228 Works

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 2.2.2

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 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...

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.

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,...

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...

The Open PHACTS Discovery Platform from a network biology perspective

Chris Evelo, Egon Willighagen, Nick Lynch, Bryn Williams Jones, Antonis Loizou, Stian Soiland-Reyes, Ryan Miller, Anna Gaulton, George Papadatos, Lee Harland, Carole Goble, Peter Woollard, Gerhard Ecker, Daniela Digles & Stefan Senger
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 workstreams. Also central to the Open PHACTS Discovery Platform is the development of identity resolution and identity...

The BridgeDb framework

Egon Willighagen, Jonathan Mélius, Brenninkmeijer Christian, Stian Soiland-Reyes, Anwesha Bohler, Martina Kutmon, Andra Waagmeester, Alex Pico, Anders Riutta, Alasdair Gray, Christ Leemans, Colin Batchelor, Ola Spjuth, Nuno Nunes, Chris Evelo & Carole Goble
 
What is BridgeDb? Biological systems consist of many thousands of genes, proteins, and metabolites. Our collective knowledge about these entities is collected in many hundreds of disparate databases, each focusing on particular themes of knowledge or types of experiments. Importantly, to capture this focus, each database uses its own definition of the key entities and have a matching collection of entity identifiers. Linking all these identifiers requires a flexible tool that provides identifier mappings (IDmaps)...

Enanomapper Applications To Support The Risk Assessment Of Nanomaterials

Lucian Farcal, Philip Doganis, George Drakakis, Haralambos Sarimveis, Micha Rautenberg, Christoph Helma, Denis Gebele, Nikolay Kochev, Vedrin Jeliazkov, Nina Jeliazkova, Malahat Mousavi, Bengt Fadeel, Vesa Hongisto, Penny Nymark, Pekka Kohonen, Roland Grafström, Jiakang Chang, Gareth Owen, Friederike Ehrhart, Linda Rieswijk, Egon Willighagen, Spela Hardy & Barry Hardy
The infrastructure developed within eNanoMapper project aims to support the data management in the area of nano safety 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. By merging the expertise of partners in statistical and data mining tools and in predictive toxicology, biology and nanotechnology research, eNanoMapper developed resources and...

Cdk/Cdk: Cdk 1.5.15

John Mayfield, Egon Willighagen, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Tomáš Pluskal, Yap Chun Wei, Daniel Szisz, Mark Williamson, Nikolay Kochev, Nina Jeliazkova, Arvid Berg, Alex Clark, Ralf Stephan, Oliver Stueker, Kdole, Klas Jönsson, Kaibioinfo, Dmitry Katsubo, AndyHowlettGitHub, Uli Köhler, Cyrus Harmon, Sambitgaan … & LuisFF
The Chemistry Development Kit

Cdk/Cdk: Cdk 2.0

John Mayfield, Egon Willighagen, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Tomáš Pluskal, Kazuya Ujihara, Yap Chun Wei, Daniel Szisz, Mark Williamson, Nikolay Kochev, Nina Jeliazkova, Arvid Berg, Alex Clark, Ralf Stephan, Oliver Stueker, Kdole, Klas Jönsson, Kaibioinfo, Dmitry Katsubo, AndyHowlettGitHub, Uli Köhler, Cyrus Harmon … & LuisFF
The Chemistry Development Kit

Cdk/Cdk: Cdk 2.0

John Mayfield, Egon Willighagen, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Tomáš Pluskal, Kazuya Ujihara, Yap Chun Wei, Daniel Szisz, Mark Williamson, Nikolay Kochev, Nina Jeliazkova, Arvid Berg, Alex Clark, Ralf Stephan, Oliver Stueker, Kdole, Klas Jönsson, Kaibioinfo, Dmitry Katsubo, AndyHowlettGitHub, Uli Köhler, Cyrus Harmon … & LuisFF
The Chemistry Development Kit

Cdk/Cdk: Cdk 1.5.14

John Mayfield, Egon Willighagen 0000-0001-7542-0286, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Tomáš Pluskal, Yap Chun Wei, Daniel Szisz, Mark Williamson, Nikolay Kochev, Nina Jeliazkova, Arvid Berg, Alex Clark, Ralf Stephan, Klas Jönsson, Kdole, Stephan Beisken, Kaibioinfo, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Cyrus Harmon, Uli Köhler … & PeterOdeus
The Chemistry Development Kit

cdk: CDK Release 1.5.11

Egon Willighagen, John May, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Yap Chun Wei, Daniel Szisz, Stephan Beisken, Tomáš Pluskal, Mark Williamson, Arvid Berg, Aclarkxyz, Ralf Stephan, Ngn, Klas Jönsson, Dmitry Katsubo, Oliver Stueker, AndyHowlettGitHub, Uli Köhler, Cyrus Harmon, Sambitgaan, Zachcp, Rafeli … & Carl Mäsak
https://github.com/cdk/cdk/wiki/1.5.11-Release-Notes

cdk: CDK Release 1.5.12

John May, Egon Willighagen, Rajarshi Guha, Gilleain Torrance, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Yap Chun Wei, Daniel Szisz, Stephan Beisken, Tomáš Pluskal, Mark Williamson, Arvid Berg, Alex Clark, Ralf Stephan, Nina Jeliazkova, Klas Jönsson, Kdole, AndyHowlettGitHub, Dmitry Katsubo, Oliver Stueker, Uli Köhler, Cyrus Harmon, Sambitgaan, Zachcp … & Carl Mäsak
1.5.12 Release Note

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

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

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