Services

Semantic annotation

UoB will work closely with the interested parties to semantically annotate raw, processed and/or published data using established ontologies, but focusing on the widely accepted eNanoMapper (eNM) ontology. UoB will work with Users to build the workflows needed to identify the appropriate ontological terms to link to their datasets and assist with the establishment and addition into ontologies of any missing terms or branch of terms fitting their data. In this way, UoB will help ensure the highest possible degree of data FAIRness and interoperability. For further information please contact Anastasios (Tassos) Papadiamantis.


Category:
Experimental Workflows Design & Implementation, Data Processing & Analysis, Data Storage & Online Accessibility
Type:
Data curation tool, Semantic annotation tool, Data warehouse, Knowledge base
Applicability domain:
Ontologies, Hazard assessment, Exposure assessment, Risk assessment, Risk characterisation, Bioinformatics
Topic:
Read-across, (Quantitative) structure-activity relationship (SAR / QSAR), Protein and small molecule corona analysis, Information extraction, Identifier mapping, Kinetics / biokinetics, Predictive modelling, Omics data analysis, Physicochemical characterisation of nanomaterials, Toxicology, Ecotoxicology
Targeted industry:
Food and feed, Cosmetics, Drugs, Nanotechnology, Chemicals, Other consumer products, Automotives, Textiles, Constructions
Targeted users:
Data managers, Researchers, Students, Risk assessors, Data modellers
Access type:
Remote
Support contact:

Provided by:
University of Birmingham
Login required:
Yes

Transnational access

The NanoCommons Transnational Access (TA) is the ability of nanosafety researchers from industry, academia and regulatory bodies to access the state-of-the-art NanoCommons expertise free of charge and take advantage of the NanoCommons services, facilities and knowledge to advance their work, solve problems and take their research to the next level.

Apply for Transnational Access →


Resources & Training materials

Presentation
The NanoCommons knowledge infrastructure built to support the research communities, industrial users and regulators in the area of nanomaterials safety assessment
Thomas Exner, Dieter Maier, Ivan Stambolic, Joh Dokler, Lucian Farcal, Egon Willighagen, Anastasios Papadiamantis and Iseult Lynch
9 Oct 2019
Abstract:

NanoCommons (Horizon 2020 INFRAIA, project no. 731032) aims to provide a standardised, reproducible and interoperable way to access available data, knowledge, analysis and modelling tools that have been adapted and verified as suitable for application to nanomaterials.
One of the major goals is to reduce the fragmentation of nanosafety related data and knowledge by aligning and semantically linking available resources major European and international nanosafety projects and infrastructures, providing new harmonized resources when needed and ensuring access following the FAIR principles (Findable, Accessible, Interoperable and Re-usable) whenever possible in an open and free manner. Outputs to be shared via the NanoCommons knowledge infrastructure include: i) Central data access to stored data or linked data sources via a variety of mechanisms (e.g. web interfaces, application programming interfaces), ii) Metadata-rich datasets from experiments and modelling/simulations, iii) Protocols and Standard Operating Procedures, iv) Quality Assurance, v) Concepts, guidance and templates for data curation, vi) Automated annotation pipelines, and vii) Data standards. This integrated design offers easy and harmonized access to a variety of datasets (physicochemical, hazard, exposure, fate) as well as data management, data mining and data visualisation tools to researchers from academia and industry, as well as regulators, ensuring their optimal use and joint development.

Additional materials:
Slides

Target audience: Data providers, Bioinformaticians, Data modellers, Regulators, Data owners, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)
Organisations involved: UoB, EwC, BIOMAX, UM
Presentation
Presentation
Introduction to the eNanoMapper ontology
Luke Slater, University of Birmingham
9 Oct 2018
Abstract:

Presentation on the structure, content and usage of the eNanoMapper ontology.


Target audience: Data providers, Software developers, Bioinformaticians, Data modellers, Regulators, General public, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB
Presentation
Video
Using the NanoCommons Knowledge portal for templates and annotation upload
Beatrix Gerhard Ivan Stambolic Deiter Meier
9 Oct 2018
Abstract:

Presentation on the use of the NanoCommons Knowledge portal for templates and annotation upload. Presented during the 1st NanoCommons Hackathon on the Ontological annotation of datasets.


Target audience: Data providers, Bioinformaticians, Data modellers, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: BIOMAX
Video
Presentation
Using the NanoCommons Knowledge portal for templates and annotation upload
Beatrix Gerhard Ivan Stambolic Dieter Meier
9 Oct 2018
Abstract:

Presentation on the use of the NanoCommons Knowledge portal for templates and annotation upload. Presented during the 1st NanoCommons Hackathon on the Ontological annotation of datasets.


Target audience: Data providers, Bioinformaticians, Data modellers, Regulators, Data owners, Data managers, Students, Researchers, Risk assessors
Open access: yes
Licence: Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
Organisations involved: BIOMAX
Presentation
Video
Introduction to the eNanoMapper Ontology
Luke Slater
9 Oct 2018
Abstract:

Presentation on the eNanoMapper ontology, its structure and use for annotating nanosafety and nanotechnology data. The presentation took place during the 1st NanoCommons hackathon on the ontological annotation of datasets, Athens, Greece, Oct 2018.


Target audience: Data providers, Bioinformaticians, Data modellers, Data owners, Data managers, Researchers
Open access: yes
Licence: Attribution 4.0 International (CC BY 4.0)
Organisations involved: UoB
Video
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