BridgeDbR
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R package for the BridgeDb Java library making identifier mapping functionality available in the R environment.
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BridgeDb Java
Java library for identifier mapping
117
mentions
18
contributors
Cite this software
What BridgeDb Java can do for you
BridgeDb Java is a library that maps identifiers from one source to another. For example, it can map NCBI Gene identifiers to Ensembl gene identifiers, and DOIs to PubMed identifiers.
For example, the following code shows how identifiers for the ChEBI data source
can be used:
DataSource chebi = DataSource.getExistingByFullName("ChEBI");
assertNotNull(chebi);
assertEquals("urn:miriam:chebi:1234", chebi.getMiriamURN("1234"));
assertEquals("chebi", chebi.getCompactIdentifierPrefix());
Keywords
Programming languages
License
</>Source code
Participating organisations
Mentions
Book section
11- 1.WikiPathways: Integrating Pathway Knowledge with Clinical DataAuthor(s): Denise N. Slenter, Martina Kutmon, Egon L. WillighagenPublished in Physician's Guide to the Diagnosis, Treatment, and Follow-Up of Inherited Metabolic Diseases by Springer International Publishing in 2022, page: 1457-146610.1007/978-3-030-67727-5_73
- 2.Design and Analysis of Offshore Macroalgae BiorefineriesAuthor(s): Alexander Golberg, Alexander Liberzon, Edward Vitkin, Zohar YakhiniPublished in Methods in Molecular Biology, Biofuels from Algae by Springer New York in 2018, page: 9-3310.1007/7651_2018_127
- 3.Clustering and Network Analysis of Reverse Phase Protein Array DataAuthor(s): Adam ByronPublished in Methods in Molecular Biology, Molecular Profiling by Springer New York in 2017, page: 171-19110.1007/978-1-4939-6990-6_12
- 4.Plant Pathway DatabasesAuthor(s): Pankaj Jaiswal, Björn UsadelPublished in Plant Bioinformatics, Methods in Molecular Biology by Springer New York in 2016, page: 71-8710.1007/978-1-4939-3167-5_4
- 5.Taking Bioinformatics to Systems MedicineAuthor(s): Antoine H. C. van Kampen, Perry D. MoerlandPublished in Methods in Molecular Biology, Systems Medicine by Springer New York in 2016, page: 17-4110.1007/978-1-4939-3283-2_2
- 6.Scientific Lenses to Support Multiple Views over Linked Chemistry DataAuthor(s): Colin Batchelor, Christian Y. A. Brenninkmeijer, Christine Chichester, Mark Davies, Daniela Digles, Ian Dunlop, Chris T. Evelo, Anna Gaulton, Carole Goble, Alasdair J. G. Gray, Paul Groth, Lee Harland, Karen Karapetyan, Antonis Loizou, John P. Overington, Steve Pettifer, Jon Steele, Robert Stevens, Valery Tkachenko, Andra Waagmeester, Antony Williams, Egon L. WillighagenPublished in The Semantic Web – ISWC 2014, Lecture Notes in Computer Science by Springer International Publishing in 2014, page: 98-11310.1007/978-3-319-11964-9_7
- 7.Hox Protein Interactions: Screening and Network BuildingAuthor(s): Isabelle Bergiers, Barbara Lambert, Sarah Daakour, Jean-Claude Twizere, René RezsohazyPublished in Methods in Molecular Biology, Hox Genes by Springer New York in 2014, page: 319-34810.1007/978-1-4939-1242-1_20
- 8.Genome-Scale Model Management and ComparisonAuthor(s): Stephan Pabinger, Zlatko TrajanoskiPublished in Methods in Molecular Biology, Systems Metabolic Engineering by Humana Press in 2013, page: 3-1610.1007/978-1-62703-299-5_1
- 9.Open PHACTS: A Semantic Knowledge Infrastructure for Public and Commercial Drug Discovery ResearchAuthor(s): Lee HarlandPublished in Lecture Notes in Computer Science, Knowledge Engineering and Knowledge Management by Springer Berlin Heidelberg in 2012, page: 1-710.1007/978-3-642-33876-2_1
- 10.Building disease and target knowledge with Semantic MediaWikiAuthor(s): Lee Harland, Catherine Marshall, Ben Gardner, Meiping Chang, Rich Head, Philip VerdematoPublished in Open Source Software in Life Science Research by Elsevier in 2012, page: 391-42010.1533/9781908818249.391
- 11.Sustainable Model BuildingAuthor(s): Falko Krause, Marvin Schulz, Neil Swainston, Wolfram LiebermeisterPublished in Methods in Enzymology, Methods in Systems Biology by Elsevier in 2011, page: 371-39510.1016/b978-0-12-385118-5.00019-0
Journal articles
99- 1.MetaboAnnotator: an efficient toolbox to annotate metabolites in genome-scale metabolic reconstructionsAuthor(s): Ines Thiele, German Preciat, Ronan M T FlemingPublished in Bioinformatics by Oxford University Press (OUP) in 2022, page: 4831-483210.1093/bioinformatics/btac596
- 2.A Simple Standard for Sharing Ontological Mappings (SSSOM)Author(s): Nicolas Matentzoglu, James P Balhoff, Susan M Bello, Chris Bizon, Matthew Brush, Tiffany J Callahan, Christopher G Chute, William D Duncan, Chris T Evelo, Davera Gabriel, John Graybeal, Alasdair Gray, Benjamin M Gyori, Melissa Haendel, Henriette Harmse, Nomi L Harris, Ian Harrow, Harshad B Hegde, Amelia L Hoyt, Charles T Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Koehler, Thomas Liener, Qinqin Long, James Malone, James A McLaughlin, Julie A McMurry, Sierra Moxon, Monica C Munoz-Torres, David Osumi-Sutherland, James A Overton, Bjoern Peters, Tim Putman, Núria Queralt-Rosinach, Kent Shefchek, Harold Solbrig, Anne Thessen, Tania Tudorache, Nicole Vasilevsky, Alex H Wagner, Christopher J MungallPublished in Database by Oxford University Press (OUP) in 202210.1093/database/baac035
- 3.A Community-Driven, Openly Accessible Molecular Pathway Integrating Knowledge on Malignant Pleural MesotheliomaAuthor(s): Marvin Martens, Franziska Kreidl, Friederike Ehrhart, Didier Jean, Merlin Mei, Holly M. Mortensen, Alistair Nash, Penny Nymark, Chris T. Evelo, Ferdinando CercielloPublished in Frontiers in Oncology by Frontiers Media SA in 202210.3389/fonc.2022.849640
- 4.Unifying the identification of biomedical entities with the BioregistryAuthor(s): Charles Tapley Hoyt, Meghan Balk, Tiffany J. Callahan, Daniel Domingo-Fernández, Melissa A. Haendel, Harshad B. Hegde, Daniel S. Himmelstein, Klas Karis, John Kunze, Tiago Lubiana, Nicolas Matentzoglu, Julie McMurry, Sierra Moxon, Christopher J. Mungall, Adriano Rutz, Deepak R. Unni, Egon Willighagen, Donald Winston, Benjamin M. GyoriPublished in Scientific Data by Springer Science and Business Media LLC in 202210.1038/s41597-022-01807-3
- 5.MSMetaEnhancer: A Python package for mass spectra metadata annotationAuthor(s): Matej Troják, Helge Hecht, Martin Čech, Elliott James PricePublished in Journal of Open Source Software by The Open Journal in 2022, page: 449410.21105/joss.04494
- 6.Integrative OMICS Data-Driven Procedure Using a Derivatized Meta-Analysis ApproachAuthor(s): Karla Cervantes-Gracia, Richard Chahwan, Holger HusiPublished in Frontiers in Genetics by Frontiers Media SA in 202210.3389/fgene.2022.828786
- 7.European Registry of Materials: global, unique identifiers for (undisclosed) nanomaterialsAuthor(s): Jeaphianne van Rijn, Antreas Afantitis, Mustafa Culha, Maria Dusinska, Thomas E. Exner, Nina Jeliazkova, Eleonora Marta Longhin, Iseult Lynch, Georgia Melagraki, Penny Nymark, Anastasios G. Papadiamantis, David A. Winkler, Hulya Yilmaz, Egon WillighagenPublished in Journal of Cheminformatics by Springer Science and Business Media LLC in 202210.1186/s13321-022-00614-7
- 8.A systematically derived overview of the non-ubiquitous pathways and genes that define the molecular and genetic signature of the healthy trabecular meshworkAuthor(s): Ilona Liesenborghs, Johannes S.A.G. Schouten, Martina Kutmon, Theo G.M.F. Gorgels, Chris T. Evelo, Wouter H.G. Hubens, Henny J.M. Beckers, Carroll A.B. Webers, Lars M.T. EijssenPublished in Genomics by Elsevier BV in 2022, page: 11028010.1016/j.ygeno.2022.110280
- 9.BridgeDb and Wikidata: a powerful combination generating interoperable open research (BridgeDb)Author(s): Egon Willighagen, Martina Kutmon, Marvin Martens, Denise SlenterPublished in Research Ideas and Outcomes by Pensoft Publishers in 202210.3897/rio.8.e83031
- 10.Knowledge-Driven Approaches to Create the MTox700+ Metabolite Panel for Predicting ToxicityAuthor(s): Elena Sostare, Thomas N Lawson, Lucy R Saunders, John K Colbourne, Ralf J M Weber, Tomasz Sobanski, Mark R ViantPublished in Toxicological Sciences by Oxford University Press (OUP) in 2022, page: 208-22010.1093/toxsci/kfac007
- 11.Interpreting the lipidome: bioinformatic approaches to embrace the complexityAuthor(s): Jennifer E. Kyle, Lucila Aimo, Alan J. Bridge, Geremy Clair, Maria Fedorova, J. Bernd Helms, Martijn R. Molenaar, Zhixu Ni, Matej Orešič, Denise Slenter, Egon Willighagen, Bobbie-Jo M. Webb-RobertsonPublished in Metabolomics by Springer Science and Business Media LLC in 202110.1007/s11306-021-01802-6
- 12.Bacting: a next generation, command line version of BioclipseAuthor(s): Egon WillighagenPublished in Journal of Open Source Software by The Open Journal in 2021, page: 255810.21105/joss.02558
- 13.Complex Portal 2022: new curation frontiersAuthor(s): Birgit H M Meldal, Livia Perfetto, Colin Combe, Tiago Lubiana, João Vitor Ferreira Cavalcante, Hema Bye-A-Jee, Andra Waagmeester, Noemi del-Toro, Anjali Shrivastava, Elisabeth Barrera, Edith Wong, Bernhard Mlecnik, Gabriela Bindea, Kalpana Panneerselvam, Egon Willighagen, Juri Rappsilber, Pablo Porras, Henning Hermjakob, Sandra OrchardPublished in Nucleic Acids Research by Oxford University Press (OUP) in 2021, page: D578-D58610.1093/nar/gkab991
- 14.Quo Vadis Caenorhabditis elegans Metabolomics—A Review of Current Methods and Applications to Explore Metabolism in the NematodeAuthor(s): Liesa Salzer, Michael WittingPublished in Metabolites by MDPI AG in 2021, page: 28410.3390/metabo11050284
- 15.Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive ReviewAuthor(s): Fotis A. Baltoumas, Sofia Zafeiropoulou, Evangelos Karatzas, Mikaela Koutrouli, Foteini Thanati, Kleanthi Voutsadaki, Maria Gkonta, Joana Hotova, Ioannis Kasionis, Pantelis Hatzis, Georgios A. PavlopoulosPublished in Biomolecules by MDPI AG in 2021, page: 124510.3390/biom11081245
- 16.COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanismsAuthor(s): Marek Ostaszewski, Anna Niarakis, Alexander Mazein, Inna Kuperstein, Robert Phair, Aurelio Orta‐Resendiz, Vidisha Singh, Sara Sadat Aghamiri, Marcio Luis Acencio, Enrico Glaab, Andreas Ruepp, Gisela Fobo, Corinna Montrone, Barbara Brauner, Goar Frishman, Luis Cristóbal Monraz Gómez, Julia Somers, Matti Hoch, Shailendra Kumar Gupta, Julia Scheel, Hanna Borlinghaus, Tobias Czauderna, Falk Schreiber, Arnau Montagud, Miguel Ponce de Leon, Akira Funahashi, Yusuke Hiki, Noriko Hiroi, Takahiro G Yamada, Andreas Dräger, Alina Renz, Muhammad Naveez, Zsolt Bocskei, Francesco Messina, Daniela Börnigen, Liam Fergusson, Marta Conti, Marius Rameil, Vanessa Nakonecnij, Jakob Vanhoefer, Leonard Schmiester, Muying Wang, Emily E Ackerman, Jason E Shoemaker, Jeremy Zucker, Kristie Oxford, Jeremy Teuton, Ebru Kocakaya, Gökçe Yağmur Summak, Kristina Hanspers, Martina Kutmon, Susan Coort, Lars Eijssen, Friederike Ehrhart, Devasahayam Arokia Balaya Rex, Denise Slenter, Marvin Martens, Nhung Pham, Robin Haw, Bijay Jassal, Lisa Matthews, Marija Orlic‐Milacic, Andrea Senff-Ribeiro, Karen Rothfels, Veronica Shamovsky, Ralf Stephan, Cristoffer Sevilla, Thawfeek Varusai, Jean‐Marie Ravel, Rupsha Fraser, Vera Ortseifen, Silvia Marchesi, Piotr Gawron, Ewa Smula, Laurent Heirendt, Venkata Satagopam, Guanming Wu, Anders Riutta, Martin Golebiewski, Stuart Owen, Carole Goble, Xiaoming Hu, Rupert W Overall, Dieter Maier, Angela Bauch, Benjamin M Gyori, John A Bachman, Carlos Vega, Valentin Grouès, Miguel Vazquez, Pablo Porras, Luana Licata, Marta Iannuccelli, Francesca Sacco, Anastasia Nesterova, Anton Yuryev, Anita de Waard, Denes Turei, Augustin Luna, Ozgun Babur, Sylvain Soliman, Alberto Valdeolivas, Marina Esteban‐Medina, Maria Peña‐Chilet, Kinza Rian, Tomáš Helikar, Bhanwar Lal Puniya, Dezso Modos, Agatha Treveil, Marton Olbei, Bertrand De Meulder, Stephane Ballereau, Aurélien Dugourd, Aurélien Naldi, Vincent Noël, Laurence Calzone, Chris Sander, Emek Demir, Tamas Korcsmaros, Tom C Freeman, Franck Augé, Jacques S Beckmann, Jan Hasenauer, Olaf Wolkenhauer, Egon L Willighagen, Alexander R Pico, Chris T Evelo, Marc E Gillespie, Lincoln D Stein, Henning Hermjakob, Peter D'Eustachio, Julio Saez‐Rodriguez, Joaquin Dopazo, Alfonso Valencia, Hiroaki Kitano, Emmanuel Barillot, Charles Auffray, Rudi Balling, Reinhard SchneiderPublished in Molecular Systems Biology by Springer Science and Business Media LLC in 202110.15252/msb.202110387
- 17.A protocol for adding knowledge to Wikidata: aligning resources on human coronavirusesAuthor(s): Andra Waagmeester, Egon L. Willighagen, Andrew I. Su, Martina Kutmon, Jose Emilio Labra Gayo, Daniel Fernández-Álvarez, Quentin Groom, Peter J. Schaap, Lisa M. Verhagen, Jasper J. KoehorstPublished in BMC Biology by Springer Science and Business Media LLC in 202110.1186/s12915-020-00940-y
- 18.WikiPathways: connecting communitiesAuthor(s): Marvin Martens, Ammar Ammar, Anders Riutta, Andra Waagmeester, Denise N Slenter, Kristina Hanspers, Ryan A. Miller, Daniela Digles, Elisson N Lopes, Friederike Ehrhart, Lauren J Dupuis, Laurent A Winckers, Susan L Coort, Egon L Willighagen, Chris T Evelo, Alexander R Pico, Martina KutmonPublished in Nucleic Acids Research by Oxford University Press (OUP) in 2020, page: D613-D62110.1093/nar/gkaa1024
- 19.Distributed flux balance analysis simulations of serial biomass fermentation by two organismsAuthor(s): Edward Vitkin, Amichai Gillis, Mark Polikovsky, Barak Bender, Alexander Golberg, Zohar YakhiniPublished in PLOS ONE by Public Library of Science (PLoS) in 2020, page: e022736310.1371/journal.pone.0227363
- 20.Biospytial: spatial graph-based computing for ecological Big DataAuthor(s): Juan M Escamilla Molgora, Luigi Sedda, Peter M AtkinsonPublished in GigaScience by Oxford University Press (OUP) in 202010.1093/gigascience/giaa039
- 21.Suggestions for Standardized Identifiers for Fatty Acyl Compounds in Genome Scale Metabolic Models and Their Application to the WormJam Caenorhabditis elegans ModelAuthor(s): Michael WittingPublished in Metabolites by MDPI AG in 2020, page: 13010.3390/metabo10040130
- 22.Identification of genes and miRNA associated with idiopathic recurrent pregnancy loss: an exploratory data mining studyAuthor(s): Wael Bahia, Ismael Soltani, Anouar Abidi, Anis Haddad, Salima Ferchichi, Samia Menif, Wassim Y. AlmawiPublished in BMC Medical Genomics by Springer Science and Business Media LLC in 202010.1186/s12920-020-00730-z
- 23.cPEA: a parallel method to perform pathway enrichment analysis using multiple pathways databasesAuthor(s): Giuseppe Agapito, Mario CannataroPublished in Soft Computing by Springer Science and Business Media LLC in 2020, page: 17561-1757210.1007/s00500-020-05243-6
- 24.Improving lipid mapping in Genome Scale Metabolic Networks using ontologiesAuthor(s): Nathalie Poupin, Florence Vinson, Arthur Moreau, Aurélie Batut, Maxime Chazalviel, Benoit Colsch, Laetitia Fouillen, Sarah Guez, Spiro Khoury, Jessica Dalloux-Chioccioli, Anthony Tournadre, Pauline Le Faouder, Corinne Pouyet, Pierre Van Delft, Fanny Viars, Justine Bertrand-Michel, Fabien JourdanPublished in Metabolomics by Springer Science and Business Media LLC in 202010.1007/s11306-020-01663-5
- 25.Wikidata as a knowledge graph for the life sciencesAuthor(s): Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M Good, Malachi Griffith, Obi L Griffith, Kristina Hanspers, Henning Hermjakob, Toby S Hudson, Kevin Hybiske, Sarah M Keating, Magnus Manske, Michael Mayers, Daniel Mietchen, Elvira Mitraka, Alexander R Pico, Timothy Putman, Anders Riutta, Nuria Queralt-Rosinach, Lynn M Schriml, Thomas Shafee, Denise Slenter, Ralf Stephan, Katherine Thornton, Ginger Tsueng, Roger Tu, Sabah Ul-Hasan, Egon Willighagen, Chunlei Wu, Andrew I SuPublished in eLife by eLife Sciences Publications, Ltd in 202010.7554/elife.52614
- 26.Identification of Biological Pathways Contributing to Marbling in Skeletal Muscle to Improve Beef Cattle BreedingAuthor(s): Zahra Roudbari, Susan L. Coort, Martina Kutmon, Lars Eijssen, Jonathan Melius, Tomasz Sadkowski, Chris T. EveloPublished in Frontiers in Genetics by Frontiers Media SA in 202010.3389/fgene.2019.01370
- 27.Biobtree: A tool to search and map bioinformatics identifiers and special keywordsAuthor(s): Tamer GurPublished in F1000Research by F1000 Research Ltd in 2020, page: 14510.12688/f1000research.17927.4
- 28.gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:ProfilerAuthor(s): Liis Kolberg, Uku Raudvere, Ivan Kuzmin, Jaak Vilo, Hedi PetersonPublished in F1000Research by F1000 Research Ltd in 2020, page: 70910.12688/f1000research.24956.2
- 29.Deep gene selection method to select genes from microarray datasets for cancer classificationAuthor(s): Russul Alanni, Jingyu Hou, Hasseeb Azzawi, Yong XiangPublished in BMC Bioinformatics by Springer Science and Business Media LLC in 201910.1186/s12859-019-3161-2
- 30.Ontology mapping for semantically enabled applicationsAuthor(s): Ian Harrow, Rama Balakrishnan, Ernesto Jimenez-Ruiz, Simon Jupp, Jane Lomax, Jane Reed, Martin Romacker, Christian Senger, Andrea Splendiani, Jabe Wilson, Peter WoollardPublished in Drug Discovery Today by Elsevier BV in 2019, page: 2068-207510.1016/j.drudis.2019.05.020
- 31.The EFI Web Resource for Genomic Enzymology Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic PathwaysAuthor(s): Rémi Zallot, Nils Oberg, John A. GerltPublished in Biochemistry by American Chemical Society (ACS) in 2019, page: 4169-418210.1021/acs.biochem.9b00735
- 32.Ontology-based metabolomics data integration with quality controlAuthor(s): Patricia Buendia, Ray M Bradley, Thomas J Taylor, Emma L Schymanski, Gary J Patti, Mansur R KabukaPublished in Bioanalysis by Future Science Ltd in 2019, page: 1139-115410.4155/bio-2018-0303
- 33.A bioinformatics workflow to decipher transcriptomic data from vitamin D studiesAuthor(s): Amadeo Muñoz García, Lars M. Eijssen, Martina Kutmon, Chaitra Sarathy, Ardi Cengo, Martin Hewison, Chris T. Evelo, Michael Lenz, Susan L. CoortPublished in The Journal of Steroid Biochemistry and Molecular Biology by Elsevier BV in 2019, page: 28-3510.1016/j.jsbmb.2019.01.003
- 34.Identification of microRNAs in skeletal muscle associated with lung cancer cachexiaAuthor(s): Wouter R.P.H. van de Worp, Annemie M.W.J. Schols, Anne‐Marie C. Dingemans, Céline M.H. Op den Kamp, Juliette H.R.J. Degens, Marco C.J.M. Kelders, Susan Coort, Henry C. Woodruff, Gueorqui Kratassiouk, Annick Harel‐Bellan, Jan Theys, Ardy van Helvoort, Ramon C.J. LangenPublished in Journal of Cachexia, Sarcopenia and Muscle by Wiley in 2019, page: 452-46310.1002/jcsm.12512
- 35.CyTargetLinker app update: A flexible solution for network extension in CytoscapeAuthor(s): Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, Susan L. CoortPublished in F1000Research by F1000 Research Ltd in 2019, page: 74310.12688/f1000research.14613.2
- 36.Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genesAuthor(s): Friederike Ehrhart, Susan L. Coort, Lars Eijssen, Elisa Cirillo, Eric E. Smeets, Nasim Bahram Sangani, Chris T. Evelo, Leopold M.G. CurfsPublished in The World Journal of Biological Psychiatry by Informa UK Limited in 2019, page: 712-72510.1080/15622975.2019.1593501
- 37.Beyond Pathway Analysis: Identification of Active Subnetworks in Rett SyndromeAuthor(s): Ryan A. Miller, Friederike Ehrhart, Lars M. T. Eijssen, Denise N. Slenter, Leopold M. G. Curfs, Chris T. Evelo, Egon L. Willighagen, Martina KutmonPublished in Frontiers in Genetics by Frontiers Media SA in 201910.3389/fgene.2019.00059
- 38.PathMe: merging and exploring mechanistic pathway knowledgeAuthor(s): Daniel Domingo-Fernández, Sarah Mubeen, Josep Marín-Llaó, Charles Tapley Hoyt, Martin Hofmann-ApitiusPublished in BMC Bioinformatics by Springer Science and Business Media LLC in 201910.1186/s12859-019-2863-9
- 39.Integration among databases and data sets to support productive nanotechnology: Challenges and recommendationsAuthor(s): Sandra Karcher, Egon L. Willighagen, John Rumble, Friederike Ehrhart, Chris T. Evelo, Martin Fritts, Sharon Gaheen, Stacey L. Harper, Mark D. Hoover, Nina Jeliazkova, Nastassja Lewinski, Richard L. Marchese Robinson, Karmann C. Mills, Axel P. Mustad, Dennis G. Thomas, Georgia Tsiliki, Christine Ogilvie HendrenPublished in NanoImpact by Elsevier BV in 2018, page: 85-10110.1016/j.impact.2017.11.002
- 40.Evaluation and comparison of bioinformatic tools for the enrichment analysis of metabolomics dataAuthor(s): Anna Marco-Ramell, Magali Palau-Rodriguez, Ania Alay, Sara Tulipani, Mireia Urpi-Sarda, Alex Sanchez-Pla, Cristina Andres-LacuevaPublished in BMC Bioinformatics by Springer Science and Business Media LLC in 201810.1186/s12859-017-2006-0
- 41.Providing gene-to-variant and variant-to-gene database identifier mappings to use with BridgeDb mapping services.Author(s): Friederike Ehrhart, Jonathan Melius, Elisa Cirillo, Martina Kutmon, Egon L. Willighagen, Susan L. Coort, Leopold M.G. Curfs, Chris T. EveloPublished in F1000Research by F1000 Research Ltd in 2018, page: 139010.12688/f1000research.15708.1
- 42.Introducing WikiPathways as a Data-Source to Support Adverse Outcome Pathways for Regulatory Risk Assessment of Chemicals and NanomaterialsAuthor(s): Marvin Martens, Tim Verbruggen, Penny Nymark, Roland Grafström, Lyle D. Burgoon, Hristo Aladjov, Fernando Torres Andón, Chris T. Evelo, Egon L. WillighagenPublished in Frontiers in Genetics by Frontiers Media SA in 201810.3389/fgene.2018.00661
- 43.BED: a Biological Entity Dictionary based on a graph data modelAuthor(s): Patrice Godard, Jonathan van EyllPublished in F1000Research by F1000 Research Ltd in 2018, page: 19510.12688/f1000research.13925.3
- 44.Prader-Willi syndrome and Angelman syndrome: Visualisation of the molecular pathways for two chromosomal disordersAuthor(s): Friederike Ehrhart, Kelly J. M. Janssen, Susan L. Coort, Chris T. Evelo, Leopold M. G. CurfsPublished in The World Journal of Biological Psychiatry by Informa UK Limited in 2018, page: 670-68210.1080/15622975.2018.1439594
- 45.CyTargetLinker app update: A flexible solution for network extension in CytoscapeAuthor(s): Martina Kutmon, Friederike Ehrhart, Egon L. Willighagen, Chris T. Evelo, Susan L. CoortPublished in F1000Research by F1000 Research Ltd in 2018, page: 74310.12688/f1000research.14613.1
- 46.Identifier Mapping in Cytoscape: idmapperAuthor(s): Adam Treister, Alexander R. PicoPublished in F1000Research by F1000 Research Ltd in 2018, page: 72510.12688/f1000research.14807.1
- 47.Lilikoi: an R package for personalized pathway-based classification modeling using metabolomics dataAuthor(s): Fadhl M AlAkwaa, Breck Yunits, Sijia Huang, Hassam Alhajaji, Lana X GarmirePublished in GigaScience by Oxford University Press (OUP) in 201810.1093/gigascience/giy136
- 48.BED: a Biological Entity Dictionary based on a graph data modelAuthor(s): Patrice Godard, Jonathan van EyllPublished in F1000Research by F1000 Research Ltd in 2018, page: 19510.12688/f1000research.13925.1
- 49.Pathway analysis of transcriptomic data shows immunometabolic effects of vitamin DAuthor(s): Amadeo Muñoz Garcia, Martina Kutmon, Lars Eijssen, Martin Hewison, Chris T Evelo, Susan L CoortPublished in Journal of Molecular Endocrinology by Bioscientifica in 2018, page: 95-10810.1530/jme-17-0186
- 50.The future of metabolomics in ELIXIRAuthor(s): Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez, Warwick B. Dunn, Timothy M. D. Ebbels, Franck Giacomoni, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Jose L. Izquierdo-Garcia, Rafael C. Jimenez, Fabien Jourdan, Namrata Kale, Maria I. Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Nicholas K. Moschonas, Steffen Neumann, Claire O’Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M. Salek, Susanna-Assunta Sansone, Venkata Satagopam, Daniel Schober, Ruth Shimmo, Rachel A. Spicer, Ola Spjuth, Etienne A. Thévenot, Mark R. Viant, Ralf J. M. Weber, Egon L. Willighagen, Gianluigi Zanetti, Christoph SteinbeckPublished in F1000Research by F1000 Research Ltd in 2017, page: 164910.12688/f1000research.12342.1
Other
7- 1.Unifying the Identification of Biomedical Entities with the BioregistryAuthor(s): Charles Tapley Hoyt, Meghan Balk, Tiffany J. Callahan, Daniel Domingo-Fernández, Melissa A. Haendel, Harshad B. Hegde, Daniel S. Himmelstein, Klas Karis, John Kunze, Tiago Lubiana, Nicolas Matentzoglu, Julie McMurry, Sierra Moxon, Christopher J. Mungall, Adriano Rutz, Deepak R. Unni, Egon Willighagen, Donald Winston, Benjamin M. GyoriPublished by Cold Spring Harbor Laboratory in 202210.1101/2022.07.08.499378
- 2.A protocol for adding knowledge to Wikidata, a case reportAuthor(s): Andra Waagmeester, Egon L. Willighagen, Andrew I Su, Martina Kutmon, Jose Emilio Labra Gayo, Daniel Fernández-Álvarez, Quentin Groom, Peter J. Schaap, Lisa M. Verhagen, Jasper J. KoehorstPublished by Cold Spring Harbor Laboratory in 202010.1101/2020.04.05.026336
- 3.Wikidata as a FAIR knowledge graph for the life sciencesAuthor(s): Andra Waagmeester, Gregory Stupp, Sebastian Burgstaller-Muehlbacher, Benjamin M. Good, Malachi Griffith, Obi Griffith, Kristina Hanspers, Henning Hermjakob, Toby S. Hudson, Kevin Hybiske, Sarah M. Keating, Magnus Manske, Michael Mayers, Daniel Mietchen, Elvira Mitraka, Alexander R. Pico, Timothy Putman, Anders Riutta, Núria Queralt-Rosinach, Lynn M. Schriml, Thomas Shafee, Denise Slenter, Ralf Stephan, Katherine Thornton, Ginger Tsueng, Roger Tu, Sabah Ul-Hasan, Egon Willighagen, Chunlei Wu, Andrew I. SuPublished by Cold Spring Harbor Laboratory in 201910.1101/799684
- 4.Integrated analysis of human transcriptome data for Rett syndrome finds a network of involved genesAuthor(s): Friederike Ehrhart, Susan L. Coort, Lars Eijssen, Elisa Cirillo, Eric E. Smeets, Nasim Bahram Sangani, Chris T. Evelo, Leopold M.G. CurfsPublished by Cold Spring Harbor Laboratory in 201810.1101/274258
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- 7.Automatic OpenAPI to Bio.tools ConversionAuthor(s): Egon Willighagen, Jonathan MéliusPublished by Cold Spring Harbor Laboratory in 201710.1101/170274
Contributors
Contact person
EW
MPvI
Martijn P van Iersel
AP
Alexander Pico
TK
Thomas Kelder
JG
Jianjiong Gao
IH
Isaac Ho
KH
Kristina Hanspers
BC
Bruce Conklin
CE
Chris Evelo
HB
Helena Basaric
Maastricht University
EW
Egon Willighagen
Maastricht University
CB
Christian Brenninkmeijer
AG
Alasdair Gray
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BridgeDb and Wikidata
a powerful combination generating interoperable open research
Updated 3 months ago
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