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Expanding the eNanoMapper Ontology – ICBO2020

Poster Presentations, PublicationsOctober 12, 2020

Poster by Laurent Winckers (University of Maastricht), presented during 11th International Conference on Biomedical Ontologies. Abstract The NanoCommons Knowledgebase, https://www.nanocommons.eu/nanocommonsknowedge-base/, is an essential component of nanoinformatics and based on an agreed ontology. NanoCommons has continued to expand and develop the eNanoMapper (ENM) ontology to aid toxicological data management for NMs. Ontological mapping facilitates the organization,…

When Would Immunologists Consider a Nanomaterial to be Safe? Recommendations for Planning Studies on Nanosafety

PublicationsApril 2, 2020

Abstract The immune system is professional in recognizing and responding to non‐self, including nanomaterials. Immune responses by professional and nonprofessional immune cells are thus nearly inevitable upon exposure of cells and organisms to such materials. The state of research into taking the immune system into account in nanosafety studies is reviewed and three aspects in…

Driving the nanoinformatics wave

PublicationsMarch 16, 2020

The NanoCommons (https://www.nanocommons.eu/) research e-infrastructure and NanoSolveIT (https://nanosolveit.eu/) projects are developing the knowledge management and nanoinformatics tools to support in silico nanosafety assessment (published in Scitech Europa www.scitecheuropa.eu) DOI: http://doi.org/10.5281/zenodo.3765525 You can access the article here.

Zeta‐Potential Read‐Across Model Utilizing Nanodescriptors Extracted via the NanoXtract Image Analysis Tool Available on the Enalos Nanoinformatics Cloud Platform

PublicationsMarch 16, 2020

Abstract Zeta potential is one of the most critical properties of nanomaterials (NMs) which provides an estimation of the surface charge, and therefore electrostatic stability in medium and, in practical terms, influences the NM’s tendency to form agglomerates and to interact with cellular membranes. This paper describes a robust and accurate read‐across model to predict…

The rise of the nanomaterial metabolite corona, and emergence of the complete corona

PublicationsFebruary 24, 2020

Abstract Bio–nano interactions are a promising area of research, focused particularly on the interactions between proteins and nanomaterials (NMs). These interactions lead to the formation of the protein corona, a layer of proteins adsorbed to the surface of NMs; this corona determines the way in which cells within organisms “recognise” and interact with NMs. Corona…

Extensive rewiring of the EGFR network in colorectal cancer cells expressing transforming levels of KRASG13D

PublicationsJanuary 24, 2020

Abstract Protein-protein-interaction networks (PPINs) organize fundamental biological processes, but how oncogenic mutations impact these interactions and their functions at a network-level scale is poorly understood. Here, we analyze how a common oncogenic KRAS mutation (KRASG13D) affects PPIN structure and function of the Epidermal Growth Factor Receptor (EGFR) network in colorectal cancer (CRC) cells. Mapping >6000…

D10.3 – Initial version of NanoCommons Sustainability Plan

Deliverables, OutputsJanuary 9, 2020

The NanoCommons deliverable “D10.3 – Initial version of NanoCommons Sustainability Plan” is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). During the first year of the project a strategy was developed for ensuring sustainability of the NanoCommons research infrastructure and including the tools and services…

D10.2 – Interactions Needs and Goals of Nano Safety Projects and Programs

Deliverables, OutputsJanuary 9, 2020

The updated NanoCommons deliverable “D10.2 – Interactions Needs and Goals of Nano Safety Projects and Programs” is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). The Horizon 2020 (H2020) project NanoCommons is establishing a long-term infrastructure to benefit nanotechnology and nanosafety research. This means that…

D6.1 – A workflow and checklist for experimental design and informatics workflow for risk assessment for use in WP9

Deliverables, OutputsJanuary 9, 2020

The NanoCommons deliverable “D6.1 – A workflow and checklist for experimental design and informatics workflow for risk assessment for use in WP9” is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). The development of safe and effective nanomaterials (NMs) is highly important for both industry…

D5.5 – A workflow and checklist of key information needed from modelling tool owners to facilitate integration into KB

Deliverables, OutputsJanuary 9, 2020

The NanoCommons deliverable “D5.5 – A workflow and checklist of key information needed from modelling tool owners to facilitate integration into KB” is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). This deliverable is part of Work Package 5 (WP5), which aims to integrate state-of-the-art…

D5.4 – First predictive nanoQSAR models integrated into NanoCommons KnowledgeBase

Deliverables, OutputsJanuary 9, 2020

The NanoCommons deliverable “D5.4 – First predictive nanoQSAR models integrated into NanoCommons KnowledgeBase” is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). This Deliverable report (D5.4) presents the services that have been developed and are available through the NanoCommons infrastructure for generating and validating nano-specific…

D5.3. – First raw data processing and knowledge extraction tools integrated into KB and first theoretical descriptor calculation services available

Deliverables, OutputsJanuary 9, 2020

The NanoCommons deliverable “D5.3. – First raw data processing and knowledge extraction tools integrated into KB and first theoretical descriptor calculation services available” is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). This Deliverable (D5.3) focuses on (i) tools developed for processing of raw data…

D5.2 – First big data (omics) analysis and mining tools integrated into KnowledgeBase

Deliverables, OutputsJanuary 8, 2020

The NanoCommons deliverable “D5.2 – First big data (omics) analysis and mining tools integrated into KnowledgeBase” is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). The current deliverable is part of Work Package 5 (WP5) Joint Research Activity 3 (JRA3) – Analysis and Modelling Tools,…

D5.1 – Initial Knowledge Infrastructure Functionalities and Services Implemented

Deliverables, OutputsJanuary 8, 2020

The updated NanoCommons deliverable D5.1 – Initial Knowledge Infrastructure Functionalities and Services Implemented is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). The scope of Work Package 5 (WP5) is the integration of the state-of-the-art tools for data management, mining, handling, analysis and predictive modelling…

D4.4 – First version of data warehouse and collaborative knowledge infrastructure

Deliverables, OutputsJanuary 8, 2020

The updated NanoCommons deliverable “D4.4 – First version of data warehouse and collaborative knowledge infrastructure” is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). Deliverable 4.4 is part of Task 4.2 that deals with the development of the NanoCommons Knowledge Base and Warehouse that aims…

D4.3 – Initial NanoCommons Ontology

Deliverables, OutputsJanuary 8, 2020

The NanoCommons deliverable D4.1 – Initial NanoCommons Ontology is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). This deliverable describes the outcomes of the first 18 months of work on the NanoCommons Ontology, which builds on and expands the FP7-funded eNanoMapper ontology. With significantly fewer…

D2.2 – 1st set of Stakeholder Workshops and Report on Stakeholder feedback on the usability of NanoCommons portal and tools

Deliverables, OutputsJanuary 8, 2020

The NanoCommons deliverable “D2.2 – 1st set of Stakeholder Workshops and Report on Stakeholder feedback on the usability of NanoCommons portal and tools” is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). Deliverable 2.2 is part of Work Package 2 (WP2) ‘Community building’. WP2 supports…

D2.1 – 1st Annual conference and nano-exploitation day, stakeholder workshop and User call

Deliverables, OutputsJanuary 8, 2020

The NanoCommons deliverable D2.1 – 1st annual conference and nanoexploitation day, stakeholder workshop and user call is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). This deliverable is part of Work Package 2 (WP2) Networking Activity 1: Community building, and it presents the actions performed…

Deliverable report 1.2 – Dissemination strategy

Deliverables, OutputsJanuary 8, 2020

The NanoCommons dissemination strategy (Deliverable Report D1.2) is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). The NanoCommons Dissemination strategy provides guidance and direction for all partners on the required dissemination activities, and ensures a unified approach across the entire consortium. The aim of the…

NanoCommons informational brochure

Dissemination, OutputsJanuary 8, 2020

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NanoCommons Rollup

Dissemination, Dissemination, Outputs, OutputsJanuary 8, 2020

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NanoCommons TA flyer

Dissemination, OutputsJanuary 8, 2020

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Semantic Interoperability and Characterization of Data Provenance in Computational Molecular Engineering

PublicationsDecember 19, 2019

Abstract By introducing a common representational system for metadata that describe the employed simulation workflows, diverse sources of data and platforms in computational molecular engineering, such as workflow management systems, can become interoperable at the semantic level. To achieve semantic interoperability, the present work introduces two ontologies that provide a formal specification of the entities…

Deliverable D10.1 v2.0: Second version of NanoCommons Data Management Plan

Deliverables, OutputsSeptember 10, 2019

The updated NanoCommons data management plan (Deliverable Report D10.1 v.20) is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). This deliverable presents the initial data management plan (DMP) for the starting community research infrastructure NanoCommons. It is a living document that will be updated over the…

Release 6 of the eNanoMapper ontology

Outputs, Outputs, PublicationsSeptember 1, 2019

Version 6.0 of the NanoCommons sponsored eNanoMapper ontology is now online! Version 6 of the eNanoMapper Ontology (ENM) was released on the 30th August 2019. ENM now covers 12732 classes, compared with 12531 classes in version 5. What’s new in version 6 New NCIT version (submission 82 instead of 41 on BioPortal) Includes OECD Testing…

An Integrative Computational Approach for a Prioritization of Key Transcription Regulators Associated With Nanomaterial-Induced Toxicity

PublicationsJuly 14, 2019

Abstract A rapid increase of new nanomaterial (NM) products poses new challenges for their risk assessment. Current traditional methods for estimating potential adverse health effect of NMs are complex, time consuming, and expensive. In order to develop new prediction tests for nanotoxicity evaluation, a systems biology approach, and data from high-throughput omics experiments can be…

Read-across predictions of nanoparticle hazard endpoints: a mathematical optimization approach

Outputs, Outputs, PublicationsJuly 5, 2019

NanoCommons supported paper: Read-across predictions of nanoparticle hazard endpoints: a mathematical optimization approach Abstract In the present study, a novel read-across methodology for the prediction of toxicity related end-points of engineered nanomaterials (ENMs) is developed. The proposed method lies in the interface between the two main read-across approaches, namely the analogue and the grouping methods,…

European Registry of Materials Hackathon – Oral Presentation

Oral Presentations, OutputsJuly 4, 2019

Egon Willighagen from the University of Maastricht has given a presentation on the need for FAIR (Findable, Accessible, Interoperable and Reusable) identifiers for nanomaterials used in nanosafety, nanomedicine and nanotechnology research. The presentation was given during the 4th NanoCommons General Assembly that took place in Limassol, Cyprus in July 2019. The presentation is available…

Mapping connections in signaling networks with ambiguous modularity

PublicationsMay 23, 2019

Abstract Modular Response Analysis (MRA) is a suite of methods that under certain assumptions permits the precise reconstruction of both the directions and strengths of connections between network modules from network responses to perturbations. Standard MRA assumes that modules are insulated, thereby neglecting the existence of inter-modular protein complexes. Such complexes sequester proteins from different…

Modeling cell line-specific recruitment of signaling proteins to the insulin-like growth factor 1 receptor

PublicationsJanuary 17, 2019

Abstract Receptor tyrosine kinases (RTKs) typically contain multiple autophosphorylation sites in their cytoplasmic domains. Once activated, these autophosphorylation sites can recruit downstream signaling proteins containing Src homology 2 (SH2) and phosphotyrosine-binding (PTB) domains, which recognize phosphotyrosine-containing short linear motifs (SLiMs). These domains and SLiMs have polyspecific or promiscuous binding activities. Thus, multiple signaling proteins may…

A safe-by-design tool for functionalised nanomaterials through the Enalos Nanoinformatics Cloud platform

Outputs, PublicationsNovember 10, 2018

NanoCommons supported paper: A safe-by-design tool for functionalised nanomaterials through the Enalos Nanoinformatics Cloud platform Abstract Multi-walled carbon nanotubes are currently used in numerous industrial applications and products, therefore fast and accurate evaluation of their biological and toxicological effects is of utmost importance. Computational methods and techniques, previously applied in the area of cheminformatics for…

Release 5 of the eNanoMapper ontology

Outputs, Outputs, PublicationsSeptember 14, 2018

The first NanoCommons sponsored eNanoMapper ontology is now online! Version 5 of the eNanoMapper Ontology (ENM) was released on the 13th of September 2018. ENM now covers 12531 classes, compared with 10881 classes in version 4. What’s new in version 5 Now based on BFO 2 New 3rd party ontology versions Includes most JRC nanomaterials…

Dissecting RAF Inhibitor Resistance by Structure-based Modeling Reveals Ways to Overcome Oncogenic RAS Signaling

PublicationsAugust 22, 2018

Abstract Clinically used RAF inhibitors are ineffective in RAS mutant tumors because they enhance homo- and heterodimerization of RAF kinases, leading to paradoxical activation of ERK signaling. Overcoming enhanced RAF dimerization and the resulting resistance is a challenge for drug design. Combining multiple inhibitors could be more effective, but it is unclear how the best combinations can…

Deliverable 10.1 – Initial Draft of NanoCommons Data Management Plan

DeliverablesJuly 28, 2018

The first NanoCommons draft data management plan (Deliverable Report 10.1) is now available to view online. The report is available under the Creative Commons Attribution 4.0 International Licence (CC BY 4.0). This deliverable presents the initial data management plan (DMP) for the starting community research infrastructure NanoCommons. It is a living document that will be updated over the course of…

The EU NanoSafety Cluster as Linked Data visualised with Scholia

PublicationsJuly 9, 2018

At a recent hackathon organised by the European Research Council, GeneWiki, and others, a group of 25 researchers came together in Berlin to work on ontologically modelling research grants in Wikidata. During this meeting the EU NanoSafety Cluster was used as use case study, resulting in new linked data around the cluster. The Scholia platform was extended with a Project…

Data management in nanosafety research: From bench to database thus streamlining analysis and publication – OpenTox Asia 2018

Oral Presentations, PresentationsMay 27, 2018

Tassos Papadiamantis of the University of Birmingham presented NanoCommons’ data management goals and approach. His presentation focused on the need of data management in nanosafety research and how it can cover all aspects of the nanosafety data lifecycle, starting from experimental planning and reaching FAIR data. Data management can also ensure that collected data stay safe, can be…

The Odyssey of data curation… Or how to make curation fun and promote data harmonisation – NSC Scientific Meeting 2018

Oral Presentations, Presentations, PublicationsMarch 24, 2018

Tassos Papadiamantis (University of Birmingham) gave a presentation on data curation automation and harmonisation, the CEINT NanoInformatics Knowledge Commons (NIKC) curation templates and the use of online lab-books during every day experimental practice during the EU NanoSafety Cluster Scientific Meeting that took place in Athens, Greece. in conjunction with the NanoFASE consortium meeting, was a member…