71 Works

Ambit.Js: Release 0.0.2

Egon Willighagen
Second release: extended support for the Substance API initial support for the Bundle API examples online at http://enanomapper.github.io/ambit.js/ API documentation online at http://enanomapper.github.io/ambit.js/api/

Bodr: Bodr 10

Egon Willighagen
Release notes are available from: http://chem-bla-ics.blogspot.co.uk/2013/08/the-blue-obelisk-data-repositorys-10.html

Capturing reuse in altmetrics

Egon Willighagen
A brief idea

Ops4J: Release 0.0.1

Egon Willighagen, StaffanArvidsson & Peter Ansell
First release of the Java client for Open PHACTS that I created some time ago for the R package ("ropenphacts") and the Bioclipse manager. support for the 1.4 and 1.5 API

Doi For Wprdf Paper

Andrawaag, Egon Willighagen, Alexander Pico & Anders Riutta
Java source for conversion of WikiPathways GPML to triples

Edamontology/Edamontology: Edam 1.18

Hervé Ménager, Matúš Kalaš & Egon Willighagen
EDAM_1.18.owl See the detailed change log for additions, deprecations, and changes in relations between concepts. EDAM_1.18 includes: various refactoring including concepts deprecations within the Operation branch to make this more simple and improve usability new attribute to provide tips e.g. in bio.tools UI indicating "organisational classes", i.e. higher-level concepts which primarily structure the hierarchy and are not normally recommended for annotation. Changed 37 concepts changed (37 Operations) Deprecated 16 concepts deprecated (16 Operations) Fixed 1...

Edamontology/Edamontology: Edam 1.18

Hervé Ménager, Matúš Kalaš & Egon Willighagen
EDAM_1.18.owl See the detailed change log for additions, deprecations, and changes in relations between concepts. EDAM_1.18 includes: various refactoring including concepts deprecations within the Operation branch to make this more simple and improve usability new attribute to provide tips e.g. in bio.tools UI indicating "organisational classes", i.e. higher-level concepts which primarily structure the hierarchy and are not normally recommended for annotation. Changed 37 concepts changed (37 Operations) Deprecated 16 concepts deprecated (16 Operations) Fixed 1...

Enanomapper/Ontologies: Final Release Of Enanomapper Ontology

JKChang, Janna Hastings, Egon Willighagen, Fehrhart & Lrieswijk
v4.0 of the eNanoMapper Ontology (ENM) covers 10,881 classes, compared with 8407 classes in version 3. What's new in eNM V4.0: 162 New modelling-related terms selected by NTUA have been added to cover experimental and calculated (image analysis and algorithm-derived) descriptors. Around 200 new terms have been added as a result of input from the NanoSafety Cluster Community (NANoREG, Nano WG and NECID etc.). As a byproduct of the development of the eNanoMapper Ontology, interaction...

Deliverable Report D1.1 Requirements Analysis And Systems Design

Barry Hardy Markus Hegi
The objective of WP 1 is, to enable the communication between the eNanoMapper project and the wider nanosafety community and to ensure the alignment of the objectives of eNanoMapper with the needs of the community. At the start of the project, an extensive requirements analysis was conducted and based on the results, an overall system design was worked out. The process was based on the methodology of Contextual Design and included five steps, each building...

Deliverable Report D2.1 Framework And Infrastructure For Ontology Development, Versioning And Dissemination

Egon Willighagen Janna Hastings
The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe by design” engineered nanomaterial development. Work Package 2 of this effort will develop and disseminate 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 technical infrastructure that has been created in order to support...

Scholia - March 2017

Finn Årup Nielsen, Daniel Mietchen & Egon Willighagen
Scholia Python package, including its web service. Packaged for workshop paper March 2017.

Enanomapper/Ontologies: Final Release Of Enanomapper Ontology

JKChang, Janna Hastings, Egon Willighagen, Fehrhart & Lrieswijk
v4.0 of the eNanoMapper Ontology (ENM) covers 10,881 classes, compared with 8407 classes in version 3. What's new in eNM V4.0: 162 New modelling-related terms selected by NTUA have been added to cover experimental and calculated (image analysis and algorithm-derived) descriptors. Around 200 new terms have been added as a result of input from the NanoSafety Cluster Community (NANoREG, Nano WG and NECID etc.). As a byproduct of the development of the eNanoMapper Ontology, interaction...

ops.js: OPS.js 4.0.0 for Open PHACTS 1.4 API

Ian Dunlop, Egon Willighagen, Elblood, Andrawaag & PANDORINO
Javascript library for requesting information from the Open PHACTS API and parsing responses. Version 4.0.0 is compatible with the 1.4 API (and should be backwards compatible with 1.3). Includes Disease API calls and compound/target batch. New release created due to change of response from pathways by target.

ops.js: OPS.js 5.0.0 for Open PHACTS 1.4 API

Ian Dunlop, Egon Willighagen, Elblood, Andrawaag & PANDORINO
Javascript library for requesting information from the Open PHACTS API and parsing responses. Version 5.0.0 is compatible with the 1.4 API (and may be backwards compatible with 1.3 for most API calls). New release created due to change of response from target & compound class pharmacology.

rrdf: Release 2.2.1

Egon Willighagen, Ryan Kohl & Carl Boettiger
This release has the following changes: adds (unit) testing with the testthat package adds a tripleCount(store) method some documentation improvements typo in package description now lists all formats in asString() add.data.triple() and load.rdf() should now stop() when exceptions happen (closes #10) add.data.triple() now checks the data type given sparql.remote() now discusses bif:contains (closes #32) now uses missing() instead of is.null() for input checking (addresses #34)

ops.js: OPS.js 3.0.0 for Open PHACTS 1.4 API

Ian Dunlop, Elblood, Egon Willighagen & Andrawaag
Javascript library for requesting information from the Open PHACTS API and parsing responses. Version 3.0.0 is compatible with the 1.4 API (and should be backwards compatible with 1.3). Includes Disease API calls and compound/target batch.

Rrdf: Release 2.1.2

Egon Willighagen, Richard Zijdeman, Ryan Kohl, Carl Boettiger & Davide Ceolin
This release has the following changes: updated documentation datatypes or properties now also include double, NOTATION, and QName

Deliverable Report D5.6 User Application For Conformance To Reporting And Curation Standards

Jiakang Chang Linda Rieswijk
The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe by design” engineered nanomaterial development. Within the nanosafety domain several projects have initiated the development of standards for data reporting and curation. With this deliverable we show how the ontology can be used to test the data completeness within the eNanoMapper database, according to these approved standards, which is tested with the use of SPARQL queries. To...

Deliverable Report D2.2 Ontology Content Types And Existing Community Efforts

Gareth Owen Janna Hastings
The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe by design” engineered nanomaterial development. Work Package 2 of this effort will develop and disseminate 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 primary content areas within the nanomaterial safety domain which need...

Deliverable Report D2.3 Ontology Initial Release

Egon Willighagen Janna Hastings
The eNanoMapper project aims to build an ontology and database to collate and describe data relevant for “safe 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 initial release of the ontology, including the content and organization,...

Rrdf: Release 2.1.2

Egon Willighagen, Richard Zijdeman, Ryan Kohl, Carl Boettiger & Davide Ceolin
This release has the following changes: updated documentation datatypes or properties now also include double, NOTATION, and QName

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).

Rregrs: Release 0.0.3

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

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

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...

Resource Types

  • Software
    45
  • Text
    25
  • Dataset
    1

Publication Year

  • 2017
    17
  • 2016
    14
  • 2015
    29
  • 2014
    11

Data Centers

  • ZENODO - Research. Shared.
    71