%***************************************************************************% % % % Copyright (C) 2005, 2006 Sampo Pyysalo, Sophie Aubin % % See file "LICENSE" for information about commercial use of this system % % % %***************************************************************************% % This file contains regular expressions that are used to match % tokens not found in the dictionary. Each regex is given a name which % determines the disjuncts assigned when the regex matches; this name % must be defined in the dictionary along with the appropriate disjuncts. % Note that the order of the regular expressions matters: matches will % be attempted in the order in which the regexs appear in this file, % and only the first match will be used. % Numbers. % XXX, we need to add utf8 U+00A0 "no-break space" % The ":" is included here so we allow "10:30" to be a number % % This one matches the original LG rule. % NUMBERS: /^[0-9][0-9:.,]+$/ % This allows more, e.g. "-5" and "5-10" and "9+/-6.5" NUMBERS: /^[0-9:.,-]*[0-9]([0-9:.,-]|\+\/-[0-9:.,-])*$/ % "10(3)" exponent (used in PubMed) NUMBERS: /^[0-9:.,-]*[0-9][0-9:.,-]*\([0-9:.,-]*[0-9][0-9:.,-]*\)$/ % Roman numerals % The first expr has the potential(?) problem that it matches an empty % string, this should be fixed. ROMAN-NUMERAL-WORDS: /^M*(CM|D?C{0,3}|CD)(XC|L?X{0,3}|XL)(IX|V?I{0,3}|IV)$/ % ROMAN-NUMERAL-WORDS: /^M*(CM|D?C{0,3}|CD){1}(XC|L?X{0,3}|XL)(IX|V?I{0,3}|IV)$/ % ROMAN-NUMERAL-WORDS: /^M*(CM|D?C{0,3}|CD)(XC|L?X{0,3}|XL){1}(IX|V?I{0,3}|IV)$/ % ROMAN-NUMERAL-WORDS: /^M*(CM|D?C{0,3}|CD)(XC|L?X{0,3}|XL)(IX|V?I{0,3}|IV){1}$/ % Greek letters with numbers GREEK-LETTER-AND-NUMBER: /^(alpha|beta|gamma|delta|epsilon|zeta|eta|theta|iota|kappa|lambda|mu|nu|xi|omicron|pi|rho|sigma|tau|upsilon|phi|chi|psi|omega)\-?[0-9]+$/ PL-GREEK-LETTER-AND-NUMBER: /^(alpha|beta|gamma|delta|epsilon|zeta|eta|theta|iota|kappa|lambda|mu|nu|xi|omicron|pi|rho|sigma|tau|upsilon|phi|chi|psi|omega)s\-?[0-9]+$/ % Some "safe" derived units. Simple units are in dictionary. % The idea here is for the regex to match something that is almost % certainly part of a derived unit, and allow the rest to be % anything; this way we can capture difficult derived units such % as "mg/kg/day" and even oddities such as "micrograms/mouse/day" % without listing them explicitly. % TODO: add more. % Some (real) misses from these: % micrograms.kg-1.h-1 microM-1 J/cm2 %/day mN/m cm/yr % m/s days/week ml/s degrees/sec cm/sec cm/s mm/s N/mm (is that a unit?) % cuts/minute clicks/s beats/minute x/week W/kg/W %/patient-year % microIU/ml degrees/s counts/mm2 cells/mm3 tumors/mouse % mm/sec ml/hr mJ/cm(2) m2/g amol/mm2 animals/group % h-1 min-1 day-1 cm-1 mg-1 kg-1 mg.m-2.min-1 ms.cm-1 g-1 % sec-1 ms-1 ml.min.-1kg-1 ml.hr-1 % also, both kilometer and kilometers seem to be absent(!) % remember "mm"! UNITS: /^([npmk]|nano|pico|milli|micro|kilo)?(g|grams?)\// % grams/anything UNITS: /^([fnmp]|femto|nano|micro|pico|mu)?mol(es)?\// % mol/anything UNITS: /^[a-zA-Z\/.]+\/((m|micro)?[lLg]|kg|mol|min|day|h)$/ % common endings % common endings, except in the style "mg.kg-1" instead of "mg/kg". UNITS: /^[a-zA-Z\/.1-]+\.((m|micro)?[lLg]|kg|mol|min|day|h)(-1|\(-1\))$/ % combinations of numbers and units, e.g. "50-kDa", "1-2h" % TODO: Clean up and check that these are up-to-date wrt the % dictionary-recognized units; this is quite a mess currently. % TODO: Extend the "number" part of the regex to allow anything % that the NUMBER regex matches. % One problem here is a failure to split up the expression ... % e.g. "2hr" becomes 2 - ND - hr with the ND link. But 2-hr is treated % as a single word ('I is a 2-hr wait') NUMBER-AND-UNIT: /^[0-9.,-]+(msec|s|min|hour|h|hr|day|week|wk|month|year|yr|kDa|kilodalton|base|kilobase|base-pair|kD|kd|kDa|bp|nt|kb|mm|mg|cm|nm|g|Hz|ms|kg|ml|mL|km|microm|\%)$/ % fold-words. Matches NUMBER-fold, where NUMBER can be either numeric % or a spelled-out number, and the hyphen is optional. Note that for % spelled-out numbers, anything is allowed between the "initial" number % and "fold" to catch e.g. "two-to-three fold" ("fourteen" etc. are absent % as the prefix "four" is sufficient to match). FOLD-WORDS: /^[0-9.,:-]*[0-9]([0-9.,:-]|\([0-9.,:-]*[0-9][0-9.,:-]*\)|\+\/-)*-?fold$/ FOLD-WORDS: /^(one|two|three|four|five|six|seven|eight|nine|ten|eleven|twelve|thirteen|fifteen|twenty|thirty|fifty|hundred|thousand|million).*fold$/ % Plural proper nouns. PL-CAPITALIZED-WORDS: /^[[:upper:]].*[^iuoys]s$/ % Other proper nouns. CAPITALIZED-WORDS: /^[[:upper:]]/ % Nouns ending -ation stubbed out in BioLG, stub out here ... %ATION-WORDS: /..ation$/ ING-WORDS: /..ing$/ % plurals or verb-s. S-WORDS: /[^iuoys]s$/ % Verbs ending -ed. ED-WORDS: /..ed$/ % Advebs ending -ly. LY-WORDS: /..ly$/ % Extension by LIPN 11/10/2005 % nouns -- typically seen in (bio-)chemistry texts % synthetase, kinase % 5-(hydroxymethyl)-2’-deoxyuridine % hydroxyethyl, hydroxymethyl % septation, reguion % isomaltotetraose, isomaltotriose % glycosylphosphatidylinositol % iodide, oligodeoxynucleotide % chronicity, hypochromicity MC-NOUN-WORDS: /..ase$/ MC-NOUN-WORDS: /..ine?$/ MC-NOUN-WORDS: /..yl$/ MC-NOUN-WORDS: /..ion$/ MC-NOUN-WORDS: /..ose$/ MC-NOUN-WORDS: /..ol$/ MC-NOUN-WORDS: /..ide$/ MC-NOUN-WORDS: /..ity$/ % replicon, intron C-NOUN-WORDS: /..o[rn]$/ % adjectives % exogenous, heterologous % intermolecular, intramolecular % glycolytic, ribonucleic, uronic % ribosomal, ribsosomal % nonpermissive, thermosensitive % inducible, metastable ADJ-WORDS: /..ous$/ ADJ-WORDS: /..ar$/ ADJ-WORDS: /..ic$/ ADJ-WORDS: /..al$/ ADJ-WORDS: /..ive$/ ADJ-WORDS: /..ble$/ % latin (postposed) adjectives % influenzae, tarentolae % pentosaceus, luteus, carnosus LATIN-ADJ-WORDS: /..ae$/ LATIN-ADJ-WORDS: /..us$/ % must appear after -ous in this file % latin (postposed) adjectives or latin plural noun % brevis, israelensis % japonicum, tabacum, xylinum LATIN-ADJ-P-NOUN-WORDS: /..is?$/ LATIN-ADJ-S-NOUN-WORDS: /..um$/ % Hyphenated words. In the original LG morpho-guessing system that % predated the regex-based system, hyphenated words were detected % before ING-WORDS, S-WORDS etc., causing e.g. "cross-linked" to be % treated as a HYPHENATED-WORD (a generic adjective/noun), and % never a verb. To return to this ordering, move this regex just % after the CAPITALIZED-WORDS regex. HYPHENATED-WORDS: /^[[:alpha:][:digit:],.][[:alpha:][:digit:],.-]*-[[:alpha:][:digit:],.-]*[[:alpha:][:digit:],.]$/ % proteins often end "ase", so we'll assume those things are names. % removed, too many false positives. % NAME: /ase$/