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paper.bib
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@article{wong2021capturing,
title={Capturing scientific knowledge in computable form},
author={Wong, Jeffrey V and Franz, Max and Siper, Metin Can and Fong, Dylan and Durupinar, Funda and Dallago, Christian and Luna, Augustin and Giorgi, John M and Rodchenkov, Igor and Babur, {\"O}zg{\"u}n and others},
journal={bioRxiv},
year={2021},
publisher={Cold Spring Harbor Laboratory},
doi={10.1101/2021.03.10.382333}
}
@article{cerami2010pathway,
title={Pathway Commons, a web resource for biological pathway data},
author={Cerami, Ethan G and Gross, Benjamin E and Demir, Emek and Rodchenkov, Igor and Babur, {\"O}zg{\"u}n and Anwar, Nadia and Schultz, Nikolaus and Bader, Gary D and Sander, Chris},
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publisher={Oxford University Press},
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@article{gyori2017word,
title={From word models to executable models of signaling networks using automated assembly},
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@article{pafilis2009reflect,
title={Reflect: augmented browsing for the life scientist},
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@article{berriz2008synergizer,
title={The Synergizer service for translating gene, protein and other biological identifiers},
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journal={Bioinformatics},
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@article{mering2003string,
title={STRING: a database of predicted functional associations between proteins},
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@article{mostafavi2008genemania,
title={GeneMANIA: a real-time multiple association network integration algorithm for predicting gene function},
author={Mostafavi, Sara and Ray, Debajyoti and Warde-Farley, David and Grouios, Chris and Morris, Quaid},
journal={Genome biology},
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year={2008},
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}
@article{reimand2007g,
title={g: Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments},
author={Reimand, J{\"u}ri and Kull, Meelis and Peterson, Hedi and Hansen, Jaanus and Vilo, Jaak},
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volume={35},
number={suppl\_2},
pages={W193--W200},
year={2007},
publisher={Oxford University Press},
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}
@article{cote2007protein,
title={The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases},
author={C{\^o}t{\'e}, Richard G and Jones, Philip and Martens, Lennart and Kerrien, Samuel and Reisinger, Florian and Lin, Quan and Leinonen, Rasko and Apweiler, Rolf and Hermjakob, Henning},
journal={BMC bioinformatics},
volume={8},
number={1},
pages={1--14},
year={2007},
publisher={Springer},
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}
@article{juty2012identifiers,
title={Identifiers. org and MIRIAM Registry: community resources to provide persistent identification},
author={Juty, Nick and Le Novere, Nicolas and Laibe, Camille},
journal={Nucleic acids research},
volume={40},
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publisher={Oxford University Press},
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}
@article{abeysooriya2021gene,
title={Gene name errors: lessons not learned},
author={Abeysooriya, Mandhri and Soria, Megan and Kasu, Mary Sravya and Ziemann, Mark},
journal={bioRxiv},
year={2021},
publisher={Cold Spring Harbor Laboratory},
doi={10.1101/2021.03.30.437702}
}
@misc{groundingswagger,
author = {Max Franz and Jeffrey V Wong and Metin Can Siper},
title = {Pathway Commons Grounding Search Service},
year = {2021},
publisher = {GitHub},
journal = {GitHub documentation},
url = {https://grounding.baderlab.org}
}
@misc{githubRepoReadme,
author = {Max Franz and Jeffrey V Wong and Metin Can Siper},
title = {GitHub: Pathway Commons Grounding Search Service},
year = {2021},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/PathwayCommons/grounding-search}
}
@article{gene2pubmed,
title={Entrez Gene: gene-centered information at NCBI},
author={Maglott, Donna and Ostell, Jim and Pruitt, Kim D and Tatusova, Tatiana},
journal={Nucleic acids research},
volume={39},
number={suppl\_1},
pages={D52--D57},
year={2010},
publisher={Oxford University Press},
doi={10.1093/nar/gki031}
}