48 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

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...

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

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

BridgeDbR

Christ Leemans , Egon Willighagen, Anwesha Bohler, Lars Eijssen

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

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

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).

RDFIO (3.0.2) Demo Virtual Machine

Samuel Lampa, Egon Willighagen, Pekka Kohonen, ALISON KING, Denny Vrandečić, Roland Grafström & Ola Spjuth
A virtual machine demonstrating the RDFIO extension [1] for for enabling import, export and SPARQL querying in Semantic MediaWiki [2] wikis, as recently published in [3]. The script to generate this virtual machine is available in [4].
Instructions
1. Download the .ova file2. Import the .ova file in a virtual machine player like VirtualBox of VMWare3. Start the virtual machine4. Log in as Ubuntu (no password required, but it is "changethis..." if you need it)5. Highly recommended...

RDFIO (3.0.2) Demo Virtual Machine

Samuel Lampa, Egon Willighagen, Pekka Kohonen, ALISON KING, Denny Vrandečić, Roland Grafström & Ola Spjuth
A virtual machine demonstrating the RDFIO extension [1] for for enabling import, export and SPARQL querying in Semantic MediaWiki [2] wikis, as recently published in [3]. The script to generate this virtual machine is available in [4].
Instructions
1. Download the .ova file2. Import the .ova file in a virtual machine player like VirtualBox of VMWare3. Start the virtual machine4. Log in as Ubuntu (no password required, but it is "changethis..." if you need it)5. Highly recommended...

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.

Resource Types

  • Software
    48

Publication Year

  • 2017
    15
  • 2016
    3
  • 2015
    21
  • 2014
    9

Data Centers

  • ZENODO - Research. Shared.
    45
  • figshare Academic Research System
    2
  • National Cancer Institute, Bioconductor
    1