https://search.data.enanomapper.net

Click on CALIBRATE icon to go to the H2020 CALIBRATE database

• The Calibrate database is accessible only to project partners.

• The logos on the right indicate which projects the data contents comes from.

Ask your WP leader for database access

• In case you don't have user and password
• In case you have used eNanoMapper database from another project (e.g. NanoReg2)
• In case you have self-registered - while registration is open to anybody, the new users has to be approved (and be project members)! Self registration will not grant access to the database !

Main project page

• Once logged in, the main project page appears. There are several links to the Search, Template Wizard, User guide (this page), etc.

Click on the Search link to go to the Search page

Search page

• On the search page there is a search box on the top right , a summary panel on the left and the results are shown at the main panel.

• The database includes results from multiple sources.

There are several summaries at the left panel:

• Project
• Study providers
• Nanomaterial type
• Nanomaterials
• Protocols
• Protocol annotation
• Method
• Method annotation
• P-Chem
• Tox
• Ecotox
• Cell
• Experiment year
• References
• Endpoint
• Endpoint annotation
• Release

Every panel is expandable and shows the types of elements found for the particular query

Expand the Projects panel and click on CALIBRATE. This will filter the results and only data generated by CALIBRATE project will be shown.

The filters can be combined.

Expand the Nanomaterial type panel and select silicon dioxide. These are ontology terms assigned to each material , e.g. NPO_373

The panels show the types and counts of elements found for the particular query

i.e, the CALIBRATE project and silicon dioxide materials in this case.

The Methods panel shown indicate there is CALIBRATE data for silicon dioxide measured by these methods. The Method annotation panel contains the ontology terms denoting the same methods.

Exploring the data

Per material - click the Material and Study details link for particular material

Export data for all query results - Export tab

Compact summary report

• select Compact data report from the dropdown menu, click on XLSX icon and finally click on Download filtered entries as XLSX

The report is an Excel file

• Try exporting the same data into different report layouts (select from the dropdown menu).

Data export

Select the TXT icon and click on Download filtered entries as TSV

The result is a spreadsheet (.txt , tab separated text file)

Predefined queries

Select Physicochemical studies and click Apply. This will change the active query and will select all materials with physico-chemical characterisations.

This query could be further refined using the widgets at the left, and data exported as described.

Search by ontology terms

OBI_0302736 (comet assay) is a term defined in Ontology for Biomedical Investigations (OBI) BioPortal link

Project wise summary

• Download the summary (Excel button)

• Reports number of studies along with material and study metadata

• Generating various type of summary reports

Programmatic access (Application Programming Interface - API)

• API keys and OAuth2 plans

API documentation

• Online interactive API documentation with standard OpenAPI3 format

eNanoMapper client libraries

• Python : https://pypi.org/project/pynanomapper/
• R : https://github.com/enanomapper/renm
• JavaScript : https://github.com/enanomapper/ambit.js/
• JavaScript : https://github.com/ideaconsult/jToxKit

Jupyter notebooks

https://github.com/ideaconsult/notebooks-ambit/blob/master/enanomapper/tutorial.ipynb https://github.com/ideaconsult/notebooks-ambit/blob/master/enanomapper/summary.ipynb https://github.com/ideaconsult/notebooks-ambit/blob/master/enanomapper/explore.ipynb

Summary charts generated with explore.ipynb

Data entry

While the eNanoMapper database supports structured formats for data import (e.g. IUCLID5/6 files, W3C RDF), JSON, the data originating from NanoSafety Cluster during the last decade is predominantly provided in the form of custom spreadsheet (MS Excel) templates.

To steer the spreadsheet layout design towards harmonization, while retaining the user friendliness and the features deemed important by the labs, we provide a
Template Wizard

Template Wizard

• Log into the project database at the Nanosafety Data Interface

• Use the Template Wizard menu and select physchem, ecotox, in-vitro, exposure and release templates or literature curation templates.

• Fill in the relevant options in the web form and click Download

• Fill in the template

• Upload the file a dedicated results location, as agreed within the project

The files will be taken from the agreed results location, assigned a NMDataParser configuration and imported into project-specific eNanoMapper database instance, using the eNanoMapper FAIRification workflow

• The Template Wizard will provide optional download of NMDataParser configurations for users willing to import data to eNanoMapper database on their own.

• List of all templates

• More about enanoMapper data entry workflow. Additional templates will be added according to WP suggestions.

This guide is available at Help/User guide