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\title{Enriched Genic Interaction Extraction Challenge\\Data Format}
\author{}
\date{}

\begin{document}
\maketitle
\section{File Structure}

LLL challenge training data and the linguistic information are represented as follows. The file consists of the following fields (one field by line): 

\begin{itemize}
  \item ID: unique identifier of the Pubmed abstract that contains
    the sentence and the sentence position number
  \item sentence: the original sentence
  \item words: sequence of the sentence words
  \item agents: list of the agents of the genic interactions
  \item targets: list of the targets of the genic interactions
  \item genic\_interactions: list of the interactions described in the
      sentence.
  \item lemmas: list of identified canonical form of words 
  \item syntactic\_relations: list of the syntactic relations in the
      sentence. See the Syntactic Analysis Guidelines for more information about this field
\end{itemize}

\section{Field Structure}

A tab separates each element of a field:

\subsection*{ID}

 The ID field contains the abstract PubMed ID (PMID) which the sentence is
extracted from and it contains the sentence number in this abstract.

\begin{center}
\begin{tabular}[!]{|lll|}
\hline
ID & (tabulation)& 11011148-1\\
\hline
\end{tabular}
\end{center}

\subsection*{SENTENCE}

This field contains the sentence.

\begin{center}
\begin{tabular}[!]{|lll|}
\hline
sentence & (tabulation) & ykuD was transcribed by SigK RNA \\
& & polymerase from T4 of sporulation.\\
\hline
\end{tabular}
\end{center}

\subsection*{WORDS, AGENTS, TARGETS, GENIC\_INTERACTIONS, LEMMAS, SYNTACTIC\_RELATIONS}

Other fields are organised according to the following format :

\begin{center}
\begin{tabular}[!]{|lll|}
\hline
Field\_Name & (tabulation) & predicate1(argument1\_1,argument1\_2,...)\\
& (tabulation)&  predicate2(argument2\_1,argument2\_2,$\dots$)\\
& (tabulation) & $\dots$ \\
\hline
\end{tabular}
\end{center}


\subsection*{EXAMPLE WORDS}

\begin{center}
\begin{tabular}[!]{|ll|}
\hline
words & word(0,'ykuD',0,3) word(1,'was',5,7) word(2,'transcribed',9,19)\\
&word(3,'by',21,22) word(4,'SigK',24,27) word(5,'RNA',29,31)\\
&word(6,'polymerase',33,42) word(7,'from',44,47) word(8,'T4',49,50)\\
&word(9,'of',52,53) word(10,'sporulation',55,65)\\
\hline
\end{tabular}
\end{center}

\section{Predicate Description}

\subsection*{WORD}
The predicate "word" refers to a word of the sentence and accepts four arguments:\\
{\bf word(id\_word,'string\_word',start\_word,end\_word)}

\begin{center}
\begin{tabular}[!]{|l|l|}
\hline
id\_word & integer, unique word id\\
string\_word & string, the actual word\\
start\_word & integer, position of the first character in the sentence (starting at 0)\\
end\_word & integer, position of the last character in the sentence (starting at 0)\\
\hline
\end{tabular}
\end{center}

\subsection*{AGENT}
The predicate "agent" refers to the agent of the genic interaction. 
It accepts one argument: {\bf agent(id\_word)}

\begin{center}
\begin{tabular}[!]{|l|l|}
\hline
id\_word & integer, id of the word the agent refers to\\
\hline
\end{tabular}
\end{center}


\subsection*{TARGET}
 The predicate "target" refers to the target of the genic interaction.
It accepts one argument: {\bf target(id\_word) }

\begin{center}
\begin{tabular}[!]{|l|l|}
\hline
id\_word & integer, id of the word the target refers to\\
\hline
\end{tabular}
\end{center}

\subsection*{GENIC\_INTERACTION}
The predicate "genic\_interaction" refers to an
interaction between an agent and a target: {\bf genic\_interaction(id\_word1,id\_word2)}

\begin{center}
\begin{tabular}[!]{|l|l|}
\hline
id\_word1 & integer, id of the word the agent refers to\\
id\_word2 & integer, id of the word the target refers to\\
\hline
\end{tabular}
\end{center}

\subsection*{LEMMAS}
The predicate "lemma" refers to the normalized form (lemma) of a word.

{\bf lemma(id\_word,'string\_lemma')}
\begin{center}
\begin{tabular}[!]{|l|l|}
\hline
id\_word & integer, id of the word the lemma refers to\\
string\_lemma & string,the lemma of the word\\
\hline
\end{tabular}
\end{center}

\subsection*{SYNTACTIC\_RELATION}
The predicate "relation" refers to the normalized form (lemma) of a word.
See the Syntactic Analysis Guidelines for more information.

{\bf relation('string\_relation',id\_word1,id\_word2)}

\begin{center}
\begin{tabular}[!]{|l|l|}
\hline
string\_relation & string, the information contained in a syntactic relation\\
		&(function of the relation:morpho-syntactic nature of the 2 words)\\
id\_word1 & integer, id of the first word (the head) linked by the relation\\
id\_word2 & integer, id of the second word (the expension) linked by the relation\\
\hline
\end{tabular}
\end{center}


\section{Example}

\begin{tabular}[!]{ll}
ID& 10747015-5\\

sentence& Localization of SpoIIE was shown to be dependent on the essential cell\\ 
&division protein FtsZ.\\
words&	word(0,'Localization',0,11)	word(1,'of',13,14)	word(2,'SpoIIE',16,21)\\
&word(3,'was',23,25) word(4,'shown',27,31)	word(5,'to',33,34)	word(6,'be',36,37)\\	
&word(7,'dependent',39,47)	word(8,'on',49,50)  word(9,'the',52,54)\\	
&word(10,'essential',56,64)   word(11,'cell',66,69)	word(12,'division',71,78)\\
& word(13,'protein',80,86)	word(14,'FtsZ',88,91)\\
lemmas&	lemma(0,'localization')	lemma(1,'of')	lemma(2,'spoIIE')	lemma(3,'be')\\
&lemma(4,'show')  lemma(5,'to')	lemma(6,'be')	lemma(7,'dependent')\\	
&lemma(8,'on')	lemma(9,'the')	lemma(10,'essential')\\	
&lemma(11,'cell')	lemma(12,'division')	lemma(13,'protein')	lemma(14,'ftsZ')\\	
syntactic\_relations&	relation('comp\_of:N-N',0,2)	relation('mod\_att:N-ADJ',13,10)\\
&relation('mod\_pred:N-ADJ',0,7)  relation('mod\_att:N-N',14,13)\\
&relation('mod\_att:N-N',12,11) relation('mod\_att:N-N',13,12)\\
&relation('comp\_on:ADJ-N',7,14)\\
agents& agent(14)\\
targets& target(2)\\
genic\_interactions& genic\_interaction(14,2)\\
\end{tabular}
\end{document}
