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njahn82/docCN.Rmd

Last active August 29, 2015 14:12
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Sample output
Raw
docCN.md

Example:

Load package

require(devtools)
devtools::install_github("njahn82/rcrossref")
## Downloading github repo njahn82/rcrossref@master
## Installing rcrossref
## '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla CMD INSTALL  \
##   '/private/var/folders/_q/dzf38j_16pqghrqt1b4z52300000gn/T/RtmpTvGQyH/devtools94725c43723/njahn82-rcrossref-72d95cb'  \
##   --library='/Library/Frameworks/R.framework/Versions/3.1/Resources/library'  \
##   --install-tests 
## 
## Reloading installed rcrossref

Retrieve metadata content type application/vnd.crossref.unixsd+xml

library(rcrossref)
doc <- cr_cn("10.1186/1471-2164-14-714", "crossref-tdm")

Show crm-fields

require(XML)
 XML::xpathSApply(doc, "//r:crm-item", namespaces = c(r = "http://www.crossref.org/qrschema/3.0"), xmlAttrs)
##      [,1]             [,2]          [,3]        [,4]          [,5]        
## name "publisher-name" "prefix-name" "member-id" "citation-id" "journal-id"
## type "string"         "string"      "number"    "number"      "number"    
##      [,6]                [,7]           [,8]          [,9]           
## name "deposit-timestamp" "owner-prefix" "last-update" "citedby-count"
## type "number"            "string"       "date"        "number"

Retrieve Citedby count

xpathSApply(doc, "//r:crm-item[@name='citedby-count']", namespaces = c(r = "http://www.crossref.org/qrschema/3.0"), xmlValue)
## [1] "11"

Print full XML

doc
## <?xml version="1.0" encoding="UTF-8"?>
## <crossref_result xmlns="http://www.crossref.org/qrschema/3.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" version="3.0" xsi:schemaLocation="http://www.crossref.org/qrschema/3.0 http://www.crossref.org/schema/queryResultSchema/crossref_query_output3.0.xsd">
##   <query_result>
##     <head>
##       <doi_batch_id>none</doi_batch_id>
##     </head>
##     <body>
##       <query status="resolved">
##         <doi type="journal_article">10.1186/1471-2164-14-714</doi>
##         <crm-item name="publisher-name" type="string">Springer Science + Business Media</crm-item>
##         <crm-item name="prefix-name" type="string">Springer (Biomed Central Ltd.)</crm-item>
##         <crm-item name="member-id" type="number">297</crm-item>
##         <crm-item name="citation-id" type="number">64889155</crm-item>
##         <crm-item name="journal-id" type="number">5911</crm-item>
##         <crm-item name="deposit-timestamp" type="number">20131107140123</crm-item>
##         <crm-item name="owner-prefix" type="string">10.1186</crm-item>
##         <crm-item name="last-update" type="date">2013-11-07 09:01:48.0</crm-item>
##         <crm-item name="citedby-count" type="number">11</crm-item>
##         <doi_record>
##           <crossref xmlns="http://www.crossref.org/xschema/1.1" xsi:schemaLocation="http://www.crossref.org/xschema/1.1 http://doi.crossref.org/schemas/unixref1.1.xsd">
##             <journal>
##               <journal_metadata language="en">
##                 <full_title>BMC Genomics</full_title>
##                 <abbrev_title>BMC Genomics</abbrev_title>
##                 <abbrev_title>BMC Genomics</abbrev_title>
##                 <issn media_type="print">1471-2164</issn>
##               </journal_metadata>
##               <journal_issue>
##                 <publication_date media_type="print">
##                   <year>2013</year>
##                 </publication_date>
##                 <journal_volume>
##                   <volume>14</volume>
##                 </journal_volume>
##                 <issue>1</issue>
##               </journal_issue>
##               <journal_article publication_type="full_text">
##                 <titles>
##                   <title>Comprehensive discovery and characterization of small RNAs in Corynebacterium glutamicum ATCC 13032</title>
##                 </titles>
##                 <contributors>
##                   <person_name sequence="first" contributor_role="author">
##                     <given_name>Almut</given_name>
##                     <surname>Mentz</surname>
##                   </person_name>
##                   <person_name sequence="additional" contributor_role="author">
##                     <given_name>Armin</given_name>
##                     <surname>Neshat</surname>
##                   </person_name>
##                   <person_name sequence="additional" contributor_role="author">
##                     <given_name>Katharina</given_name>
##                     <surname>Pfeifer-Sancar</surname>
##                   </person_name>
##                   <person_name sequence="additional" contributor_role="author">
##                     <given_name>Alfred</given_name>
##                     <surname>Pühler</surname>
##                   </person_name>
##                   <person_name sequence="additional" contributor_role="author">
##                     <given_name>Christian</given_name>
##                     <surname>Rückert</surname>
##                   </person_name>
##                   <person_name sequence="additional" contributor_role="author">
##                     <given_name>Jörn</given_name>
##                     <surname>Kalinowski</surname>
##                   </person_name>
##                 </contributors>
##                 <publication_date media_type="print">
##                   <year>2013</year>
##                 </publication_date>
##                 <pages>
##                   <first_page>714</first_page>
##                 </pages>
##                 <publisher_item>
##                   <identifier id_type="pii">1471-2164-14-714</identifier>
##                 </publisher_item>
##                 <doi_data>
##                   <doi>10.1186/1471-2164-14-714</doi>
##                   <resource>http://www.biomedcentral.com/1471-2164/14/714</resource>
##                 </doi_data>
##                 <citation_list>
##                   <citation key="10.1186/1471-2164-14-714-B1">
##                     <doi>10.1007/s00253-011-3686-4</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B2">
##                     <doi>10.1016/S0168-1656(03)00149-4</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B3">
##                     <doi>10.1016/S0168-1656(03)00154-8</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B4">
##                     <doi>10.1007/s00253-003-1328-1</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B5">
##                     <doi>10.1016/j.jbiotec.2006.12.013</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B6">
##                     <doi>10.1093/nar/gkr883</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B7">
##                     <doi>10.4161/rna.8.3.14421</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B8">
##                     <doi>10.1111/j.1574-6968.2007.01024.x</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B10">
##                     <doi>10.1093/nar/gkl837</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B11">
##                     <doi>10.1186/1471-2164-13-384</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B12">
##                     <doi>10.1038/nrmicro2730</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B13">
##                     <doi>10.1016/j.sbi.2012.04.005</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B14">
##                     <doi>10.1016/j.molcel.2011.08.022</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B16">
##                     <doi>10.1016/j.cell.2009.01.043</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B17">
##                     <doi>10.1016/j.mib.2007.03.008</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B18">
##                     <doi>10.1073/pnas.1113521108</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B19">
##                     <doi>10.1016/j.mib.2007.03.005</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B20">
##                     <doi>10.1073/pnas.0409169102</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B21">
##                     <doi>10.1093/nar/gki715</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B22">
##                     <doi>10.1093/nar/gkg867</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B23">
##                     <doi>10.1016/j.mib.2009.07.006</doi>
##                   </citation>
##                   <citation key="-">
##                     <doi>10.1007/978-1-61779-089-8_5</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B26">
##                     <doi>10.1038/nature08756</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B27">
##                     <doi>10.1038/nrg2484</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B28">
##                     <doi>10.1038/nmeth.1529</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B29">
##                     <doi>10.1016/j.ijmm.2013.04.002</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B30">
##                     <doi>10.1093/bioinformatics/btr151</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B31">
##                     <doi>10.1126/science.1102216</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B32">
##                     <doi>10.1038/nbt1053</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B33">
##                     <doi>10.1016/j.jbiotec.2011.01.017</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B34">
##                     <doi>10.1186/1471-2164-13-445</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B35">
##                     <doi>10.1016/j.bbrc.2005.04.073</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B36">
##                     <doi>10.1128/JB.00112-09</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B37">
##                     <doi>10.1101/gr.849004</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B39">
##                     <doi>10.1186/gb-2007-8-2-r22</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B40">
##                     <doi>10.1073/pnas.0308014101</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B41">
##                     <doi>10.1093/bioinformatics/17.12.1123</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B44">
##                     <doi>10.1128/JB.188.2.724-732.2006</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B47">
##                     <doi>10.1186/1471-2164-9-483</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B48">
##                     <doi>10.1128/JB.00382-07</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B50">
##                     <doi>10.1128/JB.01596-06</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B51">
##                     <doi>10.1186/1471-2199-8-104</doi>
##                   </citation>
##                   <citation key="-">
##                     <doi>10.1099/mic.0.025841-0</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B53">
##                     <doi>10.1128/JB.01338-09</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B54">
##                     <doi>10.1007/s00253-007-0929-5</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B55">
##                     <doi>10.1186/gb-2010-11-3-r31</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B56">
##                     <doi>10.1093/bioinformatics/btk010</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B57">
##                     <doi>10.1371/journal.ppat.1002342</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B58">
##                     <doi>10.1261/rna.034116.112</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B59">
##                     <doi>10.1093/nar/gkq101</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B60">
##                     <doi>10.1186/1471-2164-11-245</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B61">
##                     <doi>10.1146/annurev-genet-102209-163523</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B62">
##                     <doi>10.1093/nar/gkr033</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B63">
##                     <doi>10.1128/JB.186.20.6698-6705.2004</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B65">
##                     <doi>10.1016/0022-2836(92)90621-P</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B66">
##                     <doi>10.1111/j.1365-2958.2010.07161.x</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B67">
##                     <doi>10.1128/JB.00619-06</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B68">
##                     <doi>10.1016/j.tig.2005.04.009</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B69">
##                     <doi>10.1016/j.jmb.2005.10.079</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B70">
##                     <doi>10.1261/rna.7286705</doi>
##                   </citation>
##                   <citation key="-">
##                     <doi>10.1186/1471-2105-8-172</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B73">
##                     <doi>10.1186/1471-2164-12-383</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B74">
##                     <doi>10.1371/journal.pone.0007668</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B75">
##                     <doi>10.1111/j.1365-2958.2009.06777.x</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B76">
##                     <doi>10.1093/nar/gkl453</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B77">
##                     <doi>10.1261/rna.033324.112</doi>
##                   </citation>
##                   <citation key="-">
##                     <doi>10.1099/mic.0.062059-0</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B79">
##                     <doi>10.1093/nar/gkn898</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B80">
##                     <doi>10.1146/annurev.micro.62.081307.162948</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B81">
##                     <doi>10.1093/nar/27.10.2063</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B82">
##                     <doi>10.1038/289751a0</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B83">
##                     <doi>10.1016/j.tig.2005.03.002</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B84">
##                     <doi>10.1128/AEM.00262-08</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B85">
##                     <doi>10.1101/gr.2289704</doi>
##                   </citation>
##                   <citation key="10.1186/1471-2164-14-714-B86">
##                     <doi>10.4161/rna.17212</doi>
##                   </citation>
##                 </citation_list>
##               </journal_article>
##             </journal>
##           </crossref>
##         </doi_record>
##       </query>
##     </body>
##   </query_result>
## </crossref_result>
##
Raw
docCN.Rmd
Example:
### Load package
```{r}
require(devtools)
devtools::install_github("njahn82/rcrossref")
```
### Retrieve metadata content type `application/vnd.crossref.unixsd+xml`
```{r}
library(rcrossref)
doc <- cr_cn("10.1186/1471-2164-14-714", "crossref-tdm")
```
### Show crm-fields
```{r}
require(XML)
XML::xpathSApply(doc, "//r:crm-item", namespaces = c(r = "http://www.crossref.org/qrschema/3.0"), xmlAttrs)
```
### Retrieve Citedby count
```{r}
xpathSApply(doc, "//r:crm-item[@name='citedby-count']", namespaces = c(r = "http://www.crossref.org/qrschema/3.0"), xmlValue)
```
### Print full XML
```{r}
doc
```
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