Appendix

Appendix

Property Axioms

Table 1: Entity Mention Axioms (Abstract Syntax)

label(EntityMention, Label)
hasFrameType(EntityMention, FrameType)
hasObjectType(EntityMention,ObjectType)
hasMentionType(EntityMention,MentionType)
fromSentence(EntityMention,Sentence)
hasXref(EntityMention,XRef)
hasStartPosition(EntityMention,StartPosition)
hasEndPosition(EntityMention,EndPosition)

Table 2: Event Mention Axioms (Abstract Syntax)

label (EventMention,Label)
hasFrameType(EventMention,FrameType)
hasObjectType(EventMention, ObjectType)
hasMentionType(EventMention, MentionType)
hasMentionSubType(EventMention, MentionType)
fromSentence(EventMention, Sentence)
hasContext(EventMention,Context)
hasTrigger(EventMention,Trigger)
hasArgument(EventMention,Argument)
hasStartPosition(EventMention, StartPosition)
hasEndPosition(EventMention,EndPosition)
boolIsHypothesis(EventMention, IsHypothesisBoolean)
boolIsDirect(EventMention,IsDirectBoolean)
foundBy(EventMention,Finder)

Table 3: Passage Axioms (Abstract Syntax)

hasFrameType(Passage, FrameType)
hasObjectType (Passage, ObjectType)
hasMetaObject (Passage, MetaObject)
hasStartPosition(Passage, StartPosition)
hasEndPosition(Passage,EndPosition)
hasIndex (Passage, Index)
hasContent(Passage, Content)
hasSectionID (Passage,SectionID)
hasSectionName(Passage, SectionName)

Table 4: Sentence Axioms (Abstract Syntax)

hasFrameType(Sentence, FrameType)
hasObjectType (Sentence, ObjectType)
fromPassage (Sentence, Passage)
hasMetaObject (Sentence, MetaObject)
hasStartPosition(Sentence, StartPosition)
hasEndPosition(Sentence,EndPosition)
hasContent(Sentence, Content)

Table 5: Context Axioms (Abstract Syntax)

hasFrameType(Sentence, FrameType)
hasObjectType (Sentence, ObjectType)
hasScope (Context, Sentence)
hasFacet (Context, Facet)

Evaluation Results

Table 6: Entity-Event Duality Extractions

Label	Entity MT	Event MT	Event MST	Sentence
TA	protein	activation	positive-activation	Overall , TA , TDH and SDH expression were low prior to E-15, but increased more then four-fold by E-17.
KO	simple-chemical	activation	negative-activation	Pramipexole treatment lowered V max in WT but not D 3 KO mice ; however , D 3 KO mice had lower V max for [ 3 H ] DA uptake .
cholesterol	simple-chemical	protein-modification	hydroxylation	The ’ classical ’ pathway begins with the 7alpha hydroxylation of cholesterol and operates entirely in the liver showed normal histone H3 hypoacetylation and K4 H3 hypomethylation in spite of the very low levels of DNA methylation in this CpG island region .
GTP	protein	protein-modification	hydrolysis	The tubulins and the actins are filament forming proteins that bind and hydrolyze GTP and ATP, respectively .
SRE	family	activation	positive-activation	Nevertheless , c-fos SRE elements with TCF sites are still activated by MKL1 and myocardin such that there may be additional elements that determine sensitivity to MKL1 activation .
APN	protein	protein-modification	glycosylation	These results indicate the Cry1Aa-APN interaction was specific and that APN glycosylation was not required for Cry1Aa binding .

Table 7: Domain Specific Entity Type Mismatch

Label	MT1	MT2	Sentence
5-HT	protein	simple-chemical	An increased 5-HT responsiveness has also been demonstrated for other serotonin receptors than 5-HT 1A and in other projection areas than hippocampus.
niacin	protein	simple-chemical	Some 18.2% of the niacin subjects indicated that they found niacin to be intolerable and would never take it again.
Hh	protein	simple-chemical	Our finding that, in endothelial cells in Matrigel IP mRNA levels decrease while HPtc-1 levels increase demonstrates that a mechanism other than Hh signaling can modulate the expression of these Hh target genes.
HIV-1	species	site	The major co-receptors required for entry of HIV-1 are the chemokine receptor molecules CCR-5 ( R5 HIV-1 isolates ) and CXCR-4 ( X4 HIV-1 isolates ) , which are used by monocytes and macrophage- tropic and T-cell tropic HIV-1 viruses, respectively.
HT	protein	cellline	Using HT prevalence data from the NHAHES III study , an estimated lambda S value is about 28 for HT .
Sec	protein	cellline	The five Campylobacter strains analyzed in this study have the Sec dependent and Sec independent ( twin-arginine translocation ‘ TAT ’ ) protein export pathways for the secretion of proteins across the inner and periplasmic membrane .

Table 8: Domain Specific Event Subtype Mismatch

Label	MST1	MST2	Sentence
histone	acetylation	methylation	Trichostatin A ( TSA ) and 5-aza-deoxy-cytadine ( 5-aza-dC ) have been found to increase histone acetylation and decrease DNA methylation , respectively .
ADP	acetylation	methylation	The physical characteristics of the histones are precisely regulated in the cell by an elaborate network of post-translational modifications that include acetylation , methylation , phosphorylation , ubiquitination and ADP ribosylation .
H3	acetylation	methylation	Our ChIP analysis of the inactive X at the SYBL1 locus in an ICF female ( PT3 ) also showed normal histone H3 hypoacetylation and K4 H3 hypomethylation in spite of the very low levels of DNA methylation in this CpG island region .
Foxo3a	phosphorylation	translocation	In conditions in which the PI3K and Akt survival and growth pathway is activated , Foxo3a is phosphorylated by Akt and exported to the cytoplasm where it is sequestrated by the 14-3-3 protein .
Ik-B	phosphorylation	ubiquitination	Upon activation by cytokines , Ik-B is phosphorylated , dissociates from the NF-kB , and is subsequently ubiquitinated and degraded .

Table 9: Reciprocal Event Inconsistency Examples

Label	MT1	MT2	Sentence
Tat	acetylation	deacetylation	Future efforts will analyze in additional molecular detail the role of Tat acetylation and deacetylation in HIV transcription and replication .
AR	acetylation	deacetylation	We have previously shown Tip60 co-associates with HDAC1 upon the active PSA promoter directly acetylates the AR and attenuates HDAC1 mediated AR deacetylation .
IRS-1	acetylation	deacetylation	Indeed , the acetyl transferase Tip60 has been reported to bind to the PH domain of IRS-1 , suggesting the IRS-1 could be acetylated and deacetylated under different conditions .
MAGEA1	methylation	demethylation	The MAGEA1 gene was fully hypermethylated in all four cases of the normal liver tissues but significantly demethylated in HCC tissues ( 21/28 , 75 % ) .
apyrase	glycosylation	deglycosylation	Essentially , glycosylation and deglycosylation of the ecto apyrase ( HB6 ) monomer and the consequences for homodimer formation have been regarded as an on-off switch for ecto nucleotidase activity .