85 Works

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.

ops.js: OPS.js 6.0.2 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 6.0.2 is compatible with the Open PHACTS 1.5 API (and should be backwards compatible with 1.4 for most API calls).

RRegrs: Release 0.0.4

Cristian R Munteanu, Egon Willighagen, GTsiliki, Jseoane & Carlos Fernandez-Lozano
This release: adds testing using the testthat package removed the dependency on doMC so that it should install on Windows now (where doMC is not available) added the tutorial PDF so that it is part of the distribution now allows absolute paths now to point to the data adds additional parameter value checking

BridgeDb: BridgeDb 2.1.0 released

Egon Willighagen, Christian Y. Brenninkmeijer, Alexander Pico & Martina Summer-Kutmon
ChangeLog 2.1.0 (2015-08-06) Update SwissLipids, BRENDA and wikidata Update InChiKey to PRIMARY id Fix designations for KEGG Reactome and PubChem-bioassay Added the InChIKey as DataSource, allowing at some point WikiPathways to be searched on InChIKey Added SwissLipids Added more detail on how to get DataSource's Also compiles the BatchMapper now Added 'Plasmodium falciparum' to the Organism enumeration Added alternative methods that allow getting attributes not just from the data source of the Xref, but from...

ops.js: OPS.js 6.1.2 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 6.1.2 is compatible with the Open PHACTS 1.5 API (and should be backwards compatible with 1.4 for most API calls).

ops.js: OPS.js 6.1.3 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 6.1.3 is compatible with the Open PHACTS 1.5 API (and should be backwards compatible with 1.4 for most API calls).

RRegrs: Release 0.0.5

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

eNanoMapper Ontology

Jiakang Chang, Egon Willighagen, Friederike Ehrhart, Linda Rieswijk, Gareth Owen & Janna Hastings
The eNanoMapper ontology covers the full scope of terminology needed to support research into nanomaterial safety. It builds on multiple pre-existing external ontologies such as the NanoParticle Ontology.

Openphacts/Ops_Linkeddataapi: Open Phacts Linked Data Api 2.1.0

Fundatureanu-Sever, Randy Kerber, Stian Soiland-Reyes, Ian Dunlop, Antonis Loizou, Ronald Siebes, Egon Willighagen & Paul Groth
This release improves and extends the earlier versions. New API methods are included around interactions.

Openphacts/Ops_Linkeddataapi: Open Phacts Linked Data Api 2.1.0

Fundatureanu-Sever, Randy Kerber, Stian Soiland-Reyes, Ian Dunlop, Antonis Loizou, Ronald Siebes, Egon Willighagen & Paul Groth
This release improves and extends the earlier versions. New API methods are included around interactions.

Deliverable Report D6.2 Enanomapper Year 2 Dissemination Report

Friederike Ehrhart Bengt Fadeel
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, and other training events. In the second year of the project, the project partners have produced additional online seminars or webinars on selected topics as well as tutorials on tools developed in other...

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: 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

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...

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.

Cdk/Cdk: Patch Release Of 2.1

John Mayfield, Egon Willighagen, Rajarshi Guha, Gilleain Torrance, Kazuya Ujihara, Syed Asad Rahman, Jonathan Alvarsson, Mbv31602, Tomáš Pluskal, Yap Chun Wei, Daniel Szisz, Mark J. Williamson, Nikolay Kochev, Nina Jeliazkova, Arvid Berg, Alex Clark, Ralf Stephan, Oliver Stueker, Kdole, Klas Jönsson, Kaibioinfo, Dmitry Katsubo, AndyHowlettGitHub, Uli Köhler, Cyrus Harmon … & Philopon
This patch release removes the SNAPSHOT dependency.

Cdk/Cdk: Cdk 2.1

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

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

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