med2ris - Online in the Cloud

PROGRAM:

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.

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