Mixup - "Little" language for creating annotations for text.

At the simplest level, Mixup is a pattern language for Spans (i.e. token sequences). Each expression is defined relative to labeling called a {@link edu.cmu.minorthird.text.TextLabels}. From the ground up:

Extraction with Mixup

Mixup is normally used for extraction, not matching. For extraction, every Mixup expression should contain matching left and right square brackets. For each Span that the expression is matched against, and for every possible way the expression can be matched, a subspan of the tokens matching the RPCS's inside the square brackets will be extracted.

For example:

Mixup Programs

The MixupProgram class allows a series of statements to be executed, one after another, in order to modify a text labeling. Most of these statements are based on evaluating Mixup patterns, and then modifying the labels in response to those patterns.
The types of Mixup statements are:

An Example Mixup Program

Here's an extended example. 
  
//=============================================================================
// Extract phrases about cells from biomedical captions.
//
// known current bugs:
//  need better sentence-starting rules, not using stems
//  (sentence start should be based on linguistically proper use of ":")
//  need to discard things with unbalanced parens
// undesirable examples:        
//  "in Hela-tet Of f cells" extracts "f cells"
//  "in contrast cells" extracts "in contrast cells"
//  "respective cells" extracts "respective cells"
//=============================================================================

// words that might start a plural noun phrase about cells
defDict pluralStart = ,, no, with, within, from, of, the, these, all, in, on, only, for, by, to, other, 
        have, indicate, represent, show, and, or;

// end of a plural noun phrase about cells - ie, a plural cell-related noun
defDict pluralEnd = cells,strains,clones;

// end of a singular noun phrase about cells
defDict singEnd = cell,strain,clone;

// start of a singular noun phrase about cells
defDict singStart = ,, with, from, of, the, in, on, or, a, an, each, to, other, indicate, represent, 
        and, or, per;

// numbers
defDict number = one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve,
        thirteen, fourteen, fifteen, sixteen, seventeen, eighteen, nineteen, twenty;

// simplify syntax for these, since there's no good way to quote them
defDict openParen = (;
defDict closeParen = );

// 'context' is anything near a cell end.  This is used to restrict search

defSpanType end =: ... [a(pluralEnd)] ... || ... [a(singEnd)] ...;
defSpanType context =: any+ [ any{15} @end any{2}] ... ||  [ any{,15} @end any{2}] ... ;

// the start of a sentence might have a panel label like (a) before it.

defSpanType sentStart =context: ... ['.' a(openParen) !a(closeParen){1,4} a(closeParen)] ... ;
defSpanType sentStart =context: ... ['.' ] re('^[A-Z]') ... ;

// something to ignore (not extract) that precedes a plural noun phrase

defSpanType ignoredPluralStart =context: ... [stem:a(pluralStart)]  ...;
defSpanType ignoredPluralStart =context: ... [stem:a(pluralStart) a(number) ] ...; 
defSpanType ignoredPluralStart =context: ... [stem:a(pluralStart) re('^[0-9]+$') ] ...; 
defSpanType ignoredPluralStart =context: ... [@sentStart] ...;

// something to ignore (not extract) that precedes a singular noun phrase

defSpanType ignoredSingStart =context: ... [stem:a(singStart)] ...;
defSpanType ignoredSingStart =context: ... [@sentStart] ...;

// don't allow 'breaks' (commands, periods, etc) in the adjectives that qualify a 
// cell-related noun.

defDict breakPunct = ,, .;
defSpanType qualifiers =context: 
        ... [{1,8}] ...;

// finally define noun phrases as start,qualifiers,end

defSpanType cell =context: ... @ignoredPluralStart [@qualifiers a(pluralEnd)] ... ;
defSpanType cell =context: ... @ignoredSingStart [@qualifiers a(singEnd)] ... ;

// other cases seem to be like 'strain XY123' and 'strain XY123-fobar'

defSpanType cell =context: ... ['strain' re('^[A-Z]+[0-9]+$') '-' any] ... ;
defSpanType cell =context: ... ['strain' re('^[A-Z]+[0-9]+$') !'-'] ... ;

Last modified: Sun Feb 08 20:31:21 Eastern Standard Time 2004