Revision as of 16:34, 20 May 2013

Note that complete details on the Annotation Query Language (AQL) are available on the IBM website. We summarize some of the queries used specifically in our work here.

Annotation Query Language

create dictionary Buprenorphine_dict as 
(
       'Buprel', 'Buprenex', 
       'Buprenorphine', 
       'Buprenorphine analgesic', 
       'Buprenorphine opioid dependence', 'Probuphine', 
       'Subbies', 
       'Suboxone', 'Suboxone film', 
       'Suboxone tablet', 'Subs', 
       'Subutex', 'Temgesic', 
       'film', 'films', 'strip', 
       'strips', 
       'sub', 'tecs', 'tex',
       'Zubsolv'
);

create view Buprenorphine_view as 
   extract
   dictionaries 'Buprenorphine_dict'
   on D.text as buprenorphine
   from Document D;

create dictionary demonstrative_pronoun_dict as 
(
   'this', 'that', 
   'these', 'those'	
);

create dictionary personal_pronoun_dict as 
(
   'i', 'me','you',
   'she','her',
   'he','him',
   'it',
   'we','us',
   'they','them'
);

create dictionary possessive_pronoun_dict as 
(
   'my', 'your',
   'our', 'ours', 'your','yours',
   'his','her', 'hers',
   'its',
   'their','theirs',
   'mine'
);

create dictionary reflexive_pronoun_dict as 
(
   'myself', 'ourselves',
   'yourself','yourselves',
   'himself','herself',
   'itself','themselves'
);

create dictionary relative_pronoun_dict as 
(
  'that', 'which', 'who', 'whom', 'whose',
  'whichever', 'whoever', 'whomever'
);

create dictionary interrogative_pronoun_dict as 
(
   'what', 'who', 'whom', 'which', 'whose'
);

create dictionary indefinite_pronoun_dict as 
(
    'anybody', 'anyone','anything',
    'each','either',
    'everybody','everyone','everything',
    'neither','nobody','no one','nothing','one',
    'somebody','someone','something',
    'both','few','many','several',
    'all','any','most','none','some'
);

create view Pronounview as 
    extract 
    dictionaries 
     'personal_pronoun_dict' and 'relative_pronoun_dict' and 
     'demonstrative_pronoun_dict' and  'indefinite_pronoun_dict' and 
     'reflexive_pronoun_dict' and 'interrogative_pronoun_dict' and  
     'possessive_pronoun_dict'
    on D.text as match
from Document D;

The following production DrugPronounview detects an ENTITY followed by a PRONOUN (e.g. bupe I took.)

create view DrugPronounview as
    select CombineSpans(D.drug,P.match) as match
    from  'Drug_view' D,'Pronounview' P
    where 
  FollowsTok( D.drug,P.match, 0, 4);

The following Nonterminal NUMERIC_AMOUNT detects numeric amounts (e.g. 10, 7/7, 80-90, 0.002, 2.5)

create view NUMERIC_AMOUNT as
  extract 
    regex /\d{1,3}\.?(\/|\\|-|=)?\d*/
  on D.text as numberunit
 from Document D;

The following Nonterminal detects a unit, same as Unit_dict

create view OnlyUnitView as
  select RightContextTok(N.numberunit,1) as unit
   from NUMERIC_AMOUNT N
   where ContainsDict('Unit_dict',RightContextTok(N.numberunit,1))
 and ContainsRegex(/\d{1,3}\.?(-|\s|\(|=|\/|\\)?\d*/,N.numberunit);

The following production NUMERIC_AMOUNT_UNIT detects an amount followed by a unit (e.g. 300mg, 1/2CC, 37.5mg, 80-90mg)

create view NUMERIC_AMOUNT_UNIT as
    select CombineSpans(NA.numberunit, U.unit) as match
    from NUMERIC_AMOUNT NA, OnlyUnitView U
    where 
     FollowsTok(NA.numberunit, U.unit, 0, 1);

create dictionary wordedAmount_dict as 
(
 'one','once','two','twice',
 'three','thrice','four','five',
 'six','seven','eight','nine',
 'ten','eleven','twelve','thirteen',
 'fourteen','fifteen','sixteen',
 'seventeen','eighteen','nineteen',
 'twenty','thirty','forty','fifty',
 'sixty','seventy','eighty','ninty',
 'hundred'
);

The following Nonterminal detects a WordedAmount, same as wordedAmount_dict

create view WordedAmount as
   extract 
      dictionary 'wordedAmount_dict'
      on D.text as match
   from Document D;

create dictionary Unit_dict as 
 (
	 'cc', 'ccs',
	 'cubic c', 'cubic cs',
	 'cubic centimeter', 'cubic centimeters',
	 'cubic centimetres', 'cubic centimetre', 
	 'cubic centi-meter', 'cubic centi-meters',
	 'cubic centi-metre', 'cubic centi-metres',
	 
	 'bag', 'bags',
	 
	 'lb', 'lbs',
	 'pound', 'pounds',
	 
	 'g', 'gs',
	 'gm', 'gms',
	 'gram', 'grams',
	 
	 'mg', 'mgs',
	 'milligram', 'milligrams',
	 'milli-gram', 'milli-grams',
 
	 'kg', 'kgs',
	 'kilogram', 'kilograms',
	 'kilo-gram', 'kilo-grams',
 	
	 'ug', 'ugs',
	 'mcg', 'mcgs',
	 'microgram', 'micrograms',
	 'micro-gram', 'micro-grams',

	 'litre', 'litres',
	 'liter', 'liters',

	 'ml','mls',
	 'millilitre', 'millilitres',
	 'milliliter', 'milliliters',
	 'milli-litre', 'milli-litres',
	 'milli-liter', 'milli-liters',

	  'mcl','mcls',
	  'microlitre', 'microlitres',
	  'microliter', 'microliters',
	  'micro-litre', 'micro-litres',
	  'micro-liter', 'micro-liters',
	 
	  'oz', 'ozs',
	  'ounce', 'ounces',
     
	  'tablet', 'tablets',
	  'tab', 'tabs'
);

create view Unit_view as 
    extract
     dictionaries 'Unit_dict'
   on D.text as unit
 from Document D;

The following production WORDED_NUMERIC_AMOUNT_UNIT detects a dosage expressed as a word followed by a unit (e.g. four mg, six milligrams)

create view WORDED_NUMERIC_AMOUNT_UNIT as
    select CombineSpans(WN.match, U.unit) as match
    from WordedAmount WN, Unit_view U
    where 
      FollowsTok(WN.match, U.unit, 0, 1); 

The following Nonterminal DosageView combines all dosage expressions (e.g. 37.5mg, 80-90mg, four mg, six milligrams)

create view DosageView as 
 (select N.match from NUMERIC_AMOUNT_UNIT N)
  union all
 (select W.match from WORDED_NUMERIC_AMOUNT_UNIT W);

create view DrugPronounDosageView as
    select CombineSpans(D.match,N.match) as match
    from DrugPronounview D, NUMERIC_AMOUNT_UNIT N
    where 
  FollowsTok( D.match,N.match, 0, 4);

create dictionary pastperiodDeterminer as
(
	 'ago','prior',' previous','since','before','last','past' 
);

create dictionary presentperiodDeterminer as
(
	 'now','about','around','several','couple','every','all','this'
);

create dictionary futureperiodDeterminer as
(
 	 'next','later','after'
);

create dictionary hourtimeIndicator as
(
	 'hour', 'hours', 'hrs','hr'
);

create dictionary minutetimeIndicator as
(
	 'minute', 'minutes', 'mins','min'
);

create dictionary secondtimeIndicator as
(
	 'second', 'seconds', 'sec', 'secs'
);

create dictionary decadedurationIndicator as 
(
	 'decade','decades'
);

create dictionary yeardurationIndicator as 
(
	 'year', 'years', 'yrs','yr', 'annum'
);

create dictionary monthdurationIndicator as 
(
	 'month', 'months', 'mnth','mths','mo'
);

create dictionary weekdurationIndicator as 
(
	 'wk','week', 'weeks','wks'
);

create dictionary daydurationIndicator as 
(
    'day', 'days',
	 'night','nights','nite','nites',
	  'morning','mornings','mornin',
	 'evening','evenings',
	 'afternoon','noon'
);

The following Nonterminal detects a PAST_PERIOD_DETERMINER, same as pastperiodDeterminer

create view PAST_PERIOD_DETERMINER as
extract 
	 dictionary 'pastperiodDeterminer'
	 on D.text as match
from Document D;

The following Nonterminal detects a PRESENT_PERIOD_DETERMINER, same as presentperiodDeterminer

create view PRESENT_PERIOD_DETERMINER as
extract 
	 dictionary 'presentperiodDeterminer'
	 on D.text as match
from Document D;

The following Nonterminal detects a FUTURE_PERIOD_DETERMINER, same as futureperiodDeterminer

create view FUTURE_PERIOD_DETERMINER as
extract 
	 dictionary 'futureperiodDeterminer'
	 on D.text as match
from Document D;

The following Nonterminal PERIOD_DETERMINER combines all period expressions

create view PERIOD_DETERMINER as
extract 
	 dictionaries 'pastperiodDeterminer' 
	 and 'presentperiodDeterminer' 
	 and 'futureperiodDeterminer'
	 on D.text as match
from Document D;

The following Nonterminal TIME_INTERVAL combines all time expressions

create view TIME_INTERVAL as
extract 
	 dictionaries 'hourtimeIndicator' 
	 and 'minutetimeIndicator' 
	 and 'secondtimeIndicator'
	 on D.text as match
from Document D;

The following Nonterminal DURATION_INDICATOR combines all duration expressions

create view DURATION_INDICATOR as
extract 
	 dictionaries 'decadedurationIndicator' 
	 and 'yeardurationIndicator'
	 and 'monthdurationIndicator' 
	 and 'weekdurationIndicator' 
	 and 'daydurationIndicator'
	 on D.text as match
from Document D;

The following production DURATION_PAST_PERIOD detects a Duration identifier followed by a time when (e.g. years ago, weeks prior)

create view DURATION_PAST_PERIOD as
select CombineSpans(DI.match, PSD.match) as match
from DURATION_INDICATOR DI, PAST_PERIOD_DETERMINER PSD 
where
	 FollowsTok(DI.match, PSD.match, 0, 1);

The following production DURATION_PRESENT_PERIOD detects a Duration identifier followed by a time when

create view DURATION_PRESENT_PERIOD as
select CombineSpans(DI.match, PPD.match) as match
from DURATION_INDICATOR DI, PRESENT_PERIOD_DETERMINER PPD 
where
	 FollowsTok(DI.match, PPD.match, 0, 1);	

The following production DURATION_FUTURE_PERIOD detects a Duration identifier followed by a time when (e.g. weeks later, days after)

create view DURATION_FUTURE_PERIOD as
select CombineSpans(DI.match, FD.match) as match
from DURATION_INDICATOR DI, FUTURE_PERIOD_DETERMINER FD 
where
	 FollowsTok(DI.match, FD.match, 0, 1);

The following production PAST_PERIOD_DURATION detects a time when, followed by a Duration (e.g. last year, previous day)

create view PAST_PERIOD_DURATION as
select CombineSpans(PSD.match, DI.match) as match
from PAST_PERIOD_DETERMINER PSD , DURATION_INDICATOR DI 
where
	 FollowsTok(PSD.match, DI.match, 0, 1);

The following production PRESENT_PERIOD_DURATION detects a time when, followed by a Duration(e.g. about a year, around a month)

create view PRESENT_PERIOD_DURATION as
select CombineSpans(PPD.match, DI.match) as match 
from PRESENT_PERIOD_DETERMINER PPD , DURATION_INDICATOR DI 
where
	 FollowsTok(PPD.match, DI.match, 0, 1);

The following production FUTURE_PERIOD_DURATION detects a time when, followed by a Duration (e.g. later years, next day)

create view FUTURE_PERIOD_DURATION as
select CombineSpans(FD.match, DI.match) as match
from FUTURE_PERIOD_DETERMINER FD, DURATION_INDICATOR DI 
where
	 FollowsTok(FD.match, DI.match, 0, 1);	

The following production TIME_PAST_PERIOD detects a Time indicator followed by a time when (e.g. hours ago, minutes before)

create view TIME_PAST_PERIOD as
select CombineSpans(TI.match, PSD.match) as match
from TIME_INTERVAL TI, PAST_PERIOD_DETERMINER PSD 
where
	 FollowsTok(TI.match, PSD.match, 0, 1);

The following production TIME_PRESENT_PERIOD detects a Time indicator followed by a time when (e.g. hours now)

create view TIME_PRESENT_PERIOD as
select CombineSpans(TI.match, PPD.match) as match
from TIME_INTERVAL TI, PRESENT_PERIOD_DETERMINER PPD 
where
	 FollowsTok(TI.match, PPD.match, 0, 1);	

The following production TIME_FUTURE_PERIOD detects a Time indicator followed by a time when (e.g. hours later, minutes after)

create view TIME_FUTURE_PERIOD as
select CombineSpans(TI.match, FD.match) as match
from TIME_INTERVAL TI, FUTURE_PERIOD_DETERMINER FD 
where
	 FollowsTok(TI.match, FD.match, 0, 1);

The following production PAST_PERIOD_TIME detects a time when followed by a Time indicator (e.g. last hour, last minutes)

create view PAST_PERIOD_TIME as
select CombineSpans(PSD.match, TI.match) as match
from PAST_PERIOD_DETERMINER PSD, TIME_INTERVAL TI  
where
	 FollowsTok(PSD.match, TI.match, 0, 1);

The following production PRESENT_PERIOD_TIME detects a time when followed by a Time indicator (e.g. several hour, couple of minutes)

create view PRESENT_PERIOD_TIME as
select CombineSpans(PPD.match, TI.match) as match
from PRESENT_PERIOD_DETERMINER PPD, TIME_INTERVAL TI  
where
	 FollowsTok(PPD.match, TI.match, 0, 1);

-------------------------------------------------------------------

-- (e.g. next hour, after a minute)
-------------------------------------------------------------------
create view FUTURE_PERIOD_TIME as
select CombineSpans(FD.match, TI.match) as match
from FUTURE_PERIOD_DETERMINER FD, TIME_INTERVAL TI  
where
	 FollowsTok(FD.match, TI.match, 0, 1);

--------------------------------------------------------

-- e.g. 5 minutes ago 
--------------------------------------------------------
create view AMOUNT_TIME_PAST_PERIOD as
select CombineSpans(A.match, TSP.match) as match
from AMOUNT A, TIME_PAST_PERIOD TSP
where 
	 FollowsTok(A.match, TSP.match, 0, 1);

--------------------------------------------------------

-- e.g. 10 hours now
--------------------------------------------------------
create view AMOUNT_TIME_PRESENT_PERIOD as
select CombineSpans(A.match, TPP.match) as match
from AMOUNT A, TIME_PRESENT_PERIOD TPP
where 
	 FollowsTok(A.match, TPP.match, 0, 1);

--------------------------------------------------------

-- e.g. 5 minutes later 
--------------------------------------------------------	
create view AMOUNT_TIME_FUTURE_PERIOD as
select CombineSpans(A.match, TFP.match) as match
from AMOUNT A, TIME_FUTURE_PERIOD TFP
where 
	 FollowsTok(A.match, TFP.match, 0, 1);

--------------------------------------------------------

-- e.g. 15 seconds 
--------------------------------------------------------
create view AMOUNT_TIME as
select CombineSpans(A.match, T.match) as match
from AMOUNT A, TIME_INTERVAL T
where 
	 FollowsTok(A.match, T.match, 0, 1);

--------------------------------------------------------

-- e.g. last 2 hours, past 2 minutes 
--------------------------------------------------------
create view PAST_PERIOD_AMOUNT_TIME as
select CombineSpans(PSD.match, AT.match) as match
from PAST_PERIOD_DETERMINER PSD, AMOUNT_TIME AT
where 
	 FollowsTok(PSD.match, AT.match, 0, 1);

--------------------------------------------------------

-- e.g. around 2 hours 
--------------------------------------------------------	
create view PRESENT_PERIOD_AMOUNT_TIME as
select CombineSpans(PPD.match, AT.match) as match
from PRESENT_PERIOD_DETERMINER PPD, AMOUNT_TIME AT
where 
	 FollowsTok(PPD.match, AT.match, 0, 1);

--------------------------------------------------------

-- e.g. next 15 seconds, after 2 minutes 
--------------------------------------------------------	
create view FUTURE_PERIOD_AMOUNT_TIME as
select CombineSpans(FD.match, AT.match) as match
from FUTURE_PERIOD_DETERMINER FD, AMOUNT_TIME AT
where 
	 FollowsTok(FD.match, AT.match, 0, 1);

--------------------------------------------------------

-- e.g. 5 years ago 
--------------------------------------------------------		
create view AMOUNT_DURATION_PAST_PERIOD as
select CombineSpans(A.match, DSP.match) as match
from AMOUNT A, DURATION_PAST_PERIOD DSP
where 
	 FollowsTok(A.match, DSP.match, 0, 1);

--------------------------------------------------------

-- e.g. 5 years now
--------------------------------------------------------	
create view AMOUNT_DURATION_PRESENT_PERIOD as
select CombineSpans(A.match, DPP.match) as match
from AMOUNT A, DURATION_PRESENT_PERIOD DPP
where 
	 FollowsTok(A.match, DPP.match, 0, 1);

--------------------------------------------------------

-- e.g. 5 years later, 9 months after 
--------------------------------------------------------	
create view AMOUNT_DURATION_FUTURE_PERIOD as
select CombineSpans(A.match, DFP.match) as match
from AMOUNT A, DURATION_FUTURE_PERIOD DFP
where 
	 FollowsTok(A.match, DFP.match, 0, 1);

--------------------------------------------------------

-- e.g. 15 months 
--------------------------------------------------------
create view AMOUNT_DURATION as
select CombineSpans(A.match, DI.match) as match
from AMOUNT A, DURATION_INDICATOR DI
where 
	 FollowsTok(A.match, DI.match, 0, 1);

--------------------------------------------------------

-- e.g. last 15 weeks, last 2 years 
--------------------------------------------------------
create view PAST_PERIOD_AMOUNT_DURATION as
select CombineSpans(PSD.match, AD.match) as match
from PAST_PERIOD_DETERMINER PSD, AMOUNT_DURATION AD
where 
	 FollowsTok(PSD.match, AD.match, 0, 1);

--------------------------------------------------------

-- e.g. about 3 monts, around five years 
--------------------------------------------------------
create view PRESENT_PERIOD_AMOUNT_DURATION as
select CombineSpans(PPD.match, AD.match) as match
from PRESENT_PERIOD_DETERMINER PPD, AMOUNT_DURATION AD
where 
	 FollowsTok(PPD.match, AD.match, 0, 1);

--------------------------------------------------------

-- e.g. next 15 weeks, after 2 years 
--------------------------------------------------------	
create view FUTURE_PERIOD_AMOUNT_DURATION as
select CombineSpans(FPD.match, AD.match) as match
from FUTURE_PERIOD_DETERMINER FPD, AMOUNT_DURATION AD
where 
	 FollowsTok(FPD.match, AD.match, 0, 1);

create view DURATION_PERIOD as
(select DSP.* from DURATION_PAST_PERIOD DSP)
union all 
(select DPP.* from DURATION_PRESENT_PERIOD DPP)
union all 
(select DFP.* from DURATION_FUTURE_PERIOD DFP);

create view PERIOD_DURATION as
(select PSD.* from PAST_PERIOD_DURATION PSD)
union all 
(select PPD.* from PRESENT_PERIOD_DURATION PPD)
union all
(select FPD.* from FUTURE_PERIOD_DURATION FPD);

create view TIME_PERIOD as
(select TSP.* from TIME_PAST_PERIOD TSP)
union all 
(select TPP.* from TIME_PRESENT_PERIOD TPP)
union all 
(select TFP.* from TIME_FUTURE_PERIOD TFP);

create view PERIOD_TIME as
(select PST.* from PAST_PERIOD_TIME PST)
union all 
(select PPT.* from PRESENT_PERIOD_TIME PPT)
union all 
(select FPT.* from FUTURE_PERIOD_TIME FPT);

create view AMOUNT_TIME_PERIOD as
(select ATSP.* from AMOUNT_TIME_PAST_PERIOD ATSP)
union all 
(select ATPP.* from AMOUNT_TIME_PRESENT_PERIOD ATPP)
union all 
(select ATFP.* from AMOUNT_TIME_FUTURE_PERIOD ATFP);

create view PERIOD_AMOUNT_TIME as
(select PSAT.* from PAST_PERIOD_AMOUNT_TIME PSAT)
union all 
(select PPAT.* from PRESENT_PERIOD_AMOUNT_TIME PPAT)
union all 
(select FPAT.* from FUTURE_PERIOD_AMOUNT_TIME FPAT);

create view AMOUNT_DURATION_PERIOD as
(select ADSP.* from AMOUNT_DURATION_PAST_PERIOD ADSP)
union all 
(select ADPP.* from AMOUNT_DURATION_PRESENT_PERIOD ADPP)
union all 
(select AFDP.* from AMOUNT_DURATION_FUTURE_PERIOD AFDP);

create view PERIOD_AMOUNT_DURATION as
(select PSAD.* from PAST_PERIOD_AMOUNT_DURATION PSAD)
union all
(select PPAD.* from PRESENT_PERIOD_AMOUNT_DURATION PPAD)
union all
(select FPAD.* from FUTURE_PERIOD_AMOUNT_DURATION FPAD);

create view Intervalview as
(select AD.* from AMOUNT_DURATION AD)
union all
(select AT.* from AMOUNT_TIME AT)
union all
(select DP.* from DURATION_PERIOD DP)
union all
(select DP.* from PERIOD_DURATION DP)
union all
(select TP.* from TIME_PERIOD TP)
union all
(select PT.* from PERIOD_TIME PT)
union all
(select ATP.* from AMOUNT_TIME_PERIOD ATP)
union all
(select PAT.* from PERIOD_AMOUNT_TIME PAT)
union all
(select ADP.* from AMOUNT_DURATION_PERIOD ADP)
union all
(select PAD.* from PERIOD_AMOUNT_DURATION PAD);

create view DrugPronounDosageIntervalView as
select CombineSpans(D.match,I.match) as match
from DrugPronounDosageView D, Intervalview I
where 
FollowsTok( D.match,I.match, 0, 4);