Automatic extraction of microorganisms and their habitats from free text using text mining workflows

Automatic extraction of microorganisms and their habitats from free text using text mining workflows

In this paper we illustrate the usage of text mining workflows to automatically extract instances of microorganisms and their habitats from free text; these entries can then be curated and added to different databases. To this end, we use a Conditional Random Field (CRF) based classifier, as part of...

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Main Authors: Kolluru BalaKrishna, Nakjang Sirintra, Hirt Robert P., Wipat Anil, Ananiadou Sophia
Format: Article
Language:English
Published: De Gruyter 2011-06-01
Series:Journal of Integrative Bioinformatics
Online Access:https://doi.org/10.1515/jib-2011-184
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spelling doaj-c8e4349176cd4e88a4983f0aa04f8b172021-09-06T19:40:31ZengDe GruyterJournal of Integrative Bioinformatics1613-45162011-06-018217618610.1515/jib-2011-184biecoll-jib-2011-184Automatic extraction of microorganisms and their habitats from free text using text mining workflowsKolluru BalaKrishna0Nakjang Sirintra1Hirt Robert P.2Wipat Anil3Ananiadou Sophia4National Centre for Text Mining, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK United Kingdom of Great Britain and Northern IrelandInstitute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK United Kingdom of Great Britain and Northern IrelandInstitute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, United Kingdom of Great Britain and Northern IrelandInstitute for Cell and Molecular Biosciences, University of Newcastle, Newcastle upon Tyne, NE2 4HH, UK United Kingdom of Great Britain and Northern IrelandNational Centre for Text Mining, University of Manchester, 131 Princess Street, Manchester M1 7DN, UK United Kingdom of Great Britain and Northern IrelandIn this paper we illustrate the usage of text mining workflows to automatically extract instances of microorganisms and their habitats from free text; these entries can then be curated and added to different databases. To this end, we use a Conditional Random Field (CRF) based classifier, as part of the workflows, to extract the mention of microorganisms, habitats and the inter-relation between organisms and their habitats.https://doi.org/10.1515/jib-2011-184
collection DOAJ
language English
format Article
sources DOAJ
author Kolluru BalaKrishna
Nakjang Sirintra
Hirt Robert P.
Wipat Anil
Ananiadou Sophia
spellingShingle Kolluru BalaKrishna
Nakjang Sirintra
Hirt Robert P.
Wipat Anil
Ananiadou Sophia
Automatic extraction of microorganisms and their habitats from free text using text mining workflows
Journal of Integrative Bioinformatics
author_facet Kolluru BalaKrishna
Nakjang Sirintra
Hirt Robert P.
Wipat Anil
Ananiadou Sophia
author_sort Kolluru BalaKrishna
title Automatic extraction of microorganisms and their habitats from free text using text mining workflows
title_short Automatic extraction of microorganisms and their habitats from free text using text mining workflows
title_full Automatic extraction of microorganisms and their habitats from free text using text mining workflows
title_fullStr Automatic extraction of microorganisms and their habitats from free text using text mining workflows
title_full_unstemmed Automatic extraction of microorganisms and their habitats from free text using text mining workflows
title_sort automatic extraction of microorganisms and their habitats from free text using text mining workflows
publisher De Gruyter
series Journal of Integrative Bioinformatics
issn 1613-4516
publishDate 2011-06-01
description In this paper we illustrate the usage of text mining workflows to automatically extract instances of microorganisms and their habitats from free text; these entries can then be curated and added to different databases. To this end, we use a Conditional Random Field (CRF) based classifier, as part of the workflows, to extract the mention of microorganisms, habitats and the inter-relation between organisms and their habitats.
url https://doi.org/10.1515/jib-2011-184
work_keys_str_mv AT kollurubalakrishna automaticextractionofmicroorganismsandtheirhabitatsfromfreetextusingtextminingworkflows
AT nakjangsirintra automaticextractionofmicroorganismsandtheirhabitatsfromfreetextusingtextminingworkflows
AT hirtrobertp automaticextractionofmicroorganismsandtheirhabitatsfromfreetextusingtextminingworkflows
AT wipatanil automaticextractionofmicroorganismsandtheirhabitatsfromfreetextusingtextminingworkflows
AT ananiadousophia automaticextractionofmicroorganismsandtheirhabitatsfromfreetextusingtextminingworkflows
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