116 Works

A Transcriptomics Data-Driven Gene Space Accurately Predicts Liver Cytopathology And Drug-Induced Liver Injury

Pekka Kohonen, Juuso Parkkinen, Egon Willighagen, Rebecca Ceder, Krister Wennerberg, Samuel Kaski & Roland Grafström
Predicting unanticipated harmful effects of chemicals and drug molecules is a difficult and costly task. Here we utilize a “big data compacting and data fusion”- concept to capture diverse adverse outcomes on cellular and organismal levels.  The approach generates from transcriptomics data set a “predictive toxicogenomics space” (PTGS) tool composed of 1331 genes distributed over 14 overlapping cytotoxicity-related gene space components. Involving approximately 2.5 x 108 data points and 1300 compounds to construct and validate...

Rregrs: Release 0.0.4

Cristian R Munteanu, Egon Willighagen, GTsiliki, Jseoane & Carlos Fernandez-Lozano
This release: adds testing using the testthat package removed the dependency on doMC so that it should install on Windows now (where doMC is not available) added the tutorial PDF so that it is part of the distribution now allows absolute paths now to point to the data adds additional parameter value checking

Bridgedb: Bridgedb V2.0.0 Released

Christian Y. Brenninkmeijer, Egon Willighagen, Alexander Pico & Martina Summer-Kutmon
ChangeLog 2.0.0 (2014-11-21) Added the upcoming 10 alphanum ID format for Uniprot, see http://www.uniprot.org/docs/sp_soon.htm (2013-11-22) Added XMetDB (http://www.xmetdb.org/) as data source Removes redundant Sp code from build list Add Sugar Beet and Barley Added web service method to retrieve datasources.txt file Added ability to write a DataSource file in txt format Changed BioDataSource.init calls to DataSourceTxt.init() calls Split read funtionality out of Depricated BioDataSource UrnBased changed to mirianBase None miriam UrnBase no longer allowed Although...

Report Of The Service Integration With Openrisknet - Initial Deployment (Deliverable 4.1)

Danyel Jennen, Tim Dudgeon, Haralambos Sarimveis, Philip Doganis, Pantelis Karatzas, Micha Rautenberg, Egon Willighagen & Thomas Exner
This report describes the status of selection of services of high priority for the OpenRiskNet infrastructure and their integration including active services provided by the consortium, associated partners and other third parties.

Report Of The Service Integration With Openrisknet - Initial Deployment (Deliverable 4.1)

Danyel Jennen, Tim Dudgeon, Haralambos Sarimveis, Philip Doganis, Pantelis Karatzas, Micha Rautenberg, Egon Willighagen & Thomas Exner
This report describes the status of selection of services of high priority for the OpenRiskNet infrastructure and their integration including active services provided by the consortium, associated partners and other third parties.

Bridgedb: Bridgedb V2.0.0 Released

Christian Y. Brenninkmeijer, Egon Willighagen, Alexander Pico & Martina Summer-Kutmon
ChangeLog 2.0.0 (2014-11-21) Added the upcoming 10 alphanum ID format for Uniprot, see http://www.uniprot.org/docs/sp_soon.htm (2013-11-22) Added XMetDB (http://www.xmetdb.org/) as data source Removes redundant Sp code from build list Add Sugar Beet and Barley Added web service method to retrieve datasources.txt file Added ability to write a DataSource file in txt format Changed BioDataSource.init calls to DataSourceTxt.init() calls Split read funtionality out of Depricated BioDataSource UrnBased changed to mirianBase None miriam UrnBase no longer allowed Although...

Rregrs: Release 0.0.3

Cristian R Munteanu, GTsiliki, Egon Willighagen, Jseoane & Carlos Fernandez-Lozano
Fixed to complete the full author list

Ops.Js: Ops.Js 5.0.2 For Open Phacts 1.5 Api

Ian Dunlop, Egon Willighagen, Elblood, Andrawaag, Stian Soiland-Reyes & PANDORINO
Javascript library for requesting information from the Open PHACTS API and parsing responses. Version 5.0.2 is compatible with the Open PHACTS 1.5 API (and should be backwards compatible with 1.4 for most API calls). This is the last of the jquery based OPS.js, future versions will be NodeJS based.

Ops.Js: Ops.Js 6.0.1 For Open Phacts 1.5 Api

Ian Dunlop, Egon Willighagen, Elblood, Andrawaag, Stian Soiland-Reyes & PANDORINO
NodeJS based JavaScript library for requesting and parsing information from the Open PHACTS API. Version 6.0.1 is compatible with the Open PHACTS 1.5 API (and should be backwards compatible with 1.4 for most API calls). This is the first release of the NodeJS based OPS.js which can run in either a browser or a NodeJS based server side app.

Ops.Js: Ops.Js 6.0.2 For Open Phacts 1.5 Api

Ian Dunlop, Egon Willighagen, Elblood, Andrawaag, Stian Soiland-Reyes & PANDORINO
NodeJS based JavaScript library for requesting and parsing information from the Open PHACTS API. Version 6.0.2 is compatible with the Open PHACTS 1.5 API (and should be backwards compatible with 1.4 for most API calls).

Rregrs: Release 0.0.4

Cristian R Munteanu, Egon Willighagen, GTsiliki, Jseoane & Carlos Fernandez-Lozano
This release: adds testing using the testthat package removed the dependency on doMC so that it should install on Windows now (where doMC is not available) added the tutorial PDF so that it is part of the distribution now allows absolute paths now to point to the data adds additional parameter value checking

Bridgedb: Bridgedb 2.1.0 Released

Egon Willighagen, Christian Y. Brenninkmeijer, Alexander Pico & Martina Summer-Kutmon
ChangeLog 2.1.0 (2015-08-06) Update SwissLipids, BRENDA and wikidata Update InChiKey to PRIMARY id Fix designations for KEGG Reactome and PubChem-bioassay Added the InChIKey as DataSource, allowing at some point WikiPathways to be searched on InChIKey Added SwissLipids Added more detail on how to get DataSource's Also compiles the BatchMapper now Added 'Plasmodium falciparum' to the Organism enumeration Added alternative methods that allow getting attributes not just from the data source of the Xref, but from...

Ops.Js: Ops.Js 6.1.2 For Open Phacts 1.5 Api

Ian Dunlop, Egon Willighagen, Elblood, Andrawaag, Stian Soiland-Reyes & PANDORINO
NodeJS based JavaScript library for requesting and parsing information from the Open PHACTS API. Version 6.1.2 is compatible with the Open PHACTS 1.5 API (and should be backwards compatible with 1.4 for most API calls).

Deliverable Report D6.3 Enanomapper Tutorials

Philip Doganis Lucian Farcal
The applications developed within eNanoMapper are complemented by a set of support materials, dedicated to users (experimentalists, data managers, etc.) and developers. Various tools were used to document the development and testing phase (described in previous reports on specific applications), while the guidance materials dedicated to users were incorporated in presentations at different face-toface meetings, workshops, trainings, online seminars and other similar dissemination activities which facilitated the interactions and information exchanges between eNanoMapper developers and...

Deliverable Report D5.4 User Application For Importing Nanosafety Cluster Data

Nikolay Kochev Nina Jeliazkova
The aim of this work is to analyze and choose technical options to implement application and user interfaces for the import of available data from various EU Nanosafety Cluster (EU NSC) projects. Applications are subjected to integrated testing (Task 5.2) and, depending on licenses, data are released for user testing and evaluation (Task 1.4). eNanoMapper has been in contact with various NanoSafety Cluster projects for importing data. Most of this data is expected to be...

Deliverable Report D5.5 User Application For Searching And Downloading Enanomapper Data

Nikolay Kochev Nina Jeliazkova
Searching and downloading nanomaterial data was identified from requirements analysis as one of the top priority use cases for users within the Nano Safety community. The search modes include both free text and structured search, which appeal to different types of users. The typical structured search requires combining queries on chemical composition and query on physicochemical characterization and bioassay outcomes. The preferred way of displaying the search result is a summary, with a subsequent drill...

Deliverable Raport D4.2 Descriptor Calculation Algorithms And Methods

Georgia Tsiliki Philip Doganis
This deliverable focuses on extensions to the OpenTox descriptor calculation services, in order to account for the supra-molecular pattern (size, shape, porosity and irregularity of the surface area and coatings) governing the activities, effects and properties of ENMs. New descriptors have been derived by applying image analysis techniques on raw microscopy nanomaterial images. The quantummechanical semi-empirical calculation services using the MOPAC open-source software have been adapted and tested on the special requirements of ENM. Experimentally...

Deliverable Raport D4.4 Mechanism-Ofaction Modelling Tools

Penny Nymark Friederike Ehrhart
This deliverable describes the mechanistic modelling task which was developed within WP 4 of eNanoMapper project. Three main issues were handled in this task: 1) we initiated a ENMs portal with nanosafety-relevant pathways to WikiPathways, an open database for biological pathways, as a basis for pathway analysis; 2) we established workflows for ENMs data analysis, (mainly transcriptomics data), to reveal the significantly and differently affected biological pathways by a variety of exposure scenarios and ENMs...

Deliverable Report D1.4 User Guidance

Lucian Farcal Micha Rautenberg
The Provision of User Guidance (on data input, access to data, tool use, experimental design, model building) was developed from an early stage of development and was improved throughout the project with a final version that is made available in this deliverable, D1.4. User guidance and training was implemented through online tutorials, meetings, face-to-face workshops and conferences (organised by WP6). An eNanoMapper dictionary with the definitions of terms and abbreviations has been developed and deployed.

Deliverable Report D2.4 Ontology Final Release

Egon Willighagen Linda Rieswijk
The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safety by design” engineered nanomaterial development. Work Package 2 of this effort is developing and disseminating a comprehensive ontology for the nanosafety domain, encompassing nanomaterials and all information relating to their characterization, as well as relevant experimental paradigms, biological interactions and safety information. This deliverable report describes the work undertaken for the final release of the ontology (Task...

Deliverable Report D3.2 Data Management System With Extended Search Capabilities

Nikolay Kochev Nina Jeliazkova
The eNanoMapper prototype database, described in the eNanoMapper report “Technical specification and initial implementation of the protocol and data management web services” (2015), was extended with new search functionality: chemically-aware search, several options for searching experimental data, semantic search including SPARQL endpoint free text search, supported by eNanoMapper ontology and annotated database entries. The types of the new queries are informed by the list of scientific questions identified through the requirements analysis and during the...

Deliverable Report D3.3 Modules And Services For Linking And Integration With Third Party Databases

Micha Rautenberg Egon Willighagen
Understanding the biological effects of nanomaterials needs at least insight into the physicochemical identity; recent research has however shown how important the biological identity is in fully understanding the biological mechanisms. This requires, however, interlinking nanomaterial databases with databases from other domains. This deliverable reports on our efforts outlined in Tasks 3.4 and 3.6 to implement the Linked Data ideas to data in the nanosafety community, taking into account this recent guidance document, experimenting with...

Rregrs: Version 0.0.5

Cristian R Munteanu, Egon Willighagen, GTsiliki, Jseoane & Carlos Fernandez-Lozano
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

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/

Registration Year

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