MBR Files | |
Users are responsible for compliance with all applicable MEDLINE®/PubMed® and other NLM Databases License Agreements. The MEDLINE citations included in this MEDLINE Baseline Repository were retrieved in their respective years and represent a static view of MEDLINE at that time. |
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Available Files: The following files have been made available from the MEDLINE Baseline Repository and include all of the generated files we create during our processing of each baseline. We have used GNU's gzip utility to compress the larger files and used the Unix tar command to compile the files into a single download. The compressed files can be expanded using either GNU's gunzip utility or WinZip. WinZip will also be able to understand the tar files and separate out the files as appropriate. To download each file, simply move your cursor over the file icon for the file you wish to download, press the right mouse button and select the "Save Link Target as ..." option. The frequency count files represent a complete count of the MEDLINE baseline for each category. For example, the MH_freq_count file represents a count for each unique MeSH Heading found in MEDLINE for the given baseline year. We include an overall count for each term and a count of when the term has been starred (considered an IM or Index Medicus index term which represents the most significant points of an article) when applicable (MH and SH terms only). We provide at least two versions of each frequency count category which is just a sorting difference - MH_freq_count is ordered by the overall frequency count for each term, while MH_freq_alpha is ordered in alphabetical order by MeSH Heading. The MH_major_freq_count is sorted using the count of when each term has been starred. The README file associated with each baseline explains in greater detail the format of each of the files. The raw data files represent the files we generated to use in our MEDLINE Baseline Repository Query tool database and it was felt that others might find these files useful and by providing them here, we help eliminate the duplication of effort. The README file associated with each baseline explains in greater detail the format of each of the files. We also provide two files where we look at the MeSH Headings assigned to the completed citations during the given baseline or year. The "hist" file is a frequency count of MeSH Headings based on their assigned MeSH Treecodes. The "histST" file is a frequency count of MeSH Headings based on their UMLS Semantic Types and more specifically, their UMLS Semantic Groupings (groups of Semantic Types). We have also included several graphs to help illustrate this data. The related MeSH Vocabulary data files are also included here to make sure that you have available all of the year specific data you might need for your research. It's unclear whether the SemGroups.txt file is updated each year, as the Semantic Types change, or is static. This file has grouped the UMLS Semantic Types into 15 (currently) high-level categories. We are using this file to see if we can detect patterns in how the MeSH Headings are assigned in MEDLINE. The papers: "Aggregating UMLS semantic types for reducing conceptual complexity. McCray AT, Burgun A, Bodenreider O; Medinfo. 2001;10(Pt 1):216-20." and "Exploring semantic groups through visual approaches., Bodenreider O, McCray AT; Journal of Biomedical Informatics. 2003; 36(6):414-432." provide much greater detail on the grouping of the Semantic Types. Both papers can be found at the Lister Hill National Center for Biomedical Communications web site (http://lhncbc.nlm.nih.gov) under the "Publications & Lectures" section. The Unique Words from the baseline files are the latest addition to the Repository starting with the 2009 Medline Baseline. We use a very simplified idea of a word -- we throw away anything with all numbers, throws away anything with non-ascii characters, and breaks at anything that is not alphanumeric. The "words" files contains single words and bigram words. The bigram words are made up of a sliding window using the last "valid" word and the current word - so you get something like "last current" where we simply added a space. We also ignore a short (313) list of stop words, so they are not included in the various lists. Each of the "words" files also contains a frequency count for each item. Also, please note that we only look at the Title and Abstract fields to generate our list of words - we have ignored the MeSH Heading fields. One or more of the following tools may be needed to access the files located on this page after they have been downloaded. The need depends on your current computer resources.
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Item | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 |
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DTD (Document Type Definition) Files | |||||||||||||||
DTDs (gzipped tar) |
(3.7 kb) |
(3.8 kb) |
(4.4 kb) |
(4.1 kb) |
(6.1 kb) |
(4.3 kb) |
(129 kb) |
(6.2 kb) |
(8.4 kb) |
(7.8 kb) |
(7 kb) |
(7 kb) |
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Frequency Count Files | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 |
README |
(2.2 kb) |
(2.2 kb) |
(2.2 kb) |
(2.2 kb) |
(2.2 kb) |
(2.2 kb) |
(2.2 kb) |
(2.2 kb) |
(2.2 kb) |
(2.2 kb) |
(2.2 kb) |
(2.4 kb) |
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Summary |
(228 by) |
(228 by) |
(228 by) |
(228 by) |
(228 by) |
(228 by) |
(228 by) |
(228 by) |
(228 by) |
(228 by) |
(228 by) |
(228 by) |
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Chemical_freq_alpha |
(1.5 mb) |
(1.5 mb) |
(1.6 mb) |
(1.7 mb) |
(1.85 mb) |
(2.0 mb) |
(2.1 mb) |
(2.2 mb) |
(2.2 mb) |
(2.3 mb) |
(3.2 mb) |
(3.3 mb) |
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Chemical_freq_count |
(1.5 mb) |
(1.6 mb) |
(1.7 mb) |
(1.8 mb) |
(1.92 mb) |
(2.1 mb) |
(2.2 mb) |
(2.3 mb) |
(2.3 mb) |
(2.4 mb) |
(3.3 mb) |
(3.4 mb) |
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MH_freq_alpha |
(207 kb) |
(215 kb) |
(226 kb) |
(232 kb) |
(245 kb) |
(256 kb) |
(385 kb) |
(392 kb) |
(400 kb) |
(409 kb) |
(521 kb) |
(472 kb) |
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MH_freq_count |
(219 kb) |
(227 kb) |
(239 kb) |
(246 kb) |
(260 kb) |
(270 kb) |
(373 kb) |
(381 kb) |
(388 kb) |
(397 kb) |
(506 kb) |
(503 kb) |
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MH_major_freq_count |
(218 kb) |
(226 kb) |
(239 kb) |
(246 kb) |
(260 kb) |
(271 kb) |
(378 kb) |
(385 kb) |
(393 kb) |
(403 kb) |
(512 kb) |
(509 kb) |
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MH_SH_freq_alpha |
(2 mb) |
(2.1 mb) |
(2.2 mb) |
(2.3 mb) |
(2.37 mb) |
(2.45 mb) |
(2.52 mb) |
(2.60 mb) |
(2.65 mb) |
(2.71 mb) |
(4.3 mb) |
(4.2 mb) |
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MH_SH_freq_count |
(3 mb) |
(3.1 mb) |
(3.3 mb) |
(3.4 mb) |
(3.5 mb) |
(3.67 mb) |
(3.78 mb) |
(3.90 mb) |
(3.99 mb) |
(4.08 mb) |
(6.5 mb) |
(6.4 mb) |
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MH_SH_major_freq_count |
(3 mb) |
(3.2 mb) |
(3.29 mb) |
(3.41 mb) |
(3.54 mb) |
(3.68 mb) |
(3.79 mb) |
(3.91 mb) |
(4 mb) |
(4.1 mb) |
(6.5 mb) |
(6.4 mb) |
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SH_freq_alpha |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.5 kb) |
(1.6 kb) |
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SH_freq_count |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.5 kb) |
(1.6 kb) |
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SH_major_freq_count |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.3 kb) |
(1.5 kb) |
(1.6 kb) |
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Raw Data Files | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 |
README |
(3.1 kb) |
(3.1 kb) |
(3.1 kb) |
(3.1 kb) |
(3.4 kb) |
(3.4 kb) |
(3.4 kb) |
(3.4 kb) |
(3.4 kb) |
(3.4 kb) |
(3.4 kb) |
(3.4 kb) |
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Summary |
(136 by) |
(136 by) |
(136 by) |
(136 by) |
(136 by) |
(162 by) |
(163 by) |
(163 by) |
(197 by) |
(197 by) |
(199 by) |
(199 by) |
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Chemical_items |
(162 mb) |
(180 mb) |
(195 mb) |
(207 mb) |
(229 mb) |
(243 mb) |
(260 mb) |
(276 mb) |
(291 mb) |
(307 mb) |
(309 mb) |
(325 mb) |
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ID_items |
(42 mb) |
(45 mb) |
(48 mb) |
(52 mb) |
(57 mb) |
(61 mb) |
(68 mb) |
(73 mb) |
(77 mb) |
(83 mb) |
(85 mb) |
(91 mb) |
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Full_MH_SH_items |
(995 mb) |
(1 gb) |
(1.1 gb) |
(1.2 gb) |
(1.3 gb) |
(1.3 gb) |
(1.4 gb) |
(1.4 gb) |
(1.5 gb) |
(1.6 gb) |
(1.7 gb) |
(1.7 gb) |
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MH_items |
(1.5 gb) |
(1.7 gb) |
(1.7 gb) |
(1.9 gb) |
(2.1 gb) |
(2.1 gb) |
(2.2 gb) |
(2.4 gb) |
(2.5 gb) |
(2.6 gb) |
(2.7 gb) |
(2.8 gb) |
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MH_SH_items |
(511 mb) |
(544 mb) |
(580 mb) |
(610 mb) |
(660 mb) |
(702 mb) |
(749 mb) |
(795 mb) |
(841 mb) |
(887 mb) |
(893 mb) |
(942 mb) |
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SH_items |
(161 mb) |
(175 mb) |
(188 mb) |
(188 mb) |
(214 mb) |
(233 mb) |
(260 mb) |
(283 mb) |
(305 mb) |
(326 mb) |
(334 mb) |
(357 mb) |
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Histogram/Summary Files | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 |
README |
(2.9 kb) |
(2.9 kb) |
(2.9 kb) |
(2.9 kb) |
(2.9 kb) |
(2.9 kb) |
(2.9 kb) |
(2.9 kb) |
(2.9 kb) |
(2.9 kb) |
(2.9 kb) |
(2.9 kb) |
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hist |
(4.8 kb) |
(4.8 kb) |
(4.9 kb) |
(4.8 kb) |
(4.5 kb) |
(4.4 kb) |
(4.4 kb) |
(4.6 kb) |
(4.7 kb) |
(4.8 kb) |
(4.7 kb) |
(4.7 kb) |
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Graph of hist File |
(5.1 kb) |
(5.1 kb) |
(5.0 kb) |
(5.1 kb) |
(5.4 kb) |
(7.4 kb) |
(6.1 kb) |
(202 kb) |
(464 kb) |
(465 kb) |
(245 kb) |
(120 kb) |
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Graph of Combined hist Files | N/A | N/A |
(5.8 kb) |
(6.4 kb) |
(8 kb) |
(44 kb) |
(10 kb) |
(134 kb) |
(235 kb) |
(546 kb) |
(352 kb) |
(125 kb) |
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histST |
(309 by) |
(309 by) |
(309 by) |
(311 by) |
(311 by) |
(311 by) |
(312 by) |
(313 by) |
(314 by) |
(314 by) |
(314 by) |
(315 by) |
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Graph of histST File |
(3.8 kb) |
(3.8 kb) |
(3.8 kb) |
(3.8 kb) |
(3.7 kb) |
(4.9 kb) |
(3.7 kb) |
(90 kb) |
(61 kb) |
(61 kb) |
(60 kb) |
(59 kb) |
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Graph of Combined histST Files | N/A | N/A |
(4.7 kb) |
(5.2 kb) |
(6.2 kb) |
(38 kb) |
(7.8 kb) |
(79 kb) |
(82 kb) |
(84 kb) |
(83 kb) |
(81 kb) |
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hist_Full | N/A | N/A |
(33.2 kb) |
(34.2 kb) |
(33.7 kb) |
(33.9 kb) |
(34.6 kb) |
(36.6 kb) |
(37.6 kb) |
(39 kb) |
(40 kb) |
(40 kb) |
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Graph of hist_Full File | N/A | N/A |
(24.1 kb) |
(24.7 kb) |
(27.1 kb) |
(218 kb) |
(27.9 kb) |
(71 kb) |
(77.8 kb) |
(77.8 kb) |
(77 kb) |
(47 kb) |
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histST_Full | N/A | N/A |
(4.2 kb) |
(4.3 kb) |
(4.4 kb) |
(4.5 kb) |
(4.6 kb) |
(4.7 kb) |
(4.8 kb) |
(4.9 kb) |
(5 kb) |
(5.1 kb) |
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Graph of histST_Full File | N/A | N/A |
(24.1 kb) |
(24.8 kb) |
(24.8 kb) |
(210 kb) |
(27.3 kb) |
(119 kb) |
(129 kb) |
(112 kb) |
(136 kb) |
(60 kb) |
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Related MeSH Files | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 |
Access to All MeSH Files | Memorandum of Understanding | ||||||||||||||
README |
(1.3 kb) |
(1 kb) |
(1 kb) |
(1 kb) |
(1.1 kb) |
(1.1 kb) |
(1.1 kb) |
(1.1 kb) |
(1.1 kb) |
(1.1 kb) |
(1.1 kb) |
(1.1 kb) |
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streeYYYY.bin |
(642 kb) |
(678 kb) |
(699 kb) |
(715 kb) |
(767 kb) |
(787 kb) |
(804 kb) |
(819 kb) |
(833 kb) |
(852 kb) |
(847 kb) |
(858 kb) |
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UMLS Semantic Groups File | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 |
SemGroups.txt |
(5.8 kb) |
(5.8 kb) |
(5.8 kb) |
(5.8 kb) |
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Unique Words from Medline Baseline | 2002 | 2003 | 2004 | 2005 | 2006 | 2007 | 2008 | 2009 | 2010 | 2011 | 2012 | 2013 | 2014 | 2015 | 2016 |
readme | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
(974 by) |
(1.2 kb) |
(774 by) |
(774 by) |
(774 by) |
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singleWords | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
(9.7 mb) |
(11 mb) |
(11 mb) |
(11 mb) |
(12 mb) |
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bigramWords | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
(175 mb) |
(239 mb) |
(180 mb) |
(188 mb) |
(198 mb) |
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wrd_stop | N/A | N/A | N/A | N/A | N/A | N/A | N/A |
(1.9 kb) |
Last Modified: February 01, 2013 | ii-public2 | |||||||||||||||||||||||||||||
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Lister Hill National Center for Biomedical Communications | U.S. National Library of Medicine | National Institutes of Health | ||||||||||||||||||||||||||||
Department of Health and Human Services |