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article_​grabber_​pubmed

PubMed Query Samplehasabstract[text] AND ("humans"[MeSH Terms] OR "humans"[All Fields] OR "human"[All Fields]) AND (("genes"[MeSH Terms] OR "genes"[All Fields] OR "gene"[All Fields]) OR chromosome region[All Fields] OR ("dna"[MeSH Terms] OR "dna"[All Fields]) OR ("genomics"[MeSH Terms] OR "genomics"[All Fields] OR "genomic"[All Fields] OR "genome"[MeSH Terms] OR "genome"[All Fields]) OR ("exome"[MeSH Terms] OR "exome"[All Fields]) OR transcript[All Fields] OR locus[All Fields] OR loci[All Fields] OR variant[All Fields] OR variation[All Fields] OR ("mutation"[MeSH Terms] OR "mutation"[All Fields]) OR ("polymorphism, genetic"[MeSH Terms] OR ("polymorphism"[All Fields] AND "genetic"[All Fields]) OR "genetic polymorphism"[All Fields] OR "polymorphism"[All Fields]) OR SNP[All Fields] OR CNV[All Fields] OR ("indel mutation"[MeSH Terms] OR ("indel"[All Fields] AND "mutation"[All Fields]) OR "indel mutation"[All Fields] OR "indel"[All Fields]) OR monogenic[All Fields] OR ("genotype"[MeSH Terms] OR "genotype"[All Fields]) OR ("alleles"[MeSH Terms] OR "alleles"[All Fields] OR "allele"[All Fields]) OR mutational spectrum[All Fields] OR copy-number variations[All Fields] OR rare variants[All Fields] OR ("genetic therapy"[MeSH Terms] OR ("genetic"[All Fields] AND "therapy"[All Fields]) OR "genetic therapy"[All Fields] OR "genetic"[All Fields]) OR ("biomarkers"[MeSH Terms] OR "biomarkers"[All Fields] OR "biomarker"[All Fields]) OR ("pharmacogenetics"[MeSH Terms] OR "pharmacogenetics"[All Fields] OR "pharmacogenomics"[All Fields]) OR ("pharmacogenetics"[MeSH Terms] OR "pharmacogenetics"[All Fields]) OR ("nutrigenomics"[MeSH Terms] OR "nutrigenomics"[All Fields]) OR ("nutrigenomics"[MeSH Terms] OR "nutrigenomics"[All Fields] OR "nutrigenetics"[All Fields]) OR complex trait[All Fields] OR ("genome-wide association study"[MeSH Terms] OR ("genome-wide"[All Fields] AND "association"[All Fields] AND "study"[All Fields]) OR "genome-wide association study"[All Fields] OR "gwas"[All Fields]) OR ("association"[MeSH Terms] OR "association"[All Fields]) OR germline[All Fields] OR ("diploidy"[MeSH Terms] OR "diploidy"[All Fields] OR "somatic"[All Fields]) OR mosaic[All Fields] OR ("mosaicism"[MeSH Terms] OR "mosaicism"[All Fields]) OR Novo, De[Full Author Name] OR ("congenital"[Subheading] OR "congenital"[All Fields]) OR ("family"[MeSH Terms] OR "family"[All Fields] OR "familial"[All Fields]) OR hereditary[All Fields] OR inherited[All Fields]) AND 1990/02 : 2016/04 [EDAT]
This process fetches documents (abstracts) from a source, in this case Pubmed. The query for abstract retrieval resides in an external configuration file, passed as parameter. Output is cleaned up and formatted as CSV delimited file.
Document Data Extractor
write log
CSV Writer (deprecated)
garbage delimiters
Java Snippet
set query dates
Java Snippet
get query
File Reader (deprecated)
select cols
Column Filter
Column Resorter
year and url
Java Snippet
Document Grabber
writeformatted
CSV Writer (deprecated)
format colnames
Column Rename (deprecated)

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Created by: peleitor
Created at: 2018-03-30
On NodePit since: 2020-05-10
Last update: 2026-08-02
Created with KNIME version: v5.8.3

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