bibliography_V2.bib

@Article{field2008,
  author = {Field, D. and Garrity, G. and Gray, T. and Morrison, N. and Selengut, J. and Sterk, P. and Tatusova, T. and Thomson, N. and Allen, M. J. and Angiuoli, S. V. and Ashburner, M. and Axelrod, N. and Baldauf, S. and Ballard, S. and Boore, J. and Cochrane, G. and Cole, J. and Dawyndt, P. and De Vos, P. and DePamphilis, C. and others},
  title = {The minimum information about a genome sequence (MIGS) specification},
  journal = {Nature biotechnology},
  volume = {26},
  number = {5},
  pages = {541--547},
  year = {2008},
  url = {https://doi.org/10.1038/nbt1360},
}

@Article{bowers2017,
  author = {Bowers, R. and Kyrpides, N. and Stepanauskas, R. and others},
  title = {Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea},
  journal = {Nat Biotechnol},
  volume = {35},
  pages = {725--731},
  year = {2017},
  url = {https://doi.org/10.1038/nbt.3893},
}

@Article{murray2020,
  author = {Murray, A. E. and Freudenstein, J. and Gribaldo, S. and others},
  title = {Roadmap for naming uncultivated Archaea and Bacteria},
  journal = {Nat Microbiol},
  volume = {5},
  pages = {987--994},
  year = {2020},
  url = {https://doi.org/10.1038/s41564-020-0733-x},
}

@Article{yilmaz2011,
  author = {Yilmaz, Pelin and others},
  title = {Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications},
  journal = {Nature biotechnology},
  volume = {29},
  number = {5},
  pages = {415--420},
  year = {2011},
  url = {https://doi.org/10.1038/nbt.1823},
}

@Online{nfdi,
  title = {German National Research Data Infrastructure},
  url = {https://www.nfdi.de/?lang=en},
  urldate = {Accessed on 2023-03-21},
  year = { },
}

@Online{nfdi_microbiota,
  title = {NFDI4Microbiota},
  url = {https://nfdi4microbiota.de/},
  urldate = {Accessed on 2023-03-21},
  year = {},
}

@Online{mims_package,
  title = {MIMS: metagenome/environmental, human-associated; version 6.0 Package},
  url = {https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIMS.me.human-associated.5.0/},
  urldate = {Accessed on 2023-08-07},
  year = {},
}

@Online{gsc_mixs_human_associated,
  title = {GSC MIxS human associated; ENA Checklist: ERC000014},
  url = {https://www.ebi.ac.uk/ena/browser/view/ERC000014},
  urldate = {Accessed on 2023-07-31},
  year = {},
}

@Online{ena_marine_microalgae,
  title = {ENA Marine Microalgae Checklist; Checklist: ERC000043},
  url = {https://www.ebi.ac.uk/ena/browser/view/ERC000043},
  urldate = {Accessed on 2023-07-28},
  year = {},
}

@Online{gsc_mixs_water,
  title = {GSC MIxS water; ENA Checklist: ERC000024},
  url = {https://www.ebi.ac.uk/ena/browser/view/ERC000024},
  urldate = {Accessed on 2023-07-28},
  year = {},
}

@Online{ena_tara_oceans,
  title = {ENA Tara Oceans; Checklist: ERC000030},
  url = {https://www.ebi.ac.uk/ena/browser/view/ERC000030},
  urldate = {Accessed on 2023-08-07},
  year = {},
}

@Article{morrison2007,
  author = {Morrison, Norman and Bearden, Daniel and Bundy, Jacob G. and Collette, Timothy and Currie, Fraser and Davey, Matthew and Dominguez, Migdalia and Foster, Jill and Goodacre, Royston and Griffin, Julian and others},
  title = {Standard reporting requirements for biological samples in metabolomics experiments: environmental context},
  journal = {Metabolomics},
  year = {2007},
  volume = {3},
  number = {2},
  pages = {203--210},
  doi = {10.1007/s11306-007-0067-1},
  url = {https://doi.org/10.1007/s11306-007-0067-1},
}

@Online{field_migs,
  title = {The minimum information about a genome sequence (MIGS) specification},
  author = {Field, D. and Garrity, G. and Gray, T. and Morrison, N. and Selengut, J. and Sterk, P. and Tatusova, T. and Thomson, N. and Allen, M. J. and Angiuoli, S. V. and Ashburner, M. and Axelrod, N. and Baldauf, S. and Ballard, S. and Boore, J. and Cochrane, G. and Cole, J. and Dawyndt, P. and De Vos, P. and DePamphilis, C. and Edwards, R. and Faruque, N. and Feldman, R. and Gilbert, J. and Gilna, P. and Glöckner, F. O. and Goldstein, P. and Guralnick, R. and Haft, D. and Hancock, D. and Hermjakob, H. and Hertz-Fowler, C. and Hugenholtz, P. and Joint, I. and Kagan, L. and Kane, M. and Kennedy, J. and Kowalchuk, G. and Kottmann, R. and Kolker, E. and Kravitz, S. and Kyrpides, N. and Leebens-Mack, J. and Lewis, S. E. and Li, K. and Lister, A. L. and Lord, P. and Maltsev, N. and Markowitz, V. and Martiny, J. and Methe, B. and Mizrachi, I. and Moxon, R. and Nelson, K. and Parkhill, J. and Proctor, L. and White, O. and Sansone, S. A. and Spiers, A. and Stevens, R. and Swift, P. and Taylor, C. and Tateno, Y. and Tett, A. and Turner, S. and Ussery, D. and Vaughan, B. and Ward, N. and Whetzel, T. and San Gil, I. and Wilson, G. and Wipat, A.},
  year = {2008},
  journal = {Nature Biotechnology},
  volume = {26},
  number = {5},
  pages = {541-547},
  url = {https://doi.org/10.1038/nbt1360},
}

@Online{kottmann_gcdml,
  title = {A standard MIGS/MIMS compliant XML Schema: Toward the development of the Genomic Contextual Data Markup Language (GCDML)},
  author = {Kottmann, R. and Gray, T. and Murphy, S. and Kagan, L. and Kravitz, S. and Lombardot, T. and Field, D. and Glöckner, F. O. and Genomic Standards Consortium},
  year = {2008},
  journal = {OMICS: A Journal of Integrative Biology},
  volume = {12},
  number = {2},
  pages = {115-121},
  url = {https://doi.org/10.1089/omi.2008.0A10},
}

@Online{gsc_water_mims,
  title = {GSC MIxS: WaterMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/WaterMIMS/},
  urldate = {Accessed on 2023-08-07},
  year = {},
}

@Online{gsc_built_env_mims,
  title = {GSC MIxS: BuiltEnvironmentMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/BuiltEnvironmentMIMS/},
  urldate = {Accessed on 2023-08-09},
  year = {},
}

@Online{gsc_plant_assoc_mims,
  title = {GSC MIxS: Plant-associatedMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/Plant-associatedMIMS/},
  urldate = {Accessed on 2023-08-08},
  year = {},
}

@Article{envo_ontology,
  title = {The environment ontology: Contextualising biological and biomedical entities},
  author = {Buttigieg, P. L. and Morrison, N. and Smith, B. and Mungall, C. J. and Lewis, S. E. and ENVO Consortium},
  year = {2013},
  journal = {Journal of Biomedical Semantics},
  volume = {4},
  number = {1},
  pages = {43},
  doi = {10.1186/2041-1480-4-43},
}

@Online{gsc_agriculture_mims,
  title = {GSC MIxS: AgricultureMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/AgricultureMIMS/},
  urldate = {Accessed on 2023-08-08},
  year = {},
}

@Online{gsc_symbiont_assoc_mims,
  title = {GSC MIxS: Symbiont-associatedMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/Symbiont-associatedMIMS/},
  urldate = {Accessed on 2023-08-08},
  year = {},
}

@Online{us_omb_race,
  title = {U.S. Office of Management and Budget (OMB): About the Topic of Race},
  url = {https://www.census.gov/topics/population/race/about.html},
  urldate = {Accessed on 2023-08-07},
  year = {},
}

@Online{gsc_human_gut_mims,
  title = {GSC MIxS: Human-gutMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/Human-gutMIMS/},
  urldate = {Accessed on 2023-08-01},
  year = {},
}

@Online{gsc_human_oral_mims,
  title = {GSC MIxS: Human-oralMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/Human-oralMIMS/},
  urldate = {Accessed on 2023-08-01},
  year = {},
}

@Online{gsc_human_skin_mims,
  title = {GSC MIxS: Human-skinMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/Human-skinMIMS/},
  urldate = {Accessed on 2023-08-01},
  year = {},
}

@Online{gsc_human_vaginal_mims,
  title = {GSC MIxS: Human-vaginalMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/Human-vaginalMIMS/},
  urldate = {Accessed on 2023-08-01},
  year = {},
}

@Online{gsc_host_assoc_mims,
  title = {GSC MIxS: Host-associatedMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/Host-associatedMIMS/},
  urldate = {Accessed on 2023-07-31},
  year = {},
}

@Online{gsc_human_assoc_mims,
  title = {GSC MIxS: Human-associatedMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/Human-associatedMIMS/},
  urldate = {Accessed on 2023-08-01},
  year = {},
}

@Online{gsc_misc_env_mims,
  title = {GSC MIxS: MiscellaneousNaturalOrArtificialEnvironmentMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/MiscellaneousNaturalOrArtificialEnvironmentMIMS/},
  urldate = {Accessed on 2023-08-09},
  year = {},
}

@Online{gsc_sediment_mims,
  title = {GSC MIxS: SedimentMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/SedimentMIMS/},
  urldate = {Accessed on 2023-08-09},
  year = {},
}

@Online{gsc_soil_mims,
  title = {GSC MIxS: SoilMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/SoilMIMS/},
  urldate = {Accessed on 2023-08-09},
  year = {},
}

@Online{gsc_wastewater_sludge_mims,
  title = {GSC MIxS: WastewaterSludgeMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/WastewaterSludgeMIMS/},
  urldate = {Accessed on 2023-08-09},
  year = {},
}

@Online{gsc_microbial_mat_biofilm_mims,
  title = {GSC MIXS: MicrobialMatBiofilmMIMS},
  url = {https://genomicsstandardsconsortium.github.io/mixs/MicrobialMatBiofilmMIMS/},
  urldate = {Accessed on 2023-08-09},
  year = {},
}

@Online{gold_ecosystem_classification,
  title = {GOLD Ecosystem Classification paths},
  url = {https://gold.jgi.doe.gov/ecosystem_classification},
  urldate = {Accessed on 2023-08-02},
  year = {},
}

@Online{gsc_migs_bacteria,
  title = {GSC MIXS: MIGSBacteria},
  url = {https://genomicsstandardsconsortium.github.io/mixs/MIGSBacteria/},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@Online{ena_metadata_platform,
  title = {ENA Metadata Validation: Platform},
  url = {https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#platform},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@Online{ena_metadata_instrument,
  title = {ENA Metadata Validation: Instrument},
  url = {https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#instrument},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@Online{ena_metadata_source,
  title = {ENA Metadata Validation: Source},
  url = {https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#source},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@Online{ena_metadata_strategy,
  title = {ENA Metadata Validation: Strategy},
  url = {https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#strategy},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@Online{ena_metadata_selection,
  title = {ENA Metadata Validation: Selection},
  url = {https://ena-docs.readthedocs.io/en/latest/submit/reads/webin-cli.html#selection},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@Online{gsc_mixs_mimarks_specimen,
  title = {GSC MIXS: MIMARKSSpecimen},
  url = {https://genomicsstandardsconsortium.github.io/mixs/MIMARKSSpecimen/},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@Online{ena_submit_read_alignments,
  title = {ENA How to Submit Other Analyses: Submitting Read Alignments},
  url = {https://ena-docs.readthedocs.io/en/latest/submit/analyses/read-alignments.html},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@Online{gsc_mixs_mimag,
  title = {GSC MIXS: MIMAG},
  url = {https://genomicsstandardsconsortium.github.io/mixs/MIMAG/},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@online{Miuvig,
  title = {{Minimum Information About an Uncultivated Virus Genome (Miuvig)}},
  url = {https://genomicsstandardsconsortium.github.io/mixs/0010012/},
  urldate = {Accessed on 2023-12-05},
  year = {},
}

@software{fair_cookbook,
author = {Rocca-Serra, Philippe and J G Gray, Alasdair and Delfin Rossaro, Alejandra and Splendiani, Andrea and Zaliani, Andrea and Pippow, Andreas and Cambon-Thomsen, Anne and Sedani, Ashni and Goble, Carole and Evelo, Chris and Kee Ong, Chuang and Wood, Colin and Pommier, Cyril and J. B. Clarke, Daniel and Welter, Danielle and Henderson, David and Batista, Dominique and Reilly, Dorothy and Alharbi, Ebtisam and van der Horst, Eelke and Willighagen, Egon and Reynares, Emiliano and Vos, Emma and LeFloch, Erwan and Marin del Pico, Eva and Ronzano, Francesco and Kroh, Franziska and Xu, Fuqi and Backianathan, Gabriel and Papadotas, George and Witt, Gesa and Hurst, Hannah and Van Vlijmen, Herman and Emam, Ibrahim and Liyanage, Isuru and Neefs, Jean-Marc and Strubel, Jolanda and Quast, Karsten and van Bochove, Kees and Dauth, Kurt and Furlong, Laura and Garcia, Leyla and Giovanni, Lucas and Kohler, Manfred and Pruess, Manuela and Ibberson, Mark and Cook, Martin and Courtot, Melanie and d'Arcy, Mike and Juty, Nick and Lynch, Nick and Engkvist, Ola and Deniz Beyan, Oya and Peeters, Paul and Woollard, Peter and Papadopoulos, Petros and Gribbon, Philip and Sahay, Ratnesh and Giessmann, Robert and Verbeeck, Rudi and Capella Gutierrez, Salvador and Lusher, Scott and Beier, Sebastian and Singh, Sukhi and Sansone, Susanna-Assunta and Plasterer, Tom and Burdett, Tony and Abbassi-Daloii, Tooba and Goldmann, Ulrich and Grouès, Valentin and Ioannidis, Vassilios and P. Satagopam, Venkata and Sedlyarov, Vitaly and Gu, Wei and Gaidya, Yojana and Warnes, Zachary},
license = {CC-BY-4.0},
month = apr,
title = {{The FAIR Cookbook}},
url = {https://github.com/FAIRplus/the-fair-cookbook/},
version = {0.1.0},
year = {2022}
}

@Online{ena_metagenome_assemblies,
  title = {{ENA Submitting Metagenome Assemblies}},
  url = {https://ena-docs.readthedocs.io/en/latest/submit/assembly/metagenome.html},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@article{shakya2019advances,
  author = {Shakya, Migun and Quince, Christopher and Campbell, James H and Yang, Zamin K},
  title = {Advances and Challenges in Metatranscriptomic Analysis},
  journal = {Frontiers in Genetics},
  volume = {10},
  pages = {904},
  year = {2019},
  doi = {10.3389/fgene.2019.00904},
  date = {2019-09-25},
}

@online{ena_transcriptome_assembly,
  title = {ENA Submitting Transcriptome Assemblies},
  url = {https://ena-docs.readthedocs.io/en/latest/submit/assembly/transcriptome.html},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@online{tsa_database,
  title = {Transcriptome Shotgun Assembly Sequence Database},
  url = {https://www.ncbi.nlm.nih.gov/genbank/tsa/},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@online{proteomexchange_guidelines,
  title = {Data Submission Guidelines for the ProteomeXchange Consortium V3.0.1},
  url = {https://www.proteomexchange.org/docs/guidelines_px.pdf},
  note = {PDF document},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@online{pride,
  title = {{PRIDE}: PRoteomics {IDEntifications} Database},
  url = {https://www.ebi.ac.uk/pride/markdownpage/submitdatapage#submit_dataset},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@online{peptideatlas,
  title = {PeptideAtlas},
  url = {https://peptideatlas.org/},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@online{massive,
  title = {{MassIVE}: Mass Spectrometry Interactive Virtual Environment},
  url = {https://massive.ucsd.edu/ProteoSAFe/static/massive.jsp},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@online{iprox,
  title = {iProX: Integrated Proteome Resources},
  url = {https://www.iprox.cn/page/helpEn.html#pag5},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@article{jpostrepo,
  author = {Shujiro Okuda and Yu Watanabe and Yuki Moriya and Shin Kawano and Tadashi Yamamoto and Masaki Matsumoto and Tomoyo Takami and Daiki Kobayashi and Norie Araki and Akiyasu C. Yoshizawa and Tsuyoshi Tabata and Naoyuki Sugiyama and Susumu Goto and Yasushi Ishihama},
  title = {{jPOSTrepo}: an international standard data repository for proteomes},
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  number = {D1},
  pages = {D1107-D1111},
  year = {2017},
  doi = {10.1093/nar/gkw1080},
}

@article{taylor2007miape,
  author = {Taylor, Chris and Paton, Norman and Lilley, Kathryn and Binz, Pierre-Alain and Julian, Randall K and Jones, Andrew R and Zhu, Weimin and Apweiler, Rolf and Aebersold, Ruedi and Deutsch, Eric W},
  title = {The minimum information about a proteomics experiment ({MIAPE})},
  journal = {Nature Biotechnology},
  volume = {25},
  number = {8},
  pages = {887--893},
  year = {2007},
  doi = {10.1038/nbt1329},
  url = {https://doi.org/10.1038/nbt1329},
}

@online{metabolomexchange,
  title = {MetabolomeXchange},
  url = {http://www.metabolomexchange.org/site/#/},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@article{metabolights,
  title = {MetaboLights: a resource evolving in response to the needs of its scientific community},
  author = {Haug, Kenneth and Cochrane, Keeva and Nainala, Venkata Chandrasekhar and Williams, Mark and Chang, Jiakang and Jayaseelan, Kalai Vanii and O’Donovan, Claire},
  journal = {Nucleic Acids Research},
  year = {2020},
  volume = {},
  pages = {},
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  pmid = {31691833},
}

@article{ara2015metabolonote,
  title = {Metabolonote: a wiki-based database for managing hierarchical metadata of metabolome analyses},
  author = {Ara, Takeshi and Enomoto, Mizuki and Arita, Masanori and Ikeda, Chisato and Kera, Kenichiro and Yamada, Masanobu and Nishioka, Toshio and Ikeda, Takamasa and Nihei, Yohei and Shibata, Daisuke and Kanaya, Shigehiko and Sakurai, Nozomu},
  journal = {Front. Bioeng. Biotechnol.},
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  year = {2015},
  doi = {10.3389/fbioe.2015.00038},
}

@article{sud2016metabolomics,
  title = {Metabolomics Workbench: An international repository for metabolomics data and metadata, metabolite standards, protocols, tutorials and training, and analysis tools},
  author = {Sud, Manish and Fahy, Eoin and Cotter, Dawn and Azam, Kenan and Vadivelu, Ilango and Burant, Charles and Edison, Arthur and Fiehn, Oliver and Higashi, Richard and Nair, Karin S and Sumner, Susan and Subramaniam, Shankar},
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  pmid = {26467476},
  pmcid = {PMC4702780},
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@article{fiehn2007metabolomics,
  title = {The metabolomics standards initiative (MSI)},
  author = {Fiehn, Oliver and Robertson, Donald and Griffin, Julian and van der Werf, Mari{\"e}t J and Nikolau, Basil and Morrison, Neil and Sumner, Lloyd W and Goodacre, Royston and Hardy, Nigel W and Taylor, Chris and others},
  journal = {Metabolomics},
  year = {2007},
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@online{ena_common_run_errors,
  title = {Common Run Submission Errors},
  url = {https://ena-docs.readthedocs.io/en/latest/faq/runs.html},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@online{geo_submission_guide,
  title = {Submitting high-throughput sequence data to GEO},
  url = {https://www.ncbi.nlm.nih.gov/geo/info/seq.html},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@online{sra_quick_start_guide,
  title = {SRA Submission Quick Start Guide},
  url = {https://anonsvn.ncbi.nlm.nih.gov/repos/v1/trunk/sra/doc/SRA_1-1/SRA_Quick_Start_Guide.pdf},
  urldate = {Accessed on 2023-08-10},
  year = {},
}

@online{sra_tools,
  title = {SRA-tools},
  url = {https://github.com/ncbi/sra-tools/tree/master},
  urldate = {Accessed on 2023-08-10},
  year = {},
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@article{mitchell2020mgnify,
  title = {MGnify: the microbiome analysis resource in 2020},
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  journal = {Nucleic Acids Research},
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}

@article{meyer2008metagenomics,
  title = {The Metagenomics RAST server — A public resource for the automatic phylogenetic and functional analysis of metagenomes},
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  url = {https://help.mg-rast.org/user_manual.html#data-hygiene},
}

@article{bassi2007biopython,
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