23 Works

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

Accessing biological data in R with semantic web technologies

Egon Willighagen
Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in...

Accessing biological data in R with semantic web technologies

Egon Willighagen
Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness show advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be use in...

Accessing biological data in R with semantic web technologies

Egon Willighagen
Background. Semantic Web technologies are increasingly used in biological database systems. The improved expressiveness shows advantages in tracking provenance and allowing knowledge to be more explicitly annotated. The list of semantic web standards needs a complementary set of tools to handle data in those formats to use them in bioinformatics workflows. Methods. The approach proposed in this paper uses the Apache Jena library to create an environment where semantic web technologies can be used in...

Doi For Wprdf Paper

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

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...

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 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.

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...

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...

Summary of the Spring 2014 NSC Database Survey

Axel P. Mustad, Bart Smeets, Nina Jeliazkova, Vedrin Jeliazkov & Egon Willighagen

Summary of the Spring 2014 NSC Database Survey

Axel P. Mustad, Bart Smeets, Nina Jeliazkova, Vedrin Jeliazkov & Egon Willighagen

Blue Obelisk Data Repository 10

Egon Willighagen, Geoff Hutchinson, Carsten Niehaus, Jörg Buchwald, Martin Pfeiffer, Daniel Leidert & Jean Brefort

Blue Obelisk Data Repository 10

Egon Willighagen, Geoff Hutchinson, Carsten Niehaus, Jörg Buchwald, Martin Pfeiffer, Daniel Leidert & Jean Brefort

PathVisioRPC

Anwesha Bohler, Martijn P Van Iersel, Martina Kutmon, Lars Eijssen, Magali Jaillard, Egon Willighagen & Chris T Evelo

PathVisioRPC

Anwesha Bohler, Martijn P Van Iersel, Martina Kutmon, Lars Eijssen, Magali Jaillard, Egon Willighagen & Chris T Evelo

cdk: CDK Release 1.5.9

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Daniel Szisz, Stephan Beisken, Yap Chun Wei, Mark Williamson, Arvid Berg, Ralf Stephan, Ngn, Aclarkxyz, KlasJoensson, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Tomas-Pluskal, Uli Köhler, Cyrus Harmon, Sambitgaan, Rafeli, PeterOdeus … & Carl Mäsak
Full Release Notes

cdk: CDK Release 1.5.10

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Daniel Szisz, Stephan Beisken, Yap Chun Wei, Mark Williamson, Tomas-Pluskal, Arvid Berg, Ralf Stephan, Ngn, Aclarkxyz, KlasJoensson, AndyHowlettGitHub, Dmitry Katsubo, Oliver Stueker, Uli Köhler, Cyrus Harmon, Sambitgaan, Rafeli, PeterOdeus … & Carl Mäsak
https://github.com/cdk/cdk/wiki/1.5.10-Release-Notes

cdk: CDK Release 1.5.7

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Daniel Szisz, Stephan Beisken, Yap Chun Wei, Mark Williamson, Arvid Berg, Rwst, Ngn, Aclarkxyz, KlasJoensson, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Tomas-Pluskal, Uli Köhler, Cyrus Harmon, Sambitgaan, Rafeli, PeterOdeus … & Carl Mäsak
1.5.7 Release Notes

cdk: CDK Release 1.5.8

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Daniel Szisz, Stephan Beisken, Yap Chun Wei, Mark Williamson, Arvid Berg, Rwst, Ngn, Aclarkxyz, KlasJoensson, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Tomas-Pluskal, Uli Köhler, Cyrus Harmon, Sambitgaan, Rafeli, PeterOdeus … & Carl Mäsak
1.5.8 Release Notes

Resource Types

  • Software
    9
  • Dataset
    8
  • Text
    6

Publication Year

  • 2014
    23

Data Centers

  • ZENODO - Research. Shared.
    11
  • figshare Academic Research System
    8
  • PeerJ
    3
  • Faculty of 1000 Research Ltd
    1