269 Works

POSTER<< Chemistry Identifier Mapping to Pathway Databases using Ontologies: Expanding metabolomics analysis in WikiPathways with ChEBI >>POSTER

De Sl, Egon Willighagen & Https://Orcid.Org/0000-0002-5301-3142
Poster presented
at BioSB 2018 (https://www.aanmelder.nl/biosb2018#.WwrDKKSFOM8 )
and
at the 11th International Conference on Chemical Structures, May 27-31 2018, Noordwijkerhout, The Netherlands (http://www.int-conf-chem-structures.org/registration.html).

POSTER<< Chemistry Identifier Mapping to Pathway Databases using Ontologies: Expanding metabolomics analysis in WikiPathways with ChEBI >>POSTER

De Sl, Egon Willighagen & Https://Orcid.Org/0000-0002-5301-3142
Poster presented
at BioSB 2018 (https://www.aanmelder.nl/biosb2018#.WwrDKKSFOM8 )
and
at the 11th International Conference on Chemical Structures, May 27-31 2018, Noordwijkerhout, The Netherlands (http://www.int-conf-chem-structures.org/registration.html).

MCDCalc Values for Enantioselective α-Amidoalkylation Reac.

H. Gonzalez-Diaz, Cristian Robert Munteanu, Carlos Fernandez-Lozano & Egon Willighagen
Data set of MCDCalc Descriptors for Chiral Brønsted Acid-Catalyzed Enantioselective α-Amidoalkylation Reactions

MCDCalc Values for Enantioselective α-Amidoalkylation Reac.

H. Gonzalez-Diaz, Cristian Robert Munteanu, Carlos Fernandez-Lozano & Egon Willighagen
Data set of MCDCalc Descriptors for Chiral Brønsted Acid-Catalyzed Enantioselective α-Amidoalkylation Reactions

Validation of the Predictive Toxicogenomics Space with cell culture data

Pekka Kohonen, Roland Grafström, Egon Willighagen, Juuso Parkkinen, Samuel Kaski & Krister Wennerberg
Cell culture for in vitro cytotoxicity predictions. To validate the predictive performance of the PTGS, a set of CMap instances for 38 compounds that were not included in the NCI-60 data set were assessed. MCF7 (ATCC® HTB22™), PC­3 (ATCC® CRL­1435™) and HL­60 (ATCC® CCL­240™) cell lines were obtained directly from American Type Culture Collection (LGC Promochem AB) and maintained at 37 °C with 5 % CO2 in a humidified incubator according to provider’s instructions. Cell...

Example wiki content for RDFIO demonstrator I: OrphaNet data imported into Semantic MediaWiki

Samuel Lampa, Egon Willighagen, Pekka Kohonen, ALISON KING, Denny Vrandečić, Roland Grafström & Ola Spjuth
This file is a MediaWiki XML dump of the wiki content generated for Demonstrator I in the RDFIO article [1], importing the open part of the OrphaNet dataset [2], converted to RDF in the Bio2RDF project [3].
They are exported using a command like:

cd WIKIDIR
php maintenance/dumpBackup.php --current | gzip -c > FILENAME.xml.gz

They can be imported into a Semantic MediaWiki enabled MediaWiki wiki, using the command:

cd WIKIDIR
php maintenance/importDump.php FILENAME.xml.gz

License information

See this page for information and links to...

Example wiki content for RDFIO demonstrator I: OrphaNet data imported into Semantic MediaWiki

Samuel Lampa, Egon Willighagen, Pekka Kohonen, ALISON KING, Denny Vrandečić, Roland Grafström & Ola Spjuth
This file is a MediaWiki XML dump of the wiki content generated for Demonstrator I in the RDFIO article [1], importing the open part of the OrphaNet dataset [2], converted to RDF in the Bio2RDF project [3].
They are exported using a command like:

cd WIKIDIR
php maintenance/dumpBackup.php --current | gzip -c > FILENAME.xml.gz

They can be imported into a Semantic MediaWiki enabled MediaWiki wiki, using the command:

cd WIKIDIR
php maintenance/importDump.php FILENAME.xml.gz

License information

See this page for information and links to...

Example wiki content for RDFIO demonstrator II: DrugMet data imported into Semantic MediaWiki

Samuel Lampa, Egon Willighagen, Pekka Kohonen, ALISON KING, Denny Vrandečić, Roland Grafström & Ola Spjuth
This file is a MediaWiki XML dump of the wiki content generated for Demonstrator II in the RDFIO article [1], importing the open part of the DrugMet dataset, extracted from WikiData [2].
They are exported using a command like:

cd WIKIDIR
php maintenance/dumpBackup.php --current | gzip -c > FILENAME.xml.gz

They can be imported into a Semantic MediaWiki enabled MediaWiki wiki, using the command:

cd WIKIDIR
php maintenance/importDump.php FILENAME.xml.gz

License information

See the WikiData front page page for information about the license of data...

Example wiki content for RDFIO demonstrator II: DrugMet data imported into Semantic MediaWiki

Samuel Lampa, Egon Willighagen, Pekka Kohonen, ALISON KING, Denny Vrandečić, Roland Grafström & Ola Spjuth
This file is a MediaWiki XML dump of the wiki content generated for Demonstrator II in the RDFIO article [1], importing the open part of the DrugMet dataset, extracted from WikiData [2].
They are exported using a command like:

cd WIKIDIR
php maintenance/dumpBackup.php --current | gzip -c > FILENAME.xml.gz

They can be imported into a Semantic MediaWiki enabled MediaWiki wiki, using the command:

cd WIKIDIR
php maintenance/importDump.php FILENAME.xml.gz

License information

See the WikiData front page page for information about the license of data...

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...

MOESM1 of PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

Gang Fu, Colin Batchelor, Michel Dumontier, Janna Hastings, Egon Willighagen & Evan Bolton
Additional file 1. The supporting information for the paper entitled: PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.

Open chemistry registry and mapping platform based on open source cheminformatics toolkits

Valery Tkachenko, Denise Slenter, Nina Jeliazkova, Anna Gaulton, Antony Williams, Christoph Steinbeck, Chris Evelo & Egon Willighagen
Presentation at the American Chemical Society Fall meeting Aug 2017

Open chemistry registry and mapping platform based on open source cheminformatics toolkits

Valery Tkachenko, Denise Slenter, Nina Jeliazkova, Anna Gaulton, Antony Williams, Christoph Steinbeck, Chris Evelo & Egon Willighagen
Presentation at the American Chemical Society Fall meeting Aug 2017

Development of the eNanoMapper ontology and usability within the nanosafety domain

Linda Rieswijk, Thies Oosterwijk, Janna Hastings, Friederike Ehrhart, Chris Evelo & Egon Willighagen
The FP7 EU-funded eNanoMapper project aims to develop computational solutions to support the challenge of human risk assessment of engineered nanomaterials. These solutions could support the design of new, safe and environment-friendly engineered nanomaterials as well as the assessment of existing materials. One of the focuses of the eNanomapper project is on the development and dissemination of a comprehensive ontology for the nanosafety domain. This ontology aims to encompass all information related to the characterization...

Blue Obelisk Data Repository 10

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

Summary of the Spring 2014 NSC Database Survey

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

Creating biological pathways for WikiPathways using PathVisio

Friederike Ehrhart, Martina Kutmon, Egon Willighagen, Kristina Hanspers, Alexander Pico, Linda Rieswijk & Penny Nymark
Introduction This tutorial shows users how to make a biological (or biochemical) pathway for WikiPathways using the software PathVisio. The information and images are derived from help pages of WikiPathways with some recent updates. Pathways can be created from e.g. comprehensive images in reviews showing the interactions of genes, proteins and metabolites in a good graphical way. Pathways can show molecular biological interactions like signal cascades, enzyme reactions, transport mechanisms of “healthy” pathways, drug or...

Creating biological pathways for WikiPathways using PathVisio

Friederike Ehrhart, Martina Kutmon, Egon Willighagen, Kristina Hanspers, Alexander Pico, Linda Rieswijk & Penny Nymark
Introduction This tutorial shows users how to make a biological (or biochemical) pathway for WikiPathways using the software PathVisio. The information and images are derived from help pages of WikiPathways with some recent updates. Pathways can be created from e.g. comprehensive images in reviews showing the interactions of genes, proteins and metabolites in a good graphical way. Pathways can show molecular biological interactions like signal cascades, enzyme reactions, transport mechanisms of “healthy” pathways, drug or...

MOESM1 of PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

Gang Fu, Colin Batchelor, Michel Dumontier, Janna Hastings, Egon Willighagen & Evan Bolton
Additional file 1. The supporting information for the paper entitled: PubChemRDF: towards the semantic annotation of PubChem compound and substance databases.

PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

Gang Fu, Colin Batchelor, Michel Dumontier, Janna Hastings, Egon Willighagen & Evan Bolton
Abstract Background PubChem is an open repository for chemical structures, biological activities and biomedical annotations. Semantic Web technologies are emerging as an increasingly important approach to distribute and integrate scientific data. Exposing PubChem data to Semantic Web services may help enable automated data integration and management, as well as facilitate interoperable web applications. Description This work, one of a series covering the PubChemRDF project, describes an approach to translate PubChem Substance and Compound information into...

Blue Obelisk Data Repository 10

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

Summary of the Spring 2014 NSC Database Survey

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

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

  • Dataset
    71
  • Text
    69
  • Software
    66
  • Collection
    39
  • Image
    13
  • Audiovisual
    6
  • Other
    5

Publication Year

  • 2018
    25
  • 2017
    75
  • 2016
    50
  • 2015
    68
  • 2014
    23
  • 2013
    19
  • 2012
    7
  • 2011
    2

Registration Year

  • 2018
    33
  • 2017
    116
  • 2016
    66
  • 2015
    28
  • 2014
    15
  • 2013
    7
  • 2012
    4

Data Centers

  • figshare Academic Research System
    157
  • ZENODO - Research. Shared.
    99
  • Faculty of 1000 Research Ltd
    6
  • National Cancer Institute, Bioconductor
    2
  • ResearchGate
    2
  • U.S. Environmental Protection Agency
    2
  • University of Cambridge
    1