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BioTextQuest+: a knowledge integration platform for literature mining and concept discovery

N. Papanikolaou, G. A. Pavlopoulos, E. Pafilis, T. Theodosiou, R. Schneider, V. P. Satagopam, C. A. Ouzounis, A. G. Eliopoulos, V. J. Promponas, I. Iliopoulos
<span title="2015-02-11">2015</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
The above article contained an incorrect email address for the corresponding author, Ioannis Iliopoulos, the correct email address is iliopj@med.uoc.gr V C The Author 2015.  ...  For Permissions, please e-mail: journals.permissions@oup.com 979 Bioinformatics, 31(6), 2015, 979 doi: 10.1093/bioinformatics/btv029 Advance Access Publication Date: 11 February 2015 Erratum Downloaded  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btv029">doi:10.1093/bioinformatics/btv029</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25673338">pmid:25673338</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s4piy3qqsrbzxo2teu2bqrhyiy">fatcat:s4piy3qqsrbzxo2teu2bqrhyiy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729203211/https://watermark.silverchair.com/btv029.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAb0wggG5BgkqhkiG9w0BBwagggGqMIIBpgIBADCCAZ8GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMquoVXdJuWghqZyXoAgEQgIIBcJBPRPH5IifhaoqIXulvUzk2dAJxmVNkUzK4w2_1vTjh_umUR2RL2IClRmmZgxRIRBt6bRunmSfOBcbCxUDD0Gk_xorikd-XOeUmWXJ5dH6CmLWD3UDYBHUYmxe3F0ogejSnu3UK5518bNpA2ld5XYAiqXSLVMrbuLrVUF0nIMXSiVcSxMOb1pIOe4pMlDtyDmXDw5Egzx4eysF-ck5kBfoT98gF-ZZsC2Ci3myILuts4feT0u8GlUzMvR_KC6_dZFA5wN3Y-PXr1YzOulCh0zoASRwyaFgK2Bc4vt1mPZw8pXk8IK5_LxSjrzEfueLF3jgiaWizFltgvYbRBmPcMASSRWAS8ANpyzLqxu7oX5rigDVg8U4wFxHEttqjqkfSo5fImfBclPyyOLsTyt2EqVDi4dK_CHEiP7mocalnWYddLuLgQ-9DAYPLIgi4lmXigzsPOSWVkAvrU0gGS3asgs4KHGSP_NkLXvvvgXfnlFOF" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fe/12/fe12b3a3703f999ebc16bac06c5619f1ae549568.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btv029"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

BioTextQuest + : a knowledge integration platform for literature mining and concept discovery

Nikolas Papanikolaou, Georgios A. Pavlopoulos, Evangelos Pafilis, Theodosios Theodosiou, Reinhard Schneider, Venkata P. Satagopam, Christos A. Ouzounis, Aristides G. Eliopoulos, Vasilis J. Promponas, Ioannis Iliopoulos
<span title="2014-08-06">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
, functional annotation, document clustering and data integration towards literature mining and concept discovery.  ...  We demonstrate the functionality of BioTextQuest + through several exemplary research scenarios including author disambiguation, functional term enrichment, knowledge acquisition and concept discovery  ...  ACKNOWLEDGEMENTS The authors wish to thank the four anonymous reviewers for invaluable comments. I.I. and V.P.S. would like to thank I. Manolakis for fruitful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btu524">doi:10.1093/bioinformatics/btu524</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25100685">pmid:25100685</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gyf7y7qvxfbb5maq4ofsrrh25a">fatcat:gyf7y7qvxfbb5maq4ofsrrh25a</a> </span>
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DrugQuest - a text mining workflow for drug association discovery

Nikolas Papanikolaou, Georgios A. Pavlopoulos, Theodosios Theodosiou, Ioannis S. Vizirianakis, Ioannis Iliopoulos
<span title="">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Conclusions: DrugQuest is a text mining tool for knowledge discovery: it is designed to cluster DrugBank records based on text attributes in order to find new associations between drugs.  ...  Text mining and data integration methods are gaining ground in the field of health sciences due to the exponential growth of bio-medical literature and information stored in biological databases.  ...  Discussion DrugQuest is a concept discovery tool mainly designed for finding new associations between known drugs but also for providing concise summation of a large corpus of drug-related knowledge.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-016-1041-6">doi:10.1186/s12859-016-1041-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27295093">pmid:27295093</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4905607/">pmcid:PMC4905607</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ss7fan4ucrgplgdudidmq7adwm">fatcat:ss7fan4ucrgplgdudidmq7adwm</a> </span>
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Biomolecular Relationships Discovered from Biological Labyrinth and Lost in Ocean of Literature: Community Efforts Can Rescue Until Automated Artificial Intelligence Takes Over

Rajinder Gupta, Shrikant S. Mantri
<span title="2016-03-31">2016</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
TABLE 1 | 1 Informational (viz. data used, parameters for evaluation and working platform) and statistical (viz. f-value, recall and precision) insights for a few literature mining tools with their brief  ...  ISSUES IN LITERATURE TEXT MINING Let's have a deeper look into major concerns in biological literature mining: (A) Non-standard naming conventions: The absence of any standard naming convention(s) for  ...  Conflict of Interest Statement: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest  ... 
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Developing computational biology at meridian 23° E, and a little eastwards

Christos A Ouzounis
<span title="2018-11-14">2018</span> <i title="BMC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kga3wj5jurhgflm5yjfqv2bnyy" style="color: black;">Journal of Biological Research - Thessaloniki</a> </i> &nbsp;
The strong tradition of open access for large volumes of raw data, collections of complex results and high-quality algorithm implementations in bioinformatics makes the field a unique, special case of  ...  A key element in this transformation is the field of bioinformatics, that has-in the meanwhile-permeated pretty much all of biological and biomedical research and is now emerging as a key inter-disciplinary  ...  Acknowledgements The author thanks his colleagues and co-authors at the Centre for Research & Technology Hellas (CERTH), the Aristotle University of Thessaloniki (AUTH), the Democritus University of Thrace  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40709-018-0091-5">doi:10.1186/s40709-018-0091-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30460210">pmid:30460210</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6237004/">pmcid:PMC6237004</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uj6bqtrhe5dnbj4gjq7t24txyq">fatcat:uj6bqtrhe5dnbj4gjq7t24txyq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429092151/https://jbiolres.biomedcentral.com/track/pdf/10.1186/s40709-018-0091-5" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e3/e6/e3e69d473968a50eda71d92ca3e208a7c4be69ae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s40709-018-0091-5"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6237004" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Tissue-Specific Methylation Biosignatures for Monitoring Diseases: An In Silico Approach

Makrina Karaglani, Maria Panagopoulou, Ismini Baltsavia, Paraskevi Apalaki, Theodosis Theodosiou, Ioannis Iliopoulos, Ioannis Tsamardinos, Ekaterini Chatzaki
<span title="2022-03-09">2022</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
Tissue-specific gene methylation events are key to the pathogenesis of several diseases and can be utilized for diagnosis and monitoring.  ...  Highly performing and low feature number biosignatures were built with automated machine learning, including: (1) a five-gene biosignature discriminating BrCa tissue from healthy tissues (AUC 0.987 and  ...  The literature searching of biosignature genes was performed using BioTextQuest(+), a platform for knowledge integration, literature mining and concept discovery [96] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms23062959">doi:10.3390/ijms23062959</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35328380">pmid:35328380</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8952417/">pmcid:PMC8952417</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/buujgcjvjvb6diya3anzrzt2bu">fatcat:buujgcjvjvb6diya3anzrzt2bu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220321194310/https://mdpi-res.com/d_attachment/ijms/ijms-23-02959/article_deploy/ijms-23-02959-v2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f0/0f/f00f6d8ccb42aea5da877fc2f15a37c08c3465e6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms23062959"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8952417" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CONDITION-SPECIFIC DIFFERENTIAL SUBNETWORK ANALYSIS FOR BIOLOGICAL SYSTEMS

Deepali Jhamb, Xiaowen Liu, Mathew Palakal, David Stocum, Lang Li, Yunlong Liu
<span title="">2015</span> <span class="release-stage">unpublished</span>
Briefly, an innovative algorithm was designed to mine the condition-specific (or context-specific) knowledge from the biomedical literature which and integrate it with the high throughput data.  ...  Most importantly, to our knowledge none of the studies so far has logically integrated context-specific text mining and high throughput datasets in a systems biology framework to compare subnetworks across  ...  for condition-specific data extraction from biomedical literature.  ... 
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Biomedical knowledge base construction from text and its applications in knowledge-based systems [article]

Patrick Ernst, Universität Des Saarlandes, Universität Des Saarlandes
<span title="2018-03-20">2018</span>
KnowLife's One-stop Health Portal is an exploration platform with the goal of comprising knowledge on all health-related aspects in an integrated manner.  ...  The main goal of this thesis is to develop principled methods for building such a KB and enabling knowledge-centric applications.  ...  the Open PHACTS project [199] , a pharmacological information platform for drug discovery, offer Knowledge Bases with annotated text corpora to facilitate approaches for these use cases.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.22028/d291-27105">doi:10.22028/d291-27105</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ctjjzvcdnjantlzlzjfq4ayonq">fatcat:ctjjzvcdnjantlzlzjfq4ayonq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200221195144/https://publikationen.sulb.uni-saarland.de/bitstream/20.500.11880/26987/1/ClassicThesis.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fc/50/fc508e25802e9907f52ff7bbbcbc76903520e19e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.22028/d291-27105"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>