Risultati finali
Report on quantitative weight of evidence methods and software specifications final version
Safety assessment tools - first versionSoftware implementation of the quantitative weight of evidence methods developed in Task 8.5, as described in deliverable 8.6.
Initial Data and Knowledge Management PlanOutline for eTRANSAFE data and knowledge management policy especially referring to research data quality sharing and security
D3.9 Progress on preclinical and clinical data donations - action stemming from the Mid-term reviewStemming from the MidTerm Review recommendations to improve project implementation this deliverable provides an update on the progress of data gathering and the actions taken to ensure the quantity and quality of clinical and preclinical data donated The report will serve to monitor the progress of data donation and extraction WP3 Update on data sharing via SEND format WP4 Update on access to access to clinical data WP6
First version of knowledge gathering servicesRelease of the first version of the knowledge bases including a description of the initial overarching system architecture of these services.
Report on SEND data sharing exercise – first versionThe report will include the timelines and the amount of expected data donations, specifying which data will be provided already in SEND format, which data can be obtained in non-SEND format and which report data need to be converted. In addition, the report will set out the principles for curating SEND formatted data including, but not limited to, units conversion, synonym management (controlled terminologies) and data summarisation/ aggregation.
Safety assessment tools - intermediate releaseSoftware implementation of the quantitative weight of evidence methods developed in Task 85 as described in deliverable 86
Project guidelines for sharing of preclinical safety data between industry / academia and guidelines for safety model validationReport on project requirements analysis, survey of existing guidelines and participant/stakeholder requirements for model validation and iSSC consultation to adopt project guidelines for data sharing and data management, including a data classification system, and model validation.
Knowledge Hub and API specifications - first versionReport describing the software specifications of the knowledge hub and the application program interface.
Consensus position paper on predictive model validations based on stakeholder board opinionPosition paper summarising best practice for validation and use of predictive toxicology models and data classification published for external community consultation (including OECD/ICH)
First version of complete translational systemRelease of the first version of the translational system including integration and visualisation
Report on synergies with related initiativesThis document will report on the relationships established to promote alignment and collaboration with other EUinternational projects and initiatives
Report on quantitative weight of evidence methods and software specifications - first versionReport describing the specifications of the software developed for supporting the quantitative weight of evidence computational methods obtained in Task 8.5.
Advanced data mining module - intermediate releaseSoftware implemented in a standard module supporting advanced data mining from the knowledge hub. In addition, this software (so called “Gateway” to Knowledge Hub) will provide centralized access to most of the eTRANSAFE databases and tools.
Guidelines for sharing of safety data and model validations consulted with OECD/ICH and other stakeholders and publishedPublication of final guidelines for safety data sharing and model validation subsequent to extensive external consultation
Report on knowledge gathering by analysing preclinical dataReport to provide details on the evolution of the knowledge gained through the analysis of preclinical data as more studies are absorbed into the system.
Final report on results of use casesFinal report on the Use Cases
Report on SEND data sharing exercise – third versionUpdate on data sharing via SEND format.
Report on quantitative weight of evidence methods and software specifications - final versionReport describing the characteristics of the software developed for supporting the quantitative weight of evidence computational methods obtained in Task 85
Final Data and Knowledge Management Plan including innovation-based access to consortium dataFinal document describing the different data processed and the uses identified by the Consortium
Report on SEND data sharing exercise – fourth versionUpdate on data sharing via SEND format.
Report on release of integrated textual data, identifier and semantic integration services, integrated ontologies, and ontology management and access services to consortiumReport on release of integrated textual data, identifier and semantic integration services, integrated ontologies, and ontology management and access services to consortium, covering input from Task 5.1, 5.2 and 5.3.
Report on knowledge gathering by analysing preclinical data – final versionReport to provide details on the evolution of the knowledge gained through the analysis of preclinical data as more studies are absorbed into the system.
Report on consortium needs, available assets and documented knowledge hub (WP9) interfacesRequirements analysis: report on consortium needs, available assets, shared pipelines and documented knowledge hub (WP9) interfaces of (1) identifier, ontology and semantic integration services, (2) ontologies and ontology management, available assets, and interfaces to the ontologies, (3) available sources of unstructured information including historical report data, and available assets and key data providers in the consortium, including input from Task 5.1, 5.2 and 5.3.
List on high priority translational safety biomarkersReport on the list of high priority translational safety biomarkers that bridge between in vitro systems animal models and the human situation based on integration of the mode of action information with coregulated gene network analysis and bioinformatics approaches
Quantitative pharmaco-toxico mode-of-action landscapeComprehensive compilation on the concentration response relationship on mode of action at the pharmacological and toxicological level for chemicals that cover the relevant chemical drug space related to adverse drug reactions
Second version of knowledge gathering servicesRelease of the second version of the knowledge bases
Computational read-across workflows- first versionCompilation of computational workflows implementing read across techniques (chemical grouping or analogue identification) for relevant toxic endpoints developed in Task 8.1. The deliverable comprises, for every workflow, both the computational implementation and the documentation, following the guidelines developed in WP2.
Project communication plan and initial tool setA plan for dissemination that includes the communication objectives, target audiences, activities to be carried out and tools that will support their implementation, with connections among these components. It will also include an initial set of communication materials.
Final report on knowledge extraction and data integration in drug safety assessmentFinal report on knowledge extraction and data integration across all services in support of drug safety assessment
Advanced data mining module - first versionSoftware implemented in a standard module supporting advanced data mining from the knowledge hub. In addition, this software (so called “Gateway” to Knowledge Hub) will provide centralized access to most of the eTRANSAFE databases and tools.
Report on data gathering, processing and database – second versionThis report will serve to monitor the progress of data donation and extraction; the evolution and development of the database and the incorporation of 3rd party databases into the system.
Tools for the translational assessment of predictive modelsCollection of computational tools and methods aimed to assess the translational capability of predictive models developed from preclinical data
Data export and reporting module - first versionSoftware implemented in a standard module allowing to export data extracted from knowledge hub and to generate reports in standard formats relevant for toxicology.
Deployment of a data infrastructure for consortium partner accessAn informatics infrastructure suitable for hosting databases in containerized form will be released and made available to the consortium partners for Internet access.
Report on data gathering, processing and database - final versionThis report will serve to monitor the progress of data donation and extraction the evolution and development of the database and the incorporation of 3rd party databases into the system
Report on compound similarity serviceReport documenting the compound similarity service used in Use Case 3 (in collaboration with WP8).
Project AssessmentHalfway through the project an assessment of the degree of fulfillment of the project objectives will be carried out and reported in this deliverable
Visualisation module - final versionSoftware implemented in a standard module for the interactive visualization of data accessible through the knowledge hub
Report on read-across approaches and software specificationsReport describing advances in read-across techniques and similarity metrics for chemical compounds.
Predictive models repository - first versionCompilation of in silico predictive models and read-across workflows generated in Task 8.3 and 8.1, implemented in one or more standard modules.
Report on SEND data sharing exercise - final versionFinal update on data sharing via SEND format
Report on the evaluation of priority safety biomarkersReport on the practical evaluation of priority safety biomarkers in both animal models and the human situation
Visualisation module - first versionSoftware implemented in a standard module for the interactive visualization of data accessible through the knowledge hub.
Report on SEND data sharing exercise – second versionUpdate to the report on data shared through SEND.
Report on user requirements and system specifications of database(s)"This report will result from a series of user questionnaires and interviews based on expected use cases. User Requirements and specifications will be classified according to ""essential"", ""important"", ""nice-to-have"". The report will also summarise the security requirements and technical specification for the solution."
Report on data gathering, processing and database – third versionThis report will serve to monitor the progress of data donation and extraction; the evolution and development of the database and the incorporation of 3rd party databases into the system.
Knowledge Hub and API specifications – intermediate releaseReport describing the software specifications of the knowledge hub and the application program interface.
Translational adverse outcome pathways for human adversityA report describing AOPs for the most prevalent human adversities and the comparison of the mechanistic understanding of these AOPs between human and animal models
Machine-learning models - first versionCompilation of predictive models based on machine-learning methods developed in Task 8.2. The deliverable comprises, for every model, both the model implementation and the documentation, following the guidelines developed in WP2.
Methodology, analysis of existing related initiatives, and tools for implementationA roadmap of synergies with other projects/networks will be established, followed by implementation of the most relevant collaborations.
Predictive models repository - final versionCompilation of in silico predictive models and readacross workflows generated in Task 83 and 81 implemented in one or more standard modules
Report on the procedures for the data donation, extraction, curation and normalisation, ontology mapping, and access to pertinent datasetsThis report will describe the pharmaco-toxicological endpoints identified for extraction or collection, how they have been prioritized, the details of extraction (granularity) and the commitment of the different partners in terms of number of reports (confidential & non-confidential). In addition, the report will describe the procedures to be established for quality assurance (e.g. establishment of Clearing House) as well as data curation, normalisation and controlled terminology mapping and assign the responsibilities to achieve these tasks.
Pubblicazioni
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Giulia Callegaro, Johannes P. Schimming, Janet Piñero González, Steven J. Kunnen, Lukas Wijaya, Panuwat Trairatphisan, Linda van den Berk, Kim Beetsma, Laura I. Furlong, Jeffrey J. Sutherland, Jennifer Mollon, James L. Stevens, and Bob van de Water
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Chemistry Central
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Editore:
Chemistry Central
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Computational and Structural Biotechnology Journal, Numero 19, 2021, Pagina/e 2960-2967, ISSN 2001-0370
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Nucleic Acids Research, 2019, ISSN 0305-1048
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Ferran Sanz, François Pognan, Thomas Steger-Hartmann, Carlos Díaz, Shoji Asakura, Alexander Amberg, Nathalie Bécourt-Lhote, Niklas Blomberg, Nicolas Bosc, Katharine Briggs, Frank Bringezu, Claire Brulle-Wohlhueter, Søren Brunak, Ruud Bueters, Giulia Callegaro, Salvador Capella-Gutierrez, Emilio Centeno, Javier Corvi, Mark T. D. Cronin, Philip Drew, Guillemette Duchateau-Nguyen, Gerhard F. Ecke
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Nature Publishing Group
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Chemistry Central
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Joaquim Aguirre-Plans, Janet Piñero, Terezinha Souza, Giulia Callegaro, Steven J. Kunnen, Ferran Sanz, Narcis Fernandez-Fuentes, Laura I. Furlong, Emre Guney, Baldo Oliva
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Biology Direct, Numero 16/1, 2021, ISSN 1745-6150
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10.1186/s13062-020-00288-x
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10.1016/j.cmpb.2023.107345
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Ferran Sanz, François Pognan, Thomas Steger-Hartmann, Carlos Díaz, Montserrat Cases, Manuel Pastor, Philippe Marc, Joerg Wichard, Katharine Briggs, David K. Watson, Thomas Kleinöder, Chihae Yang, Alexander Amberg, Maria Beaumont, Anthony J. Brookes, Søren Brunak, Mark T. D. Cronin, Gerhard F. Ecker, Sylvia Escher, Nigel Greene, Antonio Guzmán, Anne Hersey, Pascale Jacques, Lieve Lammens, Jord
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Editore:
Springer Spektrum | Springer-Verlag GmbH
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10.14573/altex.2011181
Autori:
Jordi Amengol-Estapé, Felipe Soares, Montserrat Marimon, Martin Krallinger
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Genomics & Informatics, Numero 17/2, 2019, Pagina/e e15, ISSN 2234-0742
Editore:
Korea Genome Organization
DOI:
10.5808/gi.2019.17.2.e15
Autori:
Janet Piñero; Ferran Sanz; Narcis Fernandez-Fuentes; Joaquim Aguirre-Plans
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Journal of molecular biology, Numero 1, 2019, ISSN 0022-2836
Editore:
Academic Press
DOI:
10.1016/j.jmb.2019.02.027
Autori:
Wanda van der Stel, Huan Yang, Nanette G Vrijenhoek, Johannes P Schimming, Giulia Callegaro, Giada Carta, Salihanur Darici, Johannes Delp, Anna Forsby, Andrew White, Sylvia le Dévédec, Marcel Leist, Paul Jennings, Joost B Beltman, Bob van de Water, Erik H J Danen
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Archives of Toxicology, 2021, ISSN 1432-0738
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Springer
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10.1007/s00204-021-03160-7
Autori:
Frank Bringezu, José Carlos Gómez-Tamayo, Manuel Pastor
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Computational Toxicology, Numero 20, 2021, Pagina/e 100189, ISSN 2468-1113
Editore:
ScienceDirect, Elsevier
DOI:
10.1016/j.comtox.2021.100189
Autori:
Olivier J.M. Béquignon, Gopal Pawar, Bob van de Water, Mark T.D. Cronin, Gerard J.P. van Westen
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Systems Medicine, 2021, Pagina/e 308-329, ISBN 9780128160787
Editore:
Elsevier
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Manuel Pastor, Ferran Sanz, Frank Bringezu
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Editore:
Springer Nature
DOI:
10.1007/978-1-0716-1960-5_5issn:1064-3745
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