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Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?

Publication Date: September 14, 2011
Journal: PLOS ONE
Authors: Devabhaktuni Srikrishna & Marc A. Coram
Volume: 6
Issue: 9
Pages: e24920
DOI: https://dx.plos.org/10.1371/journal.pone.0024920
Publisher URL: http://journals.plos.org/plosone/article?id=10.1371%2Fjournal.pone.0024920
PubMed: http://www.ncbi.nlm.nih.gov/pubmed/21935487
PubMed Central: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3173492
Europe PMC: http://europepmc.org/abstract/MED/21935487
Scopus: 80052829301
Mendeley: http://www.mendeley.com/research/using-noun-phrases-navigating-biomedical-literature-pubmed-updates-we-losing-track

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Figshare10 Dec 12:09 UTC

Figshare

{"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/371189/Table_S1.pdf", "https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/371376/Table_S2.pdf"], "description"=>"<div>Author-supplied citations are a fraction of the related literature for a paper. The “related citations” on PubMed is typically dozens or hundreds of results long, and does not offer hints why these results are related. Using noun phrases derived from the sentences of the paper, we show it is possible to more transparently navigate to PubMed updates through search terms that can associate a paper with its citations. The algorithm to generate these search terms involved automatically extracting noun phrases from the paper using natural language processing tools, and ranking them by the number of occurrences in the paper compared to the number of occurrences on the web. We define search queries having at least one instance of overlap between the author-supplied citations of the paper and the top 20 search results as citation validated (CV). When the overlapping citations were written by same authors as the paper itself, we define it as CV-S and different authors is defined as CV-D. For a systematic sample of 883 papers on PubMed Central, at least one of the search terms for 86% of the papers is CV-D versus 65% for the top 20 PubMed “related citations.” We hypothesize these quantities computed for the 20 million papers on PubMed to differ within 5% of these percentages. Averaged across all 883 papers, 5 search terms are CV-D, and 10 search terms are CV-S, and 6 unique citations validate these searches. Potentially related literature uncovered by citation-validated searches (either CV-S or CV-D) are on the order of ten per paper – many more if the remaining searches that are not citation-validated are taken into account. The significance and relationship of each search result to the paper can only be vetted and explained by a researcher with knowledge of or interest in that paper. </div>", "links"=>[], "tags"=>["noun", "phrases", "navigating", "biomedical", "updates", "are", "losing"], "article_id"=>133339, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Science Policy"], "users"=>["Devabhaktuni Srikrishna", "Marc A. Coram"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0024920"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/Using_Noun_Phrases_for_Navigating_Biomedical_Literature_on_Pubmed_How_Many_Updates_Are_We_Losing_Track_of_/133339", "title"=>"Using Noun Phrases for Navigating Biomedical Literature on Pubmed: How Many Updates Are We Losing Track of?", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2011-09-14 00:55:39"}
{"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/735809/Figure_1.tif"], "description"=>"The axes are on a log-scale; a quantile regression curve runs through the scatterplot. Phrases that most representative of the document's contents are along the upper boundary; they have high document count for their web count. Less relevant phrases fall below.", "links"=>[], "tags"=>["counts", "phrases", "detection"], "article_id"=>406164, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Science Policy"], "users"=>["Devabhaktuni Srikrishna", "Marc A. Coram"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0024920.g001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Document_and_web_counts_for_phrases_appearing_in_an_example_paper_about_nuclear_detection_technologies_/406164", "title"=>"Document and web counts for phrases appearing in an example paper about nuclear detection technologies.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-14 01:42:44"}
{"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/735880/Figure_2.tif"], "description"=>"We rank them based on the number of occurrences of the term in the paper itself (document count) and inversely to the number of occurrences of that same term on the web (web count). To visually aid in phrase selection the ranked phrases are further split into three columns while maintaining the ranking in each column: those which occur on the web more than 10 million times (broad), those which occur between 100 and 10 million times (specific), and those which occur less than 100 times (rare).", "links"=>[], "tags"=>["ranking", "noun", "phrases", "death-1", "heterologous", "prime-boost", "vaccines"], "article_id"=>406232, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Science Policy"], "users"=>["Devabhaktuni Srikrishna", "Marc A. Coram"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0024920.g002"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_The_ranking_of_noun_phrases_for_the_paper_8220_Programmed_cell_death_1_PD_1_at_the_heart_of_heterologous_prime_boost_vaccines_and_regulation_of_CD8_T_cell_immunity_8221_/406232", "title"=>"The ranking of noun phrases for the paper, “Programmed cell death-1 (PD-1) at the heart of heterologous prime-boost vaccines and regulation of CD8+ T cell immunity.”", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-14 01:43:52"}
{"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/735937/Figure_3.tif"], "description"=>"For 883 papers, this figure shows the number of PubMed search terms per paper which are validated by citations from different authors (CV-D), which ranges from 0 to well over 20 in some cases out of a maximum possible of 40 (20 from each of the specific and rare lists). The search results which are not author-supplied citations in these CV-D searches can in turn be used to suggest related literature for the paper.", "links"=>[], "tags"=>["validated", "citations"], "article_id"=>406300, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Science Policy"], "users"=>["Devabhaktuni Srikrishna", "Marc A. Coram"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0024920.g003"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Searches_validated_by_citations_by_different_authors_/406300", "title"=>"Searches validated by citations by different authors.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-14 01:45:00"}
{"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/735987/Figure_4.tif"], "description"=>"For 883 papers, this figure shows the total number of different citations from the paper that validate all the search terms for each paper. Each paper may have multiple search terms whose top 20 search results are validated by citations. This number ranges from 0 to well over 20 citations across the papers.", "links"=>[], "tags"=>["validate"], "article_id"=>406354, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Science Policy"], "users"=>["Devabhaktuni Srikrishna", "Marc A. Coram"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0024920.g004"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Citations_that_validate_the_search_terms_for_each_paper_/406354", "title"=>"Citations that validate the search terms for each paper.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-14 01:45:54"}
{"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/736033/Figure_5.tif"], "description"=>"For 883 papers, this figure shows the total number of different citations from the paper that validate the top 20 “related citations” from PubMed for each paper. This number ranges from 0 to well over 20 citations across the papers. This number ranges from 0 to well over 10 citations across the papers.", "links"=>[], "tags"=>["citations"], "article_id"=>406396, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Science Policy"], "users"=>["Devabhaktuni Srikrishna", "Marc A. Coram"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0024920.g005"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Validating_citations_per_paper_for_PubMed_s_8220_related_citations_8221_/406396", "title"=>"Validating citations per paper for PubMed's “related citations”.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-14 01:46:36"}
{"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/736087/Figure_6.tif"], "description"=>"For 883 papers, the figure shows how many different search terms have more than 10 and more than 100 search results. Each of the search results that are not already citations may be potentially related literature, whose relationship is indicated via the search term.", "links"=>[], "tags"=>["Computational biology", "computer science", "science policy", "mathematics"], "article_id"=>406447, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Science Policy"], "users"=>["Devabhaktuni Srikrishna", "Marc A. Coram"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0024920.g006"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_Non_overlapping_search_results_/406447", "title"=>"Non-overlapping search results.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2011-09-14 01:47:27"}
{"files"=>["https://s3-eu-west-1.amazonaws.com/pstorage-plos-3567654/736134/Table_1.xls"], "description"=>"PubMed “related citations” versus ranked noun phrases.", "links"=>[], "tags"=>["ranked", "noun"], "article_id"=>406494, "categories"=>["Information And Computing Sciences", "Mathematics", "Biological Sciences", "Science Policy"], "users"=>["Devabhaktuni Srikrishna", "Marc A. Coram"], "doi"=>["http://dx.doi.org/10.1371/journal.pone.0024920.t001"], "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"http://figshare.com/articles/_PubMed_8220_related_citations_8221_versus_ranked_noun_phrases_/406494", "title"=>"PubMed “related citations” versus ranked noun phrases.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2011-09-14 01:48:14"}

PMC Usage Stats 186917 Jan 16:15 UTC

PMC Usage Stats | Further Information

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{"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2013", "month"=>"11"}
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{"unique-ip"=>"8", "full-text"=>"9", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"2"}
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{"unique-ip"=>"15", "full-text"=>"18", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"5"}
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{"unique-ip"=>"13", "full-text"=>"16", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"4"}
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{"unique-ip"=>"5", "full-text"=>"5", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"6"}
{"unique-ip"=>"13", "full-text"=>"12", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"7"}
{"unique-ip"=>"15", "full-text"=>"28", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"3"}
{"unique-ip"=>"18", "full-text"=>"36", "pdf"=>"4", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"2"}
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{"unique-ip"=>"14", "full-text"=>"14", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"9"}
{"unique-ip"=>"21", "full-text"=>"24", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2015", "month"=>"10"}
{"unique-ip"=>"13", "full-text"=>"15", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"2", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"7"}
{"unique-ip"=>"11", "full-text"=>"13", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"8"}
{"unique-ip"=>"27", "full-text"=>"25", "pdf"=>"2", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"1", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2014", "month"=>"9"}
{"unique-ip"=>"19", "full-text"=>"18", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"10", "supp-data"=>"4", "cited-by"=>"0", "year"=>"2014", "month"=>"10"}
{"unique-ip"=>"7", "full-text"=>"8", "pdf"=>"0", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"0", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2016", "month"=>"2"}
{"unique-ip"=>"15", "full-text"=>"19", "pdf"=>"1", "abstract"=>"0", "scanned-summary"=>"0", "scanned-page-browse"=>"0", "figure"=>"5", "supp-data"=>"0", "cited-by"=>"0", "year"=>"2014", "month"=>"11"}
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Relative Metric 36449305 Apr 19:02 UTC

Relative Metric

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F1000Prime13 Jan 12:33 UTC

F1000Prime

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