'\" t
.\"     Title: med2ris
.\"    Author: [see the "Author" section]
.\" Generator: DocBook XSL Stylesheets v1.76.1 <http://docbook.sf.net/>
.\"      Date: 2005-10-16
.\"    Manual: RefDB Manual
.\"    Source: RefDB Manual
.\"  Language: English
.\"
.TH "MED2RIS" "1" "2005\-10\-16" "RefDB Manual" "RefDB Manual"
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.SH "NAME"
med2ris \- converts Medline/Pubmed bibliographic data to the RIS format
.SH "SYNOPSIS"
.HP \w'\fBmed2ris\fR\ 'u
\fBmed2ris\fR [\-e\ \fIlogdest\fR] [\-f\ \fIfrom\-encoding\fR] [\-h] [\-i] [\-l\ \fIloglevel\fR] [\-L\ \fIlogfile\fR] [\-o\ \fIfile\fR] [\-O\ \fIfile\fR] [\-q] [\-t\ \fIto\-encoding\fR] [\-T\ \fItype\fR] [\-y\ \fIpath\fR]
.SH "DESCRIPTION"
.PP
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
\m[blue]\fBPubMedArticle DTD\fR\m[]\&\s-2\u[1]\d\s+2\&. In most cases med2ris is able to automatically detect the input data type\&.
.SH "OPTIONS"
.PP
\fB\-e\fR \fIlog\-destination\fR
.RS 4
log\-destination can have the values 0, 1, or 2, or the equivalent strings
\fIstderr\fR,
\fIsyslog\fR, or
\fIfile\fR, 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
\fB\-L\fR
option\&.
.RE
.PP
\fB\-f\fR \fIfrom\-encoding\fR
.RS 4
Select the input character encoding\&. Supported encodings are platform\-dependent and can usually be found in iconv_open(3)\&. If no encodings are specified,
\fBISO\-8859\-1\fR
aka Latin\-1 is assumed\&.
.RE
.PP
\fB\-h\fR
.RS 4
Displays help and usage screen, then exits\&.
.RE
.PP
\fB\-i\fR
.RS 4
Output additional information about unknown or unused tags\&. Mainly useful to debug the conversion if the input format has changed\&.
.RE
.PP
\fB\-l\fR \fIlog\-level\fR
.RS 4
Specify the priority up to which events are logged\&. This is either a number between
0
and
7
or one of the strings
\fIemerg\fR,
\fIalert\fR,
\fIcrit\fR,
\fIerr\fR,
\fIwarning\fR,
\fInotice\fR,
\fIinfo\fR,
\fIdebug\fR, respectively (see also Log level definitions)\&.
\fB\-1\fR
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\&.
.RE
.PP
\fB\-L\fR \fIlog\-file\fR
.RS 4
Specify the full path to a log file that will receive the log messages\&. Typically this would be
/var/log/refdba\&.
.RE
.PP
\fB\-o\fR \fIfile\fR
.RS 4
Send output to
\fIfile\fR\&. If
\fIfile\fR
exists, its contents will be overwritten\&.
.RE
.PP
\fB\-O\fR \fIfile\fR
.RS 4
Send output to
\fIfile\fR\&. If
\fIfile\fR
exists, the output will be appended\&.
.RE
.PP
\fB\-q\fR
.RS 4
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\&.
.RE
.PP
\fB\-t\fR \fIto\-encoding\fR
.RS 4
Select the output character encoding\&. Supported encodings are platform\-dependent and can usually be found in iconv_open(3)\&. If no encodings are specified,
\fBISO\-8859\-1\fR
aka Latin\-1 is assumed\&.
.RE
.PP
\fB\-T\fR \fItype\fR
.RS 4
Overrides the automatic type detection\&. Allowed values for
\fItype\fR
are "tag" and "xml" for the tagged Pubmed format and the XML Pubmed format, respectively\&.
.RE
.PP
\fB\-y\fR \fIconfdir\fR
.RS 4
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\*(Aqt need the
\fB\-y\fR
option unless you use precompiled binaries in unusual locations, e\&.g\&. by relocating a rpm package\&.
.RE
.SH "CONFIGURATION"
.PP
\fBmed2ris\fR
evaluates the file
med2risrc
to initialize itself\&.
.sp
.it 1 an-trap
.nr an-no-space-flag 1
.nr an-break-flag 1
.br
.B Table\ \&1.\ \&med2risrc
.TS
allbox tab(:);
lB lB lB.
T{
Variable
T}:T{
Default
T}:T{
Comment
T}
.T&
l l l
l l l
l l l
l l l
l l l
l l l
l l l
l l l.
T{
outfile
T}:T{
(none)
T}:T{
The default output file name\&.
T}
T{
outappend
T}:T{
t
T}:T{
Determines whether output is appended (\fIt\fR) to an existing file or overwrites (\fIf\fR) an existing file\&.
T}
T{
unmapped
T}:T{
t
T}:T{
If set to \fIt\fR, unknown tags in the input data will be output following a <unmapped> tag; the resulting data can be inspected and then be sent through \fBsed\fR to strip off these additional lines\&. If set to \fIf\fR, unknown tags will be gracefully ignored\&.
T}
T{
from_enc
T}:T{
ISO\-8859\-1
T}:T{
The character encoding of the input data
T}
T{
to_enc
T}:T{
ISO\-8859\-1
T}:T{
The character encoding of the output data
T}
T{
logfile
T}:T{
/var/log/med2ris\&.log
T}:T{
The full path of a custom log file\&. This is used only if logdest is set appropriately\&.
T}
T{
logdest
T}:T{
1
T}:T{
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\&.
T}
T{
loglevel
T}:T{
6
T}:T{
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\&.
T}
.TE
.sp 1
.SH "DATA PROCESSING"
.PP
Keywords with multiple MeSH subheadings are split into multiple keywords with one MeSH subheading each\&. This simplifies searching for MeSH subheadings greatly\&.
.PP
\fBmed2ris\fR
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\&.
.SH "FILES"
.PP
PREFIX/etc/refdb/med2risrc
.RS 4
The global configuration file of med2ris\&.
.RE
.PP
$HOME/\&.med2risrc
.RS 4
The user configuration file of med2ris\&.
.RE
.SH "SEE ALSO"
.PP
\fBRefDB\fR
(7),
\fBbib2ris\fR
(1),
\fBdb2ris\fR
(1),
\fBen2ris\fR
(1),
\fBmarc2ris\fR
(1)\&.
.PP
\fIRefDB manual (local copy) \fR
PREFIX/share/doc/refdb\-<version>/refdb\-manual/index\&.html
.PP
\fIRefDB manual (web) \fR
<\m[blue]\fBhttp://refdb\&.sourceforge\&.net/manual/index\&.html\fR\m[]>
.PP
\fIRefDB on the web \fR
<\m[blue]\fBhttp://refdb\&.sourceforge\&.net/\fR\m[]>
.SH "AUTHOR"
.PP
med2ris was written by Markus Hoenicka <markus@mhoenicka\&.de>\&.
.SH "NOTES"
.IP " 1." 4
PubMedArticle DTD
.RS 4
\%http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_020114.dtd
.RE