116 Works

Rregrs: Release 0.0.5

Georgia Tsiliki, Cristian R. Munteanu, José A. Seoane, Carlos Fernandez-Lozano, Haralambos Sarimveis & Egon Willighagen
Bug in function ScalingDS: normalization Incomplete option in function ScalingDS: standarization Bug in plot 4, function SVMRFEreg Bug in function RFRFEreg, removed abs() from resids calculation Bug in function LASSOreg, removed abs() from resids calculation

Bridgedb: Bridgedb 2.1.2 Open Phacts Internal Release

Egon Willighagen, Christian Y. Brenninkmeijer, Alexander Pico, Martina Summer-Kutmon & JonathanMELIUS
Internal BridgeDB release for Open PHACTS 2.0. Also available from myGrid's Maven repository Build info: http://build.mygrid.org.uk/ci/view/OpenPHACTS/job/ops-BridgeDb/59/

Deliverable Report D6.2 Enanomapper Year 2 Dissemination Report

Friederike Ehrhart Bengt Fadeel
The key objectives of WP6 are to disseminate and raise awareness of the scientific results, tools and applications developed in the eNanoMapper project among the user communities in academia and industry, and to provide training on these eNanoMapper tools, through online seminars, and other training events. In the second year of the project, the project partners have produced additional online seminars or webinars on selected topics as well as tutorials on tools developed in other...

Dataset Descriptions For The Open Pharmacological Space

Christian Brenninkmeijer, Chris Evelo, Carole Goble, Alasdair J G Gray, Lee Harland, Robert Stevens, Andra Waagmeester & Egon Willighagen
This is a specification for the metadata to described datasets, and the linksets that relate them, to enable their use within the Open PHACTS discovery platform. The specification defines the metadata properties that are expected to describe datasets and linksets; detailing the creation and publication of the dataset. Details of deploying dataset descriptions and an exchange format for linkset files are also given.

Dataset Descriptions For The Open Pharmacological Space

Christian Brenninkmeijer, Chris Evelo, Carole Goble, Alasdair J G Gray, Lee Harland, Robert Stevens, Andra Waagmeester & Egon Willighagen
This is a specification for the metadata to described datasets, and the linksets that relate them, to enable their use within the Open PHACTS discovery platform. The specification defines the metadata properties that are expected to describe datasets and linksets; detailing the creation and publication of the dataset. Details of deploying dataset descriptions and an exchange format for linkset files are also given.

Openphacts/Ops_Linkeddataapi: Open Phacts Linked Data Api 2.1.0

Fundatureanu-Sever, Randy Kerber, Stian Soiland-Reyes, Ian Dunlop, Antonis Loizou, Ronald Siebes, Egon Willighagen & Paul Groth
This release improves and extends the earlier versions. New API methods are included around interactions.

Openphacts/Ops_Linkeddataapi: Open Phacts Linked Data Api 2.1.0

Fundatureanu-Sever, Randy Kerber, Stian Soiland-Reyes, Ian Dunlop, Antonis Loizou, Ronald Siebes, Egon Willighagen & Paul Groth
This release improves and extends the earlier versions. New API methods are included around interactions.

Final Definition Of Case Studies (Deliverable 1.3)

Paul Jennings, Thomas Exner, Lucian Farcal, Noffisat Oki, Harry Sarimveis, Philip Doganis, Danyel Jennen, Daan Geerke, Egon Willighagen, Frederic Bois, Micha Rautenberg, Tim Dudgeon & Barry Hardy
OpenRiskNet case studies are used to test and evaluate solutions provided by the project to the predictive toxicology and risk assessment community, especially regarding the usability of the developed Application Programming Interfaces (APIs) and the interoperability layer. These case studies will demonstrate the capabilities to satisfy the requirements of the different stakeholder groups, including researchers, risk assessors and regulators and present real-world applications such as systems biology approaches for grouping compounds, read-across applications using chemical...

Final Definition Of Case Studies (Deliverable 1.3)

Paul Jennings, Thomas Exner, Lucian Farcal, Noffisat Oki, Harry Sarimveis, Philip Doganis, Danyel Jennen, Daan Geerke, Egon Willighagen, Frederic Bois, Micha Rautenberg, Tim Dudgeon & Barry Hardy
OpenRiskNet case studies are used to test and evaluate solutions provided by the project to the predictive toxicology and risk assessment community, especially regarding the usability of the developed Application Programming Interfaces (APIs) and the interoperability layer. These case studies will demonstrate the capabilities to satisfy the requirements of the different stakeholder groups, including researchers, risk assessors and regulators and present real-world applications such as systems biology approaches for grouping compounds, read-across applications using chemical...

Initial Api Version Provided To Providers Of Services (Deliverable 2.2)

Micha Rautenberg, Andreas Karwath, Stefan Kramer, Tim Dudgeon, Ola Spjuth, Daniel Bachler, Thomas Exner, Joh Dokler, Haralambos Sarimveis, Angelos Valsamis, Philip Doganis, Egon Willighagen & Frederic Bois
This document reports the work towards the first version of the OpenRiskNet application programming interfaces (APIs) to be released to all partners of the consortium and associated partners for feedback and usage. Based on the diversity of the requirement foreseeable when developing the case studies to validate the infrastructure with real-world applications across all areas of predictive toxicology and risk assessment, a bottom-up approach to start with existing APIs and then harmonize them and bring...

Initial Api Version Provided To Providers Of Services (Deliverable 2.2)

Micha Rautenberg, Andreas Karwath, Stefan Kramer, Tim Dudgeon, Ola Spjuth, Daniel Bachler, Thomas Exner, Joh Dokler, Haralambos Sarimveis, Angelos Valsamis, Philip Doganis, Egon Willighagen & Frederic Bois
This document reports the work towards the first version of the OpenRiskNet application programming interfaces (APIs) to be released to all partners of the consortium and associated partners for feedback and usage. Based on the diversity of the requirement foreseeable when developing the case studies to validate the infrastructure with real-world applications across all areas of predictive toxicology and risk assessment, a bottom-up approach to start with existing APIs and then harmonize them and bring...

Report On Deployment Of Virtual Infrastructures With Service Discovery And Container Orchestration (Deliverable 2.3)

Ola Spjuth, Tim Dudgeon, Daniel Bachler, Denis Gebele, Micha Rautenberg, Jonathan Alvarsson, Pantelis Karatzas, Egon Willighagen, Chris Evelo, Marvin Martens & Thomas Exner
This report documents the Demonstrator for the Deliverable 2.3, describing the deployment of virtual infrastructure and applications making up the OpenRiskNet Virtual Research Environment (VRE). It outlines the system analysis, deployment fundamentals, service discovery, and a list of the currently available services. The production reference instance is deployed on the Swedish Science Cloud (SSC), and end user access is available at https://home.prod.openrisknet.org.

Report On Deployment Of Virtual Infrastructures With Service Discovery And Container Orchestration (Deliverable 2.3)

Ola Spjuth, Tim Dudgeon, Daniel Bachler, Denis Gebele, Micha Rautenberg, Jonathan Alvarsson, Pantelis Karatzas, Egon Willighagen, Chris Evelo, Marvin Martens & Thomas Exner
This report documents the Demonstrator for the Deliverable 2.3, describing the deployment of virtual infrastructure and applications making up the OpenRiskNet Virtual Research Environment (VRE). It outlines the system analysis, deployment fundamentals, service discovery, and a list of the currently available services. The production reference instance is deployed on the Swedish Science Cloud (SSC), and end user access is available at https://home.prod.openrisknet.org.

Deliverable Report D5.7 Final Report On User Applications

Lucian Farcal, Philip Doganis, Georgia Tsiliki, Haralambos Sarimveis, Nina Jeliazkova, Egon Willighagen, Linda Rieswijk, Penny Nymark, Micha Rautenberg, Christoph Helma, Maja Brajnik & Barry Hardy
Deliverable 5.7 reports on the Tasks 5.3 and 5.9 on the user applications achievements. The application infrastructure developed within eNanoMapper project aims to support the data management in the area of nanosafety research and to enable an integrated approach for the risk assessment of nanomaterials. To achieve these, eNanoMapper developed an ontology, a data infrastructure and modelling tools with applicability in risk assessment of nanomaterials. eNanoMapper developed resources and tools for predicting toxicity of nanomaterials...

Deliverable Report D6.6 Enanomapper Final Dissemination Report

Bengt Fadeel Malahat Mousavi
The key objectives of WP6 are to disseminate and raise awareness of the scientific results, tools and applications developed in the eNanoMapper project among the user communities in academia and industry, and to provide training on these eNanoMapper tools, through online seminars, tutorials, and training events (workshops). In the third year of the project, the partners have produced a series of tutorials on tools developed in the technical workpackages and organized several workshops including the...

Deliverable Report D5.7 Final Report On User Applications

Philip Doganis Lucian Farcal
Deliverable 5.7 reports on the Tasks 5.3 and 5.9 on the user applications achievements. The application infrastructure developed within eNanoMapper project aims to support the data management in the area of nanosafety research and to enable an integrated approach for the risk assessment of nanomaterials. To achieve these, eNanoMapper developed an ontology, a data infrastructure and modelling tools with applicability in risk assessment of nanomaterials. eNanoMapper developed resources and tools for predicting toxicity of nanomaterials...

Deliverable Report D3.1 Technical Specification And Initial Implementation Of The Protocol And Data Management Web Services

Bengt Fadeel Philip Doganis
We reviewed the current state of the art of availability and requirements for nanomaterial databases, through reviewing the literature, online resources, engaging in discussions with the NanoSafety Cluster working groups and using the results of a community-based requirement analysis. The eNanoMapper data architecture was developed and consists of a set of web services, providing access to experimental protocols and data, search service and modules, facilitating linking and data transfer between third party databases. This design...

Enabling Open Science: Wikidata For Research

Daniel Mietchen, Gregor Hagedorn, Egon Willighagen, Mariano Rico, Asuncion Gomez-Perez, Eduard Aibar, Karima Rafes, Cécile Germain, Alastair Dunning, Lydia Pintscher, Daniel Kinzler & Anonymous
Wiki4R will create an innovative virtual research environment (VRE) for Open Science at scale, engaging both professional researchers and citizen data scientists in new and potentially transformative forms of collaboration. It is based on the realizations that (1) the structured parts of the Web itself can be regarded as a VRE, (2) such environments depend on communities, (3) closed environments are limited in their capacity to nurture thriving communities. Wiki4R will therefore integrate Wikidata, the...

Bridgedb/Bridgedb: Bridgedb 2.3.0

Christian Y. Brenninkmeijer, Egon Willighagen, Stian Soiland-Reyes, Anders Riutta, Ian Dunlop, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
Major BridgeDb release, to be picked up by all downstream projects and users. The changes include an update for the PICR client, better documentation, updated Open PHACTS URIs, minor updates to various data sources, added "Brachypodium distachyon" as recognized species, removed Uniprot-SwissProt as data source (just use Uniprot-TrEMBL), and the URL of the webservice can now be changed from the command line.

Bridgedb/Bridgedb: Bridgedb 2.2.0 Released

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Anders Riutta, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
Major BridgeDb release, to be picked up by all downstream projects and users. The changes include more liberal loading of Derby files, new data sources (EPA CompTox Dashboard, BRENDA Ligands, MetaboLights), updated link out patterns, and the QC tool reports more information, including the overall identifier and mapping counts. Furthermore, it includes a considerable amount of work by the Open PHACTS projects, as detailed in a few past internal releases.

Bridgedb/Bridgedb: Bridgedb 2.2.1

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Anders Riutta, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
BridgeDb v2.2.1 is a minor bug fix release since v2.2.0. Fixes: IDMapperUniprot does not follow relative redirects org.bridgedb jars published in Maven Central The release to Maven Central mean you do no longer need to compile BridgeDb or add a <repository> to use BridgeDb JARs as a binary dependencies. The Maven build system will take care of transitive dependencies (e.g. other parts of BridgeDb that is needed) The below examples assume you need just org.bridgedb.bio,...

Bridgedb/Bridgedb: Bridgedb 2.2.2

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Anders Riutta, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
BridgeDb v2.2.2 is a minor bug fix release since v2.2.1. Fixes: recognition of the new HMDB identifiers reduces the size of Ant-based distributions (with jars that support OSGi) fixed the MIRIAM urn for some UniProt identifiers

Bridgedb: Bridgedb 2.1.1 Released

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Alexander Pico, Anders Riutta, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
Minor release that adds ChEMBL and KNApSAcK as data sources, and adds name and synonym support for the Biomart driver.

Enabling Open Science: Wikidata For Research

Daniel Mietchen, Gregor Hagedorn, Egon Willighagen, Mariano Rico, Asuncion Gomez-Perez, Eduard Aibar, Karima Rafes, Cécile Germain, Alastair Dunning, Lydia Pintscher, Daniel Kinzler & Anonymous
Wiki4R will create an innovative virtual research environment (VRE) for Open Science at scale, engaging both professional researchers and citizen data scientists in new and potentially transformative forms of collaboration. It is based on the realizations that (1) the structured parts of the Web itself can be regarded as a VRE, (2) such environments depend on communities, (3) closed environments are limited in their capacity to nurture thriving communities. Wiki4R will therefore integrate Wikidata, the...

Openrisknet, An Open E-Infrastructure To Support Data Sharing, Knowledge Integration And In Silico Analysis And Modelling In Risk Assessment

Thomas Exner, Joh Dokler, Daniel Bachler, Lucian Farcal, Chris Evelo, Egon Willighagen, Marc Jacobs, Philip Doganis, Haralambos Sarimveis, Iseult Lynch, Stefan Kramer, Cedric Notredame, Danyel Jennen, Georgios Gkoutos, Ola Spjuth, Paul Jennings, Tim Dudgeon, Frederic Bois & Barry Hardy
OpenRiskNet (https://openrisknet.org/) is an EU funded infrastructure project with the main objective to develop an open e-infrastructure providing resources and services to a variety of industries requiring risk assessment, including chemicals, cosmetic ingredients, drugs and nanomaterials. The OpenRiskNet approach is to work on different case studies to test and evaluate requirements to overcome the fragmentation of data and tools and to provide solutions improving the harmonization of data, usability and interoperability of application programming interfaces...

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