Literature Knowledge: Extract, digitize

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Literature KnowledgeExtract, digitize
explore
Textin articles
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(No Transcript)
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Vocab.
ANNOTATOR Steven Vercruysse SOURCE H. Stals,
D. Inze (2001). When plants cells decide to
divide SPECIES plants //comment SPECIES
Arabidopsis.cell_culture.MM1 SETTING
sucrose_starvation SUBJECT G1-entry, G1-S
transition SUBJECT
Mode-definitions
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Vocab.
ANNOTATOR Steven Vercruysse SOURCE H. Stals,
D. Inze (2001). When plants cells decide to
divide SPECIES plants //comment SPECIES
Arabidopsis.cell_culture.MM1 SETTING
sucrose_starvation SUBJECT G1-entry, G1-S
transition SUBJECT A ( B source(Wang et al.
(1998). ICK1, ...) A ( B (A,B,C) ( ABC
// Symbol ( means element
of. Aaa.Bbb high // Symbol .
means attribute. A -tgt AP //
Symbol means modifier.
Mode-definitions
Introductory examples
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Vocab.
ANNOTATOR Steven Vercruysse SOURCE H. Stals,
D. Inze (2001). When plants cells decide to
divide SPECIES plants //comment SPECIES
Arabidopsis.cell_culture.MM1 SETTING
sucrose_starvation SUBJECT G1-entry, G1-S
transition SUBJECT A ( B source(Wang et al.
(1998). ICK1, ...) A ( B (A,B,C) ( ABC
// Symbol ( means element
of. Aaa.Bbb high // Symbol .
means attribute. A -tgt AP //
Symbol means modifier. A -gt B A
- B A gt B HYP A - C _at_timeX Arab X
-gt Y Yeast A lt-gt B mammals X1 lt-a-gt X2P, a
-gt Y Arab yeast.geneX -gt geneY ArabCDKB11
cell_division --, CycX.expr
Mode-definitions
Introductory examples
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Vocab.
A B A ! B A h B ABC.subid 4 ABCD gt 3
ABC 3 A -gt B -gt C A -gt (B -gt C) A -gt B
-tgt C D B -tgt C A -gt (t1 -gt t2) A -gt
B.expr (A,B,C).subid -gt D //Equiv. to
"(A.subid,B.subid,C.subid) -gt D". A -gt (B -gt
BP) AP,T14P,Y15 -gt (B-gtC)
Relations
Stimulation, transformation
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Vocab.
A B A ! B A h B ABC.subid 4 ABCD gt 3
ABC 3 A -gt B -gt C A -gt (B -gt C) A -gt B
-tgt C D B -tgt C A -gt (t1 -gt t2) A -gt
B.expr (A,B,C).subid -gt D //Equiv. to
"(A.subid,B.subid,C.subid) -gt D". A -gt (B -gt
BP) AP,T14P,Y15 -gt (B-gtC) A \ B -gt
D A \ (B,C) -gt D _at_time (A\B u (C n D)) X
-gt Y Aactive -gt (BNoteB -gt CNoteC)
Relations
Stimulation, transformation
Sets
Notes
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Vocab.
A B A ! B A h B ABC.subid 4 ABCD gt 3
ABC 3 A -gt B -gt C A -gt (B -gt C) A -gt B
-tgt C D B -tgt C A -gt (t1 -gt t2) A -gt
B.expr (A,B,C).subid -gt D //Equiv. to
"(A.subid,B.subid,C.subid) -gt D". A -gt (B -gt
BP) AP,T14P,Y15 -gt (B-gtC) A \ B -gt
D A \ (B,C) -gt D _at_time (A\B u (C n D)) X
-gt Y Aactive -gt (BNoteB -gt
CNoteC) (A,B) -gt C (A,B) -gt (C,D) (A,B) - (A
-gt B) (A,B) -gt (t -gt t.next) (A,B) gt Y (A,B)
-gt (A lt-gt B) A -gt (P -gt B) A -gt (B -gt X)
Relations
Stimulation, transformation
Sets
Notes
Sets Control
Shorthands
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Vocab.
A sgt B //Cf. Kohns zigzag arrow notation A
sgt B //(Equivalent) A s B A -..-gt B
//Cf. Kitanos dash-dotted arrow notation A -..-
B (A,B) sgt (C,D) A -o B (A,B) -o (A -gt
B) (A,B) -o (A lt-gt B)
Transcription, translation
Enzymatic stim.
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Vocab.
A sgt B //Cf. Kohns zigzag arrow notation A
sgt B //(Equivalent) A s B A -..-gt B
//Cf. Kitanos dash-dotted arrow notation A -..-
B (A,B) sgt (C,D) A -o B (A,B) -o (A -gt
B) (A,B) -o (A lt-gt B) A lt-gt B (A,B) lt-gt
(C,D) A lt-a-gt B , a-C (A,B) -gt (C
lt-e-gt D , e-(E,F) , e-gtC) !( A -gt B )
_at_tm !( (A,B) -gt (C,D) ) species ! A -gt B
Transcription, translation
Enzymatic stim.
Binding extensions
Denial
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Vocab.
A sgt B //Cf. Kohns zigzag arrow notation A
sgt B //(Equivalent) A s B A -..-gt B
//Cf. Kitanos dash-dotted arrow notation A -..-
B (A,B) sgt (C,D) A -o B (A,B) -o (A -gt
B) (A,B) -o (A lt-gt B) A lt-gt B (A,B) lt-gt
(C,D) A lt-a-gt B , a-C (A,B) -gt (C
lt-e-gt D , e-(E,F) , e-gtC) !( A -gt B )
_at_tm !( (A,B) -gt (C,D) ) species ! A -gt B HYP
A-gtB species A-gtB sp1, sp2 A-gtB _at_ tm
A-gtB _at_locabc A-gtB abc
AB speciesabc AB settingabc AB species
_at_tm A-gtB sp1, sp2 _at_tm _at_locabc
(A,B) -gt (C,D) HYP sp1, sp2 setting _at_tm
(sp3.A, sp4.B) -gt (C,D) _at_locabc
Transcription, translation
Enzymatic stim.
Binding extensions
Denial
A-gtB _at_ tm A-gtB _at_locabc A-gtB _at_ tm
_at_locabc B _at_tm C-- _at_tm Dgt0 _at_tm Elt0 _at_tm F
note _at_tm G high _at_(intv4\intv5)
Prefixes
Postfixes
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Vocab.
è A _at_tm species è A è A A -gt B A lt-gt
C è A -gt B lt-gt C è A A -gt B
A lt-gt C è A A -gt B gt A lt-gt C è A
A.expr high _at_tm èmany A lt-gt B èmost A
( B è A (A B) !C E gt F è A A B
!C (E gt F) è A A (B (!C D)) (E gt
F) è A1\A2 è z à B1\B2 (Alt-d-gtB,
d-gtC) - E à A A ( B à A ( B à
A.prop è B A.prop -gt B
Quantifiers (exists / for all) logic
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Vocab.
è A _at_tm species è A è A A -gt B A lt-gt
C è A -gt B lt-gt C è A A -gt B
A lt-gt C è A A -gt B gt A lt-gt C è A
A.expr high _at_tm èmany A lt-gt B èmost A
( B è A (A B) !C E gt F è A A B
!C (E gt F) è A A (B (!C D)) (E gt
F) è A1\A2 è z à B1\B2 (Alt-d-gtB,
d-gtC) - E à A A ( B à A ( B à
A.prop è B A.prop -gt B Arabgene
Aconstant, Bequal, Cincrease, D ,
E Arabgene,gene-- A, B, C--, Dgt0,
Elt0, F0, G note Arabgene Khigh,
Lmedium, Mlow, Nconstant, P ,
Qvariable Arabgene Thigh _at_timeX, V0
_at_locLc note2, Wconstant _at_(G1,S)
Quantifiers (exists / for all) logic
Transgenics
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Vocab.
è A _at_tm species è A è A A -gt B A lt-gt
C è A -gt B lt-gt C è A A -gt B
A lt-gt C è A A -gt B gt A lt-gt C è A
A.expr high _at_tm èmany A lt-gt B èmost A
( B è A (A B) !C E gt F è A A B
!C (E gt F) è A A (B (!C D)) (E gt
F) è A1\A2 è z à B1\B2 (Alt-d-gtB,
d-gtC) - E à A A ( B à A ( B à
A.prop è B A.prop -gt B Arabgene
Aconstant, Bequal, Cincrease, D ,
E Arabgene,gene-- A, B, C--, Dgt0,
Elt0, F0, G note Arabgene Khigh,
Lmedium, Mlow, Nconstant, P ,
Qvariable Arabgene Thigh _at_timeX, V0
_at_locLc note2, Wconstant _at_(G1,S) Abc.expr
offsetG1.begin, 0h low, 0h-8h , 8h-12h
, 12h-22h -- Abc.expr G1.begin low, G1
, S.begin - 1h medium, S.begin 1h high
Quantifiers (exists / for all) logic
Transgenics
Time-series
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• Very extensive vocabulary yet mainly pretty
  intuitive
• For modelling genetic networks

• Notation inspired by
• 1. Kohn diagrams and
• 2. Kitanos graphical notation

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Literature KnowledgeExtract, digitize
explore
Textin articles
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• Three merits
• Text-input - broad vocab. for modellers
• Intermediate data-repres. - gt possible
  other format output
• Graphical repres. - Relation-graph browser,
  dynamical

• For now quick way to write down information,
• to visualize explore
• - No demand yet for exact ontology-terminology

• Context (1. Viewing information gathered in
  vicinity 2. SUBJECT-def.).
• HYPs

• Link with text-mining other curation tools

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• Short clarifying demo

BEWARE ! ) First time demo of linked
pipeline Visualizer (graph browser) NOT
FINISHED! - Please extrapolate a bit
- Share feature suggestions