From 886fddd98a63ed4c8cb63f7e8de0780f1c9c7a16 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Tue, 3 Mar 2015 13:26:55 -0500 Subject: [PATCH 01/44] Fixes mesh-rdf #110, put warnings against the use of the chunking script. --- README.md | 20 ++++++++++++-------- bin/mesh-xml2rdf.pl | 4 ++++ 2 files changed, 16 insertions(+), 8 deletions(-) diff --git a/README.md b/README.md index a3cedbc6..3d9043dd 100755 --- a/README.md +++ b/README.md @@ -1,6 +1,7 @@ -# MeSH® RDF +# MeSH® RDF -***Status: Beta. Feedback is [welcome](https://github.com/HHS/meshrdf/issues).*** +***Status: pre-beta. Feedback is welcome, but please bear in mind that the data model is +subject to change.*** This repository contains a set of XSLT files that transform MeSH XML into RDF, and also contains the content for the technical documentation pages, deployed as a set of GitHub pages, at @@ -87,13 +88,16 @@ XSLT conversions. The conversion scripts are: * mesh-xml2rdf.sh - For unix, this shell script will brute-force convert each of the three - main MeSH XML files into RDF N-Triples format, and put the results into the *out* directory + main MeSH XML files into RDF N-Triples format, and put the results into the *$MESHRDF_HOME/out* + directory. * mesh-xml2rdf.bat - This does the same thing, but can be run from Windows. -* mesh-xml2rdf.pl - [To do: fix this to work with the MESHRDF_HOME env. var.] - This Perl script takes a completely different approach, that is useful - for doing the conversions on less-powerful machines. It first chops up each of the - input XML files into manageable sized chunks, and then runs each chunk through the - XSLTs separately. It should run on any machine that has Perl installed. + +There is one other script that takes a different approach, that was useful for +doing the conversions on less-powerful machines. The Perl script mesh-xml2rdf.pl first +chops up each of the input XML files into manageable sized chunks, and then runs each chunk +through the XSLTs separately. ***Note, however, that because of the way it chunks the input +files, it fails to create a lot of meshv:broader links between the various tree nodes. +Therefore, this should not be used in production.*** ### Generating and converting the sample files diff --git a/bin/mesh-xml2rdf.pl b/bin/mesh-xml2rdf.pl index abc95852..766d211f 100755 --- a/bin/mesh-xml2rdf.pl +++ b/bin/mesh-xml2rdf.pl @@ -1,5 +1,9 @@ #! /usr/bin/env perl +# THIS SCRIPT SHOULD NOT BE USED IN PRODUCTION. +# Because of the way this script chunks the input files, it fails to create a lot +# of meshv:broader links between the various tree nodes. +# # The aim of this script is to provide a means to run the XSLTs against the very huge MeSH XML # files, on machines that have limited memory. For each of the inputs qual, desc, and supp, it will # * split the input XML into chunks From 793025e2389eea8fef99e0e366f8ef74b1aa1632 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Tue, 3 Mar 2015 14:12:49 -0500 Subject: [PATCH 02/44] Add caveats about missing meshv:broader links in samples --- README.md | 5 ++ samples/make-samples.pl | 5 ++ samples/qual-samples.xml | 109 --------------------------------------- samples/supp-samples.xml | 2 +- 4 files changed, 11 insertions(+), 110 deletions(-) diff --git a/README.md b/README.md index 3d9043dd..29d839fc 100755 --- a/README.md +++ b/README.md @@ -126,6 +126,11 @@ Finally, either of the scripts *convert-samples.sh* (for Unix) or *convert-sampl (for Windows) can be used to convert the sample XML files into RDF, the final output being *samples.nt*. +***Note, though, that the generated RDF will be missing a lot of meshv:broader +relationships, because those are generated from the tree node identifiers to link between +various records. Since the sample files contain only a subset of the records, most of +these cannot be generated.*** + ## Project directory structure diff --git a/samples/make-samples.pl b/samples/make-samples.pl index 9e13e045..c2b908bd 100755 --- a/samples/make-samples.pl +++ b/samples/make-samples.pl @@ -1,9 +1,14 @@ #! /usr/bin/env perl +# # This script will create subsets of the main MeSH XML files, with just a discrete set of # sample records. The input XML files are assumed to be in the `data` subdirectory of the # directory pointed to by the $MESHRDF_HOME environment variable. The list of records to # extract are listed in the samples-list.txt file. # +# NOTE: The resultant RDF will not include many meshv:broader relationships, because those +# are generated from links between various records, and since the sample files contain only +# a subset of the records, these cannot be generated. +# # This should be run from the samples directory of the repository, and it will overrite the # *-samples.xml files. # diff --git a/samples/qual-samples.xml b/samples/qual-samples.xml index 117da42b..a7e12ab2 100644 --- a/samples/qual-samples.xml +++ b/samples/qual-samples.xml @@ -1222,113 +1222,4 @@ - - Q000628 - - therapy - - - 1973 - 12 - 27 - - - 2003 - 07 - 22 - - - 1966 - 01 - 01 - - - 2004 - 2005 - 2006 - 2007 - 2008 - 2009 - 2010 - 2011 - 2012 - 2013 - 2014 - - subhead only; for general or unspecified therapy & multiple therapies; for tissue therapy & therapy with biological products; not for drug therapy ( =/drug therapy), nor for diet therapy ( = /diet therapy), nor for surgical therapy ( = /surgery), nor for radiotherapy ( = /radiotherapy), nor for rehabilitative therapy ( = /rehabilitation); indexing policy: Manual 19.8.72; DF: /ther or /TH - - 66; used with Category C & F 1966-74; C & F3 1975-87; C, F3 & SMOKING 1988; C, F3 & SMOKING+ 1989; C & F3 1990 forward - - search policy: Online Manual; use: main heading/TH or TH (SH) or SUBS APPLY TH - - - Y11 - - - C01 - C02 - C03 - C04 - C05 - C06 - C07 - C08 - C09 - C10 - C11 - C12 - C13 - C14 - C15 - C16 - C17 - C18 - C19 - C20 - C21 - C22 - C23 - C24 - C25 - C26 - F03 - - - nlm - schulmaj - nelsons - - - - M0030821 - - therapy - - Used with diseases for therapeutic interventions except drug therapy, diet therapy, radiotherapy, and surgery, for which specific subheadings exist. The concept is also used for articles and books dealing with multiple therapies. - - - - T169 - Functional Concept - - - - - T061268 - therapy - TH - THER - - - T061269 - treatment - - - T061270 - disease management - - - - - diff --git a/samples/supp-samples.xml b/samples/supp-samples.xml index dada2d55..695dcb1f 100644 --- a/samples/supp-samples.xml +++ b/samples/supp-samples.xml @@ -19,7 +19,7 @@ 2013A 2014 - 9 + 10 From 83ab746f52fa8b6e8f8b1dbd2867f44cbcde2601 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Tue, 3 Mar 2015 14:44:34 -0500 Subject: [PATCH 03/44] Fixes mesh-rdf #107, strip datatype off of activeMeSHYear --- xslt/common.xsl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/xslt/common.xsl b/xslt/common.xsl index da1a047a..e702b0a3 100755 --- a/xslt/common.xsl +++ b/xslt/common.xsl @@ -259,7 +259,7 @@ activeMeSHYear - + From 3a2325d98858dda730d8c39aeef508a42cde933d Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Tue, 3 Mar 2015 15:38:18 -0500 Subject: [PATCH 04/44] Fixes mesh-rdf #108. --- README.md | 3 ++- bin/mesh-xml2rdf.sh | 12 +++++++++--- 2 files changed, 11 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 29d839fc..78fb7b41 100755 --- a/README.md +++ b/README.md @@ -90,7 +90,8 @@ The conversion scripts are: * mesh-xml2rdf.sh - For unix, this shell script will brute-force convert each of the three main MeSH XML files into RDF N-Triples format, and put the results into the *$MESHRDF_HOME/out* directory. -* mesh-xml2rdf.bat - This does the same thing, but can be run from Windows. +* mesh-xml2rdf.bat - This does the same thing (mostly), but can be run from Windows. Note that + the unix shell script sorts and uniques the output, whereas this one does not. There is one other script that takes a different approach, that was useful for doing the conversions on less-powerful machines. The Perl script mesh-xml2rdf.pl first diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index 51d9d582..4cc5eb2f 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -6,10 +6,16 @@ # separately. mkdir -p $MESHRDF_HOME/out + java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/qual2014.xml \ - -xsl:xslt/qual.xsl > $MESHRDF_HOME/out/qual2014.nt + -xsl:xslt/qual.xsl > $MESHRDF_HOME/out/qual2014-dups.nt +sort -u $MESHRDF_HOME/out/qual2014-dups.nt > $MESHRDF_HOME/out/qual2014.nt + java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/desc2014.xml \ - -xsl:xslt/desc.xsl > $MESHRDF_HOME/out/desc2014.nt + -xsl:xslt/desc.xsl > $MESHRDF_HOME/out/desc2014-dups.nt +sort -u $MESHRDF_HOME/out/desc2014-dups.nt > $MESHRDF_HOME/out/desc2014.nt + java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/supp2014.xml \ - -xsl:xslt/supp.xsl > $MESHRDF_HOME/out/supp2014.nt + -xsl:xslt/supp.xsl > $MESHRDF_HOME/out/supp2014-dups.nt +sort -u $MESHRDF_HOME/out/supp2014-dups.nt > $MESHRDF_HOME/out/supp2014.nt From cf2093df97f13f743dd741889110deec5bb08027 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Tue, 3 Mar 2015 17:35:01 -0500 Subject: [PATCH 05/44] Add language param to literal template (see mesh-rdf issue #104) --- xslt/common.xsl | 12 +++++++++++- 1 file changed, 11 insertions(+), 1 deletion(-) diff --git a/xslt/common.xsl b/xslt/common.xsl index e702b0a3..3c2874bf 100755 --- a/xslt/common.xsl +++ b/xslt/common.xsl @@ -111,7 +111,17 @@ - + + + + + + + + + + + From dc57edce8b8065dfbc11ea80cad5a0fe27e2773c Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Wed, 4 Mar 2015 11:06:11 -0500 Subject: [PATCH 06/44] Fixes mesh-rdf #108 again. Combine the three output files into one, and gzip them. --- README.md | 3 ++- bin/mesh-xml2rdf.bat | 6 +++--- bin/mesh-xml2rdf.sh | 11 +++++------ 3 files changed, 10 insertions(+), 10 deletions(-) diff --git a/README.md b/README.md index 78fb7b41..57688ab3 100755 --- a/README.md +++ b/README.md @@ -89,7 +89,8 @@ The conversion scripts are: * mesh-xml2rdf.sh - For unix, this shell script will brute-force convert each of the three main MeSH XML files into RDF N-Triples format, and put the results into the *$MESHRDF_HOME/out* - directory. + directory. It produces mesh2014.nt, which is the RDF in N-triples format, and mesh2014.nt.gz, + a gzipped version. * mesh-xml2rdf.bat - This does the same thing (mostly), but can be run from Windows. Note that the unix shell script sorts and uniques the output, whereas this one does not. diff --git a/bin/mesh-xml2rdf.bat b/bin/mesh-xml2rdf.bat index e6370f48..f676762b 100644 --- a/bin/mesh-xml2rdf.bat +++ b/bin/mesh-xml2rdf.bat @@ -6,9 +6,9 @@ rem separately. mkdir %MESHRDF_HOME%\out java -Xmx2G -jar %SAXON_JAR% -s:%MESHRDF_HOME%/data/qual2014.xml ^ - -xsl:xslt/qual.xsl > %MESHRDF_HOME%/out/qual2014.nt + -xsl:xslt/qual.xsl > %MESHRDF_HOME%/out/mesh2014.nt java -Xmx2G -jar %SAXON_JAR% -s:%MESHRDF_HOME%/data/desc2014.xml ^ - -xsl:xslt/desc.xsl > %MESHRDF_HOME%/out/desc2014.nt + -xsl:xslt/desc.xsl >> %MESHRDF_HOME%/out/mesh2014.nt java -Xmx2G -jar %SAXON_JAR% -s:%MESHRDF_HOME%/data/supp2014.xml ^ - -xsl:xslt/supp.xsl > %MESHRDF_HOME%/out/supp2014.nt + -xsl:xslt/supp.xsl >> %MESHRDF_HOME%/out/mesh2014.nt diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index 4cc5eb2f..48e249bd 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -8,14 +8,13 @@ mkdir -p $MESHRDF_HOME/out java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/qual2014.xml \ - -xsl:xslt/qual.xsl > $MESHRDF_HOME/out/qual2014-dups.nt -sort -u $MESHRDF_HOME/out/qual2014-dups.nt > $MESHRDF_HOME/out/qual2014.nt + -xsl:xslt/qual.xsl > $MESHRDF_HOME/out/mesh2014-dups.nt java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/desc2014.xml \ - -xsl:xslt/desc.xsl > $MESHRDF_HOME/out/desc2014-dups.nt -sort -u $MESHRDF_HOME/out/desc2014-dups.nt > $MESHRDF_HOME/out/desc2014.nt + -xsl:xslt/desc.xsl >> $MESHRDF_HOME/out/mesh2014-dups.nt java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/supp2014.xml \ - -xsl:xslt/supp.xsl > $MESHRDF_HOME/out/supp2014-dups.nt -sort -u $MESHRDF_HOME/out/supp2014-dups.nt > $MESHRDF_HOME/out/supp2014.nt + -xsl:xslt/supp.xsl >> $MESHRDF_HOME/out/mesh2014-dups.nt +sort -u $MESHRDF_HOME/out/mesh2014-dups.nt > $MESHRDF_HOME/out/mesh2014.nt +gzip -k mesh2014.nt From bd3f2e50c0763f0121a4fb490f04ad93c6189b45 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Mon, 30 Mar 2015 14:40:50 -0400 Subject: [PATCH 07/44] mesh-rdf issue 102 - more specific names for broader et al --- OxygenProject.xpr | 4 ++-- meta/vocab.ttl | 41 +++++++++++++++++++++++++++++------------ xslt/common.xsl | 47 +++++++++++++++++++++++++---------------------- 3 files changed, 56 insertions(+), 36 deletions(-) mode change 100755 => 100644 OxygenProject.xpr diff --git a/OxygenProject.xpr b/OxygenProject.xpr old mode 100755 new mode 100644 index 1cb94d1b..de763963 --- a/OxygenProject.xpr +++ b/OxygenProject.xpr @@ -1,9 +1,9 @@ - + - + validation.scenario.associations diff --git a/meta/vocab.ttl b/meta/vocab.ttl index fc3e55c0..657d3036 100755 --- a/meta/vocab.ttl +++ b/meta/vocab.ttl @@ -53,20 +53,37 @@ meshv:identifier a rdf:Property ; rdfs:domain rdfs:Class ; rdfs:range rdfs:Literal . -meshv:broader a rdf:Property , owl:ObjectProperty ; - rdfs:domain rdfs:Class ; - rdfs:range rdfs:Class ; - rdfs:subPropertyOf meshv:broaderTransitive ; - owl:inverseOf meshv:narrower . -meshv:narrower a rdf:Property , owl:ObjectProperty ; - rdfs:domain rdfs:Class ; - rdfs:range rdfs:Class ; - owl:inverseOf meshv:broader . -meshv:broaderTransitive a rdf:Property , owl:ObjectProperty , owl:TransitiveProperty ; - rdfs:domain rdfs:Class ; - rdfs:range rdfs:Class . + + +meshv:broaderConcept a rdf:Property , owl:ObjectProperty ; + rdfs:domain meshv:Concept ; + rdfs:range meshv:Concept ; + owl:inverseOf meshv:narrowerConcept . + +meshv:narrowerConcept a rdf:Property , owl:ObjectProperty ; + rdfs:domain meshv:Concept ; + rdfs:range meshv:Concept ; + owl:inverseOf meshv:broaderConcept . + +meshv:relatedConcept a rdf:Property , owl:ObjectProperty ; + rdfs:domain meshv:Concept ; + rdfs:range meshv:Concept . + +meshv:broaderDescriptor a rdf:Property , owl:ObjectProperty ; + rdfs:domain meshv:Descriptor ; + rdfs:range meshv:Descriptor . + +meshv:broaderQualifier a rdf:Property , owl:ObjectProperty ; + rdfs:domain meshv:Qualifier ; + rdfs:range meshv:Qualifier . + +meshv:broaderTreeNumber a rdf:Propery , owl:TransitiveProperty; + rdfs:domain meshv:TreeNumber ; + rdfs:range meshv:TreeNumber . + + # In issue #36, we discussed this, and decided not to create individual subclasses of meshv:Term. diff --git a/xslt/common.xsl b/xslt/common.xsl index 3c2874bf..3ea9383e 100755 --- a/xslt/common.xsl +++ b/xslt/common.xsl @@ -183,6 +183,7 @@ --> + @@ -195,6 +196,7 @@ related + @@ -417,11 +419,11 @@ Every time we reify a TreeNumber that has a dot in it, we'll create a triple - to link it to its parent with meshv:broaderTransitive. + to link it to its parent with meshv:broaderTreeNumber. - broaderTransitive + broaderTreeNumber @@ -431,8 +433,9 @@ - - + + + Also create a simple meshv:broader relationship between this descriptor and @@ -440,28 +443,28 @@ - broader + broaderDescriptor - - - - - Also create a simple meshv:broader relationship between this qualifier and - the qualifier that has the parent tree number - - - - broader - - - - - - + + + + + Also create a simple meshv:broader relationship between this qualifier and + the qualifier that has the parent tree number + + + + broaderQualifier + + + + + + @@ -765,7 +768,7 @@ - + From df3a93ef3c92e8db981045d323255c29e93f61a8 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Mon, 30 Mar 2015 15:41:11 -0400 Subject: [PATCH 08/44] mesh-rdf issue 104, added lang='en' to several literals --- xslt/common.xsl | 25 ++++++++++++++----------- xslt/desc.xsl | 6 +++--- xslt/qual.xsl | 2 +- xslt/supp.xsl | 2 +- 4 files changed, 19 insertions(+), 16 deletions(-) diff --git a/xslt/common.xsl b/xslt/common.xsl index 3ea9383e..33482e1b 100755 --- a/xslt/common.xsl +++ b/xslt/common.xsl @@ -80,7 +80,10 @@ ' - + + + + @@ -289,7 +292,7 @@ annotation - + @@ -308,7 +311,7 @@ historyNote - + @@ -323,7 +326,7 @@ onlineNote - + @@ -408,7 +411,7 @@ label - + @@ -580,7 +583,7 @@ label - + @@ -657,7 +660,7 @@ scopeNote - + @@ -713,7 +716,7 @@ label - + @@ -913,7 +916,7 @@ prefLabel - + @@ -1007,7 +1010,7 @@ abbreviation - + @@ -1086,7 +1089,7 @@ altLabel - + diff --git a/xslt/desc.xsl b/xslt/desc.xsl index 574cc5f2..2ae9402b 100755 --- a/xslt/desc.xsl +++ b/xslt/desc.xsl @@ -81,7 +81,7 @@ label - + @@ -170,7 +170,7 @@ publicMeSHNote - + @@ -281,7 +281,7 @@ considerAlso - + diff --git a/xslt/qual.xsl b/xslt/qual.xsl index 5e6d36d9..33334d33 100755 --- a/xslt/qual.xsl +++ b/xslt/qual.xsl @@ -85,7 +85,7 @@ label - + diff --git a/xslt/supp.xsl b/xslt/supp.xsl index d7017ec5..14516456 100755 --- a/xslt/supp.xsl +++ b/xslt/supp.xsl @@ -73,7 +73,7 @@ label - + From 7bb9291c9a56fae306d967103cbea5d6662629cd Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Mon, 30 Mar 2015 17:00:17 -0400 Subject: [PATCH 09/44] mesh-rdf issue 39 - vocabulary.owl is now the official ontology --- meta/vocab.ttl | 547 -------------------------------------------- meta/vocabulary.owl | 118 ++++++++-- 2 files changed, 98 insertions(+), 567 deletions(-) delete mode 100755 meta/vocab.ttl diff --git a/meta/vocab.ttl b/meta/vocab.ttl deleted file mode 100755 index 657d3036..00000000 --- a/meta/vocab.ttl +++ /dev/null @@ -1,547 +0,0 @@ -@prefix meshv: . -@prefix rdfs: . -@prefix rdf: . -@prefix owl: . - -meshv:Descriptor a rdfs:Class . - -meshv:TopicalDescriptor a rdfs:Class ; - rdfs:subClassOf meshv:Descriptor . - -meshv:PublicationType a rdfs:Class ; - rdfs:subClassOf meshv:Descriptor . - -meshv:CheckTag a rdfs:Class ; - rdfs:subClassOf meshv:Descriptor . - -meshv:GeographicalDescriptor a rdfs:Class ; - rdfs:subClassOf meshv:Descriptor . - -meshv:Qualifier a rdfs:Class . - -meshv:DescriptorQualifierPair a rdfs:Class . - -meshv:AllowedDescriptorQualifierPair a rdfs:Class ; - rdfs:subClassOf meshv:DescriptorQualifierPair . - -meshv:DisallowedDescriptorQualifierPair a rdfs:Class ; - rdfs:subClassOf meshv:DescriptorQualifierPair . - -meshv:Concept a rdfs:Class . - -meshv:Term a rdfs:Class . - -meshv::SupplementaryConceptRecord a rdfs:Class . - -meshv:SCR_Chemical rdfs:subClassOf meshv:SupplementaryConceptRecord . - -meshv:SCR_Protocol rdfs:subClassOf meshv:SupplementaryConceptRecord . - -meshv:SCR_Disease rdfs:subClassOf meshv:SupplementaryConceptRecord . - - -meshv:preferredTerm a rdf:Property ; - rdfs:subPropertyOf meshv:term . - -meshv:prefLabel a rdf:Property ; - rdfs:subPropertyOf rdfs:label . - -meshv:altLabel a rdf:Property ; - rdfs:subPropertyOf rdfs:label . - -meshv:identifier a rdf:Property ; - rdfs:domain rdfs:Class ; - rdfs:range rdfs:Literal . - - - - - -meshv:broaderConcept a rdf:Property , owl:ObjectProperty ; - rdfs:domain meshv:Concept ; - rdfs:range meshv:Concept ; - owl:inverseOf meshv:narrowerConcept . - -meshv:narrowerConcept a rdf:Property , owl:ObjectProperty ; - rdfs:domain meshv:Concept ; - rdfs:range meshv:Concept ; - owl:inverseOf meshv:broaderConcept . - -meshv:relatedConcept a rdf:Property , owl:ObjectProperty ; - rdfs:domain meshv:Concept ; - rdfs:range meshv:Concept . - -meshv:broaderDescriptor a rdf:Property , owl:ObjectProperty ; - rdfs:domain meshv:Descriptor ; - rdfs:range meshv:Descriptor . - -meshv:broaderQualifier a rdf:Property , owl:ObjectProperty ; - rdfs:domain meshv:Qualifier ; - rdfs:range meshv:Qualifier . - -meshv:broaderTreeNumber a rdf:Propery , owl:TransitiveProperty; - rdfs:domain meshv:TreeNumber ; - rdfs:range meshv:TreeNumber . - - - - -# In issue #36, we discussed this, and decided not to create individual subclasses of meshv:Term. -# Leaving the code here, just in case they ever change their minds. -#meshv:Abbreviation a rdfs:Class ; -# rdfs:subClassOf meshv:Term . -#meshv:EmbeddedAbbreviation a rdfs:Class ; -# rdfs:subClassOf meshv:Term . -#meshv:Acronym a rdfs:Class ; -# rdfs:subClassOf meshv:Term . -#meshv:EmbeddedAcronym a rdfs:Class ; -# rdfs:subClassOf meshv:Term . -#meshv:Eponym a rdfs:Class ; -# rdfs:subClassOf meshv:Term . -#meshv:LabNumber a rdfs:Class ; -# rdfs:subClassOf meshv:Term . -#meshv:ProperName a rdfs:Class ; -# rdfs:subClassOf meshv:Term . -#meshv:TradeName a rdfs:Class ; -# rdfs:subClassOf meshv:Term . - - -# meshv::EntryCombination rdf:type rdfs:Class . -# meshv::IndexingData rdf:type rdfs:Class . -# meshv::MappedData rdf:type rdfs:Class . -# meshv::Qualifier rdf:type rdfs:Class . -# meshv::SemanticType rdf:type rdfs:Class . -# -# meshv::abbreviation rdfs:domain meshv::Qualifier . -# meshv::abbreviation rdfs:domain meshv::Term . -# meshv::abbreviation rdfs:Literal . -# meshv::abbreviation rdf:type rdf:Property . -# meshv::abbreviation dcterms:identifier 'abbreviation' . -# meshv::abbreviation rdfs:label 'abbreviation' . -# -# meshv::activemeshv:Year rdfs:domain meshv::Descriptor . -# meshv::activemeshv:Year rdfs:domain meshv::Qualifier . -# meshv::activemeshv:Year rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::activemeshv:Year rdfs:range rdfs:Literal . -# meshv::activemeshv:Year rdf:type rdf:Property . -# meshv::activemeshv:Year dcterms:identifier 'activemeshv:Year' . -# meshv::activemeshv:Year rdfs:label 'activemeshv:Year' . -# -# meshv::allowableQualifier rdfs:domain meshv::Descriptor . -# meshv::allowableQualifier rdfs:range meshv::Qualifier . -# meshv::allowableQualifier rdf:type rdf:Property . -# meshv::allowableQualifier dcterms:identifier 'allowableQualifier' . -# meshv::allowableQualifier rdfs:label 'allowableQualifier' . -# -# meshv::allowedTreeNode rdfs:domain meshv::Qualifier . -# meshv::allowedTreeNode rdfs:range rdfs:Literal . -# meshv::allowedTreeNode rdf:type rdf:Property . -# meshv::allowedTreeNode dcterms:identifier 'allowedTreeNode' . -# meshv::allowedTreeNode rdfs:label 'allowedTreeNode' . -# -# meshv::annotation rdfs:domain meshv::Descriptor . -# meshv::annotation rdfs:domain meshv::Qualifier . -# meshv::annotation rdfs:range rdfs:Literal . -# meshv::annotation rdf:type rdf:Property . -# meshv::annotation dcterms:identifier 'annotation' . -# meshv::annotation rdfs:label 'annotation' . -# -# meshv::CASN1_label rdfs:domain meshv::Concept . -# meshv::CASN1_label rdfs:range rdfs:Literal . -# meshv::CASN1_label rdf:type rdf:Property . -# meshv::CASN1_label dcterms:identifier 'CASN1_label' . -# meshv::CASN1_label rdfs:label 'CASN1_label' . -# -# meshv::concept1 rdfs:domain meshv::ConceptRelation . -# meshv::concept1 rdfs:range meshv::Concept . -# meshv::concept1 rdf:type rdf:Property . -# meshv::concept1 dcterms:identifier 'concept1' . -# meshv::concept1 rdfs:label 'concept1' . -# -# meshv::concept2 rdfs:domain meshv::ConceptRelation . -# meshv::concept2 rdfs:range meshv::Concept . -# meshv::concept2 rdf:type rdf:Property . -# meshv::concept2 dcterms:identifier 'concept2' . -# meshv::concept2 rdfs:label 'concept2' . -# -# meshv::concept rdfs:domain meshv::Descriptor . -# meshv::concept rdfs:domain meshv::Qualifier . -# meshv::concept rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::concept rdfs:range meshv::Concept . -# meshv::concept rdf:type rdf:Property . -# meshv::concept dcterms:identifier 'concept' . -# meshv::concept rdfs:label 'concept' . -# -# meshv::conceptRelation rdfs:domain meshv::Concept . -# meshv::conceptRelation rdfs:range meshv::ConceptRelation . -# meshv::conceptRelation rdf:type rdf:Property . -# meshv::conceptRelation dcterms:identifier 'conceptRelation' . -# meshv::conceptRelation rdfs:label 'conceptRelation' . -# -# meshv::considerAlso rdfs:domain meshv::Descriptor . -# meshv::considerAlso rdfs:range rdfs:Literal . -# meshv::considerAlso rdf:type rdf:Property . -# meshv::considerAlso dcterms:identifier 'considerAlso' . -# meshv::considerAlso rdfs:label 'considerAlso' . -# -# meshv::dateCreated rdfs:domain meshv::Descriptor . -# meshv::dateCreated rdfs:domain meshv::Qualifier . -# meshv::dateCreated rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::dateCreated rdfs:domain meshv::Term . -# meshv::dateCreated rdfs:domain meshv::TermData . -# meshv::dateCreated rdfs:range rdfs:Literal . -# meshv::dateCreated rdf:type rdf:Property . -# meshv::dateCreated dcterms:identifier 'dateCreated' . -# meshv::dateCreated rdfs:label 'dateCreated' . -# -# meshv::dateEstablished rdfs:domain meshv::Descriptor . -# meshv::dateEstablished rdfs:domain meshv::Qualifier . -# meshv::dateEstablished rdfs:range rdfs:Literal . -# meshv::dateEstablished rdf:type rdf:Property . -# meshv::dateEstablished dcterms:identifier 'dateEstablished' . -# meshv::dateEstablished rdfs:label 'dateEstablished' . -# -# meshv::dateRevised rdfs:domain meshv::Descriptor . -# meshv::dateRevised rdfs:domain meshv::Qualifier . -# meshv::dateRevised rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::dateRevised rdfs:range rdfs:Literal . -# meshv::dateRevised rdf:type rdf:Property . -# meshv::dateRevised dcterms:identifier 'dateRevised' . -# meshv::dateRevised rdfs:label 'dateRevised' . -# -# meshv::DescriptorClass rdfs:domain meshv::Descriptor . -# meshv::descriptorClass rdfs:range rdfs:Literal . -# meshv::descriptorClass rdf:type rdf:Property . -# meshv::descriptorClass dcterms:identifier 'descriptorClass' . -# meshv::descriptorClass rdfs:label 'descriptorClass' . -# -# meshv::ECINDescriptor rdfs:domain meshv::EntryCombination . -# meshv::ECINDescriptor rdfs:range meshv::Descriptor . -# meshv::ECINDescriptor rdf:type rdf:Property . -# meshv::ECINDescriptor dcterms:identifier 'ECINDescriptor' . -# meshv::ECINDescriptor rdfs:label 'ECINDescriptor' . -# -# meshv::ECINQualifier rdfs:domain meshv::EntryCombination . -# meshv::ECINQualifier rdfs:range meshv::Qualifier . -# meshv::ECINQualifier rdf:type rdf:Property . -# meshv::ECINQualifier dcterms:identifier 'ECINQualifier' . -# meshv::ECINQualifier rdfs:label 'ECINQualifier' . -# -# meshv::ECOUTDescriptor rdfs:domain meshv::EntryCombination . -# meshv::ECOUTDescriptor rdfs:range meshv::Descriptor . -# meshv::ECOUTDescriptor rdf:type rdf:Property . -# meshv::ECOUTDescriptor dcterms:identifier 'ECOUTDescriptor' . -# meshv::ECOUTDescriptor rdfs:label 'ECOUTDescriptor' . -# -# meshv::ECOUTQualifier rdfs:domain meshv::EntryCombination . -# meshv::ECOUTQualifier rdfs:range meshv::Qualifier . -# meshv::ECOUTQualifier rdf:type rdf:Property . -# meshv::ECOUTQualifier dcterms:identifier 'ECOUTQualifier' . -# meshv::ECOUTQualifier rdfs:label 'ECOUTQualifier' . -# -# meshv::entryCombination rdfs:domain meshv::Descriptor . -# meshv::entryCombination rdfs:range meshv::EntryCombination . -# meshv::entryCombination rdf:type rdf:Property . -# meshv::entryCombination dcterms:identifier 'entryCombination' . -# meshv::entryCombination rdfs:label 'entryCombination' . -# -# meshv::entryVersion rdfs:domain meshv::Term . -# meshv::entryVersion rdfs:domain meshv::TermData . -# meshv::entryVersion rdfs:range rdfs:Literal . -# meshv::entryVersion rdf:type rdf:Property . -# meshv::entryVersion dcterms:identifier 'entryVersion' . -# meshv::entryVersion rdfs:label 'entryVersion' . -# -# meshv::frequency rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::frequency rdfs:range rdfs:Literal . -# meshv::frequency rdf:type rdf:Property . -# meshv::frequency dcterms:identifier 'frequency' . -# meshv::frequency rdfs:label 'frequency' . -# -# meshv::historyNote rdfs:domain meshv::Descriptor . -# meshv::historyNote rdfs:domain meshv::Qualifier . -# meshv::historyNote rdfs:range rdfs:Literal . -# meshv::historyNote rdf:type rdf:Property . -# meshv::historyNote dcterms:identifier 'historyNote' . -# meshv::historyNote rdfs:label 'historyNote' . -# -# meshv::indexingData rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::indexingData rdfs:range meshv::IndexingData -# meshv::indexingData rdf:type rdf:Property . -# meshv::indexingData dcterms:identifier 'indexingData' . -# meshv::indexingData rdfs:label 'indexingData' . -# -# meshv::indexingDescriptor rdfs:domain meshv::IndexingData -# meshv::indexingDescriptor rdfs:range meshv::Descriptor . -# meshv::indexingDescriptor rdf:type rdf:Property . -# meshv::indexingDescriptor dcterms:identifier 'indexingDescriptor' . -# meshv::indexingDescriptor rdfs:label 'indexingDescriptor' . -# -# meshv::indexingQualifier rdfs:domain meshv::IndexingData -# meshv::indexingQualifier rdfs:range meshv::Qualifier . -# meshv::indexingQualifier rdf:type rdf:Property . -# meshv::indexingQualifier dcterms:identifier 'indexingQualifier' . -# meshv::indexingQualifier rdfs:label 'indexingQualifier' . -# -# meshv::isConceptPreferredTerm rdfs:domain meshv::Term . -# meshv::isConceptPreferredTerm rdfs:domain meshv::TermData . -# meshv::isConceptPreferredTerm rdfs:range rdfs:Literal . -# meshv::isConceptPreferredTerm rdf:type rdf:Property . -# meshv::isConceptPreferredTerm dcterms:identifier 'isConceptPreferredTerm' . -# meshv::isConceptPreferredTerm rdfs:label 'isConceptPreferredTerm' . -# -# meshv::isDescriptorStarred rdfs:domain meshv::MappedData -# meshv::isDescriptorStarred rdfs:range rdfs:Literal . -# meshv::isDescriptorStarred rdf:type rdf:Property . -# meshv::isDescriptorStarred dcterms:identifier 'isDescriptorStarred' . -# meshv::isDescriptorStarred rdfs:label 'isDescriptorStarred' . -# -# meshv::isMappedToDescriptor rdfs:domain meshv::MappedData -# meshv::isMappedToDescriptor rdfs:range meshv::Descriptor . -# meshv::isMappedToDescriptor rdf:type rdf:Property . -# meshv::isMappedToDescriptor dcterms:identifier 'isMappedToDescriptor' . -# meshv::isMappedToDescriptor rdfs:label 'isMappedToDescriptor' . -# -# meshv::isMappedToQualifier rdfs:domain meshv::MappedData -# meshv::isMappedToQualifier rdfs:range meshv::Qualifier . -# meshv::isMappedToQualifier rdf:type rdf:Property . -# meshv::isMappedToQualifier dcterms:identifier 'isMappedToQualifier' . -# meshv::isMappedToQualifier rdfs:label 'isMappedToQualifier' . -# -# meshv::isPermutedTerm rdfs:domain meshv::Term . -# meshv::isPermutedTerm rdfs:domain meshv::TermData . -# meshv::isPermutedTerm rdfs:range rdfs:Literal . -# meshv::isPermutedTerm rdf:type rdf:Property . -# meshv::isPermutedTerm dcterms:identifier 'isPermutedTerm' . -# meshv::isPermutedTerm rdfs:label 'isPermutedTerm' . -# -# meshv::isPreferredConcept rdfs:domain meshv::Concept -# meshv::isPreferredConcept rdfs:range rdfs:Literal . -# meshv::isPreferredConcept rdf:type rdf:Property . -# meshv::isPreferredConcept dcterms:identifier 'isPreferredConcept' . -# meshv::isPreferredConcept rdfs:label 'isPreferredConcept' . -# -# meshv::isQualifierStarred rdfs:domain meshv::MappedData -# meshv::isQualifierStarred rdfs:range rdfs:Literal . -# meshv::isQualifierStarred rdf:type rdf:Property . -# meshv::isQualifierStarred dcterms:identifier 'isQualifierStarred' . -# meshv::isQualifierStarred rdfs:label 'isQualifierStarred' . -# -# meshv::isQualifierType rdfs:domain meshv::Qualifier . -# meshv::isQualifierType rdfs:range rdfs:Literal . -# meshv::isQualifierType rdf:type rdf:Property . -# meshv::isQualifierType dcterms:identifier 'isQualifierType' . -# meshv::isQualifierType rdfs:label 'isQualifierType' . -# -# meshv::isRecordPreferredTerm rdfs:domain meshv::Term . -# meshv::isRecordPreferredTerm rdfs:domain meshv::TermData . -# meshv::isRecordPreferredTerm rdfs:range rdfs:Literal . -# meshv::isRecordPreferredTerm rdf:type rdf:Property . -# meshv::isRecordPreferredTerm dcterms:identifier 'isRecordPreferredTerm' . -# meshv::isRecordPreferredTerm rdfs:label 'isRecordPreferredTerm' . -# -# meshv::lexicalTag rdfs:domain meshv::Term . -# meshv::lexicalTag rdfs:domain meshv::TermData . -# meshv::lexicalTag rdfs:range rdfs:Literal . -# meshv::lexicalTag rdf:type rdf:Property . -# meshv::lexicalTag dcterms:identifier 'lexicalTag' . -# meshv::lexicalTag rdfs:label 'lexicalTag' . -# -# meshv::mappedData rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::mappedData rdfs:range meshv::MappedData -# meshv::mappedData rdf:type rdf:Property . -# meshv::mappedData dcterms:identifier 'mappedData' . -# meshv::mappedData rdfs:label 'mappedData' . -# -# meshv::note rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::note rdfs:range rdfs:Literal . -# meshv::note rdf:type rdf:Property . -# meshv::note dcterms:identifier 'note' . -# meshv::note rdfs:label 'note' . -# -# meshv::onlineNote rdfs:domain meshv::Descriptor . -# meshv::onlineNote rdfs:domain meshv::Qualifier . -# meshv::onlineNote rdfs:range rdfs:Literal . -# meshv::onlineNote rdf:type rdf:Property . -# meshv::onlineNote dcterms:identifier 'onlineNote' . -# meshv::onlineNote rdfs:label 'onlineNote' . -# -# meshv::pharmacologicalAction rdfs:domain meshv::Descriptor . -# meshv::pharmacologicalAction rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::pharmacologicalAction rdfs:range meshv::Descriptor . -# meshv::pharmacologicalAction rdf:type rdf:Property . -# meshv::pharmacologicalAction dcterms:identifier 'pharmacologicalAction' . -# meshv::pharmacologicalAction rdfs:label 'pharmacologicalAction' . -# -# meshv::previousIndexing rdfs:domain meshv::Descriptor . -# meshv::previousIndexing rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::previousIndexing rdfs:range rdfs:Literal . -# meshv::previousIndexing rdf:type rdf:Property . -# meshv::previousIndexing dcterms:identifier 'previousIndexing' . -# meshv::previousIndexing rdfs:label 'previousIndexing' . -# -# meshv::printFlag rdfs:domain meshv::Term . -# meshv::printFlag rdfs:domain meshv::TermData . -# meshv::printFlag rdfs:range rdfs:Literal . -# meshv::printFlag rdf:type rdf:Property . -# meshv::printFlag dcterms:identifier 'printFlag' . -# meshv::printFlag rdfs:label 'printFlag' . -# -# meshv::publicmeshv:Note rdfs:domain meshv::Descriptor . -# meshv::publicmeshv:Note rdfs:range rdfs:Literal . -# meshv::publicmeshv:Note rdf:type rdf:Property . -# meshv::publicmeshv:Note dcterms:identifier 'publicmeshv:Note' . -# meshv::publicmeshv:Note rdfs:label 'publicmeshv:Note' . -# -# meshv::recordAuthorizer rdfs:domain meshv::Descriptor . -# meshv::recordAuthorizer rdfs:domain meshv::Qualifier . -# meshv::recordAuthorizer rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::recordAuthorizer rdfs:range rdfs:Literal . -# meshv::recordAuthorizer rdf:type rdf:Property . -# meshv::recordAuthorizer dcterms:identifier 'recordAuthorizer' . -# meshv::recordAuthorizer rdfs:label 'recordAuthorizer' . -# -# meshv::recordMaintainer rdfs:domain meshv::Descriptor . -# meshv::recordMaintainer rdfs:domain meshv::Qualifier . -# meshv::recordMaintainer rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::recordMaintainer rdfs:range rdfs:Literal . -# meshv::recordMaintainer rdf:type rdf:Property . -# meshv::recordMaintainer dcterms:identifier 'recordMaintainer' . -# meshv::recordMaintainer rdfs:label 'recordMaintainer' . -# -# meshv::recordOriginator rdfs:domain meshv::Descriptor . -# meshv::recordOriginator rdfs:domain meshv::Qualifier . -# meshv::recordOriginator rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::recordOriginator rdfs:range rdfs:Literal . -# meshv::recordOriginator rdf:type rdf:Property . -# meshv::recordOriginator dcterms:identifier 'recordOriginator' . -# meshv::recordOriginator rdfs:label 'recordOriginator' . -# -# meshv::registryNumber rdfs:domain meshv::Concept . -# meshv::registryNumber rdfs:range rdfs:Literal . -# meshv::registryNumber rdf:type rdf:Property . -# meshv::registryNumber dcterms:identifier 'registryNumber' . -# meshv::registryNumber rdfs:label 'registryNumber' . -# -# meshv::relatedRegistryNumber rdfs:domain meshv::Concept . -# meshv::relatedRegistryNumber rdfs:range rdfs:Literal . -# meshv::relatedRegistryNumber rdf:type rdf:Property . -# meshv::relatedRegistryNumber dcterms:identifier 'relatedRegistryNumber' . -# meshv::relatedRegistryNumber rdfs:label 'relatedRegistryNumber' . -# -# meshv::relationAttribute rdfs:domain meshv::ConceptRelation . -# meshv::relationAttribute rdfs:range rdfs:Literal . -# meshv::relationAttribute rdf:type rdf:Property . -# meshv::relationAttribute dcterms:identifier 'relationAttribute' . -# meshv::relationAttribute rdfs:label 'relationAttribute' . -# -# meshv::relation rdfs:domain meshv::ConceptRelation . -# meshv::relation rdfs:range rdfs:Literal . -# meshv::relation rdf:type rdf:Property . -# meshv::relation dcterms:identifier 'relation' . -# meshv::relation rdfs:label 'relation' . -# -# meshv::runningHead rdfs:domain meshv::Descriptor . -# meshv::runningHead rdfs:range rdfs:Literal . -# meshv::runningHead rdf:type rdf:Property . -# meshv::runningHead dcterms:identifier 'runningHead' . -# meshv::runningHead rdfs:label 'runningHead' . -# -# meshv::SCRClass rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::SCRClass rdfs:range rdfs:Literal . -# meshv::SCRClass rdf:type rdf:Property . -# meshv::SCRClass dcterms:identifier 'SCRClass' . -# meshv::SCRClass rdfs:label 'SCRClass' . -# -# meshv::semanticType rdfs:domain meshv::Concept . -# meshv::semanticType rdfs:range meshv::SemanticType . -# meshv::semanticType rdf:type rdf:Property . -# meshv::semanticType dcterms:identifier 'semanticType' . -# meshv::semanticType rdfs:label 'semanticType' . -# -# meshv::sortVersion rdfs:domain meshv::Term . -# meshv::sortVersion rdfs:domain meshv::TermData . -# meshv::sortVersion rdfs:range rdfs:Literal . -# meshv::sortVersion rdf:type rdf:Property . -# meshv::sortVersion dcterms:identifier 'sortVersion' . -# meshv::sortVersion rdfs:label 'sortVersion' . -# -# meshv::source rdfs:domain meshv::SupplementaryConceptRecord . -# meshv::source rdfs:range rdfs:Literal . -# meshv::source rdf:type rdf:Property . -# meshv::source dcterms:identifier 'source' . -# meshv::source rdfs:label 'source' . -# -# meshv::termData rdfs:domain meshv::Term . -# meshv::termData rdfs:range meshv::TermData . -# meshv::termData rdf:type rdf:Property . -# meshv::termData dcterms:identifier 'termData' . -# meshv::termData rdfs:label 'termData' . -# -# meshv::term rdfs:domain meshv::Concept . -# meshv::term rdfs:range meshv::Term . -# meshv::term rdf:type rdf:Property . -# meshv::term dcterms:identifier 'term' . -# meshv::term rdfs:label 'term' . -# -# meshv::thesaurusID rdfs:domain meshv::TermData . -# meshv::thesaurusID rdfs:range rdfs:Literal . -# meshv::thesaurusID rdf:type rdf:Property . -# meshv::thesaurusID dcterms:identifier 'thesaurusID' . -# meshv::thesaurusID rdfs:label 'thesaurusID' . -# -# meshv::treeNumber rdfs:domain meshv::Descriptor . -# meshv::treeNumber rdfs:domain meshv::Qualifier . -# meshv::treeNumber rdfs:range rdfs:Literal . -# meshv::treeNumber rdf:type rdf:Property . -# meshv::treeNumber dcterms:identifier 'treeNumber' . -# meshv::treeNumber rdfs:label 'treeNumber' . -# -# -# -# -# -# rdfs:label rdfs:domain meshv::Concept -# rdfs:label rdfs:domain meshv::Descriptor . -# rdfs:label rdfs:domain meshv::Qualifier . -# rdfs:label rdfs:domain meshv::SemanticType . -# rdfs:label rdfs:domain meshv::SupplementaryConceptRecord . -# rdfs:label rdfs:domain meshv::Term . -# rdfs:label rdfs:domain meshv::TermData . -# rdfs:label rdfs:range rdfs:Literal . -# -# rdfs:seeAlso rdfs:domain meshv::Descriptor . -# rdfs:seeAlso rdfs:range meshv::Descriptor . -# -# skos:broader rdfs:domain meshv::Descriptor . -# skos:broader rdfs:domain meshv::Qualifier . -# skos:broader rdfs:range meshv::Descriptor . -# skos:broader rdfs:range meshv::Qualifier . -# -# skos:scopeNote rdfs:domain meshv::Concept . -# skos:scopeNote rdfs:range rdfs:Literal . -# -# dcterms:identifier rdfs:domain meshv::Concept . -# dcterms:identifier rdfs:domain meshv::Descriptor . -# dcterms:identifier rdfs:domain meshv::Qualifier . -# dcterms:identifier rdfs:domain meshv::SemanticType . -# dcterms:identifier rdfs:domain meshv::SupplementaryConceptRecord . -# dcterms:identifier rdfs:domain meshv::Term . -# dcterms:identifier rdfs:domain meshv::TermData . -# dcterms:identifier rdfs:range rdfs:Literal . -# -# -# -# meshv::DescriptorQualifierPair rdf:type rdfs:Class . -# -# meshv::has_descriptor rdfs:domain meshv::DescriptorQualifierPair . -# meshv::has_descriptor rdfs:range meshv::Descriptor . -# meshv::has_descriptor rdf:type rdf:Property . -# meshv::has_descriptor dcterms:identifier 'has_descriptor' . -# meshv::has_descriptor rdfs:label 'has_descriptor' . -# -# meshv::has_qualifier rdfs:domain meshv::DescriptorQualifierPair . -# meshv::has_qualifier rdfs:range meshv::Qualifier . -# meshv::has_qualifier rdf:type rdf:Property . -# meshv::has_qualifier dcterms:identifier 'has_qualifier' . -# meshv::has_qualifier rdfs:label 'has_qualifier' . diff --git a/meta/vocabulary.owl b/meta/vocabulary.owl index 914e3a3c..92b73195 100644 --- a/meta/vocabulary.owl +++ b/meta/vocabulary.owl @@ -11,10 +11,10 @@ @@ -83,7 +83,16 @@ - + + + + + + + + + + @@ -101,10 +110,7 @@ - - - - + @@ -127,6 +133,9 @@ + + + @@ -463,12 +472,20 @@ + + + + + - - - + + + + + + @@ -482,16 +499,77 @@ - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -527,7 +605,7 @@ Concept - MeSH concepts are meanings. Many MeSH concepts contain synonymous terms. meshv:Concept identifiers begin with â€M’ such as M0000013 (Congenital Abnormalities). + MeSH concepts are smeanings. Many MeSH concepts contain synonymous terms. meshv:Concept identifiers begin with â€M’ such as M0000013 (Congenital Abnormalities). @@ -763,5 +841,5 @@ - + From c41dd77e19ad2dac655c4f1925e89fed3336ff3d Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Mon, 27 Apr 2015 15:04:52 -0400 Subject: [PATCH 10/44] Change script to append -T argument to avoid /tmp exhaustion and fix gzip to work properly for my copy of gzip. --- bin/mesh-xml2rdf.sh | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index 48e249bd..c2de5ec9 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -16,5 +16,5 @@ java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/desc2014.xml \ java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/supp2014.xml \ -xsl:xslt/supp.xsl >> $MESHRDF_HOME/out/mesh2014-dups.nt -sort -u $MESHRDF_HOME/out/mesh2014-dups.nt > $MESHRDF_HOME/out/mesh2014.nt -gzip -k mesh2014.nt +sort -u -T$MESHRDF_HOME/out $MESHRDF_HOME/out/mesh2014-dups.nt > $MESHRDF_HOME/out/mesh2014.nt +gzip -c $MESHRDF_HOME/out/mesh2014.nt > $MESHRDF_HOME/out/mesh2014.nt.gz From fbb6e7fc54db40d8c1962d11d93bf6e2dc0fba82 Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Mon, 27 Apr 2015 17:27:27 -0400 Subject: [PATCH 11/44] Parameterize fetch-mesh-xml.sh and mesh-xml2rdf.sh with YEAR (and URI) --- bin/fetch-mesh-xml.sh | 32 ++++++++++++++++++++++---------- bin/mesh-xml2rdf.sh | 33 ++++++++++++++++++++++++--------- 2 files changed, 46 insertions(+), 19 deletions(-) diff --git a/bin/fetch-mesh-xml.sh b/bin/fetch-mesh-xml.sh index 6d4acc09..7fc4e494 100755 --- a/bin/fetch-mesh-xml.sh +++ b/bin/fetch-mesh-xml.sh @@ -1,13 +1,25 @@ #!/bin/sh -mkdir -p $MESHRDF_HOME/data - -wget ftp://ftp.nlm.nih.gov/online/mesh/2014/desc2014.dtd -O $MESHRDF_HOME/data/desc2014.dtd -wget ftp://ftp.nlm.nih.gov/online/mesh/2014/desc2014.xml -O $MESHRDF_HOME/data/desc2014.xml -wget ftp://ftp.nlm.nih.gov/online/mesh/2014/pa2014.dtd -O $MESHRDF_HOME/data/pa2014.dtd -wget ftp://ftp.nlm.nih.gov/online/mesh/2014/pa2014.xml -O $MESHRDF_HOME/data/pa2014.xml -wget ftp://ftp.nlm.nih.gov/online/mesh/2014/qual2014.dtd -O $MESHRDF_HOME/data/qual2014.dtd -wget ftp://ftp.nlm.nih.gov/online/mesh/2014/qual2014.xml -O $MESHRDF_HOME/data/qual2014.xml -wget ftp://ftp.nlm.nih.gov/online/mesh/2014/supp2014.dtd -O $MESHRDF_HOME/data/supp2014.dtd -wget ftp://ftp.nlm.nih.gov/online/mesh/2014/supp2014.xml -O $MESHRDF_HOME/data/supp2014.xml +if [ -z "$MESHRDF_HOME" ]; then + echo "Please define MESHRDF_HOME environment variable" 1>&2 + exit 1 +fi + +mkdir -p "$MESHRDF_HOME/data" + +# Can override default URI with MESHRDF_URI environment variable +URI=${MESHRDF_URI:-ftp://ftp.nlm.nih.gov/online/mesh/2014} + +# CAn override default year with MESHRDF_YEAR environment variable +YEAR=${MESHRDF_YEAR:-2014} + +wget "$URI/desc$YEAR.dtd" -O "$MESHRDF_HOME/data/desc$YEAR.dtd" +wget "$URI/desc$YEAR.xml" -O "$MESHRDF_HOME/data/desc$YEAR.xml" +wget "$URI/pa$YEAR.dtd" -O "$MESHRDF_HOME/data/pa$YEAR.dtd" +wget "$URI/pa$YEAR.xml" -O "$MESHRDF_HOME/data/pa$YEAR.xml" +wget "$URI/qual$YEAR.dtd" -O "$MESHRDF_HOME/data/qual$YEAR.dtd" +wget "$URI/qual$YEAR.xml" -O "$MESHRDF_HOME/data/qual$YEAR.xml" +wget "$URI/supp$YEAR.dtd" -O "$MESHRDF_HOME/data/supp$YEAR.dtd" +wget "$URI/supp$YEAR.xml" -O "$MESHRDF_HOME/data/supp$YEAR.xml" + diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index c2de5ec9..d7dbc268 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -5,16 +5,31 @@ # huge XML files into manageable chunks, and then passes each chunk through XSLT # separately. -mkdir -p $MESHRDF_HOME/out +if [ -z "$MESHRDF_HOME" ]; then + echo "Please define MESHRDF_HOME environment variable" 1>&2 + exit 1 +fi -java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/qual2014.xml \ - -xsl:xslt/qual.xsl > $MESHRDF_HOME/out/mesh2014-dups.nt +if [ -z "$SAXON_JAR" ]; then + echo "Please define SAXON_JAR environment variable" 1>&2 + exit 1 +fi -java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/desc2014.xml \ - -xsl:xslt/desc.xsl >> $MESHRDF_HOME/out/mesh2014-dups.nt +# Can override default year with MESHRDF_YEAR environment variable +YEAR=${MESHRDF_YEAR:-2014} -java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/supp2014.xml \ - -xsl:xslt/supp.xsl >> $MESHRDF_HOME/out/mesh2014-dups.nt +# Use year to modify $MESHRDF_HOME/xslt/mesh-rdf-prefixes.ent -sort -u -T$MESHRDF_HOME/out $MESHRDF_HOME/out/mesh2014-dups.nt > $MESHRDF_HOME/out/mesh2014.nt -gzip -c $MESHRDF_HOME/out/mesh2014.nt > $MESHRDF_HOME/out/mesh2014.nt.gz +mkdir -p "$MESHRDF_HOME/out" + +java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/qual$YEAR.xml \ + -xsl:xslt/qual.xsl > $MESHRDF_HOME/out/mesh$YEAR-dups.nt + +java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/desc$YEAR.xml \ + -xsl:xslt/desc.xsl >> $MESHRDF_HOME/out/mesh$YEAR-dups.nt + +java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/supp$YEAR.xml \ + -xsl:xslt/supp.xsl >> $MESHRDF_HOME/out/mesh$YEAR-dups.nt + +sort -u -T$MESHRDF_HOME/out $MESHRDF_HOME/out/mesh$YEAR-dups.nt > $MESHRDF_HOME/out/mesh$YEAR.nt +gzip -c $MESHRDF_HOME/out/mesh$YEAR.nt > $MESHRDF_HOME/out/mesh$YEAR.nt.gz From ed64843f6a20a72d34eb4c8f1c13c1961b969d18 Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Tue, 28 Apr 2015 16:16:21 -0400 Subject: [PATCH 12/44] https://github.com/HHS/mesh-rdf/issues/52 suggests that there may not need to be a separate path pattern to use for our own use and the publics. Therefore, default the URI to depend on the year, and continue to allow scripts to override it. --- bin/fetch-mesh-xml.sh | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/bin/fetch-mesh-xml.sh b/bin/fetch-mesh-xml.sh index 7fc4e494..ae7f4ebb 100755 --- a/bin/fetch-mesh-xml.sh +++ b/bin/fetch-mesh-xml.sh @@ -7,12 +7,12 @@ fi mkdir -p "$MESHRDF_HOME/data" -# Can override default URI with MESHRDF_URI environment variable -URI=${MESHRDF_URI:-ftp://ftp.nlm.nih.gov/online/mesh/2014} - # CAn override default year with MESHRDF_YEAR environment variable YEAR=${MESHRDF_YEAR:-2014} +# Can override default URI with MESHRDF_URI environment variable +URI=${MESHRDF_URI:-ftp://ftp.nlm.nih.gov/online/mesh/$YEAR} + wget "$URI/desc$YEAR.dtd" -O "$MESHRDF_HOME/data/desc$YEAR.dtd" wget "$URI/desc$YEAR.xml" -O "$MESHRDF_HOME/data/desc$YEAR.xml" wget "$URI/pa$YEAR.dtd" -O "$MESHRDF_HOME/data/pa$YEAR.dtd" From 5766db9724e08ddf8aa2f79878ba362aadf944ad Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Tue, 28 Apr 2015 18:09:42 -0400 Subject: [PATCH 13/44] Changes to parameterize the fetch and convert of MESH XML These changes also tolerate a $MESHRDF_HOME that includes spaces --- .gitignore | 1 + bin/mesh-xml2rdf.sh | 45 ++++++++++++++----- ...xes.ent => mesh-rdf-prefixes.ent.template} | 2 +- 3 files changed, 37 insertions(+), 11 deletions(-) rename xslt/{mesh-rdf-prefixes.ent => mesh-rdf-prefixes.ent.template} (80%) diff --git a/.gitignore b/.gitignore index a81a23c7..f7a5f4bf 100755 --- a/.gitignore +++ b/.gitignore @@ -2,3 +2,4 @@ Saxon*.zip saxon9he data out +xslt/mesh-rdf-prefixes.ent diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index d7dbc268..b24d96f9 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -1,9 +1,12 @@ #!/bin/sh +# # This script will convert all of the MeSH XML to RDF, assuming that your machine has # enough memory and resources. -# Another option is to use the Perl script convert-all.pl, which first chops up the +# +# Another option is to use the Perl script mesh-rdf2xml.pl, which first chops up the # huge XML files into manageable chunks, and then passes each chunk through XSLT # separately. +# if [ -z "$MESHRDF_HOME" ]; then echo "Please define MESHRDF_HOME environment variable" 1>&2 @@ -18,18 +21,40 @@ fi # Can override default year with MESHRDF_YEAR environment variable YEAR=${MESHRDF_YEAR:-2014} -# Use year to modify $MESHRDF_HOME/xslt/mesh-rdf-prefixes.ent +# Can override default Mesh prefix and output file with MESHRDF_PREFIX environment variable +PREFIX=${MESHRDF_PREFIX:-mesh/$YEAR} +OUT=`echo $PREFIX | sed -e 's,/,,'` + +# substitute the prefix into the DTD entity file +sed -e "s,MESHRDF_PATH,$PREFIX,g" xslt/mesh-rdf-prefixes.ent.template > xslt/mesh-rdf-prefixes.ent +if [ $? -ne 0 ]; then + echo "Error creating xslt/mesh-rdf-prefixes.ent from template" 1>&2 + exit 1 +fi mkdir -p "$MESHRDF_HOME/out" -java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/qual$YEAR.xml \ - -xsl:xslt/qual.xsl > $MESHRDF_HOME/out/mesh$YEAR-dups.nt +java -Xmx2G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/qual$YEAR.xml" \ + -xsl:xslt/qual.xsl > "$MESHRDF_HOME/out/$OUT-dups.nt" +if [ $? -ne 0 ]; then + echo "Error converting $MESHRDF_HOME/data/qual$YEAR.xml" 1>&2 + exit 1 +fi + +java -Xmx2G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/desc$YEAR.xml" \ + -xsl:xslt/desc.xsl >> "$MESHRDF_HOME/out/$OUT-dups.nt" +if [ $? -ne 0 ]; then + echo "Error converting $MESHRDF_HOME/data/desc$YEAR.xml" + exit 1 +fi -java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/desc$YEAR.xml \ - -xsl:xslt/desc.xsl >> $MESHRDF_HOME/out/mesh$YEAR-dups.nt -java -Xmx2G -jar $SAXON_JAR -s:$MESHRDF_HOME/data/supp$YEAR.xml \ - -xsl:xslt/supp.xsl >> $MESHRDF_HOME/out/mesh$YEAR-dups.nt +java -Xmx2G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/supp$YEAR.xml" \ + -xsl:xslt/supp.xsl >> "$MESHRDF_HOME/out/$OUT-dups.nt" +if [ $? -ne 0 ]; then + echo "Error converting $MESHRDF_HOME/data/supp$YEAR.xml" + exit 1 +fi -sort -u -T$MESHRDF_HOME/out $MESHRDF_HOME/out/mesh$YEAR-dups.nt > $MESHRDF_HOME/out/mesh$YEAR.nt -gzip -c $MESHRDF_HOME/out/mesh$YEAR.nt > $MESHRDF_HOME/out/mesh$YEAR.nt.gz +sort -u -T"$MESHRDF_HOME/out" "$MESHRDF_HOME/out/$OUT-dups.nt" > "$MESHRDF_HOME/out/$OUT.nt" +gzip -c "$MESHRDF_HOME/out/$OUT.nt" > "$MESHRDF_HOME/out/$OUT.nt.gz" diff --git a/xslt/mesh-rdf-prefixes.ent b/xslt/mesh-rdf-prefixes.ent.template similarity index 80% rename from xslt/mesh-rdf-prefixes.ent rename to xslt/mesh-rdf-prefixes.ent.template index 409bed26..9de3556b 100755 --- a/xslt/mesh-rdf-prefixes.ent +++ b/xslt/mesh-rdf-prefixes.ent.template @@ -1,4 +1,4 @@ - + From 5e55914d47652cf2678e352e5aba320d4b3955dc Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Wed, 29 Apr 2015 16:44:54 -0400 Subject: [PATCH 14/44] Parameterize mesh-xml2rdf.pl with the same environment variables used for mesh-xml2rdf.sh --- bin/mesh-xml2rdf.pl | 21 ++++++++++++++++++++- 1 file changed, 20 insertions(+), 1 deletion(-) diff --git a/bin/mesh-xml2rdf.pl b/bin/mesh-xml2rdf.pl index 766d211f..63bb1f1a 100755 --- a/bin/mesh-xml2rdf.pl +++ b/bin/mesh-xml2rdf.pl @@ -22,6 +22,7 @@ use strict; + my $LINES_PER_CHUNK = 500000; my $meshrdf_home = $ENV{MESHRDF_HOME}; my $saxon_jar = $ENV{SAXON_JAR}; @@ -31,11 +32,27 @@ my $out_dir = "$meshrdf_home/out"; mkdir $out_dir; # if it didn't exist already +my $YEAR = ($ENV{MESHRDF_YEAR} || "2014"); +my $PREFIX = ($ENV{MESHRDF_PREFIX} || "mesh/$YEAR"); + +# substitute the prefix into the file +my $prefix_file= "$meshrdf_home/xslt/mesh-rdf-prefixes.ent"; +my $prefix_template = "$prefix_file.template"; + +open(INPUT, '<', $prefix_template) || die "$prefix_template: $!"; +open(OUTPUT, '>', $prefix_file) || die "$prefix_file: $!"; +while () { + s{MESHRDF_PATH}{$PREFIX}g; + print OUTPUT $_; +} +close INPUT; +close OUTPUT; + my @sets = qw( qual desc supp ); # First, chunk up the XML foreach my $set (@sets) { - my $xml_file = "$meshrdf_home/data/$set" . "2014.xml"; + my $xml_file = "$meshrdf_home/data/$set" . "$YEAR.xml"; my $xml_chunk_base = "$out_dir/$set-"; my $state = 0; # init @@ -109,6 +126,8 @@ print "$xml_file split into $chunk_num chunks\n"; } + + # Next, run the transforms foreach my $set (@sets) { foreach my $xml_chunk_file (<$out_dir/$set-*.xml>) { From f2e47853953ae3c247c35684cd8b64e3ea855fa5 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Mon, 4 May 2015 12:32:48 -0400 Subject: [PATCH 15/44] broaderTreeNumber -> parentTreeNumber --- README.md | 2 +- xslt/common.xsl | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 57688ab3..80b18345 100755 --- a/README.md +++ b/README.md @@ -166,7 +166,7 @@ Decide on a directory where you will install virtuoso, and set the $VIRTUOSO_HOM Checkout source from github: - git clone git://github.com/openlink/virtuoso-opensource.git + git clone https://github.com/openlink/virtuoso-opensource.git cd virtuoso-opensource git checkout develop/7 # should say already on develop/7 diff --git a/xslt/common.xsl b/xslt/common.xsl index 33482e1b..528a003d 100755 --- a/xslt/common.xsl +++ b/xslt/common.xsl @@ -422,11 +422,11 @@ Every time we reify a TreeNumber that has a dot in it, we'll create a triple - to link it to its parent with meshv:broaderTreeNumber. + to link it to its parent with meshv:parentTreeNumber. - broaderTreeNumber + parentTreeNumber From 549ab3f97be2f77f98e228fdcf02def9830070b1 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Mon, 4 May 2015 13:24:49 -0400 Subject: [PATCH 16/44] Remove support for windows --- README.md | 37 ++++------- bin/mesh-xml2rdf.bat | 14 ---- bin/mesh-xml2rdf.pl | 123 ------------------------------------ samples/.gitignore | 1 + samples/convert-samples.bat | 7 -- samples/convert-samples.sh | 3 +- 6 files changed, 17 insertions(+), 168 deletions(-) delete mode 100644 bin/mesh-xml2rdf.bat delete mode 100755 bin/mesh-xml2rdf.pl delete mode 100644 samples/convert-samples.bat diff --git a/README.md b/README.md index 80b18345..d935ae80 100755 --- a/README.md +++ b/README.md @@ -11,8 +11,13 @@ Please see that technical documentation for details about the data model, and ho RDF version of MeSH relates to the XML from which it derives. The rest of this README describes how to set up a development environment, perform the -transformations yourself, if you are interested in doing that. All the instructions assume -that you're running on a Unix-like operating system, in a bash shell. +transformations yourself, if you are interested in doing that. + +All the instructions assume +that you're running on a Unix-like operating system, in a bash shell. If you have a Windows +machine, we recommend that you install [cygwin](https://www.cygwin.com/). Please let us know +(by opening a GitHub issue here) if you have problems. + ## Quick start @@ -75,9 +80,6 @@ Where *repository-dir* is the base directory of this repository. If your version of Saxon is in a different location, then, of course, set this environment variable appropriately. -On Windows: - - set SAXON_JAR=*repository-dir*\saxon\saxon9he.jar ### Converting the complete MeSH data set @@ -85,21 +87,11 @@ On Windows: There are a few conversion scripts in the repository which you can use to run the XSLT conversions. -The conversion scripts are: - -* mesh-xml2rdf.sh - For unix, this shell script will brute-force convert each of the three - main MeSH XML files into RDF N-Triples format, and put the results into the *$MESHRDF_HOME/out* - directory. It produces mesh2014.nt, which is the RDF in N-triples format, and mesh2014.nt.gz, - a gzipped version. -* mesh-xml2rdf.bat - This does the same thing (mostly), but can be run from Windows. Note that - the unix shell script sorts and uniques the output, whereas this one does not. +The conversion script is *mesh-xml2rdf.sh*. This shell script will brute-force convert each of +the three main MeSH XML files into RDF N-Triples format, and put the results into the +*$MESHRDF_HOME/out* directory. It produces *mesh2014.nt*, which is the RDF in N-triples format, and +*mesh2014.nt.gz*, a gzipped version. -There is one other script that takes a different approach, that was useful for -doing the conversions on less-powerful machines. The Perl script mesh-xml2rdf.pl first -chops up each of the input XML files into manageable sized chunks, and then runs each chunk -through the XSLTs separately. ***Note, however, that because of the way it chunks the input -files, it fails to create a lot of meshv:broader links between the various tree nodes. -Therefore, this should not be used in production.*** ### Generating and converting the sample files @@ -124,11 +116,10 @@ file, if any of those changes. So, keep in mind that these samples in the repos used for testing/demo purposes, and are not necessarily up-to-date with the latest MeSH release. -Finally, either of the scripts *convert-samples.sh* (for Unix) or *convert-samples.bat* -(for Windows) can be used to convert the sample XML files into RDF, the final output -being *samples.nt*. +Finally, the script *convert-samples.sh* can be used to convert the sample XML files into +RDF, the final output being *samples.nt*. -***Note, though, that the generated RDF will be missing a lot of meshv:broader +***Note that the generated RDF will be missing a lot of meshv:parentTreeNumber relationships, because those are generated from the tree node identifiers to link between various records. Since the sample files contain only a subset of the records, most of these cannot be generated.*** diff --git a/bin/mesh-xml2rdf.bat b/bin/mesh-xml2rdf.bat deleted file mode 100644 index f676762b..00000000 --- a/bin/mesh-xml2rdf.bat +++ /dev/null @@ -1,14 +0,0 @@ -rem This script will convert all of the MeSH XML to RDF, assuming that your machine has -rem enough memory and resources. -rem Another option is to use the Perl script convert-all.pl, which first chops up the -rem huge XML files into manageable chunks, and then passes each chunk through XSLT -rem separately. - -mkdir %MESHRDF_HOME%\out -java -Xmx2G -jar %SAXON_JAR% -s:%MESHRDF_HOME%/data/qual2014.xml ^ - -xsl:xslt/qual.xsl > %MESHRDF_HOME%/out/mesh2014.nt -java -Xmx2G -jar %SAXON_JAR% -s:%MESHRDF_HOME%/data/desc2014.xml ^ - -xsl:xslt/desc.xsl >> %MESHRDF_HOME%/out/mesh2014.nt -java -Xmx2G -jar %SAXON_JAR% -s:%MESHRDF_HOME%/data/supp2014.xml ^ - -xsl:xslt/supp.xsl >> %MESHRDF_HOME%/out/mesh2014.nt - diff --git a/bin/mesh-xml2rdf.pl b/bin/mesh-xml2rdf.pl deleted file mode 100755 index 766d211f..00000000 --- a/bin/mesh-xml2rdf.pl +++ /dev/null @@ -1,123 +0,0 @@ -#! /usr/bin/env perl - -# THIS SCRIPT SHOULD NOT BE USED IN PRODUCTION. -# Because of the way this script chunks the input files, it fails to create a lot -# of meshv:broader links between the various tree nodes. -# -# The aim of this script is to provide a means to run the XSLTs against the very huge MeSH XML -# files, on machines that have limited memory. For each of the inputs qual, desc, and supp, it will -# * split the input XML into chunks -# * run each chunk through the XSLT, producing a chunk of RDF in n-triples format -# * (TBD) concatenate those n-triples together. -# The last step is "TBD", because it might turn out to be easier to load the triples into a triple -# store if they remain in manageable chunk sizes. -# -# Before running this, make sure you have two environment variables set: -# - MESHRDF_HOME should point to the directory where the the work will be done. -# The `data` subdirectory is assumed to hold the source XML files, and the output -# files will be written to `out`. -# - SAXON_JAR should point to the saxon jar file. -# Finally, make sure that your current directory is the hhs/meshrdf repository directory, as this -# script refers to the XSLT files in the xslt directory by their relative paths. - -use strict; - -my $LINES_PER_CHUNK = 500000; -my $meshrdf_home = $ENV{MESHRDF_HOME}; -my $saxon_jar = $ENV{SAXON_JAR}; -if (!$meshrdf_home || !$saxon_jar) { - die "You must first define the environment variables MESHRDF_HOME and SAXON_JAR."; -} -my $out_dir = "$meshrdf_home/out"; -mkdir $out_dir; # if it didn't exist already - -my @sets = qw( qual desc supp ); - -# First, chunk up the XML -foreach my $set (@sets) { - my $xml_file = "$meshrdf_home/data/$set" . "2014.xml"; - my $xml_chunk_base = "$out_dir/$set-"; - - my $state = 0; # init - open( my $XML_FILE, '<' , $xml_file ) or die( "Can't open $xml_file for reading ($!)" ); - print "Chunking $set\n"; - - my $wrapper_line; - my $wrapper_element_name; - my $chunk_num = 0; - my $item_element_name; - my $CHUNK_FILE; - my $chunk_line_num; - while (my $line = <$XML_FILE>) { - chomp $line; - - # Initial state - if ($state == 0) { - if ($line =~ /^\<(\w+) /) { - $wrapper_element_name = $1; - $wrapper_line = $line; - #print "wrapper_line = '$wrapper_line'; wrapper_element_name = '$wrapper_element_name'\n"; - $state = 1; # Ready to start the first chunk file - } - } - - # Ready to start a new chunk. $CHUNK_FILE is not open. - elsif ($state == 1) { - #print "state == 1, line is '$line'\n"; - # If we see the closing tag of the whole file, just get out - if ($line =~ /^\s*\<\/$wrapper_element_name\>/) { - $state = 3; - } - if ($line =~ /^\<(\w+) /) { - $item_element_name = $1; - my $chunk_file = $xml_chunk_base . sprintf("%03d", $chunk_num) . '.xml'; - $chunk_num++; - open($CHUNK_FILE, ">", $chunk_file) or die("Can't open $chunk_file for writing ($!)"); - print " Writing $chunk_file\n"; - print $CHUNK_FILE $wrapper_line . "\n"; - print $CHUNK_FILE $line . "\n"; - $chunk_line_num = 0; - $state = 2; # Writing chunk - } - } - - # Writing chunk - elsif ($state == 2) { - print $CHUNK_FILE $line . "\n"; - $chunk_line_num++; - # If we see the closing tag of the whole file - if ($line =~ /^\s*\<\/$wrapper_element_name\>/) { - close $CHUNK_FILE; - $state = 3; # Done - } - # Otherwise, if we are outside the min. lines per chunk, and we see the closing tag of - # an item, then close this chunk and get ready to start a new one. - elsif ($chunk_line_num > $LINES_PER_CHUNK && - $line =~ /^\s*\<\/$item_element_name\>/) - { - print $CHUNK_FILE "\n"; - close $CHUNK_FILE; - $state = 1; # Ready for next chunk - } - } - - elsif ($state == 3) { - last; - } - } - close $xml_file; - print "$xml_file split into $chunk_num chunks\n"; -} - -# Next, run the transforms -foreach my $set (@sets) { - foreach my $xml_chunk_file (<$out_dir/$set-*.xml>) { - $xml_chunk_file =~ /-(\d+)/; - my $num_str = $1; - my $nt_chunk_file = "$out_dir/$set-$num_str.nt"; - print "Converting $xml_chunk_file -> $nt_chunk_file\n"; - my $cmd = "java -Xmx2G -jar $saxon_jar -s:$xml_chunk_file -xsl:xslt/$set.xsl > $nt_chunk_file"; - print "Executing '$cmd'\n"; - system $cmd; - } -} diff --git a/samples/.gitignore b/samples/.gitignore index 343af4d9..6e1a564f 100644 --- a/samples/.gitignore +++ b/samples/.gitignore @@ -1 +1,2 @@ *samples.nt +samples-dups.nt diff --git a/samples/convert-samples.bat b/samples/convert-samples.bat deleted file mode 100644 index de02021d..00000000 --- a/samples/convert-samples.bat +++ /dev/null @@ -1,7 +0,0 @@ -rem This script will convert the sample XML files, which contain all the entities listed -rem in sample-list.txt. - -java -jar %SAXON_JAR% -s:qual-samples.xml -xsl:../xslt/qual.xsl > qual-samples.nt -java -jar %SAXON_JAR% -s:desc-samples.xml -xsl:../xslt/desc.xsl > desc-samples.nt -java -jar %SAXON_JAR% -s:supp-samples.xml -xsl:../xslt/supp.xsl > supp-samples.nt -type qual-samples.nt desc-samples.nt supp-samples.nt > samples.nt diff --git a/samples/convert-samples.sh b/samples/convert-samples.sh index 12e52241..0a4571dd 100755 --- a/samples/convert-samples.sh +++ b/samples/convert-samples.sh @@ -5,4 +5,5 @@ java -jar $SAXON_JAR -s:qual-samples.xml -xsl:../xslt/qual.xsl > qual-samples.nt java -jar $SAXON_JAR -s:desc-samples.xml -xsl:../xslt/desc.xsl > desc-samples.nt java -jar $SAXON_JAR -s:supp-samples.xml -xsl:../xslt/supp.xsl > supp-samples.nt -cat qual-samples.nt desc-samples.nt supp-samples.nt > samples.nt +cat qual-samples.nt desc-samples.nt supp-samples.nt > samples-dups.nt +sort -u samples-dups.nt > samples.nt \ No newline at end of file From dc4e15ad53a71aae2a76df28dabbaf116beab957 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Mon, 4 May 2015 15:46:20 -0400 Subject: [PATCH 17/44] Tweak parameterization of shell scripts a little bit --- README.md | 44 +++++++++++++++++++++++------ bin/mesh-xml2rdf.sh | 27 +++++++++++------- xslt/mesh-rdf-prefixes.ent.template | 2 +- 3 files changed, 54 insertions(+), 19 deletions(-) diff --git a/README.md b/README.md index d935ae80..ea02ce31 100755 --- a/README.md +++ b/README.md @@ -31,6 +31,7 @@ Next, you can either explore this repository using the included sample XML files relatively small), or, if you need complete and up-to-date data, you can download the latest MeSH XML files from the NLM server. The latter option is described first. + ### Getting the MeSH XML files Since the complete MeSH data files are quite large, we assume that they'll be kept @@ -42,7 +43,7 @@ $MESHRDF_HOME to point to that location. For example, You can run the script *bin/fetch-mesh-xml.sh*, which downloads all the XML and corresponding DTD files from the NLM FTP server. It saves them to the *data* subdirectory of $MESHRDF_HOME. -It downloads the following: +By default, it downloads the following: * desc2014.dtd * desc2014.xml @@ -53,6 +54,16 @@ It downloads the following: * supp2014.dtd * supp2014.xml +If you want to download a different year's data, set the MESHRDF_YEAR environment variable +before executing the script. For example, + + MESHRDF_YEAR=2015 bin/fetch-mesh-xml.sh + +***Note that at the time of this writing, the 2015 MeSH XML files have not yet been deployed +to that location.*** To specify the actual location for these files, use this command line: + + MESHRDF_YEAR=2015 MESHRDF_URI=ftp://ftp.nlm.nih.gov/online/mesh/.xmlmesh bin/fetch-mesh-xml.sh + ### Getting Saxon @@ -81,17 +92,33 @@ If your version of Saxon is in a different location, then, of course, set this e appropriately. - ### Converting the complete MeSH data set -There are a few conversion scripts in the repository which you can use to run the -XSLT conversions. - -The conversion script is *mesh-xml2rdf.sh*. This shell script will brute-force convert each of +The conversion script is *mesh-xml2rdf.sh*. This shell script will run the XSLTs to convert each of the three main MeSH XML files into RDF N-Triples format, and put the results into the -*$MESHRDF_HOME/out* directory. It produces *mesh2014.nt*, which is the RDF in N-triples format, and -*mesh2014.nt.gz*, a gzipped version. +*$MESHRDF_HOME/out* directory. +By default, it looks for 2014 data files, and will produce *mesh.nt*, which is the +RDF in N-triples format, and *mesh.nt.gz*, a gzipped version. Also by default, these +data files will have RDF URIs that do not include the year. For example, the descriptor for +Ofloxacin would have the URI http://id.nlm.nih.gov/mesh/D015242. + +As with the fetch script, described above, you can use the MESHRDF_YEAR environment variable +to specify that it convert a different set of data files. For example: + + MESHRDF_YEAR=2015 bin/mesh-xml2rdf.sh + +This uses the 2015 data files to produce the "current" RDF output files *out/mesh.nt* +and *out/mesh.nt.gz*. + +To produce RDF data that has URIs with the year, then you should also set the +MESHRDF_URI_YEAR variable to "yes". Thus, the following uses the 2015 MeSH XML files to +generate the data that has RDF URIs that include the year: + + MESHRDF_YEAR=2015 MESHRDF_URI_YEAR=yes bin/mesh-xml2rdf.sh + +In this case, the output data files will be written to *out/mesh-2015.nt* and +*out/mesh-2015.nt.gz*. ### Generating and converting the sample files @@ -181,6 +208,7 @@ documentation](http://data-gov.tw.rpi.edu/wiki/How_to_install_virtuoso_sparql_en $VIRTUOSO_HOME/bin/isql 1111 dba SQL> shutdown(); + ## Technical documentation on GitHub pages The gh-pages branch of this repository is used to generate the technical documentation diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index b24d96f9..2f0e0681 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -3,10 +3,9 @@ # This script will convert all of the MeSH XML to RDF, assuming that your machine has # enough memory and resources. # -# Another option is to use the Perl script mesh-rdf2xml.pl, which first chops up the -# huge XML files into manageable chunks, and then passes each chunk through XSLT -# separately. -# +# + + if [ -z "$MESHRDF_HOME" ]; then echo "Please define MESHRDF_HOME environment variable" 1>&2 @@ -21,9 +20,17 @@ fi # Can override default year with MESHRDF_YEAR environment variable YEAR=${MESHRDF_YEAR:-2014} -# Can override default Mesh prefix and output file with MESHRDF_PREFIX environment variable -PREFIX=${MESHRDF_PREFIX:-mesh/$YEAR} -OUT=`echo $PREFIX | sed -e 's,/,,'` +# Override the default Mesh prefix and output file by setting MESHRDF_URI_YEAR to "yes" +if [ "$MESHRDF_URI_YEAR" = "yes" ]; then + PREFIX=mesh/$YEAR + OUT=mesh$YEAR +else + PREFIX=mesh + OUT=mesh +fi + +#echo PREFIX = $PREFIX +#echo OUT = $OUT # substitute the prefix into the DTD entity file sed -e "s,MESHRDF_PATH,$PREFIX,g" xslt/mesh-rdf-prefixes.ent.template > xslt/mesh-rdf-prefixes.ent @@ -34,14 +41,14 @@ fi mkdir -p "$MESHRDF_HOME/out" -java -Xmx2G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/qual$YEAR.xml" \ +java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/qual$YEAR.xml" \ -xsl:xslt/qual.xsl > "$MESHRDF_HOME/out/$OUT-dups.nt" if [ $? -ne 0 ]; then echo "Error converting $MESHRDF_HOME/data/qual$YEAR.xml" 1>&2 exit 1 fi -java -Xmx2G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/desc$YEAR.xml" \ +java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/desc$YEAR.xml" \ -xsl:xslt/desc.xsl >> "$MESHRDF_HOME/out/$OUT-dups.nt" if [ $? -ne 0 ]; then echo "Error converting $MESHRDF_HOME/data/desc$YEAR.xml" @@ -49,7 +56,7 @@ if [ $? -ne 0 ]; then fi -java -Xmx2G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/supp$YEAR.xml" \ +java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/supp$YEAR.xml" \ -xsl:xslt/supp.xsl >> "$MESHRDF_HOME/out/$OUT-dups.nt" if [ $? -ne 0 ]; then echo "Error converting $MESHRDF_HOME/data/supp$YEAR.xml" diff --git a/xslt/mesh-rdf-prefixes.ent.template b/xslt/mesh-rdf-prefixes.ent.template index 9de3556b..ed3e19a1 100755 --- a/xslt/mesh-rdf-prefixes.ent.template +++ b/xslt/mesh-rdf-prefixes.ent.template @@ -1,5 +1,5 @@ - + From 77769035a29ba866db16aa0ced1cb1808bc25354 Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Fri, 8 May 2015 16:20:33 -0400 Subject: [PATCH 18/44] Add vocabulary.ttl generated by WebProtege to the repository. --- meta/vocabulary.ttl | 755 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 755 insertions(+) create mode 100644 meta/vocabulary.ttl diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl new file mode 100644 index 00000000..8b018373 --- /dev/null +++ b/meta/vocabulary.ttl @@ -0,0 +1,755 @@ +@prefix : . +@prefix owl: . +@prefix rdf: . +@prefix xml: . +@prefix xsd: . +@prefix rdfs: . +@base . + + rdf:type owl:Ontology ; + + 1 ; + + "May 7, 2015 1:58:22 PM"^^xsd:dateTime ; + + rdfs:comment "Ontology supporting next generation (2015) of http://id.nlm.nih.gov/"^^xsd:string , + "This ontology was generated from an ontology revision in WebProtege http://webprotege.stanford.edu"^^xsd:string ; + + "system"^^xsd:string . + + +################################################################# +# +# Annotation properties +# +################################################################# + + +### http://purl.org/dc/terms/description + + rdf:type owl:AnnotationProperty . + + + + + +################################################################# +# +# Object Properties +# +################################################################# + + +### http://id.nlm.nih.gov/mesh/vocab#allowableQualifier + + rdf:type owl:ObjectProperty ; + + rdfs:range . + + + +### http://id.nlm.nih.gov/mesh/vocab#allowedTreeNode + + rdf:type owl:ObjectProperty ; + + rdfs:label "allowedTreeNode" ; + + "Name of a subcategory in the MeSH Trees indicating, that for most Descriptors in that subcategory, the allowed Qualifiers on the Descriptor include the Qualifier. This value does not impact Descriptors permitted with a given Qualifier, but is a statistical summary of Descriptors permitted with the Qualifier." ; + + rdfs:range . + + + +### http://id.nlm.nih.gov/mesh/vocab#broader + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#broaderConcept + + rdf:type owl:ObjectProperty ; + + rdfs:range ; + + rdfs:domain ; + + rdfs:subPropertyOf . + + + +### http://id.nlm.nih.gov/mesh/vocab#broaderDescriptor + + rdf:type owl:ObjectProperty ; + + rdfs:domain ; + + rdfs:range ; + + rdfs:subPropertyOf . + + + +### http://id.nlm.nih.gov/mesh/vocab#broaderQualifier + + rdf:type owl:ObjectProperty ; + + rdfs:range ; + + rdfs:domain ; + + rdfs:subPropertyOf . + + + +### http://id.nlm.nih.gov/mesh/vocab#broaderTreeNumber + + rdf:type owl:ObjectProperty , + owl:TransitiveProperty ; + + rdfs:domain ; + + rdfs:range ; + + rdfs:subPropertyOf . + + + +### http://id.nlm.nih.gov/mesh/vocab#concept + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#hasDescriptor + + rdf:type owl:ObjectProperty ; + + rdfs:range . + + + +### http://id.nlm.nih.gov/mesh/vocab#hasQualifier + + rdf:type owl:ObjectProperty ; + + rdfs:range . + + + +### http://id.nlm.nih.gov/mesh/vocab#indexerConsiderAlso + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#mappedTo + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#narrowerConcept + + rdf:type owl:ObjectProperty ; + + rdfs:domain ; + + rdfs:range . + + + +### http://id.nlm.nih.gov/mesh/vocab#pharmacologicalAction + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#preferredConcept + + rdf:type owl:ObjectProperty ; + + rdfs:subPropertyOf . + + + +### http://id.nlm.nih.gov/mesh/vocab#preferredMappedTo + + rdf:type owl:ObjectProperty ; + + rdfs:subPropertyOf . + + + +### http://id.nlm.nih.gov/mesh/vocab#preferredTerm + + rdf:type owl:ObjectProperty ; + + rdfs:subPropertyOf . + + + +### http://id.nlm.nih.gov/mesh/vocab#previousIndexing + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#recordPreferredTerm + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#related + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#relatedConcept + + rdf:type owl:ObjectProperty ; + + rdfs:range ; + + rdfs:domain . + + + +### http://id.nlm.nih.gov/mesh/vocab#seeAlso + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#semanticType + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#term + + rdf:type owl:ObjectProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#treeNumber + + rdf:type owl:ObjectProperty ; + + rdfs:range . + + + +### http://id.nlm.nih.gov/mesh/vocab#useInstead + + rdf:type owl:ObjectProperty . + + + + + +################################################################# +# +# Data properties +# +################################################################# + + +### http://id.nlm.nih.gov/mesh/vocab#abbreviation + + rdf:type owl:DatatypeProperty ; + + rdfs:label "abbreviation" . + + + +### http://id.nlm.nih.gov/mesh/vocab#activeMeSHYear + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#altLabel + + rdf:type owl:DatatypeProperty ; + + rdfs:label "altLabel" ; + + "alternative label" ; + + owl:propertyDisjointWith ; + + rdfs:subPropertyOf rdfs:label . + + + +### http://id.nlm.nih.gov/mesh/vocab#annotation + + rdf:type owl:DatatypeProperty ; + + rdfs:label "annotation" . + + + +### http://id.nlm.nih.gov/mesh/vocab#casn1_label + + rdf:type owl:DatatypeProperty ; + + rdfs:label "casn1_label" . + + + +### http://id.nlm.nih.gov/mesh/vocab#considerAlso + + rdf:type owl:DatatypeProperty ; + + rdfs:label "considerAlso" . + + + +### http://id.nlm.nih.gov/mesh/vocab#dateCreated + + rdf:type owl:DatatypeProperty ; + + rdfs:label "dateCreated" . + + + +### http://id.nlm.nih.gov/mesh/vocab#dateEstablished + + rdf:type owl:DatatypeProperty ; + + rdfs:label "dateEstablished" . + + + +### http://id.nlm.nih.gov/mesh/vocab#dateRevised + + rdf:type owl:DatatypeProperty ; + + rdfs:label "dateRevised" . + + + +### http://id.nlm.nih.gov/mesh/vocab#entryVersion + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#frequency + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#historyNote + + rdf:type owl:DatatypeProperty ; + + rdfs:label "historyNote" . + + + +### http://id.nlm.nih.gov/mesh/vocab#identifier + + rdf:type owl:DatatypeProperty ; + + rdfs:label "identifier" . + + + +### http://id.nlm.nih.gov/mesh/vocab#lexicalTag + + rdf:type owl:DatatypeProperty ; + + rdfs:label "lexicalTag" . + + + +### http://id.nlm.nih.gov/mesh/vocab#note + + rdf:type owl:DatatypeProperty ; + + rdfs:label "note" . + + + +### http://id.nlm.nih.gov/mesh/vocab#onlineNote + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#prefLabel + + rdf:type owl:DatatypeProperty ; + + rdfs:label "prefLabel" ; + + "preferred label." ; + + rdfs:subPropertyOf rdfs:label . + + + +### http://id.nlm.nih.gov/mesh/vocab#previousIndexing + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#printFlag + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#publicMeSHNote + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#recordAuthorizer + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#recordMaintainer + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#recordOriginator + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#registryNumber + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#relatedRegistryNumber + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#runningHead + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#scopeNote + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#sortVersion + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#source + + rdf:type owl:DatatypeProperty . + + + +### http://id.nlm.nih.gov/mesh/vocab#thesaurusID + + rdf:type owl:DatatypeProperty . + + + +### http://www.w3.org/2000/01/rdf-schema#label + +rdfs:label rdf:type owl:DatatypeProperty . + + + + + +################################################################# +# +# Classes +# +################################################################# + + +### http://id.nlm.nih.gov/mesh/vocab#AllowedDescriptorQualifierPair + + rdf:type owl:Class ; + + rdfs:label "MeSH AllowedDescriptorQualifierPair" ; + + rdfs:subClassOf ; + + owl:disjointWith ; + + "A combined MeSH descriptor and qualifier, where the pairing is allowed by MeSH rules. These URIs are a mash up of the descriptor and qualifier identifiers, such as D000236Q000235." . + + + +### http://id.nlm.nih.gov/mesh/vocab#CheckTag + + rdf:type owl:Class ; + + rdfs:label "MeSH CheckTag" ; + + rdfs:subClassOf ; + + owl:disjointWith , + , + ; + + "A special class of descriptor singled out because they are so frequently applied to biomedical literature. There are only 2 Descriptors that are members of the class meshv:CheckTag: D005260 (Male) and D008297 (Female). These two Descriptors do not have tree numbers. " . + + + +### http://id.nlm.nih.gov/mesh/vocab#Concept + + rdf:type owl:Class ; + + rdfs:label "MeSH Concept" ; + + rdfs:subClassOf owl:Thing ; + + owl:disjointWith , + , + , + , + , + , + ; + + "MeSH concepts are smeanings. Many MeSH concepts contain synonymous terms. meshv:Concept identifiers begin with â€M’ such as M0000013 (Congenital Abnormalities)." . + + + +### http://id.nlm.nih.gov/mesh/vocab#Descriptor + + rdf:type owl:Class ; + + rdfs:label "MeSH Descriptor" ; + + rdfs:subClassOf owl:Thing ; + + owl:disjointWith , + , + , + , + , + ; + + "MeSH Descriptors are a cluster of one or more concepts used to describe what a publication is about. meshv:Descriptor is the parent class of meshv:TopicalDescriptor, meshv:GeographicDescriptor, meshv:PublicationType, and meshv:CheckTag." . + + + +### http://id.nlm.nih.gov/mesh/vocab#DescriptorQualifierPair + + rdf:type owl:Class ; + + rdfs:label "MeSH DescriptorQualifierPair" ; + + rdfs:subClassOf owl:Thing ; + + owl:disjointWith , + , + , + , + ; + + "A combined MeSH descriptor and qualifier pair. Allowed pairs belong to the class meshv:AllowedDescriptorQualifierPair. Disallowed pairs belong to the class meshv:DisallowedDescriptorQualifierPair." . + + + +### http://id.nlm.nih.gov/mesh/vocab#DisallowedDescriptorQualifierPair + + rdf:type owl:Class ; + + rdfs:label "MeSH DisallowedDescriptorQualifierPair" ; + + rdfs:subClassOf ; + + "A combined MeSH descriptor and qualifier where the pairing is not allowed by MeSH rules, such as Abdomen/radiography." . + + + +### http://id.nlm.nih.gov/mesh/vocab#GeographicalDescriptor + + rdf:type owl:Class ; + + rdfs:label "MeSH GeographicalDescriptor" ; + + rdfs:subClassOf ; + + owl:disjointWith , + ; + + "A descriptor that references places or regions of the world, such as D001061 (Appalachian Region)." . + + + +### http://id.nlm.nih.gov/mesh/vocab#PublicationType + + rdf:type owl:Class ; + + rdfs:label "MeSH PublicationType" ; + + rdfs:subClassOf ; + + owl:disjointWith ; + + "A special class of descriptor that describes what type of publication a resource is as opposed to what it is about. All MeSH Publication Types are in the V tree." . + + + +### http://id.nlm.nih.gov/mesh/vocab#Qualifier + + rdf:type owl:Class ; + + rdfs:label "MeSH Qualifier" ; + + rdfs:subClassOf owl:Thing ; + + owl:disjointWith , + , + , + ; + + "Also known as MeSH Subheadings, these provide context to the use of a MeSH Heading." . + + + +### http://id.nlm.nih.gov/mesh/vocab#SCR_Chemical + + rdf:type owl:Class ; + + rdfs:label "MeSH SCR Chemical" ; + + rdfs:subClassOf ; + + owl:disjointWith , + ; + + "These are chemicals, drugs, enzymes, vitamins, etc." . + + + +### http://id.nlm.nih.gov/mesh/vocab#SCR_Disease + + rdf:type owl:Class ; + + rdfs:label "MeSH SCR Disease" ; + + rdfs:subClassOf ; + + owl:disjointWith ; + + "SCR Diseases were originally brought into MeSH from a list maintained by the Office of Rare Diseases Research." . + + + +### http://id.nlm.nih.gov/mesh/vocab#SCR_Protocol + + rdf:type owl:Class ; + + rdfs:label "MeSH SCR Protocol" ; + + rdfs:subClassOf ; + + "MeSH protocols are therapies in the domain of cancer treatment" . + + + +### http://id.nlm.nih.gov/mesh/vocab#SemanticType + + rdf:type owl:Class ; + + rdfs:label "MeSH SemanticType" ; + + rdfs:subClassOf owl:Thing ; + + owl:disjointWith , + , + ; + + "A semantic type provides broad categorization for meshv:Concept classes, such as Disease or Syndrome, Medical Device, etc." . + + + +### http://id.nlm.nih.gov/mesh/vocab#SupplementaryConceptRecord + + rdf:type owl:Class ; + + rdfs:label "MeSH SupplementaryConceptRecord " ; + + rdfs:subClassOf owl:Thing ; + + owl:disjointWith , + ; + + "Supplementary Concepts are created in MeSH to aid in searching the large volume of mainly chemicals and drugs. meshv:SupplementaryConceptRecord has three sub-classes: meshv:RegularSubstance, meshv:SCR_Protocol, and meshv:SCR_Disease." . + + + +### http://id.nlm.nih.gov/mesh/vocab#Term + + rdf:type owl:Class ; + + rdfs:label "MeSH Term" ; + + rdfs:subClassOf owl:Thing ; + + owl:disjointWith ; + + "MeSH terms provide synonymous names for MeSH concepts. Terms have T identifiers, and are considered either preferred or lexical variants." . + + + +### http://id.nlm.nih.gov/mesh/vocab#TopicalDescriptor + + rdf:type owl:Class ; + + rdfs:label "MeSH TopicalDescriptor" ; + + rdfs:subClassOf ; + + "Topical Descriptors indicate the subject of an indexed item such as a journal article. See D063926 (Drug Hypersensitivity Syndrome) for an example." . + + + +### http://id.nlm.nih.gov/mesh/vocab#TreeNumber + + rdf:type owl:Class ; + + rdfs:label "MeSH TreeNumber" ; + + rdfs:subClassOf owl:Thing ; + + "Tree Numbers are used to organize MeSH Descriptors in a broader-than/narrower-than manner." . + + + +### http://www.w3.org/2002/07/owl#Thing + +owl:Thing rdfs:subClassOf owl:Thing . + + + + +### Generated by the OWL API (version 3.5.0) http://owlapi.sourceforge.net + From 5b8045b5d324d1d2c3b943fba947bb79949032e1 Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Tue, 12 May 2015 14:40:41 -0400 Subject: [PATCH 19/44] Change scripts to exit if errors occur. --- bin/fetch-mesh-xml.sh | 2 +- bin/mesh-xml2rdf.sh | 16 +++++++++++----- 2 files changed, 12 insertions(+), 6 deletions(-) diff --git a/bin/fetch-mesh-xml.sh b/bin/fetch-mesh-xml.sh index ae7f4ebb..5711ce7a 100755 --- a/bin/fetch-mesh-xml.sh +++ b/bin/fetch-mesh-xml.sh @@ -1,4 +1,4 @@ -#!/bin/sh +#!/bin/sh -e if [ -z "$MESHRDF_HOME" ]; then echo "Please define MESHRDF_HOME environment variable" 1>&2 diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index 2f0e0681..b082c2b1 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -5,8 +5,6 @@ # # - - if [ -z "$MESHRDF_HOME" ]; then echo "Please define MESHRDF_HOME environment variable" 1>&2 exit 1 @@ -51,17 +49,25 @@ fi java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/desc$YEAR.xml" \ -xsl:xslt/desc.xsl >> "$MESHRDF_HOME/out/$OUT-dups.nt" if [ $? -ne 0 ]; then - echo "Error converting $MESHRDF_HOME/data/desc$YEAR.xml" + echo "Error converting $MESHRDF_HOME/data/desc$YEAR.xml" 1>&2 exit 1 fi - java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/supp$YEAR.xml" \ -xsl:xslt/supp.xsl >> "$MESHRDF_HOME/out/$OUT-dups.nt" if [ $? -ne 0 ]; then - echo "Error converting $MESHRDF_HOME/data/supp$YEAR.xml" + echo "Error converting $MESHRDF_HOME/data/supp$YEAR.xml" 1>&2 exit 1 fi sort -u -T"$MESHRDF_HOME/out" "$MESHRDF_HOME/out/$OUT-dups.nt" > "$MESHRDF_HOME/out/$OUT.nt" +if [ $? -ne 0 ]; then + echo "Error deduplicating $MESHRDF_HOME/out/$OUT-dups.nt" 1>&2 + exit 1 +fi + gzip -c "$MESHRDF_HOME/out/$OUT.nt" > "$MESHRDF_HOME/out/$OUT.nt.gz" +if [ $? -ne 0 ]; then + echo "Error compressing $MESHRDF_HOME/out/$OUT.nt" 1>&2 + exit 1 +fi From 1d9356e03d4daca9bb7218b7f32bb48966c8c4c4 Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Tue, 12 May 2015 14:41:11 -0400 Subject: [PATCH 20/44] Commit meta/vocabulary.ttl produced using Protege 5.0 Beta on Desktop. --- meta/vocabulary.ttl | 305 +++++++++++++++++++++----------------------- 1 file changed, 148 insertions(+), 157 deletions(-) diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl index 8b018373..ed8fcd9d 100644 --- a/meta/vocabulary.ttl +++ b/meta/vocabulary.ttl @@ -1,4 +1,4 @@ -@prefix : . +@prefix : . @prefix owl: . @prefix rdf: . @prefix xml: . @@ -6,43 +6,34 @@ @prefix rdfs: . @base . - rdf:type owl:Ontology ; - - 1 ; - - "May 7, 2015 1:58:22 PM"^^xsd:dateTime ; - - rdfs:comment "Ontology supporting next generation (2015) of http://id.nlm.nih.gov/"^^xsd:string , - "This ontology was generated from an ontology revision in WebProtege http://webprotege.stanford.edu"^^xsd:string ; - - "system"^^xsd:string . + rdf:type :Ontology . -################################################################# -# -# Annotation properties -# -################################################################# +################################################################# +# +# Annotation properties +# +################################################################# ### http://purl.org/dc/terms/description - rdf:type owl:AnnotationProperty . + rdf:type :AnnotationProperty . -################################################################# -# -# Object Properties -# -################################################################# +################################################################# +# +# Object Properties +# +################################################################# ### http://id.nlm.nih.gov/mesh/vocab#allowableQualifier - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:range . @@ -50,7 +41,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#allowedTreeNode - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:label "allowedTreeNode" ; @@ -62,13 +53,13 @@ ### http://id.nlm.nih.gov/mesh/vocab#broader - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#broaderConcept - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:range ; @@ -80,7 +71,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#broaderDescriptor - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:domain ; @@ -92,7 +83,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#broaderQualifier - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:range ; @@ -104,8 +95,8 @@ ### http://id.nlm.nih.gov/mesh/vocab#broaderTreeNumber - rdf:type owl:ObjectProperty , - owl:TransitiveProperty ; + rdf:type :ObjectProperty , + :TransitiveProperty ; rdfs:domain ; @@ -117,13 +108,13 @@ ### http://id.nlm.nih.gov/mesh/vocab#concept - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#hasDescriptor - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:range . @@ -131,7 +122,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#hasQualifier - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:range . @@ -139,19 +130,19 @@ ### http://id.nlm.nih.gov/mesh/vocab#indexerConsiderAlso - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#mappedTo - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#narrowerConcept - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:domain ; @@ -161,13 +152,13 @@ ### http://id.nlm.nih.gov/mesh/vocab#pharmacologicalAction - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#preferredConcept - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:subPropertyOf . @@ -175,7 +166,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#preferredMappedTo - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:subPropertyOf . @@ -183,7 +174,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#preferredTerm - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:subPropertyOf . @@ -191,25 +182,25 @@ ### http://id.nlm.nih.gov/mesh/vocab#previousIndexing - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#recordPreferredTerm - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#related - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#relatedConcept - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:range ; @@ -219,25 +210,25 @@ ### http://id.nlm.nih.gov/mesh/vocab#seeAlso - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#semanticType - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#term - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . ### http://id.nlm.nih.gov/mesh/vocab#treeNumber - rdf:type owl:ObjectProperty ; + rdf:type :ObjectProperty ; rdfs:range . @@ -245,22 +236,22 @@ ### http://id.nlm.nih.gov/mesh/vocab#useInstead - rdf:type owl:ObjectProperty . + rdf:type :ObjectProperty . -################################################################# -# -# Data properties -# -################################################################# +################################################################# +# +# Data properties +# +################################################################# ### http://id.nlm.nih.gov/mesh/vocab#abbreviation - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "abbreviation" . @@ -268,19 +259,19 @@ ### http://id.nlm.nih.gov/mesh/vocab#activeMeSHYear - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#altLabel - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "altLabel" ; "alternative label" ; - owl:propertyDisjointWith ; + :propertyDisjointWith ; rdfs:subPropertyOf rdfs:label . @@ -288,7 +279,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#annotation - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "annotation" . @@ -296,7 +287,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#casn1_label - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "casn1_label" . @@ -304,7 +295,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#considerAlso - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "considerAlso" . @@ -312,7 +303,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#dateCreated - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "dateCreated" . @@ -320,7 +311,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#dateEstablished - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "dateEstablished" . @@ -328,7 +319,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#dateRevised - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "dateRevised" . @@ -336,19 +327,19 @@ ### http://id.nlm.nih.gov/mesh/vocab#entryVersion - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#frequency - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#historyNote - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "historyNote" . @@ -356,7 +347,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#identifier - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "identifier" . @@ -364,7 +355,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#lexicalTag - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "lexicalTag" . @@ -372,7 +363,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#note - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "note" . @@ -380,13 +371,13 @@ ### http://id.nlm.nih.gov/mesh/vocab#onlineNote - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#prefLabel - rdf:type owl:DatatypeProperty ; + rdf:type :DatatypeProperty ; rdfs:label "prefLabel" ; @@ -398,106 +389,106 @@ ### http://id.nlm.nih.gov/mesh/vocab#previousIndexing - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#printFlag - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#publicMeSHNote - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#recordAuthorizer - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#recordMaintainer - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#recordOriginator - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#registryNumber - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#relatedRegistryNumber - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#runningHead - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#scopeNote - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#sortVersion - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#source - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#thesaurusID - rdf:type owl:DatatypeProperty . + rdf:type :DatatypeProperty . ### http://www.w3.org/2000/01/rdf-schema#label -rdfs:label rdf:type owl:DatatypeProperty . +rdfs:label rdf:type :DatatypeProperty . -################################################################# -# -# Classes -# -################################################################# +################################################################# +# +# Classes +# +################################################################# ### http://id.nlm.nih.gov/mesh/vocab#AllowedDescriptorQualifierPair - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH AllowedDescriptorQualifierPair" ; rdfs:subClassOf ; - owl:disjointWith ; + :disjointWith ; "A combined MeSH descriptor and qualifier, where the pairing is allowed by MeSH rules. These URIs are a mash up of the descriptor and qualifier identifiers, such as D000236Q000235." . @@ -505,15 +496,15 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#CheckTag - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH CheckTag" ; rdfs:subClassOf ; - owl:disjointWith , - , - ; + :disjointWith , + , + ; "A special class of descriptor singled out because they are so frequently applied to biomedical literature. There are only 2 Descriptors that are members of the class meshv:CheckTag: D005260 (Male) and D008297 (Female). These two Descriptors do not have tree numbers. " . @@ -521,19 +512,19 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#Concept - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH Concept" ; - rdfs:subClassOf owl:Thing ; + rdfs:subClassOf :Thing ; - owl:disjointWith , - , - , - , - , - , - ; + :disjointWith , + , + , + , + , + , + ; "MeSH concepts are smeanings. Many MeSH concepts contain synonymous terms. meshv:Concept identifiers begin with â€M’ such as M0000013 (Congenital Abnormalities)." . @@ -541,18 +532,18 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#Descriptor - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH Descriptor" ; - rdfs:subClassOf owl:Thing ; + rdfs:subClassOf :Thing ; - owl:disjointWith , - , - , - , - , - ; + :disjointWith , + , + , + , + , + ; "MeSH Descriptors are a cluster of one or more concepts used to describe what a publication is about. meshv:Descriptor is the parent class of meshv:TopicalDescriptor, meshv:GeographicDescriptor, meshv:PublicationType, and meshv:CheckTag." . @@ -560,17 +551,17 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#DescriptorQualifierPair - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH DescriptorQualifierPair" ; - rdfs:subClassOf owl:Thing ; + rdfs:subClassOf :Thing ; - owl:disjointWith , - , - , - , - ; + :disjointWith , + , + , + , + ; "A combined MeSH descriptor and qualifier pair. Allowed pairs belong to the class meshv:AllowedDescriptorQualifierPair. Disallowed pairs belong to the class meshv:DisallowedDescriptorQualifierPair." . @@ -578,7 +569,7 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#DisallowedDescriptorQualifierPair - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH DisallowedDescriptorQualifierPair" ; @@ -590,14 +581,14 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#GeographicalDescriptor - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH GeographicalDescriptor" ; rdfs:subClassOf ; - owl:disjointWith , - ; + :disjointWith , + ; "A descriptor that references places or regions of the world, such as D001061 (Appalachian Region)." . @@ -605,13 +596,13 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#PublicationType - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH PublicationType" ; rdfs:subClassOf ; - owl:disjointWith ; + :disjointWith ; "A special class of descriptor that describes what type of publication a resource is as opposed to what it is about. All MeSH Publication Types are in the V tree." . @@ -619,16 +610,16 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#Qualifier - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH Qualifier" ; - rdfs:subClassOf owl:Thing ; + rdfs:subClassOf :Thing ; - owl:disjointWith , - , - , - ; + :disjointWith , + , + , + ; "Also known as MeSH Subheadings, these provide context to the use of a MeSH Heading." . @@ -636,14 +627,14 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#SCR_Chemical - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH SCR Chemical" ; rdfs:subClassOf ; - owl:disjointWith , - ; + :disjointWith , + ; "These are chemicals, drugs, enzymes, vitamins, etc." . @@ -651,13 +642,13 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#SCR_Disease - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH SCR Disease" ; rdfs:subClassOf ; - owl:disjointWith ; + :disjointWith ; "SCR Diseases were originally brought into MeSH from a list maintained by the Office of Rare Diseases Research." . @@ -665,7 +656,7 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#SCR_Protocol - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH SCR Protocol" ; @@ -677,15 +668,15 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#SemanticType - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH SemanticType" ; - rdfs:subClassOf owl:Thing ; + rdfs:subClassOf :Thing ; - owl:disjointWith , - , - ; + :disjointWith , + , + ; "A semantic type provides broad categorization for meshv:Concept classes, such as Disease or Syndrome, Medical Device, etc." . @@ -693,14 +684,14 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#SupplementaryConceptRecord - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH SupplementaryConceptRecord " ; - rdfs:subClassOf owl:Thing ; + rdfs:subClassOf :Thing ; - owl:disjointWith , - ; + :disjointWith , + ; "Supplementary Concepts are created in MeSH to aid in searching the large volume of mainly chemicals and drugs. meshv:SupplementaryConceptRecord has three sub-classes: meshv:RegularSubstance, meshv:SCR_Protocol, and meshv:SCR_Disease." . @@ -708,13 +699,13 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#Term - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH Term" ; - rdfs:subClassOf owl:Thing ; + rdfs:subClassOf :Thing ; - owl:disjointWith ; + :disjointWith ; "MeSH terms provide synonymous names for MeSH concepts. Terms have T identifiers, and are considered either preferred or lexical variants." . @@ -722,7 +713,7 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#TopicalDescriptor - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH TopicalDescriptor" ; @@ -734,11 +725,11 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://id.nlm.nih.gov/mesh/vocab#TreeNumber - rdf:type owl:Class ; + rdf:type :Class ; rdfs:label "MeSH TreeNumber" ; - rdfs:subClassOf owl:Thing ; + rdfs:subClassOf :Thing ; "Tree Numbers are used to organize MeSH Descriptors in a broader-than/narrower-than manner." . @@ -746,10 +737,10 @@ rdfs:label rdf:type owl:DatatypeProperty . ### http://www.w3.org/2002/07/owl#Thing -owl:Thing rdfs:subClassOf owl:Thing . - +:Thing rdfs:subClassOf :Thing . -### Generated by the OWL API (version 3.5.0) http://owlapi.sourceforge.net + +### Generated by the OWL API (version 3.5.1) http://owlapi.sourceforge.net From 39e3d9b38e6761c0843f9e74220779894cbb5b13 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Wed, 20 May 2015 17:07:17 -0400 Subject: [PATCH 21/44] Remove classes and predicates per mesh-rdf issue #119 --- meta/vocabulary.owl | 83 -------------------------------------- samples/convert-samples.sh | 14 +++++++ xslt/common.xsl | 41 +++++++++++-------- xslt/desc.xsl | 3 +- xslt/qual.xsl | 3 +- 5 files changed, 43 insertions(+), 101 deletions(-) diff --git a/meta/vocabulary.owl b/meta/vocabulary.owl index 92b73195..0345edc2 100644 --- a/meta/vocabulary.owl +++ b/meta/vocabulary.owl @@ -58,9 +58,6 @@ - - - @@ -76,9 +73,6 @@ - - - @@ -139,9 +133,6 @@ - - - @@ -154,9 +145,6 @@ - - - @@ -205,30 +193,15 @@ - - - - - - - - - - - - - - - @@ -295,10 +268,6 @@ - - - - @@ -347,10 +316,6 @@ - - - - @@ -371,10 +336,6 @@ - - - - @@ -391,10 +352,6 @@ - - - - @@ -419,10 +376,6 @@ - - - - @@ -447,18 +400,6 @@ - - - - - - - - - - - - @@ -530,10 +471,6 @@ - - - - @@ -702,16 +639,6 @@ SCR_Protocol MeSH SCR Protocol - - - SemanticType - A semantic type provides broad categorization for meshv:Concept classes, such as Disease or Syndrome, Medical Device, etc. - - - - SemanticType - MeSH SemanticType - SupplementaryConceptRecord @@ -757,16 +684,6 @@ abbreviation abbreviation - - - allowedTreeNode - Name of a subcategory in the MeSH Trees indicating, that for most Descriptors in that subcategory, the allowed Qualifiers on the Descriptor include the Qualifier. This value does not impact Descriptors permitted with a given Qualifier, but is a statistical summary of Descriptors permitted with the Qualifier. - - - - allowedTreeNode - allowedTreeNode - altLabel diff --git a/samples/convert-samples.sh b/samples/convert-samples.sh index 0a4571dd..3cd4945a 100755 --- a/samples/convert-samples.sh +++ b/samples/convert-samples.sh @@ -2,6 +2,20 @@ # This script will convert the sample XML files, which contain all the entities listed # in sample-list.txt. +# Can override default year with MESHRDF_YEAR environment variable +YEAR=${MESHRDF_YEAR:-2014} + +# Override the default Mesh prefix and output file by setting MESHRDF_URI_YEAR to "yes" +if [ "$MESHRDF_URI_YEAR" = "yes" ]; then + PREFIX=mesh/$YEAR + OUT=mesh$YEAR +else + PREFIX=mesh + OUT=mesh +fi + +sed -e "s,MESHRDF_PATH,$PREFIX,g" ../xslt/mesh-rdf-prefixes.ent.template > ../xslt/mesh-rdf-prefixes.ent + java -jar $SAXON_JAR -s:qual-samples.xml -xsl:../xslt/qual.xsl > qual-samples.nt java -jar $SAXON_JAR -s:desc-samples.xml -xsl:../xslt/desc.xsl > desc-samples.nt java -jar $SAXON_JAR -s:supp-samples.xml -xsl:../xslt/supp.xsl > supp-samples.nt diff --git a/xslt/common.xsl b/xslt/common.xsl index 528a003d..e2ab09b7 100755 --- a/xslt/common.xsl +++ b/xslt/common.xsl @@ -265,7 +265,7 @@ + Removed: see https://github.com/HHS/mesh-rdf/issues/119 @@ -280,6 +280,7 @@ + --> + Removed: see https://github.com/HHS/mesh-rdf/issues/119 @@ -490,9 +491,9 @@ - + -/-> @@ -508,9 +509,9 @@ - + -/-> @@ -526,6 +527,7 @@ + --> @@ -667,6 +669,9 @@ + + -\-> This relation states that a concept has a semantic type. @@ -688,9 +693,9 @@ - + -\-> Specifies the class of the semantic type resource. @@ -702,9 +707,9 @@ - + -\-> This rule states the a semantic type unique identifier has a semantic type name. @@ -722,9 +727,9 @@ - + -\-> This rule states that a semantic type has a unique identifier. @@ -739,7 +744,10 @@ - + --> + + + @@ -946,7 +954,7 @@ + Removed: see https://github.com/HHS/mesh-rdf/issues/119 This relation states that a term has a print flag. @@ -960,6 +968,7 @@ + --> + Removed: see https://github.com/HHS/mesh-rdf/issues/119 @@ -307,6 +307,7 @@ + --> diff --git a/xslt/qual.xsl b/xslt/qual.xsl index 33334d33..d7fe001d 100755 --- a/xslt/qual.xsl +++ b/xslt/qual.xsl @@ -93,7 +93,7 @@ + Removed: see https://github.com/HHS/mesh-rdf/issues/119 @@ -108,6 +108,7 @@ + --> From 60f18f35a310e23a9028d9739299d69d1466afd8 Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Wed, 20 May 2015 17:25:01 -0400 Subject: [PATCH 22/44] Respond to issue 112, make 2015 the default in github.com/HHS/meshrdf, at least my branch. --- bin/fetch-mesh-xml.sh | 2 +- bin/mesh-xml2rdf.sh | 2 +- samples/desc-samples.xml | 4064 +++++++++++++++++++------------------- samples/make-samples.pl | 4 +- samples/qual-samples.xml | 6 + samples/sample-list.txt | 2 +- samples/supp-samples.xml | 1375 +++++++------ 7 files changed, 2722 insertions(+), 2733 deletions(-) diff --git a/bin/fetch-mesh-xml.sh b/bin/fetch-mesh-xml.sh index 5711ce7a..19301370 100755 --- a/bin/fetch-mesh-xml.sh +++ b/bin/fetch-mesh-xml.sh @@ -8,7 +8,7 @@ fi mkdir -p "$MESHRDF_HOME/data" # CAn override default year with MESHRDF_YEAR environment variable -YEAR=${MESHRDF_YEAR:-2014} +YEAR=${MESHRDF_YEAR:-2015} # Can override default URI with MESHRDF_URI environment variable URI=${MESHRDF_URI:-ftp://ftp.nlm.nih.gov/online/mesh/$YEAR} diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index b082c2b1..a120bdc9 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -16,7 +16,7 @@ if [ -z "$SAXON_JAR" ]; then fi # Can override default year with MESHRDF_YEAR environment variable -YEAR=${MESHRDF_YEAR:-2014} +YEAR=${MESHRDF_YEAR:-2015} # Override the default Mesh prefix and output file by setting MESHRDF_URI_YEAR to "yes" if [ "$MESHRDF_URI_YEAR" = "yes" ]; then diff --git a/samples/desc-samples.xml b/samples/desc-samples.xml index f75bad9d..18ad0b96 100644 --- a/samples/desc-samples.xml +++ b/samples/desc-samples.xml @@ -21,259 +21,260 @@ 2014 + 2015 - Q000008 + Q000096 - administration & dosage + biosynthesis - AD + BI - Q000009 + Q000627 - adverse effects + therapeutic use - AE + TU - Q000031 + Q000633 - analogs & derivatives + toxicity - AA + TO - Q000032 + Q000176 - analysis + diagnostic use - AN + DU - Q000037 + Q000506 - antagonists & inhibitors + poisoning - AI + PO - Q000096 + Q000008 - biosynthesis + administration & dosage - BI + AD - Q000097 + Q000009 - blood + adverse effects - BL + AE - Q000134 + Q000819 - cerebrospinal fluid + agonists - CF + AG - Q000138 + Q000097 - chemical synthesis + blood - CS + BL - Q000145 + Q000134 - classification + cerebrospinal fluid - CL + CF - Q000176 + Q000138 - diagnostic use + chemical synthesis - DU + CS - Q000191 + Q000744 - economics + contraindications - EC + CT - Q000266 + Q000737 - history + chemistry - HI + CH - Q000276 + Q000652 - immunology + urine - IM + UR - Q000302 + Q000528 - isolation & purification + radiation effects - IP + RE - Q000378 + Q000266 - metabolism + history - ME + HI - Q000493 + Q000031 - pharmacokinetics + analogs & derivatives - PK + AA - Q000494 + Q000032 - pharmacology + analysis - PD + AN - Q000506 + Q000037 - poisoning + antagonists & inhibitors - PO + AI - Q000528 + Q000145 - radiation effects + classification - RE + CL - Q000592 + Q000191 - standards + economics - ST + EC - Q000600 + Q000276 - supply & distribution + immunology - SD + IM - Q000627 + Q000302 - therapeutic use + isolation & purification - TU + IP - Q000633 + Q000378 - toxicity + metabolism - TO + ME - Q000652 + Q000494 - urine + pharmacology - UR + PD - Q000737 + Q000592 - chemistry + standards - CH + ST - Q000744 + Q000600 - contraindications + supply & distribution - CT + SD - Q000819 + Q000493 - agonists + pharmacokinetics - AG + PK 91(75); was A 23187 1975-90 (see under ANTIBIOTICS 1975-83) @@ -447,34 +448,44 @@ 2012 2013 2014 + 2015 - Q000601 + Q000502 - surgery + physiology - SU + PH - Q000736 + Q000503 - ultrasonography + physiopathology - US + PP - Q000821 + Q000531 - virology + radionuclide imaging - VI + RI + + + + Q000294 + + innervation + + + IR @@ -485,6 +496,33 @@ AB + + + Q000821 + + virology + + + VI + + + + Q000736 + + ultrasonography + + + US + + + + Q000528 + + radiation effects + + + RE + Q000033 @@ -521,15 +559,6 @@ GD - - - Q000294 - - innervation - - - IR - Q000382 @@ -559,56 +588,29 @@ - Q000502 + Q000601 - physiology + surgery - PH + SU - - - Q000503 + + GEN: prefer specifics; abdom muscles = ABDOMINAL MUSCLES but RECTUS ABDOMINIS is available; abdominal pain = ABDOMINAL PAIN; abrupt dis requiring emerg surg = ABDOMEN, ACUTE + + + + + + D000005 + + Abdomen + + + + Q000293 - physiopathology - - - PP - - - - Q000528 - - radiation effects - - - RE - - - - Q000531 - - radionuclide imaging - - - RI - - - GEN: prefer specifics; abdom muscles = ABDOMINAL MUSCLES but RECTUS ABDOMINIS is available; abdominal pain = ABDOMINAL PAIN; abrupt dis requiring emerg surg = ABDOMEN, ACUTE - - - - - - D000005 - - Abdomen - - - - Q000293 - - injuries + injuries @@ -711,250 +713,251 @@ 2014 + 2015 - Q000008 + Q000627 - administration & dosage + therapeutic use - AD + TU - Q000009 + Q000633 - adverse effects + toxicity - AE + TO - Q000031 + Q000176 - analogs & derivatives + diagnostic use - AA + DU - Q000032 + Q000506 - analysis + poisoning - AN + PO - Q000037 + Q000008 - antagonists & inhibitors + administration & dosage - AI + AD - Q000097 + Q000009 - blood + adverse effects - BL + AE - Q000134 + Q000819 - cerebrospinal fluid + agonists - CF + AG - Q000138 + Q000097 - chemical synthesis + blood - CS + BL - Q000145 + Q000134 - classification + cerebrospinal fluid - CL + CF - Q000176 + Q000138 - diagnostic use + chemical synthesis - DU + CS - Q000191 + Q000744 - economics + contraindications - EC + CT - Q000266 + Q000737 - history + chemistry - HI + CH - Q000276 + Q000652 - immunology + urine - IM + UR - Q000302 + Q000528 - isolation & purification + radiation effects - IP + RE - Q000378 + Q000266 - metabolism + history - ME + HI - Q000493 + Q000031 - pharmacokinetics + analogs & derivatives - PK + AA - Q000494 + Q000032 - pharmacology + analysis - PD + AN - Q000506 + Q000037 - poisoning + antagonists & inhibitors - PO + AI - Q000528 + Q000145 - radiation effects + classification - RE + CL - Q000592 + Q000191 - standards + economics - ST + EC - Q000600 + Q000276 - supply & distribution + immunology - SD + IM - Q000627 + Q000302 - therapeutic use + isolation & purification - TU + IP - Q000633 + Q000378 - toxicity + metabolism - TO + ME - Q000652 + Q000494 - urine + pharmacology - UR + PD - Q000737 + Q000592 - chemistry + standards - CH + ST - Q000744 + Q000600 - contraindications + supply & distribution - CT + SD - Q000819 + Q000493 - agonists + pharmacokinetics - AG + PK 1965; for ACEPHEN use MECLOFENOXATE 1990-2002 @@ -1494,331 +1497,332 @@ 2014 + 2015 - Q000097 + Q000503 - blood + physiopathology - BL + PP - Q000134 + Q000530 - cerebrospinal fluid + radiography - CF + RA - Q000139 + Q000531 - chemically induced + radionuclide imaging - CI + RI - Q000145 + Q000534 - classification + rehabilitation - CL + RH - Q000150 + Q000201 - complications + enzymology - CO + EN - Q000175 + Q000209 - diagnosis + etiology - DI + ET - Q000178 + Q000401 - diet therapy + mortality - DH + MO - Q000188 + Q000453 - drug therapy + epidemiology - DT + EP - Q000191 + Q000517 - economics + prevention & control - EC + PC - Q000196 + Q000097 - embryology + blood - EM + BL - Q000201 + Q000134 - enzymology + cerebrospinal fluid - EN + CF - Q000208 + Q000139 - ethnology + chemically induced - EH + CI - Q000209 + Q000178 - etiology + diet therapy - ET + DH - Q000235 + Q000188 - genetics + drug therapy - GE + DT - Q000266 + Q000628 - history + therapy - HI + TH - Q000276 + Q000523 - immunology + psychology - IM + PX - Q000378 + Q000652 - metabolism + urine - ME + UR - Q000382 + Q000821 - microbiology + virology - MI + VI - Q000401 + Q000736 - mortality + ultrasonography - MO + US - Q000451 + Q000662 - nursing + veterinary - NU + VE - Q000453 + Q000266 - epidemiology + history - EP + HI - Q000469 + Q000145 - parasitology + classification - PS + CL - Q000473 + Q000150 - pathology + complications - PA + CO - Q000503 + Q000175 - physiopathology + diagnosis - PP + DI - Q000517 + Q000191 - prevention & control + economics - PC + EC - Q000523 + Q000196 - psychology + embryology - PX + EM - Q000530 + Q000208 - radiography + ethnology - RA + EH - Q000531 + Q000235 - radionuclide imaging + genetics - RI + GE - Q000532 + Q000276 - radiotherapy + immunology - RT + IM - Q000534 + Q000378 - rehabilitation + metabolism - RH + ME - Q000601 + Q000382 - surgery + microbiology - SU + MI - Q000628 + Q000451 - therapy + nursing - TH + NU - Q000652 + Q000469 - urine + parasitology - UR + PS - Q000662 + Q000473 - veterinary + pathology - VE + PA - Q000736 + Q000532 - ultrasonography + radiotherapy - US + RT - Q000821 + Q000601 - virology + surgery - VI + SU @@ -2024,52 +2028,71 @@ 2014 + 2015 - Q000008 + Q000627 - administration & dosage + therapeutic use - AD + TU - Q000009 + Q000633 - adverse effects + toxicity - AE + TO - Q000031 + Q000176 - analogs & derivatives + diagnostic use - AA + DU - Q000032 + Q000506 - analysis + poisoning - AN + PO - Q000037 + Q000008 - antagonists & inhibitors + administration & dosage - AI + AD + + + + Q000009 + + adverse effects + + + AE + + + + Q000819 + + agonists + + + AG @@ -2100,174 +2123,156 @@ - Q000145 + Q000744 - classification + contraindications - CL + CT - Q000176 + Q000737 - diagnostic use + chemistry - DU + CH - Q000191 + Q000652 - economics + urine - EC + UR - Q000266 + Q000528 - history + radiation effects - HI + RE - Q000276 + Q000266 - immunology + history - IM + HI - Q000302 + Q000031 - isolation & purification + analogs & derivatives - IP + AA - Q000378 + Q000032 - metabolism + analysis - ME + AN - Q000493 + Q000037 - pharmacokinetics + antagonists & inhibitors - PK + AI - Q000494 - - pharmacology - - - PD - - - - Q000506 - - poisoning - - - PO - - - - Q000528 + Q000145 - radiation effects + classification - RE + CL - Q000592 + Q000191 - standards + economics - ST + EC - Q000600 + Q000276 - supply & distribution + immunology - SD + IM - Q000627 + Q000302 - therapeutic use + isolation & purification - TU + IP - Q000633 + Q000378 - toxicity + metabolism - TO + ME - Q000652 + Q000494 - urine + pharmacology - UR + PD - Q000737 + Q000592 - chemistry + standards - CH + ST - Q000744 + Q000600 - contraindications + supply & distribution - CT + SD - Q000819 + Q000493 - agonists + pharmacokinetics - AG + PK 65(64) @@ -2748,6 +2753,7 @@ 2012 2013 2014 + 2015 NIM as check tag; Manual 18.7+; relation to /vet: Manual 19.8.81 @@ -2864,271 +2870,243 @@ Anti-Bacterial Agents - 2014 - 06 - 26 + 1999 + 01 + 01 - 2003 - 07 - 09 + 2014 + 06 + 25 - 2004 - 2005 - 2006 - 2007 - 2008 - 2009 - 2010 - 2011 - 2012 - 2013 - 2014 + 2015 - Q000008 - - administration & dosage - - - AD - - - - Q000009 + Q000096 - adverse effects + biosynthesis - AE + BI - Q000032 + Q000627 - analysis + therapeutic use - AN + TU - Q000037 + Q000633 - antagonists & inhibitors + toxicity - AI + TO - Q000096 + Q000176 - biosynthesis + diagnostic use - BI + DU - Q000097 + Q000506 - blood + poisoning - BL + PO - Q000134 + Q000008 - cerebrospinal fluid + administration & dosage - CF + AD - Q000138 + Q000009 - chemical synthesis + adverse effects - CS + AE - Q000145 + Q000097 - classification + blood - CL + BL - Q000176 + Q000134 - diagnostic use + cerebrospinal fluid - DU + CF - Q000191 + Q000138 - economics + chemical synthesis - EC + CS - Q000266 + Q000744 - history + contraindications - HI + CT - Q000276 + Q000737 - immunology + chemistry - IM + CH - Q000302 + Q000652 - isolation & purification + urine - IP + UR - Q000378 + Q000528 - metabolism + radiation effects - ME + RE - Q000493 + Q000266 - pharmacokinetics + history - PK + HI - Q000494 + Q000032 - pharmacology + analysis - PD + AN - Q000506 + Q000145 - poisoning + classification - PO + CL - Q000528 + Q000191 - radiation effects + economics - RE + EC - Q000592 + Q000276 - standards + immunology - ST + IM - Q000600 + Q000302 - supply & distribution + isolation & purification - SD + IP - Q000627 + Q000378 - therapeutic use + metabolism - TU + ME - Q000633 + Q000494 - toxicity + pharmacology - TO + PD - Q000652 + Q000592 - urine + standards - UR + ST - Q000737 + Q000600 - chemistry + supply & distribution - CH + SD - Q000744 + Q000493 - contraindications + pharmacokinetics - CT - - - - Q000819 - - agonists - - - AG + PK GEN or unspecified; resistance to antibiotics = DRUG RESISTANCE, BACTERIAL or specifics; preop use of antibiotics for prev of infect: index under ANTIBIOTIC PROPHYLAXIS (IM) + specific antibiotic /ther use (IM) @@ -3142,7 +3120,7 @@ nlm - bears + pashj chodan @@ -3365,9 +3343,9 @@ Career Mobility - 2014 - 06 - 26 + 1999 + 01 + 01 1999 @@ -3380,21 +3358,7 @@ 01 - 2000 - 2001 - 2002 - 2003 - 2004 - 2005 - 2006 - 2007 - 2008 - 2009 - 2010 - 2011 - 2012 - 2013 - 2014 + 2015 no qualif @@ -3408,7 +3372,7 @@ specific occupation (1966-1971) - I01.880.840.200 + I01.880.853.996.200 N01.824.175 N01.824.547.330 N04.452.677.300 @@ -3651,331 +3615,332 @@ 2014 + 2015 - Q000097 + Q000503 - blood + physiopathology - BL + PP - Q000134 + Q000530 - cerebrospinal fluid + radiography - CF + RA - Q000139 + Q000531 - chemically induced + radionuclide imaging - CI + RI - Q000145 + Q000534 - classification + rehabilitation - CL + RH - Q000151 + Q000201 - congenital + enzymology - CN + EN - Q000175 + Q000209 - diagnosis + etiology - DI + ET - Q000178 + Q000401 - diet therapy + mortality - DH + MO - Q000188 + Q000453 - drug therapy + epidemiology - DT + EP - Q000191 + Q000517 - economics + prevention & control - EC + PC - Q000196 + Q000097 - embryology + blood - EM + BL - Q000201 + Q000134 - enzymology + cerebrospinal fluid - EN + CF - Q000208 + Q000139 - ethnology + chemically induced - EH + CI - Q000209 + Q000151 - etiology + congenital - ET + CN - Q000235 + Q000178 - genetics + diet therapy - GE + DH - Q000266 + Q000188 - history + drug therapy - HI + DT - Q000276 + Q000628 - immunology + therapy - IM + TH - Q000378 + Q000523 - metabolism + psychology - ME + PX - Q000382 + Q000652 - microbiology + urine - MI + UR - Q000401 + Q000821 - mortality + virology - MO + VI - Q000451 + Q000736 - nursing + ultrasonography - NU + US - Q000453 + Q000662 - epidemiology + veterinary - EP + VE - Q000469 + Q000266 - parasitology + history - PS + HI - Q000473 + Q000145 - pathology + classification - PA + CL - Q000503 + Q000175 - physiopathology + diagnosis - PP + DI - Q000517 + Q000191 - prevention & control + economics - PC + EC - Q000523 + Q000196 - psychology + embryology - PX + EM - Q000530 + Q000208 - radiography + ethnology - RA + EH - Q000531 + Q000235 - radionuclide imaging + genetics - RI + GE - Q000532 + Q000276 - radiotherapy + immunology - RT + IM - Q000534 + Q000378 - rehabilitation + metabolism - RH + ME - Q000601 + Q000382 - surgery + microbiology - SU + MI - Q000628 + Q000451 - therapy + nursing - TH + NU - Q000652 + Q000469 - urine + parasitology - UR + PS - Q000662 + Q000473 - veterinary + pathology - VE + PA - Q000736 + Q000532 - ultrasonography + radiotherapy - US + RT - Q000821 + Q000601 - virology + surgery - VI + SU GEN or unspecified; prefer specifics; pregnancy of diabetic patients = PREGNANCY IN DIABETICS but do not confuse with DIABETES, GESTATIONAL: see note there; PREDIABETIC STATE is also available & includes subclinical diabetes; /diet ther: consider coord with DIABETIC DIET but see note there; alloxan- & streptozocin-induced diabetes: see note on DIABETES MELLITUS, EXPERIMENTAL @@ -4121,142 +4086,143 @@ 2014 + 2015 - Q000145 + Q000941 - classification + ethics - CL + ES - Q000191 + Q000401 - economics + mortality - EC + MO - Q000266 + Q000744 - history + contraindications - HI + CT - Q000295 + Q000656 - instrumentation + utilization - IS + UT - Q000379 + Q000523 - methods + psychology - MT + PX - Q000401 + Q000706 - mortality + statistics & numerical data - MO + SN - Q000451 + Q000639 - nursing + trends - NU + TD - Q000523 + Q000662 - psychology + veterinary - PX + VE - Q000592 + Q000266 - standards + history - ST + HI - Q000639 + Q000145 - trends + classification - TD + CL - Q000656 + Q000191 - utilization + economics - UT + EC - Q000662 + Q000295 - veterinary + instrumentation - VE + IS - Q000706 + Q000379 - statistics & numerical data + methods - SN + MT - Q000744 + Q000451 - contraindications + nursing - CT + NU - Q000941 + Q000592 - ethics + standards - ES + ST general only: prefer /drug ther with disease term: Manual 19.7+, 19.8.26; note entry term CHEMOTHERAPY: prefer specific chemical or chemical group, e.g., chemotherapy of lymphoma = LYMPHOMA /drug ther + ANTINEOPLASTIC AGENTS /ther use, not DRUG THERAPY @@ -4423,52 +4389,44 @@ 2012 2013 2014 + 2015 - Q000033 - - anatomy & histology - - - AH - - - - Q000098 + Q000503 - blood supply + physiopathology - BS + PP - Q000166 + Q000530 - cytology + radiography - CY + RA - Q000187 + Q000531 - drug effects + radionuclide imaging - DE + RI - Q000196 + Q000557 - embryology + secretion - EM + SE @@ -4481,75 +4439,75 @@ - Q000254 + Q000294 - growth & development + innervation - GD + IR - Q000276 + Q000166 - immunology + cytology - IM + CY - Q000294 + Q000648 - innervation + ultrastructure - IR + UL - Q000378 + Q000737 - metabolism + chemistry - ME + CH - Q000382 + Q000187 - microbiology + drug effects - MI + DE - Q000469 + Q000637 - parasitology + transplantation - PS + TR - Q000473 + Q000821 - pathology + virology - PA + VI - Q000503 + Q000736 - physiopathology + ultrasonography - PP + US @@ -4562,75 +4520,84 @@ - Q000530 + Q000033 - radiography + anatomy & histology - RA + AH - Q000531 + Q000098 - radionuclide imaging + blood supply - RI + BS - Q000557 + Q000196 - secretion + embryology - SE + EM - Q000637 + Q000254 - transplantation + growth & development - TR + GD - Q000648 + Q000276 - ultrastructure + immunology - UL + IM - Q000736 + Q000378 - ultrasonography + metabolism - US + ME - Q000737 + Q000382 - chemistry + microbiology - CH + MI - Q000821 + Q000469 - virology + parasitology - VI + PS + + + + Q000473 + + pathology + + + PA inflammation of the eye = ENDOPHTHALMITIS or specific -ITIS terms in Category C11, Eye Diseases; COMPOUND EYE, ARTHROPOD is available for arthropods @@ -4828,52 +4795,44 @@ 2014 + 2015 - Q000002 - - abnormalities - - - AB - - - - Q000033 + Q000502 - anatomy & histology + physiology - AH + PH - Q000166 + Q000503 - cytology + physiopathology - CY + PP - Q000187 + Q000530 - drug effects + radiography - DE + RA - Q000196 + Q000531 - embryology + radionuclide imaging - EM + RI @@ -4886,75 +4845,75 @@ - Q000254 + Q000002 - growth & development + abnormalities - GD + AB - Q000276 + Q000166 - immunology + cytology - IM + CY - Q000378 + Q000648 - metabolism + ultrastructure - ME + UL - Q000382 + Q000737 - microbiology + chemistry - MI + CH - Q000469 + Q000187 - parasitology + drug effects - PS + DE - Q000473 + Q000637 - pathology + transplantation - PA + TR - Q000502 + Q000821 - physiology + virology - PH + VI - Q000503 + Q000736 - physiopathology + ultrasonography - PP + US @@ -4967,66 +4926,75 @@ - Q000530 + Q000033 - radiography + anatomy & histology - RA + AH - Q000531 + Q000196 - radionuclide imaging + embryology - RI + EM - Q000637 + Q000254 - transplantation + growth & development - TR + GD - Q000648 + Q000276 - ultrastructure + immunology - UL + IM - Q000736 + Q000378 - ultrasonography + metabolism - US + ME - Q000737 + Q000382 - chemistry + microbiology - CH + MI - Q000821 + Q000469 - virology + parasitology - VI + PS + + + + Q000473 + + pathology + + + PA @@ -5100,43 +5068,44 @@ 2012 2013 2014 + 2015 - Q000002 + Q000502 - abnormalities + physiology - AB + PH - Q000033 + Q000503 - anatomy & histology + physiopathology - AH + PP - Q000098 + Q000530 - blood supply + radiography - BS + RA - Q000196 + Q000531 - embryology + radionuclide imaging - EM + RI @@ -5149,102 +5118,102 @@ - Q000382 + Q000002 - microbiology + abnormalities - MI + AB - Q000469 + Q000821 - parasitology + virology - PS + VI - Q000473 + Q000736 - pathology + ultrasonography - PA + US - Q000502 + Q000528 - physiology + radiation effects - PH + RE - Q000503 + Q000033 - physiopathology + anatomy & histology - PP + AH - Q000528 + Q000098 - radiation effects + blood supply - RE + BS - Q000530 + Q000196 - radiography + embryology - RA + EM - Q000531 + Q000382 - radionuclide imaging + microbiology - RI + MI - Q000601 + Q000469 - surgery + parasitology - SU + PS - Q000736 + Q000473 - ultrasonography + pathology - US + PA - Q000821 + Q000601 - virology + surgery - VI + SU usually NIM as site; soft parts = FACE, bones = FACIAL BONES or specifics; /abnorm permitted but FACIAL BONES /abnorm is more likely; facial fractures: see note on FACIAL BONES; craniofacial dysmorphism & craniofacial fibrous dysplasia & long face syndrome: see note also on FACIAL BONES @@ -5383,6 +5352,7 @@ 2014 + 2015 check tag only for female organs, diseases, physiol processes, genetics, etc.; do not confuse with WOMEN as a social, cultural, political, economic force; Manual 18.9+, 34.12; 35.6.2 CATALOG: do not use: for indexers only @@ -5458,43 +5428,71 @@ 2012 2013 2014 + 2015 - Q000008 + Q000627 - administration & dosage + therapeutic use - AD + TU - Q000009 + Q000633 - adverse effects + toxicity - AE + TO - Q000032 + Q000176 - analysis + diagnostic use - AN + DU - Q000037 + Q000506 - antagonists & inhibitors + poisoning - AI + PO + + + + Q000008 + + administration & dosage + + + AD + + + + Q000009 + + adverse effects + + + AE + + + + Q000819 + + agonists + + + AG @@ -5525,174 +5523,147 @@ - Q000145 + Q000744 - classification + contraindications - CL + CT - Q000176 + Q000737 - diagnostic use + chemistry - DU + CH - Q000191 + Q000652 - economics + urine - EC + UR - Q000266 + Q000528 - history + radiation effects - HI + RE - Q000276 - - immunology - - - IM - - - - Q000302 - - isolation & purification - - - IP - - - - Q000378 - - metabolism - - - ME - - - - Q000493 + Q000266 - pharmacokinetics + history - PK + HI - Q000494 + Q000032 - pharmacology + analysis - PD + AN - Q000506 + Q000037 - poisoning + antagonists & inhibitors - PO + AI - Q000528 + Q000145 - radiation effects + classification - RE + CL - Q000592 + Q000191 - standards + economics - ST + EC - Q000600 + Q000276 - supply & distribution + immunology - SD + IM - Q000627 + Q000302 - therapeutic use + isolation & purification - TU + IP - Q000633 + Q000378 - toxicity + metabolism - TO + ME - Q000652 + Q000494 - urine + pharmacology - UR + PD - Q000737 + Q000592 - chemistry + standards - CH + ST - Q000744 + Q000600 - contraindications + supply & distribution - CT + SD - Q000819 + Q000493 - agonists + pharmacokinetics - AG + PK = iron(III) or Fe(III), as Fe2O3, FeCl3; iron(II) or Fe(II) = FERROUS COMPOUNDS; hematinics; DF: FERRIC CPDS @@ -5811,6 +5782,7 @@ 2012 2013 2014 + 2015 @@ -5903,133 +5875,134 @@ 2012 2013 2014 + 2015 - Q000033 + Q000502 - anatomy & histology + physiology - AH + PH - Q000187 + Q000503 - drug effects + physiopathology - DE + PP - Q000196 + Q000530 - embryology + radiography - EM + RA - Q000254 + Q000531 - growth & development + radionuclide imaging - GD + RI - Q000294 + Q000557 - innervation + secretion - IR + SE - Q000382 + Q000294 - microbiology + innervation - MI + IR - Q000469 + Q000187 - parasitology + drug effects - PS + DE - Q000502 + Q000821 - physiology + virology - PH + VI - Q000503 + Q000528 - physiopathology + radiation effects - PP + RE - Q000528 + Q000033 - radiation effects + anatomy & histology - RE + AH - Q000530 + Q000196 - radiography + embryology - RA + EM - Q000531 + Q000254 - radionuclide imaging + growth & development - RI + GD - Q000557 + Q000382 - secretion + microbiology - SE + MI - Q000821 + Q000469 - virology + parasitology - VI + PS heart as pump, not tissue (MYOCARDIUM); qualif permitted: /anat /drug eff /embryol (FETAL HEART also exists) /growth /innerv (HEART CONDUCTION SYSTEM also exists) /microbiol /parasitol /physiol (see also ATRIAL FUNCTION & VENTRICULAR FUNCTION & their specifics; see also MYOCARDIAL CONTRACTION & its specifics) /physiopathol /rad eff /radiogr (do not confuse with ANGIOCARDIOGRAPHY) /radionuclide /virol; /blood supply = CORONARY VESSELS but consider also CORONARY CIRCULATION; /drug eff: consider also MYOCARDIAL DEPRESSANTS see ANTI-ARRHYTHMIA AGENTS & CARDIOTONIC AGENTS; /transpl = HEART TRANSPLANTATION: do not coord with TRANSPLANTATION, HOMOLOGOUS unless particularly discussed; /ultrasonogr = ECHOCARDIOGRAPHY or ECHOCARDIOGRAPHY, DOPPLER; inotropism: INOTROPISM, CARDIAC see MYOCARDIAL CONTRACTION & INOTROPIC AGENTS, POSITIVE CARDIAC are available but see MYOCARDIAL CONTRACTION note; chronotropism: see HEART RATE note; DIASTOLE & SYSTOLE are also available; heart-lung prep: index HEART /physiol (probably NIM); Manual 21.48+; carditis = MYOCARDITIS; mural thrombosis: index HEART DISEASE (IM) + THROMBOSIS (IM) @@ -6525,340 +6498,341 @@ 2012 2013 2014 + 2015 - Q000097 + Q000503 - blood + physiopathology - BL + PP - Q000134 + Q000530 - cerebrospinal fluid + radiography - CF + RA - Q000139 + Q000531 - chemically induced + radionuclide imaging - CI + RI - Q000145 + Q000534 - classification + rehabilitation - CL + RH - Q000150 + Q000201 - complications + enzymology - CO + EN - Q000151 + Q000209 - congenital + etiology - CN + ET - Q000175 + Q000401 - diagnosis + mortality - DI + MO - Q000178 + Q000453 - diet therapy + epidemiology - DH + EP - Q000188 + Q000517 - drug therapy + prevention & control - DT + PC - Q000191 + Q000097 - economics + blood - EC + BL - Q000196 + Q000134 - embryology + cerebrospinal fluid - EM + CF - Q000201 + Q000139 - enzymology + chemically induced - EN + CI - Q000208 + Q000151 - ethnology + congenital - EH + CN - Q000209 + Q000178 - etiology + diet therapy - ET + DH - Q000235 + Q000188 - genetics + drug therapy - GE + DT - Q000266 + Q000628 - history + therapy - HI + TH - Q000276 + Q000523 - immunology + psychology - IM + PX - Q000378 + Q000652 - metabolism + urine - ME + UR - Q000382 + Q000821 - microbiology + virology - MI + VI - Q000401 + Q000736 - mortality + ultrasonography - MO + US - Q000451 + Q000662 - nursing + veterinary - NU + VE - Q000453 + Q000266 - epidemiology + history - EP + HI - Q000469 + Q000145 - parasitology + classification - PS + CL - Q000473 + Q000150 - pathology + complications - PA + CO - Q000503 + Q000175 - physiopathology + diagnosis - PP + DI - Q000517 + Q000191 - prevention & control + economics - PC + EC - Q000523 + Q000196 - psychology + embryology - PX + EM - Q000530 + Q000208 - radiography + ethnology - RA + EH - Q000531 + Q000235 - radionuclide imaging + genetics - RI + GE - Q000532 + Q000276 - radiotherapy + immunology - RT + IM - Q000534 + Q000378 - rehabilitation + metabolism - RH + ME - Q000601 + Q000382 - surgery + microbiology - SU + MI - Q000628 + Q000451 - therapy + nursing - TH + NU - Q000652 + Q000469 - urine + parasitology - UR + PS - Q000662 + Q000473 - veterinary + pathology - VE + PA - Q000736 + Q000532 - ultrasonography + radiotherapy - US + RT - Q000821 + Q000601 - virology + surgery - VI + SU 2000(1966) @@ -7306,25 +7280,26 @@ 2014 + 2015 - Q000002 + Q000502 - abnormalities + physiology - AB + PH - Q000033 + Q000002 - anatomy & histology + abnormalities - AH + AB @@ -7344,6 +7319,42 @@ CF + + + Q000523 + + psychology + + + PX + + + + Q000652 + + urine + + + UR + + + + Q000821 + + virology + + + VI + + + + Q000033 + + anatomy & histology + + + AH + Q000145 @@ -7416,24 +7427,6 @@ PS - - - Q000502 - - physiology - - - PH - - - - Q000523 - - psychology - - - PX - Q000601 @@ -7443,24 +7436,6 @@ SU - - - Q000652 - - urine - - - UR - - - - Q000821 - - virology - - - VI - NIM as check tag only; Manual 18.8+; Homo sp. other than Homo sapiens are indexed HOMO see HOMINIDAE @@ -7581,241 +7556,242 @@ 2014 + 2015 - Q000008 + Q000502 - administration & dosage + physiology - AD + PH - Q000009 + Q000627 - adverse effects + therapeutic use - AE + TU - Q000032 + Q000633 - analysis + toxicity - AN + TO - Q000097 + Q000176 - blood + diagnostic use - BL + DU - Q000134 + Q000506 - cerebrospinal fluid + poisoning - CF + PO - Q000145 + Q000008 - classification + administration & dosage - CL + AD - Q000172 + Q000009 - deficiency + adverse effects - DF + AE - Q000176 + Q000819 - diagnostic use + agonists - DU + AG - Q000191 + Q000097 - economics + blood - EC + BL - Q000266 + Q000134 - history + cerebrospinal fluid - HI + CF - Q000276 + Q000744 - immunology + contraindications - IM + CT - Q000302 + Q000172 - isolation & purification + deficiency - IP + DF - Q000378 + Q000737 - metabolism + chemistry - ME + CH - Q000493 + Q000652 - pharmacokinetics + urine - PK + UR - Q000494 + Q000528 - pharmacology + radiation effects - PD + RE - Q000502 + Q000266 - physiology + history - PH + HI - Q000506 + Q000032 - poisoning + analysis - PO + AN - Q000528 + Q000145 - radiation effects + classification - RE + CL - Q000592 + Q000191 - standards + economics - ST + EC - Q000600 + Q000276 - supply & distribution + immunology - SD + IM - Q000627 + Q000302 - therapeutic use + isolation & purification - TU + IP - Q000633 + Q000378 - toxicity + metabolism - TO + ME - Q000652 + Q000494 - urine + pharmacology - UR + PD - Q000737 + Q000592 - chemistry + standards - CH + ST - Q000744 + Q000600 - contraindications + supply & distribution - CT + SD - Q000819 + Q000493 - agonists + pharmacokinetics - AG + PK Fe-56; Fe(II) = FERROUS COMPOUNDS, Fe(III) = FERRIC COMPOUNDS; /defic: permitted but consider ANEMIA, IRON DEFICIENCY; pneumoconiosis caused by iron particles = SIDEROSIS; /metab: consider also IRON OVERLOAD; metabolic disorders = IRON METABOLISM DISORDERS @@ -7991,6 +7967,7 @@ 2012 2013 2014 + 2015 not used for indexing or cataloging @@ -8058,390 +8035,390 @@ Neoplasms - 2014 - 06 - 26 + 1999 + 01 + 01 - 2013 - 07 - 10 + 2014 + 06 + 13 - 2014 + 2015 - Q000097 + Q000503 - blood + physiopathology - BL + PP - Q000098 + Q000530 - blood supply + radiography - BS + RA - Q000134 + Q000531 - cerebrospinal fluid + radionuclide imaging - CF + RI - Q000139 + Q000534 - chemically induced + rehabilitation - CI + RH - Q000145 + Q000557 - classification + secretion - CL + SE - Q000150 + Q000201 - complications + enzymology - CO + EN - Q000151 + Q000209 - congenital + etiology - CN + ET - Q000175 + Q000401 - diagnosis + mortality - DI + MO - Q000178 + Q000453 - diet therapy + epidemiology - DH + EP - Q000188 + Q000517 - drug therapy + prevention & control - DT + PC - Q000191 + Q000097 - economics + blood - EC + BL - Q000196 + Q000134 - embryology + cerebrospinal fluid - EM + CF - Q000201 + Q000139 - enzymology + chemically induced - EN + CI - Q000208 + Q000151 - ethnology + congenital - EH + CN - Q000209 + Q000178 - etiology + diet therapy - ET + DH - Q000235 + Q000188 - genetics + drug therapy - GE + DT - Q000266 + Q000628 - history + therapy - HI + TH - Q000276 + Q000648 - immunology + ultrastructure - IM + UL - Q000378 + Q000737 - metabolism + chemistry - ME + CH - Q000382 + Q000523 - microbiology + psychology - MI + PX - Q000401 + Q000652 - mortality + urine - MO + UR - Q000451 + Q000821 - nursing + virology - NU + VI - Q000453 + Q000736 - epidemiology + ultrasonography - EP + US - Q000469 + Q000662 - parasitology + veterinary - PS + VE - Q000473 + Q000266 - pathology + history - PA + HI - Q000503 + Q000098 - physiopathology + blood supply - PP + BS - Q000517 + Q000145 - prevention & control + classification - PC + CL - Q000523 + Q000150 - psychology + complications - PX + CO - Q000530 + Q000175 - radiography + diagnosis - RA + DI - Q000531 + Q000191 - radionuclide imaging + economics - RI + EC - Q000532 + Q000196 - radiotherapy + embryology - RT + EM - Q000534 + Q000208 - rehabilitation + ethnology - RH + EH - Q000557 + Q000235 - secretion + genetics - SE + GE - Q000601 + Q000276 - surgery + immunology - SU + IM - Q000628 + Q000378 - therapy + metabolism - TH + ME - Q000648 + Q000382 - ultrastructure + microbiology - UL + MI - Q000652 + Q000451 - urine + nursing - UR + NU - Q000662 + Q000469 - veterinary + parasitology - VE + PS - Q000736 + Q000473 - ultrasonography + pathology - US + PA - Q000737 + Q000532 - chemistry + radiotherapy - CH + RT - Q000821 + Q000601 - virology + surgery - VI + SU - general; prefer specifics; policy: Manual section 24; qualifier / nurs = the patient, ONCOLOGY NURSING = the oncologic specialty; qualifier / radiother = the patient, RADIATION ONCOLOGY = the specialty; familial: consider also NEOPLASTIC SYNDROMES, HEREDITARY; metastatic cancer of unknown origin: index under NEOPLASM METASTASIS + general; prefer specifics; policy: see Manual Chapter 24; familial: consider also NEOPLASTIC SYNDROMES, HEREDITARY; metastatic cancer of unknown origin: index under NEOPLASM METASTASIS /diagnosis was NEOPLASM DIAGNOSIS 1964-65; /etiology was NEOPLASM ETIOLOGY 1964-65; /immunology was NEOPLASM IMMUNOLOGY 1964-65; /radiotherapy was NEOPLASM RADIOTHERAPY 1964-65; /therapy was NEOPLASM THERAPY 1964-65; NEOPLASM STATISTICS was heading 1964-65; CARCINOGENESIS was heading 1977 @@ -8592,13 +8569,13 @@ - + M0014585 - M0014586 + M0014584 - + M0014585 - M0014584 + M0014586 @@ -8657,6 +8634,43 @@ + + M0014584 + + Cancer + + + + T191 + Neoplastic Process + + + + + M0014585 + M0014584 + + + + + T027925 + Cancer + + 1974 + 03 + 30 + + + BIOETHICS (1974) + POPLINE (1978) + + + + T027925 + Cancers + + + M0014586 @@ -8669,7 +8683,7 @@ - + M0014585 M0014586 @@ -8711,43 +8725,6 @@ - - M0014584 - - Cancer - - - - T191 - Neoplastic Process - - - - - M0014585 - M0014584 - - - - - T027925 - Cancer - - 1974 - 03 - 30 - - - BIOETHICS (1974) - POPLINE (1978) - - - - T027925 - Cancers - - - @@ -8772,250 +8749,251 @@ 2012 2013 2014 + 2015 - Q000002 + Q000502 - abnormalities + physiology - AB + PH - Q000033 + Q000503 - anatomy & histology + physiopathology - AH + PP - Q000098 + Q000530 - blood supply + radiography - BS + RA - Q000166 + Q000531 - cytology + radionuclide imaging - CY + RI - Q000187 + Q000557 - drug effects + secretion - DE + SE - Q000196 + Q000201 - embryology + enzymology - EM + EN - Q000201 + Q000294 - enzymology + innervation - EN + IR - Q000254 + Q000002 - growth & development + abnormalities - GD + AB - Q000276 + Q000166 - immunology + cytology - IM + CY - Q000293 + Q000648 - injuries + ultrastructure - IN + UL - Q000294 + Q000737 - innervation + chemistry - IR + CH - Q000378 + Q000187 - metabolism + drug effects - ME + DE - Q000382 + Q000637 - microbiology + transplantation - MI + TR - Q000469 + Q000821 - parasitology + virology - PS + VI - Q000473 + Q000736 - pathology + ultrasonography - PA + US - Q000502 + Q000528 - physiology + radiation effects - PH + RE - Q000503 + Q000033 - physiopathology + anatomy & histology - PP + AH - Q000528 + Q000098 - radiation effects + blood supply - RE + BS - Q000530 + Q000196 - radiography + embryology - RA + EM - Q000531 + Q000254 - radionuclide imaging + growth & development - RI + GD - Q000557 + Q000276 - secretion + immunology - SE + IM - Q000601 + Q000293 - surgery + injuries - SU + IN - Q000637 + Q000378 - transplantation + metabolism - TR + ME - Q000648 + Q000382 - ultrastructure + microbiology - UL + MI - Q000736 + Q000469 - ultrasonography + parasitology - US + PS - Q000737 + Q000473 - chemistry + pathology - CH + PA - Q000821 + Q000601 - virology + surgery - VI + SU /innerv = probably OCULOMOTOR NERVE but consider also ABDUCENS NERVE & TROCHLEAR NERVE; paralysis = OCULOMOTOR PARALYSIS see OPHTHALMOPLEGIA; /growth: coord with MUSCLE DEVELOPMENT; /embryol: coord with MUSCLE DEVELOPMENT if pertinent @@ -9098,43 +9076,89 @@ 2012 2013 2014 + 2015 - Q000145 + Q000502 + + physiology + + + PH + + + + Q000201 + + enzymology + + + EN + + + + Q000166 + + cytology + + + CY + + + + Q000648 + + ultrastructure + + + UL + + + + Q000737 + + chemistry + + + CH + + + + Q000187 - classification + drug effects - CL + DE - Q000166 + Q000821 - cytology + virology - CY + VI - Q000187 + Q000528 - drug effects + radiation effects - DE + RE - Q000201 + Q000145 - enzymology + classification - EN + CL @@ -9190,51 +9214,6 @@ PY - - - Q000502 - - physiology - - - PH - - - - Q000528 - - radiation effects - - - RE - - - - Q000648 - - ultrastructure - - - UL - - - - Q000737 - - chemistry - - - CH - - - - Q000821 - - virology - - - VI - use YEAST, DRIED for brewer's yeast or baker's yeast used as a nutritional supplement or therapeutically @@ -9463,250 +9442,251 @@ 2012 2013 2014 + 2015 - Q000002 + Q000502 - abnormalities + physiology - AB + PH - Q000033 + Q000503 - anatomy & histology + physiopathology - AH + PP - Q000098 + Q000530 - blood supply + radiography - BS + RA - Q000166 + Q000531 - cytology + radionuclide imaging - CY + RI - Q000187 + Q000557 - drug effects + secretion - DE + SE - Q000196 + Q000201 - embryology + enzymology - EM + EN - Q000201 + Q000294 - enzymology + innervation - EN + IR - Q000254 + Q000002 - growth & development + abnormalities - GD + AB - Q000276 + Q000166 - immunology + cytology - IM + CY - Q000293 + Q000648 - injuries + ultrastructure - IN + UL - Q000294 + Q000737 - innervation + chemistry - IR + CH - Q000378 + Q000187 - metabolism + drug effects - ME + DE - Q000382 + Q000637 - microbiology + transplantation - MI + TR - Q000469 + Q000821 - parasitology + virology - PS + VI - Q000473 + Q000736 - pathology + ultrasonography - PA + US - Q000502 + Q000528 - physiology + radiation effects - PH + RE - Q000503 + Q000033 - physiopathology + anatomy & histology - PP + AH - Q000528 + Q000098 - radiation effects + blood supply - RE + BS - Q000530 + Q000196 - radiography + embryology - RA + EM - Q000531 + Q000254 - radionuclide imaging + growth & development - RI + GD - Q000557 + Q000276 - secretion + immunology - SE + IM - Q000601 + Q000293 - surgery + injuries - SU + IN - Q000637 + Q000378 - transplantation + metabolism - TR + ME - Q000648 + Q000382 - ultrastructure + microbiology - UL + MI - Q000736 + Q000469 - ultrasonography + parasitology - US + PS - Q000737 + Q000473 - chemistry + pathology - CH + PA - Q000821 + Q000601 - virology + surgery - VI + SU GEN: prefer specifics @@ -9805,6 +9785,7 @@ 2012 2013 2014 + 2015 not used for indexing since 1989; prior to 1989 used for skin manifest of non-skin diseases @@ -9907,6 +9888,7 @@ 2012 2013 2014 + 2015 no qualif; "the unconscious" or unconscious behavior: do not confuse with UNCONSCIOUSNESS, the physiol loss of consciousness; DF: UNCONSCIOUS @@ -10013,14 +9995,14 @@ Ofloxacin - 2014 - 06 - 26 + 1988 + 05 + 16 - 2013 - 07 - 08 + 2014 + 06 + 17 1989 @@ -10028,53 +10010,71 @@ 01 - 2014 + 2015 - Q000008 + Q000627 + + therapeutic use + + + TU + + + + Q000633 + + toxicity + + + TO + + + + Q000176 - administration & dosage + diagnostic use - AD + DU - Q000009 + Q000506 - adverse effects + poisoning - AE + PO - Q000031 + Q000008 - analogs & derivatives + administration & dosage - AA + AD - Q000032 + Q000009 - analysis + adverse effects - AN + AE - Q000037 + Q000819 - antagonists & inhibitors + agonists - AI + AG @@ -10105,174 +10105,156 @@ - Q000145 - - classification - - - CL - - - - Q000176 - - diagnostic use - - - DU - - - - Q000191 + Q000744 - economics + contraindications - EC + CT - Q000266 + Q000737 - history + chemistry - HI + CH - Q000276 + Q000652 - immunology + urine - IM + UR - Q000302 + Q000528 - isolation & purification + radiation effects - IP + RE - Q000378 + Q000266 - metabolism + history - ME + HI - Q000493 + Q000031 - pharmacokinetics + analogs & derivatives - PK + AA - Q000494 + Q000032 - pharmacology + analysis - PD + AN - Q000506 + Q000037 - poisoning + antagonists & inhibitors - PO + AI - Q000528 + Q000145 - radiation effects + classification - RE + CL - Q000592 + Q000191 - standards + economics - ST + EC - Q000600 + Q000276 - supply & distribution + immunology - SD + IM - Q000627 + Q000302 - therapeutic use + isolation & purification - TU + IP - Q000633 + Q000378 - toxicity + metabolism - TO + ME - Q000652 + Q000494 - urine + pharmacology - UR + PD - Q000737 + Q000592 - chemistry + standards - CH + ST - Q000744 + Q000600 - contraindications + supply & distribution - CT + SD - Q000819 + Q000493 - agonists + pharmacokinetics - AG + PK 89 @@ -10309,6 +10291,14 @@ + + + D065609 + + Cytochrome P-450 CYP1A2 Inhibitors + + + D03.438.810.835.322.500 @@ -10356,15 +10346,15 @@ M0023430 - M0023432 + M0333652 M0023430 - M0333652 + M0333653 M0023430 - M0333653 + M0023432 M0023430 @@ -10496,43 +10486,6 @@ - - M0023432 - - Tarivid - - 0 - - - T109 - Organic Chemical - - - T121 - Pharmacologic Substance - - - - - M0023430 - M0023432 - - - - - T044630 - Tarivid - - 1989 - 06 - 09 - - - NLM (1990) - - - - M0333652 @@ -10623,6 +10576,43 @@ + + M0023432 + + Tarivid + + 0 + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0023430 + M0023432 + + + + + T044630 + Tarivid + + 1989 + 06 + 09 + + + NLM (1990) + + + + M0333650 @@ -10735,6 +10725,7 @@ 2012 2013 2014 + 2015 @@ -10748,147 +10739,147 @@ - Q000009 + Q000941 - adverse effects + ethics - AE + ES - Q000145 + Q000401 - classification + mortality - CL + MO - Q000191 + Q000009 - economics + adverse effects - EC + AE - Q000266 + Q000744 - history + contraindications - HI + CT - Q000295 + Q000656 - instrumentation + utilization - IS + UT - Q000379 + Q000523 - methods + psychology - MT + PX - Q000401 + Q000706 - mortality + statistics & numerical data - MO + SN - Q000451 + Q000639 - nursing + trends - NU + TD - Q000523 + Q000662 - psychology + veterinary - PX + VE - Q000592 + Q000266 - standards + history - ST + HI - Q000639 + Q000145 - trends + classification - TD + CL - Q000656 + Q000191 - utilization + economics - UT + EC - Q000662 + Q000295 - veterinary + instrumentation - VE + IS - Q000706 + Q000379 - statistics & numerical data + methods - SN + MT - Q000744 + Q000451 - contraindications + nursing - CT + NU - Q000941 + Q000592 - ethics + standards - ES + ST for general design, methodology, economics, etc. of randomized controlled trials; a different heading RANDOMIZED CONTROLLED TRIAL is used for reports of a specific randomized trial @@ -11072,6 +11063,7 @@ 2012 2013 2014 + 2015 @@ -11103,93 +11095,93 @@ - Q000145 + Q000331 - classification + legislation & jurisprudence - CL + LJ - Q000191 + Q000941 - economics + ethics - EC + ES - Q000266 + Q000656 - history + utilization - HI + UT - Q000331 + Q000706 - legislation & jurisprudence + statistics & numerical data - LJ + SN - Q000592 + Q000639 - standards + trends - ST + TD - Q000600 + Q000266 - supply & distribution + history - SD + HI - Q000639 + Q000145 - trends + classification - TD + CL - Q000656 + Q000191 - utilization + economics - UT + EC - Q000706 + Q000592 - statistics & numerical data + standards - SN + ST - Q000941 + Q000600 - ethics + supply & distribution - ES + SD CATALOG: use NAF entry @@ -11335,6 +11327,7 @@ 2012 2013 2014 + 2015 this heading is used as a Publication Type; CATALOG: do not use @@ -11408,6 +11401,7 @@ 2012 2013 2014 + 2015 this heading is used as a Publication Type; for original report of the conduct or results of a specific randomized controlled trial; a different heading RANDOMIZED CONTROLLED TRIALS AS TOPIC is used for general design, methodology, economics, etc. of randomized controlled trials @@ -11478,6 +11472,7 @@ 2014 + 2015 this heading is used as a Publication Type; review articles as a bibliographic form are indexed under the main heading REVIEW LITERATURE AS TOPIC @@ -11739,6 +11734,7 @@ 2012 2013 2014 + 2015 @@ -11842,106 +11838,107 @@ 2012 2013 2014 + 2015 - Q000145 + Q000941 - classification + ethics - CL + ES - Q000191 + Q000656 - economics + utilization - EC + UT - Q000266 + Q000706 - history + statistics & numerical data - HI + SN - Q000295 + Q000639 - instrumentation + trends - IS + TD - Q000379 + Q000662 - methods + veterinary - MT + VE - Q000592 + Q000266 - standards + history - ST + HI - Q000639 + Q000145 - trends + classification - TD + CL - Q000656 + Q000191 - utilization + economics - UT + EC - Q000662 + Q000295 - veterinary + instrumentation - VE + IS - Q000706 + Q000379 - statistics & numerical data + methods - SN + MT - Q000941 + Q000592 - ethics + standards - ES + ST GEN or unspecified; prefer specifics; used for tests of drugs, food, environ pollutants, etc.; when the test itself is emphasized; coord IM with substance /tox (IM); toxic eff of a specific substance = specific substance /tox; DF: TOX TESTS @@ -12039,8 +12036,18 @@ 2013 2013A 2014 + 2015 + + + Q000534 + + rehabilitation + + + RH + Q000145 @@ -12086,15 +12093,6 @@ SN - - - Q000534 - - rehabilitation - - - RH - 98 @@ -12256,6 +12254,7 @@ 2012 2013 2014 + 2015 used for searching: indexers and catalogers apply specifics @@ -12339,6 +12338,7 @@ 2013 2014 + 2015 this heading is used as a Publication Type. Used by catalogers only. CATALOG: Use when 20% or more of the content consists of statistical data. If presented in tabular form use also the Publication Type TABLES; statistics as a subject is indexed under the main heading STATISTICS AS TOPIC @@ -12419,340 +12419,341 @@ 2012 2013 2014 + 2015 - Q000097 + Q000503 - blood + physiopathology - BL + PP - Q000134 + Q000530 - cerebrospinal fluid + radiography - CF + RA - Q000139 + Q000531 - chemically induced + radionuclide imaging - CI + RI - Q000145 + Q000534 - classification + rehabilitation - CL + RH - Q000150 + Q000201 - complications + enzymology - CO + EN - Q000151 + Q000209 - congenital + etiology - CN + ET - Q000175 + Q000401 - diagnosis + mortality - DI + MO - Q000178 + Q000453 - diet therapy + epidemiology - DH + EP - Q000188 + Q000517 - drug therapy + prevention & control - DT + PC - Q000191 + Q000097 - economics + blood - EC + BL - Q000196 + Q000134 - embryology + cerebrospinal fluid - EM + CF - Q000201 + Q000139 - enzymology + chemically induced - EN + CI - Q000208 + Q000151 - ethnology + congenital - EH + CN - Q000209 + Q000178 - etiology + diet therapy - ET + DH - Q000235 + Q000188 - genetics + drug therapy - GE + DT - Q000266 + Q000628 - history + therapy - HI + TH - Q000276 + Q000523 - immunology + psychology - IM + PX - Q000378 + Q000652 - metabolism + urine - ME + UR - Q000382 + Q000821 - microbiology + virology - MI + VI - Q000401 + Q000736 - mortality + ultrasonography - MO + US - Q000451 + Q000662 - nursing + veterinary - NU + VE - Q000453 + Q000266 - epidemiology + history - EP + HI - Q000469 + Q000145 - parasitology + classification - PS + CL - Q000473 + Q000150 - pathology + complications - PA + CO - Q000503 + Q000175 - physiopathology + diagnosis - PP + DI - Q000517 + Q000191 - prevention & control + economics - PC + EC - Q000523 + Q000196 - psychology + embryology - PX + EM - Q000530 + Q000208 - radiography + ethnology - RA + EH - Q000531 + Q000235 - radionuclide imaging + genetics - RI + GE - Q000532 + Q000276 - radiotherapy + immunology - RT + IM - Q000534 + Q000378 - rehabilitation + metabolism - RH + ME - Q000601 + Q000382 - surgery + microbiology - SU + MI - Q000628 + Q000451 - therapy + nursing - TH + NU - Q000652 + Q000469 - urine + parasitology - UR + PS - Q000662 + Q000473 - veterinary + pathology - VE + PA - Q000736 + Q000532 - ultrasonography + radiotherapy - US + RT - Q000821 + Q000601 - virology + surgery - VI + SU general only; prefer /compl with specific type of diabetes + specific complication: Manual 23.25.3.1 @@ -12889,6 +12890,7 @@ 2014 + 2015 for all articles noted as resulting from extramural research at any NIH institute; CATALOG: do not use @@ -12977,6 +12979,7 @@ 2012 2013 2014 + 2015 not used for indexing or cataloging @@ -13088,106 +13091,107 @@ 2012 2013 2014 + 2015 - Q000145 + Q000364 - classification + manpower - CL + MA - Q000191 + Q000331 - economics + legislation & jurisprudence - EC + LJ - Q000266 + Q000941 - history + ethics - HI + ES - Q000331 + Q000706 - legislation & jurisprudence + statistics & numerical data - LJ + SN - Q000364 + Q000639 - manpower + trends - MA + TD - Q000379 + Q000266 - methods + history - MT + HI - Q000458 + Q000145 - organization & administration + classification - OG + CL - Q000592 + Q000191 - standards + economics - ST + EC - Q000639 + Q000379 - trends + methods - TD + MT - Q000706 + Q000458 - statistics & numerical data + organization & administration - SN + OG - Q000941 + Q000592 - ethics + standards - ES + ST 2012 diff --git a/samples/make-samples.pl b/samples/make-samples.pl index c2b908bd..d853f76b 100755 --- a/samples/make-samples.pl +++ b/samples/make-samples.pl @@ -20,6 +20,8 @@ my $meshrdf_home = $ENV{MESHRDF_HOME}; die "You must first define the environment variables MESHRDF_HOME." if !$meshrdf_home; +my $meshrdf_year = ($ENV{MESHRDF_YEAR} || 2015); + my @sets = qw( qual desc supp ); if (@ARGV) { @@ -75,7 +77,7 @@ foreach my $set (@sets) { my $set_data = $set_info{$set}; my $sample_list = $set_data->{sample_list}; - my $xml_file = "$meshrdf_home/data/$set" . "2014.xml"; + my $xml_file = "$meshrdf_home/data/$set" . "$meshrdf_year.xml"; my $sample_file = "$set-samples.xml"; my $state = 0; # init diff --git a/samples/qual-samples.xml b/samples/qual-samples.xml index a7e12ab2..c9e9583d 100644 --- a/samples/qual-samples.xml +++ b/samples/qual-samples.xml @@ -31,6 +31,7 @@ 2012 2013 2014 + 2015 subhead only; for routes of administration, timing, amounts of doses; not for "dosage" in Romance languages ( = /analysis) ; see MeSH scope note in Introduction; indexing policy: Manual 19.8.2; DF: /admin or /AD @@ -123,6 +124,7 @@ 2012 2013 2014 + 2015 subhead only; includes treatment or prevention by drugs & chemicals; includes therapy with antibiotics; not for immunotherapy nor for tissue therapy ( = /therapy); see MeSH scope note in Introduction; indexing policy: Manual 19.8.26; DF: /drug ther or /DT @@ -236,6 +238,7 @@ 2012 2013 2014 + 2015 subhead only; by physical trauma only; includes "wounds", "trauma"; for "lesion" in Romance languages; not for cell damage ( = /pathology); indexing policy: Manual 19.8.38; DF: /inj or /IN @@ -356,6 +359,7 @@ 2012 2013 2014 + 2015 subhead only; includes "legal", "laws", "government regulations","statutes", "ordinances", "medicolegal", "judicial", "juridical", "suits", "avoidance of suits", "litigation", "court decisions"; indexing policy: Manual 19.8.42; DF: /legis or /LJ @@ -809,6 +813,7 @@ 2012 2013 2014 + 2015 subhead only; with diseases & geographicals only; includes "incidence", "frequency", "prevalence", "occurrence", "outbreaks"; not for "mortality" ( = /mortality); not for "statistics" on non-disease terms ( = /statist); see MeSH scope note in Introduction; indexing policy: Manual 19.8.31; DF: /epidemiol or /EP CATALOG: may be subdivided geographically @@ -1164,6 +1169,7 @@ 2012 2013 2014 + 2015 subhead only; for treatment or preventive use of drugs or physical agents in clinical or experimental human or animal disease; indexing policy: Manual 19.8.71; DF: /ther use or /TU diff --git a/samples/sample-list.txt b/samples/sample-list.txt index 09f079ad..cf94156d 100755 --- a/samples/sample-list.txt +++ b/samples/sample-list.txt @@ -1,4 +1,4 @@ -# Samples 2014 MeSH records that span the three record types (Descriptor, Qualifier, SCR) and classes, +# Samples MeSH records that span the three record types (Descriptor, Qualifier, SCR) and classes, # such as Geographic, Publication Type, and Check tag for Descriptors; and Chemical, Protocol, and # Disease for SCRs diff --git a/samples/supp-samples.xml b/samples/supp-samples.xml index 695dcb1f..4976167b 100644 --- a/samples/supp-samples.xml +++ b/samples/supp-samples.xml @@ -18,8 +18,9 @@ 2013 2013A 2014 + 2015 - 10 + 13 @@ -196,6 +197,7 @@ 2012 2013 2014 + 2015 contains scopolamine camphorate mixture with (-)-atropine camphorate @@ -312,6 +314,7 @@ 2012 2013 2014 + 2015 chemotherapy protocol consisting of above cpds @@ -425,6 +428,7 @@ 2012 2013 2014 + 2015 mixture of derivs of 2-hydroxyethylrutoside @@ -492,30 +496,21 @@ - C017472 + C111106 - lonazolac + 7-methylguanosine 5'-diphosphate - 1979 - 01 - 01 + 1998 + 03 + 30 - 2009 - 11 + 2013 + 02 12 - 1989 - 1990 - 1991 - 1992 - 1993 - 1994 - 1995 - 1996 - 1997 1998 1999 2000 @@ -524,224 +519,137 @@ 2002 2003 2004 - 2004A 2005 2006 2007 - 2007A 2008 2009 2010 2011 2012 2013 + 2013A + 2013B 2014 + 2015 - RN given refers to parent cpd - - 33 - - ACETIC ACIDS (79-82) - + 18 - *D011720 + D006153 - Pyrazoles + Guanosine Diphosphate + + *Q000031 + + analogs & derivatives + + - D011448 + D012314 - Prostaglandin Antagonists + RNA Cap Analogs - - - - D000894 - - Anti-Inflammatory Agents, Non-Steroidal - - - - - Z Rheumatol 37(7-8):254;1978 + Cell 1997 Jun 13;89(6):951-61 - nlm - system - bears + vanlenb + benjersb + benjersb - M0068239 + M0287822 - lonazolac + 7-methylguanosine 5'-diphosphate - 53808-88-1 + 104809-16-7 - T109 - Organic Chemical - - - T121 - Pharmacologic Substance + T114 + Nucleic Acid, Nucleoside, or Nucleotide - - 75821-71-5 (Ca salt) - - M0068239 - M0313426 - - - M0068239 - M0463994 - - - M0068239 - M0068237 + M0287822 + M0068363 - T098242 - lonazolac + T317827 + 7-methylguanosine 5'-diphosphate - NLM (1979) + NLM (1998) - T098239 - 3-(4-chlorophenyl)-1-phenylpyrazole-4-acetic acid - - NLM (1979) - - - - - - M0313426 - - lonazolac calcium salt - - 75821-71-5 - - - T109 - Organic Chemical - - - T121 - Pharmacologic Substance - - - - - M0068239 - M0313426 - - - - - T343426 - lonazolac calcium salt + T837273 + m(7)GDP - 1999 - 08 - 18 + 2013 + 02 + 12 - NLM (1979) + NLM (2013) - - - - M0463994 - - Argun - - - - T109 - Organic Chemical - - - T121 - Pharmacologic Substance - - - - - M0068239 - M0463994 - - - - - T581962 - Argun - - 2004 - 04 - 08 - + + T317826 + 7-methyl-GDP - DE + NLM (1998) - T581963 - Merckle Brand of Lonazolac Calcium Salt + T835181 + 7-methylguanosine diphosphate - 2004 - 04 - 08 + 2013 + 01 + 04 - NLM (2004) + NLM (2013) - M0068237 + M0068363 - Irriten + RNA,delta messenger(7)GDP + 0 - T109 - Organic Chemical - - - T121 - Pharmacologic Substance + T114 + Nucleic Acid, Nucleoside, or Nucleotide - M0068239 - M0068237 + M0287822 + M0068363 - - T098240 - Irriten + + T098365 + RNA,delta messenger(7)GDP NLM (1979) @@ -751,196 +659,35 @@ - C111106 + C012211 - 7-methylguanosine 5'-diphosphate + ubenimex - 1998 - 03 - 30 + 1976 + 01 + 01 - 2013 - 02 - 12 + 2012 + 11 + 05 - 1998 - 1999 - 2000 - 2001 - 2001A - 2002 - 2003 - 2004 - 2005 - 2006 - 2007 - 2008 - 2009 - 2010 - 2011 - 2012 2013 - 2013A - 2013B 2014 + 2015 - 17 + growth inhibitor; RN given refers to ((L-Leu)-(S-(R*,S*)))-isomer; structure + + 750 + + DIPEPTIDES (76-79) + - D006153 - - Guanosine Diphosphate - - - - *Q000031 - - analogs & derivatives - - - - - - - - D012314 - - RNA Cap Analogs - - - - - - Cell 1997 Jun 13;89(6):951-61 - - - vanlenb - benjersb - benjersb - - - - M0287822 - - 7-methylguanosine 5'-diphosphate - - 104809-16-7 - - - T114 - Nucleic Acid, Nucleoside, or Nucleotide - - - - - M0287822 - M0068363 - - - - - T317827 - 7-methylguanosine 5'-diphosphate - - NLM (1998) - - - - T837273 - m(7)GDP - - 2013 - 02 - 12 - - - NLM (2013) - - - - T317826 - 7-methyl-GDP - - NLM (1998) - - - - T835181 - 7-methylguanosine diphosphate - - 2013 - 01 - 04 - - - NLM (2013) - - - - - - M0068363 - - RNA,delta messenger(7)GDP - - 0 - - - T114 - Nucleic Acid, Nucleoside, or Nucleotide - - - - - M0287822 - M0068363 - - - - - T098365 - RNA,delta messenger(7)GDP - - NLM (1979) - - - - - - - - C012211 - - ubenimex - - - 1976 - 01 - 01 - - - 2012 - 11 - 05 - - - 2013 - 2014 - - growth inhibitor; RN given refers to ((L-Leu)-(S-(R*,S*)))-isomer; structure - - 745 - - DIPEPTIDES (76-79) - - - - - D007930 + D007930 Leucine @@ -1399,6 +1146,7 @@ 2012 2013 2014 + 2015 1 @@ -1511,6 +1259,7 @@ 2012 2013 2014 + 2015 Russian drug, geriatric preparation @@ -1644,6 +1393,7 @@ 2012 2013 2014 + 2015 11 @@ -1889,6 +1639,7 @@ 2013 2014 + 2015 cpd is acetaminophen acetate @@ -1973,368 +1724,58 @@ - - C014792 + + C564178 - reproterol + Horner Syndrome, Congenital - 1977 - 01 - 01 - - 2012 11 05 + + + 2013 + 11 + 06 - 2013 2014 + 2015 - RN given refers to cpd without isomeric designation; structure - - 62 + 0 - D004338 - - Drug Combinations - - - - - - D009921 - - Metaproterenol - - - - *Q000031 - - analogs & derivatives - - - - - - D013806 + D006732 - Theophylline + Horner Syndrome - *Q000031 + *Q000151 - analogs & derivatives + congenital - - - - D000318 - - Adrenergic beta-Agonists - - - - - - D001993 - - Bronchodilator Agents - - - - - - Arzneim Forsch 28(1):765;1978 - Birth Defects 1979;15(4):541 - Curr Med Res Opin 1979;6(5):364 - Dtsch Med Wochenschr 102(16):619;1977 - Dtsch Med Wochenschr 104(29):1041;1979 - Med Welt 30(23):897;1979 - Respiration 1979;38(5):280 - - nlm + jarnotm system chodan - M0063597 + M0564478 - reproterol + Horner Syndrome, Congenital - 11941YC6RN + 0 - T109 - Organic Chemical - - - T121 - Pharmacologic Substance - - - - 13055-82-8 (mono-HCl) - 54063-54-6 (reproterol) - 62401-83-6 ((-)-isomer) - - - - M0063597 - M0312623 - - - M0063597 - M0063596 - - - M0063597 - M0312622 - - - M0063597 - M0475022 - - - - - T093600 - reproterol - - FDA SRS (2013) - INN (19XX) - USAN (1977) - - - - - - M0312623 - - reproterol, (-)-isomer - - 62401-83-6 - - - T109 - Organic Chemical - - - T121 - Pharmacologic Substance - - - - - M0063597 - M0312623 - - - - - T342623 - reproterol, (-)-isomer - - 1999 - 08 - 18 - - - NLM (1977) - - - - - - M0063596 - - Bronchospasmin - - - - T109 - Organic Chemical - - - T121 - Pharmacologic Substance - - - - - M0063597 - M0063596 - - - - - T093599 - Bronchospasmin - - DE - - - - T616841 - Viatris brand of reproterol monohydrochloride - - 2004 - 11 - 01 - - - NLM (2004) - - - - - - M0312622 - - reproterol monohydrochloride - - 13055-82-8 - - - T109 - Organic Chemical - - - T121 - Pharmacologic Substance - - - - - M0063597 - M0312622 - - - - - T342622 - reproterol monohydrochloride - - 1999 - 08 - 18 - - - NLM (1977) - - - - - - M0475022 - - Epiferol - - - - T109 - Organic Chemical - - - T121 - Pharmacologic Substance - - - - - M0063597 - M0475022 - - - - - T616842 - Epiferol - - 2004 - 11 - 01 - - - ES - - - - T616843 - Juventus brand of reproterol monohydrochloride - - 2004 - 11 - 01 - - - NLM (2004) - - - - - - - - C564178 - - Horner Syndrome, Congenital - - - 2012 - 11 - 05 - - - 2013 - 11 - 06 - - - 2014 - - 0 - - - - D006732 - - Horner Syndrome - - - - *Q000151 - - congenital - - - - - - jarnotm - system - chodan - - - - M0564478 - - Horner Syndrome, Congenital - - 0 - - - T047 - Disease or Syndrome + T047 + Disease or Syndrome @@ -2371,6 +1812,7 @@ 2014 + 2015 Familial Dandy-Walker malformation associated with macrocephaly, facial anomalies, developmental delay, and brain stem dysgenesis. @@ -2459,6 +1901,7 @@ 2014 + 2015 alkaloid from Fritillaria shuchengensis; structure in first source @@ -2528,6 +1971,7 @@ 2014 + 2015 1 @@ -2606,6 +2050,7 @@ 2014 + 2015 mutation in TYK2 @@ -2722,6 +2167,7 @@ 2014 + 2015 anti-inflammatory and cytotoxic sterol from Penicillium purpurogenum; structure in first source @@ -2785,13 +2231,14 @@ 01 - 2012 - 11 - 05 + 2014 + 10 + 27 2013 2014 + 2015 RN given refers to parent cpd(2S-(2alpha,5alpha,6beta(S*)))-isomer @@ -2836,7 +2283,7 @@ nlm - system + pashj chodan @@ -2900,18 +2347,18 @@ - T076567 - metampicillin + T076565 + 6-(2-methyleneamino-2-phenylacetamido)penicillanic acid - FDA SRS (2013) - INN (19XX) NLM (1970) - T076565 - 6-(2-methyleneamino-2-phenylacetamido)penicillanic acid + T076567 + metampicillin + FDA SRS (2013) + INN (19XX) NLM (1970) @@ -2952,18 +2399,6 @@ ES - - T613921 - Inexfa brand of methampicillin, sodium salt - - 2004 - 10 - 18 - - - NLM (2004) - - @@ -3119,18 +2554,6 @@ ES - - T613923 - Serra Pamies brand of methampicillin, sodium salt - - 2004 - 10 - 18 - - - NLM (2004) - - @@ -3204,4 +2627,558 @@ + + C014792 + + reproterol + + + 1977 + 01 + 01 + + + 2014 + 10 + 28 + + + 2013 + 2014 + 2015 + + RN given refers to cpd without isomeric designation; structure + + 62 + + + + D004338 + + Drug Combinations + + + + + + D009921 + + Metaproterenol + + + + *Q000031 + + analogs & derivatives + + + + + + D013806 + + Theophylline + + + + *Q000031 + + analogs & derivatives + + + + + + + + D000318 + + Adrenergic beta-Agonists + + + + + + D001993 + + Bronchodilator Agents + + + + + + Arzneim Forsch 28(1):765;1978 + Birth Defects 1979;15(4):541 + Curr Med Res Opin 1979;6(5):364 + Dtsch Med Wochenschr 102(16):619;1977 + Dtsch Med Wochenschr 104(29):1041;1979 + Med Welt 30(23):897;1979 + Respiration 1979;38(5):280 + + + nlm + pbutler + chodan + + + + M0063597 + + reproterol + + 11941YC6RN + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + 13055-82-8 (mono-HCl) + 54063-54-6 (reproterol) + 62401-83-6 ((-)-isomer) + + + + M0063597 + M0312623 + + + M0063597 + M0063596 + + + M0063597 + M0312622 + + + M0063597 + M0475022 + + + + + T093600 + reproterol + + FDA SRS (2013) + INN (19XX) + USAN (1977) + + + + + + M0312623 + + reproterol, (-)-isomer + + 62401-83-6 + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0063597 + M0312623 + + + + + T342623 + reproterol, (-)-isomer + + 1999 + 08 + 18 + + + NLM (1977) + + + + + + M0063596 + + Bronchospasmin + + 0 + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0063597 + M0063596 + + + + + T093599 + Bronchospasmin + + DE + + + + + + M0312622 + + reproterol monohydrochloride + + 13055-82-8 + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0063597 + M0312622 + + + + + T342622 + reproterol monohydrochloride + + 1999 + 08 + 18 + + + NLM (1977) + + + + + + M0475022 + + Epiferol + + 0 + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0063597 + M0475022 + + + + + T616842 + Epiferol + + 2004 + 11 + 01 + + + ES + + + + + + + + C017472 + + lonazolac + + + 1979 + 01 + 01 + + + 2014 + 11 + 02 + + + 1989 + 1990 + 1991 + 1992 + 1993 + 1994 + 1995 + 1996 + 1997 + 1998 + 1999 + 2000 + 2001 + 2001A + 2002 + 2003 + 2004 + 2004A + 2005 + 2006 + 2007 + 2007A + 2008 + 2009 + 2010 + 2011 + 2012 + 2013 + 2014 + 2015 + + RN given refers to parent cpd + + 33 + + ACETIC ACIDS (79-82) + + + + + *D011720 + + Pyrazoles + + + + + + + + D011448 + + Prostaglandin Antagonists + + + + + + + + D000894 + + Anti-Inflammatory Agents, Non-Steroidal + + + + + + Z Rheumatol 37(7-8):254;1978 + + + nlm + pashj + chodan + + + + M0068239 + + lonazolac + + 13097143QI + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + 53808-88-1 + 75821-71-5 (Ca salt) + + + + M0068239 + M0313426 + + + M0068239 + M0463994 + + + M0068239 + M0068237 + + + + + T098242 + lonazolac + + FDA SRS (2015) + INN (19XX) + NLM (1979) + USAN (19XX) + + + + T098239 + 3-(4-chlorophenyl)-1-phenylpyrazole-4-acetic acid + + NLM (1979) + + + + + + M0313426 + + lonazolac calcium salt + + 75821-71-5 + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0068239 + M0313426 + + + + + T343426 + lonazolac calcium salt + + 1999 + 08 + 18 + + + NLM (1979) + + + + + + M0463994 + + Argun + + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0068239 + M0463994 + + + + + T581962 + Argun + + 2004 + 04 + 08 + + + DE + + + + T581963 + Merckle Brand of Lonazolac Calcium Salt + + 2004 + 04 + 08 + + + NLM (2004) + + + + + + M0068237 + + Irriten + + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0068239 + M0068237 + + + + + T098240 + Irriten + + NLM (1979) + + + + + + From 34d47f94ab6e361daf6628bacf6dd139877bd2e7 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Thu, 21 May 2015 10:17:29 -0400 Subject: [PATCH 23/44] 2014 -> 2015 in convert-samples.sh --- samples/convert-samples.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/samples/convert-samples.sh b/samples/convert-samples.sh index 3cd4945a..3ecfd9b7 100755 --- a/samples/convert-samples.sh +++ b/samples/convert-samples.sh @@ -3,7 +3,7 @@ # in sample-list.txt. # Can override default year with MESHRDF_YEAR environment variable -YEAR=${MESHRDF_YEAR:-2014} +YEAR=${MESHRDF_YEAR:-2015} # Override the default Mesh prefix and output file by setting MESHRDF_URI_YEAR to "yes" if [ "$MESHRDF_URI_YEAR" = "yes" ]; then From dfa9c92a1a310e54dcfcc089881d5b4caf85f7e3 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Thu, 21 May 2015 10:55:59 -0400 Subject: [PATCH 24/44] issue 104 - language label updates --- xslt/common.xsl | 12 ++++++------ xslt/supp.xsl | 4 ++-- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/xslt/common.xsl b/xslt/common.xsl index e2ab09b7..6f96696b 100755 --- a/xslt/common.xsl +++ b/xslt/common.xsl @@ -347,7 +347,7 @@ previousIndexing - + @@ -621,7 +621,7 @@ casn1_label - + @@ -946,7 +946,7 @@ lexicalTag - + @@ -1037,7 +1037,7 @@ sortVersion - + @@ -1055,7 +1055,7 @@ entryVersion - + @@ -1073,7 +1073,7 @@ thesaurusID - + diff --git a/xslt/supp.xsl b/xslt/supp.xsl index 14516456..7fd27a04 100755 --- a/xslt/supp.xsl +++ b/xslt/supp.xsl @@ -90,7 +90,7 @@ note - + @@ -184,7 +184,7 @@ source - + From 67a02a0ae6393bc4f0d352ca54ebf5f56396d935 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Tue, 26 May 2015 12:43:47 -0400 Subject: [PATCH 25/44] Cosmetic: add comments about env. vars. --- bin/mesh-xml2rdf.sh | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index a120bdc9..da01cfce 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -3,7 +3,11 @@ # This script will convert all of the MeSH XML to RDF, assuming that your machine has # enough memory and resources. # -# +# It is parameterized according to the following environment variables: +# - MESHRDF_YEAR - default is "2015". Set this to override the *source* data. In other +# words, this is used to determine which XML files are used as input. +# - MESHRDF_URI_YEAR - no default. If this is set to "yes", then the generated URIs will +# include the year. if [ -z "$MESHRDF_HOME" ]; then echo "Please define MESHRDF_HOME environment variable" 1>&2 From a55093a28c7e77191932d9361bb354186ef327f7 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Tue, 26 May 2015 12:44:06 -0400 Subject: [PATCH 26/44] Issue #132 - fix encoding --- samples/desc-samples.xml | 766 ++++++++++++++++++++++++++++++++++----- samples/sample-list.txt | 1 + samples/supp-samples.xml | 2 +- xslt/desc.xsl | 2 +- xslt/qual.xsl | 2 +- xslt/supp.xsl | 2 +- 6 files changed, 690 insertions(+), 85 deletions(-) diff --git a/samples/desc-samples.xml b/samples/desc-samples.xml index 18ad0b96..57cbb2f5 100644 --- a/samples/desc-samples.xml +++ b/samples/desc-samples.xml @@ -718,246 +718,246 @@ - Q000627 + Q000032 - therapeutic use + analysis - TU + AN - Q000633 + Q000037 - toxicity + antagonists & inhibitors - TO + AI - Q000176 + Q000145 - diagnostic use + classification - DU + CL - Q000506 + Q000191 - poisoning + economics - PO + EC - Q000008 + Q000276 - administration & dosage + immunology - AD + IM - Q000009 + Q000302 - adverse effects + isolation & purification - AE + IP - Q000819 + Q000378 - agonists + metabolism - AG + ME - Q000097 + Q000494 - blood + pharmacology - BL + PD - Q000134 + Q000592 - cerebrospinal fluid + standards - CF + ST - Q000138 + Q000600 - chemical synthesis + supply & distribution - CS + SD - Q000744 + Q000493 - contraindications + pharmacokinetics - CT + PK - Q000737 + Q000627 - chemistry + therapeutic use - CH + TU - Q000652 + Q000633 - urine + toxicity - UR + TO - Q000528 + Q000176 - radiation effects + diagnostic use - RE + DU - Q000266 + Q000506 - history + poisoning - HI + PO - Q000031 + Q000008 - analogs & derivatives + administration & dosage - AA + AD - Q000032 + Q000009 - analysis + adverse effects - AN + AE - Q000037 + Q000819 - antagonists & inhibitors + agonists - AI + AG - Q000145 + Q000097 - classification + blood - CL + BL - Q000191 + Q000134 - economics + cerebrospinal fluid - EC + CF - Q000276 + Q000138 - immunology + chemical synthesis - IM + CS - Q000302 + Q000744 - isolation & purification + contraindications - IP + CT - Q000378 + Q000737 - metabolism + chemistry - ME + CH - Q000494 + Q000652 - pharmacology + urine - PD + UR - Q000592 + Q000528 - standards + radiation effects - ST + RE - Q000600 + Q000266 - supply & distribution + history - SD + HI - Q000493 + Q000031 - pharmacokinetics + analogs & derivatives - PK + AA 1965; for ACEPHEN use MECLOFENOXATE 1990-2002 @@ -5743,6 +5743,610 @@ + + D005840 + + Gentian Violet + + + 1999 + 01 + 01 + + + 2013 + 07 + 08 + + + 2014 + 2015 + + + + + Q000627 + + therapeutic use + + + TU + + + + Q000633 + + toxicity + + + TO + + + + Q000176 + + diagnostic use + + + DU + + + + Q000506 + + poisoning + + + PO + + + + Q000008 + + administration & dosage + + + AD + + + + Q000009 + + adverse effects + + + AE + + + + Q000819 + + agonists + + + AG + + + + Q000097 + + blood + + + BL + + + + Q000134 + + cerebrospinal fluid + + + CF + + + + Q000138 + + chemical synthesis + + + CS + + + + Q000744 + + contraindications + + + CT + + + + Q000737 + + chemistry + + + CH + + + + Q000652 + + urine + + + UR + + + + Q000528 + + radiation effects + + + RE + + + + Q000266 + + history + + + HI + + + + Q000032 + + analysis + + + AN + + + + Q000037 + + antagonists & inhibitors + + + AI + + + + Q000145 + + classification + + + CL + + + + Q000191 + + economics + + + EC + + + + Q000276 + + immunology + + + IM + + + + Q000302 + + isolation & purification + + + IP + + + + Q000378 + + metabolism + + + ME + + + + Q000494 + + pharmacology + + + PD + + + + Q000592 + + standards + + + ST + + + + Q000600 + + supply & distribution + + + SD + + + + Q000493 + + pharmacokinetics + + + PK + + + D25-26 qualif + + + + + D000891 + + Anti-Infective Agents, Local + + + + + + D02.092.146.400 + + + nlm + system + kilbourj + + + + M0009174 + + Gentian Violet + + Methanaminium, N-(4-(bis(4-(dimethylamino)phenyl)methylene)-2,5-cyclohexadien-1-ylidene)-N-methyl-, chloride + J4Z741D6O5 + A dye that is a mixture of violet rosanilinis with antibacterial, antifungal, and anthelmintic properties. + + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + T130 + Indicator, Reagent, or Diagnostic Aid + + + + 548-62-9 (Gentian Violet) + + + + M0009174 + M0474260 + + + M0009174 + M0474262 + + + M0009174 + M0351187 + + + M0009174 + M0474261 + + + + + T017674 + Gentian Violet + + 1999 + 01 + 01 + + + FDA SRS (2014) + USP (19XX) + + + + T017674 + Violet, Gentian + + + T017677 + Methylrosaniline Chloride + + 1974 + 03 + 30 + + + FDA SRS (2014) + UNK (19XX) + + + + T017677 + Chloride, Methylrosaniline + + + T017676 + Methyl Violet + + 1974 + 03 + 30 + + + UNK (19XX) + + + + T017676 + Violet, Methyl + + + T017673 + Crystal Violet + + 1974 + 03 + 30 + + + FDA SRS (2014) + UNK (19XX) + + + + T017673 + Violet, Crystal + + + T017675 + Hexamethylpararosaniline Chloride + + 1980 + 08 + 25 + + + UNK (19XX) + + + + T017675 + Chloride, Hexamethylpararosaniline + + + + + M0474260 + + Gentiaanviolet FNA + + 0 + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0009174 + M0474260 + + + + + T614213 + Gentiaanviolet FNA + + 2004 + 10 + 19 + + + NL + + + + T614213 + FNA, Gentiaanviolet + + + T614214 + FNA Brand of Gentian Violet + + 2004 + 10 + 19 + + + NLM (2006) + + + + + + M0474262 + + Vigencial + + 0 + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0009174 + M0474262 + + + + + T614217 + Vigencial + + 2004 + 10 + 19 + + + ES + + + + T614218 + Estedi Brand of Gentian Violet + + 2004 + 10 + 19 + + + NLM (2006) + + + + + + M0351187 + + C.I. 42555 + + 0 + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + T130 + Indicator, Reagent, or Diagnostic Aid + + + + + M0009174 + M0351187 + + + + + T017672 + C.I. 42555 + + 1980 + 08 + 25 + + + UNK (19XX) + + + + + + M0474261 + + Kristallviolett-Lösung + + 0 + + + T109 + Organic Chemical + + + T121 + Pharmacologic Substance + + + + + M0009174 + M0474261 + + + + + T614215 + Kristallviolett-Lösung + + 2004 + 10 + 19 + + + DE + + + + T614215 + Kristallviolett Lösung + + + T614216 + Dr. K. Hollborn Brand of Gentian Violet + + 2004 + 10 + 19 + + + NLM (2006) + + + + + + D005858 diff --git a/samples/sample-list.txt b/samples/sample-list.txt index cf94156d..6b528265 100755 --- a/samples/sample-list.txt +++ b/samples/sample-list.txt @@ -37,6 +37,7 @@ D005138 Eyebrows D005260 Female D005290 Ferric Compounds D005145 Face +D005840 Gentian Violet # has non-ascii characters in concept "Kristallviolett-Lšsung" D005858 Germany D006321 Heart D006732 Horner Syndrome diff --git a/samples/supp-samples.xml b/samples/supp-samples.xml index 4976167b..3f57173e 100644 --- a/samples/supp-samples.xml +++ b/samples/supp-samples.xml @@ -20,7 +20,7 @@ 2014 2015 - 13 + 14 diff --git a/xslt/desc.xsl b/xslt/desc.xsl index 816c3f0d..5d9c242c 100755 --- a/xslt/desc.xsl +++ b/xslt/desc.xsl @@ -12,7 +12,7 @@ xmlns:xsl="http://www.w3.org/1999/XSL/Transform"> - + diff --git a/xslt/qual.xsl b/xslt/qual.xsl index d7fe001d..9193c589 100755 --- a/xslt/qual.xsl +++ b/xslt/qual.xsl @@ -11,7 +11,7 @@ xmlns:xsl="http://www.w3.org/1999/XSL/Transform"> - + diff --git a/xslt/supp.xsl b/xslt/supp.xsl index 7fd27a04..e6f52468 100755 --- a/xslt/supp.xsl +++ b/xslt/supp.xsl @@ -12,7 +12,7 @@ xmlns:xsl="http://www.w3.org/1999/XSL/Transform"> - + From 19cacc68b35c5cb2123aba0e0a5d923afc201809 Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Tue, 26 May 2015 16:40:36 -0400 Subject: [PATCH 27/44] Convert vocabulary.owl to vocabulary.ttl with Protege 5.0.0-beta-17 --- meta/vocabulary.ttl | 76 +-------------------------------------------- 1 file changed, 1 insertion(+), 75 deletions(-) diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl index ed8fcd9d..fc04e1e5 100644 --- a/meta/vocabulary.ttl +++ b/meta/vocabulary.ttl @@ -39,18 +39,6 @@ -### http://id.nlm.nih.gov/mesh/vocab#allowedTreeNode - - rdf:type :ObjectProperty ; - - rdfs:label "allowedTreeNode" ; - - "Name of a subcategory in the MeSH Trees indicating, that for most Descriptors in that subcategory, the allowed Qualifiers on the Descriptor include the Qualifier. This value does not impact Descriptors permitted with a given Qualifier, but is a statistical summary of Descriptors permitted with the Qualifier." ; - - rdfs:range . - - - ### http://id.nlm.nih.gov/mesh/vocab#broader rdf:type :ObjectProperty . @@ -214,12 +202,6 @@ -### http://id.nlm.nih.gov/mesh/vocab#semanticType - - rdf:type :ObjectProperty . - - - ### http://id.nlm.nih.gov/mesh/vocab#term rdf:type :ObjectProperty . @@ -257,12 +239,6 @@ -### http://id.nlm.nih.gov/mesh/vocab#activeMeSHYear - - rdf:type :DatatypeProperty . - - - ### http://id.nlm.nih.gov/mesh/vocab#altLabel rdf:type :DatatypeProperty ; @@ -393,36 +369,12 @@ -### http://id.nlm.nih.gov/mesh/vocab#printFlag - - rdf:type :DatatypeProperty . - - - ### http://id.nlm.nih.gov/mesh/vocab#publicMeSHNote rdf:type :DatatypeProperty . -### http://id.nlm.nih.gov/mesh/vocab#recordAuthorizer - - rdf:type :DatatypeProperty . - - - -### http://id.nlm.nih.gov/mesh/vocab#recordMaintainer - - rdf:type :DatatypeProperty . - - - -### http://id.nlm.nih.gov/mesh/vocab#recordOriginator - - rdf:type :DatatypeProperty . - - - ### http://id.nlm.nih.gov/mesh/vocab#registryNumber rdf:type :DatatypeProperty . @@ -435,12 +387,6 @@ -### http://id.nlm.nih.gov/mesh/vocab#runningHead - - rdf:type :DatatypeProperty . - - - ### http://id.nlm.nih.gov/mesh/vocab#scopeNote rdf:type :DatatypeProperty . @@ -521,7 +467,6 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith , , , - , , , ; @@ -540,7 +485,6 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith , , - , , , ; @@ -558,7 +502,6 @@ rdfs:label rdf:type :DatatypeProperty . rdfs:subClassOf :Thing ; :disjointWith , - , , , ; @@ -616,8 +559,7 @@ rdfs:label rdf:type :DatatypeProperty . rdfs:subClassOf :Thing ; - :disjointWith , - , + :disjointWith , , ; @@ -666,22 +608,6 @@ rdfs:label rdf:type :DatatypeProperty . -### http://id.nlm.nih.gov/mesh/vocab#SemanticType - - rdf:type :Class ; - - rdfs:label "MeSH SemanticType" ; - - rdfs:subClassOf :Thing ; - - :disjointWith , - , - ; - - "A semantic type provides broad categorization for meshv:Concept classes, such as Disease or Syndrome, Medical Device, etc." . - - - ### http://id.nlm.nih.gov/mesh/vocab#SupplementaryConceptRecord rdf:type :Class ; From 896d54a7ce98ea16f55b11ce070fb1d75bf9d3b0 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Wed, 27 May 2015 14:49:37 -0400 Subject: [PATCH 28/44] Fixes #34 --- .gitignore | 1 - bin/mesh-xml2rdf.sh | 25 ++++------- xslt/common.xsl | 42 ++++++++++++------- xslt/desc.xsl | 16 +++---- ...xes.ent.template => mesh-rdf-prefixes.ent} | 3 +- xslt/qual.xsl | 9 +++- xslt/supp.xsl | 6 +-- 7 files changed, 55 insertions(+), 47 deletions(-) rename xslt/{mesh-rdf-prefixes.ent.template => mesh-rdf-prefixes.ent} (59%) diff --git a/.gitignore b/.gitignore index f7a5f4bf..a81a23c7 100755 --- a/.gitignore +++ b/.gitignore @@ -2,4 +2,3 @@ Saxon*.zip saxon9he data out -xslt/mesh-rdf-prefixes.ent diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index da01cfce..a067c17a 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -7,7 +7,8 @@ # - MESHRDF_YEAR - default is "2015". Set this to override the *source* data. In other # words, this is used to determine which XML files are used as input. # - MESHRDF_URI_YEAR - no default. If this is set to "yes", then the generated URIs will -# include the year. +# include the year, and the output file will be mesh.nt; otherwise, the URIs will +# not include the year, and the output file will be mesh.nt. if [ -z "$MESHRDF_HOME" ]; then echo "Please define MESHRDF_HOME environment variable" 1>&2 @@ -22,43 +23,35 @@ fi # Can override default year with MESHRDF_YEAR environment variable YEAR=${MESHRDF_YEAR:-2015} -# Override the default Mesh prefix and output file by setting MESHRDF_URI_YEAR to "yes" +# Set the output file name, and the parameter that controls the RDF URIs, +# according to whether or not MESHRDF_URI_YEAR is "yes" if [ "$MESHRDF_URI_YEAR" = "yes" ]; then - PREFIX=mesh/$YEAR OUT=mesh$YEAR + URI_YEAR_PARAM=uri-year-segment=$YEAR else - PREFIX=mesh OUT=mesh + URI_YEAR_PARAM= fi -#echo PREFIX = $PREFIX -#echo OUT = $OUT - -# substitute the prefix into the DTD entity file -sed -e "s,MESHRDF_PATH,$PREFIX,g" xslt/mesh-rdf-prefixes.ent.template > xslt/mesh-rdf-prefixes.ent -if [ $? -ne 0 ]; then - echo "Error creating xslt/mesh-rdf-prefixes.ent from template" 1>&2 - exit 1 -fi mkdir -p "$MESHRDF_HOME/out" java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/qual$YEAR.xml" \ - -xsl:xslt/qual.xsl > "$MESHRDF_HOME/out/$OUT-dups.nt" + -xsl:xslt/qual.xsl $URI_YEAR_PARAM > "$MESHRDF_HOME/out/$OUT-dups.nt" if [ $? -ne 0 ]; then echo "Error converting $MESHRDF_HOME/data/qual$YEAR.xml" 1>&2 exit 1 fi java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/desc$YEAR.xml" \ - -xsl:xslt/desc.xsl >> "$MESHRDF_HOME/out/$OUT-dups.nt" + -xsl:xslt/desc.xsl $URI_YEAR_PARAM >> "$MESHRDF_HOME/out/$OUT-dups.nt" if [ $? -ne 0 ]; then echo "Error converting $MESHRDF_HOME/data/desc$YEAR.xml" 1>&2 exit 1 fi java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/supp$YEAR.xml" \ - -xsl:xslt/supp.xsl >> "$MESHRDF_HOME/out/$OUT-dups.nt" + -xsl:xslt/supp.xsl $URI_YEAR_PARAM >> "$MESHRDF_HOME/out/$OUT-dups.nt" if [ $? -ne 0 ]; then echo "Error converting $MESHRDF_HOME/data/supp$YEAR.xml" 1>&2 exit 1 diff --git a/xslt/common.xsl b/xslt/common.xsl index 6f96696b..d49d3936 100755 --- a/xslt/common.xsl +++ b/xslt/common.xsl @@ -12,6 +12,18 @@ xmlns:xs="&xs;" exclude-result-prefixes="xs f"> + + + + + + + + + + + + - + diff --git a/xslt/desc.xsl b/xslt/desc.xsl index 5d9c242c..a1811c09 100755 --- a/xslt/desc.xsl +++ b/xslt/desc.xsl @@ -23,7 +23,7 @@ Transformation rule: meshv:identifier --> - + @@ -90,7 +90,7 @@ - + @@ -113,7 +113,7 @@ Create a DescriptorQualifierPair resource --> - + @@ -180,7 +180,7 @@ - + @@ -210,7 +210,7 @@ hasDescriptor - + @@ -226,7 +226,7 @@ hasQualifier - + @@ -242,7 +242,7 @@ useInstead - + @@ -263,7 +263,7 @@ seeAlso - + diff --git a/xslt/mesh-rdf-prefixes.ent.template b/xslt/mesh-rdf-prefixes.ent similarity index 59% rename from xslt/mesh-rdf-prefixes.ent.template rename to xslt/mesh-rdf-prefixes.ent index ed3e19a1..a8e17d8b 100755 --- a/xslt/mesh-rdf-prefixes.ent.template +++ b/xslt/mesh-rdf-prefixes.ent @@ -1,5 +1,4 @@ - - + diff --git a/xslt/qual.xsl b/xslt/qual.xsl index 9193c589..c483f38f 100755 --- a/xslt/qual.xsl +++ b/xslt/qual.xsl @@ -15,12 +15,17 @@ + + mesh-prefix = ' + + ' + - + @@ -102,7 +107,7 @@ allowedTreeNode - + diff --git a/xslt/supp.xsl b/xslt/supp.xsl index e6f52468..0e508937 100755 --- a/xslt/supp.xsl +++ b/xslt/supp.xsl @@ -19,7 +19,7 @@ - + @@ -139,7 +139,7 @@ - + indexerConsiderAlso - + From 065ecc568f15900dd70b088364bb24f56c42d1e4 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Wed, 27 May 2015 14:59:34 -0400 Subject: [PATCH 29/44] Fix mesh-xml2rdf.sh script to cd /Users/maloneyc/git/hhs/meshrdf --- bin/mesh-xml2rdf.sh | 1 + 1 file changed, 1 insertion(+) diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index a067c17a..898da3d4 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -14,6 +14,7 @@ if [ -z "$MESHRDF_HOME" ]; then echo "Please define MESHRDF_HOME environment variable" 1>&2 exit 1 fi +cd $MESHRDF_HOME if [ -z "$SAXON_JAR" ]; then echo "Please define SAXON_JAR environment variable" 1>&2 From 765588c23205476582a8e4ba23d8733967bfe172 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Wed, 27 May 2015 16:13:49 -0400 Subject: [PATCH 30/44] Add copying over of vocabulary and void files; directory structure to match FTP site --- bin/mesh-xml2rdf.sh | 40 ++++++++++++++++++++++++++-------------- 1 file changed, 26 insertions(+), 14 deletions(-) diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index 898da3d4..6467a320 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -1,14 +1,20 @@ #!/bin/sh # # This script will convert all of the MeSH XML to RDF, assuming that your machine has -# enough memory and resources. +# enough memory and resources. It will also copy over the vocabulary and void files. # # It is parameterized according to the following environment variables: # - MESHRDF_YEAR - default is "2015". Set this to override the *source* data. In other # words, this is used to determine which XML files are used as input. -# - MESHRDF_URI_YEAR - no default. If this is set to "yes", then the generated URIs will -# include the year, and the output file will be mesh.nt; otherwise, the URIs will -# not include the year, and the output file will be mesh.nt. +# - MESHRDF_URI_YEAR +# By default: +# - the generated URIs will not include the year, +# - the output file will be named mesh.nt, and +# - it will be put into the output directory $MESHRDF_HOME/out +# If this is set to "yes", then: +# - the generated URIs will include the year, +# - the output file will be have the name meshYYYY.nt, and +# - it will be put into the output directory $MESHRDF_HOME/out/YYYY if [ -z "$MESHRDF_HOME" ]; then echo "Please define MESHRDF_HOME environment variable" 1>&2 @@ -27,45 +33,51 @@ YEAR=${MESHRDF_YEAR:-2015} # Set the output file name, and the parameter that controls the RDF URIs, # according to whether or not MESHRDF_URI_YEAR is "yes" if [ "$MESHRDF_URI_YEAR" = "yes" ]; then - OUT=mesh$YEAR + OUTDIR=$MESHRDF_HOME/out/$YEAR + OUTFILE=$OUTDIR/mesh$YEAR URI_YEAR_PARAM=uri-year-segment=$YEAR else - OUT=mesh + OUTDIR=$MESHRDF_HOME/out + OUTFILE=$OUTDIR/mesh URI_YEAR_PARAM= fi -mkdir -p "$MESHRDF_HOME/out" +mkdir -p $OUTDIR java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/qual$YEAR.xml" \ - -xsl:xslt/qual.xsl $URI_YEAR_PARAM > "$MESHRDF_HOME/out/$OUT-dups.nt" + -xsl:xslt/qual.xsl $URI_YEAR_PARAM > "$OUTFILE-dups.nt" if [ $? -ne 0 ]; then echo "Error converting $MESHRDF_HOME/data/qual$YEAR.xml" 1>&2 exit 1 fi java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/desc$YEAR.xml" \ - -xsl:xslt/desc.xsl $URI_YEAR_PARAM >> "$MESHRDF_HOME/out/$OUT-dups.nt" + -xsl:xslt/desc.xsl $URI_YEAR_PARAM >> "$OUTFILE-dups.nt" if [ $? -ne 0 ]; then echo "Error converting $MESHRDF_HOME/data/desc$YEAR.xml" 1>&2 exit 1 fi java -Xmx4G -jar $SAXON_JAR -s:"$MESHRDF_HOME/data/supp$YEAR.xml" \ - -xsl:xslt/supp.xsl $URI_YEAR_PARAM >> "$MESHRDF_HOME/out/$OUT-dups.nt" + -xsl:xslt/supp.xsl $URI_YEAR_PARAM >> "$OUTFILE-dups.nt" if [ $? -ne 0 ]; then echo "Error converting $MESHRDF_HOME/data/supp$YEAR.xml" 1>&2 exit 1 fi -sort -u -T"$MESHRDF_HOME/out" "$MESHRDF_HOME/out/$OUT-dups.nt" > "$MESHRDF_HOME/out/$OUT.nt" +sort -u -T"$OUTDIR" "$OUTFILE-dups.nt" > "$OUTFILE.nt" if [ $? -ne 0 ]; then - echo "Error deduplicating $MESHRDF_HOME/out/$OUT-dups.nt" 1>&2 + echo "Error deduplicating $OUTFILE-dups.nt" 1>&2 exit 1 fi -gzip -c "$MESHRDF_HOME/out/$OUT.nt" > "$MESHRDF_HOME/out/$OUT.nt.gz" +gzip -c "$OUTFILE.nt" > "$OUTFILE.nt.gz" if [ $? -ne 0 ]; then - echo "Error compressing $MESHRDF_HOME/out/$OUT.nt" 1>&2 + echo "Error compressing $OUTFILE.nt" 1>&2 exit 1 fi + +cp $MESHRDF_HOME/meta/vocabulary.ttl $OUTDIR +cp $MESHRDF_HOME/meta/void.ttl $OUTDIR + From 590c4790efe6b1bfbcc9e60963d129414be43934 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Wed, 27 May 2015 16:14:55 -0400 Subject: [PATCH 31/44] Remove vocabulary.owl. .ttl file is now the master --- meta/vocabulary.owl | 762 -------------------------------------------- 1 file changed, 762 deletions(-) delete mode 100644 meta/vocabulary.owl diff --git a/meta/vocabulary.owl b/meta/vocabulary.owl deleted file mode 100644 index 0345edc2..00000000 --- a/meta/vocabulary.owl +++ /dev/null @@ -1,762 +0,0 @@ - - - - - - - -]> - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AllowedDescriptorQualifierPair - A combined MeSH descriptor and qualifier, where the pairing is allowed by MeSH rules. These URIs are a mash up of the descriptor and qualifier identifiers, such as D000236Q000235. - - - - AllowedDescriptorQualifierPair - MeSH AllowedDescriptorQualifierPair - - - - CheckTag - A special class of descriptor singled out because they are so frequently applied to biomedical literature. There are only 2 Descriptors that are members of the class meshv:CheckTag: D005260 (Male) and D008297 (Female). These two Descriptors do not have tree numbers. - - - - CheckTag - MeSH CheckTag - - - - Concept - MeSH concepts are smeanings. Many MeSH concepts contain synonymous terms. meshv:Concept identifiers begin with â€M’ such as M0000013 (Congenital Abnormalities). - - - - Concept - MeSH Concept - - - - Descriptor - MeSH Descriptors are a cluster of one or more concepts used to describe what a publication is about. meshv:Descriptor is the parent class of meshv:TopicalDescriptor, meshv:GeographicDescriptor, meshv:PublicationType, and meshv:CheckTag. - - - - Descriptor - MeSH Descriptor - - - - DescriptorQualifierPair - A combined MeSH descriptor and qualifier pair. Allowed pairs belong to the class meshv:AllowedDescriptorQualifierPair. Disallowed pairs belong to the class meshv:DisallowedDescriptorQualifierPair. - - - - DescriptorQualifierPair - MeSH DescriptorQualifierPair - - - - DisallowedDescriptorQualifierPair - A combined MeSH descriptor and qualifier where the pairing is not allowed by MeSH rules, such as Abdomen/radiography. - - - - DisallowedDescriptorQualifierPair - MeSH DisallowedDescriptorQualifierPair - - - - GeographicalDescriptor - A descriptor that references places or regions of the world, such as D001061 (Appalachian Region). - - - - GeographicalDescriptor - MeSH GeographicalDescriptor - - - - PublicationType - A special class of descriptor that describes what type of publication a resource is as opposed to what it is about. All MeSH Publication Types are in the V tree. - - - - PublicationType - MeSH PublicationType - - - - Qualifier - Also known as MeSH Subheadings, these provide context to the use of a MeSH Heading. - - - - Qualifier - MeSH Qualifier - - - - SCR_Chemical - These are chemicals, drugs, enzymes, vitamins, etc. - - - - SCR_Chemical - MeSH SCR Chemical - - - - SCR_Disease - SCR Diseases were originally brought into MeSH from a list maintained by the Office of Rare Diseases Research. - - - - SCR_Disease - MeSH SCR Disease - - - - SCR_Protocol - MeSH protocols are therapies in the domain of cancer treatment - - - - SCR_Protocol - MeSH SCR Protocol - - - - SupplementaryConceptRecord - Supplementary Concepts are created in MeSH to aid in searching the large volume of mainly chemicals and drugs. meshv:SupplementaryConceptRecord has three sub-classes: meshv:RegularSubstance, meshv:SCR_Protocol, and meshv:SCR_Disease. - - - - SupplementaryConceptRecord - MeSH SupplementaryConceptRecord - - - - Term - MeSH terms provide synonymous names for MeSH concepts. Terms have T identifiers, and are considered either preferred or lexical variants. - - - - Term - MeSH Term - - - - TopicalDescriptor - Topical Descriptors indicate the subject of an indexed item such as a journal article. See D063926 (Drug Hypersensitivity Syndrome) for an example. - - - - TopicalDescriptor - MeSH TopicalDescriptor - - - - TreeNumber - Tree Numbers are used to organize MeSH Descriptors in a broader-than/narrower-than manner. - - - - TreeNumber - MeSH TreeNumber - - - - abbreviation - abbreviation - - - - altLabel - alternative label - - - - altLabel - altLabel - - - - annotation - annotation - - - - casn1_label - casn1_label - - - - considerAlso - considerAlso - - - - dateCreated - dateCreated - - - - dateEstablished - dateEstablished - - - - dateRevised - dateRevised - - - - historyNote - historyNote - - - - identifier - identifier - - - - lexicalTag - lexicalTag - - - - note - note - - - - prefLabel - preferred label. - - - - prefLabel - prefLabel - - - - - - - From 7482bfbe47e642a478c4f04fc1c5adfde820c7e6 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Thu, 28 May 2015 14:27:04 -0400 Subject: [PATCH 32/44] Fix error with vocabulary URI prefix --- xslt/mesh-rdf-prefixes.ent | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/xslt/mesh-rdf-prefixes.ent b/xslt/mesh-rdf-prefixes.ent index a8e17d8b..d560fca5 100755 --- a/xslt/mesh-rdf-prefixes.ent +++ b/xslt/mesh-rdf-prefixes.ent @@ -1,4 +1,4 @@ - + From f1e4df487956635650800149d421c0417ae8e22c Mon Sep 17 00:00:00 2001 From: Steve Emrick Date: Thu, 28 May 2015 16:56:36 -0400 Subject: [PATCH 33/44] 5/28/2015 SPE Added class/predicate definitions Added meshv:parentTreeNumber Removed meshv:broaderTreeNumber Removed meshv:narrower --- meta/vocabulary.ttl | 267 ++++++++++++++++++++++++++++++-------------- 1 file changed, 184 insertions(+), 83 deletions(-) diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl index fc04e1e5..4239b3ca 100644 --- a/meta/vocabulary.ttl +++ b/meta/vocabulary.ttl @@ -9,11 +9,11 @@ rdf:type :Ontology . -################################################################# -# -# Annotation properties -# -################################################################# +################################################################# +# +# Annotation properties +# +################################################################# ### http://purl.org/dc/terms/description @@ -24,17 +24,19 @@ -################################################################# -# -# Object Properties -# -################################################################# +################################################################# +# +# Object Properties +# +################################################################# ### http://id.nlm.nih.gov/mesh/vocab#allowableQualifier rdf:type :ObjectProperty ; + "Relates Descriptors to Qualifiers. A specific Qualifier allowed in combination with the Descriptor." ; + rdfs:range . @@ -49,10 +51,12 @@ rdf:type :ObjectProperty ; - rdfs:range ; + "Relates 2 instances of the meshv:Concept class, one of which is broader than the other." ; rdfs:domain ; + rdfs:range ; + rdfs:subPropertyOf . @@ -61,6 +65,8 @@ rdf:type :ObjectProperty ; + "Relates 2 instances of the meshv:Descriptor class, one of which is broader than the other." ; + rdfs:domain ; rdfs:range ; @@ -81,22 +87,11 @@ -### http://id.nlm.nih.gov/mesh/vocab#broaderTreeNumber - - rdf:type :ObjectProperty , - :TransitiveProperty ; - - rdfs:domain ; - - rdfs:range ; - - rdfs:subPropertyOf . - - - ### http://id.nlm.nih.gov/mesh/vocab#concept - rdf:type :ObjectProperty . + rdf:type :ObjectProperty ; + + "Relates Descriptors, Qualifiers or SupplementaryConceptRecords to Concepts. Designates a member of a collection of Concepts for a Descriptor, Qualifier or SCR." . @@ -104,6 +99,8 @@ rdf:type :ObjectProperty ; + "Relates DescriptorQualifierPairs to Descriptors." ; + rdfs:range . @@ -112,19 +109,25 @@ rdf:type :ObjectProperty ; + "Relates DescriptorQualifierPairs to Qualifiers." ; + rdfs:range . ### http://id.nlm.nih.gov/mesh/vocab#indexerConsiderAlso - rdf:type :ObjectProperty . + rdf:type :ObjectProperty ; + + "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. A Descriptor or DescriptorQualifierPair that is usually broader than the SupplementaryConceptRecord, and which is suggested as an indexing guideline for addition to the citation if pertinent to the article being indexed." . ### http://id.nlm.nih.gov/mesh/vocab#mappedTo - rdf:type :ObjectProperty . + rdf:type :ObjectProperty ; + + "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. A Descriptor or DescriptorQualifierPair that is a parent (not the main parent; lacks an asterisk designation in the Source XML) for the SupplementaryConceptRecord and that is automatically added to the journal citation for which the SupplementaryConceptRecord is indexed. See also meshv:preferredMappedTo." . @@ -132,15 +135,32 @@ rdf:type :ObjectProperty ; + "Relates 2 instances the of meshv:Concept class, one of which is narrower than the other." ; + rdfs:domain ; rdfs:range . +### http://id.nlm.nih.gov/mesh/vocab#parentTreeNumber + + rdf:type :ObjectProperty , + :TransitiveProperty ; + + "Relates 2 instances of meshv:treeNumber classes, one of which is the immediate parent of the other." ; + + rdfs:range ; + + rdfs:domain . + + + ### http://id.nlm.nih.gov/mesh/vocab#pharmacologicalAction - rdf:type :ObjectProperty . + rdf:type :ObjectProperty ; + + "Relates Descriptors or SupplementaryConceptRecords to Descriptors. Reference to a Descriptor describing observed biological activity of an exogenously administered chemical represented by a Descriptor or SupplementaryConceptRecord." . @@ -148,6 +168,8 @@ rdf:type :ObjectProperty ; + "Relates Descriptors or Supplementary Concept Records to Concepts. The preferred concept is frequently a broader concept that includes narrower sub-concepts, but may also be one among several distinct concepts. The preferred concept is selected as the primary or most prominent representation among the concepts in the literature. meshv:preferredConcept is a subproperty of meshv:concept." ; + rdfs:subPropertyOf . @@ -156,6 +178,8 @@ rdf:type :ObjectProperty ; + "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. Designates a Descriptor or DescriptorQualifierPair that is a main parent (includes an asterisk designation in the Source XML) for the SupplementaryConceptRecord and that is automatically added to the journal citation for which the SupplementaryConceptRecord is indexed. meshv:preferredMappedTo is a subproperty of meshv:mappedTo." ; + rdfs:subPropertyOf . @@ -164,25 +188,27 @@ rdf:type :ObjectProperty ; + "Relates Concepts to Terms. The Term in this relationship expresses the most relevant name of the Concept. meshv:preferredTerm is a subproperty of meshv:term." ; + rdfs:subPropertyOf . ### http://id.nlm.nih.gov/mesh/vocab#previousIndexing - rdf:type :ObjectProperty . + rdf:type :ObjectProperty ; + + rdfs:label "previousIndexing" ; + + "A property of Descriptors and Supplementary Concept Records. Free-text information referring to Descriptors or DescriptorQualifierPairs that were used to index the concept in MEDLINE before the Descriptor was created. Intended to enable users of new Descriptors to find similar concepts indexed before the Descriptor was created. Includes a date or date range. May include descriptive text referring to a group of Descriptors as “specifics”. Data are not maintained when a Descriptor or Qualifier name changes. DUI D005290 example: Iron (1966-1974). Also used for SupplementaryConceptRecords to refer to the Descriptor or DescriptorQualifierPair to which the SupplementaryConceptRecord was previously mapped." . ### http://id.nlm.nih.gov/mesh/vocab#recordPreferredTerm - rdf:type :ObjectProperty . - - - -### http://id.nlm.nih.gov/mesh/vocab#related - - rdf:type :ObjectProperty . + rdf:type :ObjectProperty ; + + "Relates Descriptors, Qualifiers or SupplementaryConceptRecords to Terms. Indicates that the Term is the preferred term for a Descriptor, Qualifier, or SupplementaryConceptRecord." . @@ -190,6 +216,8 @@ rdf:type :ObjectProperty ; + "Relates one Concept to another. A semantic relationship between two Concepts, usually between the preferred Concept and subordinate Concept(s) where one is neither broader nor narrower in meaning." ; + rdfs:range ; rdfs:domain . @@ -198,13 +226,17 @@ ### http://id.nlm.nih.gov/mesh/vocab#seeAlso - rdf:type :ObjectProperty . + rdf:type :ObjectProperty ; + + "Relates one Descriptor to another. Reference to a specific Descriptor to which a user is referred by a 'see related' cross-reference." . ### http://id.nlm.nih.gov/mesh/vocab#term - rdf:type :ObjectProperty . + rdf:type :ObjectProperty ; + + "Relates Concepts to Terms. Each Concept has a set of entry terms and a preferred term that are related to the Concept." . @@ -212,30 +244,36 @@ rdf:type :ObjectProperty ; + "Relates Descriptors or Qualifiers to TreeNumbers. Alpha-numeric string referring to location within a Descriptor or Qualifier hierarchy. Used for browsing the MeSH vocabulary and for inclusive searches by retrieval systems using MeSH. (Note that the Trees hierarchy is not represented using subelements. The hierarchy is represented by the TreeNumber itself.) Up to thirteen hierarchical levels." ; + rdfs:range . ### http://id.nlm.nih.gov/mesh/vocab#useInstead - rdf:type :ObjectProperty . + rdf:type :ObjectProperty ; + + "Relates DisallowedDescriptorQualifierPairs to Descriptors or AllowedDescriptorQualifierPairs. Descriptor or DescriptorQualifierPair recommended in place of the prohibited combination." . -################################################################# -# -# Data properties -# -################################################################# +################################################################# +# +# Data properties +# +################################################################# ### http://id.nlm.nih.gov/mesh/vocab#abbreviation rdf:type :DatatypeProperty ; - rdfs:label "abbreviation" . + rdfs:label "abbreviation" ; + + "A property of Terms. Two-letter, uppercase abbreviation for a Qualifier term." . @@ -245,7 +283,7 @@ rdfs:label "altLabel" ; - "alternative label" ; + "A property of Terms. A lexical variant for a Term’s prefLabel. meshv:altLabel is a subproperty of rdfs:label" ; :propertyDisjointWith ; @@ -257,7 +295,9 @@ rdf:type :DatatypeProperty ; - rdfs:label "annotation" . + rdfs:label "annotation" ; + + "A property of Descriptors or Qualifiers. Free-text information for indexers and catalogers concerning the use of the Descriptor or Qualifier." . @@ -265,7 +305,9 @@ rdf:type :DatatypeProperty ; - rdfs:label "casn1_label" . + rdfs:label "casn1_label" ; + + "A property of Concepts. Free-text of the Chemical Abstracts Type N1 Name which is the systematic name used in the Chemical Abstracts Chemical Substance and Formula Indexes. The systematic name is a unique name assigned to a chemical substance to represent its structure. First available in 1995." . @@ -273,7 +315,9 @@ rdf:type :DatatypeProperty ; - rdfs:label "considerAlso" . + rdfs:label "considerAlso" ; + + "A property of Descriptors. Free-text information that refers a user from a Descriptor to other terms which have related roots." . @@ -281,7 +325,9 @@ rdf:type :DatatypeProperty ; - rdfs:label "dateCreated" . + rdfs:label "dateCreated" ; + + "A property of Descriptors, Qualifiers, SupplementaryConceptRecords or Terms. Date in YYYY-MM-DD format when a Descriptor, Qualifer, SupplementaryConceptRecord or Term was first added to MeSH provisionally. This timestamp may be a year behind the dateEstablished. Upon conversion to a new MeSH maintenance system in 1999, a default value of 1999-01-01 was supplied." . @@ -289,7 +335,9 @@ rdf:type :DatatypeProperty ; - rdfs:label "dateEstablished" . + rdfs:label "dateEstablished" ; + + "A property of Descriptors or Qualifiers. Date in YYYY-MM-DD format when the Descriptor or Qualifier became effective for use; set to YYYY-01-01 where YYYY = year of introduction to MeSH." . @@ -297,19 +345,29 @@ rdf:type :DatatypeProperty ; - rdfs:label "dateRevised" . + rdfs:label "dateRevised" ; + + "A property of Descriptors, Qualifiers, or SupplementaryConceptRecords. Indicates that a revision was made to Descriptor, Qualifier, or SupplementaryConceptRecord data in YYYY-MM-DD format." . ### http://id.nlm.nih.gov/mesh/vocab#entryVersion - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "entryVersion" ; + + "A property of Terms. Used for internal NLM processing only." . ### http://id.nlm.nih.gov/mesh/vocab#frequency - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "frequency" ; + + "A property of SupplementaryConceptRecords. Number of citations indexed with a SupplementaryConceptRecord in MEDLINE/PubMed. Automatically updated monthly in the XML. See also meshv:source definition." . @@ -317,7 +375,9 @@ rdf:type :DatatypeProperty ; - rdfs:label "historyNote" . + rdfs:label "historyNote" ; + + "A property of Descriptors or Qualifiers. Free-text information that traces the concept in MeSH and is deemed helpful for the online searcher. Headings and entry terms are entered in upper case. Initial characters refer to the year in which the Descriptor or Qualifier was created in MeSH in its current form (i.e., with the same preferred term). A date in parentheses indicates the oldest creation date of terms, provisional headings (before 1975), or minor headings (before 1991), which are reflected in bibliographic citations. Entries without a year date were created between 1963 and 1966." . @@ -325,7 +385,9 @@ rdf:type :DatatypeProperty ; - rdfs:label "identifier" . + rdfs:label "identifier" ; + + "A property of Descriptors, Qualifiers, SupplementaryConceptRecords, Concepts, Terms and SemanticTypes. Descriptor identifier is a 7 or 10 alphanumeric starting with the letter D. Qualifier identifier is a 7 or 10 alphanumeric starting with the letter Q. SupplementaryConceptRecord identifier is a 7 or 10 alphanumeric starting with the letter C. Concept identifier is an 8 or 10 alphanumeric starting with the letter M. Term identifier is a 7 or 10 alphanumeric starting with the letter T. The 10 alphanumeric format was implemented for new identifiers created on or after about May 19, 2014." . @@ -333,7 +395,9 @@ rdf:type :DatatypeProperty ; - rdfs:label "lexicalTag" . + rdfs:label "lexicalTag" ; + + "A property of Terms. A 3-letter value that indicates the lexical category. Valid values with their meanings in parentheses are: ABB (Abbreviation); ABX (Embedded abbreviation); ACR (Acronym); ACX (Embedded acronym); EPO (Eponym); LAB (Lab number); NAM (Proper name); NON (None); and TRD (Trade name). Note that in the XML, a Permuted Term will always have the same Lexical Tag value as the term from which it is generated." . @@ -341,13 +405,19 @@ rdf:type :DatatypeProperty ; - rdfs:label "note" . + rdfs:label "note" ; + + "A property of SupplementaryConceptRecords. Free-text narrative giving information about the SupplementaryConceptRecord, and may include information such as the registryNumber." . ### http://id.nlm.nih.gov/mesh/vocab#onlineNote - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "onlineNote" ; + + "A property of Descriptors and Qualifiers. Free-text information intended to direct the MeSH online searcher to alternate search terms. Superseded by a more detailed historyNote when onlineNote is not present." . @@ -357,7 +427,7 @@ rdfs:label "prefLabel" ; - "preferred label." ; + "A property of Terms. The preferred string for the term. meshv:prefLabel is a subproperty of rdfs:label." ; rdfs:subPropertyOf rdfs:label . @@ -365,49 +435,80 @@ ### http://id.nlm.nih.gov/mesh/vocab#previousIndexing - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "previousIndexing" ; + + "A property of Descriptors and Supplementary Concept Records. Free-text information referring to Descriptors or DescriptorQualifierPairs that were used to index the concept in MEDLINE before the Descriptor was created. Intended to enable users of new Descriptors to find similar concepts indexed before the Descriptor was created. Includes a date or date range. May include descriptive text referring to a group of Descriptors as “specifics”. Data are not maintained when a Descriptor or Qualifier name changes. DUI D005290 example: Iron (1966-1974). Also used for SupplementaryConceptRecords to refer to the Descriptor or DescriptorQualifierPair to which the SupplementaryConceptRecord was previously mapped." . ### http://id.nlm.nih.gov/mesh/vocab#publicMeSHNote - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "publicMeSHNote" ; + + "A property of Descriptors. Free-text information about the history of changes to the Descriptor that may be helpful to the user of the printed Index Medicus publication (ceased in 2005). This includes the date the Descriptor was created in MeSH, changes in the preferred term, earlier status as an SupplementaryConceptRecord, etc. Unlike the History Note, this note reflects the MeSH vocabulary printed at that point in time, not as updated for online databases. Applies only to TopicalDescriptors. MeSH Descriptor labels are in upper case." . ### http://id.nlm.nih.gov/mesh/vocab#registryNumber - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "registryNumber" ; + + "A property of Concepts. A unique identifier from one of these sources: Enzyme Commission (Example: EC 2.4.2.17; Example for Partial enzyme number: EC 1.4.3.-); Chemical Abstracts Service (CAS) (Example: 7004-12-8); FDA Substance Registration System Unique Identifier (UNII) in 10-character format (Example: R16CO5Y76E); or the value of 0 if no match is available from the previous sources. A single MeSH Concept can only have one Registry Number. Used for Concepts related to Descriptors in the D Category Drugs and Chemicals and for SupplementaryConceptRecords." . ### http://id.nlm.nih.gov/mesh/vocab#relatedRegistryNumber - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "relatedRegistryNumber" ; + + "A property of Concepts. An additional unique identifier for chemicals, which is sometimes followed by a label in parentheses. Multiple Related Registry Numbers are allowed for each Concept. For example, these might be salts and/or stereoisomers of the parent compound. Used for Concepts related to Descriptors in the D Category Drugs and Chemicals and for SupplementaryConceptRecords." . ### http://id.nlm.nih.gov/mesh/vocab#scopeNote - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "scopeNote" ; + + "A property of Concepts. Free-text narrative giving the scope and meaning (definition) of a Concept." . ### http://id.nlm.nih.gov/mesh/vocab#sortVersion - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "sortVersion" ; + + "A property of Terms. Custom version of a Term label used to sort properly in a print product; format is all uppercase." . ### http://id.nlm.nih.gov/mesh/vocab#source - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "source" ; + + "A property of SupplementaryConceptRecords. Citation reference string in which the SupplementaryConceptRecord was first found. Single occurrence if SupplementaryConceptRecord created since 1980; frequency reports total citations indexed with the term in MEDLINE/PubMed. Possible multiple occurrences if SupplementaryConceptRecord created prior to 1980; term not found on those citations in MEDLINE/PubMed. Number of multiple Source occurrences need to be added to Frequency count for grand total of citations to articles discussing the SCR." . ### http://id.nlm.nih.gov/mesh/vocab#thesaurusID - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + "thesaurusID" , + "A property of Terms. Name of a Thesaurus in which the term occurs. The value 'NLM' is equivalent to MeSH." . @@ -419,11 +520,11 @@ rdfs:label rdf:type :DatatypeProperty . -################################################################# -# -# Classes -# -################################################################# +################################################################# +# +# Classes +# +################################################################# ### http://id.nlm.nih.gov/mesh/vocab#AllowedDescriptorQualifierPair @@ -471,7 +572,7 @@ rdfs:label rdf:type :DatatypeProperty . , ; - "MeSH concepts are smeanings. Many MeSH concepts contain synonymous terms. meshv:Concept identifiers begin with â€M’ such as M0000013 (Congenital Abnormalities)." . + "MeSH concepts are meanings. Many MeSH concepts contain synonymous terms. meshv:Concept identifiers begin with 'M' such as M0000013, 'Congenital Abnormalities'." . @@ -506,7 +607,7 @@ rdfs:label rdf:type :DatatypeProperty . , ; - "A combined MeSH descriptor and qualifier pair. Allowed pairs belong to the class meshv:AllowedDescriptorQualifierPair. Disallowed pairs belong to the class meshv:DisallowedDescriptorQualifierPair." . + "A combined MeSH descriptor and qualifier pair. Allowed pairs (according to MeSH rules) belong to the class meshv:AllowedDescriptorQualifierPair. Disallowed pairs belong to the class meshv:DisallowedDescriptorQualifierPair." . @@ -533,7 +634,7 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith , ; - "A descriptor that references places or regions of the world, such as D001061 (Appalachian Region)." . + "A descriptor that references places or regions of the world, such as D001061, 'Appalachian Region'." . @@ -547,7 +648,7 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith ; - "A special class of descriptor that describes what type of publication a resource is as opposed to what it is about. All MeSH Publication Types are in the V tree." . + "A special class of descriptor that describes what type of publication a resource is as opposed to what it is about. All MeSH Publication Types are in the V tree." . @@ -563,7 +664,7 @@ rdfs:label rdf:type :DatatypeProperty . , ; - "Also known as MeSH Subheadings, these provide context to the use of a MeSH Heading." . + "Also known as Subheadings, these provide context to the use of a MeSH Heading." . @@ -604,7 +705,7 @@ rdfs:label rdf:type :DatatypeProperty . rdfs:subClassOf ; - "MeSH protocols are therapies in the domain of cancer treatment" . + "MeSH protocols are therapies in the domain of cancer treatment." . @@ -633,7 +734,7 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith ; - "MeSH terms provide synonymous names for MeSH concepts. Terms have T identifiers, and are considered either preferred or lexical variants." . + "MeSH terms provide synonymous names for MeSH concepts. Terms have 'T' identifiers, and are considered either preferred or lexical variants, such as 'Congenital Abnormalities' as opposed to 'Abnormality, Congenital'." . @@ -645,7 +746,7 @@ rdfs:label rdf:type :DatatypeProperty . rdfs:subClassOf ; - "Topical Descriptors indicate the subject of an indexed item such as a journal article. See D063926 (Drug Hypersensitivity Syndrome) for an example." . + "Topical Descriptors indicate the subject of an indexed item such as a journal article. See D063926, 'Drug Hypersensitivity Syndrome', for an example." . @@ -667,6 +768,6 @@ rdfs:label rdf:type :DatatypeProperty . - -### Generated by the OWL API (version 3.5.1) http://owlapi.sourceforge.net + +### Generated by the OWL API (version 3.5.0) http://owlapi.sourceforge.net From c8d317e4b3351896d5651eb90d89695da1ecb18c Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Thu, 28 May 2015 17:13:34 -0400 Subject: [PATCH 34/44] add 'dct' prefix --- meta/vocabulary.ttl | 156 +++++++++++++++++++++++--------------------- 1 file changed, 82 insertions(+), 74 deletions(-) diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl index 4239b3ca..300e8e69 100644 --- a/meta/vocabulary.ttl +++ b/meta/vocabulary.ttl @@ -1,4 +1,5 @@ @prefix : . +@prefix dct: . @prefix owl: . @prefix rdf: . @prefix xml: . @@ -18,7 +19,7 @@ ### http://purl.org/dc/terms/description - rdf:type :AnnotationProperty . +dct:description rdf:type :AnnotationProperty . @@ -35,7 +36,7 @@ rdf:type :ObjectProperty ; - "Relates Descriptors to Qualifiers. A specific Qualifier allowed in combination with the Descriptor." ; + dct:description "Relates Descriptors to Qualifiers. A specific Qualifier allowed in combination with the Descriptor." ; rdfs:range . @@ -51,12 +52,12 @@ rdf:type :ObjectProperty ; - "Relates 2 instances of the meshv:Concept class, one of which is broader than the other." ; - - rdfs:domain ; + dct:description "Relates 2 instances of the meshv:Concept class, one of which is broader than the other." ; rdfs:range ; + rdfs:domain ; + rdfs:subPropertyOf . @@ -65,7 +66,7 @@ rdf:type :ObjectProperty ; - "Relates 2 instances of the meshv:Descriptor class, one of which is broader than the other." ; + dct:description "Relates 2 instances of the meshv:Descriptor class, one of which is broader than the other." ; rdfs:domain ; @@ -91,7 +92,7 @@ rdf:type :ObjectProperty ; - "Relates Descriptors, Qualifiers or SupplementaryConceptRecords to Concepts. Designates a member of a collection of Concepts for a Descriptor, Qualifier or SCR." . + dct:description "Relates Descriptors, Qualifiers or SupplementaryConceptRecords to Concepts. Designates a member of a collection of Concepts for a Descriptor, Qualifier or SCR." . @@ -99,7 +100,7 @@ rdf:type :ObjectProperty ; - "Relates DescriptorQualifierPairs to Descriptors." ; + dct:description "Relates DescriptorQualifierPairs to Descriptors." ; rdfs:range . @@ -109,7 +110,7 @@ rdf:type :ObjectProperty ; - "Relates DescriptorQualifierPairs to Qualifiers." ; + dct:description "Relates DescriptorQualifierPairs to Qualifiers." ; rdfs:range . @@ -119,7 +120,7 @@ rdf:type :ObjectProperty ; - "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. A Descriptor or DescriptorQualifierPair that is usually broader than the SupplementaryConceptRecord, and which is suggested as an indexing guideline for addition to the citation if pertinent to the article being indexed." . + dct:description "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. A Descriptor or DescriptorQualifierPair that is usually broader than the SupplementaryConceptRecord, and which is suggested as an indexing guideline for addition to the citation if pertinent to the article being indexed." . @@ -127,7 +128,7 @@ rdf:type :ObjectProperty ; - "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. A Descriptor or DescriptorQualifierPair that is a parent (not the main parent; lacks an asterisk designation in the Source XML) for the SupplementaryConceptRecord and that is automatically added to the journal citation for which the SupplementaryConceptRecord is indexed. See also meshv:preferredMappedTo." . + dct:description "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. A Descriptor or DescriptorQualifierPair that is a parent (not the main parent; lacks an asterisk designation in the Source XML) for the SupplementaryConceptRecord and that is automatically added to the journal citation for which the SupplementaryConceptRecord is indexed. See also meshv:preferredMappedTo." . @@ -135,7 +136,7 @@ rdf:type :ObjectProperty ; - "Relates 2 instances the of meshv:Concept class, one of which is narrower than the other." ; + dct:description "Relates 2 instances the of meshv:Concept class, one of which is narrower than the other." ; rdfs:domain ; @@ -148,7 +149,7 @@ rdf:type :ObjectProperty , :TransitiveProperty ; - "Relates 2 instances of meshv:treeNumber classes, one of which is the immediate parent of the other." ; + dct:description "Relates 2 instances of meshv:treeNumber classes, one of which is the immediate parent of the other." ; rdfs:range ; @@ -160,7 +161,7 @@ rdf:type :ObjectProperty ; - "Relates Descriptors or SupplementaryConceptRecords to Descriptors. Reference to a Descriptor describing observed biological activity of an exogenously administered chemical represented by a Descriptor or SupplementaryConceptRecord." . + dct:description "Relates Descriptors or SupplementaryConceptRecords to Descriptors. Reference to a Descriptor describing observed biological activity of an exogenously administered chemical represented by a Descriptor or SupplementaryConceptRecord." . @@ -168,7 +169,7 @@ rdf:type :ObjectProperty ; - "Relates Descriptors or Supplementary Concept Records to Concepts. The preferred concept is frequently a broader concept that includes narrower sub-concepts, but may also be one among several distinct concepts. The preferred concept is selected as the primary or most prominent representation among the concepts in the literature. meshv:preferredConcept is a subproperty of meshv:concept." ; + dct:description "Relates Descriptors or Supplementary Concept Records to Concepts. The preferred concept is frequently a broader concept that includes narrower sub-concepts, but may also be one among several distinct concepts. The preferred concept is selected as the primary or most prominent representation among the concepts in the literature. meshv:preferredConcept is a subproperty of meshv:concept." ; rdfs:subPropertyOf . @@ -178,7 +179,7 @@ rdf:type :ObjectProperty ; - "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. Designates a Descriptor or DescriptorQualifierPair that is a main parent (includes an asterisk designation in the Source XML) for the SupplementaryConceptRecord and that is automatically added to the journal citation for which the SupplementaryConceptRecord is indexed. meshv:preferredMappedTo is a subproperty of meshv:mappedTo." ; + dct:description "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. Designates a Descriptor or DescriptorQualifierPair that is a main parent (includes an asterisk designation in the Source XML) for the SupplementaryConceptRecord and that is automatically added to the journal citation for which the SupplementaryConceptRecord is indexed. meshv:preferredMappedTo is a subproperty of meshv:mappedTo." ; rdfs:subPropertyOf . @@ -188,7 +189,7 @@ rdf:type :ObjectProperty ; - "Relates Concepts to Terms. The Term in this relationship expresses the most relevant name of the Concept. meshv:preferredTerm is a subproperty of meshv:term." ; + dct:description "Relates Concepts to Terms. The Term in this relationship expresses the most relevant name of the Concept. meshv:preferredTerm is a subproperty of meshv:term." ; rdfs:subPropertyOf . @@ -196,11 +197,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#previousIndexing - rdf:type :ObjectProperty ; - - rdfs:label "previousIndexing" ; - - "A property of Descriptors and Supplementary Concept Records. Free-text information referring to Descriptors or DescriptorQualifierPairs that were used to index the concept in MEDLINE before the Descriptor was created. Intended to enable users of new Descriptors to find similar concepts indexed before the Descriptor was created. Includes a date or date range. May include descriptive text referring to a group of Descriptors as “specifics”. Data are not maintained when a Descriptor or Qualifier name changes. DUI D005290 example: Iron (1966-1974). Also used for SupplementaryConceptRecords to refer to the Descriptor or DescriptorQualifierPair to which the SupplementaryConceptRecord was previously mapped." . + rdf:type :ObjectProperty . @@ -208,7 +205,7 @@ rdf:type :ObjectProperty ; - "Relates Descriptors, Qualifiers or SupplementaryConceptRecords to Terms. Indicates that the Term is the preferred term for a Descriptor, Qualifier, or SupplementaryConceptRecord." . + dct:description "Relates Descriptors, Qualifiers or SupplementaryConceptRecords to Terms. Indicates that the Term is the preferred term for a Descriptor, Qualifier, or SupplementaryConceptRecord." . @@ -216,7 +213,7 @@ rdf:type :ObjectProperty ; - "Relates one Concept to another. A semantic relationship between two Concepts, usually between the preferred Concept and subordinate Concept(s) where one is neither broader nor narrower in meaning." ; + dct:description "Relates one Concept to another. A semantic relationship between two Concepts, usually between the preferred Concept and subordinate Concept(s) where one is neither broader nor narrower in meaning." ; rdfs:range ; @@ -228,7 +225,7 @@ rdf:type :ObjectProperty ; - "Relates one Descriptor to another. Reference to a specific Descriptor to which a user is referred by a 'see related' cross-reference." . + dct:description "Relates one Descriptor to another. Reference to a specific Descriptor to which a user is referred by a 'see related' cross-reference." . @@ -236,7 +233,7 @@ rdf:type :ObjectProperty ; - "Relates Concepts to Terms. Each Concept has a set of entry terms and a preferred term that are related to the Concept." . + dct:description "Relates Concepts to Terms. Each Concept has a set of entry terms and a preferred term that are related to the Concept." . @@ -244,7 +241,7 @@ rdf:type :ObjectProperty ; - "Relates Descriptors or Qualifiers to TreeNumbers. Alpha-numeric string referring to location within a Descriptor or Qualifier hierarchy. Used for browsing the MeSH vocabulary and for inclusive searches by retrieval systems using MeSH. (Note that the Trees hierarchy is not represented using subelements. The hierarchy is represented by the TreeNumber itself.) Up to thirteen hierarchical levels." ; + dct:description "Relates Descriptors or Qualifiers to TreeNumbers. Alpha-numeric string referring to location within a Descriptor or Qualifier hierarchy. Used for browsing the MeSH vocabulary and for inclusive searches by retrieval systems using MeSH. (Note that the Trees hierarchy is not represented using subelements. The hierarchy is represented by the TreeNumber itself.) Up to thirteen hierarchical levels." ; rdfs:range . @@ -254,7 +251,7 @@ rdf:type :ObjectProperty ; - "Relates DisallowedDescriptorQualifierPairs to Descriptors or AllowedDescriptorQualifierPairs. Descriptor or DescriptorQualifierPair recommended in place of the prohibited combination." . + dct:description "Relates DisallowedDescriptorQualifierPairs to Descriptors or AllowedDescriptorQualifierPairs. Descriptor or DescriptorQualifierPair recommended in place of the prohibited combination." . @@ -273,7 +270,7 @@ rdfs:label "abbreviation" ; - "A property of Terms. Two-letter, uppercase abbreviation for a Qualifier term." . + dct:description "A property of Terms. Two-letter, uppercase abbreviation for a Qualifier term." . @@ -283,7 +280,7 @@ rdfs:label "altLabel" ; - "A property of Terms. A lexical variant for a Term’s prefLabel. meshv:altLabel is a subproperty of rdfs:label" ; + dct:description "A property of Terms. A lexical variant for a Term’s prefLabel. meshv:altLabel is a subproperty of rdfs:label" ; :propertyDisjointWith ; @@ -297,7 +294,7 @@ rdfs:label "annotation" ; - "A property of Descriptors or Qualifiers. Free-text information for indexers and catalogers concerning the use of the Descriptor or Qualifier." . + dct:description "A property of Descriptors or Qualifiers. Free-text information for indexers and catalogers concerning the use of the Descriptor or Qualifier." . @@ -307,7 +304,7 @@ rdfs:label "casn1_label" ; - "A property of Concepts. Free-text of the Chemical Abstracts Type N1 Name which is the systematic name used in the Chemical Abstracts Chemical Substance and Formula Indexes. The systematic name is a unique name assigned to a chemical substance to represent its structure. First available in 1995." . + dct:description "A property of Concepts. Free-text of the Chemical Abstracts Type N1 Name which is the systematic name used in the Chemical Abstracts Chemical Substance and Formula Indexes. The systematic name is a unique name assigned to a chemical substance to represent its structure. First available in 1995." . @@ -317,7 +314,7 @@ rdfs:label "considerAlso" ; - "A property of Descriptors. Free-text information that refers a user from a Descriptor to other terms which have related roots." . + dct:description "A property of Descriptors. Free-text information that refers a user from a Descriptor to other terms which have related roots." . @@ -327,7 +324,7 @@ rdfs:label "dateCreated" ; - "A property of Descriptors, Qualifiers, SupplementaryConceptRecords or Terms. Date in YYYY-MM-DD format when a Descriptor, Qualifer, SupplementaryConceptRecord or Term was first added to MeSH provisionally. This timestamp may be a year behind the dateEstablished. Upon conversion to a new MeSH maintenance system in 1999, a default value of 1999-01-01 was supplied." . + dct:description "A property of Descriptors, Qualifiers, SupplementaryConceptRecords or Terms. Date in YYYY-MM-DD format when a Descriptor, Qualifer, SupplementaryConceptRecord or Term was first added to MeSH provisionally. This timestamp may be a year behind the dateEstablished. Upon conversion to a new MeSH maintenance system in 1999, a default value of 1999-01-01 was supplied." . @@ -337,7 +334,7 @@ rdfs:label "dateEstablished" ; - "A property of Descriptors or Qualifiers. Date in YYYY-MM-DD format when the Descriptor or Qualifier became effective for use; set to YYYY-01-01 where YYYY = year of introduction to MeSH." . + dct:description "A property of Descriptors or Qualifiers. Date in YYYY-MM-DD format when the Descriptor or Qualifier became effective for use; set to YYYY-01-01 where YYYY = year of introduction to MeSH." . @@ -347,7 +344,7 @@ rdfs:label "dateRevised" ; - "A property of Descriptors, Qualifiers, or SupplementaryConceptRecords. Indicates that a revision was made to Descriptor, Qualifier, or SupplementaryConceptRecord data in YYYY-MM-DD format." . + dct:description "A property of Descriptors, Qualifiers, or SupplementaryConceptRecords. Indicates that a revision was made to Descriptor, Qualifier, or SupplementaryConceptRecord data in YYYY-MM-DD format." . @@ -357,7 +354,7 @@ rdfs:label "entryVersion" ; - "A property of Terms. Used for internal NLM processing only." . + dct:description "A property of Terms. Used for internal NLM processing only." . @@ -367,7 +364,7 @@ rdfs:label "frequency" ; - "A property of SupplementaryConceptRecords. Number of citations indexed with a SupplementaryConceptRecord in MEDLINE/PubMed. Automatically updated monthly in the XML. See also meshv:source definition." . + dct:description "A property of SupplementaryConceptRecords. Number of citations indexed with a SupplementaryConceptRecord in MEDLINE/PubMed. Automatically updated monthly in the XML. See also meshv:source definition." . @@ -377,7 +374,7 @@ rdfs:label "historyNote" ; - "A property of Descriptors or Qualifiers. Free-text information that traces the concept in MeSH and is deemed helpful for the online searcher. Headings and entry terms are entered in upper case. Initial characters refer to the year in which the Descriptor or Qualifier was created in MeSH in its current form (i.e., with the same preferred term). A date in parentheses indicates the oldest creation date of terms, provisional headings (before 1975), or minor headings (before 1991), which are reflected in bibliographic citations. Entries without a year date were created between 1963 and 1966." . + dct:description "A property of Descriptors or Qualifiers. Free-text information that traces the concept in MeSH and is deemed helpful for the online searcher. Headings and entry terms are entered in upper case. Initial characters refer to the year in which the Descriptor or Qualifier was created in MeSH in its current form (i.e., with the same preferred term). A date in parentheses indicates the oldest creation date of terms, provisional headings (before 1975), or minor headings (before 1991), which are reflected in bibliographic citations. Entries without a year date were created between 1963 and 1966." . @@ -387,7 +384,7 @@ rdfs:label "identifier" ; - "A property of Descriptors, Qualifiers, SupplementaryConceptRecords, Concepts, Terms and SemanticTypes. Descriptor identifier is a 7 or 10 alphanumeric starting with the letter D. Qualifier identifier is a 7 or 10 alphanumeric starting with the letter Q. SupplementaryConceptRecord identifier is a 7 or 10 alphanumeric starting with the letter C. Concept identifier is an 8 or 10 alphanumeric starting with the letter M. Term identifier is a 7 or 10 alphanumeric starting with the letter T. The 10 alphanumeric format was implemented for new identifiers created on or after about May 19, 2014." . + dct:description "A property of Descriptors, Qualifiers, SupplementaryConceptRecords, Concepts, Terms and SemanticTypes. Descriptor identifier is a 7 or 10 alphanumeric starting with the letter D. Qualifier identifier is a 7 or 10 alphanumeric starting with the letter Q. SupplementaryConceptRecord identifier is a 7 or 10 alphanumeric starting with the letter C. Concept identifier is an 8 or 10 alphanumeric starting with the letter M. Term identifier is a 7 or 10 alphanumeric starting with the letter T. The 10 alphanumeric format was implemented for new identifiers created on or after about May 19, 2014." . @@ -397,7 +394,7 @@ rdfs:label "lexicalTag" ; - "A property of Terms. A 3-letter value that indicates the lexical category. Valid values with their meanings in parentheses are: ABB (Abbreviation); ABX (Embedded abbreviation); ACR (Acronym); ACX (Embedded acronym); EPO (Eponym); LAB (Lab number); NAM (Proper name); NON (None); and TRD (Trade name). Note that in the XML, a Permuted Term will always have the same Lexical Tag value as the term from which it is generated." . + dct:description "A property of Terms. A 3-letter value that indicates the lexical category. Valid values with their meanings in parentheses are: ABB (Abbreviation); ABX (Embedded abbreviation); ACR (Acronym); ACX (Embedded acronym); EPO (Eponym); LAB (Lab number); NAM (Proper name); NON (None); and TRD (Trade name). Note that in the XML, a Permuted Term will always have the same Lexical Tag value as the term from which it is generated." . @@ -407,7 +404,7 @@ rdfs:label "note" ; - "A property of SupplementaryConceptRecords. Free-text narrative giving information about the SupplementaryConceptRecord, and may include information such as the registryNumber." . + dct:description "A property of SupplementaryConceptRecords. Free-text narrative giving information about the SupplementaryConceptRecord, and may include information such as the registryNumber." . @@ -417,7 +414,7 @@ rdfs:label "onlineNote" ; - "A property of Descriptors and Qualifiers. Free-text information intended to direct the MeSH online searcher to alternate search terms. Superseded by a more detailed historyNote when onlineNote is not present." . + dct:description "A property of Descriptors and Qualifiers. Free-text information intended to direct the MeSH online searcher to alternate search terms. Superseded by a more detailed historyNote when onlineNote is not present." . @@ -427,7 +424,7 @@ rdfs:label "prefLabel" ; - "A property of Terms. The preferred string for the term. meshv:prefLabel is a subproperty of rdfs:label." ; + dct:description "A property of Terms. The preferred string for the term. meshv:prefLabel is a subproperty of rdfs:label." ; rdfs:subPropertyOf rdfs:label . @@ -435,11 +432,7 @@ ### http://id.nlm.nih.gov/mesh/vocab#previousIndexing - rdf:type :DatatypeProperty ; - - rdfs:label "previousIndexing" ; - - "A property of Descriptors and Supplementary Concept Records. Free-text information referring to Descriptors or DescriptorQualifierPairs that were used to index the concept in MEDLINE before the Descriptor was created. Intended to enable users of new Descriptors to find similar concepts indexed before the Descriptor was created. Includes a date or date range. May include descriptive text referring to a group of Descriptors as “specifics”. Data are not maintained when a Descriptor or Qualifier name changes. DUI D005290 example: Iron (1966-1974). Also used for SupplementaryConceptRecords to refer to the Descriptor or DescriptorQualifierPair to which the SupplementaryConceptRecord was previously mapped." . + rdf:type :DatatypeProperty . @@ -449,7 +442,7 @@ rdfs:label "publicMeSHNote" ; - "A property of Descriptors. Free-text information about the history of changes to the Descriptor that may be helpful to the user of the printed Index Medicus publication (ceased in 2005). This includes the date the Descriptor was created in MeSH, changes in the preferred term, earlier status as an SupplementaryConceptRecord, etc. Unlike the History Note, this note reflects the MeSH vocabulary printed at that point in time, not as updated for online databases. Applies only to TopicalDescriptors. MeSH Descriptor labels are in upper case." . + dct:description "A property of Descriptors. Free-text information about the history of changes to the Descriptor that may be helpful to the user of the printed Index Medicus publication (ceased in 2005). This includes the date the Descriptor was created in MeSH, changes in the preferred term, earlier status as an SupplementaryConceptRecord, etc. Unlike the History Note, this note reflects the MeSH vocabulary printed at that point in time, not as updated for online databases. Applies only to TopicalDescriptors. MeSH Descriptor labels are in upper case." . @@ -459,7 +452,7 @@ rdfs:label "registryNumber" ; - "A property of Concepts. A unique identifier from one of these sources: Enzyme Commission (Example: EC 2.4.2.17; Example for Partial enzyme number: EC 1.4.3.-); Chemical Abstracts Service (CAS) (Example: 7004-12-8); FDA Substance Registration System Unique Identifier (UNII) in 10-character format (Example: R16CO5Y76E); or the value of 0 if no match is available from the previous sources. A single MeSH Concept can only have one Registry Number. Used for Concepts related to Descriptors in the D Category Drugs and Chemicals and for SupplementaryConceptRecords." . + dct:description "A property of Concepts. A unique identifier from one of these sources: Enzyme Commission (Example: EC 2.4.2.17; Example for Partial enzyme number: EC 1.4.3.-); Chemical Abstracts Service (CAS) (Example: 7004-12-8); FDA Substance Registration System Unique Identifier (UNII) in 10-character format (Example: R16CO5Y76E); or the value of 0 if no match is available from the previous sources. A single MeSH Concept can only have one Registry Number. Used for Concepts related to Descriptors in the D Category Drugs and Chemicals and for SupplementaryConceptRecords." . @@ -469,7 +462,7 @@ rdfs:label "relatedRegistryNumber" ; - "A property of Concepts. An additional unique identifier for chemicals, which is sometimes followed by a label in parentheses. Multiple Related Registry Numbers are allowed for each Concept. For example, these might be salts and/or stereoisomers of the parent compound. Used for Concepts related to Descriptors in the D Category Drugs and Chemicals and for SupplementaryConceptRecords." . + dct:description "A property of Concepts. An additional unique identifier for chemicals, which is sometimes followed by a label in parentheses. Multiple Related Registry Numbers are allowed for each Concept. For example, these might be salts and/or stereoisomers of the parent compound. Used for Concepts related to Descriptors in the D Category Drugs and Chemicals and for SupplementaryConceptRecords." . @@ -479,7 +472,7 @@ rdfs:label "scopeNote" ; - "A property of Concepts. Free-text narrative giving the scope and meaning (definition) of a Concept." . + dct:description "A property of Concepts. Free-text narrative giving the scope and meaning (definition) of a Concept." . @@ -489,7 +482,7 @@ rdfs:label "sortVersion" ; - "A property of Terms. Custom version of a Term label used to sort properly in a print product; format is all uppercase." . + dct:description "A property of Terms. Custom version of a Term label used to sort properly in a print product; format is all uppercase." . @@ -499,7 +492,7 @@ rdfs:label "source" ; - "A property of SupplementaryConceptRecords. Citation reference string in which the SupplementaryConceptRecord was first found. Single occurrence if SupplementaryConceptRecord created since 1980; frequency reports total citations indexed with the term in MEDLINE/PubMed. Possible multiple occurrences if SupplementaryConceptRecord created prior to 1980; term not found on those citations in MEDLINE/PubMed. Number of multiple Source occurrences need to be added to Frequency count for grand total of citations to articles discussing the SCR." . + dct:description "A property of SupplementaryConceptRecords. Citation reference string in which the SupplementaryConceptRecord was first found. Single occurrence if SupplementaryConceptRecord created since 1980; frequency reports total citations indexed with the term in MEDLINE/PubMed. Possible multiple occurrences if SupplementaryConceptRecord created prior to 1980; term not found on those citations in MEDLINE/PubMed. Number of multiple Source occurrences need to be added to Frequency count for grand total of citations to articles discussing the SCR." . @@ -507,8 +500,8 @@ rdf:type :DatatypeProperty ; - "thesaurusID" , - "A property of Terms. Name of a Thesaurus in which the term occurs. The value 'NLM' is equivalent to MeSH." . + dct:description "A property of Terms. Name of a Thesaurus in which the term occurs. The value 'NLM' is equivalent to MeSH." , + "thesaurusID" . @@ -537,7 +530,7 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith ; - "A combined MeSH descriptor and qualifier, where the pairing is allowed by MeSH rules. These URIs are a mash up of the descriptor and qualifier identifiers, such as D000236Q000235." . + dct:description "A combined MeSH descriptor and qualifier, where the pairing is allowed by MeSH rules. These URIs are a mash up of the descriptor and qualifier identifiers, such as D000236Q000235." . @@ -553,7 +546,7 @@ rdfs:label rdf:type :DatatypeProperty . , ; - "A special class of descriptor singled out because they are so frequently applied to biomedical literature. There are only 2 Descriptors that are members of the class meshv:CheckTag: D005260 (Male) and D008297 (Female). These two Descriptors do not have tree numbers. " . + dct:description "A special class of descriptor singled out because they are so frequently applied to biomedical literature. There are only 2 Descriptors that are members of the class meshv:CheckTag: D005260 (Male) and D008297 (Female). These two Descriptors do not have tree numbers. " . @@ -572,7 +565,7 @@ rdfs:label rdf:type :DatatypeProperty . , ; - "MeSH concepts are meanings. Many MeSH concepts contain synonymous terms. meshv:Concept identifiers begin with 'M' such as M0000013, 'Congenital Abnormalities'." . + dct:description "MeSH concepts are meanings. Many MeSH concepts contain synonymous terms. meshv:Concept identifiers begin with 'M' such as M0000013, 'Congenital Abnormalities'." . @@ -590,7 +583,7 @@ rdfs:label rdf:type :DatatypeProperty . , ; - "MeSH Descriptors are a cluster of one or more concepts used to describe what a publication is about. meshv:Descriptor is the parent class of meshv:TopicalDescriptor, meshv:GeographicDescriptor, meshv:PublicationType, and meshv:CheckTag." . + dct:description "MeSH Descriptors are a cluster of one or more concepts used to describe what a publication is about. meshv:Descriptor is the parent class of meshv:TopicalDescriptor, meshv:GeographicDescriptor, meshv:PublicationType, and meshv:CheckTag." . @@ -607,7 +600,7 @@ rdfs:label rdf:type :DatatypeProperty . , ; - "A combined MeSH descriptor and qualifier pair. Allowed pairs (according to MeSH rules) belong to the class meshv:AllowedDescriptorQualifierPair. Disallowed pairs belong to the class meshv:DisallowedDescriptorQualifierPair." . + dct:description "A combined MeSH descriptor and qualifier pair. Allowed pairs (according to MeSH rules) belong to the class meshv:AllowedDescriptorQualifierPair. Disallowed pairs belong to the class meshv:DisallowedDescriptorQualifierPair." . @@ -619,7 +612,7 @@ rdfs:label rdf:type :DatatypeProperty . rdfs:subClassOf ; - "A combined MeSH descriptor and qualifier where the pairing is not allowed by MeSH rules, such as Abdomen/radiography." . + dct:description "A combined MeSH descriptor and qualifier where the pairing is not allowed by MeSH rules, such as Abdomen/radiography." . @@ -634,7 +627,7 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith , ; - "A descriptor that references places or regions of the world, such as D001061, 'Appalachian Region'." . + dct:description "A descriptor that references places or regions of the world, such as D001061, 'Appalachian Region'." . @@ -648,7 +641,7 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith ; - "A special class of descriptor that describes what type of publication a resource is as opposed to what it is about. All MeSH Publication Types are in the V tree." . + dct:description "A special class of descriptor that describes what type of publication a resource is as opposed to what it is about. All MeSH Publication Types are in the V tree." . @@ -664,7 +657,7 @@ rdfs:label rdf:type :DatatypeProperty . , ; - "Also known as Subheadings, these provide context to the use of a MeSH Heading." . + dct:description "Also known as Subheadings, these provide context to the use of a MeSH Heading." . @@ -679,7 +672,7 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith , ; - "These are chemicals, drugs, enzymes, vitamins, etc." . + dct:description "These are chemicals, drugs, enzymes, vitamins, etc." . @@ -693,7 +686,7 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith ; - "SCR Diseases were originally brought into MeSH from a list maintained by the Office of Rare Diseases Research." . + dct:description "SCR Diseases were originally brought into MeSH from a list maintained by the Office of Rare Diseases Research." . @@ -705,7 +698,7 @@ rdfs:label rdf:type :DatatypeProperty . rdfs:subClassOf ; - "MeSH protocols are therapies in the domain of cancer treatment." . + dct:description "MeSH protocols are therapies in the domain of cancer treatment." . @@ -720,7 +713,7 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith , ; - "Supplementary Concepts are created in MeSH to aid in searching the large volume of mainly chemicals and drugs. meshv:SupplementaryConceptRecord has three sub-classes: meshv:RegularSubstance, meshv:SCR_Protocol, and meshv:SCR_Disease." . + dct:description "Supplementary Concepts are created in MeSH to aid in searching the large volume of mainly chemicals and drugs. meshv:SupplementaryConceptRecord has three sub-classes: meshv:RegularSubstance, meshv:SCR_Protocol, and meshv:SCR_Disease." . @@ -734,7 +727,7 @@ rdfs:label rdf:type :DatatypeProperty . :disjointWith ; - "MeSH terms provide synonymous names for MeSH concepts. Terms have 'T' identifiers, and are considered either preferred or lexical variants, such as 'Congenital Abnormalities' as opposed to 'Abnormality, Congenital'." . + dct:description "MeSH terms provide synonymous names for MeSH concepts. Terms have 'T' identifiers, and are considered either preferred or lexical variants, such as 'Congenital Abnormalities' as opposed to 'Abnormality, Congenital'." . @@ -746,7 +739,7 @@ rdfs:label rdf:type :DatatypeProperty . rdfs:subClassOf ; - "Topical Descriptors indicate the subject of an indexed item such as a journal article. See D063926, 'Drug Hypersensitivity Syndrome', for an example." . + dct:description "Topical Descriptors indicate the subject of an indexed item such as a journal article. See D063926, 'Drug Hypersensitivity Syndrome', for an example." . @@ -758,7 +751,7 @@ rdfs:label rdf:type :DatatypeProperty . rdfs:subClassOf :Thing ; - "Tree Numbers are used to organize MeSH Descriptors in a broader-than/narrower-than manner." . + dct:description "Tree Numbers are used to organize MeSH Descriptors in a broader-than/narrower-than manner." . @@ -769,5 +762,20 @@ rdfs:label rdf:type :DatatypeProperty . -### Generated by the OWL API (version 3.5.0) http://owlapi.sourceforge.net + +################################################################# +# +# Annotations +# +################################################################# + + + rdfs:label "previousIndexing" ; + + dct:description "A property of Descriptors and Supplementary Concept Records. Free-text information referring to Descriptors or DescriptorQualifierPairs that were used to index the concept in MEDLINE before the Descriptor was created. Intended to enable users of new Descriptors to find similar concepts indexed before the Descriptor was created. Includes a date or date range. May include descriptive text referring to a group of Descriptors as “specifics”. Data are not maintained when a Descriptor or Qualifier name changes. DUI D005290 example: Iron (1966-1974). Also used for SupplementaryConceptRecords to refer to the Descriptor or DescriptorQualifierPair to which the SupplementaryConceptRecord was previously mapped." . + + + + +### Generated by the OWL API (version 3.5.1) http://owlapi.sourceforge.net From 4699e39c8a74a488e6c51c749be85065f5c1c01c Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Fri, 29 May 2015 09:47:45 -0400 Subject: [PATCH 35/44] add versionInfo --- meta/vocabulary.ttl | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl index 300e8e69..b2407915 100644 --- a/meta/vocabulary.ttl +++ b/meta/vocabulary.ttl @@ -7,7 +7,9 @@ @prefix rdfs: . @base . - rdf:type :Ontology . + rdf:type :Ontology ; + + :versionInfo "0.9-dev" . ################################################################# From 8348ee488b08e90eb6b143f5d6398d9590d414f0 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Mon, 1 Jun 2015 15:21:49 -0400 Subject: [PATCH 36/44] Add owl:versionInfo to void.ttl, too --- meta/void.ttl | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/meta/void.ttl b/meta/void.ttl index 46e4640f..d7df9968 100644 --- a/meta/void.ttl +++ b/meta/void.ttl @@ -3,6 +3,7 @@ @prefix freq: . @prefix rdf: . @prefix rdfs: . +@prefix owl: . @prefix void: . @prefix xsd: . @prefix : . @@ -13,7 +14,9 @@ dcterms:description "This is the VoID description for MeSH RDF datasets."; dcterms:creator "U.S. National Library of Medicine" ; dcterms:date "2014-11-01"^^xsd:date ; - foaf:primaryTopic . + foaf:primaryTopic ; + owl:versionInfo "0.9-dev" . + # Metadata description of the Dataset From eb38d2c5f831a3c6b1148a7bedcae98fdb09211e Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Tue, 2 Jun 2015 13:43:52 -0400 Subject: [PATCH 37/44] Get vocabulary and void version and setup hardlinks As a sub-part of issues #144 and #147, update bin/mesh-xml2rdf.sh to do the following: - Get the version of the vocabulary.ttl and void.ttl files. - Create hard link for the versioned files. --- bin/mesh-xml2rdf.sh | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index 6467a320..6e79f7d4 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -81,3 +81,19 @@ fi cp $MESHRDF_HOME/meta/vocabulary.ttl $OUTDIR cp $MESHRDF_HOME/meta/void.ttl $OUTDIR +cd $OUTDIR + +vocab_version=`awk '$1~/versionInfo/ { gsub(/"/, "", $2); print $2 }' vocabulary.ttl` +if [ -z "$vocab_version" ]; then + echo "Unable to determine vocabulary.ttl version" 1>&2 + exit 1 +fi + +void_version=`awk '$1~/versionInfo/ { gsub(/"/, "", $2); print $2 }' void.ttl` +if [ -z "$void_version" ]; then + echo "Unable to determine void.ttl version" 1>&2 +fi + +ln -f void.ttl void_$vocab_version.ttl +ln -f vocabulary.ttl vocabulary_$vocab_version.ttl + From 31405d479961612825d884979eea93a222216440 Mon Sep 17 00:00:00 2001 From: Chris Maloney Date: Tue, 2 Jun 2015 15:53:38 -0400 Subject: [PATCH 38/44] Fix 114 - recordPreferredTerm -> preferredTerm --- meta/vocabulary.ttl | 4 ++-- xslt/common.xsl | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl index b2407915..62cfeea1 100644 --- a/meta/vocabulary.ttl +++ b/meta/vocabulary.ttl @@ -203,9 +203,9 @@ dct:description rdf:type :AnnotationProperty . -### http://id.nlm.nih.gov/mesh/vocab#recordPreferredTerm +### http://id.nlm.nih.gov/mesh/vocab#preferredTerm - rdf:type :ObjectProperty ; + rdf:type :ObjectProperty ; dct:description "Relates Descriptors, Qualifiers or SupplementaryConceptRecords to Terms. Indicates that the Term is the preferred term for a Descriptor, Qualifier, or SupplementaryConceptRecord." . diff --git a/xslt/common.xsl b/xslt/common.xsl index d49d3936..d18a9851 100755 --- a/xslt/common.xsl +++ b/xslt/common.xsl @@ -995,7 +995,7 @@ - recordPreferredTerm + preferredTerm From cc5415e9a590cf5074c6b327b9831d43cff01e20 Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Thu, 4 Jun 2015 12:56:54 -0400 Subject: [PATCH 39/44] Add the cns-disease-2014AB.nt file for the language sample. --- .gitignore | 4 +++- data/cns-disease-2014AB.nt | 15 +++++++++++++++ 2 files changed, 18 insertions(+), 1 deletion(-) create mode 100644 data/cns-disease-2014AB.nt diff --git a/.gitignore b/.gitignore index a81a23c7..989223a6 100755 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,6 @@ Saxon*.zip saxon9he -data +data/*.xml +data/*.dtd +data/readme* out diff --git a/data/cns-disease-2014AB.nt b/data/cns-disease-2014AB.nt new file mode 100644 index 00000000..0797f5ca --- /dev/null +++ b/data/cns-disease-2014AB.nt @@ -0,0 +1,15 @@ + "nemoci centr\u00E1ln\u00EDho nervov\u00E9ho syst\u00E9mu"@cs . + "Ziekte, centraalzenuwstelsel-"@nl . + "Central Nervous System Diseases"@en . + "Keskushermoston sairaudet"@fi . + "Maladie du syst\u00E8me nerveux central"@fr . + "Zentralnervensystemkrankheiten"@de . + "Malattie del sistema nervoso centrale"@it . + "\u4E2D\u67A2\u795E\u7D4C\u7CFB\u75BE\u60A3"@ja . + "Sykdommer i sentralnervesystemet"@no . + "Choroby OUN"@pl . + "Doen\u00E7as do Sistema Nervoso Central"@pt . + "\u041D\u0415\u0420\u0412\u041D\u041E\u0419 \u0421\u0418\u0421\u0422\u0415\u041C\u042B \u0426\u0415\u041D\u0422\u0420\u0410\u041B\u042C\u041D\u041E\u0419 \u0411\u041E\u041B\u0415\u0417\u041D\u0418"@ru . + "SREDI\u0160NJI \u017DIV\u010CANI SUSTAV, BOLESTI"@hr . + "Enfermedades del Sistema Nervioso Central"@es . + "Centrala nervsystemets sjukdomar"@sv . From 5f25adcec119a65e27c3618c5d9d89af5e0d1437 Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Thu, 4 Jun 2015 14:46:59 -0400 Subject: [PATCH 40/44] Append cns-diseases-2014AB.nt to the dups file before sort Addresses https://github.com/HHS/mesh-rdf/issues/150. Not sure how to itemize an issue in another repository. --- bin/mesh-xml2rdf.sh | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/bin/mesh-xml2rdf.sh b/bin/mesh-xml2rdf.sh index 6e79f7d4..76b6f8ff 100755 --- a/bin/mesh-xml2rdf.sh +++ b/bin/mesh-xml2rdf.sh @@ -36,10 +36,12 @@ if [ "$MESHRDF_URI_YEAR" = "yes" ]; then OUTDIR=$MESHRDF_HOME/out/$YEAR OUTFILE=$OUTDIR/mesh$YEAR URI_YEAR_PARAM=uri-year-segment=$YEAR + URI_PREFIX="http://id.nlm.nih.gov/mesh/$YEAR" else OUTDIR=$MESHRDF_HOME/out OUTFILE=$OUTDIR/mesh URI_YEAR_PARAM= + URI_PREFIX="http://id.nlm.nih.gov/mesh" fi @@ -66,6 +68,11 @@ if [ $? -ne 0 ]; then exit 1 fi +if [ -f "$MESHRDF_HOME/data/cns-disease-2014AB.nt" ]; then + sed -e "s,http://id.nlm.nih.gov/mesh,$URI_PREFIX," \ + "$MESHRDF_HOME/data/cns-disease-2014AB.nt" >> "$OUTFILE-dups.nt" +fi + sort -u -T"$OUTDIR" "$OUTFILE-dups.nt" > "$OUTFILE.nt" if [ $? -ne 0 ]; then echo "Error deduplicating $OUTFILE-dups.nt" 1>&2 From 44d4b3a1d8cd0519feba3bbdc0016e336831dafd Mon Sep 17 00:00:00 2001 From: "david.anderson3" Date: Mon, 8 Jun 2015 17:42:07 -0400 Subject: [PATCH 41/44] Update to vocabulary.ttl descriptions --- meta/vocabulary.ttl | 24 +++++++++--------------- 1 file changed, 9 insertions(+), 15 deletions(-) diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl index 62cfeea1..0fad5dd9 100644 --- a/meta/vocabulary.ttl +++ b/meta/vocabulary.ttl @@ -54,7 +54,7 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; - dct:description "Relates 2 instances of the meshv:Concept class, one of which is broader than the other." ; + dct:description "Relates one Concept to another. A semantic relationship between two Concepts, usually between the preferred concept and subordinate concept(s) where one is broader in meaning. Example: M0024816 is broader than M0024811." ; rdfs:range ; @@ -68,7 +68,7 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; - dct:description "Relates 2 instances of the meshv:Descriptor class, one of which is broader than the other." ; + dct:description "Relates one Descriptor to another. The immediate parent Descriptor(s) of a given Descriptor based on the TreeNumber hierarchy. Example: both DUI D007254 (Information Science) and DUI D008491 (Medical Informatics Applications) are parents of DUI D016247 (Information Storage and Retrieval)." ; rdfs:domain ; @@ -82,6 +82,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + dct:description "Relates one Qualifier to another. The immediate parent Qualifier(s) of a given Qualifier based on the TreeNumber hierarchy. Example: QUI Q000458 (organization & administration) is a parent of QUI Q000592 (standards)." ; + rdfs:range ; rdfs:domain ; @@ -138,7 +140,7 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; - dct:description "Relates 2 instances the of meshv:Concept class, one of which is narrower than the other." ; + dct:description "Relates one Concept to another. A semantic relationship between the preferred concept and subordinate concept(s) where one is narrower in meaning. Example: M0353609 is narrower with respect to M0000001." ; rdfs:domain ; @@ -151,7 +153,7 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty , :TransitiveProperty ; - dct:description "Relates 2 instances of meshv:treeNumber classes, one of which is the immediate parent of the other." ; + dct:description "Relates one TreeNumber to another. Immediate “parent” TreeNumber, meaning one level higher in the TreeNumber hierarchy. Example: D03.438.221 is a parent of D03.438.221.173." ; rdfs:range ; @@ -191,7 +193,7 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; - dct:description "Relates Concepts to Terms. The Term in this relationship expresses the most relevant name of the Concept. meshv:preferredTerm is a subproperty of meshv:term." ; + dct:description "Relates Concepts, Descriptors, Qualifiers or SupplementaryConceptRecords to Terms. Indicates that the Term is the preferred term for a Concept, Descriptor, Qualifier, or SupplementaryConceptRecord." ; rdfs:subPropertyOf . @@ -203,19 +205,11 @@ dct:description rdf:type :AnnotationProperty . -### http://id.nlm.nih.gov/mesh/vocab#preferredTerm - - rdf:type :ObjectProperty ; - - dct:description "Relates Descriptors, Qualifiers or SupplementaryConceptRecords to Terms. Indicates that the Term is the preferred term for a Descriptor, Qualifier, or SupplementaryConceptRecord." . - - - ### http://id.nlm.nih.gov/mesh/vocab#relatedConcept rdf:type :ObjectProperty ; - dct:description "Relates one Concept to another. A semantic relationship between two Concepts, usually between the preferred Concept and subordinate Concept(s) where one is neither broader nor narrower in meaning." ; + dct:description "Relates one Concept to another. A semantic relationship between two Concepts, usually between the preferred Concept and subordinate Concept(s) where one is neither broader nor narrower in meaning. Example: M0000562 is related to M0000561" ; rdfs:range ; @@ -386,7 +380,7 @@ dct:description rdf:type :AnnotationProperty . rdfs:label "identifier" ; - dct:description "A property of Descriptors, Qualifiers, SupplementaryConceptRecords, Concepts, Terms and SemanticTypes. Descriptor identifier is a 7 or 10 alphanumeric starting with the letter D. Qualifier identifier is a 7 or 10 alphanumeric starting with the letter Q. SupplementaryConceptRecord identifier is a 7 or 10 alphanumeric starting with the letter C. Concept identifier is an 8 or 10 alphanumeric starting with the letter M. Term identifier is a 7 or 10 alphanumeric starting with the letter T. The 10 alphanumeric format was implemented for new identifiers created on or after about May 19, 2014." . + dct:description "A property of Descriptors, Qualifiers, SupplementaryConceptRecords, Concepts and Terms. Descriptor identifier is a 7 or 10 alphanumeric starting with the letter D. Qualifier identifier is a 7 or 10 alphanumeric starting with the letter Q. SupplementaryConceptRecord identifier is a 7 or 10 alphanumeric starting with the letter C. Concept identifier is an 8 or 10 alphanumeric starting with the letter M. Term identifier is a 7 or 10 alphanumeric starting with the letter T. The 10 alphanumeric format was implemented for new identifiers created on or after about May 19, 2014." . From bdfb0227c09116286eddc1e3ea92d0a1904edb71 Mon Sep 17 00:00:00 2001 From: "david.anderson3" Date: Tue, 9 Jun 2015 09:41:43 -0400 Subject: [PATCH 42/44] Revised description. --- meta/vocabulary.ttl | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl index 0fad5dd9..5a712543 100644 --- a/meta/vocabulary.ttl +++ b/meta/vocabulary.ttl @@ -496,8 +496,7 @@ dct:description rdf:type :AnnotationProperty . rdf:type :DatatypeProperty ; - dct:description "A property of Terms. Name of a Thesaurus in which the term occurs. The value 'NLM' is equivalent to MeSH." , - "thesaurusID" . + dct:description "A property of Terms. Name of a Thesaurus in which the term occurs. The value 'NLM' is equivalent to MeSH." . From 4d0d3d23cc813e5b8e7b0223380bf181bc60cd96 Mon Sep 17 00:00:00 2001 From: "david.anderson3" Date: Tue, 9 Jun 2015 15:53:16 -0400 Subject: [PATCH 43/44] Added labels also previousIndexing was both an object property and data property. Should just be a data property, I think. --- meta/vocabulary.ttl | 69 ++++++++++++++++++++++++++++++--------------- 1 file changed, 47 insertions(+), 22 deletions(-) diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl index 5a712543..10776584 100644 --- a/meta/vocabulary.ttl +++ b/meta/vocabulary.ttl @@ -38,6 +38,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "allowableQualifier" ; + dct:description "Relates Descriptors to Qualifiers. A specific Qualifier allowed in combination with the Descriptor." ; rdfs:range . @@ -54,6 +56,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "broaderConcept" ; + dct:description "Relates one Concept to another. A semantic relationship between two Concepts, usually between the preferred concept and subordinate concept(s) where one is broader in meaning. Example: M0024816 is broader than M0024811." ; rdfs:range ; @@ -68,6 +72,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "broaderDescriptor" ; + dct:description "Relates one Descriptor to another. The immediate parent Descriptor(s) of a given Descriptor based on the TreeNumber hierarchy. Example: both DUI D007254 (Information Science) and DUI D008491 (Medical Informatics Applications) are parents of DUI D016247 (Information Storage and Retrieval)." ; rdfs:domain ; @@ -82,6 +88,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "broaderQualifier" ; + dct:description "Relates one Qualifier to another. The immediate parent Qualifier(s) of a given Qualifier based on the TreeNumber hierarchy. Example: QUI Q000458 (organization & administration) is a parent of QUI Q000592 (standards)." ; rdfs:range ; @@ -96,6 +104,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "concept" ; + dct:description "Relates Descriptors, Qualifiers or SupplementaryConceptRecords to Concepts. Designates a member of a collection of Concepts for a Descriptor, Qualifier or SCR." . @@ -104,6 +114,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "hasDescriptor" ; + dct:description "Relates DescriptorQualifierPairs to Descriptors." ; rdfs:range . @@ -114,6 +126,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "hasQualifier" ; + dct:description "Relates DescriptorQualifierPairs to Qualifiers." ; rdfs:range . @@ -124,6 +138,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "indexerConsiderAlso" ; + dct:description "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. A Descriptor or DescriptorQualifierPair that is usually broader than the SupplementaryConceptRecord, and which is suggested as an indexing guideline for addition to the citation if pertinent to the article being indexed." . @@ -132,6 +148,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "mappedTo" ; + dct:description "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. A Descriptor or DescriptorQualifierPair that is a parent (not the main parent; lacks an asterisk designation in the Source XML) for the SupplementaryConceptRecord and that is automatically added to the journal citation for which the SupplementaryConceptRecord is indexed. See also meshv:preferredMappedTo." . @@ -140,6 +158,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "narrowerConcept" ; + dct:description "Relates one Concept to another. A semantic relationship between the preferred concept and subordinate concept(s) where one is narrower in meaning. Example: M0353609 is narrower with respect to M0000001." ; rdfs:domain ; @@ -153,6 +173,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty , :TransitiveProperty ; + rdfs:label "parentTreeNumber" ; + dct:description "Relates one TreeNumber to another. Immediate “parent” TreeNumber, meaning one level higher in the TreeNumber hierarchy. Example: D03.438.221 is a parent of D03.438.221.173." ; rdfs:range ; @@ -165,6 +187,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "pharmacologicalAction" ; + dct:description "Relates Descriptors or SupplementaryConceptRecords to Descriptors. Reference to a Descriptor describing observed biological activity of an exogenously administered chemical represented by a Descriptor or SupplementaryConceptRecord." . @@ -173,6 +197,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "preferredConcept" ; + dct:description "Relates Descriptors or Supplementary Concept Records to Concepts. The preferred concept is frequently a broader concept that includes narrower sub-concepts, but may also be one among several distinct concepts. The preferred concept is selected as the primary or most prominent representation among the concepts in the literature. meshv:preferredConcept is a subproperty of meshv:concept." ; rdfs:subPropertyOf . @@ -183,6 +209,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "preferredMappedTo" ; + dct:description "Relates SupplementaryConceptRecords to Descriptors or DescriptorQualifierPairs. Designates a Descriptor or DescriptorQualifierPair that is a main parent (includes an asterisk designation in the Source XML) for the SupplementaryConceptRecord and that is automatically added to the journal citation for which the SupplementaryConceptRecord is indexed. meshv:preferredMappedTo is a subproperty of meshv:mappedTo." ; rdfs:subPropertyOf . @@ -193,22 +221,20 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "preferredTerm" ; + dct:description "Relates Concepts, Descriptors, Qualifiers or SupplementaryConceptRecords to Terms. Indicates that the Term is the preferred term for a Concept, Descriptor, Qualifier, or SupplementaryConceptRecord." ; rdfs:subPropertyOf . -### http://id.nlm.nih.gov/mesh/vocab#previousIndexing - - rdf:type :ObjectProperty . - - - ### http://id.nlm.nih.gov/mesh/vocab#relatedConcept rdf:type :ObjectProperty ; + rdfs:label "relatedConcept" ; + dct:description "Relates one Concept to another. A semantic relationship between two Concepts, usually between the preferred Concept and subordinate Concept(s) where one is neither broader nor narrower in meaning. Example: M0000562 is related to M0000561" ; rdfs:range ; @@ -221,6 +247,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "seeAlso" ; + dct:description "Relates one Descriptor to another. Reference to a specific Descriptor to which a user is referred by a 'see related' cross-reference." . @@ -229,6 +257,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "term" ; + dct:description "Relates Concepts to Terms. Each Concept has a set of entry terms and a preferred term that are related to the Concept." . @@ -237,6 +267,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "treeNumber" ; + dct:description "Relates Descriptors or Qualifiers to TreeNumbers. Alpha-numeric string referring to location within a Descriptor or Qualifier hierarchy. Used for browsing the MeSH vocabulary and for inclusive searches by retrieval systems using MeSH. (Note that the Trees hierarchy is not represented using subelements. The hierarchy is represented by the TreeNumber itself.) Up to thirteen hierarchical levels." ; rdfs:range . @@ -247,6 +279,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :ObjectProperty ; + rdfs:label "useInstead" ; + dct:description "Relates DisallowedDescriptorQualifierPairs to Descriptors or AllowedDescriptorQualifierPairs. Descriptor or DescriptorQualifierPair recommended in place of the prohibited combination." . @@ -428,7 +462,11 @@ dct:description rdf:type :AnnotationProperty . ### http://id.nlm.nih.gov/mesh/vocab#previousIndexing - rdf:type :DatatypeProperty . + rdf:type :DatatypeProperty ; + + rdfs:label "previousIndexing" ; + + dct:description "A property of Descriptors and Supplementary Concept Records. Free-text information referring to Descriptors or DescriptorQualifierPairs that were used to index the concept in MEDLINE before the Descriptor was created. Intended to enable users of new Descriptors to find similar concepts indexed before the Descriptor was created. Includes a date or date range. May include descriptive text referring to a group of Descriptors as “specifics”. Data are not maintained when a Descriptor or Qualifier name changes. DUI D005290 example: Iron (1966-1974). Also used for SupplementaryConceptRecords to refer to the Descriptor or DescriptorQualifierPair to which the SupplementaryConceptRecord was previously mapped." . @@ -496,6 +534,8 @@ dct:description rdf:type :AnnotationProperty . rdf:type :DatatypeProperty ; + rdfs:label "thesaurusID" ; + dct:description "A property of Terms. Name of a Thesaurus in which the term occurs. The value 'NLM' is equivalent to MeSH." . @@ -757,20 +797,5 @@ rdfs:label rdf:type :DatatypeProperty . - -################################################################# -# -# Annotations -# -################################################################# - - - rdfs:label "previousIndexing" ; - - dct:description "A property of Descriptors and Supplementary Concept Records. Free-text information referring to Descriptors or DescriptorQualifierPairs that were used to index the concept in MEDLINE before the Descriptor was created. Intended to enable users of new Descriptors to find similar concepts indexed before the Descriptor was created. Includes a date or date range. May include descriptive text referring to a group of Descriptors as “specifics”. Data are not maintained when a Descriptor or Qualifier name changes. DUI D005290 example: Iron (1966-1974). Also used for SupplementaryConceptRecords to refer to the Descriptor or DescriptorQualifierPair to which the SupplementaryConceptRecord was previously mapped." . - - - - ### Generated by the OWL API (version 3.5.1) http://owlapi.sourceforge.net From f86881b7ecc8c93e4ce94a480ecb90a2294b3fe4 Mon Sep 17 00:00:00 2001 From: Daniel Davis Date: Thu, 18 Jun 2015 11:39:27 -0400 Subject: [PATCH 44/44] CHange the versionInfo from "0.9-dev" to "0.9" --- meta/vocabulary.ttl | 2 +- meta/void.ttl | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/meta/vocabulary.ttl b/meta/vocabulary.ttl index 10776584..bd32e205 100644 --- a/meta/vocabulary.ttl +++ b/meta/vocabulary.ttl @@ -9,7 +9,7 @@ rdf:type :Ontology ; - :versionInfo "0.9-dev" . + :versionInfo "0.9" . ################################################################# diff --git a/meta/void.ttl b/meta/void.ttl index d7df9968..5b8dd4bd 100644 --- a/meta/void.ttl +++ b/meta/void.ttl @@ -15,7 +15,7 @@ dcterms:creator "U.S. National Library of Medicine" ; dcterms:date "2014-11-01"^^xsd:date ; foaf:primaryTopic ; - owl:versionInfo "0.9-dev" . + owl:versionInfo "0.9" . # Metadata description of the Dataset