Computing Pathways in Bio-Models Derived from Bio-Science Text Sources

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

Computing Pathways in Bio-Models Derived from Bio-Science Text Sources

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

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

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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 specfic inference rules.

Original language	English
Title of host publication	International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014, Granada, Spain, April 7-9, 2014
Editors	Ignacio Rojas, Francisco Ortuno Guzman
Number of pages	10
Place of Publication	Spanien
Publisher	Copicentro Editorial
Publication date	2015
Pages	217-226
ISBN (Print)	9788415814849
Publication status	Published - 2015
Event	2nd International Work-Conference on Bioinformatics and Biomedical Engineering - Granada, Spain Duration: 7 Apr 2014 → 9 Apr 2014 Conference number: 2 http://iwbbio.ugr.es/2014/

Conference

Conference	2nd International Work-Conference on Bioinformatics and Biomedical Engineering
Number	2
Country/Territory	Spain
City	Granada
Period	07/04/2014 → 09/04/2014
Internet address	http://iwbbio.ugr.es/2014/

Keywords

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

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Andreasen_Bulskov_Nilsson_Jensen_IWBBIO_2014_paper_26Final published version, 809 KBLicence: CC BY-NC-ND

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Cite this

@inproceedings{924187e4ec174d60a4040e41ced8be26,

title = "Computing Pathways in Bio-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 specfic inference rules.",

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

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

year = "2015",

language = "English",

isbn = "9788415814849",

pages = "217--226",

editor = "Ignacio Rojas and {Ortuno Guzman}, Francisco",

booktitle = "International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014, Granada, Spain, April 7-9, 2014",

publisher = "Copicentro Editorial",

address = "Spain",

note = "2nd International Work-Conference on Bioinformatics and Biomedical Engineering ; Conference date: 07-04-2014 Through 09-04-2014",

url = "http://iwbbio.ugr.es/2014/",

}

Andreasen, T, Bulskov, H, Nilsson, JF & Jensen, PA 2015, Computing Pathways in Bio-Models Derived from Bio-Science Text Sources. in I Rojas & F Ortuno Guzman (eds), International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014, Granada, Spain, April 7-9, 2014. Copicentro Editorial, Spanien, pp. 217-226, 2nd International Work-Conference on Bioinformatics and Biomedical Engineering, Granada, Spain, 07/04/2014.

Computing Pathways in Bio-Models Derived from Bio-Science Text Sources. / Andreasen, Troels; Bulskov, Henrik; Nilsson, Jørgen Fischer et al.
International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014, Granada, Spain, April 7-9, 2014. ed. / Ignacio Rojas; Francisco Ortuno Guzman. Spanien: Copicentro Editorial, 2015. p. 217-226.

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

TY - GEN

T1 - Computing Pathways in Bio-Models Derived from Bio-Science Text Sources

AU - Andreasen, Troels

AU - Bulskov, Henrik

AU - Nilsson, Jørgen Fischer

AU - Jensen, Per Anker

N1 - Conference code: 2

PY - 2015

Y1 - 2015

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 specfic 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 specfic inference rules.

KW - Semantic text processing in bio-informatics

KW - Bio-models using natural logic and semantic graphs

KW - Pathway computation

M3 - Article in proceedings

SN - 9788415814849

SP - 217

EP - 226

BT - International Work-Conference on Bioinformatics and Biomedical Engineering, IWBBIO 2014, Granada, Spain, April 7-9, 2014

A2 - Rojas, Ignacio

A2 - Ortuno Guzman, Francisco

PB - Copicentro Editorial

CY - Spanien

T2 - 2nd International Work-Conference on Bioinformatics and Biomedical Engineering

Y2 - 7 April 2014 through 9 April 2014

ER -