102 Works

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...

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...

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...

Enanomapper Ontology

Jiakang Chang, Egon Willighagen, Friederike Ehrhart, Linda Rieswijk, Gareth Owen & Janna Hastings
The eNanoMapper ontology covers the full scope of terminology needed to support research into nanomaterial safety. It builds on multiple pre-existing external ontologies such as the NanoParticle Ontology.

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...

Ops.Js: Ops.Js 6.1.3 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 6.1.3 is compatible with the Open PHACTS 1.5 API (and should be backwards compatible with 1.4 for most API calls).

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/

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...

Openphacts/Ops.Js: Ops.Js 7.0.0 For Open Phacts 2.1 Api

Ian Dunlop, Egon Willighagen, Stian Soiland-Reyes, Elblood, Andrawaag, PANDORINO & Morton Fox
NodeJS based JavaScript library for requesting and parsing information from the Open PHACTS API. Version 7.0.0 is compatible with the Open PHACTS 2.1 API (and should be backwards compatible with 2.0 for most API calls).

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).

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...

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.

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.

Resource Types

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    65
  • Text
    36
  • Dataset
    1

Publication Year

  • 2018
    14
  • 2017
    25
  • 2016
    15
  • 2015
    30
  • 2014
    14
  • 2013
    4

Registration Year

  • 2018
    20
  • 2017
    49
  • 2016
    3
  • 2015
    21
  • 2014
    9

Data Centers

  • Zenodo
    102