Author Archives: Johanna

Let Your Browser Do the Looking

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You found the perfect article and now need to get it in full text. Why not try a browser plug-in offering one-click access to articles available through open access or MSK Library subscriptions?

The plug-ins Kopernio and Unpaywall work similarly, harvesting content from legal, copyright-compliant sources and linking to full text where found. Kopernio finds freely available content and PDFs available through the Library, while Unpaywall focuses on open access items. Both tools offer free plugins for Chrome and Firefox.

Kopernio’s green “View PDF” icon appears on the PubMed results page under each record. You can also click the Kopernio icon at the bottom left of each record page.

From a record page in PubMed, click the UnPaywall icon on the right to access full text.

After testing both tools, I found that neither worked perfectly—on a page of PubMed search results limited to items with free full text availability, Kopernio found PDFs for 14 out of 20 articles. Unpaywall found PDFs for 9 of the same 20 results.

And don’t forget about the FullText@MSK icon. When you access a database via the MSK Library website and select a citation (first logging into remote access if you are off-site), click on FullText@MSK to see if the full text is immediately available. If it’s not, order a copy via the Library’s Document Delivery service.

Learn more about accessing full text through the Library.

Automating Genetic Variation Classification at MSK

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Researchers at MSK have developed a free online tool to automate the interpretation of genetic variants. The study, led by computational biologist Vignesh Ravichandran and supervised by Dr. Vijai Joseph, was published in February in Genetics in Medicine and reported recently by GenomeWeb.

PathoMAN logo

PathoMAN logo

Until recently only a few genes, like BRCA1 and BRCA2, were tested in people with a family history of cancer. Thanks to declining costs and technological advances, labs now offer broader gene panel testing for hereditary cancers. However, interpreting the genetic variants uncovered by sequencing is time consuming and challenging, taking up two hours for a novel variant.

In response to these challenges, the MSK team created the automated tool PathoMAN. It uses guidelines from the American College of Medical Genetics and Genomics and the Association of Molecular Pathology as a framework while aggregating publicly available records of evidence to determine clinical significance. When tested against a manually classified gold-standard set of 3,513 variants from three major commercial labs, PathoMAN concorded with 94.4% of the manually curated pathogenic variants. PathoMAN is fast and uniform, and it generates a variant curation report for one variant in 30 seconds.

The research team next plans to incorporate natural language processing into PathoMAN to allow it to add scientific literature to its analyses.

PathoMAN is openly available to the research community at http://pathoman.mskcc.org/.

Pancreatic Cancer in the Spotlight

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Last week, Jeopardy! host Alex Trebek announced that he has been diagnosed with stage four pancreatic cancer. New York Times reporter Gina Kolata spoke with experts, including MSK’s Dr. William Jarnagin, to explain the diagnosis.

Most pancreatic tumors are adenocarcinomas, an aggressive cancer with a high risk of recurrence. It is hard to diagnose because the pancreas is located deep inside the body, making biopsies difficult, and the cancer’s symptoms are generally not felt until the cancer is at an advanced stage. In recent years, treatment (surgery when possible, chemotherapy, and sometimes radiation) has improved the median survival time to 54 months.

To learn more about pancreatic cancer, including clinical trials at MSK, visit MSK’s patient information page.