A System for Computing Conceptual Pathways in Bio-medical Text Models

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

doi:10.1007/978-3-319-08326-1_27

A System for Computing Conceptual Pathways in Bio-medical Text Models

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

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

Abstract

This paper describes the key principles in a system for querying and conceptual path finding in a logic-based knowledge base. The knowledge base is extracted from textual descriptions in bio-, pharma- and medical areas. The knowledge base applies natural logic, that is, a variable-free term-algebraic form of predicate logic. Natural logics are distinguished by coming close to natural language so that propositions are readable by domain experts. The natural logic knowledge base is accompanied by an internal graph representation, where the nodes represent simple concept terms as well as compound concepts stemming from entire phrases. Path finding between concepts is facilitated by a labelled graph form that represents the knowledge base as well as the ontological information.

Original language	English
Title of host publication	Foundations of Intelligent Systems : 21st International Symposium, ISMIS 2014, Roskilde, Denmark, June 25-27, 2014. Proceedings
Editors	Troels Andreasen, Henning Christiansen, Juan-Carlos Cubero, Zbigniew W. Raś
Place of Publication	Heidelberg
Publisher	Springer Science+Business Media
Publication date	2014
Pages	264-273
ISBN (Print)	9783319083254, 3319083252
ISBN (Electronic)	9783319083261
DOIs	https://doi.org/10.1007/978-3-319-08326-1_27
Publication status	Published - 2014
Event	The 21st International Symposium on Methodologies for Intelligent Systems. ISMIS 2014 - Roskilde University, Roskilde, Denmark Duration: 25 Mar 2014 → 27 Jun 2014 Conference number: 21 http://isl.ruc.dk/ismis2014/

Conference

Conference	The 21st International Symposium on Methodologies for Intelligent Systems. ISMIS 2014
Number	21
Location	Roskilde University
Country/Territory	Denmark
City	Roskilde
Period	25/03/2014 → 27/06/2014
Internet address	http://isl.ruc.dk/ismis2014/

Series	Lecture Notes in Computer Science
ISSN	0302-9743

Access to Document

10.1007/978-3-319-08326-1_27

Handle.net

Persistent link

Cite this

Andreasen, T., Bulskov, H., Nilsson, J. F., & Jensen, P. A. (2014). A System for Computing Conceptual Pathways in Bio-medical Text Models. In T. Andreasen, H. Christiansen, J-C. Cubero, & Z. W. Raś (Eds.), Foundations of Intelligent Systems: 21st International Symposium, ISMIS 2014, Roskilde, Denmark, June 25-27, 2014. Proceedings (pp. 264-273). Springer Science+Business Media. https://doi.org/10.1007/978-3-319-08326-1_27

Andreasen, Troels ; Bulskov, Henrik ; Nilsson, Jørgen Fischer et al. / A System for Computing Conceptual Pathways in Bio-medical Text Models. Foundations of Intelligent Systems: 21st International Symposium, ISMIS 2014, Roskilde, Denmark, June 25-27, 2014. Proceedings. editor / Troels Andreasen ; Henning Christiansen ; Juan-Carlos Cubero ; Zbigniew W. Raś. Heidelberg : Springer Science+Business Media, 2014. pp. 264-273 (Lecture Notes in Computer Science).

@inproceedings{455a3b88851c44c88e3d53002b49caff,

title = "A System for Computing Conceptual Pathways in Bio-medical Text Models",

abstract = "This paper describes the key principles in a system for querying and conceptual path finding in a logic-based knowledge base. The knowledge base is extracted from textual descriptions in bio-, pharma- and medical areas. The knowledge base applies natural logic, that is, a variable-free term-algebraic form of predicate logic. Natural logics are distinguished by coming close to natural language so that propositions are readable by domain experts. The natural logic knowledge base is accompanied by an internal graph representation, where the nodes represent simple concept terms as well as compound concepts stemming from entire phrases. Path finding between concepts is facilitated by a labelled graph form that represents the knowledge base as well as the ontological information.",

keywords = "Semantic text processing in bio-informatics and medicine, Natural logic knowledge bases in bio-informatics, Generative ontologies, Path-finding in graph knowledge bases",

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

year = "2014",

doi = "10.1007/978-3-319-08326-1_27",

language = "English",

isbn = "9783319083254",

series = "Lecture Notes in Computer Science",

publisher = "Springer Science+Business Media",

pages = "264--273",

editor = "Troels Andreasen and Henning Christiansen and Juan-Carlos Cubero and Ra{\'s}, {Zbigniew W.}",

booktitle = "Foundations of Intelligent Systems",

address = "Germany",

note = "The 21st International Symposium on Methodologies for Intelligent Systems. ISMIS 2014 ; Conference date: 25-03-2014 Through 27-06-2014",

url = "http://isl.ruc.dk/ismis2014/",

}

Andreasen, T, Bulskov, H, Nilsson, JF & Jensen, PA 2014, A System for Computing Conceptual Pathways in Bio-medical Text Models. in T Andreasen, H Christiansen, J-C Cubero & ZW Raś (eds), Foundations of Intelligent Systems: 21st International Symposium, ISMIS 2014, Roskilde, Denmark, June 25-27, 2014. Proceedings. Springer Science+Business Media, Heidelberg, Lecture Notes in Computer Science, pp. 264-273, The 21st International Symposium on Methodologies for Intelligent Systems. ISMIS 2014, Roskilde, Denmark, 25/03/2014. https://doi.org/10.1007/978-3-319-08326-1_27

A System for Computing Conceptual Pathways in Bio-medical Text Models. / Andreasen, Troels; Bulskov, Henrik; Nilsson, Jørgen Fischer et al.
Foundations of Intelligent Systems: 21st International Symposium, ISMIS 2014, Roskilde, Denmark, June 25-27, 2014. Proceedings. ed. / Troels Andreasen; Henning Christiansen; Juan-Carlos Cubero; Zbigniew W. Raś. Heidelberg: Springer Science+Business Media, 2014. p. 264-273 (Lecture Notes in Computer Science).

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

TY - GEN

T1 - A System for Computing Conceptual Pathways in Bio-medical Text Models

AU - Andreasen, Troels

AU - Bulskov, Henrik

AU - Nilsson, Jørgen Fischer

AU - Jensen, Per Anker

N1 - Conference code: 21

PY - 2014

Y1 - 2014

N2 - This paper describes the key principles in a system for querying and conceptual path finding in a logic-based knowledge base. The knowledge base is extracted from textual descriptions in bio-, pharma- and medical areas. The knowledge base applies natural logic, that is, a variable-free term-algebraic form of predicate logic. Natural logics are distinguished by coming close to natural language so that propositions are readable by domain experts. The natural logic knowledge base is accompanied by an internal graph representation, where the nodes represent simple concept terms as well as compound concepts stemming from entire phrases. Path finding between concepts is facilitated by a labelled graph form that represents the knowledge base as well as the ontological information.

AB - This paper describes the key principles in a system for querying and conceptual path finding in a logic-based knowledge base. The knowledge base is extracted from textual descriptions in bio-, pharma- and medical areas. The knowledge base applies natural logic, that is, a variable-free term-algebraic form of predicate logic. Natural logics are distinguished by coming close to natural language so that propositions are readable by domain experts. The natural logic knowledge base is accompanied by an internal graph representation, where the nodes represent simple concept terms as well as compound concepts stemming from entire phrases. Path finding between concepts is facilitated by a labelled graph form that represents the knowledge base as well as the ontological information.

KW - Semantic text processing in bio-informatics and medicine

KW - Natural logic knowledge bases in bio-informatics

KW - Generative ontologies

KW - Path-finding in graph knowledge bases

U2 - 10.1007/978-3-319-08326-1_27

DO - 10.1007/978-3-319-08326-1_27

M3 - Article in proceedings

SN - 9783319083254

SN - 3319083252

T3 - Lecture Notes in Computer Science

SP - 264

EP - 273

BT - Foundations of Intelligent Systems

A2 - Andreasen, Troels

A2 - Christiansen, Henning

A2 - Cubero, Juan-Carlos

A2 - Raś, Zbigniew W.

PB - Springer Science+Business Media

CY - Heidelberg

T2 - The 21st International Symposium on Methodologies for Intelligent Systems. ISMIS 2014

Y2 - 25 March 2014 through 27 June 2014

ER -

Andreasen T, Bulskov H, Nilsson JF, Jensen PA. A System for Computing Conceptual Pathways in Bio-medical Text Models. In Andreasen T, Christiansen H, Cubero J-C, Raś ZW, editors, Foundations of Intelligent Systems: 21st International Symposium, ISMIS 2014, Roskilde, Denmark, June 25-27, 2014. Proceedings. Heidelberg: Springer Science+Business Media. 2014. p. 264-273. (Lecture Notes in Computer Science). doi: 10.1007/978-3-319-08326-1_27