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@Manual{biodbChebi,
title = {biodbChebi: biodbChebi, a library for connecting to the ChEBI Database},
author = {Pierrick Roger},
year = {2022},
note = {R package version 1.4.0},
url = {https://github.com/pkrog/biodbChebi},
}
@article{BridgeDb,
author = {van Iersel, Martijn P. and Pico, Alexander R. and Kelder, Thomas and Gao, Jianjiong and Ho, Isaac and Hanspers, Kristina and Conklin, Bruce R. and Evelo, Chris T.},
doi = {10.1186/1471-2105-11-5},
issn = {1471-2105},
journal = {BMC Bioinformatics},
month = {dec},
number = {1},
pages = {5},
pmid = {20047655},
title = {{The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services}},
url = {https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-5},
volume = {11},
year = {2010}
}
@Manual{BridgeDbR,
title = {BridgeDbR: Code for using BridgeDb identifier mapping framework from within R},
author = {Chris Leemans and Egon Willighagen and Denise Slenter and Anwesha Bohler and Lars Eijssen and Tooba Abbassi-Daloii},
year = {2022},
note = {R package version 2.8.0},
url = {https://github.com/bridgedb/BridgeDbR},
}
@article{LipidMaps,
title = {Update of the LIPID MAPS comprehensive classification system for lipids},
journal = {Journal of Lipid Research},
volume = {50},
pages = {S9-S14},
year = {2009},
issn = {0022-2275},
doi = {https://doi.org/10.1194/jlr.R800095-JLR200},
url = {https://www.sciencedirect.com/science/article/pii/S0022227520305800},
author = {Eoin Fahy and Shankar Subramaniam and Robert C. Murphy and Masahiro Nishijima and Christian R.H. Raetz and Takao Shimizu and Friedrich Spener and Gerrit {van Meer} and Michael J.O. Wakelam and Edward A. Dennis},
}
@Article{ontologyIndex,
title = {{ontologyX}: a suite of R packages for working with ontological data},
author = {Daniel Greene and Sylvia Richardson and Ernest Turro},
journal = {Bioinformatics},
year = {2017},
volume = {33},
number = {7},
pages = {1104--1106},
publisher = {{Oxford Univ Press}},
url = {https://doi.org/10.1093/bioinformatics/btw763},
doi = {10.1093/bioinformatics/btw763}
}
@article{SwissLipids,
author = {Aimo, Lucila and Liechti, Robin and Hyka-Nouspikel, Nevila and Niknejad, Anne and Gleizes, Anne and Götz, Lou and Kuznetsov, Dmitry and David, Fabrice P.A. and van der Goot, F. Gisou and Riezman, Howard and Bougueleret, Lydie and Xenarios, Ioannis and Bridge, Alan},
title = "{The SwissLipids knowledgebase for lipid biology}",
journal = {Bioinformatics},
volume = {31},
number = {17},
pages = {2860--2866},
year = {2015},
month = {05},
issn = {1367-4803},
doi = {10.1093/bioinformatics/btv285},
url = {https://doi.org/10.1093/bioinformatics/btv285},
eprint = {https://academic.oup.com/bioinformatics/article-pdf/31/17/2860/49035148/bioinformatics\_31\_17\_2860.pdf},
}
@Article{webchem,
title = {{webchem}: An {R} Package to Retrieve Chemical Information from the {W}eb},
author = {Eduard Sz\"ocs and Tam\'as Stirling and Eric R. Scott and Andreas Scharm\"uller and Ralf B. Sch\"afer},
journal = {Journal of Statistical Software},
year = {2020},
volume = {93},
number = {13},
pages = {1--17},
doi = {10.18637/jss.v093.i13},
}
@article{WikiPathwaysMartens2021,
author = {Martens, Marvin and Ammar, Ammar and Riutta, Anders and Waagmeester, Andra and Slenter, Denise N and Hanspers, Kristina and {A. Miller}, Ryan and Digles, Daniela and Lopes, Elisson N and Ehrhart, Friederike and Dupuis, Lauren J and Winckers, Laurent A and Coort, Susan L and Willighagen, Egon L. and Evelo, Chris T. and Pico, Alexander R. and Kutmon, Martina},
doi = {10.1093/nar/gkaa1024},
issn = {0305-1048},
journal = {Nucleic Acids Research},
month = {jan},
number = {D1},
pages = {D613--D621},
pmid = {33211851},
publisher = {Oxford University Press},
title = {{WikiPathways: connecting communities}},
url = {http://academic.oup.com/nar/article/46/D1/D661/4612963 https://academic.oup.com/nar/article/49/D1/D613/5992285},
volume = {49},
year = {2021}
}
@article{WikiPathwaysSlenter2018,
author = {Slenter, Denise N. and Kutmon, Martina and Hanspers, Kristina and Riutta, Anders and Windsor, Jacob and Nunes, Nuno and M{\'{e}}lius, Jonathan and Cirillo, Elisa and Coort, Susan L. and Digles, Daniela and Ehrhart, Friederike and Giesbertz, Pieter and Kalafati, Marianthi and Martens, Marvin and Miller, Ryan and Nishida, Kozo and Rieswijk, Linda and Waagmeester, Andra and Eijssen, Lars M T and Evelo, Chris T. and Pico, Alexander R. and Willighagen, Egon L.},
doi = {10.1093/nar/gkx1064},
issn = {0305-1048},
journal = {Nucleic Acids Research},
month = {jan},
number = {D1},
pages = {D661--D667},
pmid = {29136241},
title = {{WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research}},
url = {http://academic.oup.com/nar/article/46/D1/D661/4612963},
volume = {46},
year = {2018}
}