244 Works

Additional file 6: Table S2. of Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

Anwesha Bohler, Lars Eijssen, Martijn Van Iersel, Christ Leemans, Egon Willighagen, Martina Kutmon, Magali Jaillard & Chris Evelo
Gene level statistics. The lists of differentially expressed genes for each of the nine comparisons were collated into a single file, which was used for further analysis. (TXT 722 kb)

Additional file 7: Table S3. of Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

Anwesha Bohler, Lars Eijssen, Martijn Van Iersel, Christ Leemans, Egon Willighagen, Martina Kutmon, Magali Jaillard & Chris Evelo
Table containing highly enriched GO terms for bone marrow cells, PBMCs, and splenocytes. (TXT 10 kb)

Automatically visualise and analyse data on pathways using PathVisioRPC from any programming environment

Anwesha Bohler, Lars Eijssen, Martijn Van Iersel, Christ Leemans, Egon Willighagen, Martina Kutmon, Magali Jaillard & Chris Evelo
Abstract Background Biological pathways are descriptive diagrams of biological processes widely used for functional analysis of differentially expressed genes or proteins. Primary data analysis, such as quality control, normalisation, and statistical analysis, is often performed in scripting languages like R, Perl, and Python. Subsequent pathway analysis is usually performed using dedicated external applications. Workflows involving manual use of multiple environments are time consuming and error prone. Therefore, tools are needed that enable pathway analysis directly...

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

Using the RRegrs R package for automating predictive modelling

Georgia Tsiliki, Cristian R Munteanu, Jose A Seoane, Carlos Fernandez-Lozano, Haralambos Sarimveis & Egon L Willighagen

PathVisioRPC

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

Bridgedb/Bridgedb: Bridgedb 2.2.2

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Anders Riutta, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
BridgeDb v2.2.2 is a minor bug fix release since v2.2.1. Fixes: recognition of the new HMDB identifiers reduces the size of Ant-based distributions (with jars that support OSGi) fixed the MIRIAM urn for some UniProt identifiers

Bridgedb/Bridgedb: Bridgedb 2.2.0 Released

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Anders Riutta, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
Major BridgeDb release, to be picked up by all downstream projects and users. The changes include more liberal loading of Derby files, new data sources (EPA CompTox Dashboard, BRENDA Ligands, MetaboLights), updated link out patterns, and the QC tool reports more information, including the overall identifier and mapping counts. Furthermore, it includes a considerable amount of work by the Open PHACTS projects, as detailed in a few past internal releases.

Bridgedb/Bridgedb: Bridgedb 2.2.1

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Anders Riutta, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
BridgeDb v2.2.1 is a minor bug fix release since v2.2.0. Fixes: IDMapperUniprot does not follow relative redirects org.bridgedb jars published in Maven Central The release to Maven Central mean you do no longer need to compile BridgeDb or add a <repository> to use BridgeDb JARs as a binary dependencies. The Maven build system will take care of transitive dependencies (e.g. other parts of BridgeDb that is needed) The below examples assume you need just org.bridgedb.bio,...

Bridgedb/Bridgedb: Bridgedb 2.2.2

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Anders Riutta, Alexander Pico, Randy Kerber, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
BridgeDb v2.2.2 is a minor bug fix release since v2.2.1. Fixes: recognition of the new HMDB identifiers reduces the size of Ant-based distributions (with jars that support OSGi) fixed the MIRIAM urn for some UniProt identifiers

Deliverable Report D5.7 Final Report On User Applications

Lucian Farcal, Philip Doganis, Georgia Tsiliki, Haralambos Sarimveis, Nina Jeliazkova, Egon Willighagen, Linda Rieswijk, Penny Nymark, Micha Rautenberg, Christoph Helma, Maja Brajnik & Barry Hardy
Deliverable 5.7 reports on the Tasks 5.3 and 5.9 on the user applications achievements. The application infrastructure developed within eNanoMapper project aims to support the data management in the area of nanosafety research and to enable an integrated approach for the risk assessment of nanomaterials. To achieve these, eNanoMapper developed an ontology, a data infrastructure and modelling tools with applicability in risk assessment of nanomaterials. eNanoMapper developed resources and tools for predicting toxicity of nanomaterials...

Deliverable Report D6.6 Enanomapper Final Dissemination Report

Bengt Fadeel Malahat Mousavi
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, tutorials, and training events (workshops). In the third year of the project, the partners have produced a series of tutorials on tools developed in the technical workpackages and organized several workshops including the...

Deliverable Report D5.7 Final Report On User Applications

Philip Doganis Lucian Farcal
Deliverable 5.7 reports on the Tasks 5.3 and 5.9 on the user applications achievements. The application infrastructure developed within eNanoMapper project aims to support the data management in the area of nanosafety research and to enable an integrated approach for the risk assessment of nanomaterials. To achieve these, eNanoMapper developed an ontology, a data infrastructure and modelling tools with applicability in risk assessment of nanomaterials. eNanoMapper developed resources and tools for predicting toxicity of nanomaterials...

Deliverable Report D3.1 Technical Specification And Initial Implementation Of The Protocol And Data Management Web Services

Bengt Fadeel Philip Doganis
We reviewed the current state of the art of availability and requirements for nanomaterial databases, through reviewing the literature, online resources, engaging in discussions with the NanoSafety Cluster working groups and using the results of a community-based requirement analysis. The eNanoMapper data architecture was developed and consists of a set of web services, providing access to experimental protocols and data, search service and modules, facilitating linking and data transfer between third party databases. This design...

BridgeDb: BridgeDb 2.1.1 released

Christian Y. Brenninkmeijer, Stian Soiland-Reyes, Egon Willighagen, Alexander Pico, Anders Riutta, MyGrid Jenkins Build Server, Martina Summer-Kutmon & JonathanMELIUS
Minor release that adds ChEMBL and KNApSAcK as data sources, and adds name and synonym support for the Biomart driver.

Enabling Open Science: Wikidata for Research

Daniel Mietchen, Gregor Hagedorn, Egon Willighagen, Mariano Rico, Asuncion Gomez-Perez, Eduard Aibar, Karima Rafes, Cécile Germain, Alastair Dunning, Lydia Pintscher, Daniel Kinzler & Anonymous
Wiki4R will create an innovative virtual research environment (VRE) for Open Science at scale, engaging both professional researchers and citizen data scientists in new and potentially transformative forms of collaboration. It is based on the realizations that (1) the structured parts of the Web itself can be regarded as a VRE, (2) such environments depend on communities, (3) closed environments are limited in their capacity to nurture thriving communities. Wiki4R will therefore integrate Wikidata, the...

Answering scientific questions with linked European nanosafety data

Egon Willighagen, Micha Rautenberg, Denis Gebele, Linda Rieswijk, Friederike Ehrhart, Jiakang Chang, Georgios Drakakis, Penny Nymark, Pekka Kohonen, Gareth Owen, Haralambos Sarimveis, Christoph Helma & Nina Jeliazkova

MOESM1 of The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Egon Willighagen, John Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, TomĂĄĹĄ Pluskal, Miquel Rojas-ChertĂł, Ola Spjuth, Gilleain Torrance, Chris Evelo, Rajarshi Guha & Christoph Steinbeck
Additional file 1. Zip file with the source code of the benchmarks.

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Egon Willighagen, John Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomáš Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain Torrance, Chris Evelo, Rajarshi Guha & Christoph Steinbeck
Abstract Background The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however,...

The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Egon Willighagen, John Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, Tomáš Pluskal, Miquel Rojas-Chertó, Ola Spjuth, Gilleain Torrance, Chris Evelo, Rajarshi Guha & Christoph Steinbeck
Abstract Background The Chemistry Development Kit (CDK) is a widely used open source cheminformatics toolkit, providing data structures to represent chemical concepts along with methods to manipulate such structures and perform computations on them. The library implements a wide variety of cheminformatics algorithms ranging from chemical structure canonicalization to molecular descriptor calculations and pharmacophore perception. It is used in drug discovery, metabolomics, and toxicology. Over the last 10 years, the code base has grown significantly, however,...

Linking Wikidata to the Semantic Web

Andra Waagmeester, Egon Willighagen, Núria Queralt Rosinach, Elvira Mitraka, Sebastian Burgstaller-Muehlbacher, Tim E Putman, Julia Turner, Lynn M Schriml, Paul Pavlidis, Andrew I Su & Benjamin M Good
Poster described at: http://ceur-ws.org/Vol-1795/paper46.pdf
Wikidata is the linked database of Wikipedia and its sister projects from the Wikimedia foundation. Wikidata can be queried by SPARQL queries. Either through the WikiData Query Service (WDQS: http://query.wikidata.org) or its SPARQL endpoint at: https://query.wikidata.org/bigdata/namespace/wdq/sparql. Both the WDQS and the SPARQL endpoint do not allow submitting federated SPARQL queries. In our efforts to make Wikidata the central hub of linked data in the life science, being able to submit federated queries can...

Linking Wikidata to the Semantic Web

Andra Waagmeester, Egon Willighagen, Núria Queralt Rosinach, Elvira Mitraka, Sebastian Burgstaller-Muehlbacher, Tim E Putman, Julia Turner, Lynn M Schriml, Paul Pavlidis, Andrew I Su & Benjamin M Good
Poster described at: http://ceur-ws.org/Vol-1795/paper46.pdf
Wikidata is the linked database of Wikipedia and its sister projects from the Wikimedia foundation. Wikidata can be queried by SPARQL queries. Either through the WikiData Query Service (WDQS: http://query.wikidata.org) or its SPARQL endpoint at: https://query.wikidata.org/bigdata/namespace/wdq/sparql. Both the WDQS and the SPARQL endpoint do not allow submitting federated SPARQL queries. In our efforts to make Wikidata the central hub of linked data in the life science, being able to submit federated queries can...

MOESM1 of The Chemistry Development Kit (CDK) v2.0: atom typing, depiction, molecular formulas, and substructure searching

Egon Willighagen, John Mayfield, Jonathan Alvarsson, Arvid Berg, Lars Carlsson, Nina Jeliazkova, Stefan Kuhn, TomĂĄĹĄ Pluskal, Miquel Rojas-ChertĂł, Ola Spjuth, Gilleain Torrance, Chris Evelo, Rajarshi Guha & Christoph Steinbeck
Additional file 1. Zip file with the source code of the benchmarks.

Open PHACTS now offers patent information and interactions from Pathways

Chris Evelo, Egon Willighagen, Nick Lynch, Bryn Williams Jones, Antonis Loizou, Stian Soiland­Reyes, Ryan Miller, Anna Gaulton, George Papadatos, Lee Harland, Carole Goble, Peter Woollard, Gerhard Ecker, Daniela Digles & Stefan Senger
Open PHACTS background and History
Open PHACTS started as an Innovative Medicines Initiative (IMI) project in 2011. The objective was to integrate a wide range of pharmacologically related data into a central resource that is described according to standards of the semantic web community. Central to this unification was the development of an API to allow the project partners to build their own custom applications and work streams. Over the course of the IMI project, the...

Resource Types

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    64
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    56
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    39
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    5
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    20
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    2

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    7
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    117
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    66
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    28
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    7
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    4

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    145
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    6
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    1
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