Pathway Computation in Models Derived from Bio-Science Text Sources

Troels Andreasen; Henrik Bulskov Styltsvig; Per Anker Jensen; Jørgen Fischer Nilsson

doi:10.1007/978-3-319-60438-1_42

Pathway Computation in Models Derived from Bio-Science Text Sources

Troels Andreasen, Henrik Bulskov Styltsvig, Per Anker Jensen, Jørgen Fischer Nilsson

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

Abstract

This paper outlines a system, OntoScape, serving to accomplish complex inference tasks on knowledge bases and bio-models derived from life-science text corpora. The system applies so-called natural logic, a form of logic which is readable for humans. This logic affords ontological representations of complex terms appearing in the text sources. Along with logical propositions, the system applies a semantic graph representation facilitating calculation of bio-pathways. More generally, the system affords means of query answering appealing to general and domain specific inference rules.

Original language	English
Title of host publication	Foundations of Intelligent Systems : 23rd International Symposium, ISMIS 2017, Warsaw, Poland, June 26-29, 2017, Proceedings
Editors	Marzena Kryszkiewicz, Annalisa Appice, Dominik Ślęzak, Henryk Rybinski, Andrzej Skowron, Zbigniew W. Raś
Place of Publication	Cham
Publisher	Springer
Publication date	2017
Pages	424-434
ISBN (Print)	978-3-319-60437-4
ISBN (Electronic)	978-3-319-60438-1
DOIs	https://doi.org/10.1007/978-3-319-60438-1_42
Publication status	Published - 2017
Event	23rd International Symposium on Methodologies for Intelligent Systems: 23rd International Symposium - Warsaw University of Technology, Warsawa, Poland Duration: 26 Jun 2017 → 29 Jun 2017 Conference number: 23 http://ismis2017.ii.pw.edu.pl/

Conference

Conference	23rd International Symposium on Methodologies for Intelligent Systems
Number	23
Location	Warsaw University of Technology
Country	Poland
City	Warsawa
Period	26/06/2017 → 29/06/2017
Internet address	http://ismis2017.ii.pw.edu.pl/

Series	Lecture Notes in Computer Science
Number	10352
ISSN	0302-9743

Series	Lecture notes in artificial intelligence
Number	10352
ISSN	0302-9743

Keywords

Semantic text processing in bio-informatics
Bio-models using natural logic and semantic graphs
Querying and pathway computation

Cite this

Andreasen, T., Styltsvig, H. B., Jensen, P. A., & Nilsson, J. F. (2017). Pathway Computation in Models Derived from Bio-Science Text Sources. In M. Kryszkiewicz, A. Appice, D. Ślęzak, H. Rybinski, A. Skowron, & Z. W. Raś (Eds.), Foundations of Intelligent Systems : 23rd International Symposium, ISMIS 2017, Warsaw, Poland, June 26-29, 2017, Proceedings (pp. 424-434). Springer. Lecture Notes in Computer Science, No. 10352, Lecture notes in artificial intelligence, No. 10352 https://doi.org/10.1007/978-3-319-60438-1_42

Andreasen, Troels ; Styltsvig, Henrik Bulskov ; Jensen, Per Anker ; Nilsson, Jørgen Fischer. / Pathway Computation in Models Derived from Bio-Science Text Sources. Foundations of Intelligent Systems : 23rd International Symposium, ISMIS 2017, Warsaw, Poland, June 26-29, 2017, Proceedings . editor / Marzena Kryszkiewicz ; Annalisa Appice ; Dominik Ślęzak ; Henryk Rybinski ; Andrzej Skowron ; Zbigniew W. Raś. Cham : Springer, 2017. pp. 424-434 (Lecture Notes in Computer Science; No. 10352). (Lecture notes in artificial intelligence; No. 10352).

@inproceedings{ea1114b669754ac69ccb61f6f46a8267,

title = "Pathway Computation in Models Derived from Bio-Science Text Sources",

abstract = "This paper outlines a system, OntoScape, serving to accomplish complex inference tasks on knowledge bases and bio-models derived from life-science text corpora. The system applies so-called natural logic, a form of logic which is readable for humans. This logic affords ontological representations of complex terms appearing in the text sources. Along with logical propositions, the system applies a semantic graph representation facilitating calculation of bio-pathways. More generally, the system affords means of query answering appealing to general and domain specific inference rules.",

keywords = "Semantic text processing in bio-informatics, Bio-models using natural logic and semantic graphs , Querying and pathway computation , Semantic text processing in bio-informatics, Bio-models using natural logic and semantic graphs , Querying and pathway computation ",

author = "Troels Andreasen and Styltsvig, {Henrik Bulskov} and Jensen, {Per Anker} and Nilsson, {J{\o}rgen Fischer}",

year = "2017",

doi = "10.1007/978-3-319-60438-1_42",

language = "English",

isbn = "978-3-319-60437-4",

series = "Lecture Notes in Computer Science",

publisher = "Springer",

number = "10352",

pages = "424--434",

editor = "Kryszkiewicz, {Marzena } and Annalisa Appice and Dominik {\'S}l{\c e}zak and Henryk Rybinski and Andrzej Skowron and Ra{\'s}, {Zbigniew W.}",

booktitle = "Foundations of Intelligent Systems",

note = "null ; Conference date: 26-06-2017 Through 29-06-2017",

url = "http://ismis2017.ii.pw.edu.pl/",

}

Andreasen, T , Styltsvig, HB, Jensen, PA & Nilsson, JF 2017, Pathway Computation in Models Derived from Bio-Science Text Sources. in M Kryszkiewicz, A Appice, D Ślęzak, H Rybinski, A Skowron & ZW Raś (eds), Foundations of Intelligent Systems : 23rd International Symposium, ISMIS 2017, Warsaw, Poland, June 26-29, 2017, Proceedings . Springer, Cham, Lecture Notes in Computer Science, no. 10352, Lecture notes in artificial intelligence, no. 10352, pp. 424-434, 23rd International Symposium on Methodologies for Intelligent Systems, Warsawa, Poland, 26/06/2017. https://doi.org/10.1007/978-3-319-60438-1_42

Pathway Computation in Models Derived from Bio-Science Text Sources. / Andreasen, Troels ; Styltsvig, Henrik Bulskov; Jensen, Per Anker; Nilsson, Jørgen Fischer.

Foundations of Intelligent Systems : 23rd International Symposium, ISMIS 2017, Warsaw, Poland, June 26-29, 2017, Proceedings . ed. / Marzena Kryszkiewicz; Annalisa Appice; Dominik Ślęzak; Henryk Rybinski; Andrzej Skowron; Zbigniew W. Raś. Cham : Springer, 2017. p. 424-434 (Lecture Notes in Computer Science; No. 10352). (Lecture notes in artificial intelligence; No. 10352).

Research output: Chapter in Book/Report/Conference proceeding › Article in proceedings › Research › peer-review

TY - GEN

T1 - Pathway Computation in Models Derived from Bio-Science Text Sources

AU - Andreasen, Troels

AU - Styltsvig, Henrik Bulskov

AU - Jensen, Per Anker

AU - Nilsson, Jørgen Fischer

N1 - Conference code: 23

PY - 2017

Y1 - 2017

N2 - This paper outlines a system, OntoScape, serving to accomplish complex inference tasks on knowledge bases and bio-models derived from life-science text corpora. The system applies so-called natural logic, a form of logic which is readable for humans. This logic affords ontological representations of complex terms appearing in the text sources. Along with logical propositions, the system applies a semantic graph representation facilitating calculation of bio-pathways. More generally, the system affords means of query answering appealing to general and domain specific inference rules.

AB - This paper outlines a system, OntoScape, serving to accomplish complex inference tasks on knowledge bases and bio-models derived from life-science text corpora. The system applies so-called natural logic, a form of logic which is readable for humans. This logic affords ontological representations of complex terms appearing in the text sources. Along with logical propositions, the system applies a semantic graph representation facilitating calculation of bio-pathways. More generally, the system affords means of query answering appealing to general and domain specific inference rules.

KW - Semantic text processing in bio-informatics

KW - Bio-models using natural logic and semantic graphs

KW - Querying and pathway computation

KW - Semantic text processing in bio-informatics

KW - Bio-models using natural logic and semantic graphs

KW - Querying and pathway computation

U2 - 10.1007/978-3-319-60438-1_42

DO - 10.1007/978-3-319-60438-1_42

M3 - Article in proceedings

SN - 978-3-319-60437-4

T3 - Lecture Notes in Computer Science

SP - 424

EP - 434

BT - Foundations of Intelligent Systems

A2 - Kryszkiewicz, Marzena

A2 - Appice, Annalisa

A2 - Ślęzak, Dominik

A2 - Rybinski, Henryk

A2 - Skowron, Andrzej

A2 - Raś, Zbigniew W.

PB - Springer

CY - Cham

Y2 - 26 June 2017 through 29 June 2017

ER -

Andreasen T , Styltsvig HB, Jensen PA, Nilsson JF. Pathway Computation in Models Derived from Bio-Science Text Sources. In Kryszkiewicz M, Appice A, Ślęzak D, Rybinski H, Skowron A, Raś ZW, editors, Foundations of Intelligent Systems : 23rd International Symposium, ISMIS 2017, Warsaw, Poland, June 26-29, 2017, Proceedings . Cham: Springer. 2017. p. 424-434. (Lecture Notes in Computer Science; No. 10352). (Lecture notes in artificial intelligence; No. 10352). https://doi.org/10.1007/978-3-319-60438-1_42

Link to document

10.1007/978-3-319-60438-1_42