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Knowledge Graph Embedding for Ecotoxicological Effect Prediction [chapter]

Erik B. Myklebust, Ernesto Jimenez-Ruiz, Jiaoyan Chen, Raoul Wolf, Knut Erik Tollefsen
2019 Lecture Notes in Computer Science  
In this paper we explore the suitability of using a knowledge graph embedding approach for ecotoxicological effect prediction.  ...  The publicly available effect data is integrated to the knowledge graph using ontology alignment techniques.  ...  Ontology alignment. Ontology alignment is the process of finding mappings or correspondences between a source and a target ontology or knowledge graph [3] .  ... 
doi:10.1007/978-3-030-30796-7_30 fatcat:zsjv3hcuhfgfbc2elhl2ll43li

TERA: the Toxicological Effect and Risk Assessment Knowledge Graph [article]

Erik Bryhn Myklebust and Ernesto Jimenez-Ruiz and Jiaoyan Chen and Raoul Wolf and Knut Erik Tollefsen
2019 arXiv   pre-print
We also present the applications of TERA for chemical effect prediction and the potential applications within the Semantic Web community.  ...  In this paper we introduce the Toxicological Effect and Risk Assessment (TERA) knowledge graph, which aims at providing such integrated view, and the data preparation and steps followed to construct this  ...  Rudjord for their contribution in different stages of this project.  ... 
arXiv:1908.10128v5 fatcat:2zn3b2dnkrgajbr7nmo2dawdsm

Prediction of Adverse Biological Effects of Chemicals Using Knowledge Graph Embeddings [article]

Erik B. Myklebust, Ernesto Jiménez-Ruiz, Jiaoyan Chen, Raoul Wolf, Knut Erik Tollefsen
2021 arXiv   pre-print
We have applied this knowledge graph to an important task in risk assessment, namely chemical effect prediction.  ...  We have created a knowledge graph based on major data sources used in ecotoxicological risk assessment.  ...  This sub-KG was aligned using ontology alignment systems to the species taxonomy in the effects sub-KG.  ... 
arXiv:2112.04605v1 fatcat:lq3rshsrgrfqvjui4fkdfocmju

Long-read sequencing and de novo genome assembly of marine medaka (Oryzias melastigma)

Pingping Liang, Hafiz Sohaib Ahmed Saqib, Xiaomin Ni, Yingjia Shen
2020 BMC Genomics  
the ongoing and future investigations in marine ecotoxicology.  ...  of pollutants in marine and estuarine waters.  ...  Acknowledgments We thank the Coastal State Key Laboratory of Marine Environmental Science at Xiamen University for providing fish lines used in this study.  ... 
doi:10.1186/s12864-020-07042-7 pmid:32938378 pmcid:PMC7493909 fatcat:qcsyjjwguzd4hmqnvighwohwni

The Toxicogenome of Hyalella azteca: A Model for Sediment Ecotoxicology and Evolutionary Toxicology

Helen C. Poynton, Simone Hasenbein, Joshua B. Benoit, Maria S. Sepulveda, Monica F. Poelchau, Daniel S. T. Hughes, Shwetha C. Murali, Shuai Chen, Karl M. Glastad, Michael A. D. Goodisman, John H. Werren, Joseph H. Vineis (+38 others)
2018 Environmental Science and Technology  
It is the primary crustacean used in North America for sediment toxicity testing and an emerging model for molecular ecotoxicology.  ...  The genome quality and completeness is comparable with other ecotoxicological model species.  ...  For PCB126, none of the contigs were annotated prior to alignment to the genome. 618 In many cases more than one contig aligned to the same transcript; therefore, the total number (1) Chapman, P.  ... 
doi:10.1021/acs.est.8b00837 pmid:29634279 pmcid:PMC6091588 fatcat:ydnsps424za65j2u63c4appx3y

Tissue-specific transcriptome assemblies of the marine medaka Oryzias melastigma and comparative analysis with the freshwater medaka Oryzias latipes

Keng Lai, Jing-Woei Li, Simon Wang, Jill Chiu, Anna Tse, Karen Lau, Si Lok, Doris Au, William Tse, Chris Wong, Ting-Fung Chan, Richard Kong (+1 others)
2015 BMC Genomics  
Tissue-enriched genes were identified in O. melastigma, and Gene Ontology analysis demonstrated the functional specificity of the annotated genes in respective tissue.  ...  The marine medaka Oryzias melastigma has been demonstrated as a novel model for marine ecotoxicological studies.  ...  This work is supported by the State Key Laboratory in Marine Pollution (SKLMP) Seed Collaborative Research Fund (PJ: SKLMP/SCRF/0013) and Seed Funding Programme for Basic Research (HKU/SFPBR/201308159001  ... 
doi:10.1186/s12864-015-1325-7 pmid:25765076 pmcid:PMC4352242 fatcat:jphylcusorf2bdzcoy47fmfaqm

Enchytraeus albidus Microarray: Enrichment, Design, Annotation and Database (EnchyBASE)

Sara C. Novais, Joel Arrais, Pedro Lopes, Tine Vandenbrouck, Wim De Coen, Dick Roelofs, Amadeu M. V. M. Soares, Mónica J. B. Amorim, Cynthia Gibas
2012 PLoS ONE  
Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints.  ...  From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value#10 -5 ) and 37% had at least one Gene Ontology (GO) term assigned.  ...  Functional Annotation Gene ontology terms (GO) were assigned to the predicted proteins by homology blast using the same Blast2GO software [34] .  ... 
doi:10.1371/journal.pone.0034266 pmid:22558086 pmcid:PMC3338728 fatcat:37cptc7irnha7bhqx6epscc5tq

De novo transcriptome assembly of brackish water flea Diaphanosoma celebensis based on short-term cadmium and benzo[a]pyrene exposure experiments

Bo-Mi Kim, Seunghyun Kang, Ryeo-Ok Kim, Jee-Hyun Jung, Kyun-Woo Lee, Jae-Sung Rhee, Young-Mi Lee
2018 Hereditas  
Understanding the molecular effects of these pollutants may provide an alternative method to predict their toxicities. Cladocera (crustacean) are filter-feeding planktonic water flea.  ...  VMO protein (vmo1 gene) is essential in maintaining yolk and protecting eggs from microbes [23] . Effects of Cd on vitellogenesis are not fully explored in aquatic crustaceans.  ... 
doi:10.1186/s41065-018-0075-3 fatcat:flu6kqlvxvh2hjwsics7i5hcum

Applications for next-generation sequencing in fish ecotoxicogenomics

Alvine C. Mehinto, Christopher J. Martyniuk, Daniel J. Spade, Nancy D. Denslow
2012 Frontiers in Genetics  
These issues should be addressed in order to exploit the full potential of NGS in ecotoxicological studies and expand our understanding of the biology of non-model organisms.  ...  Despite the promising results obtained using these techniques in fish studies, NGS technologies are currently underused in ecotoxicogenomics and few studies have employed these methods.  ...  NGS approaches in ecotoxicogenomics will benefit from these bioinformatics tools to integrate both DNA and transcriptomics data and better predict the adverse effects in non-target aquatic organisms.  ... 
doi:10.3389/fgene.2012.00062 pmid:22539934 pmcid:PMC3336092 fatcat:zs7svvsvi5fm7pmhb4xasf4i44

Complete transcriptome assembly and annotation of a critically important amphipod species in freshwater ecotoxicological risk assessment: Gammarus fossarum

Domenico R. Caputo, Samuel C. Robson, Inge Werner, Alex T. Ford
2020 Environment International  
Because of their crucial role in ecotoxicological risk assessment, amphipods (Crustacea) are commonly employed as model species in a wide range of studies.  ...  However, despite their ecological importance, their genome has not yet been completely annotated and molecular mechanisms underlying key pathways, such as the serotonin pathway, in development of ecotoxicological  ...  Melanie Fischer (aQuaTox -Solutions, Dübendorf, Switzerland), Andrea Schifferli and Thomas Bucher (Swiss Centre for Applied Ecotoxicology, Dübendorf, Switzerland) for their valuable technical support in  ... 
doi:10.1016/j.envint.2019.105319 pmid:32028177 fatcat:svpufdrxerhaddnvo7ttvf2vty

Domain-specific Knowledge Graphs: A survey [article]

Bilal Abu-Salih
2021 arXiv   pre-print
Knowledge Graphs (KGs) have made a qualitative leap and effected a real revolution in knowledge representation.  ...  However, there is no consensus in regard to a plausible and inclusive definition of a domain-specific KG.  ...  [127] demonstrated the implication of using a domain KG and KG embeddings to improve the ecotoxicological effect prediction in the Norwegian Institute for Water Research (NIVA).  ... 
arXiv:2011.00235v3 fatcat:oc2loewqdjfgvlapy4kmult5li

The first draft genome of the aquatic model plant Lemna minor opens the route for future stress physiology research and biotechnological applications

Arne Van Hoeck, Nele Horemans, Pieter Monsieurs, Hieu Xuan Cao, Hildegarde Vandenhove, Ronny Blust
2015 Biotechnology for Biofuels  
Lemna minor, the so-called common duckweed, is a model system of these aquatic plants for ecotoxicological bioassays, genetic transformation tools and industrial applications.  ...  Interestingly, proteins involved in biosynthetic processes in response to various stimuli and hydrolase activities are enriched in the Lemna proteome in comparison with the Spirodela proteome.  ...  Therefore, the proteins of the single-exon gene models that did not supported on transcript level were aligned to the proteins from the monocot plants included in the gene prediction tool.  ... 
doi:10.1186/s13068-015-0381-1 pmid:26609323 pmcid:PMC4659200 fatcat:h2bso6dnhbgudfxjdblbzhrtga

Metagenomic sequencing of marine periphyton: taxonomic and functional insights into biofilm communities

Kemal Sanli, Johan Bengtsson-Palme, R. Henrik Nilsson, Erik Kristiansson, Magnus Alm Rosenblad, Hans Blanck, Karl M. Eriksson
2015 Frontiers in Microbiology  
Microorganisms partake in an extreme diversity of activities in the environment, and hence, constitute the prime candidates to be investigated in understanding of the progression and effects of the aforementioned  ...  Adverse effects of anthropogenic impact on the environment have become conspicuous in the past century and among others include the gradual increase in the global CO 2 levels, the contamination of air,  ...  SEQUENCE ALIGNMENT As mentioned among the approaches to gene prediction in the previous section, searching DNA sequences in databases requires the alignment of sequences to the individual sequence entries  ... 
doi:10.3389/fmicb.2015.01192 pmid:26579098 pmcid:PMC4626570 fatcat:ugx3kjdvcvdnpg4v75vwylbpxu

Epigenetic profiling to environmental stressors in model and non-model organisms: Ecotoxicology perspective

Nivedita Chatterjee, Jiwan Gim, Jinhee Choi
2018 Environmental Health and Toxicology  
Natural variation in the epigenetic profiles of species in responses to environmental stressors, nature of dose-response relationships for epigenetic effects, and how to incorporate this information into  ...  In this review, we presented the available information on epigenetics in ecotoxicological context.  ...  detoxification mechanisms (based on Gene Ontology and pathway analysis). [64] Daphnia pulex N/A Global DNA (5mc) methylation (UPLC) A significant genotype effect, an environment effect, and a genotype-environment  ... 
doi:10.5620/eht.e2018015 pmid:30286591 pmcid:PMC6182246 fatcat:sk6ee6rmpjcznjxceu2sbtmftq

A toxicology ontology roadmap

Barry Hardy
2012 ALTEX: Alternatives to Animal Experimentation  
Acknowledgements Opentox -An Open Source Predictive toxicology Framework,, was funded under the eU Seventh Framework Program: HeAltH-2007-1.3-3 Promotion, development, validation, acceptance  ...  Undertaking under grant agreement n° 115002, resources of which are composed of financial contribution from the European Union̓s Seventh Framework Programme (FP7/2007(FP7/ -2013 and eFPIA companies' in  ...  Finally, it should be highlighted that for the above to happen, the quality of the content in terms of simple and consistent formats, aligned to current ontology approaches, such as Open Biological and  ... 
doi:10.14573/altex.2012.2.129 pmid:22562486 fatcat:fhz6mn32zbcsfoz2vqv4uc6d4q
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