This file contains the positive and fallible patterns used in Extractor of MUtations (EMU).  

The patterns are written using regular expressions.
For details see the source perl code of EMU at the FTP site.


A. 
Positive Patterns
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Regular Expression for Positive Patterns
patt1  = "$left_border"."(p\\.$residue_set2(\\d+)$residue_set2)"."$right_border";
patt2  = "$left_border"."(p\\.($residue_set1)(\\d+)($residue_set1))"."$right_border";
patt3  = "$left_border"."(([cgmr])\\.([+-\\d]+)($residue_set1)($symbol_connective)($residue_set1))"."$right_border";
patt4 =    # analyzing pattern for one letter code
  "$left_border"
  . "(($position1)"
  . "($residue_set1)"
  . "($position23)"
  . "($symbol_connective)"
  . "($position23)"
  . "($residue_set1)"
  . "($position4))"
  . "$right_border";
patt5 = "(?i)"
  . "$left_border"
  . "(($position1)"
  . "($residue_set2)"
  . "($position23)"
  . "($symbol_connective|$word_connective)"
  . "($position23)"
  . "($residue_set2)"
  . "($position4))"
  . "$right_border";  
patt6 = "(?i)"
  . "$left_border"
  . "(($residue_set4)"
  . "($position23)"
  . "($symbol_connective)"
  . "($position23)"
  . "($residue_set4))"
  . "$right_border";  
patt7 = "(?i)" . "$left_border" . "($rs_connective)" . "$right_border";

B. 
Regular Expression for Fallible Patterns:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
1) The fallible patterns include Cell Line names (from Cell_line_list_short.txt from ftp).
Example: 
H69V 
L5178Y 
L89M 
T-47D 

2) Filtering of phrases recognized with the patterns patt4, patt5, patt6:
A phrase is eliminated if more than one numerical positions have been captured with any of the patterns patt4, patt5 or patt6.


C. List of terms:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

		# Variations of possible left border characters
		$left_border =
	"(?:(?:\\s+)|(?:,)|(?:\\.)|(?:-)|(?:\\/)|(?:;)|(?:=)|(?::)|(?:\\*)|(?:\\[)|(?:\\])|(?:\\{)|(?:\\})|(?:\\()|(?:\\)))";

		# Variations of possible right border characters
		$right_border =
	 "(?:(?:\\s+)|(?:,)|(?:-)|(?:\\.)|(?:;)|(?::)|(?:\\/)|(?:\\*)|(?:\\])|(?:\\})|(?:\\)))";

	# Variations of possible connectives linking wild type and mutation
		$symbol_connective =
	"(?:|(?:\\s*)|(?:\\s+to\\s+)|(?:-+to-+)|(?:\\s+(?:to|into|for|of|by)\\s+(?:a\\s+))|(?:\\s*-*(?:>)\\s*)|(?:---+))";

		# Specific RS id number for known mutations
		$rs_connective = "(?:[r|s]s\\d+(?:[a-zA-Z])*)";

		$position_patterns =
	"(?:amino acid|position|base pair|residue|nucleotide|codon)\\s*(\\d{2,})|((?:intron|exon)\\s*\\d{1,})";
		$position_patterns2 =
	"(?:amino acid|position|base pair|residue|nucleotide|codon|)\\s*((?:intron|exon|)\\s*\\d{2,})";

		# Templates for positions.
		$position23 = "[-\\(\\{\\[\\s]*(\\d{2,})[\\)\\}\\]\\-\\s]*|";

		$position1 = "\\W*$position_patterns2(\\W*)|";
		$position4 = "(\\W*)(\\d{2,})\\W*|";


		# Amino Acid match set assignments
		$residue_set1 = "[ARNDCQEGHILKMFPSTWYV]";
		$residue_set2 =
	"(Ala|Arg|Asn|Asp|Cys|Gln|Glu|Gly|His|Ile|Leu|Lys|Met|Phe|Pro|Ser|Thr|Trp|Tyr|Val|Alanine|Arginine|Asparagine|Aspartic Acid|Cysteine|Glutamic Acid|Glutamine|Glycine|Histidine|Isoleucine|Leucine|Lysine|Methionine|Phenylalanine|Proline|Serine|Threonine|Tryptophan|Tyrosine|Valine)";

		$residue_set4 = "([ACGT]{3})";

	 # List of possible words and adverbs used for connecting wild type and mutation
		my @verb_List = (
			"substit\\w*", "lead\\w*",   "replac\\w*", "chang\\w*",
			"mutat\\w*",   "devia\\w*",  "modif\\w*",  "alter\\w*",
			"switch\\w*",  "exhang\\w*", "variat\\w*", "instead\\w*"
		);
		my @adverb_List = ( "to", "into", "for", "of", "by", "with" );
		my $verb_List   = join( "|", @verb_List );
		my $adverb_List = join( "|", @adverb_List );

	# Variations of possible words and phrases linking wild type and mutation
		$word_connective =
			"(?:\\s+)" . "(?:"
		  . "(?:(?:\\w+\\s*){0,5}(?:$verb_List)\\s+)" . "|"
		  . "(?:(?:\\w+\\s*){0,5}(?:$adverb_List)(?:\\s+a)?\\s+)" . "|"
		  . "(?:(?:\\w+\\s*){0,5}(?:$verb_List)\\s+(?:$adverb_List)(?:\\s+a)?\\s+)"
		  . "|"
		  . "(?:\\s+(?:$verb_List)\\s+(?:$adverb_List)(?:\\s+a)?\\s+)" . ")";

C. Pattern examples:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
patt1: Arg53Glu
patt2: A110R
patt3: c.54A>T
patt4: (A54-->Q)
patt5: Ala94 replaced with Lys;
patt6: AAG25 to GGT
patt7: rs253452