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MED2RIS(1) | RefDB Manual | MED2RIS(1) |
NAME¶
med2ris - converts Medline/Pubmed bibliographic data to the RIS formatSYNOPSIS¶
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-destinationlog-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.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.FILES¶
PREFIX/etc/refdb/med2risrcThe 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
2005-10-16 | RefDB Manual |