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Claire Nédellec - One of the best experts on this subject based on the ideXlab platform.
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Overview of the bacteria Biotope task at BioNLP shared task
2016Co-Authors: Louise Deleger, Robert Bossy, Philippe Bessieres, Estelle Chaix, Arnaud Ferré, Claire NédellecAbstract:This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2016, which follows the previous 2013 and 2011 editions. The task focuses on the extraction of the locations (Biotopes and geographical places) of bacteria from PubMe abstracts and the characterization of bacteria and their associated habitats with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on bacteria habitats for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, the challenge organization, and the evaluation metrics. We also provide an analysis of the results obtained by participants.
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overview of the bacteria Biotope task at bionlp shared task 2016
Proceedings of the 4th BioNLP Shared Task Workshop, 2016Co-Authors: Louise Deleger, Robert Bossy, Philippe Bessieres, Estelle Chaix, Arnaud Ferré, Claire NédellecAbstract:This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2016, which follows the previous 2013 and 2011 editions. The task focuses on the extraction of the locations (Biotopes and geographical places) of bacteria from PubMe abstracts and the characterization of bacteria and their associated habitats with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on bacteria habitats for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, the challenge organization, and the evaluation metrics. We also provide an analysis of the results obtained by participants.
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Overview of the gene regulation network and the bacteria Biotope tasks in BioNLP'13 shared task
BMC Bioinformatics, 2015Co-Authors: Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessieres, Claire NédellecAbstract:BackgroundWe present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope (BB). These tasks were previously introduced in the 2011 BioNLP-ST Bacteria Track as Bacteria Gene Interaction (BI) and Bacteria Biotope (BB). The Bacteria Track was motivated by a need to develop specific BioNLP tools for fine-grained event extraction in bacteria biology. The 2013 tasks expand on the 2011 version by better addressing the biological knowledge modeling needs. New evaluation metrics were designed for the new goals. Moving beyond a list of gene interactions, the goal of the GRN task is to build a gene regulation network from the extracted gene interactions. BB'13 is dedicated to the extraction of bacteria Biotopes, i.e. bacterial environmental information, as was BB'11. BB'13 extends the typology of BB'11 to a large diversity of Biotopes, as defined by the OntoBiotope ontology. The detection of entities and events is tackled by distinct subtasks in order to measure the progress achieved by the participant systems since 2011.ResultsThis paper details the corpus preparations and the evaluation metrics, as well as summarizing and discussing the participant results. Five groups participated in each of the two tasks. The high diversity of the participant methods reflects the dynamism of the BioNLP research community.The highest scores for the GRN and BB'13 tasks are similar to those obtained by the participants in 2011, despite of the increase in difficulty. The high density of events in short text segments (multi-event extraction) was a difficult issue for the participating systems for both tasks. The analysis of the BB'13 results also shows that co-reference resolution and entity boundary detection remain major hindrances.ConclusionThe evaluation results suggest new research directions for the improvement and development of Information Extraction for molecular and environmental biology. The Bacteria Track tasks remain publicly open; the BioNLP-ST website provides an online evaluation service, the reference corpora and the evaluation tools.
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overview of the gene regulation network and the bacteria Biotope tasks in bionlp 13 shared task
BMC Bioinformatics, 2015Co-Authors: Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessieres, Claire NédellecAbstract:Background We present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope (BB). These tasks were previously introduced in the 2011 BioNLP-ST Bacteria Track as Bacteria Gene Interaction (BI) and Bacteria Biotope (BB). The Bacteria Track was motivated by a need to develop specific BioNLP tools for fine-grained event extraction in bacteria biology. The 2013 tasks expand on the 2011 version by better addressing the biological knowledge modeling needs. New evaluation metrics were designed for the new goals. Moving beyond a list of gene interactions, the goal of the GRN task is to build a gene regulation network from the extracted gene interactions. BB'13 is dedicated to the extraction of bacteria Biotopes, i.e. bacterial environmental information, as was BB'11. BB'13 extends the typology of BB'11 to a large diversity of Biotopes, as defined by the OntoBiotope ontology. The detection of entities and events is tackled by distinct subtasks in order to measure the progress achieved by the participant systems since 2011.
Cećile Lelong - One of the best experts on this subject based on the ideXlab platform.
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ZnO and TiO2 nanoparticles alter the ability of Bacillus subtilis to fight against a stress
PLoS ONE, 2020Co-Authors: Elise Eymard- Vernain, Sylvie Luche, Rabilloud, Thierry, Cećile LelongAbstract:Due to the physicochemical properties of nanoparticles, the use of nanomaterials increases over time in industrial and medical processes. We herein report the negative impact of nanoparticles, using solid growth conditions mimicking a biofilm, on the ability ofBacillus subtilisto fight against a stress. Bacteria have been exposed to sublethal doses of nanoparticles corresponding to conditions that bacteria may meet in their natural Biotopes, the upper layer of soil or the gut microbiome. The analysis of the proteomic data obtained by shotgun mass spectrometry have shown that several metabolic pathways are affected in response to nanoparticles, n-ZnO or n-TiO2, or zinc salt: the methyglyoxal and thiol metabolisms, the oxidative stress and the stringent responses. Nanoparticles being embedded in the agar medium, these impacts are the consequence of a physiological adaptation rather than a physical cell injury. Overall, these results show that nanoparticles, by altering bacterial physiology and especially the ability to resist to a stress, may have profound influences on a "good bacteria",Bacillus subtilis, in its natural Biotope and moreover, on the global equilibrium of this Biotope.
Robert Bossy - One of the best experts on this subject based on the ideXlab platform.
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Overview of the bacteria Biotope task at BioNLP shared task
2016Co-Authors: Louise Deleger, Robert Bossy, Philippe Bessieres, Estelle Chaix, Arnaud Ferré, Claire NédellecAbstract:This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2016, which follows the previous 2013 and 2011 editions. The task focuses on the extraction of the locations (Biotopes and geographical places) of bacteria from PubMe abstracts and the characterization of bacteria and their associated habitats with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on bacteria habitats for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, the challenge organization, and the evaluation metrics. We also provide an analysis of the results obtained by participants.
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overview of the bacteria Biotope task at bionlp shared task 2016
Proceedings of the 4th BioNLP Shared Task Workshop, 2016Co-Authors: Louise Deleger, Robert Bossy, Philippe Bessieres, Estelle Chaix, Arnaud Ferré, Claire NédellecAbstract:This paper presents the Bacteria Biotope task of the BioNLP Shared Task 2016, which follows the previous 2013 and 2011 editions. The task focuses on the extraction of the locations (Biotopes and geographical places) of bacteria from PubMe abstracts and the characterization of bacteria and their associated habitats with respect to reference knowledge sources (NCBI taxonomy, OntoBiotope ontology). The task is motivated by the importance of the knowledge on bacteria habitats for fundamental research and applications in microbiology. The paper describes the different proposed subtasks, the corpus characteristics, the challenge organization, and the evaluation metrics. We also provide an analysis of the results obtained by participants.
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Overview of the gene regulation network and the bacteria Biotope tasks in BioNLP'13 shared task
BMC Bioinformatics, 2015Co-Authors: Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessieres, Claire NédellecAbstract:BackgroundWe present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope (BB). These tasks were previously introduced in the 2011 BioNLP-ST Bacteria Track as Bacteria Gene Interaction (BI) and Bacteria Biotope (BB). The Bacteria Track was motivated by a need to develop specific BioNLP tools for fine-grained event extraction in bacteria biology. The 2013 tasks expand on the 2011 version by better addressing the biological knowledge modeling needs. New evaluation metrics were designed for the new goals. Moving beyond a list of gene interactions, the goal of the GRN task is to build a gene regulation network from the extracted gene interactions. BB'13 is dedicated to the extraction of bacteria Biotopes, i.e. bacterial environmental information, as was BB'11. BB'13 extends the typology of BB'11 to a large diversity of Biotopes, as defined by the OntoBiotope ontology. The detection of entities and events is tackled by distinct subtasks in order to measure the progress achieved by the participant systems since 2011.ResultsThis paper details the corpus preparations and the evaluation metrics, as well as summarizing and discussing the participant results. Five groups participated in each of the two tasks. The high diversity of the participant methods reflects the dynamism of the BioNLP research community.The highest scores for the GRN and BB'13 tasks are similar to those obtained by the participants in 2011, despite of the increase in difficulty. The high density of events in short text segments (multi-event extraction) was a difficult issue for the participating systems for both tasks. The analysis of the BB'13 results also shows that co-reference resolution and entity boundary detection remain major hindrances.ConclusionThe evaluation results suggest new research directions for the improvement and development of Information Extraction for molecular and environmental biology. The Bacteria Track tasks remain publicly open; the BioNLP-ST website provides an online evaluation service, the reference corpora and the evaluation tools.
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overview of the gene regulation network and the bacteria Biotope tasks in bionlp 13 shared task
BMC Bioinformatics, 2015Co-Authors: Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessieres, Claire NédellecAbstract:Background We present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope (BB). These tasks were previously introduced in the 2011 BioNLP-ST Bacteria Track as Bacteria Gene Interaction (BI) and Bacteria Biotope (BB). The Bacteria Track was motivated by a need to develop specific BioNLP tools for fine-grained event extraction in bacteria biology. The 2013 tasks expand on the 2011 version by better addressing the biological knowledge modeling needs. New evaluation metrics were designed for the new goals. Moving beyond a list of gene interactions, the goal of the GRN task is to build a gene regulation network from the extracted gene interactions. BB'13 is dedicated to the extraction of bacteria Biotopes, i.e. bacterial environmental information, as was BB'11. BB'13 extends the typology of BB'11 to a large diversity of Biotopes, as defined by the OntoBiotope ontology. The detection of entities and events is tackled by distinct subtasks in order to measure the progress achieved by the participant systems since 2011.
Zorana Ratkovic - One of the best experts on this subject based on the ideXlab platform.
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Overview of the gene regulation network and the bacteria Biotope tasks in BioNLP'13 shared task
BMC Bioinformatics, 2015Co-Authors: Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessieres, Claire NédellecAbstract:BackgroundWe present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope (BB). These tasks were previously introduced in the 2011 BioNLP-ST Bacteria Track as Bacteria Gene Interaction (BI) and Bacteria Biotope (BB). The Bacteria Track was motivated by a need to develop specific BioNLP tools for fine-grained event extraction in bacteria biology. The 2013 tasks expand on the 2011 version by better addressing the biological knowledge modeling needs. New evaluation metrics were designed for the new goals. Moving beyond a list of gene interactions, the goal of the GRN task is to build a gene regulation network from the extracted gene interactions. BB'13 is dedicated to the extraction of bacteria Biotopes, i.e. bacterial environmental information, as was BB'11. BB'13 extends the typology of BB'11 to a large diversity of Biotopes, as defined by the OntoBiotope ontology. The detection of entities and events is tackled by distinct subtasks in order to measure the progress achieved by the participant systems since 2011.ResultsThis paper details the corpus preparations and the evaluation metrics, as well as summarizing and discussing the participant results. Five groups participated in each of the two tasks. The high diversity of the participant methods reflects the dynamism of the BioNLP research community.The highest scores for the GRN and BB'13 tasks are similar to those obtained by the participants in 2011, despite of the increase in difficulty. The high density of events in short text segments (multi-event extraction) was a difficult issue for the participating systems for both tasks. The analysis of the BB'13 results also shows that co-reference resolution and entity boundary detection remain major hindrances.ConclusionThe evaluation results suggest new research directions for the improvement and development of Information Extraction for molecular and environmental biology. The Bacteria Track tasks remain publicly open; the BioNLP-ST website provides an online evaluation service, the reference corpora and the evaluation tools.
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overview of the gene regulation network and the bacteria Biotope tasks in bionlp 13 shared task
BMC Bioinformatics, 2015Co-Authors: Robert Bossy, Wiktoria Golik, Zorana Ratkovic, Dialekti Valsamou, Philippe Bessieres, Claire NédellecAbstract:Background We present the two Bacteria Track tasks of BioNLP 2013 Shared Task (ST): Gene Regulation Network (GRN) and Bacteria Biotope (BB). These tasks were previously introduced in the 2011 BioNLP-ST Bacteria Track as Bacteria Gene Interaction (BI) and Bacteria Biotope (BB). The Bacteria Track was motivated by a need to develop specific BioNLP tools for fine-grained event extraction in bacteria biology. The 2013 tasks expand on the 2011 version by better addressing the biological knowledge modeling needs. New evaluation metrics were designed for the new goals. Moving beyond a list of gene interactions, the goal of the GRN task is to build a gene regulation network from the extracted gene interactions. BB'13 is dedicated to the extraction of bacteria Biotopes, i.e. bacterial environmental information, as was BB'11. BB'13 extends the typology of BB'11 to a large diversity of Biotopes, as defined by the OntoBiotope ontology. The detection of entities and events is tackled by distinct subtasks in order to measure the progress achieved by the participant systems since 2011.
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Event extraction of bacteria Biotopes: a knowledge-intensive NLP-based approach
BMC Bioinformatics, 2012Co-Authors: Zorana Ratkovic, Wiktoria Golik, Pierre WarnierAbstract:Background Bacteria Biotopes cover a wide range of diverse habitats including animal and plant hosts, natural, medical and industrial environments. The high volume of publications in the microbiology domain provides a rich source of up-to-date information on bacteria Biotopes. This information, as found in scientific articles, is expressed in natural language and is rarely available in a structured format, such as a database. This information is of great importance for fundamental research and microbiology applications ( e.g ., medicine, agronomy, food, bioenergy). The automatic extraction of this information from texts will provide a great benefit to the field. Methods We present a new method for extracting relationships between bacteria and their locations using the Alvis framework. Recognition of bacteria and their locations was achieved using a pattern-based approach and domain lexical resources. For the detection of environment locations, we propose a new approach that combines lexical information and the syntactic-semantic analysis of corpus terms to overcome the incompleteness of lexical resources. Bacteria location relations extend over sentence borders, and we developed domain-specific rules for dealing with bacteria anaphors. Results We participated in the BioNLP 2011 Bacteria Biotope (BB) task with the Alvis system. Official evaluation results show that it achieves the best performance of participating systems. New developments since then have increased the F-score by 4.1 points. Conclusions We have shown that the combination of semantic analysis and domain-adapted resources is both effective and efficient for event information extraction in the bacteria Biotope domain. We plan to adapt the method to deal with a larger set of location types and a large-scale scientific article corpus to enable microbiologists to integrate and use the extracted knowledge in combination with experimental data.
Peter Weißhuhn - One of the best experts on this subject based on the ideXlab platform.
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Regional assessment of the vulnerability of Biotopes to landscape change
Global Ecology and Conservation, 2019Co-Authors: Peter WeißhuhnAbstract:Abstract To halt habitat loss, landscape planning and conservation management could benefit from a regional analysis of the spatially differing impacts caused by landscape changes. These impacts usually also differ according to the specific vulnerability of the affected Biotopes, i.e., the characteristic assemblage of plants and animals on a particular site. A vulnerability map of Biotopes will determine those with a high potential to be adversely affected and a low capacity to recover. The identification of vulnerability hot spots will provide guidance for potential protection and maintenance interventions. Following the interdisciplinary vulnerability concept, the analysis on a regional level (≈30,000 km2) was structured into Biotope exposure, Biotope sensitivity, and Biotope adaptive capacity. It involved patch and group metrics to describe the vulnerability of terrestrial, (semi-) natural Biotopes to landscape change. For the 32 Biotope groups that were distinguished within this study, a relative ranking of vulnerability level is provided. At the level of Biotope patches, spatial clusters and thematic clusters were identified. The Biotopes dependent on high water availability, such as wet meadow, riparian habitat, and peatland were found to be particularly vulnerable. Moreover, herbaceous perennials, shrubland, groves, orchard meadows, and several pristine forest types also scored high, while the majority of forest Biotope patches were less vulnerable to landscape change. The Biotope vulnerability index applied on a regional scale provided a sound overview for conservation planning. Only a few Biotope groups showed a homogenous vulnerability level across their associated patches, suggesting that management based on local contexts is needed for the majority of Biotopes.
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Indexing the vulnerability of Biotopes to landscape changes
Ecological Indicators, 2019Co-Authors: Peter WeißhuhnAbstract:Abstract Biodiversity loss is one of the great challenges of our times, and it is primarily driven by losses of natural and semi-natural areas. To avoid further biodiversity losses, landscape planning and ecosystem management could benefit from a condensed measure that tracks regional and cumulative ecological degradation from past and ongoing landscape changes. The affected species communities can be described spatially explicit by Biotopes. A vulnerability map of Biotopes will identify areas with a high potential to be adversely affected and a low capacity to recover. These vulnerability hot spots may require specific protection and maintenance interventions to be sustained. Following the interdisciplinary vulnerability concept, an indicator set related to landscape change was developed for the Biotopes of the biosphere reserve Schorfheide-Chorin (Germany), which have been mapped as vector data according to the Brandenburg mapping key. The indicator set was structured into indicators of Biotope exposure, sensitivity, and adaptive capacity. It covered patch metrics, like the size, the fractal dimension, and the amount of similar patches in the surrounding of each patch, as well as class metrics, like the mesh size, the state of endangerment and the average dispersal range of each Biotope type. The resulting vulnerability index covered a Biotope area of around 130,000 ha, and the study area could be extended readily. European Biotopes are already mapped and monitored across large areas, primarily for nature conservation purposes. The Biotope vulnerability index developed within this study is intended for application at large spatial scales and has the potential for a straightforward transfer to Biotope maps from other German federal states and European regions.
