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jeter.js
function accept(aref)
{
var i;
var article= aref.medlineCitation.article;
if(! article ) return false;
var abstractE = article.getAbstract();
if(!abstractE) return false;
for(i=0;i< abstractE.abstractText.size();++i)
{
if(abstractE.abstractText.get(i).value.contains("code.google")) return true;
}
return false;
}
accept(article);
Raw
journal_bioinformatics.xml
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<ArticleTitle>SNP calling by sequencing pooled samples.</ArticleTitle>
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<ArticleTitle>A graph-based approach for designing extensible pipelines.</ArticleTitle>
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<ArticleTitle>A new strategy for better genome assembly from very short reads.</ArticleTitle>
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<PubmedArticle>
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<ArticleTitle>AIGO: towards a unified framework for the analysis and the inter-comparison of GO functional annotations.</ArticleTitle>
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<PubmedArticle>
<MedlineCitation Status="MEDLINE" Owner="NLM">
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<Article PubModel="Electronic">
<ArticleTitle>An integrated workflow for robust alignment and simplified quantitative analysis of NMR spectrometry data.</ArticleTitle>
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<PubmedArticle>
<MedlineCitation Status="MEDLINE" Owner="NLM">
<PMID Version="1">21846404</PMID>
<Article PubModel="Electronic">
<ArticleTitle>Prediction of conformational B-cell epitopes from 3D structures by random forests with a distance-based feature.</ArticleTitle>
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<PubmedArticle>
<MedlineCitation Status="MEDLINE" Owner="NLM">
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<ArticleTitle>AMS 3.0: prediction of post-translational modifications.</ArticleTitle>
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<PubmedArticle>
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<PMID Version="1">19900301</PMID>
<Article PubModel="Electronic">
<ArticleTitle>bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics.</ArticleTitle>
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<ArticleTitle>BSMAP: whole genome bisulfite sequence MAPping program.</ArticleTitle>
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Raw
run.sh
java -jar dist-1.128/pubmeddump.jar '"Bioinformatics"[Journal]' | java -jar dist-1.128/pubmedfilterjs.jar -f jeter.js | java -jar dist-1.128/skipxmlelements.jar -e '(element.localName=="PubmedArticle" || element.localName=="MedlineCitation" || element.localName=="PMID" || element.localName=="PubmedArticleSet"|| element.localName=="Article" || element.localName=="ArticleTitle"? 1:0)' > result.xml
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