Open Access Datasets

In 2016, the JRC released its Data Catalogue which addresses, among others, the legal obligations from the European Commission's Reuse Decision (EC, 2011), which ensures that the European Commission as a producer and holder of public sector information sets an example by applying the same set of rules that it would like to be implemented at Member State level.

TSAR allows to track in

a transparent manner

the progress of an

alternative method,

from the early phases

of the validation

process to its eventual

inclusion into the

regulatory framework

The developers of

QSARs are welcome

to submit their

models to the JRC

database using the

QSAR Model Reporting

Format (QMRF)

CHAPTER 6

The JRC Data Catalogue therefore aims to complement the JRC Policy on Open Access to Scientific Publications and Supporting Guidance, and to promote open access to research data in the context of Horizon 2020. The main purposes of the JRC Data Catalogue are to: • Provide a central overview of data that is produced by

the JRC (alone or in collaboration with third parties) and that can be shared with the public.

• Act as a single channel for automatically feeding the EU Open Data portal with relevant metadata to be published there.

• Contribute to the JRC's new role with respect to knowledge management.

In the reporting period, EURL ECVAM published five data- sets/portals in the JRC Data Catalogue in its collection: • ChemAgora (see section 6.1.4.1)

• EURL ECVAM Fish In Vitro Intrinsic Clearance Database (see section 2.7.4.1)

• EURL ECVAM Genotoxicity and Carcinogenicity Con- solidated Database of Ames Positive Chemicals (see section section 6.1.4.2)

• Inventory of the 3Rs knowledge sources (see section 6.1.4.3)

• Supplementary materials of the Nanocomput project (Worth et al., 2017b).

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m EURL ECVAM collection in the JRC Data Catalogue: data. jrc.ec.europa.eu/collection/id-0088

m EU Open Data Portal: data.europa.eu/euodp/en/home

m ChemAgora: chemagora.jrc.ec.europa.eu/chemagora

m EURL ECVAM Fish In Vitro Intrinsic Clearance Database: data.jrc.ec.europa.eu/dataset/ jrc-eurl-ecvam-fish-in-vitro-intr-clear-db

m EURL ECVAM Genotoxicity and Carcinogenicity Consolidated Database of Ames Positive Chemicals: data.jrc.ec.europa.eu/dataset/ jrc-eurl-ecvam-genotoxicity-carcinogenicity-ames

m Inventory of the 3Rs knowledge sources: data.jrc.ec.eu- ropa.eu/dataset/jrc-eurl-ecvam-eurl-ecvam-3rs

m Computational models for the safety assessment of nanomaterials: data.jrc.ec.europa.eu/dataset/ jrc-eurl-ecvam-nanocomput

6.1.4.1 ChemAgora

ChemAgora, the chemical information portal main- tained by EURL ECVAM, facilitates the online retrieval of available information on a certain chemical substance. Chemicals can be searched by their name (or parts of it), CAS Registry Number, InChIKey or chemical structure in a

series of public repositories. Making access to informa- tion on chemical substances easier across heterogeneous platforms raises the public awareness about chemical knowledge. Stakeholders in the chemical community can take more informed decisions when being fully aware of the information available about a certain substance, and people using ChemAgora have a head start when it comes to finding out many details about a chemical. In 2017, a similarity search option based on the ChEMBL Data Web Services (with the choice among 90%, 80% and 70% Tanimoto

similarity cut off) was added to the chemical struc- ture editor page of the platform; in addition, fol- lowing a request received from the National Center for Computational

Toxicology of the US EPA, the EPA CompTox Chemistry Dashboard was added to the list of chemical resources searched by ChemAgora.

As a future improvement of the platform, the idea is under consideration to extend the search functionality adding the EC number used by ECHA. The ChemAgora search engine is currently used by the Information Plat- form for Chemical Monitoring (IPCHeM) exploiting the conversion done by ChemAgora from the CAS Registry Number – the chemical identifier used by the IPCHEM portal – to the InChIKey identifier.

In the reporting period, the Journal of Chemical Informa- tion and Modeling – a journal of the American Chemical Society – published a paper about ChemAgora (Zanzi & Wittwehr, 2017). The Chemical Abstract Service (CAS), which manages the de facto standard in chemical identification numbering, is a division of the American Chemical Society, and the publication there can be considered an acknowledgement of ChemAgora as a valuable resource (see box 6.1).

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m ChemAgora: chemagora.jrc.ec.europa.eu/chemagora

m IPCHeM: ipchem.jrc.ec.europa.eu

m Chemical Abstracts Service (CAS): www.cas.org

ChemAgora, the chemical

information portal

maintained by EURL

ECVAM, facilitates the

online retrieval of available

information on a certain

chemical substance

DISSEMINATION OF INFORMATION ON ALTERNATIVES

6.1.4.2 EURL ECVAM Genotoxicity and Carcinogenicity Database of Ames Positive Chemicals

The EURL ECVAM Genotoxicity and Carcinogenicity Consolidated Database of Ames positive chemicals is a structured and highly curated database compiling avail- able genotoxicity and carcinogenicity data for 726 Ames positive chemicals originating from different sources (Corvi & Madia, 2018; Kirkland et al., 2014).

By using a harmonised format to gather the informa- tion, this database is representing a powerful resource for data analysis that is meant to be used to guide a thorough evaluation of genotoxicity and carcinogenic- ity: 1) as a resource for evaluating the predictivity of the Ames test for in vivo genotoxicity and carcino- genicity when considered alone or in association with in vitro mammalian cell assays (gene mutation and clastogenicity/ aneugenicity) and for a better charac- terisation of those cases where the Ames test leads to irrelevant ('false positive') results; but also, 2) as a platform for detailed structural characterisation of specific groups of compounds with or without car- cinogenic or genotoxic activity. Inconsistencies (e.g., contradictory data derived from different sources) and poor data quality have been addressed through rigorous curation which included expert peer review.

Since its launch, the EURL ECVAM Genotoxicity and Car- cinogenicity Database represents a reference database for both the regulatory and scientific communities as demonstrated by its contribution to a number of activ- ities (see section 6.1.5 in Zuang et al., 2017). Recently, this dataset

(9286 data points) was i n c o r p o r a t e d into the new version of the QSAR Tool- box that was released by OECD to support governments, chemical indus- try and other

stakeholders in filling gaps in (eco)toxicity data needed for assessing the hazards of chemicals. It also contrib- uted to the recently published EFSA Scientific Opinion on "Reflection on interpretation of some aspects related to genotoxicity assessment" where it has been the basis to conduct an analysis of the sensitivity of unscheduled DNA synthesis in transgenic and comet genotoxicity assays to detect carcinogens (EFSA, 2017).

JRC portal ChemAgora simplifies access to chemical data

The JRC's ChemAgora web portal provides search capabilities to retrieve chemical data from a plethora of online resources enabling users to access both regulatory information on chem- icals and public databases on chemical properties. ChemAgora is intended to support chemical risk assessment activities by assisting stakeholders to gain a quick overview of globally avail- able data about chemicals they are interested in. This speeds up the process of data discovery and saves valuable resources. ChemAgora, through an on-the-fly search, informs whether a chemical features in any of 17 external data sources or the OECD eChemPortal (featuring another 30 external sources), and provides clickable links leading to the third-party website pages containing the information. These third-party data sources con- tain regulatory and scientific chemical information and typically use the CAS Registry Number (CASRN, a registered trademark of the American Chemical Society) as the substance identifier.

Box 6.1

ChemAgora can also map InChIKeys to CASRNs, which bridges the gap between regulatory and scientific environments. The ChemAgora portal has gained the recognition of the Amer- ican Chemical Society (ACS) as highlighted in a recent ACS publication, "Journal of Chemical Modelling and Information" (Zanzi & Wittwehr, 2017).

The EURL ECVAM

Genotoxicity and

Carcinogenicity Consolidated

Database of Ames

positive chemicals is

a database compiling

available genotoxicity and

carcinogenicity data for 726

Ames positive chemicals

CHAPTER 6

The database is a living project with possibilities of con- tinuous update as new genotoxicity and carcinogenicity data are made available. The database is currently being extended to include additional curated data from more than 200 new chemicals with Ames negative results.

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m EURL ECVAM Genotoxicity and Carcinogenicity Consolidated Database of Ames Positive Chemicals: data.jrc.ec.europa.eu/dataset/ jrc-eurl-ecvam-genotoxicity-carcinogenicity-ames

m QSAR Toolbox: www.oecd.org/chemicalsafety/risk-assess- ment/oecd-qsar-toolbox.htm

6.1.4.3 Inventory of Three Rs Knowledge Sources

In response to the European Citizens' Initiative (ECI) "Stop Vivisection", in 2015, the European Commission identified four actions to accelerate the development and uptake of non-animal approaches (EC, 2015). Action 1 of the European Commission's response aimed to conduct an assessment of current technologies, information sources and networks from all relevant sectors with potential impact on the advancement of the Three Rs. To support this action the JRC's EURL ECVAM had undertaken a review to map Three Rs knowledge, determine how knowledge is shared and to identify opportu- nities to improve on the current situation. This review was performed by build- ing an inventory of knowledge sources and carrying out a survey of the users of the knowledge sources. The out- come of the review was summarised in a study by Holley et al., 2016 (see also section 5.2 in Zuang et al., 2017), whilst in December 2017 the inventory comprising 800 knowledge sources relevant to the Three Rs was made publicly available (Holley et al., 2017). More details on the inventory of 3Rs knowl- edge sources can be found in box 6.2.

The Three Rs knowledge sources inventory should be viewed as a snapshot of the status of knowledge sources available and as a starting point for further analysis of knowledge sharing strategies.

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m ECI "Stop Vivisection": ec.europa.eu/citizens-initiative/ public/initiatives/successful/details/2012/000007

m Inventory of the Thee Rs knowledge sources: data.jrc. ec.europa.eu/dataset/jrc-eurl-ecvam-eurl-ecvam-3rs