import java.io.*;
import java.util.*;
import java.sql.*;
import java.math.*;
import java.text.*;
import java.net.*;
import java.lang.*;
public class RemoveReplace extends Thread
{
String db_connection = "jdbc:mysql://dblocation.org/umls";
String db_user = "xxxx";
String db_password = "xxxx";
Connection dbConn = null;
Hashtable nodes = new Hashtable( );
public RemoveReplace( ) throws IOException {
try {
Class.forName( "com.mysql.jdbc.Driver" ).newInstance();
} catch( Exception e ) {
System.err.println( "Unable to load mm.mysql driver." );
e.printStackTrace( );
}
try {
dbConn = DriverManager.getConnection( db_connection, db_user, db_password );
dbConn.setAutoCommit( true );
} catch (Throwable t) {
t.printStackTrace();
return;
}
}
String geo_table[] = { "gds_title", "gse_title", "gse_desc", "gsm_title", "gsm_desc", "gsm_source", "gsm_keyword" };
String geo_key[] = { "gds", "gse", "gse", "gsm", "gsm", "gsm", "gsm" };
String geo_text[] = { "title", "title", "description", "title", "description", "source", "keyword" };
public void searchText( String text ) throws IOException, SQLException {
System.out.println( ">>> Regexp '" + text + "' appears in:\n" );
int count = 0;
for( int i = 0; i < geo_table.length; i++ ) {
Statement stmt = dbConn.createStatement( );
ResultSet rset = stmt.executeQuery( "select a." + geo_key[i] + ", a." + geo_text[i] + " from " +
"geo." + geo_table[i] + " as a " +
"where a." + geo_text[i] + " regexp '" + text + "'" );
while( rset.next( ) ) {
System.out.println( geo_table[i] + " " + rset.getString(1) + ": " + rset.getString(2) );
count ++;
}
}
System.out.println( ">>> Total found: " + count + "\n" );
}
public void moveBackRemoved( ) throws IOException, SQLException {
for( int i = 0; i < geo_table.length; i++ ) {
Statement stmt = dbConn.createStatement( );
stmt.executeUpdate( "insert into geo." + geo_table[i] + "_sui " +
"select * from geo." + geo_table[i] + "_sui_removed" );
}
}
public void dropRemoved( ) throws IOException, SQLException {
for( int i = 0; i < geo_table.length; i++ ) {
Statement stmt = dbConn.createStatement( );
stmt.executeUpdate( "drop table if exists " +
"geo." + geo_table[i] + "_sui_removed" );
}
}
public void tightenTables( ) throws IOException, SQLException {
Statement stmt = dbConn.createStatement( );
for( int i = 0; i < geo_table.length; i++ ) {
stmt.executeUpdate( "drop table if exists temp.tighten_" + geo_table[i] + "_sui" );
stmt.executeUpdate( "create table temp.tighten_" + geo_table[i] + "_sui" +
" select distinct * from geo." + geo_table[i] + "_sui" );
stmt.executeUpdate( "delete from geo." + geo_table[i] + "_sui" );
stmt.executeUpdate( "insert into geo." + geo_table[i] + "_sui select * from temp.tighten_" + geo_table[i] + "_sui" );
}
}
public void removeWhereText( String removeSui, String text ) throws IOException, SQLException {
System.out.println( ">>> Regexp '" + text + "' and String " + removeSui + " appear in:\n" );
int count = 0;
for( int i = 0; i < geo_table.length; i++ ) {
Statement stmt = dbConn.createStatement( );
stmt.executeUpdate( "create table if not exists " +
"geo." + geo_table[i] + "_sui_removed like geo." + geo_table[i] + "_sui" );
stmt.executeUpdate( "insert into geo." + geo_table[i] + "_sui_removed " +
"select b.* from " +
" geo." + geo_table[i] + " as a " +
" inner join geo." + geo_table[i] + "_sui as b on a." + geo_key[i] + "=b." + geo_key[i] +
" where a." + geo_text[i] + " regexp '" + text + "' and b.sui = '" + removeSui + "'" );
ResultSet rset = stmt.executeQuery( "select a." + geo_key[i] + ", a." + geo_text[i] + " from " +
" geo." + geo_table[i] + " as a " +
" inner join geo." + geo_table[i] + "_sui as b on a." + geo_key[i] + "=b." + geo_key[i] +
" where a." + geo_text[i] + " regexp '" + text + "' and b.sui = '" + removeSui + "'" );
while( rset.next( ) ) {
System.out.println( geo_table[i] + " " + rset.getString(1) + ": " + rset.getString(2) );
count ++;
}
stmt.executeUpdate( "delete from geo." + geo_table[i] + "_sui using " +
" geo." + geo_table[i] + ", " +
" geo." + geo_table[i] + "_sui " +
" where " +
" geo." + geo_table[i] + "." + geo_key[i] + " = geo." + geo_table[i] + "_sui." + geo_key[i] + " and " +
" geo." + geo_table[i] + "." + geo_text[i] + " regexp '" + text + "' and " +
" geo." + geo_table[i] + "_sui.sui = '" + removeSui + "'" );
}
System.out.println( ">>> Total found: " + count + "\n" );
}
public void removeWherePhrase( String removeSui, String text ) throws IOException, SQLException {
System.out.println( ">>> Regexp '" + text + "' and String " + removeSui + " appear in:\n" );
int count = 0;
for( int i = 0; i < geo_table.length; i++ ) {
Statement stmt = dbConn.createStatement( );
stmt.executeUpdate( "create table if not exists " +
"geo." + geo_table[i] + "_sui_removed like geo." + geo_table[i] + "_sui" );
stmt.executeUpdate( "insert into geo." + geo_table[i] + "_sui_removed " +
"select b.* from " +
" geo." + geo_table[i] + " as a " +
" inner join geo." + geo_table[i] + "_sui as b on a." + geo_key[i] + "=b." + geo_key[i] +
" where b.phrase regexp '" + text + "' and b.sui = '" + removeSui + "'" );
ResultSet rset = stmt.executeQuery( "select a." + geo_key[i] + ", b.phrase from " +
" geo." + geo_table[i] + " as a " +
" inner join geo." + geo_table[i] + "_sui as b on a." + geo_key[i] + "=b." + geo_key[i] +
" where b.phrase regexp '" + text + "' and b.sui = '" + removeSui + "'" );
while( rset.next( ) ) {
System.out.println( geo_table[i] + " " + rset.getString(1) + ": " + rset.getString(2) );
count ++;
}
stmt.executeUpdate( "delete from geo." + geo_table[i] + "_sui using " +
" geo." + geo_table[i] + ", " +
" geo." + geo_table[i] + "_sui " +
" where " +
" geo." + geo_table[i] + "." + geo_key[i] + " = geo." + geo_table[i] + "_sui." + geo_key[i] + " and " +
" geo." + geo_table[i] + "_sui.phrase regexp '" + text + "' and " +
" geo." + geo_table[i] + "_sui.sui = '" + removeSui + "'" );
}
System.out.println( ">>> Total found: " + count + "\n" );
}
public void removeAllWithPhrase( String text ) throws IOException, SQLException {
System.out.println( ">>> Regexp '" + text + " appear in:\n" );
int count = 0;
for( int i = 0; i < geo_table.length; i++ ) {
Statement stmt = dbConn.createStatement( );
stmt.executeUpdate( "create table if not exists " +
"geo." + geo_table[i] + "_sui_removed like geo." + geo_table[i] + "_sui" );
stmt.executeUpdate( "insert into geo." + geo_table[i] + "_sui_removed " +
"select b.* from " +
" geo." + geo_table[i] + " as a " +
" inner join geo." + geo_table[i] + "_sui as b on a." + geo_key[i] + "=b." + geo_key[i] +
" where b.phrase regexp '" + text + "' " );
ResultSet rset = stmt.executeQuery( "select a." + geo_key[i] + ", b.phrase from " +
" geo." + geo_table[i] + " as a " +
" inner join geo." + geo_table[i] + "_sui as b on a." + geo_key[i] + "=b." + geo_key[i] +
" where b.phrase regexp '" + text + "' " );
while( rset.next( ) ) {
System.out.println( geo_table[i] + " " + rset.getString(1) + ": " + rset.getString(2) );
count ++;
}
stmt.executeUpdate( "delete from geo." + geo_table[i] + "_sui using " +
" geo." + geo_table[i] + ", " +
" geo." + geo_table[i] + "_sui " +
" where " +
" geo." + geo_table[i] + "." + geo_key[i] + " = geo." + geo_table[i] + "_sui." + geo_key[i] + " and " +
" geo." + geo_table[i] + "_sui.phrase regexp '" + text + "'" );
}
System.out.println( ">>> Total found: " + count + "\n" );
}
public void addWhereText( String findSui, String findText, String addSui ) throws IOException, SQLException {
System.out.println( ">>> Regexp '" + findText + "' and String " + findSui + " appear in:\n" );
int count = 0;
for( int i = 0; i < geo_table.length; i++ ) {
PreparedStatement stmt2 = dbConn.prepareStatement( "insert into temp.toBeAdded" + geo_table[i] + " set " + geo_key[i] + " = ?, " +
" sui = ?, phrase = ?, score = ?" );
Statement stmt = dbConn.createStatement( );
stmt.executeUpdate( "create table temp.toBeAdded" + geo_table[i] + " like geo." + geo_table[i] + "_sui" );
ResultSet rset = stmt.executeQuery( "select a." + geo_key[i] + ", a." + geo_text[i] + ", " +
" b.phrase, b.score " +
" from " +
" geo." + geo_table[i] + " as a " +
" inner join geo." + geo_table[i] + "_sui as b on a." + geo_key[i] + "=b." + geo_key[i] +
" where a." + geo_text[i] + " regexp '" + findText + "' and b.sui = '" + findSui + "'" );
while( rset.next( ) ) {
System.out.println( geo_table[i] + " " + rset.getString(1) + ": " + rset.getString(2) );
stmt2.setInt( 1, rset.getInt( 1 ) );
stmt2.setString( 2, addSui );
stmt2.setString( 3, rset.getString( 3 ) );
stmt2.setInt( 4, 1000 );
stmt2.executeUpdate( );
count ++;
}
stmt.executeUpdate( "delete from temp.toBeAdded" + geo_table[i] + " using temp.toBeAdded" + geo_table[i] + ", " +
" geo." + geo_table[i] + "_sui where " +
" temp.toBeAdded" + geo_table[i] + "." + geo_key[i] + " = geo." + geo_table[i] + "_sui." + geo_key[i] + " and " +
" temp.toBeAdded" + geo_table[i] + ".sui = geo." + geo_table[i] + "_sui.sui and " +
" temp.toBeAdded" + geo_table[i] + ".phrase = geo." + geo_table[i] + "_sui.phrase " );
stmt.executeUpdate( "insert into geo." + geo_table[i] + "_sui select * from temp.toBeAdded" + geo_table[i] );
stmt.executeUpdate( "drop table temp.toBeAdded" + geo_table[i] );
}
System.out.println( ">>> Total found: " + count + "\n" );
}
public void removeTextGroup( String[] sui_array, String[] text_array ) throws IOException, SQLException {
for( int i = 0; i < text_array.length; i++ ) {
for( int j = 0; j < sui_array.length; j++ ) {
removeWhereText( sui_array[j], text_array[i] );
}
}
}
public void removePhraseGroup( String[] sui_array, String[] phrase_array ) throws IOException, SQLException {
for( int i = 0; i < phrase_array.length; i++ ) {
for( int j = 0; j < sui_array.length; j++ ) {
removeWherePhrase( sui_array[j], phrase_array[i] );
}
}
}
public static void main(String[] unused) throws Exception
{
try {
RemoveReplace run = new RemoveReplace( );
run.removeWherePhrase( "S0289852", "RG" );
run.removeWherePhrase( "S1324252", "RG" );
// | C0035316 | ENG | S | L0215834 | PF | S0289852 | retinal ganglion | 0 |
// | C0565313 | ENG | P | L1103177 | PF | S1324252 | Radical gastrectomy | 0 |
run.removeWherePhrase( "S0020086", "BMC Bioinformatics" );
run.removeWherePhrase( "S0821111", "BMC Bioinformatics" );
// | C0005963 | ENG | P | L0005963 | PF | S0020086 | Bone Mineral Content | 0 |
// | C0005955 | ENG | P | L0005955 | VO | S0821111 | Bone Marrow Cell | 0 |
run.removeWherePhrase( "S0000706", "DN" );
run.removeWherePhrase( "S0001050", "DN" );
run.removeWherePhrase( "S0320503", "DN" );
// | C0011882 | ENG | P | L0011882 | VO | S0000706 | Neuropathy, diabetic | 3 |
// | C0012461 | ENG | P | L0012461 | PF | S0001050 | Dinitrocresol | 3 |
//| 760 | S0320503 | C0201987 | ENG | P | L0244964 | PF | S0320503 | Dibucaine number | 3 |
run.removeWherePhrase( "S0358988", "BG" );
run.removeWherePhrase( "S0820142", "BG" );
run.removeWherePhrase( "S0043655", "BG" );
run.removeWherePhrase( "S0018270", "BG" );
run.removeWherePhrase( "S0018688", "BG" );
run.removeWherePhrase( "S0298909", "BG" );
run.removeWherePhrase( "S0415585", "BG" );
run.removeWherePhrase( "S0138932", "BG" );
run.removeWherePhrase( "S0821148", "BG" );
run.removeWherePhrase( "S0358988", "BG" );
//| 576 | S0043655 | C0004781 | ENG | P | L0004781 | VO | S0043655 | Ganglion, Basal | 0 |
//| 576 | S0018270 | C0004972 | ENG | P | L0004972 | PF | S0018270 | Bender-Gestalt Test | 0 |
//| 576 | S0018688 | C0005220 | ENG | P | L0005220 | PF | S0018688 | beta-Galactosidase | 0 |
//| 576 | S0820142 | C0005802 | ENG | P | L0005802 | VO | S0820142 | Blood Glucose <1> | 0 |
//| 576 | S0298909 | C0005976 | ENG | S | L0018135 | VO | S0298909 | Bone graft, NOS | 3 |
//| 576 | S0415585 | C0017776 | ENG | P | L0005224 | VC | S0415585 | beta-Glucuronidase | 0 |
//| 576 | S0138932 | C0054053 | ENG | P | L0054053 | PF | S0138932 | brilliant green | 0 |
//| 576 | S0821148 | C0181075 | ENG | S | L0018135 | PF | S0821148 | Bone graft <1> | 0 |
//| 576 | S0358988 | C0230694 | ENG | S | L0286035 | PF | S0358988 | Birbeck granule | 0 |
run.removeWherePhrase( "S0405467", "SF" );
run.removeWherePhrase( "S0087857", "SF" );
run.removeWherePhrase( "S0087669", "SF" );
run.removeWherePhrase( "S0325867", "SF" );
run.removeWherePhrase( "S0084131", "SF" );
run.removeWherePhrase( "S0002392", "SF" );
run.removeWherePhrase( "S0085597", "SF" );
run.removeWherePhrase( "S0089361", "SF" );
run.removeWherePhrase( "S0088580", "SF" );
run.removeWherePhrase( "S0090619", "SF" );
run.removeWherePhrase( "S0223528", "SF" );
run.removeWherePhrase( "S1025369", "SF" );
run.removeWherePhrase( "S1030171", "SF" );
run.removeWherePhrase( "S1226749", "SF" );
//| 576 | S0405467 | C0007806 | ENG | S | L0302294 | PF | S0405467 | Spinal fluid | 3 |
//| 576 | S0087857 | C0015502 | ENG | S | L0038114 | PF | S0087857 | Stable Factor | 0 |
//| 576 | S0087669 | C0016663 | ENG | P | L0016663 | VO | S0087669 | Spontaneous Fracture | 0 |
//| 576 | S0325867 | C0019841 | ENG | S | L0249507 | PF | S0325867 | Swine Fever | 0 |
//| 576 | S0084131 | C0036285 | ENG | P | L0036285 | PF | S0084131 | Scarlet Fever | 0 |
//| 576 | S0002392 | C0036614 | ENG | S | L0036627 | PF | S0002392 | Seminal fluid | 0 |
//| 576 | S0085597 | C0036969 | ENG | S | L0036969 | PF | S0085597 | Shipping Fever | 0 |
//| 576 | S0089361 | C0037657 | ENG | S | L0038729 | PF | S0089361 | Sulfation Factor | 0 |
//| 576 | S0088580 | C0038404 | ENG | S | L0038404 | PF | S0088580 | Streptococcus faecalis | 0 |
//| 576 | S0090619 | C0039097 | ENG | P | L0039097 | PF | S0090619 | Synovial Fluid | 0 |
//| 576 | S0223528 | C0149775 | ENG | S | L0159581 | PF | S0223528 | SEIZURE FREQUENCY | 0 |
//| 576 | S1025369 | C0427406 | ENG | S | L0836784 | VO | S1025369 | Serum ferritin | 3 |
//| 576 | S1030171 | C0453863 | ENG | P | L0841141 | PF | S1030171 | Snack food | 3 |
//| 576 | S1226749 | C0597448 | ENG | P | L1018929 | PF | S1226749 | sham feeding | 0 |
run.removeWherePhrase( "S0952026", "NF" );
//| 576 | S0952026 | C0392760 | ENG | S | L0874700 | PF | S0952026 | NF | 3 |
run.removeWherePhrase( "S0143040", "chip" );
//| 576 | S0143040 | C0057856 | ENG | S | L0115588 | PF | S0143040 | CHIP | 0 |
run.removeWherePhrase( "S0138001", "BF" );
//| 576 | S0138001 | C0053844 | ENG | P | L0053844 | PF | S0138001 | blastogenic factor | 0 |
run.removeWherePhrase( "S0402628", "SRT" );
//| 576 | S0402628 | C0234742 | ENG | S | L0318097 | PF | S0402628 | SRT | 3 |
run.removeWherePhrase( "S1466930", "ORF" );
//| 136 | S1466930 | (ORF_intergenic_v1 | 684 | C0013570 | Orf <1> |
run.removeWherePhrase( "S1041533", "TL" );
//| 29 | S1041533 | in Ferea TL | 694 | C0039738 | TL |
run.removeWherePhrase( "S0466835", "ACAD" );
//| 29 | S0466835 | Proc Natl Acad Sci USA 96:9721-6 | 677 | C0268596 | ACAD |
run.removeWherePhrase( "S0509969", "SVD" );
//| 340 | S0509969 | (SVD) | 666 | C0039010 | SVD |
run.removePhraseGroup( new String[] {"S0086928", "S1437024", "S0205668", "S0320596", "S0511492",
"S0737123", "S1018955", "S1018957", "S1421396" },
new String[] {"[[:<:]]SOM[[:>:]]" } );
//| 340 | S0086928 | (SOM) | 666 | C0034839 | Somatotropin Receptor |
//| 340 | S1437024 | (SOM) | 666 | C0037668 | somatotropin RH |
//| 340 | S0205668 | (SOM) | 666 | C0074870 | somatotropin 20K |
//| 340 | S0320596 | (SOM) | 666 | C0202056 | Somatotropin measurement |
//| 340 | S0511492 | (SOM) | 666 | C0271561 | Somatotropin deficiency, NOS |
//| 340 | S0737123 | (SOM) | 666 | C0304821 | Somatotropin preparation |
//| 340 | S1018955 | (SOM) | 666 | C0370001 | SOMATOTROPIN AB |
//| 340 | S1018957 | (SOM) | 666 | C0487554 | SOMATOTROPIN AG |
//| 340 | S1421396 | (SOM) | 666 | C0636208 | somatotropin sulfoxide |
run.removePhraseGroup( new String[] {"S0007105","S0467600"},
new String[] {"[[:<:]]ABS[[:>:]]", "[[:<:]]AB[[:>:]]"} );
// S0007105 <-- C0000786: Spontaneous abortion
//| 576 | S0007105 | C0000786 | ENG | S | L0000786 | PF | S0007105 | Abortion <1> | 0 |
//| 576 | S0467600 | C0156543 | ENG | S | L0000786 | PF | S0467600 | Abortion, NOS | 3 |
run.removeWherePhrase( "S0400643", "RL" );
run.removeWherePhrase( "S0400614", "RL" );
run.removeWherePhrase( "S0726516", "RL" );
//| 576 | S0400643 | C0225706 | ENG | P | L0310843 | PF | S0400643 | Right lung, NOS | 3 |
//| 576 | S0400614 | C0230442 | ENG | P | L0310060 | PF | S0400614 | Right leg | 0 |
//| 576 | S0726516 | C0450415 | ENG | P | L0590759 | VO | S0726516 | Right lateral | 0 |
run.removeWherePhrase( "S0906049", "HZ" );
//| 576 | S0906049 | C0439482 | ENG | P | L0854953 | PF | S0906049 | Hz | 3 |
run.removeWherePhrase( "S0852831", "DD" );
//| 576 | S0852831 | C0332143 | ENG | S | L0557030 | PF | S0852831 | DD | 3 |
run.removeWherePhrase( "S0073476", "PCT" );
//| 576 | S0073476 | C0031740 | ENG | P | L0031740 | PF | S0073476 | Photochemotherapy | 0 |
run.removeWherePhrase( "S0029140", "culture" );
// | C0681854 | ENG | P | L1194008 | VW | S1864674 | culture cell study | 0 |
// | C0010453 | ENG | S | L0010453 | VO | S0029140 | Cultures | 0 |
run.removePhraseGroup( new String[] {"S0751121","S1919710","S1919711","S0100573","S0386680","S0751121",
"S1919710","S1919711","S0100573","S0386680"},
new String[] { "[ -/]Y", "^y[ ]" } );
//| 3 | S0751121 | C0041485 | ENG | P | L0041485 | VO | S0751121 | Tyrosine <1> | 0 |
//| 3 | S0386680 | C0043381 | ENG | S | L0291381 | PF | S0386680 | Male sex chromosome | 3 |
//| 3 | S1919710 | C0043405 | ENG | P | L0043405 | VO | S1919710 | Yersinia <1> | 0 |
//| 3 | S1919711 | C0043407 | ENG | s | L0043405 | PF | S1919711 | Yersinia <2> | 0 |
//| 3 | S0100573 | C0043432 | ENG | P | L0887573 | PF | S0100573 | Yttrium | 0 |
run.removeWhereText( "S0002409", "Axon Genepix" );
//| 4681 | S0002409 | C0004461 | ENG | P | L0004461 | VO | S0002409 | Axon | 0 |
run.removeWhereText( "S1344225", "GBM" );
//| 696 | S1344225 | SAGE_Duke_GBM_H1110 | 624 | C0599297 | glomerular basement membrane |
run.removeWhereText( "S0100553", "yo" );
run.removeWhereText( "S0100553", "YO" );
//| 696 | S0100553 | from a 51 yo male | 469 | C0043421 | Yohimbine |
run.removeWherePhrase( "S0032266", "DM" );
run.removeWherePhrase( "S0367334", "DM" );
//| 6768 | S0032266 | DM\\(LL\\) | 469 | C0011849 | ENG | P | L0011849 | PF | S0032266 | Diabetes Mellitus | 0 |
//| 6768 | S0367334 | DM\\(LL\\) | 469 | C0232262 | ENG | P | L0296096 | PF | S0367334 | Diastolic murmur, NOS | 3 |
run.removeWhereText( "S0678803", "\\(LL\\)" );
run.removeWhereText( "S0058982", "\\(LL\\)" );
run.removeWhereText( "S1335060", "\\(LL\\)" );
//| 6768 | S0678803 | DM\\(LL\\) | 635 | C0023448 | ENG | S | L0024294 | VO | S0678803 | Lymphoid leukaemia | 3 |
//| 6768 | S0058982 | DM\\(LL\\) | 635 | C0079748 | ENG | S | L0079748 | PF | S0058982 | Lymphoma, Lymphoblastic | 0 |
//| 6768 | S1335060 | DM\\(LL\\) | 635 | C0079764 | ENG | S | L0079748 | PF | S1335060 | Lymphoblastic lymphoma NOS | 3 |
run.removeWhereText( "S0085881", "Silicon Genetics" );
run.removeWhereText( "S0007256", "Silicon Genetics" );
run.removeWhereText( "S0007257", "Silicon Genetics" );
//| 10997 | S0085881 | (Silicon Genetics) | 527 | C0037107 | ENG | P | L0037098 | PF | S0085881 | Silicon | 0 |
//| 10997 | S0085881 | (Silicon Genetics) | 527 | C0037107 | ENG | P | L0037098 | PF | S0085881 | Silicon | 0 |
//| 10997 | S0007256 | (Silicon Genetics) | 694 | C0017398 | ENG | S | L0017398 | PF | S0007256 | Genetics <1> | 0 |
run.removeWhereText( "S0216569", " X " );
run.removeWhereText( "S0086918", " X " );
run.removeWhereText( "S0216569", " x " );
run.removeWhereText( "S0086918", " x " );
//| 10997 | S0216569 | in 0.1 x SS | 462 | C0078606 | ENG | P | L0078606 | PF | S0216569 | xanthosine | 0 |
//| 10997 | S0086918 | in 0.1 x SS | 628 | C0037658 | ENG | P | L0037658 | PF | S0086918 | Somatosensory Cortex | 0 |
run.removeWhereText( "S1432125", "dT" );
//| 10997 | S1432125 | (dT | 633 | C0001957 | ENG | S | L0298007 | PF | S1432125 | DTs | 0 |
run.removeWhereText( "S0578063", "3M" );
//| 10997 | S0578063 | 3M sodium chloride | 524 | C0332060 | ENG | P | L0475163 | PF | S0578063 | 3M | 3 |
run.removeWhereText( "S1409383", "PFU" );
//| C0600435 | ENG | P | L1176803 | PF | S1409383 | Pyrococcus furiosus | 0 |
run.removePhraseGroup( new String[] {
"S0083749", "S0083832", "S0084065", "S0084463", "S0085394", "S0086295", "S0088515", "S0088667", "S0089693",
"S0091369", "S0094017", "S0255723", "S0273880", "S0403192", "S0405936", "S1024538", "S1026620", "S1031454",
"S1033645", "S1034112", "S1034259", "S1034362", "S1034584", "S1034599", "S1034666", "S1036117", "S1424270",
"S1437440", "S1467666", "S1790457", "S1790458", "S1790475", "S1790476", "S2164981", "S2164982"},
new String[] {
"^St[ ]","^St\\\\.[ ]","^ST[ ]","^ST\\\\.[ ]",
"[ ]St[ ]","[ ]St\\\\.[ ]","[ ]ST[ ]","[ ]ST\\\\.[ ]"} );
//| 486 | S0403192 | St Louis | Saint |
//| 672 | S0739226 | St Louis | 472 | C0006736 | ENG | S | L0038372 | PF | S0739226 | Stone, NOS | 3 |
//| 672 | S1026620 | St Louis | 472 | C0009953 | ENG | S | L0036976 | PF | S1026620 | Shock Therapy <1> | 0 |
//| 672 | S0038970 | St Louis | 472 | C0014877 | ENG | P | L0014877 | PF | S0038970 | Esotropia | 0 |
//| 672 | S0255723 | St Louis | 472 | C0015260 | ENG | S | L0189329 | PF | S0255723 | Stress Test | 0 |
//| 672 | S1424270 | St Louis | 472 | C0027646 | ENG | S | L1225123 | VO | S1424270 | stage | 0 |
//| 672 | S0084065 | St Louis | 472 | C0036264 | ENG | P | L1223361 | PF | S0084065 | Scala Tympani | 0 |
//| 672 | S0084463 | St Louis | 472 | C0036435 | ENG | P | L0036435 | PF | S0084463 | Sclerotherapy | 0 |
//| 672 | S0086295 | St Louis | 472 | C0037296 | ENG | P | L0037296 | VO | S0086295 | Skin Test | 0 |
//| 672 | S1034362 | St Louis | 472 | C0038351 | ENG | P | L0038351 | VO | S1034362 | Stomach <1> | 0 |
//| 672 | S0088667 | St Louis | 472 | C0038454 | ENG | S | L0038454 | PF | S0088667 | Stroke | 0 |
//| 672 | S0089693 | St Louis | 472 | C0038887 | ENG | P | L0038887 | PF | S0089693 | Surface Tension | 0 |
//| 672 | S0091369 | St Louis | 472 | C0039239 | ENG | P | L0039239 | PF | S0091369 | Tachycardia, Sinus | 0 |
//| 672 | S0094017 | St Louis | 472 | C0040338 | ENG | P | L0040338 | PF | S0094017 | Tobacco, Smokeless | 0 |
//| 672 | S0273880 | St Louis | 472 | C0175243 | ENG | P | L0203308 | PF | S0273880 | stria terminalis | 0 |
//| 672 | S1790475 | St Louis | 472 | C0205257 | ENG | S | L0249022 | PF | S1790475 | Subtotal <1> | 0 |
//| 672 | S1034112 | St Louis | 472 | C0224166 | ENG | S | L0885811 | PF | S1034112 | Sternothyroid | 0 |
//| 672 | S1024538 | St Louis | 472 | C0224453 | ENG | S | L0884718 | PF | S1024538 | Semitendinosus | 0 |
//| 672 | S1790457 | St Louis | 472 | C0232920 | ENG | S | L0318160 | PF | S1790457 | Sterile <1> | 0 |
//| 672 | S0405936 | St Louis | 472 | C0234402 | ENG | P | L0318170 | PF | S0405936 | Stimulus, NOS | 3 |
//| 672 | S1031454 | St Louis | 472 | C0402015 | ENG | S | L0885420 | PF | S1031454 | Speech therapist | 3 |
//| 672 | S1034259 | St Louis | 472 | C0441691 | ENG | S | L0885824 | PF | S1034259 | Stimulation | 3 |
//| 672 | S1034666 | St Louis | 472 | C0442658 | ENG | P | L0885882 | PF | S1034666 | Street | 3 |
//| 672 | S1034584 | St Louis | 472 | C0445291 | ENG | P | L0885868 | PF | S1034584 | Straight | 3 |
//| 672 | S1033645 | St Louis | 472 | C0449438 | ENG | P | L0885755 | PF | S1033645 | Status | 3 |
//| 672 | S1036117 | St Louis | 472 | C0449560 | ENG | P | L0886030 | PF | S1036117 | Subtype | 3 |
//| 672 | S1437440 | St Louis | 472 | C0543467 | ENG | S | L1198899 | PF | S1437440 | surgical treatment | 0 |
//| 672 | S1790458 | St Louis | 472 | C0678108 | ENG | S | L0318160 | PF | S1790458 | sterile <2> | 0 |
//| 672 | S1467666 | St Louis | 472 | C0684248 | ENG | S | L1225123 | PF | S1467666 | Stage <2> | 0 |
//| 672 | S1790476 | St Louis | 472 | C0728939 | ENG | P | L0249022 | VO | S1790476 | Subtotal <2> | 0 |
run.removeWherePhrase( "S1424803", "\\\\(AA\\\\)" );
run.removeWherePhrase( "S1424803", "[+]AA" );
//| S1424803 | AA |
run.removePhraseGroup( new String[] { "S1788917" },
new String[] { "<{b|B)(r|R)>" } );
//| S1788917 | Br <1> |
run.removePhraseGroup( new String[] {"S0016056","S1966678","S0015155","S0013634","S0016971","S0583866","S0470807","S0812555","S1343700","S1465434"},
new String[] {"\\\\(AI\\\\)", "[ ]AI[ ]"} );
//| 351 | S0012316 | in the sperm AI SST | 635 | C0002112 | ENG | P | L0002112 | PF | S0012316 | Allergy and Immunology | 0 |
// 351 | S1966678 | in the sperm AI SST | 635 | C0003006 | ENG | P | L0003006 | VO | S1966678 | angiotensin I <1> | 0 |
// 351 | S0015155 | in the sperm AI SST | 635 | C0003504 | ENG | S | L0003494 | PF | S0015155 | Aortic Incompetence | 0 |
// 351 | S0013634 | in the sperm AI SST | 635 | C0003766 | ENG | S | L0002790 | PF | S0013634 | Anaphylatoxin Inactivator | 0 |
// 351 | S0016056 | in the sperm AI SST | 635 | C0003916 | ENG | P | L0003916 | PF | S0016056 | Artificial Intelligence | 0 |
// 351 | S0016971 | in the sperm AI SST | 635 | C0004368 | ENG | P | L0004368 | PF | S0016971 | Autoimmunity | 0 |
// 351 | S1465434 | in the sperm AI SST | 635 | C0021587 | ENG | P | L0021587 | VO | S1465434 | artificial insemination <1> | 0 |
// 351 | S0583866 | in the sperm AI SST | 635 | C0151736 | ENG | P | L0161616 | PF | S0583866 | Accidental injury | 3 |
// 351 | S0470807 | in the sperm AI SST | 635 | C0277909 | ENG | S | L0372424 | PF | S0470807 | Apical impulse | 3 |
// 351 | S0812555 | in the sperm AI SST | 635 | C0443146 | ENG | P | L0735102 | PF | S0812555 | Autoimmune | 3 |
// 351 | S1343700 | in the sperm AI SST | 635 | C0596087 | ENG | P | L1119799 | VO | S1343700 | angiogenesis inhibitor | 0 |
// 351 | S0809589 | in the sperm AI SST | 635 | C0699895 | ENG | S | L0021587 | PF | S0809589 | Artificial insemination NOS | 3 |
run.removePhraseGroup( new String[] {"S0757360", "S1348507", "S0757324", "S0517363", "S2720221", "S0087713", "S0002695", "S0757337", "S0757297",
"S0216109", "S0517353", "S0258205", "S0302846", "S0757310", "S1426804", "S2132140", "S0413560", "S1236532",
"S1326109", "S0401376", "S0504027", "S0757333", "S0757323", "S0756662", "S0757296", "S0757295", "S0757330",
"S0757358", "S2378526", "S2760577", "S0757341", "S0757334", "S0757345", "S0757309", "S0757377", "S0757340",
"S0757344", "S0757353", "S0757346", "S0757354", "S0757306", "S0757319", "S0757335", "S0757300", "S0757312",
"S0757355", "S0757318", "S0757342", "S0757313", "S0757343", "S0757331", "S0757327", "S0757299", "S0757317",
"S2760576", "S0757307", "S0757348", "S0757339", "S0757352", "S0757320", "S0757321", "S0757298", "S0757315",
"S0757359", "S1063368", "S1063359", "S1063364", "S2142152", "S1063245", "S1063209", "S1063257", "S1063252",
"S1063241", "S1063435", "S1063433", "S0757328", "S1063379", "S1063361", "S1063377", "S1063244", "S1063256",
"S1063363", "S1063437", "S1063380", "S1334593", "S0273502", "S1435049", "S1435275", "S1436862", "S1435456",
"S2070073", "S2070074", "S2142153", "S2382977", "S2378528", "S2378560", "S2378531", "S2378539", "S2378541",
"S2378536", "S2725062", "S2378538", "S2382981", "S2378530", "S2721208", "S2378524", "S2760578", "S2380947",
"S2380946", "S1029046", "S0041434" },
new String[] {"WS!"} );
//| 6803 | S1348507 | WS! | 666 | C0007457 | ENG | S | L0882851 | VCW | S1348507 | white race | 0 |
//| 6803 | S0757324 | WS! | 666 | C0031556 | ENG | S | L0590982 | PF | S0757324 | White leg | 3 |
//| 6803 | S0517363 | WS! | 666 | C0040249 | ENG | P | L0403119 | PF | S0517363 | White piedra | 0 |
//| 6803 | S2720221 | WS! | 666 | C0042527 | ENG | S | L0851534 | PF | S2720221 | Hellebore, White | 0 |
//| 6803 | S0087713 | WS! | 666 | C0043154 | ENG | P | L0080335 | VO | S0087713 | Spot, White | 0 |
//| 6803 | S0002695 | WS! | 666 | C0043155 | ENG | P | L0043155 | PF | S0002695 | White wax | 0 |
//| 6803 | S0757337 | WS! | 666 | C0043400 | ENG | P | L0602473 | PF | S0757337 | White phosphorus | 3 |
//| 6803 | S0757297 | WS! | 666 | C0052416 | ENG | S | L0514208 | PF | S0757297 | White arsenic | 3 |
//| 6803 | S0216109 | WS! | 666 | C0148747 | ENG | P | L0158430 | PF | S0216109 | white spirit | 0 |
//| 6803 | S0517353 | WS! | 666 | C0158931 | ENG | S | L0373534 | PF | S0517353 | White asphyxia | 3 |
//| 6803 | S0258205 | WS! | 666 | C0162749 | ENG | P | L0189979 | PF | S0258205 | White Pepper | 0 |
//| 6803 | S0302846 | WS! | 666 | C0188723 | ENG | S | L0227734 | PF | S0302846 | White operation | 3 |
//| 6803 | S0757310 | WS! | 666 | C0220938 | ENG | P | L0547729 | PF | S0757310 | White color | 0 |
//| 6803 | S1426804 | WS! | 666 | C0221786 | ENG | P | L1119743 | PF | S1426804 | White American | 0 |
//| 6803 | S2132140 | WS! | 666 | C0225322 | ENG | S | L1819380 | PF | S2132140 | White fat | 0 |
//| 6803 | S0413560 | WS! | 666 | C0225363 | ENG | P | L0301597 | PF | S0413560 | White fibrocartilage | 3 |
//| 6803 | S1236532 | WS! | 666 | C0234438 | ENG | S | L1025578 | PF | S1236532 | White out | 3 |
//| 6803 | S1326109 | WS! | 666 | C0239804 | ENG | P | L0305813 | PF | S1326109 | White hair | 3 |
//| 6803 | S0401376 | WS! | 666 | C0240961 | ENG | P | L0317586 | PF | S0401376 | SCLERA, WHITE | 0 |
//| 6803 | S0504027 | WS! | 666 | C0282298 | ENG | P | L0402925 | PF | S0504027 | Petrolatum, White | 0 |
//| 6803 | S0757333 | WS! | 666 | C0302229 | ENG | P | L0599684 | VC | S0757333 | White ointment | 3 |
//| 6803 | S0757323 | WS! | 666 | C0303232 | ENG | S | L0590869 | PF | S0757323 | White lead | 3 |
//| 6803 | S0756662 | WS! | 666 | C0310637 | ENG | P | L0591768 | PF | S0756662 | WHITE LINIMENT | 3 |
//| 6803 | S0757296 | WS! | 666 | C0319646 | ENG | S | L0500836 | PF | S0757296 | White amanita | 3 |
//| 6803 | S0757295 | WS! | 666 | C0319809 | ENG | S | L0496423 | VO | S0757295 | White agaric | 3 |
//| 6803 | S0757a330 | WS! | 666 | C0323312 | ENG | S | L0596934 | PF | S0757330 | White moth | 3 |
//| 6803 | S0757358 | WS! | 666 | C0324654 | ENG | P | L0609209 | PF | S0757358 | White turkey | 3 |
//| 6803 | S2378526 | WS! | 666 | C0325023 | ENG | S | L1955589 | PF | S2378526 | white bear | 0 |
//| 6803 | S2760577 | WS! | 666 | C1140552 | ENG | S | L0887481 | VO | S2760577 | White Whale <1> | 0 |
//| 6803 | S0757341 | WS! | 666 | C0325187 | ENG | S | L0605679 | PF | S0757341 | White rhinoceros | 3 |
//| 6803 | S0757334 | WS! | 666 | C0325696 | ENG | P | L0601722 | PF | S0757334 | White peafowl | 3 |
//| 6803 | S0757345 | WS! | 666 | C0325859 | ENG | P | L0607089 | PF | S0757345 | White sheathbill | 3 |
//| 6803 | S0757309 | WS! | 666 | C0326018 | ENG | S | L0547003 | PF | S0757309 | White cockatoo | 3 |
//| 6803 | S0757377 | WS! | 666 | C0326757 | ENG | P | L0571494 | PF | S0757377 | White-eye, NOS | 3 |
//| 6803 | S0757340 | WS! | 666 | C0327538 | ENG | S | L0605270 | PF | S0757340 | White rattlesnake | 3 |
//| 6803 | S0757344 | WS! | 666 | C0327628 | ENG | S | L0607079 | PF | S0757344 | White shark | 3 |
//| 6803 | S0757353 | WS! | 666 | C0327757 | ENG | S | L0607984 | PF | S0757353 | White sturgeon | 3 |
//| 6803 | S0757346 | WS! | 666 | C0328110 | ENG | S | L0607135 | PF | S0757346 | White shiner | 3 |
//| 6803 | S0757354 | WS! | 666 | C0328264 | ENG | S | L0608030 | PF | S0757354 | White sucker | 3 |
//| 6803 | S0757306 | WS! | 666 | C0328320 | ENG | S | L0538281 | PF | S0757306 | White catfish | 3 |
//| 6803 | S0757319 | WS! | 666 | C0328450 | ENG | S | L0581629 | PF | S0757319 | White hake | 3 |
//| 6803 | S0757335 | WS! | 666 | C0328721 | ENG | S | L0601976 | PF | S0757335 | White perch | 3 |
//| 6803 | S0757300 | WS! | 666 | C0328722 | ENG | S | L0521631 | PF | S0757300 | White bass | 3 |
//| 6803 | S0757312 | WS! | 666 | C0328829 | ENG | S | L0553437 | PF | S0757312 | White crappie | 3 |
//| 6803 | S0757355 | WS! | 666 | C0329007 | ENG | S | L0608032 | PF | S0757355 | White suckerfish | 3 |
//| 6803 | S0757318 | WS! | 666 | C0329108 | ENG | S | L0580814 | PF | S0757318 | White grunt | 3 |
//| 6803 | S0757342 | WS! | 666 | C0329137 | ENG | S | L0606830 | PF | S0757342 | White seabass | 3 |
//| 6803 | S0757313 | WS! | 666 | C0329153 | ENG | S | L0553938 | PF | S0757313 | White croaker | 3 |
//| 6803 | S0757343 | WS! | 666 | C0329235 | ENG | S | L0606839 | PF | S0757343 | White seaperch | 3 |
//| 6803 | S0757331 | WS! | 666 | C0329301 | ENG | S | L0597207 | PF | S0757331 | White mullet | 3 |
//| 6803 | S0757327 | WS! | 666 | C0329613 | ENG | S | L0594561 | PF | S0757327 | White marlin | 6803 | S2142152 | WS! | 666 | C0446255 | ENG | P | L0760361 | VO | S2142152 | White bryony <1> | 0 |
//| 6803 | S1063245 | WS! | 666 | C0446296 | ENG | P | L0776299 | PF | S1063245 | White cedar | 3 |
//| 6803 | S1063209 | WS! | 666 | C0446305 | ENG | P | L0741840 | PF | S1063209 | White bean | 3 |
//| 6803 | S1063257 | WS! | 666 | C0452433 | ENG | S | L0788297 | PF | S1063257 | White coffee | 3 |
//| 6803 | S1063252 | WS! | 666 | C0452525 | ENG | P | L0780567 | PF | S1063252 | White chapati | 3 |
//| 6803 | S1063241 | WS! | 666 | C0452550 | ENG | P | L0758298 | PF | S1063241 | White bread | 3 |
//| 6803 | S1063435 | WS! | 666 | C0452699 | ENG | P | L0885392 | PF | S1063435 | White spaghetti | 3 |
//| 6803 | S1063433 | WS! | 666 | C0452712 | ENG | P | L0883874 | PF | S1063433 | White rice | 3 |
//| 6803 | S0757328 | WS! | 666 | C0452888 | ENG | S | L0595226 | PF | S0757328 | White meat | 3 |
//| 6803 | S1063379 | WS! | 666 | C0452955 | ENG | P | L0882510 | PF | S1063379 | White pudding | 3 |
//| 6803 | S1063361 | WS! | 666 | C0452962 | ENG | P | L0838787 | PF | S1063361 | White fish | 3 |
//| 6803 | S1063377 | WS! | 666 | C0453007 | ENG | P | L0880602 | PF | S1063377 | White pomfret | 3 |
//| 6803 | S1063244 | WS! | 666 | C0453118 | ENG | P | L0769039 | PF | S1063244 | White cabbage | 3 |
//| 6803 | S1063256 | WS! | 666 | C0453439 | ENG | P | L0782037 | PF | S1063256 | White chocolate | 3 |
run.removeWherePhrase( "S0055922", "lab" );
//| 486 | S0055922 | of Youngs lab | 638 | C0022888 | ENG | P | L0022888 | PF | S0055922 | Labrador | 0 |
run.removeWherePhrase( "S0027715", "constitutes" );
//528 | S0027715 | constitutes | Constitution |La
run.removeWherePhrase( "S0603749", "blood" );
//| 2569 | S0603749 | blood | Blood python |
run.removeWherePhrase( "S0944118", "MP" );
run.removeWherePhrase( "S0386208", "MP" );
//| 3428 | S0944118 | MP-9 | Member of parliament | MP-9 |
//| 3503 | S0386208 | MP-DX-1 | 736 | C0247774 | ENG | S | L0269326 | PF | S0386208 | MPS-1 | 0 |
run.removeWherePhrase( "S0854576", "DX" );
run.removeWherePhrase( "S1697009", "DX" );
//| 3503 | S0854576 | MP-DX-1 | 691 | C0332139 | ENG | S | L0821415 | PF | S0854576 | DX | 3 |
//| 3503 | S1697009 | MP-DX-1 | 663 | C0717685 | ENG | P | L1318427 | PF | S1697009 | DEXTRAN 1 | 0 |
run.removeWhereText( "S0714439", "pilot studies" );
//| 6822 | S0714439 | pilot studies | Pilot
run.removeWhereText( "S1467205", "principal" );
//| 95 | S1467205 | The principal hypothesis underlying | principal <1> |T
run.removeWhereText( "S0701823", "orchestration" );
//| 683 | S0701823 | in the orchestration | Orchestrator |
run.removePhraseGroup( new String[] {"S0026949", "S0830714", "S0026958", "S0026957"},
new String[] {"[ ._,(-](C|c)[ ._,)-]", "_(C|c)_", "^(C|c)[ ._,()-]",
"[ ._,()-](C|c)$", "^(C|c)$" } );
//| 11882 | S0026949 | PGA-RnSalt_c_15w_1-m5 | 677 | C0009499 | Complement 1 |
//| 11882 | S0830714 | PGA-RnSalt_c_15w_1-m5 | 645 | C0007886 | CS |
run.removePhraseGroup( new String[] {"S0901991", "S0050039", "S1326928", "S1346262", "S0575593",
"S0166907", "S0904652", "S1657659" },
new String[] {"[^0-9][ ._,(-](H|h)[ ._,)-]", "_(H|h)_", "^(h|H)[ ._,()-]",
"[ ._,()-](h|H)$", "^(h|H)$", "^[ ._,(-](H|h)[ ._,)-]" } );
//| 12321 | S0166907 | PGA-RnSalt_h_6w_3-m5 | 688 | C0062990 | ENG | P | L0062990 | PF | S0166907 | HS 3 | 0 |
//| 12321 | S0904652 | PGA-RnSalt_h_6w_3-m5 | 623 | C0439227 | ENG | P | L0853781 | PF | S0904652 | Hour | 0 |
//| 12321 | S1657659 | PGA-RnSalt_h_6w_3-m5 | 623 | C0489786 | ENG | P | L0851473 | PF | S1657659 | HEIGHT | 0 |
//| 672 | S0901991 | for 1 h | 638 | C0011892 | ENG | P | L0019335 | VO | S0901991 | Heroin <1> | 0 |
//| 672 | S0050039 | for 1 h | 638 | C0020275 | ENG | P | L0020275 | PF | S0050039 | Hydrogen | 0 |
//| 672 | S1326928 | for 1 h | 638 | C0582517 | ENG | P | L1105470 | PF | S1326928 | henry | 3 |
//| 672 | S1346262 | for 1 h | 638 | C0599530 | ENG | P | L1121252 | PF | S1346262 | enthalpy | 0 |
//| 672 | S0575593 | for 1 h | 666 | C0700308 | ENG | S | L0456903 | PF | S0575593 | 1 H
run.removePhraseGroup( new String[] {"S1466081", "S1466082", "S1432789", "S0894296" },
new String[] {"[ ._,(-](E|e)[ ._,)-]", "_(E|e)_", "^(E|e)[ ._,()-]",
"[ ._,()-](E|e)$", "^(E|e)$", "^[ ._,(-](E|e)[ ._,)-]" } );
//| 11882 | S1466081 | (e group) | 472 | C0424589 | Energy <2> |
//| 11882 | S1466082 | (e group) | 472 | C0542479 | energy <3> |
//| 11882 | S1432789 | (e group) | 472 | C0679138 | expectation |
//| 11882 | S0894296 | (e group) | 694 | C0441833 | Group |
run.removePhraseGroup( new String[] {"S0096860"},
new String[] {"[ /._,(<-](U|u)[ /._,)>-]", "_(U|u)_", "^(U|u)[ /._,()<>-]",
"[ /._,()<>-](U|u)$", "^(U|u)$", "^[ /._,(<-](U|u)[ /._,)>-]" } );
//| 11882 | S0096860 | (Wisloff U et al | 465 | C0041928 | Uranium |
run.removeWhereText( "S1335910", "\\\\(m\\\\.o\\\\.i\\\\)" );
//| 2 | S1335910 | (m.o.i.) | Medical officer | P
run.removeWhereText( "S0381681", "judge" );
//| 486 | S0381681 | judged | Judge |
run.removeWhereText( "S2212176", "messenger" );
//| 632 | S2212176 | messenger RNA | Messenger <1> |
run.removeTextGroup( new String[] {"S0086581","S0001808","S0256391","S0729168","S1028527"},
new String[] {"SW","sw"} );
//| 2107 | S0086581 | SW-620_CL4009_COLON | Social Worker | SW-620_CL4009_COLON |
//| 2107 | S0001808 | SW-620_CL4009_COLON | 626 | C0043255 | ENG | P | L0043255 | VO | S0001808 | Stab wound | 3 |
//| 2107 | S0256391 | SW-620_CL4009_COLON | 626 | C0162459 | ENG | P | L0189478 | VO | S0256391 | Short Wave | 0 |
//| 2107 | S0729168 | SW-620_CL4009_COLON | 626 | C0359299 | ENG | P | L0607852 | PF | S0729168 | STERILE WATER | 0 |
//| 2107 | S1028527 | SW-620_CL4009_COLON | 626 | C0445259 | ENG | P | L0885030 | PF | S1028527 | Sine wave | 3 |
run.removeWhereText( "S1459401", "ng" );
//| 672 | S1459401 | 600 ng | 638 | C0694637 | ENG | P | L1217920 | PF | S1459401 | Nasogastric
run.removeWhereText( "S0000962", "guinea pig" );
//| 6555 | S0000962 | in guinea pig cages 2-3/cage rubber mats | Pig |2)
run.removeWhereText( "S0646815", "\\\\(Fisher\\\\)" );
//| 432 | S0646815 | d (Fishe | (Fisher)
run.removeWhereText( "S0046105", "home\\\\.html" );
//| 7772 | S0046105 | //cardiogenomics.med.harvard.edu/groups/proj1/pages/nk2-sd_home.html | Group Home |
run.removeTextGroup( new String[] {"S0019833","S0017958","S0020508"},
new String[] {"BC","BCS"} );
//| 502 | S0019833 | Eucalyptus grandis BC progeny | Blue Cross | Eucalyptus grandis BC progeny |
//| 1084 | S0017958 | 100 microM BCS 30 min | 462 | C0004842 | ENG | P | L0004842 | PF | S0017958 | Battered Child Syndrome | 0 |
//| 1084 | S0020508 | 100 microM BCS 30 min | 462 | C0006142 | ENG | S | L0006142 | VO | S0020508 | Breast Cancer | 0 |
run.removeWhereText( "S0788903", "et al" );
//| 486 | S0788903 | by Winzeler et al | AL |T
run.removeWhereText( "S1787838", "et al" );
//| 557 | S1787838 | in Wong et al 2003 Nat. | ETS |
run.removeWhereText( "S0936748", "MO" );
//C0026402 | ENG | S | L0312285 | PF | S0936748 | MO | 0 |
run.removeWhereText( "S0849356", "co" );
// 486 | S0849356 | (Sigma-Aldrich Co | 658 | C0454802 | ENG | P | L0787708 | PF | S0849356 | Cos | 3 |
run.removeWherePhrase( "S0022273", "CA" );
run.removeWherePhrase( "S0022354", "CA" );
run.removeWherePhrase( "S0282506", "CA" );
run.removeWherePhrase( "S0612985", "CA" );
run.removeWherePhrase( "S1788962", "CA" );
run.removeWherePhrase( "S2379725", "CA" );
// 486 | S1788962 | CA) | 611 | C0006675 | ENG | P | L0769588 | VO | S1788962 | calcium <2> | 0 |
// 486 | S0612985 | CA) | 611 | C0006826 | ENG | S | L0006826 | PF | S0612985 | Cancer <2> | 0 |
// 486 | S0022273 | CA) | 611 | C0007097 | ENG | P | L0007097 | PF | S0022273 | Carcinoma | 0 |
// 486 | S0022354 | CA) | 611 | C0018790 | ENG | S | L0007146 | PF | S0022354 | Cardiac Arrest | 0 |
// 486 | S0282506 | CA) | 611 | C0205042 | ENG | P | L0211886 | PF | S0282506 | Coronary artery | 0 |
// 486 | S2379725 | CA) | 611 | C0998265 | ENG | S | L0006826 | PF | S2379725 | Cancer <3> | 0 |
// 486 | S1788962 | CA) | 611 | C0006675 | ENG | P | L0769588 | VO | S1788962 | calcium <2> | 0 |
// 486 | S0612985 | CA) | 611 | C0006826 | ENG | S | L0006826 | PF | S0612985 | Cancer <2> | 0 |
// 486 | S0022273 | CA) | 611 | C0007097 | ENG | P | L0007097 | PF | S0022273 | Carcinoma | 0 |
// 486 | S0022354 | CA) | 611 | C0018790 | ENG | S | L0007146 | PF | S0022354 | Cardiac Arrest | 0 |
// 486 | S0282506 | CA) | 611 | C0205042 | ENG | P | L0211886 | PF | S0282506 | Coronary artery | 0 |
// 486 | S2379725 | CA) | 611 | C0998265 | ENG | S | L0006826 | PF | S2379725 | Cancer <3> | 0 |
run.removeWherePhrase( "S0047034", "HP" );
// 486 | S0047034 | by HP GeneArray Scanner | 469 | C0018738 | ENG | P | L0018738 | PF | S0047034 | Health Promotion | 0 |
run.removePhraseGroup( new String[] {"S0675396","S0395681","S2164959"},
new String[] {"pbs","PBS","leading","[ ._,()-]P$","^P[ ._,()-]"} );
//| 5960 | S0675396 | WT_PBS_1 | 631 | C0023175 | Lead <1> |
//| 5960 | S0395681 | WT_PBS_1 | 631 | C0229664 | Peripheral blood, NOS |
//| 5960 | S2164959 | WT_PBS_1 | 631 | C0947650 | LEAD <3> |
run.removePhraseGroup( new String[] {"S0041140","S0042100","S0887199"},
new String[] {"[ ._,(-](F|f)[ ._,)-]","<(F|f)>","(F|f) cell","",
"[ ._,()-](F|f)$", "^(F|f)[ ._,()-]", "=F", "=f",
"^(F|f)$", "(F|f)[/(),]" } );
//| 3384 | S0041140 | 14 d adaxial replication F | 628 | C0015895 | Fertility |
//| 3384 | S0042100 | 14 d adaxial replication F | 628 | C0016330 | Fluorine |
//| 3384 | S0887199 | 14 d adaxial replication F | 628 | C0441722 | Force |
run.removePhraseGroup( new String[] {"S1467359","S1341545","S1467358","S2074554"},
new String[] {"[ ._,(-](R|r)[ ._,)-]","<(R|r)>","(R|r) cell","",
"[ ._,()-](R|r)$", "^(R|r)[ ._,()-]",
"^(R|r)$", "(R|r)[/(),]" } );
//| 9476 | S1467359 | by R | 611 | C0237834 | Resistance <2> |
//| 9476 | S1341545 | by R | 611 | C0560562 | roentgen |
//| 9476 | S1467358 | by R | 611 | C0683598 | resistance <1> |
//| 9476 | S2074554 | by R | 611 | C0917925 | resistance <3> |
run.removePhraseGroup( new String[] {"S0017939","S2379435","S0358662","S0605369"},
new String[] {"[ ._,(-](B|b)[ ._,)-]","<(B|b)>","(b|B) cell","",
"[ ._,()-](b|B)$", "^(b|B)[ ._,()-]",
"^(b|B)$", "(b|B)[/(),]" } );
//| 10264 | S2379435 | (Mu11K-B) | 638 | C0004587 | ENG | S | L0004587 | PF | S2379435 | Bacillus <1> | 0 |
//| 10264 | S0358662 | (Mu11K-B) | 638 | C0004927 | ENG | P | L0004927 | VO | S0358662 | Behavior <1> | 0 |
//| 10264 | S0017939 | (Mu11K-B) | 638 | C0150141 | ENG | S | L0004835 | VO | S0017939 | Bath | 0 |
//| 10264 | S0605369 | (Mu11K-B) | 638 | C0337527 | ENG | P | L0531769 | VO | S0605369 | Brother, NOS | 3 |
run.removeWherePhrase( "S1017515", "(S|s)ee" );
//| C0183089 | ENG | P | L0884412 | PF | S1017515 | SAW | 0 |
run.removeWherePhrase( "S0403605", "(S|s)2" );
//| 589 | S1023549 | NOD_S2 | Second sacral nerve | NOD_S2 |
//| 4382 | S0403605 | DMD-10to12ymix-1aA-s2 | Second sacral vertebra | DMD-10to12ymix-1aA-s2 |
run.removeWherePhrase( "S1023549", "(S|s)2" );
run.removeWherePhrase( "S0372933", "(S|s)1" );
run.removeWherePhrase( "S0885337", "(S|s)1" );
//| 4020 | S0372933 | PGA-MCR-CR-12h-1aAv2-s1 | 626 | C0223598 | S0372933 | First sacral vertebra | 0
//| 4020 | S0885337 | PGA-MCR-CR-12h-1aAv2-s1 | 626 | C0501800 | S0885337 | First sacral nerve | 0
run.removeWherePhrase( "S0409546", "(S|s)3" );
run.removeWherePhrase( "S1045541", "(S|s)3" );
run.removeWherePhrase( "S0745713", "(S|s)3" );
//| 5950 | S0409546 | S3_PBS_1 | 631 | C0223600 | Third sacral vertebra | 0 |
//| 5950 | S0745713 | S3_PBS_1 | 631 | C0232237 | Third heart sound | 3 |
//| 5950 | S1045541 | S3_PBS_1 | 631 | C0501802 | Third sacral nerve | 0 |
run.removeWherePhrase( "S0373362", "(S|s)4" );
run.removeWherePhrase( "S0376013", "(S|s)4" );
run.removeWherePhrase( "S0887940", "(S|s)4" );
//| 1220 | S0373362 | PGA-MurLungHyper-Hyp10h-1bCv2-s4 | 628 | C0223601 | Fourth sacral vertebra |
//| 1220 | S0376013 | PGA-MurLungHyper-Hyp10h-1bCv2-s4 | 628 | C0232240 | HEART SOUND, FOURTH |
//| 1220 | S0887940 | PGA-MurLungHyper-Hyp10h-1bCv2-s4 | 628 | C0501803 | Fourth sacral nerve |
run.removeWherePhrase( "S0021392", "(C|c)1" );
run.removeWherePhrase( "S2164891", "(C|c)2" );
run.removeWherePhrase( "S0021404", "(C|c)3" );
run.removeWherePhrase( "S0021425", "(C|c)4" );
run.removeWherePhrase( "S0061189", "MGM" );
run.removeWherePhrase( "S1088221", "MGM" );
//| 4100 | S0061189 | PGA-MGM-ConNonHyp-1aAv2-s2 | 462 | C0025286 | Meningioma |
//| 4100 | S1088221 | PGA-MGM-ConNonHyp-1aAv2-s2 | 462 | C0439210 | milligram |
run.removeWherePhrase( "S0243514", "RST" );
//5416 | S0243514 | RST-PVH3_1 | 635 | C0152377 | Rubrospinal tract |
run.removeWherePhrase( "S0078500", "PGA" );
run.removeWherePhrase( "S0071740", "PGA" );
//| 12310 | S0078500 | PGA-RnSalt_e_6w_1-3-m5 | 622 | C0016410 | ENG | S | L0033994 | PF | S0078500 | Pteroylglutamic Acid | 0 |
//| 12310 | S0071740 | PGA-RnSalt_e_6w_1-3-m5 | 622 | C0077923 | ENG | P | L0030914 | PF | S0071740 | Pepsinogen A | 0 |
run.removeWherePhrase( "S0084666", "SC" );
run.removeWherePhrase( "S0084110", "SC" );
//| 7430 | S0084666 | in parallel 50 ml liquid SC cultures | Secretory Component |mutants grown in parallel 50 ml liquid SC cultures t
//| 7430 | S0084110 | in parallel 50 ml liquid SC cultures | Scandium |mutants
run.removePhraseGroup( new String[] {"S0324863"},
new String[] {"S-phase","\\\\(s\\\\)","S\\\\.","[ ]S[ ]","[ ]S$"} );
//| 486 | S0324863 | of S-phase cells | Second |T
//671 | S0324863 | some signal(s) | Second |M
//| 486 | S0324863 | S.cerevisiae chromosome VI | Second |T
//[ ]S[ ]
//[ ]S$
run.removePhraseGroup( new String[] {"S1966272","S2164971"},
new String[] {"\\\\(P/","p-value","[ ]P[ ]","-p-","\\\\(P\\\\)","\\\\(P<","-P"} );
run.removePhraseGroup( new String[] {"S0830714"},
new String[] {"C57","BALB/c","\\\\d[ .*]C","^C$","[ ]C[ ]","\\\\(c group\\\\)","\\\\((C|c)\\\\)",
"c-","hepatitis C","C\\\\(","C\\\\."} );
run.removePhraseGroup( new String[] {"S0002628","S0497490","S1088440","S1930826"},
new String[] {"Mol Cell","Mol Biol","Mol. Cel.","Mol. Plant"} );
//| 486 | S0002628 | (Mol | 666 | C0027962 | ENG | S | L0026386 | VO | S0002628 | Mole | 0 |
//| 486 | S0002628 | (Mol | 666 | C0349514 | ENG | S | L0026386 | VO | S0002628 | Mole | 3 |
//| 486 | S0497490 | (Mol | 666 | C0349514 | ENG | S | L0026386 | PF | S0497490 | Mole <2> | 0 |
//| 486 | S1088440 | (Mol | 666 | C0439189 | ENG | S | L0026386 | PF | S1088440 | mol | 3 |
//| 486 | S1930826 | (Mol | 666 | C0869473 | ENG | P | L0026386 | PF | S1930826 | Mole NOS | 0 |
run.removePhraseGroup( new String[] {"S0724597","S0081578"},
new String[] {"(L|l)ab"} );
//| 486 | S0724597 | of Browns lab | 638 | C0035094 | ENG | P | L0035094 | VO | S0724597 | Renin <1> | 0 |
//| 486 | S0081578 | of Browns lab | 638 | C0035100 | ENG | S | L0035094 | PF | S0081578 | Rennin | 0 |
run.removePhraseGroup( new String[] {"S0922320","S0022698","S0022987","S0007290","S0055600",
"S0055631","S1966879","S1087357","S1332573","S1219420",
"S1432501","S1430493"},
new String[] {"[ ]K[ ]","proteinase K"} );
run.removePhraseGroup( new String[] { "S1787899" },
new String[] { "/(G|g)", "/[ ](G|g)", "G\\\\.", "G-",
"(G|g)[ ]", "[ ](G|g)[ ]", "^(G|g)$", "[[:<:]](G|g)[[:>:]]" } );
//| 416 | S1787899 | G | 633 | C0162832 | GS |
run.removePhraseGroup( new String[] {"S0494052","S0057632","S0677220","S0002285","S0324511","S0931752","S0933734",
"S0495409","S0933793","S0058418","S1556763","S0391619","S0495412","S0251625",
"S0313604","S1603205","S0933755","S0324935","S0326046","S0933745","S1895044",
"S0384946","S0384973","S0384956","S0384948","S0384972","S0384950","S0678306",
"S0933754","S0933783","S0933785","S0933768","S0933764","S2119161","S0933861",
"S0933784","S0933848","S0960704","S1556764","S0933787","S1334946","S1334944",
"S1334880","S1334945","S1415289","S1450070","S0384965" },
new String[] {"/(L|l)","/[ ](L|l)","L\\\\.", "m(L|l)", "\\\\d[ ](L|l)", "L-",
"(l|L)[ ]", "", "", "[ ](L|l)[ ]", "^(L|l)$", "[[:<:]](L|l)[[:>:]]" } );
//| S0677220 | Lithium <1>
//| 16 | S0494052 | and 0.1 g/l proteina | 681 | C0024337 | ENG | S | L0399319 | PF | S0494052 | L-Lysine | 0 |
//| 16 | S0057632 | and 0.1 g/l proteina | 458 | C0023693 | ENG | P | L0023693 | PF | S0057632 | Light | 0 |
//| 16 | S0677220 | and 0.1 g/l proteina | 458 | C0023870 | ENG | P | L0023870 | VO | S0677220 | Lithium <1> | 0 |
//| 16 | S0002285 | and 0.1 g/l proteina | 458 | C0024091 | ENG | P | L0024091 | VO | S0002285 | Lumbar vertebra | 0 |
//| 16 | S0324511 | and 0.1 g/l proteina | 458 | C0205091 | ENG | P | L0248747 | PF | S0324511 | Left | 0 |
//| 16 | S0931752 | and 0.1 g/l proteina | 458 | C0302908 | ENG | S | L0591951 | PF | S0931752 | Liquid | 0 |
//| 16 | S0933734 | and 0.1 g/l proteina | 458 | C0442022 | ENG | P | L0867665 | PF | S0933734 | Lumbar | 3 |
//| 416 | S0495409 | L | 666 | C0019307 | Lumbar hernia |
//| 416 | S0933793 | L | 666 | C0024031 | Lumbar pain |
//| 416 | S0058418 | L | 666 | C0024090 | Lumbar Region |
//| 416 | S1556763 | L | 666 | C0037943 | Lumbar Puncture <1> |
//| 416 | S0391619 | L | 666 | C0149983 | OSTEOARTHRITIS, LUMBAR |
//| 416 | S0495412 | L | 666 | C0154738 | Lumbar radiculopathy, NOS |
//| 416 | S0251625 | L | 666 | C0160108 | Lumbar sprain |
//| 416 | S0313604 | L | 666 | C0196667 | Lumbar sympathectomy |
//| 416 | S1603205 | L | 666 | C0198559 | Lumbar hernioplasty |
//| 416 | S0933755 | L | 666 | C0203209 | Lumbar discogram |
//| 416 | S0324935 | L | 666 | C0205507 | Lumbar approach |
//| 416 | S0326046 | L | 666 | C0205826 | Lumbar Plexus |
//| 416 | S0933745 | L | 666 | C0223488 | Lumbar disc |
//| 416 | S1895044 | L | 666 | C0224323 | Lumbar rotator |
//| 416 | S0384946 | L | 666 | C0226408 | Lumbar artery |
//| 416 | S0384973 | L | 666 | C0226648 | Lumbar vein |
//| 416 | S0384956 | L | 666 | C0228897 | Lumbar nerve, NOS |
//| 416 | S0384948 | L | 666 | C0229020 | Lumbar ganglia |
//| 416 | S0384972 | L | 666 | C0230114 | Lumbar trigone |
//| 416 | S0384950 | L | 666 | C0231040 | Lumbar myotome |
//| 416 | S0678306 | L | 666 | C0343286 | Lumbar discitis |
//| 416 | S0933754 | L | 666 | C0408632 | Lumbar discectomy |
//| 416 | S0933783 | L | 666 | C0431307 | Lumbar meningomyelocele |
//| 416 | S0933785 | L | 666 | C0431334 | Lumbar myelocele |
//| 416 | S0933768 | L | 666 | C0431340 | Lumbar hydromyelocele |
//| 416 | S0933764 | L | 666 | C0432149 | Lumbar hemivertebra |
//| 416 | S2119161 | L | 666 | C0449183 | Lumbar intertransversalis |
//| 416 | S0933861 | L | 666 | C0450118 | Lumbar-peritoneal |
//| 416 | S0933784 | L | 666 | C0457629 | Lumbar microdiscectomy |
//| 416 | S0933848 | L | 666 | C0459574 | Lumbar triangle |
//| 416 | S0960704 | L | 666 | C0492096 | ORTHOSIS, LUMBAR
//| 416 | S1556764 | L | 666 | C0553794 | lumbar puncture <2> |
//| 416 | S0933787 | L | 666 | C0554748 | Lumbar myelogram |
//| 416 | S1334946 | L | 666 | C0556666 | Lumbar traction |
//| 416 | S1334944 | L | 666 | C0556888 | Lumbar strapping |
//| 416 | S1334880 | L | 666 | C0587051 | Lumbar mass |
//| 416 | S1334945 | L | 666 | C0589344 | Lumbar support |
//| 416 | S1415289 | L | 666 | C0600578 | Lumbar Manipulation |
//| 416 | S1450070 | L | 666 | C0685628 | Lumbar rib |
//| 416 | S0384965 | L | 666 | C0735111 | Lumbar spine |
run.removePhraseGroup( new String[] {"S0046547","S0046545","S0657751"},
new String[] {"HF"} );
//| 10241 | S0046547 | HF | 611 | C0015525 | ENG | S | L0018489 | PF | S0046547 | Hageman Factor | 0 |
//| 10241 | S0046545 | HF | 611 | C0018488 | ENG | P | L0018488 | PF | S0046545 | Hafnium | 0 |
//| 10241 | S0657751 | HF | 611 | C0019014 | ENG | P | L0019014 | VO | S0657751 | Haemofiltration | 3 |
run.removePhraseGroup( new String[] {"S0092458","S0093512","S0094295","S0095248","S0095798","S0095808",
"S0093597","S0212580","S0324989","S1049310","S1050239","S0747245",
"S1339934","S1436525"},
new String[] {"TP"} );
//| 2601 | S0078858 | D1_TP-24_C | 459 | C0034153 | Purpura, Thrombocytopenic |
//| 2601 | S0092458 | D1_TP-24_C | 459 | C0039607 | Testosterone Propionate |
//| 2601 | S0093512 | D1_TP-24_C | 459 | C0040046 | Thrombophlebitis |
//| 2601 | S0094295 | D1_TP-24_C | 459 | C0040479 | Torsades de Pointes |
//| 2601 | S0095248 | D1_TP-24_C | 459 | C0040840 | Treponema pallidum |
//| 2601 | S0095798 | D1_TP-24_C | 459 | C0041249 | Tryptophan |
//| 2601 | S0095808 | D1_TP-24_C | 459 | C0041256 | Tryptophan Pyrrolase |
//| 2601 | S0093597 | D1_TP-24_C | 459 | C0080225 | Thymopentin |
//| 2601 | S0212580 | D1_TP-24_C | 459 | C0146894 | triphosphate |
//| 2601 | S0324989 | D1_TP-24_C | 459 | C0205559 | True positive |
//| 2601 | S1049310 | D1_TP-24_C | 459 | C0223078 | Transverse process |
//| 2601 | S1050239 | D1_TP-24_C | 459 | C0458343 | Trigger point |
//| 2601 | S0747245 | D1_TP-24_C | 459 | C0555903 | Total protein |
//| 2601 | S1339934 | D1_TP-24_C | 459 | C0576464 | Terminal phalanx |
//| 2601 | S1436525 | D1_TP-24_C | 459 | C0678838 | threshold potential |
run.removePhraseGroup( new String[] {"S0064271","S0205546","S0259151","S1790417"},
new String[] {"SMA","sma"} );
//| 3072 | S0064271 | SMA_expression=yes S100_expres | 447 | C0026847 | Muscular Atrophy, Spinal |
//| 3072 | S0205546 | SMA_expression=yes S100_expres | 447 | C0074822 | somatomedin A |
//| 3072 | S0259151 | SMA_expression=yes S100_expres | 447 | C0162861 | Mesenteric Artery, Superior |
//| 3072 | S1790417 | SMA_expression=yes S100_expres | 447 | C0369998 | Smooth muscle antibody <2> |
run.removePhraseGroup( new String[] { "S0492090", "S0051442", "S0324450" },
new String[] {"[[:<:]]ie[[:>:]]"} );
//| 420 | S0492090 | (ie | 611 | C0014121 | Infective endocarditis |
//| 420 | S0051442 | (ie | 611 | C0020997 | Immunoelectrophoresis |
//| 420 | S0324450 | (ie | 611 | C0022889 | Inner ear, NOS |
run.removePhraseGroup( new String[] {"S0225455", "S1467784", "S0009437", "S0748057", "S0744480", "S0092124",
"S0094646", "S0094654", "S0095280", "S0095738", "S0212977", "S1046235", "S0410407",
"S1425514", "S0748116", "S1342632", "S1467785", "S1046095" },
new String[] {"TA","ta"} );
//<-- C0039263: Takayasu's Arteritis
run.removePhraseGroup( new String[] { "S0837367", "S0052151", "S0477368" },
new String[] { "CGS" } );
//| 9191 | S0837367 | CGS | 611 | C0018062 | Chorionic gonadotrophin, NOS |
//| 9191 | S0052151 | CGS | 611 | C0021234 | Indocyanine Green |
//| 9191 | S0477368 | CGS | 611 | C0221268 | Colloid goiter |
run.removePhraseGroup( new String[] {"S0499931","S0006593","S0066569","S0499931","S0695896"},
new String[] {"NAA","naa"} );
//| GSM9970 | S0499931 | (NAA) | Nonspecific aortoarteritis | extracted from 20 mins 0.1% ethanol treatment of 4 d old Col-0 seedling
//| 9970 | S0006593 | NAA | 611 | C0027377 | Naphthaleneacetic acid |
//| 9970 | S0066569 | NAA | 611 | C0027945 | Neutron Activation Analysis |
//| 9970 | S0499931 | NAA | 611 | C0039263 | Nonspecific aortoarteritis |
//| 9970 | S0695896 | NAA | 611 | C0301715 | Neutral amino acid |
run.removePhraseGroup( new String[] {"S1346902","S0093255","S0746132","S0095422","S2070034","S0209770","S0209614",
"S0253426","S0298913","S0742816","S2070035","S0747349"},
new String[] {"TG","tg"} );
//| 8987 | S1346902 | TNF TG-13w-m-1 | 628 | C0598934 | tumor growth |
//| 8987 | S0093255 | TNF TG-13w-m-1 | 628 | C0039902 | Thioguanine |
//| 8987 | S0746132 | TNF TG-13w-m-1 | 628 | C0040123 | Thyroglobulin <1> |
//| 8987 | S0095422 | TNF TG-13w-m-1 | 628 | C0040995 | Trigeminal Ganglion |
//| 8987 | S2070034 | TNF TG-13w-m-1 | 628 | C0041004 | Triacylglycerol <1> |
//| 8987 | S0209770 | TNF TG-13w-m-1 | 628 | C0061714 | tetraglycine |
//| 8987 | S0209614 | TNF TG-13w-m-1 | 628 | C0145263 | testosterone glucuronide |
//| 8987 | S0253426 | TNF TG-13w-m-1 | 628 | C0161899 | Total gastrectomy |
//| 8987 | S0298913 | TNF TG-13w-m-1 | 628 | C0185464 | Tendon graft |
//| 8987 | S0742816 | TNF TG-13w-m-1 | 628 | C0370059 | THROMBOGLOBULIN |
//| 8987 | S2070035 | TNF TG-13w-m-1 | 628 | C0520521 | triacylglycerol <2> |
//| 8987 | S0747349 | TNF TG-13w-m-1 | 628 | C0600086 | Toxic goiter |
run.removePhraseGroup( new String[] {"S2007281","S0019559","S0019842","S2069490","S0472027","S0604943",
"S0358573","S0819538","S0816807","S2069491"},
new String[] {"BT","bt"} );
//| 1875 | S2007281 | BT-549 | 638 | C0005695 | Bladder Tumor |
//| 1875 | S0019559 | BT-549 | 638 | C0005729 | Bleeding Time |
//| 1875 | S0019842 | BT-549 | 638 | C0005866 | Blue Tongue |
//| 1875 | S2069490 | BT-549 | 638 | C0005903 | body temperature <1> |
//| 1875 | S0472027 | BT-549 | 638 | C0006118 | BRAIN TUMOR |
//| 1875 | S0604943 | BT-549 | 638 | C0006149 | Breast tumor |
//| 1875 | S0358573 | BT-549 | 638 | C0226958 | Base of tongue |
//| 1875 | S0819538 | BT-549 | 638 | C0445452 | Bitemporal |
//| 1875 | S0816807 | BT-549 | 638 | C0521112 | Bedtime |
//| 1875 | S2069491 | BT-549 | 638 | C0886414 | Body temperature <2> |
run.removePhraseGroup( new String[] {"S0694910","S0221668","S0695607"},
new String[] {"NN","nn"} );
//| 2192 | S0694910 | PGA-FVB_NN_1-2-m5 | 623 | C0027618 | Neonatal |
//| 2192 | S0221668 | PGA-FVB_NN_1-2-m5 | 623 | C0027740 | Nerves |
//| 2192 | S0695607 | PGA-FVB_NN_1-2-m5 | 623 | C0027769 | Nerves <1> |
run.removePhraseGroup( new String[] {"S0029563","S0029563","S0621467"},
new String[] {"CF","cf"} );
run.removeWherePhrase( "S1346119", "EC" );
run.removeWherePhrase( "S0385528", "MCF" );
//| 18 | S0385528 | NHGRI_MCF-10A | 687 | C0008015 | MCF |
run.removePhraseGroup( new String[] {"S1289866","S1287286","S0895358","S0657785","S0660922","S0047406",
"S0657612","S2380885","S0048094","S0007274","S0014704","S2754842",
"S0317800","S0663463","S1789518","S0165830","S0297773","S1789517",
"S1789516","S2380886","S0001195","S0047853","S0167452","S0898984",
"S2762780" },
new String[] {"HA","ha"} );
//| 486 | S1289866 | Anti-HA monoclonal antibody HA.11 | 706 | C0018768 | ENG | S | L1072922 | PF | S1289866 | HA - Hearing aid
//| 486 | S1287286 | Anti-HA monoclonal antibody HA.11 | 706 | C0019145 | ENG | S | L1070588 | PF | S1287286 | HA - Hepatic artery | 3 |
//| 486 | S0895358 | Anti-HA monoclonal antibody HA.11 | 706 | C0115137 | ENG | S | L0849327 | PF | S0895358 | HA - Hydroxyapatite | 3 |
//| 486 | S0657785 | Anti-HA monoclonal antibody HA.11 | 626 | C0002878 | ENG | P | L0002878 | VO | S0657785 | Haemolytic anaemia | 3 |
//| 486 | S0660922 | Anti-HA monoclonal antibody HA.11 | 626 | C0003248 | ENG | S | L0281283 | VO | S0660922 | Heterophil antibody | 3 |
//| 486 | S0047406 | Anti-HA monoclonal antibody HA.11 | 626 | C0018899 | ENG | P | L1222696 | PF | S0047406 | Hemadsorption | 0 |
//| 486 | S0657612 | Anti-HA monoclonal antibody HA.11 | 626 | C0018903 | ENG | P | L1222697 | VO | S0657612 | Haemagglutination | 3 |
//| 486 | S2380885 | Anti-HA monoclonal antibody HA.11 | 626 | C0019159 | ENG | P | L0019159 | VO | S2380885 | hepatitis a <1> | 0 |
//| 486 | S0048094 | Anti-HA monoclonal antibody HA.11 | 626 | C0019338 | ENG | P | L0019338 | PF | S0048094 | Herpangina | 0 |
//| 486 | S0007274 | Anti-HA monoclonal antibody HA.11 | 626 | C0019588 | ENG | P | L0019588 | VO | S0007274 | Histamine <1> | 0 |
//| 486 | S0014704 | Anti-HA monoclonal antibody HA.11 | 626 | C0019628 | ENG | P | L0019628 | VO | S0014704 | Antigen, Histocompatibility | 0 |
//| 486 | S2754842 | Anti-HA monoclonal antibody HA.11 | 626 | C0020196 | ENG | P | L0020196 | VO | S2754842 | hyaluronic acid <1> | 0 |
//| 486 | S0317800 | Anti-HA monoclonal antibody HA.11 | 626 | C0020505 | ENG | S | L0160482 | PF | S0317800 | Hyperalimentation, NOS | 3 |
//| 486 | S0663463 | Anti-HA monoclonal antibody HA.11 | 626 | C0030548 | ENG | S | L0160482 | PF | S0663463 | Hyperalimentation <2> | 0 |
//| 486 | S1789518 | Anti-HA monoclonal antibody HA.11 | 626 | C0062044 | ENG | S | L0062044 | PF | S1789518 | H antigen <3> | 0 |
//| 486 | S0165830 | Anti-HA monoclonal antibody HA.11 | 626 | C0062725 | ENG | P | L0062725 | VC | S0165830 | hippuric acid | 0 |
//| 486 | S0297773 | Anti-HA monoclonal antibody HA.11 | 626 | C0184666 | ENG | P | L0222766 | PF | S0297773 | Hospital admission, NOS | 3 |
//| 486 | S1789517 | Anti-HA monoclonal antibody HA.11 | 626 | C0221131 | ENG | S | L0062044 | PF | S1789517 | H antigen <2> | 0 |
//| 486 | S1789516 | Anti-HA monoclonal antibody HA.11 | 626 | C0595976 | ENG | S | L0062044 | PF | S1789516 | H ANTIGEN <1> | 0 |
//| 486 | S2380886 | Anti-HA monoclonal antibody HA.11 | 626 | C1141641 | ENG | S | L0019159 | PF | S2380886 | HEPATITIS A <2> | 0 |
run.removePhraseGroup( new String[] {"S1043845","S1467861","S1043844","S0426449","S0289996","S0093568","S0093579","S0093786","S0094525",
"S0007444","S0007445","S1045222"},
new String[] {"d\\\\(T\\\\)", "T cell", "T-", "TX"} );
//| 709 | S0031549 | with oligo d(T) | 465 | C0011530 | ENG | P | L0011530 | PF | S0031549 | Deoxyribose | 0 |
//| 709 | S0631027 | with oligo d(T) | 465 | C0332517 | ENG | P | L0560040 | PF | S0631027 | Diameter | 3 |
//| 709 | S1085446 | with oligo d(T) | 465 | C0439228 | ENG | P | L0805710 | PF | S1085446 | day | 0 |
//| 709 | S1043845 | with oligo d(T) | 631 | C0005903 | ENG | s | L0039476 | PF | S1043845 | Temperature <2> | 0 |
//| 709 | S1467861 | with oligo d(T) | 631 | C0029216 | ENG | S | L1223581 | PF | S1467861 | transplantation <3> | 0 |
//| 709 | S1043844 | with oligo d(T) | 631 | C0039476 | ENG | P | L0039476 | VO | S1043844 | Temperature <1> | 0 |
//| 709 | S0426449 | with oligo d(T) | 631 | C0039798 | ENG | S | L0039798 | PF | S0426449 | therapy <1> | 0 |
//| 709 | S0289996 | with oligo d(T) | 631 | C0040061 | ENG | P | L0040061 | VO | S0289996 | thromboxane | 0 |
//| 709 | S0093568 | with oligo d(T) | 631 | C0040077 | ENG | P | L0040077 | PF | S0093568 | Thymidine | 0 |
//| 709 | S0093579 | with oligo d(T) | 631 | C0040087 | ENG | P | L0040087 | PF | S0093579 | Thymine | 0 |
//| 709 | S0093786 | with oligo d(T) | 631 | C0040223 | ENG | P | L1223556 | PF | S0093786 | Time | 0 |
//| 709 | S0094525 | with oligo d(T) | 631 | C0040597 | ENG | P | L0040597 | PF | S0094525 | Traction | 0 |
//| 709 | S0007444 | with oligo d(T) | 631 | C0040732 | ENG | S | L1223581 | PF | S0007444 | Transplantation <1> | 0 |
//| 709 | S0007445 | with oligo d(T) | 631 | C0040733 | ENG | P | L1223581 | VO | S0007445 | transplantation <2> | 0 |
//| 709 | S1045222 | with oligo d(T) | 631 | C0087111 | ENG | S | L0039798 | PF | S1045222 | Therapy, NOS | 3 |
run.removePhraseGroup( new String[] {"S0154329","S0484074","S0037143","S0370322","S0871044","S0637722","S2193314","S0426772","S0410338"},
new String[] {"EF"} );
//| 566 | S0154329 | for the EF treatment | 638 | C0059039 | ENG | S | L0122358 | PF | S0154329 | EF-T | 0 |
//| 566 | S0484074 | for the EF treatment | 472 | C0014761 | ENG | S | L0299789 | PF | S0484074 | Erythroblastosis fetalis, NOS | 3 |
//| 566 | S0037143 | for the EF treatment | 472 | C0086206 | ENG | P | L0013907 | PF | S0037143 | Elongation Factor | 0 |
//| 566 | S0370322 | for the EF treatment | 472 | C0225799 | ENG | P | L0299245 | PF | S0370322 | Endothoracic fascia, NOS | 3 |
//| 566 | S0871044 | for the EF treatment | 472 | C0264005 | ENG | S | L0299377 | PF | S0871044 | Eosinophilic fasciitis | 0 |
//| 566 | S0637722 | for the EF treatment | 472 | C0337037 | ENG | P | L0215175 | PF | S0637722 | Electric field | 3 |
//| 566 | S2193314 | for the EF treatment | 472 | C0962274 | ENG | P | L1872755 | PF | S2193314 | edema factor | 0 |
//| 566 | S0426772 | for the EF treatment | 694 | C0039798 | ENG | S | L0040807 | PF | S0426772 | treatment <2> | 0 |
//| 566 | S0410338 | for the EF treatment | 694 | C0087111 | ENG | S | L0040807 | PF | S0410338 | Treatment <1> | 0 |
run.removePhraseGroup( new String[] {"S0288990","S0637822"},
new String[] {"EI"} );
//| 566 | S0288990 | for the EI | 611 | C0014432 | ENG | P | L0014432 | VO | S0288990 | enzyme inhibitor | 0 |
//| 566 | S0288990 | for the EI | 611 | C1152555 | ENG | s | L0014432 | VO | S0288990 | enzyme inhibitor | 0 |
//| 566 | S0637822 | for the EI | 611 | C0342579 | ENG | S | L0085291 | PF | S0637822 | Electrolyte imbalance NOS | 3 |
run.removePhraseGroup( new String[] {
"S0051860","S0053003","S1556750","S0050873","S0324702","S0669471","S0918263","S0919184",
"S0919188","S1745894","S0919214","S0054102","S0289346","S0040894","S0054111","S2019824",
"S0321964","S0669495","S0324948","S1283025","S0669486","S0669482","S1325049","S0669487",
"S0669494","S1298339","S0919225","S0919253","S0919223","S0919232","S0919254","S0919211",
"S1331598","S1427371","S2232337","S2233179"},
new String[] {"IV"} );
/*
S0919214 | IV | 666 | C0002920 | Intravenous anaesthesia, NOS |
| 741 | S0054102 | IV | 666 | C0013125 | Intravenous Drip |
| 741 | S0289346 | IV | 666 | C0021440 | intravenous administration |
| 741 | S0040894 | IV | 666 | C0021910 | Feedings, Intravenous |
| 741 | S0054111 | IV | 666 | C0021912 | Intravenous Hyperalimentation |
| 741 | S2019824 | IV | 666 | C0085297 | Intravenous Antibodies |
| 741 | S0321964 | IV | 666 | C0203082 | Intravenous cholangiogram |
| 741 | S0669495 | IV | 666 | C0203108 | Intravenous pyelogram |
| 741 | S0324948 | IV | 666 | C0205520 | Intravenous route |
| 741 | S1283025 | IV | 666 | C0242904 | Intravenous anaesthetic |
| 741 | S0669486 | IV | 666 | C0346200 | Intravenous leiomyomatosis |
| 741 | S0669482 | IV | 666 | C0354566 | Intravenous heparin |
| 741 | S1325049 | IV | 666 | C0357164 | Intravenous glucose |
| 741 | S0669487 | IV | 666 | C0357168 | Intravenous nutrition |
| 741 | S0669494 | IV | 666 | C0360652 | Intravenous potassium |
| 741 | S1298339 | IV | 666 | C0398266 | Intravenous cannulation |
| 741 | S0919225 | IV | 666 | C0412158 | Intravenous cystography |
| 741 | S0919253 | IV | 666 | C0412775 | Intravenous sedation |
| 741 | S0919223 | IV | 666 | C0413365 | Intravenous chemotherapy |
| 741 | S0919232 | IV | 666 | C0413366 | Intravenous immunotherapy |
| 741 | S0919254 | IV | 666 | C0443081 | Intravenous vasodilator |
| 741 | S0919211 | IV | 666 | C0524311 | Intravenous DSA |
| 741 | S1331598 | IV | 666 | C0563322 | Intravenous steroids |
| 741 | S1427371 | IV | 666 | C0683092 | intravenous AOD |
| 741 | S2232337 | IV | 666 | C0973717 | INTRAVENOUS SETS |
| 741 | S2233179 | IV | 666 | C0991514 | Intravenous Solution |
| 741 | S0051860 | collagen IV | 638 | C0021135 | In Vitro |
| 741 | S0053003 | collagen IV | 638 | C0021494 | Injection, Intravenous |
| 741 | S1556750 | collagen IV | 638 | C0021910 | Intravenous feeding <2> |
| 741 | S0050873 | collagen IV | 638 | C0079584 | Ichthyosis Vulgaris |
| 741 | S0324702 | collagen IV | 638 | C0205281 | Invasive |
| 741 | S0669471 | collagen IV | 638 | C0348016 | Intravenous |
| 741 | S0918263 | collagen IV | 638 | C0442106 | Intervertebral |
| 741 | S0919184 | collagen IV | 638 | C0442122 | Intravaginal |
| 741 | S0919188 | collagen IV | 638 | C0442123 | Intravascular |
| 741 | S1745894 | collagen IV | 638 | C0796568 | in vivo |
*/
run.removePhraseGroup( new String[] {"S0031549","S0631027","S1085446"},
new String[] {"_D-", "[ ]d[ ]"} );
run.removePhraseGroup( new String[] {"S0035294","S0631027","S1085446","S0031549"},
new String[] {"\\\\(DS\\\\)","DS rat","DS\\\\.domain","ds-cDNA"} );
//| 12011 | S0035294 | (ds-cDNA) | 472 | C0013080 | ENG | P | L0013080 | PF | S0035294 | Down Syndrome | 0 |
//| 12011 | S0631027 | (ds-cDNA) | 472 | C0332517 | ENG | P | L0560040 | PF | S0631027 | Diameter | 3 |
//| 12011 | S1085446 | (ds-cDNA) | 472 | C0439228 | ENG | P | L0805710 | PF | S1085446 | day | 0 |
run.removeWherePhrase( "S1335228", "MA" );
//| 12011 | S1335228 | MA) | 666 | C0450172 | ENG | P | L1222939 | PF | S1335228 | mA | 3 |
run.removeWherePhrase( "S1788062", "kit" );
//| 12011 | S1788062 | kit | 666 | C0812225 | ENG | S | L1499216 | PF | S1788062 | KIT | 0 |
run.removePhraseGroup( new String[] {"S1790547","S1790548","S1044652","S0745161"},
new String[] {"Tet","TET","tet"} );
//| 457 | S1790547 | Deletions_TETs_WTs | 628 | C0039614 | ENG | P | L0039614 | VO | S1790547 | tetanus <1> | 0 |
//| 457 | S1790548 | Deletions_TETs_WTs | 628 | C0039619 | ENG | S | L0039614 | PF | S1790548 | tetanus <2> | 0 |
//| 457 | S1044a652 | Deletions_TETs_WTs | 628 | C0039644 | ENG | P | L0039644 | VO | S1044652 | Tetracycline <1> | 0 |
//| 457 | S0745161 | Deletions_TETs_WTs | 628 | C0039651 | ENG | P | L0039644 | VO | S0745161 | Tetracycline, NOS | 3 |
//run.removePhraseGroup( new String[] {"S1062665","S1061119"},
//new String[] {"wt strain,"\\\\(wt\\\\)","\\\\(WT\\\\)","[ ]W$", "[ ]W[ ]", "wt[^%]"} );
//| 457 | S1062665 | Deletions_TETs_WTs | 628 | C0005910 | ENG | s | L0043100 | PF | S1062665 | Weight <2> | 0 |
//| 457 | S1061119 | Deletions_TETs_WTs | 628 | C0043100 | ENG | P | L0043100 | VO | S1061119 | WEIGHT <1> | 0 |
run.removePhraseGroup( new String[] {"S0095801","S0095802","S0095807","S0749536","S0212999","S0212814",
"S0212991","S0212993","S0191600","S0212997","S0213004","S0529871",
"S1091084","S0749539","S1050721","S1340283","S1281852","S1339258",
"S1205900","S1421863","S1420651","S2063771"},
new String[] {"TP"} );
//| 6734 | S0095801 | (TP) | 666 | C0003806 | Tryptophan Decarboxylase |
//| 6734 | S0095802 | (TP) | 666 | C0041252 | Tryptophan Hydroxylase |
//| 6734 | S0095807 | (TP) | 666 | C0041256 | Tryptophan Oxygenase |
//| 6734 | S0749536 | (TP) | 666 | C0041258 | Tryptophan desmolase |
//| 6734 | S0212999 | (TP) | 666 | C0070361 | tryptophan pyrrolooxygenase |
//| 6734 | S0212814 | (TP) | 666 | C0077369 | tRNA, tryptophan- |
//| 6734 | S0212991 | (TP) | 666 | C0077438 | tryptophan aminotransferase |
//| 6734 | S0212993 | (TP) | 666 | C0147085 | tryptophan deaminase |
//| 6734 | S0191600 | (TP) | 666 | C0147087 | Permease, tryptophan |
//| 6734 | S0212997 | (TP) | 666 | C0147088 | tryptophan pyrolysate |
//| 6734 | S0213004 | (TP) | 666 | C0147092 | tryptophan tryptophylquinone |
//| 6734 | S0529871 | (TP) | 666 | C0300800 | tryptophan hydroxamate |
//| 6734 | S1091084 | (TP) | 666 | C0311908 | tryptophan dimethylallyltransferase |
//| 6734 | S0749539 | (TP) | 666 | C0041249 | Tryptophan product |
//| 6734 | S1050721 | (TP) | 666 | C0523957 | Tryptophan measurement, NOS |
//| 6734 | S1340283 | (TP) | 666 | C0568256 | Tryptophan poisoning |
//| 6734 | S1281852 | (TP) | 666 | C0570763 | Tryptophan allergy |
//| S1339258 Tryptophan overdose
//| S1205900 tryptophan analog
//| S1421863 tryptophan tetramate
//| S1420651 tryptophan racemase
//| S2063771 tryptophan chlorinase
//| 2569 | S1657659 | 0-6 h | 635 | C0489786 | ENG | P | L0851473 | PF | S1657659 | HEIGHT | 0 |
run.removeWherePhrase( "S2381634", "Mus musculu" ); // Muscle (tissue)
run.removeWherePhrase( "S0950542", "Mus musculu" ); // Muscle (tissue and invertebrate)
run.removeWherePhrase( "S2381635", "Mus musculu" ); // Muscle (invertebrate)
run.removeWherePhrase( "S2713521", "Mus musculu" ); // Muscle (invertebrate)
//| 2569 | S1863651 | ad libitum quantities | 491 | C0450984 | ENG | S | L0493326 | PF | S1863651 | ADS | 0 |
//| 2569 | S1787899 | 10-11 g | 658 | C0162832 | ENG | S | L1224124 | PF | S1787899 | GS | 0 |
run.removePhraseGroup( new String[] {"S0045691","S1466275","S0487302"},
new String[] {"GC"} );
/*
| 1988 | S0025170 | Tonsil GC B | 469 | C0008555 | Chromatography, Gas | 1988 | 60 |
| 1988 | S0045691 | Tonsil GC B | 469 | C0027571 | Gonococcus | 1988 | 60 |
| 1988 | S0045691 | Tonsil GC B | 469 | C0027573 | Gonococcus | 1988 | 60 |
| 1988 | S1466275 | Tonsil GC B | 469 | C0027573 | Gonococcus <1> | 1988 | 60 |
| 1988 | S0487302 | Tonsil GC B | 469 | C0282491 | Germinal Center | 1988 | 60 |
*/
run.removePhraseGroup( new String[] {"S1435954"},
new String[] {"OCT"} );
//| 1970 | S1435954 | DLCL-0036;OCT || lc5b087 | 684 | C0029279 | OCT | 1970 | 60 |
run.removeAllWithPhrase( "www\\\\." );
run.removeAllWithPhrase( "http:" );
run.removeAllWithPhrase( "\\\\.com" );
run.removeAllWithPhrase( "\\\\.org" );
run.removeAllWithPhrase( "\\\\.gov" );
run.removeAllWithPhrase( "\\\\.edu" );
run.removeAllWithPhrase( "\\\\.htm" );
run.addWhereText( "S1467528", "=(f|F)[ ]", "S0040967" );
run.addWhereText( "S1467528", "=(m|M)[ ]", "S1802267" );
run.addWhereText( "S2132569", "(m|M)uscle", "S3003095" );
//| C0026845 | ENG | P | L0026845 | VO | S2132569 | Muscle <2> | 0 | C0026845 | T024 | Tissue |
//| C0596981 | ENG | P | L1011716 | VO | S3003095 | Muscle cell | 0 | C0596981 | T025 | Cell |
} catch( Exception e ) {
e.printStackTrace();
}
}
}