PubmedMap

##Motivation

Use Pubmed Author's Affiliation to map the authors

##Compilation

Requirements / Dependencies

java 1.8 http://www.oracle.com/technetwork/java/index.html (NOT the old java 1.7 or 1.6) . Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )
GNU Make > 3.81
curl/wget
git
apache ant is only required to compile htsjdk
xsltproc http://xmlsoft.org/XSLT/xsltproc2.html

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make pubmedmap

by default, the libraries are not included in the jar file, so you shouldn't move them (https://github.com/lindenb/jvarkit/issues/15#issuecomment-140099011 ). You can create a bigger but standalone executable jar by addinging standalone=yes on the command line:

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ make pubmedmap standalone=yes

The required libraries will be downloaded and installed in the dist directory.

edit 'local.mk' (optional)

The a file local.mk can be created edited to override/add some paths.

For example it can be used to set the HTTP proxy:

http.proxy.host=your.host.com
http.proxy.port=124567

##Synopsis

$ java -jar dist/pubmedmap.jar  [options] (stdin|file)

Options

-o|--output (OUTPUT-FILE) Output file. Default:stdout.
-h|--help print help
-version|--version show version and exit

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/pubmed/PubmedMap.java

Motivation

use the Affiliation field in XML pubmed and try to insert some attributes describing the location.

Example


$ curl -s "http://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=26941271&retmode=xml" |java -jar dist/pubmedmap.jar   |\
grep domain -B 5

                 <Author>
                    <LastName>Lai</LastName>
                    <ForeName>Chih-Cheng</ForeName>
                    <Initials>CC</Initials>
                    <AffiliationInfo>
                        <Affiliation domain="tw" place="Taiwan">Department of Intensive Care Medicine, Chi Mei Medical Center, Liouying, Tainan, Taiwan.</Affiliation>
--
                    <LastName>Lee</LastName>
                    <ForeName>Meng-Tse Gabriel</ForeName>
                    <Initials>MG</Initials>
                    <Identifier Source="ORCID">http://orcid.org/0000-0002-2648-1522</Identifier>
                    <AffiliationInfo>
                        <Affiliation domain="tw" place="Taiwan">Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan.</Affiliation>
--
                    <LastName>Lee</LastName>
                    <ForeName>Shih-Hao</ForeName>
                    <Initials>SH</Initials>
                    <Identifier Source="ORCID">http://orcid.org/0000-0002-2648-1522</Identifier>
                    <AffiliationInfo>
                        <Affiliation domain="tw" place="Taiwan">Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan.</Affiliation>
--
                <Author>
                    <LastName>Hsu</LastName>
                    <ForeName>Wan-Ting</ForeName>
                    <Initials>WT</Initials>
                    <AffiliationInfo>
                        <Affiliation domain="tw" place="Taiwan">Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan.</Affiliation>
--
                <Author>
                    <LastName>Chang</LastName>
                    <ForeName>Shy-Shin</ForeName>
                    <Initials>SS</Initials>
                    <AffiliationInfo>
                        <Affiliation domain="tw" place="Taiwan">Department of Family Medicine, Chang Gung Memorial Hospital, Linkou, Taiwan Graduate Institute of Clinical Medical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.</Affiliation>
--
                <Author>
                    <LastName>Chen</LastName>
                    <ForeName>Shyr-Chyr</ForeName>
                    <Initials>SC</Initials>
                    <AffiliationInfo>
                        <Affiliation domain="tw" place="Taiwan">Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan.</Affiliation>
--
                    <LastName>Lee</LastName>
                    <ForeName>Chien-Chang</ForeName>
                    <Initials>CC</Initials>
                    <Identifier Source="ORCID">http://orcid.org/0000-0002-2648-1522</Identifier>
                    <AffiliationInfo>
                        <Affiliation domain="tw" place="Taiwan">Department of Emergency Medicine, National Taiwan University Hospital, Taipei, Taiwan Department of Emergency Medicine, National Taiwan University Hospital, Yunlin Branch, Douliou, Taiwan.</Affiliation>
 (...)