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FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases [article]

M. Delmas, O. Filangi, N. Paulhe, F. Vinson, C. Duperier, W. Garrier, P.-E. Saunier, Y. Pitarch, F. Jourdan, F. Giacomoni, C. Frainay
2021 bioRxiv   pre-print
To support this task, we introduce FORUM: a Knowledge Graph (KG) providing a semantic representation of relations between chemicals and biomedical concepts, built from a federation of life science databases  ...  A web interface to browse and download the extracted relations, as well as a SPARQL endpoint to directly probe the whole FORUM knowledge graph, are available at  ...  This project has received funding from the INRA SDN and the European Union's Horizon 2020 research and innovation program under grant agreement GOLIATH No. 825489.  ... 
doi:10.1101/2021.02.12.430944 fatcat:6oojqukebjeyzc5q6w36sj3aai

FORUM: Building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases

M Delmas, O Filangi, N Paulhe, F Vinson, C Duperier, W Garrier, P -E Saunier, Y Pitarch, F Jourdan, F Giacomoni, C Frainay, Jonathan Wren
2021 Bioinformatics  
To support this task, we introduce FORUM: a Knowledge Graph (KG) providing a semantic representation of relations between chemicals and biomedical concepts, built from a federation of life science databases  ...  and scientific literature repositories.  ...  We thank the Askelys team who provided insight and expertise on the semantic web technology, as well as our colleagues from the EMPREINTE CATI group for their technical support.  ... 
doi:10.1093/bioinformatics/btab627 pmid:34478489 pmcid:PMC8570811 fatcat:v3lnv6z4ijhnlgj46dig5upwxq

Proceedings of the China-Africa Urban Development Forum 2019

Ishmael Mensah, Hu, Liangcai (Eds.)
2020 Zenodo  
101 that green space in Ibadan can be adequately improved and sustainably managed  ...  There is a statistically significant association between ownership of personal/family cars and the frequency of public transport use.  ...  Pearson Product Moment Correlation was used to test the relationship between green space per capita and time. Charts and line graph were used to present the results.  ... 
doi:10.5281/zenodo.3975569 fatcat:sm2hh375ozhdhdfkbjjrchldre

2017 ACVIM Forum Research Abstract Program

2017 Journal of Veterinary Internal Medicine  
The objective of this study was to identify clinicopathologic features, treatment and outcome of horses with eosinophilic peritonitis.  ...  A retrospective study of medical records at the Veterinary Medical Teaching Hospital, University of California, Davis identified 8 horses with ≥10000/lL total nucleated cell count and ≥1000 eosinophils  ...  Oxidative stress plays a considerable role in the pathophysiology of multiple diseases and has been well documented as a contributor to disease in both the human and veterinary literature.  ... 
doi:10.1111/jvim.14778 fatcat:lm3hhhjfjvgbvdfm7eib5iq7t4

Abstracts of the Eighth EDCTP Forum, 6-9 November 2016

2017 BMJ Global Health  
and evaluate its association with morbidity and mortality indicators.  ...  The aim of this study is to describe access to improved water supply and sanitation infrastructure, as defined by the Joint Monitoring Programme, in the Manhiça Health Research Centre (CISM) study area  ...  Results The resulting framework counts 50 competencies required throughout the research life cycle, from assessment of scientific literature to results dissemination via project management, public engagement  ... 
doi:10.1136/bmjgh-2016-000260 pmid:28589036 pmcid:PMC5418676 fatcat:7qkdbgpmrfa45etp4b6sco35ye

2021 ACVIM Forum Research Abstract Program

2021 Journal of Veterinary Internal Medicine  
The abstracts are not peer reviewed before publication. The opinions expressed in the abstracts are those of the author(s) and may not represent the views or position of the ACVIM.  ...  The American College of Veterinary Internal Medicine (ACVIM) Forum and the Journal of Veterinary Internal Medicine (JVIM) are not responsible for the content or dosage recommendations in the abstracts.  ...  Blood glucose curves (BGCs) were retrospectively reviewed from the database of a single referral center.  ... 
doi:10.1111/jvim.16220 pmid:34351021 pmcid:PMC8692203 fatcat:g3b6gdpeyfac5iybze5vcsukni

Proceedings of the China Africa Urban Development Forum

Ishmael Mensah, Hu, Liangcai (Eds.)
2018 Zenodo  
In addition, appreciation should also be given to the research team members in the Department of Building and Real Estate of Hong Kong Polytechnic University for their constructive comments and suggestions  ...  Acknowledgments We are grateful for the support, discussion and valuable remarks of the Administration of the Southern Federal University and the scientific community of the management faculty.  ...  embedment of buildings, and carbon emission associated with transportation.  ... 
doi:10.5281/zenodo.3975559 fatcat:icigwe7oqne5pjthidm4grki2a

A Framework for Enhancing the Query and Medical Record Representations for Patient Search

Nut Limsopatham
2015 SIGIR Forum  
Limsopatham, Nut (2014) A framework for enhancing the query and medical record representations for patient search. PhD thesis.  ...  Next, the extracted association rules are stored in a database.  ...  In particular, we built a database of association rules between medical conditions extracted from existing medical resources (e.g. ontologies and health-related websites) (see Section 6.2).  ... 
doi:10.1145/2795403.2795420 fatcat:4z7m4dv4jvho5gy2hq5tqgyiyi

Suggesting disease associations for overlooked metabolites using literature from metabolic neighbours [article]

Maxime Delmas, Olivier Filangi, Christophe Duperier, Nils Paulhe, Florence Vinson, Pablo Rodriguez-Mier, Franck Giacomoni, Fabien Jourdan, Clément Frainay
2022 bioRxiv   pre-print
This task requires experts to combine their knowledge with information extracted from databases and the scientific literature.  ...  With this approach, we suggest more than 35,000 associations between 1,047 overlooked metabolites and 3,288 diseases (or disease families).  ...  Acknowledgements We are very grateful to Juliette Cooke for proofreading the manuscript.  ... 
doi:10.1101/2022.09.13.507596 fatcat:ldb52sorgrdrrad2qebn4xeeym

A Computational Approach for Mapping Heme Biology in the Context of Hemolytic Disorders

Farah Humayun, Daniel Domingo-Fernández, Ajay Abisheck Paul George, Marie-Thérèse Hopp, Benjamin F. Syllwasschy, Milena S. Detzel, Charles Tapley Hoyt, Martin Hofmann-Apitius, Diana Imhof
2020 Frontiers in Bioengineering and Biotechnology  
Using this terminology, we curated and modeled the second resource, a mechanistic knowledge graph representing the heme's interactome based on a corpus of 46 scientific articles.  ...  In summary, the presented work opens the door to the scientific community for exploring the published knowledge on heme biology.  ...  ACKNOWLEDGMENTS We would like to thank Sarah Mubeen for proofreading the article, and Amelie Wißbrock for useful scientific discussions.  ... 
doi:10.3389/fbioe.2020.00074 pmid:32211383 pmcid:PMC7069124 fatcat:ynhzizkw5vgvpnanfn2qfp5qxi

Application of Public Knowledge Discovery Tool (PKDE4J) to Represent Biomedical Scientific Knowledge

Min Song, Munui Kim, Keunyoung Kang, Yong Hwan Kim, Sieun Jeon
2018 Frontiers in Research Metrics and Analytics  
To respond to the demand to automatically extract scientific knowledge with higher precision, the public knowledge discovery tool PKDE4J (Song et al., 2015) was proposed as a flexible text-mining tool.  ...  Prior to knowledge discovery with techniques from text mining, a knowledge extraction stage is needed. A biological entity is tagged according to its type, such as gene, disease, cell, and tissue.  ... 
doi:10.3389/frma.2018.00007 fatcat:ypnjhygle5ec5edk7xsxe5kcra

Adverse Drug Reaction Discovery Using a Tumor-Biomarker Knowledge Graph

Meng Wang, Xinyu Ma, Jingwen Si, Hongjia Tang, Haofen Wang, Tunliang Li, Wen Ouyang, Liying Gong, Yongzhong Tang, Xi He, Wei Huang, Xing Liu
2021 Frontiers in Genetics  
Together with the increasing availability of large-scale literature data, machine learning has the potential to predict unknown ADRs from current knowledge.  ...  By the machine learning methods, we constructed a Tumor-Biomarker Knowledge Graph (TBKG) which contains four types of node: Tumor, Biomarker, Drug, and ADR using biomedical literatures.  ...  a dataset to study knowledge graphs for ADRs by entity extraction and relation building.  ... 
doi:10.3389/fgene.2020.625659 pmid:33584816 pmcid:PMC7873847 fatcat:g4gfk77qxjd2vao5gejwbhvt4i

Mining the pharmacogenomics literature--a survey of the state of the art

U. Hahn, K. B. Cohen, Y. Garten, N. H. Shah
2012 Briefings in Bioinformatics  
This article surveys efforts on text mining of the pharmacogenomics literature, mainly from the period 2008 to 2011.  ...  knowledge at different levels of formality and specificity, software architectures for building complex and scalable text analytics pipelines and Web services grounded to them, as well as comprehensiveways  ...  Text genre of the corpus which includes condensed texts, such as text snippets from biological or clinical databases or abstracts from scientific publications, versus full texts of scientific publications  ... 
doi:10.1093/bib/bbs018 pmid:22833496 pmcid:PMC3404399 fatcat:por4dnthkrcxjdsir6uc64kdaq

Frontiers of biomedical text mining: current progress

P. Zweigenbaum, D. Demner-Fushman, H. Yu, K. B. Cohen
2007 Briefings in Bioinformatics  
However, a number of problems at the frontiers of biomedical text mining continue to present interesting challenges and opportunities for great improvements and interesting research.  ...  It is now almost 15 years since the publication of the first paper on text mining in the genomics domain, and decades since the first paper on text mining in the medical domain.  ...  HY was supported by a Research Committee Award, a Research Growth Initiative grant, and an MiTAG award from the University of Wisconsin-Milwaukee, as well as NIH grant R01-LM009836-01A1.  ... 
doi:10.1093/bib/bbm045 pmid:17977867 pmcid:PMC2516302 fatcat:4nfbokb7lfdjbnkijw2v6754qy

What the semantic web could do for the life sciences

Eric K. Neumann, Eric Miller, John Wilbanks
2004 Drug Discovery Today BIOSILICO  
W3C semantic web technologies support flexible,extensible and evolvable knowledge transfer and reuse,enabling scientists and their organizations to increase efficiency across the scientific process.  ...  Scientific research is predicated on the effective exchange of knowledge.  ...  Scientific publications and curated databases together hold a vast amount of actionable knowledge.  ... 
doi:10.1016/s1741-8364(04)02420-5 fatcat:grqq2bxxsjb37gmxjjlbi2vrqm
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