Making project data available through eNanoMapper database ...€¦ · • FP7 eNanoMapper - A...
Transcript of Making project data available through eNanoMapper database ...€¦ · • FP7 eNanoMapper - A...
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Making project data available through eNanoMapper database: NANoREG, Nanoreg2,caLIBRAte and GraciousNina Jeliazkova, Ideaconsult Ltd., Sofia, Bulgaria
Presented by Georgia Tsiliki, ATHENA Research Center
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• Open source database and web application
• Builds upon a Chemical structure database with support for substances
• The data model supporting experimental data is capable of representing all endpoints of regulatory interests and other types of data.
• eNanoMapper ontology; developed by an experienced team at EBI. Existing ontologies are reused;
• Tools to process and import data. Export in various formats
• Searchable; Free text search based on ontology
• eNanomapper modelling; Integration of data analysis tools via API led by NTUA. WEKA, R python routines uploaded to Jaqpot platform
• Flexible data hosting architecture
ENM Summary & data solutions:eNanoMapper overview
DB
• FP7 eNanoMapper - A Database andOntology Framework forNanomaterials Design and SafetyAssessment
• Grant Agreement: 604134
• Duration: 1 Feb 2014 – 31 Jan 2017;8 partners
Ontology
Modelling
• Open source database and web application
• Builds upon a Chemical structure database with support for substances
• The data model supporting experimental data is capable of representing all endpoints of regulatory interests and other types of data.
• eNanoMapper ontology; developed by an experienced team at EBI. Existing ontologies are reused;
• Tools to process and import data. Export in various formats
• Searchable; Free text search based on ontology
• eNanomapper modelling; Integration of data analysis tools via API led by NTUA. WEKA, R python routines uploaded to Jaqpot platform
• Flexible data hosting architecture
DB
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• Challenges• Diverse data sources• Diverse data input
formats• Different data
organization• Diverse modelling
tools• Approach:
• Enable mappings!• i.e. eNanoMapper
• Physico-chemical identityDifferent analytic techniques, manufacturing conditions, batch effects, mixtures, impurities, size distribution, differences in the amount of surface modification, etc.
• Biological identityWide variety of measurements, toxicity pathways, effects of ENM coronas, modes-of-action, interactions (cell lines, assays).
• Processes requiring informationFrom raw data (science) to study summaries for regulatory purposes; linking with experimental protocols; risk assessment; grouping, safety-by-design
• Support for data analysisRequires “spreadsheet” or matrix view of data. The experimental data in the public datasets is usually not in a form appropriate for modelling (merging multiple values, conditions, similar experiments into matrix form is a challenge).
Organising the nanosafety dataeNanoMapper overview
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• https://data.enanomapper.net• Mostly literature data + partial content provided by MODENA and
MARINA projects; links to external DB• Free text search https://search.data.enanomapper.net/enm
Public eNanoMapper databaseeNanoMapper overview
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• Public• FP7 NANoREG
(2013-2017)• Restricted
• FP7 MARINA (2011-2015)
• NanoGenotox (2010- 2013)
• FP7 NanoTest(2008-2012)
• ENPRA(import ongoing)
search.data.enanomapper.neteNanoMapper database instances
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search.data.enanomapper.net/nanoregNANoREG – eNanoMapper database
Data transfer agreement NANoREG-eNanoMapper (2016)
Publicly accessible since March 2017
Open data license
Content imported from• TNO SQL database• Excel files
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https://search.enanomapper.netSearch data integration
ENM data, caNanoLab
eNanoMapperdb instance
NANoREG / TNO DB, Excel files
enanomapperdb instance (NR1 data)
MARINA files
enanomapperdb instance
MARINA
enanomapperdb instance NanoTest
enanomapperdb instance
NanoGenotox….
NANoREG NanoReg2caLIBRAteeNanoMapper
Protection (User rights)
NanoTestfiles
NanoGenotoxfiles
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Free text and faceted search
How to retrieve the data ?
Facets or filters that permit easy refinement of search
List of data resources with direct links to DB
Selected filters
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Export exampleHow to retrieve and download the data ?
• To download the search results specify “Filtered entries” and “Study results”. • Click on the TXT icon. The download button caption will change to
• “Download filtered entries as TSV” (tab separated values)• Note that only limited set of fields are exported in the TXT format. • The JSON and XML formats contain the full set of fields.
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• Application Programming Interface (API): a way computer programs talk to one another. Can be understood in terms of how a programmer sends instructions between programs.
• Access the database via any programming language , Workflow systems , Data analysis tools (R, JavaScript, Java, Ruby used by eNanomapper partners)
• eNanoMapper Tutorials: http://www.enanomapper.net/enm-tutorialshttps://github.com/enanomapper/tutorials
Mapping internal database functions to the external world
How to retrieve and analyse the data?
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• Input data files: >1,000 Excel files roughly following • IOM templates (most projects except NANoREG)• NANoREG / JRC ISA-TAB-logic files
• NANoREG / JRC are NOT ISA-TAB-NANO compliant
• Assays naming : multiple names per assay• Colony Forming• Colony Forming Assay• Colony Forming Efficiency Assay• CFE• Cell viability - Colony Forming Efficiency Assay
• Naming materials, cells , methods, etc
Data entry issuesHow the data is imported?
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An ontology is a controlled vocabulary enhanced with relationships between terms.Usage• Harmonize data from several
sources • Analysis (logical inference,
semantic search)Examples:• Is Cytotoxicity an endpoint, or
EC50 is also an endpoint? • Is TEM a protocol, or a
technology?• “Water - Fish - D. Rerio”
assay – is it the same one as “Zebrafish Embryo Toxicity Test” ?
Mapping terms: ontologyeNanoMapper overview
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Mapping data organisationseNanoMapper overview
http://ambit.sourceforge.net/enanomapper/templates/convertor_how.html
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Mapping spreadsheet content into the data model
eNanoMapper overview
JSON (JavaScript
Object Notation) is a
lightweight data-
through JSON configuration
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CompositionWhat is in a eNanoMapper database instance:
Coating
Core
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Tox/Ecotox/Env fateWhat is in a eNanoMapper database instance:
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Physchem characterisationAll projects data statistics
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BioassaysAll projects data statistics
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Future plans
WC, Cr, Ni
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Future plans
www.patrols-h2020.eu
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Future plans
Type of data:• Physical-chemical characterisation: particle size, distribution,
solubility, zeta potential…• Toxicological characterisation: ALI, submerged-cell, simulated body
fluid, ROS generation.
Type of NPs:• Engineered NPs (ZrO2, CeO, Sb-Sn Ox, SnO)• Process-generated NPs (atmospheric plasma spraying)
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WC, Cr, Ni
Engineered NPs Process-generated NPs
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Thank you!Questions?