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Import of BTMCINNES/UMLS-Interface-1.15 from CPAN.
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gitpan-cpan-distribution: UMLS-Interface
gitpan-cpan-version:      1.15
gitpan-cpan-path:         BTMCINNES/UMLS-Interface-1.15.tar.gz
gitpan-cpan-author:       BTMCINNES
gitpan-cpan-maturity:     released
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Bridget McInnes authored and Gitpan committed Oct 23, 2014
1 parent 23c0940 commit e92b632
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16 changes: 16 additions & 0 deletions CHANGELOG
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NAME
UMLS::Interface CHANGES

Changes from version 1.13 to 1.15
1. updated README documentation

2. made a change in getCuiDef.pl. The definition was not being returned
when a CUI was used as input although the term was working just fine.

3. made a change in getExtendedDef.pl. If a term was entered the
associated CUI was obtained from the SAB variable rather than the SABDEF

4. added configuration checks to getCuiDef.pl and getExtendedDef.pl

5. added ability to use ' in the term without having to escape it. For
example:

findPathToRoot.pl "Alzheimer's Disease"

Changes from version 1.11 to 1.13
1. added the STFinder module which returns the information content of a
semantic type using the isa relations in the semantic network to
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4 changes: 2 additions & 2 deletions INSTALL 100755 → 100644
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Expand Up @@ -256,6 +256,7 @@ Stage 3 - Install MySQL, if already installed go to Stage 4
<http://dev.mysql.com/doc/refman/5.1/en/adding-users.html>

Stage 4 - Install UMLS, if already installed go to Stage 5

VERSION
The UMLS-Interface requires version UMLS 2008AA or higher

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Step 1: Create the MySQL database
Log into MySQL and create a database called 'umls' as follows:

CREATE DATABASE IF NOT EXISTS umls CHARACTER SET utf8 COLLATE
utf8_unicode_ci;
CREATE DATABASE IF NOT EXISTS umls CHARACTER SET utf8 COLLATE utf8_unicode_ci;

Step 2: Modify the 'my.cnf' file.
This has been put in a different place every version or distribution
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2 changes: 1 addition & 1 deletion META.yml
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--- #YAML:1.0
name: UMLS-Interface
version: 1.13
version: 1.15
abstract: Perl interface to the Unified Medical Language System (UMLS)
author:
- Bridget McInnes <bthomson@cs.umn.edu>, Ted Pedersen <tpederse@d.umn.edu>, Serguei Pakhomov <pakh0002@umn.edu>, Siddharth Patwardhan <sidd@cs.utah.edu>
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264 changes: 170 additions & 94 deletions README 100755 → 100644
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Expand Up @@ -126,134 +126,210 @@ NAME

The methods are as follows:

my $root = $interface->root();
Returns the concept ID of the root of the tree.
my $root = $interface->root();
Returns the concept ID of the root of the tree.

my $depth = $interface->depth();
Returns the depth of the tree.
my $depth = $interface->depth();
Returns the depth of the tree.

my $version = $interface->version();
Return the version of UMLS.
my $version = $interface->version();
Return the version of UMLS.

my $bool = $interface->exists($cui);
Determines if a CUI exists
my $bool = $interface->exists($cui);
Determines if a CUI exists

my $bool = $interface->validCui($cui);
Checks if CUI is a valid concept
my $bool = $interface->validCui($cui);
Checks if CUI is a valid concept

my @array = $interface->getSab($cui);
Returns the list of sources the concept exists in
my $array = $interface->getSab($cui);
Returns the list of sources the concept exists in

my @array = $interface->getConceptList($term);
Returns the list of all CUIs of a given term
from the SAB parameter specified in the config
file or the default
my $array = $interface->getConceptList($term);
Returns the list of all CUIs of a given term
from the SAB parameter specified in the config
file or the default

my @array = $interface->getDefConceptList($term);
Returns the list of all CUIs of a given term
from the SABDEF parameter specified in the
config file or the default
my $array = $interface->getDefConceptList($term);
Returns the list of all CUIs of a given term
from the SABDEF parameter specified in the
config file or the default

my $hash = $interface->getCuiList();
Returns a list of CUIs from the source(s) specified
in the configuration file
my $array = $interface->getAllConcepts($term);
Returns the list of all CUIs of a given term
in the entire UMLS.

my $array = $interface->getCuisFromSource($sab);
Returns a list of CUIs from a specific source
my $hash = $interface->getCuiList();
Returns a list of CUIs from the source(s) specified
in the configuration file

my @array = $interface->getTermList($cui);
Returns the list of terms and their sources using
the SAB parameter in the configuration file or the
default
my $array = $interface->getCuisFromSource($sab);
Returns an list of CUIs in a specified source

my @array = $interface->getDefTermList($cui);
Returns the list of terms and their sources using
the SABDEF parameter in the configuration file or
the default
my $array = $interface->getCuisFromSource($sab);
Returns a list of CUIs from a specific source

my @array = $interface->getAllTerms($cui);
Returns the list of terms corresponding to a CUI
for all sources
my $array = $interface->getTermList($cui);
Returns the list of terms and their sources using
the SAB parameter in the configuration file or the
default

my $term = $interface->getPreferredTerms($cui);
Returns the preferred term of a CUI if that term
exists in the sources specified by the SAB parameter
in the configuration file or the default
my $array = $interface->getDefTermList($cui);
Returns the list of terms and their sources using
the SABDEF parameter in the configuration file or
the default

my $term = $interface->getPreferredTerms($cui);
Returns the preferred term of a CUI regardless
of the source information in the configuration
file
my $array = $interface->getAllTerms($cui);
Returns the list of terms corresponding to a CUI
for all sources

my @array = $interface->getParents($cui);
Returns the parent of a given CUI
my $hash = $interface->getCompounds();
Returns all the compound terms in the sources specified in
the configuration file.

my @array = $interface->getChildren($cui);
Returns the children of a given CUI
my $term = $interface->getPreferredTerms($cui);
Returns the preferred term of a CUI if that term
exists in the sources specified by the SAB parameter
in the configuration file or the default

my @array = $interface->getRelated($cui, $rel);
Returns the CUI relations of a given CUI and relation
my $term = $interface->getAllPreferredTerms($cui);
Returns the preferred term of a CUI regardless
of the source information in the configuration
file

my @array = $interface->getRelationsBetweenCuis($cui1, $cui2);
Returns the relations between two CUIs.
my $array = $interface->getParents($cui);
Returns the parent of a given CUI

my @array$interface->getRelations($cui);
Returns all of the relations associated with a CUI in
the sources specified in the configuration file
my $array = $interface->getChildren($cui);
Returns the children of a given CUI

my @array = $interface->getCuiDef($cui);
Returns the definition(s) of a given CUI
my $array = $interface->getRelated($cui, $rel);
Returns the CUI relations of a given CUI and relation

my $array = $interface->getExtendedDefinition($cui);
Returns the extended definition of a given CUI
my $array = $interface->getRelationsBetweenCuis($cui1, $cui2);
Returns the relations between two CUIs.

my @array = $interface->getSts($cui);
Returns the TUI(s) of the semantic type(s) associated
with a CUI
my $array$interface->getRelations($cui);
Returns all of the relations associated with a CUI in
the sources specified in the configuration file

my $abr = $interface->getStAbr($tui);
Returns the abbreviation of a semantic type of a TUI
my $array = $interface->getCuiDef($cui);
Returns the definition(s) of a given CUI

my $string = $interface->getStString($abr);
Returns the name of the semantic type given its
my $array = $interface->getExtendedDefinition($cui);
Returns the extended definition of a given CUI

my $def = $interface->getStDef($abr);
Returns the definition of a semantic type given its
abbreviation

my $array = $interface->pathsToRoot($cui);
Returns a list of concept IDs that denote the path from
the input CUI to the root using the source and relation
information in the configuration file
my $array = $interface->getSt($cui);
Returns the TUI(s) of the semantic type(s) associated
with a CUI

my @array = $interface->findShortestPath($cui1, $cui2);
Returns the shortest path between two CUIs
my $abr = $interface->getStAbr($tui);
Returns the abbreviation of a semantic type of a TUI

my @array = $interface->findLeastCommonSubsumer($cui1, $cui2);
Returns the least common subsumer between two CUIs
my $tui = $interface->getStTui($abr);
Returns the TUI of an abbreviation of a semantic type

my $min = $interface->findMinimumDepth($cui);
Returns the minimum depth of a CUI given the sources
and relations specified in the configuration file
my $string = $interface->getStString($abr);
Returns the name of the semantic type given its

my $max = $interface->findMaximumDepth($cui);
Returns the maximum depth of a CUI given the sources
and relations specified in the configuration file
my $def = $interface->getStDef($abr);
Returns the definition of a semantic type given its
abbreviation

my $double = $interface->getIC();
Returns the information content of a CUI
my $array = $interface->getSemanticRelation($st1, $st2);
Returns a list of semantic relation between the two
semantic types.

my $hash = $interface->returnTableNames();
Returns the mysql database table names in human and hex form
created by the package for a given configuration
my $array = $interface->getSemanticGroup($cui1);
Returns a list of semantic groups of a given CUI

$interface->dropConfigTable();
Drops the temporary table created by the UMLS-Interface
module of path information for a specified set of sources
my $array = $interface->getSemanticGroupOfSt($st);
Returns a list of semantic groups of a given semantic type

$interface->removeConfigFiles();
Removes the configuration files created by the
verbose option
my $array = $interface->pathsToRoot($cui);
Returns a list of concept IDs that denote the path from
the input CUI to the root using the source and relation
information in the configuration file

my $array = $interface->findShortestPath($cui1, $cui2);
Returns the shortest path between two CUIs

my $array = $interface->findLeastCommonSubsumer($cui1, $cui2);
Returns the least common subsumer between two CUIs

my $min = $interface->findMinimumDepth($cui);
Returns the minimum depth of a CUI given the sources
and relations specified in the configuration file

my $max = $interface->findMaximumDepth($cui);
Returns the maximum depth of a CUI given the sources
and relations specified in the configuration file

my $int = $interface->findNumberOfCloserConcepts($cui1, $cui2);
Returns the number of concepts closer to cui1 than cui2

my $double = $interface->getIC($cui);
Returns the information content of a CUI

my $double = $interface->getProbability($cui);
Returns the probability of a concept

my $int = $interface->getFrequency($cui);
Returns the frequency of a CUI that was used to calculate
its information content and probability

my $N = $interface->getN();
Returns the total number of CUIs the probabilities were
calculated with

my $hash = $interface->getPropagationCuis();
Returns a list of CUIs that the counts were propagated over

my $hash = $interface->propagateCounts(\%hash);
Returns the propagation counts of the input CUIs

my $array = $interface->stPathsToRoot($tui);
Returns all the path to the root information of the given
semantic type (TUI)

my $array = $interface->stFindShortestPath($tui1, $tui2);
Returns the shortest paths between the two semantic types
(TUIs)

my $double = $interface->getStIC($tui);
Returns the information content of a given semantic type (TUI)

my $double = $interface->getStProbability($tui);
Returns the probability of a given semantic type (TUI)

my $stN = $interface->getStN();
Returns the total number of semantic types used to
obtain the probability of a semantic type

$interface->setPropagationParameters(\%parameters);
Sets the propagation parameters

$interface->setStSmoothing();
Sets the smoothing parameter to smooth the input counts

my $hash = $interface->propagateStCounts(\%hash);
Returns the propagation counts of the input semantic types

$interface->loadStPropagationHash(\%hash);
Load the propagation hash with probability counts


my $hash = $interface->returnTableNames();
Returns the mysql database table names in human and hex form
created by the package for a given configuration

$interface->dropConfigTable();
Drops the temporary table created by the UMLS-Interface
module of path information for a specified set of sources

$interface->removeConfigFiles();
Removes the configuration files created by the
verbose option

These methods essentially expose an interface as required by the
UMLS::Similarity modules. The UMLS::Similarity modules require that any
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