e.g. by relocating a rpm package.
CONFIGURATION
med2ris evaluates the file med2risrc to initialize itself.
Table 1. med2risrc
┌──────────┬──────────────────────┬──────────────────────────────┐
│Variable │ Default │ Comment │
├──────────┼──────────────────────┼──────────────────────────────┤
│outfile │ (none) │ The default output file │
│ │ │ name. │
├──────────┼──────────────────────┼──────────────────────────────┤
│outappend │ t │ Determines whether output is │
│ │ │ appended (t) to an existing │
│ │ │ file or overwrites (f) an │
│ │ │ existing file. │
├──────────┼──────────────────────┼──────────────────────────────┤
│unmapped │ t │ If set to t, unknown tags in │
│ │ │ the input data will be │
│ │ │ output following a │
│ │ │ <unmapped> tag; the │
│ │ │ resulting data can be │
│ │ │ inspected and then be sent │
│ │ │ through sed to strip off │
│ │ │ these additional lines. If │
│ │ │ set to f, unknown tags will │
│ │ │ be gracefully ignored. │
├──────────┼──────────────────────┼──────────────────────────────┤
│from_enc │ ISO-8859-1 │ The character encoding of │
│ │ │ the input data │
├──────────┼──────────────────────┼──────────────────────────────┤
│to_enc │ ISO-8859-1 │ The character encoding of │
│ │ │ the output data │
├──────────┼──────────────────────┼──────────────────────────────┤
│logfile │ /var/log/med2ris.log │ The full path of a custom │
│ │ │ log file. This is used only │
│ │ │ if logdest is set │
│ │ │ appropriately. │
├──────────┼──────────────────────┼──────────────────────────────┤
│logdest │ 1 │ The destination of the log │
│ │ │ information. 0 = print to │
│ │ │ stderr; 1 = use the syslog │
│ │ │ facility; 2 = use a custom │
│ │ │ logfile. The latter needs a │
│ │ │ proper setting of logfile. │
├──────────┼──────────────────────┼──────────────────────────────┤
│loglevel │ 6 │ The log level up to which │
│ │ │ messages will be sent. A low │
│ │ │ setting (0) allows only the │
│ │ │ most important messages, a │
│ │ │ high setting (7) allows all │
│ │ │ messages including debug │
│ │ │ messages. -1 means nothing │
│ │ │ will be logged. │
└──────────┴──────────────────────┴──────────────────────────────┘
DATA PROCESSING
Keywords with multiple MeSH subheadings are split into multiple keywords with one MeSH subheading each.
This simplifies searching for MeSH subheadings greatly.
med2ris does not validate the input files. That is, the input files must stick to the rules of the data
sources, otherwise the conversion results are not predictable.
FILES
PREFIX/etc/refdb/med2risrc
The global configuration file of med2ris.
$HOME/.med2risrc
The user configuration file of med2ris.
SEE ALSO
RefDB (7), bib2ris (1), db2ris (1), en2ris (1), marc2ris (1).
RefDB manual (local copy) PREFIX/share/doc/refdb-<version>/refdb-manual/index.html
RefDB manual (web) <http://refdb.sourceforge.net/manual/index.html>
RefDB on the web <http://refdb.sourceforge.net/>
AUTHOR
med2ris was written by Markus Hoenicka <markus@mhoenicka.de>.
NOTES
1. PubMedArticle DTD
http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_020114.dtd