PPLRE Annotator

A PPLRE Annotator is the Annotation System used in the PPLRE Project to put some explicit Syntactic Structure and Shallow Semantic Structure to the PPLRE Corpus.

• Context:
  • Annotation includes End-of-Sentence Detection, Tokenization, Part-of-Speech Tagging, Word Sense Disambiguation, Syntactic Parsing, Named Entity Recognition, and Semantic Role Labeling.
  • Current version is v2.5
• See: PPLRE Detailed Application Design, PPLRE Annotation Issues.

---

---

Current Version

The Current version of the annotator is located at /home/shared/PSort/PPLRE/bin/Annotator/v2.5.1

---

Sample Input/Output

The following sample refers to the PubMed abstract with PSID=7181.

Sample Input

Here is the relevant portion from the source file.

 cat /home/shared/PSort/PPLRE/data/corpusHome/corpus/7181/2_AnnotatorFiles/v2.3/sourcetext.txt
 <ABSTRACT>

Virulent mycobacteria utilize surface-exposed polyketides to interact with host cells, but the mechanism by which these hydrophobic molecules are transported across the cell envelope to the surface of the bacteria is poorly understood. Phthiocerol dimycocerosate (PDIM), a surface-exposed polyketide lipid necessary for <italic>Mycobacterium tuberculosis</italic> virulence, is the product of several polyketide synthases including PpsE. Transport of PDIM requires MmpL7, a member of the MmpL family of RND permeases. Here we show that a domain of MmpL7 biochemically interacts with PpsE, the first report of an interaction between a biosynthetic enzyme and its cognate transporter. Overexpression of the interaction domain of MmpL7 acts as a dominant negative to PDIM synthesis by poisoning the interaction between synthase and transporter. This suggests that MmpL7 acts in complex with the synthesis machinery to efficiently transport PDIM across the cell membrane. Coordination of synthesis and transport may not only be a feature of MmpL-mediated transport in <italic>M. tuberculosis,</italic> but may also represent a general mechanism of polyketide export in many different microorganisms.

  </ABSTRACT>

---

Sample Output

Below are two of the resulting output files generated by the PPLRE Annotator that are most typically referenced by subsequent processes: sentences.txt and annotated.tab.

sentences.txt file

Drawn from PPLRE Corpus 7181.a

Virulent mycobacteria utilize surface-exposed polyketides to interact with host cells, but the mechanism by which these hydrophobic molecules are transported across the cell envelope to the surface of the bacteria is poorly understood. Phthiocerol dimycocerosate (PDIM), a surface-exposed polyketide lipid necessary for Mycobacterium tuberculosis virulence, is the product of several polyketide synthases including PpsE. Transport of PDIM requires MmpL7, a member of the MmpL family of RND permeases. Here we show that a domain of MmpL7 biochemically interacts with PpsE, the first report of an interaction between a biosynthetic enzyme and its cognate transporter.

---

annotated.tab file

Drawn from PPLRE Corpus 7181.a

RowID

Token

Stemmed

POS

Parse Tree

Concept Type

Concept ID

Predicate

SRL-1

SRL-2

SRL-3

SRL-4

1

Virulent

Virulent

JJ

(S1(S(S(NP*

(mono_cell

(0

(2

*

(A0*

*

*

*

2

mycobacteria

mycobacteria

NNS

*)

)

)

)

*

*)

*

*

*

3

utilize

utilize

VB

(VP*

Functional_Concept

C0042153

4

utilize

(V*)

*

*

*

4

surface-exposed

surface-exposed

JJ

(NP*

Spatial_Concept

C0205148

4

*

(A1*

*

*

*

5

polyketides

polyketides

NNS

*)

Clinical_Attribute

C0332157

4

*

*)

*

*

*

6

to

to

TO

(S(VP*

-

-

-

*

(AM-PNC*

*

*

*

7

interact

interact

VB

(VP*

Molecular_Function

C0687133

4

interact

*

(V*)

*

*

8

with

with

IN

(PP*

-

-

-

*

*

(A2*

*

*

9

host

host

NN

(NP*

(cell_type

(1

(2

*

*

*

*

*

10

cells

cell

NNS

*)))))))

)

)

)

*

*)

*)

*

*

11

,

,

,

*

-

-

-

*

*

*

*

*

12

but

but

CC

*

-

-

-

*

*

*

*

*

13

the

the

DT

(S(NP(NP*

-

-

-

*

*

*

(AM-MNR*

(A1*

14

mechanism

mechanism

NN

*)

Functional_Concept

C0441712

4

*

*

*

*)

*

15

by

by

IN

(SBAR(WHPP*

-

-

-

*

*

*

*

*

16

which

which

WDT

(WHNP*))

-

-

-

*

*

*

*

*

17

these

these

DT

(S(NP*

-

-

-

*

*

*

(A1*

*

18

hydrophobic

hydrophobic

JJ

*

(peptide

(2

(2

*

*

*

*

*

19

molecules

molecule

NNS

*)

)

)

)

*

*

*

*)

*

20

are

are

AUX

(VP*

-

-

-

*

*

*

*

*

21

transported

transport

VBN

(VP*

Cell_Function

C0005528

4

transported

*

*

(V*)

*

22

across

across

IN

(PP*

-

-

-

*

*

*

*

*

23

the

the

DT

(NP*

-

-

-

*

*

*

*

*

24

cell

cell

NN

*

(LOCALIZATION

(GO0005618

(3

*

*

*

*

*

25

envelope

envelope

NN

*))

)

)

)

*

*

*

*

*

26

to

to

TO

(PP*

-

-

-

*

*

*

*

*

27

the

the

DT

(NP(NP*

-

-

-

*

*

*

*

*

28

surface

surface

NN

*)

Spatial_Concept

C0205148

4

*

*

*

*

*

29

of

of

IN

(PP*

-

-

-

*

*

*

*

*

30

the

the

DT

(NP*

-

-

-

*

*

*

*

*

31

bacteria

bacteria

NNS

*)))))))))

mono_cell

4

2

*

*

*

*

*)

32

is

is

AUX

(VP*

-

-

-

*

*

*

*

*

33

poorly

poorly

RB

(ADVP*)

Qualitative_Concept

C0205169

4

*

*

*

*

(AM-MNR*)

34

understood

understand

VBN

(VP*)))

Mental_Process

C0162340

4

understood

*

*

*

(V*)

35

.

.

.

*))

-

-

-

*

*

36

37

Phthiocerol

Phthiocerol

NNP

(S1(S(NP(NP*

(Lipid

(C0070976

(4

*

*

38

dimycocerosate

dimycocerosate

NNP

*)

)

)

)

*

*

39

(

(

-LRB-

(PRN*

-

-

-

*

*

40

PDIM

PDIM

NNP

(NP*)

other_organic_compound

6

2

*

*

41

)

)

-RRB-

*)

-

-

-

*

*

42

,

,

,

*

-

-

-

*

*

43

a

a

DT

(NP(NP*

-

-

-

*

*

44

surface-exposed

surface-exposed

JJ

*

lipid

7

2

*

*

45

polyketide

polyketide

JJ

*

-

-

-

*

*

46

lipid

lipid

NN

*)

14742191

1

5

*

*

47

necessary

necessary

JJ

(ADJP*

Lipid

C0023779

4

*

*

48

for

for

IN

(PP*

639871

3

*

*

49

Mycobacterium

Mycobacterium

NNP

(NP*

(ORGANISM

(1773

(3

*

*

50

tuberculosis

tuberculosis

FW

*

)

)

)

*

*

51

virulence

virulence

NN

*))))

Biologic_Function

C0042765

4

*

*

52

,

,

,

*)

-

-

-

*

*

53

is

is

AUX

(VP*

-

-

-

*

*

54

the

the

DT

(NP(NP*

-

-

-

*

*

55

product

product

NN

*)

3707459

1

5

*

*

56

of

of

IN

(PP*

-

-

-

*

*

57

several

several

JJ

(NP(NP*

Quantitative_Concept

C0443302

4

*

(A2*

58

polyketide

polyketide

JJ

*

(PROTEIN

(localID_0

(1

*

*

59

synthases

synthases

NNS

*)

)

)

)

*

*)

60

including

include

VBG

(PP*

Functional_Concept

C0332257

4

including

(V*)

61

PpsE

PpsE

NNP

(NP*))))))

PROTEIN

localID_1

1

*

(A1*)

62

.

.

.

*))

-

-

-

*

*

63

64

Transport

Transport

NNP

(S1(S(NP(NP*)

Cell_Function

C0005528

4

*

(A1*

65

of

of

IN

(PP*

-

-

-

*

*

66

PDIM

PDIM

NNP

(NP*)))

PROTEIN

localID_2

1

*

*)

67

requires

require

VBZ

(VP*

2602586

1

5

requires

(V*)

68

MmpL7

MmpL7

NNP

(NP(NP*)

PROTEIN

localID_3

1

*

(A0*

69

,

,

,

*

-

-

-

*

*

70

a

a

DT

(NP(NP*

-

-

-

*

*

71

member

member

NN

*)

Population_Group

C0680022

4

*

*

72

of

of

IN

(PP*

-

-

-

*

*

73

the

the

DT

(NP(NP*

-

-

-

*

*

74

MmpL

MmpL

NNP

*

(PROTEIN

(localID_4

(1

*

*

75

family

family

NN

*)

)

)

)

*

*

76

of

of

IN

(PP*

-

-

-

*

*

77

RND

RND

JJ

(NP*

(PROTEIN

(localID_5

(1

*

*

78

permeases

permeases

NNS

*)))))))

)

)

)

*

*)

79

.

.

.

*))

-

-

-

*

*

*

80

81

Here

Here

RB

(S1(S(ADVP*)

109485

1

5

*

(AM-LOC*)

*

82

we

we

PRP

(NP*)

-

-

-

*

(A0*)

*

83

show

show

VBP

(VP*

656725

2

5

show

(V*)

*

84

that

that

IN

(SBAR*

-

-

-

*

(A1*

*

85

a

a

DT

(S(NP(NP*

-

-

-

*

*

(A1*

86

domain

domain

NN

*)

8437765

2

5

*

*

*

87

of

of

IN

(PP*

-

-

-

*

*

*

88

MmpL7

MmpL7

NNP

(NP*)))

PROTEIN

localID_3

1

*

*

*)

89

biochemically

biochemically

RB

(ADVP*)

Functional_Concept

C0205474

4

*

*

(AM-ADV*)

90

interacts

interact

VBZ

(VP*

Molecular_Function

C0687133

4

interacts

*

(V*)

91

with

with

IN

(PP*

-

-

-

*

*

(A2*

92

PpsE

PpsE

NNP

(NP(NP*)

PROTEIN

localID_1

1

*

*

*

93

,

,

,

*

-

-

-

*

*

*

94

the

the

DT

(NP(NP*

-

-

-

*

*

*

95

first

first

JJ

*

Quantitative_Concept

C0205435

4

*

*

*

96

report

report

NN

*)

Intellectual_Product

C0684224

4

*

*

*

97

of

of

IN

(PP*

-

-

-

*

*

*

98

an

an

DT

(NP(NP*

-

-

-

*

*

*

99

interaction

interaction

NN

*)

Molecular_Function

C0687133

4

*

*

*

100

between

between

IN

(PP*

-

-

-

*

*

*

101

a

a

DT

(NP(NP*

-

-

-

*

*

*

102

biosynthetic

biosynthetic

JJ

*

-

-

-

*

*

*

103

enzyme

enzyme

NN

*)

PROTEIN

638536

3

*

*

*

104

and

and

CC

*

-

-

-

*

*

*

105

its

its

PRP$

(NP*

-

-

-

*

*

*

106

cognate

cognate

JJ

*

2042649

1

5

*

*

*

107

transporter

transporter

NN

*))))))))))))

PROTEIN

localID_6

1

*

*)

*)

108

.

.

.

*))

-

-

-

*

*

*

109

---