User guide
H2020 BIORIMA - eNanoMapper database

https://search.data.enanomapper.net

Portal

Click on BIORIMA icon to go to the H2020 BIORIMA database

login

Ask your WP leader for database access

Main search page

main

There are several summaries at the left panel:

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

Expand the Projects panel and click on NANOREG1. This will filter the results and only data generated by NANOREG1 project will be shown.

search

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

filter1

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

i.e, the NANOREG1 project and silicon dioxide materials in this case.

The Methods panel shown indicate there is NANOREG1 data for silicon dioxide measured by these methods. The Method annotation panel contains the ontology terms denoting the same methods.

filter2

Exploring the data

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

study

Export data for all query results - Export tab

Compact summary report - click on Generate summary report for filtered entries

export_compact

The report is an Excel file

export_compact_results

Data export

Select TXT icon and click on Download filtered entries as TSV

export_tsv

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

export_tsv_results

Predefined queries

predefined queries

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

predefined queries results

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

pontology query

Project wise summary

summary

Programmatic access (Application Programming Interface - API)

API keys and OAuth2 plans

API documentation

Online interactive API documentations with standard OpenAPI3 format

apidocs

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

jp1

jp2

Python

https://pypi.org/project/pynanomapper/

R

https://github.com/enanomapper/renm

JavaScript

https://github.com/enanomapper/ambit.js/

https://github.com/ideaconsult/jToxKit

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

apidocs

Template Wizard

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

This guide is available at Help/User guide