information retrieval from pubmed

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Ed ▴ 230

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Last seen 10.2 years ago

Hi there, I am wondering if there is a tool (in bioconductor or not, off-topic I am sorry) that can help me retrieve, for example, all gene symbols that appears in cancer biology in the journals of the last 5 years? Many thanks! Nick [[alternative HTML version deleted]]

Cancer Cancer • 1.3k views

ADD COMMENT • link updated 10.6 years ago by Steve Lianoglou ★ 13k • written 10.6 years ago by Ed ▴ 230

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Steve Lianoglou ★ 13k

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Hi, On Fri, May 9, 2014 at 3:38 PM, Nick <edforum at="" gmail.com=""> wrote: > Hi there, > > I am wondering if there is a tool (in bioconductor or not, off-topic I am > sorry) that can help me retrieve, for example, all gene symbols that > appears in cancer biology in the journals of the last 5 years? There's the cancer census gene list: http://cancer.sanger.ac.uk/cosmic/census Which isn't exactly what you want, but it's perhaps in the same ballpark. -steve -- Steve Lianoglou Computational Biologist Genentech

ADD COMMENT • link 10.6 years ago Steve Lianoglou ★ 13k

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Hi Nick, COSMIC is generally a well curated source for your purpose. Going with Steve's suggestion, you can use the 'COSMIC.67' bioconductor package to get the cancer gene census list: data(cgc_67, package = "COSMIC.67") The Cancer Gene Census (CGC) is a list of genes that are causal to cancer, currently including ~600 genes. If you want to go a step further, you could parse the mutation calls from a number of large scale cancer sequencing studies, mainly the ICGC and TCGA. You can find the somatic mutation calls of 8 TCGA studies in the 'SomaticCancerAlterations' package, and could find the genes overlapping the mutations. Best wishes Julian

ADD REPLY • link 10.5 years ago Julian Gehring ★ 1.3k

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Hi Nick, COSMIC is generally a well curated source for your purpose. Going with Steve's suggestion, you can use the 'COSMIC.67' bioconductor package to get the cancer gene census list: data(cgc_67, package = "COSMIC.67") The Cancer Gene Census (CGC) is a list of genes that are causal to cancer, currently including ~600 genes. If you want to go a step further, you could parse the mutation calls from a number of large scale cancer sequencing studies, mainly the ICGC and TCGA. You can find the somatic mutation calls of 8 TCGA studies in the 'SomaticCancerAlterations' package, and could find the genes overlapping the mutations. Best wishes Julian

ADD REPLY • link 10.5 years ago Julian Gehring ★ 1.3k

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Hi Nick, COSMIC is generally a well curated source for your purpose. Going with Steve's suggestion, you can use the 'COSMIC.67' bioconductor package to get the cancer gene census list: data(cgc_67, package = "COSMIC.67") The Cancer Gene Census (CGC) is a list of genes that are causal to cancer, currently including ~600 genes. If you want to go a step further, you could parse the mutation calls from a number of large scale cancer sequencing studies, mainly the ICGC and TCGA. You can find the somatic mutation calls of 8 TCGA studies in the 'SomaticCancerAlterations' package, and could find the genes overlapping the mutations. Best wishes Julian

ADD REPLY • link 10.5 years ago Julian Gehring ★ 1.3k

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Thanks Julian and Steve. But I think I am more concerned with some results like after information retrieval, kind of a one step before text mining. So those genes after retrieval might just be "associated" with cancer. Is there some online tools to extract those info from like pubmed? Best, Nick On Sat, May 10, 2014 at 3:20 AM, Julian Gehring <julian.gehring@embl.de>wrote: > Hi Nick, > > COSMIC is generally a well curated source for your purpose. > > Going with Steve's suggestion, you can use the 'COSMIC.67' bioconductor > package to get the cancer gene census list: > > data(cgc_67, package = "COSMIC.67") > > The Cancer Gene Census (CGC) is a list of genes that are causal to cancer, > currently including ~600 genes. > > If you want to go a step further, you could parse the mutation calls from > a number of large scale cancer sequencing studies, mainly the ICGC and > TCGA. You can find the somatic mutation calls of 8 TCGA studies in the > 'SomaticCancerAlterations' package, and could find the genes overlapping > the mutations. > > Best wishes > Julian > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane. > science.biology.informatics.conductor > [[alternative HTML version deleted]]

ADD REPLY • link 10.5 years ago Ed ▴ 230

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