Use Pubmed Author’s Affiliation to map the authors in the world.
Usage: pubmedmap [options] Files
Options:
-h, --help
print help and exit
--helpFormat
What kind of help. One of [usage,markdown,xml].
-o, --output
Output file. Optional . Default: stdout
--version
print version and exit
${PATH}
. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew pubmedmap
The java jar file will be installed in the dist
directory.
The project is licensed under the MIT license.
Should you cite pubmedmap ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md
The current reference is:
http://dx.doi.org/10.6084/m9.figshare.1425030
Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030
use the Affiliation field in XML pubmed and try to insert some XML attributes describing the location.
$ curl -s "https://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>
(...)