2017
DOI: 10.7554/elife.28801
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Towards PubMed 2.0

Abstract: Staff from the National Center for Biotechnology Information in the US describe recent improvements to the PubMed search engine and outline plans for the future, including a new experimental site called PubMed Labs.

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Cited by 95 publications
(69 citation statements)
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“…The task of linking omics data (fields of study in biology ending in -omics such as genomics and proteomics) with scientific literature is further complicated by multiple synonyms and abbreviations used by researchers to refer to one variant, gene, disease or chemical in publications ( 7 ). Hence, finding comprehensive and contextualized information about a specific genomic variation becomes an arduous task, as researchers and healthcare professionals rely on curated databases or keyword-based search engines ( 8 , 9 ) that are not suitable for the variety of formats and complexity in which a variation can be cited in literature. Consequently, a variant-oriented semantic search system, which improves the quality (sensitivity and specificity) of search results, is greatly needed.…”
Section: Introductionmentioning
confidence: 99%
“…The task of linking omics data (fields of study in biology ending in -omics such as genomics and proteomics) with scientific literature is further complicated by multiple synonyms and abbreviations used by researchers to refer to one variant, gene, disease or chemical in publications ( 7 ). Hence, finding comprehensive and contextualized information about a specific genomic variation becomes an arduous task, as researchers and healthcare professionals rely on curated databases or keyword-based search engines ( 8 , 9 ) that are not suitable for the variety of formats and complexity in which a variation can be cited in literature. Consequently, a variant-oriented semantic search system, which improves the quality (sensitivity and specificity) of search results, is greatly needed.…”
Section: Introductionmentioning
confidence: 99%
“…These data facilitate interpretation of other patient's variants by providing classifications of variants that were previously assessed in this particular genome diagnostic lab. For other variants, after filtering for potential pathogenicity, various databases are consulted such as Human Gene Mutation Database (HGMD; Stenson et al, ), Leiden Open Variation Database (LOVD; Fokkema et al, ) and ClinVar (Landrum et al, ) as well as resources such as PubMed (Fiorini, Lipman, & Lu, ) and OMIM (Amberger, Bocchini, Schiettecatte, Scott, & Hamosh, ). In the absence of a positive hit or any clear in silico prediction of the variant effect, clinicians have to resort to contacting their peers in other diagnostic labs to determine whether they have seen these variants before.…”
Section: Introductionmentioning
confidence: 99%
“…To this end, we compare the features of PubMed Labs with those in PubMed and its current mobile version (PubMed Mobile). In doing so, we show the differences between PubMed Labs and the current ones and how it is advanced in ultimately becoming PubMed 2.0 ( 1 ). We also demonstrate that all of the features contained in PubMed Mobile are already made available and enriched in PubMed Labs.…”
Section: Introductionmentioning
confidence: 99%
“…(iv) Finally, please note that by design PubMed Labs includes only a limited set of highly used features ( 13 ) and not the entire set currently available in PubMed. Based on public testing and feedback, we will iteratively include additional functions and improve the system towards PubMed 2.0 ( 1 ) over time. PubMed Labs was first made public in October 2017 and is currently accessed by thousands of users from around the world each day.…”
Section: Introductionmentioning
confidence: 99%