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MED2RIS(1) RefDB Manual MED2RIS(1) NAME med2ris - converts Medline/Pubmed bibliographic data to the RIS format SYNOPSIS med2ris [-e logdest] [-f from-encoding] [-h] [-i] [-l loglevel] [-L log- file] [-o file] [-O file] [-q] [-t to-encoding] [-T type] [-y path] DESCRIPTION med2ris converts Pubmed reference data into RIS data. The converter under- stands both the tagged Pubmed format (which superficially resembles RIS) and the XML format according to the [1]PubMedArticle DTD. 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 in- terfere with command output. 1 will send the output to the syslog fa- cility. Keep in mind that syslog must be configured to accept log mes- sages from user programs, see the syslog(8) man page for further infor- mation. 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 plat- form-dependent and can usually be found in iconv_open(3). If no encod- ings 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 use- ful 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 defini- tions). -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 de- bug 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 com- mand-line switches. -t to-encoding Select the output character encoding. Supported encodings are plat- form-dependent and can usually be found in iconv_open(3). If no encod- ings 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 precom- piled 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 <un- | | | | mapped> tag; the re- | | | | sulting data can be | | | | inspected and then | | | | be sent through sed | | | | to strip off these | | | | additional lines. If | | | | set to f, unknown | | | | tags will be grace- | | | | fully ignored. | +-----------+----------------------+----------------------+ | from_enc | ISO-8859-1 | The character encod- | | | | ing of the input | | | | data | +-----------+----------------------+----------------------+ | to_enc | ISO-8859-1 | The character encod- | | | | ing 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 ap- | | | | propriately. | +-----------+----------------------+----------------------+ | 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 set- | | | | ting (0) allows only | | | | the most important | | | | messages, a high | | | | setting (7) allows | | | | all messages includ- | | | | ing 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 subhead- ings 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 /usr/local/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-man- ual/index.html RefDB manual (web) <[2]http://refdb.sourceforge.net/manual/index.html> RefDB on the web <[3]http://refdb.sourceforge.net/> AUTHOR med2ris was written by Markus Hoenicka <markus@mhoenicka.de>. REFERENCES 1. PubMedArticle DTD http://www.ncbi.nlm.nih.gov/entrez/query/DTD/pubmed_020114.dtd 2. http://refdb.sourceforge.net/manual/index.html http://refdb.sourceforge.net/manual/index.html 3. http://refdb.sourceforge.net/ http://refdb.sourceforge.net/ 2005-10-16 2005-10-16 MED2RIS(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | CONFIGURATION | DATA PROCESSING | FILES | SEE ALSO | AUTHOR | REFERENCES
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