


@article{Ashburner2000,
	Abstract = {Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.},
	Author = {Ashburner, Michael and Ball, Catherine A. and Blake, Judith A. and Botstein, David and Butler, Heather and Cherry, J. Michael and Davis, Allan P. and Dolinski, Kara and Dwight, Selina S. and Eppig, Janan T. and Harris, Midori A. and Hill, David P. and Issel-Tarver, Laurie and Kasarskis, Andrew and Lewis, Suzanna and Matese, John C. and Richardson, Joel E. and Ringwald, Martin and Rubin, Gerald M. and Sherlock, Gavin},
	Da = {2000/05/01},
	Date-Added = {2024-03-28 18:29:13 +0000},
	Date-Modified = {2024-03-28 18:29:13 +0000},
	Doi = {10.1038/75556},
	Id = {Ashburner2000},
	Isbn = {1546-1718},
	Journal = {Nature Genetics},
	Number = {1},
	Pages = {25--29},
	Title = {Gene Ontology: tool for the unification of biology},
	Ty = {JOUR},
	Url = {https://doi.org/10.1038/75556},
	Volume = {25},
	Year = {2000},
	Bdsk-Url-1 = {https://doi.org/10.1038/75556},
	Bdsk-Url-2 = {http://dx.doi.org/10.1038/75556}
}

@article{GO2023,
    author = {The Gene Ontology Consortium  and Aleksander, Suzi A and Balhoff, James and Carbon, Seth and Cherry, J Michael and Drabkin, Harold J and Ebert, Dustin and Feuermann, Marc and Gaudet, Pascale and Harris, Nomi L and Hill, David P and Lee, Raymond and Mi, Huaiyu and Moxon, Sierra and Mungall, Christopher J and Muruganugan, Anushya and Mushayahama, Tremayne and Sternberg, Paul W and Thomas, Paul D and Van Auken, Kimberly and Ramsey, Jolene and Siegele, Deborah A and Chisholm, Rex L and Fey, Petra and Aspromonte, Maria Cristina and Nugnes, Maria Victoria and Quaglia, Federica and Tosatto, Silvio and Giglio, Michelle and Nadendla, Suvarna and Antonazzo, Giulia and Attrill, Helen and dos Santos, Gil and Marygold, Steven and Strelets, Victor and Tabone, Christopher J and Thurmond, Jim and Zhou, Pinglei and Ahmed, Saadullah H and Asanitthong, Praoparn and Luna Buitrago, Diana and Erdol, Meltem N and Gage, Matthew C and Ali Kadhum, Mohamed and Li, Kan Yan Chloe and Long, Miao and Michalak, Aleksandra and Pesala, Angeline and Pritazahra, Armalya and Saverimuttu, Shirin C C and Su, Renzhi and Thurlow, Kate E and Lovering, Ruth C and Logie, Colin and Oliferenko, Snezhana and Blake, Judith and Christie, Karen and Corbani, Lori and Dolan, Mary E and Drabkin, Harold J and Hill, David P and Ni, Li and Sitnikov, Dmitry and Smith, Cynthia and Cuzick, Alayne and Seager, James and Cooper, Laurel and Elser, Justin and Jaiswal, Pankaj and Gupta, Parul and Jaiswal, Pankaj and Naithani, Sushma and Lera-Ramirez, Manuel and Rutherford, Kim and Wood, Valerie and De Pons, Jeffrey L and Dwinell, Melinda R and Hayman, G Thomas and Kaldunski, Mary L and Kwitek, Anne E and Laulederkind, Stanley J F and Tutaj, Marek A and Vedi, Mahima and Wang, Shur-Jen and D’Eustachio, Peter and Aimo, Lucila and Axelsen, Kristian and Bridge, Alan and Hyka-Nouspikel, Nevila and Morgat, Anne and Aleksander, Suzi A and Cherry, J Michael and Engel, Stacia R and Karra, Kalpana and Miyasato, Stuart R and Nash, Robert S and Skrzypek, Marek S and Weng, Shuai and Wong, Edith D and Bakker, Erika and Berardini, Tanya Z and Reiser, Leonore and Auchincloss, Andrea and Axelsen, Kristian and Argoud-Puy, Ghislaine and Blatter, Marie-Claude and Boutet, Emmanuel and Breuza, Lionel and Bridge, Alan and Casals-Casas, Cristina and Coudert, Elisabeth and Estreicher, Anne and Livia Famiglietti, Maria and Feuermann, Marc and Gos, Arnaud and Gruaz-Gumowski, Nadine and Hulo, Chantal and Hyka-Nouspikel, Nevila and Jungo, Florence and Le Mercier, Philippe and Lieberherr, Damien and Masson, Patrick and Morgat, Anne and Pedruzzi, Ivo and Pourcel, Lucille and Poux, Sylvain and Rivoire, Catherine and Sundaram, Shyamala and Bateman, Alex and Bowler-Barnett, Emily and Bye-A-Jee, Hema and Denny, Paul and Ignatchenko, Alexandr and Ishtiaq, Rizwan and Lock, Antonia and Lussi, Yvonne and Magrane, Michele and Martin, Maria J and Orchard, Sandra and Raposo, Pedro and Speretta, Elena and Tyagi, Nidhi and Warner, Kate and Zaru, Rossana and Diehl, Alexander D and Lee, Raymond and Chan, Juancarlos and Diamantakis, Stavros and Raciti, Daniela and Zarowiecki, Magdalena and Fisher, Malcolm and James-Zorn, Christina and Ponferrada, Virgilio and Zorn, Aaron and Ramachandran, Sridhar and Ruzicka, Leyla and Westerfield, Monte},
    title = "{The Gene Ontology knowledgebase in 2023}",
    journal = {Genetics},
    volume = {224},
    number = {1},
    pages = {iyad031},
    year = {2023},
    month = {03},
    abstract = "{The Gene Ontology (GO) knowledgebase (http://geneontology.org) is a comprehensive resource concerning the functions of genes and gene products (proteins and noncoding RNAs). GO annotations cover genes from organisms across the tree of life as well as viruses, though most gene function knowledge currently derives from experiments carried out in a relatively small number of model organisms. Here, we provide an updated overview of the GO knowledgebase, as well as the efforts of the broad, international consortium of scientists that develops, maintains, and updates the GO knowledgebase. The GO knowledgebase consists of three components: (1) the GO—a computational knowledge structure describing the functional characteristics of genes; (2) GO annotations—evidence-supported statements asserting that a specific gene product has a particular functional characteristic; and (3) GO Causal Activity Models (GO-CAMs)—mechanistic models of molecular “pathways” (GO biological processes) created by linking multiple GO annotations using defined relations. Each of these components is continually expanded, revised, and updated in response to newly published discoveries and receives extensive QA checks, reviews, and user feedback. For each of these components, we provide a description of the current contents, recent developments to keep the knowledgebase up to date with new discoveries, and guidance on how users can best make use of the data that we provide. We conclude with future directions for the project.}",
    issn = {1943-2631},
    doi = {10.1093/genetics/iyad031},
    url = {https://doi.org/10.1093/genetics/iyad031},
    eprint = {https://academic.oup.com/genetics/article-pdf/224/1/iyad031/51074934/iyad031.pdf},
}

@article{AmiGO,
    author = {Carbon, Seth and Ireland, Amelia and Mungall, Christopher J. and Shu, ShengQiang and Marshall, Brad and Lewis, Suzanna and the AmiGO Hub and the Web Presence Working Group},
    title = "{AmiGO: online access to ontology and annotation data}",
    journal = {Bioinformatics},
    volume = {25},
    number = {2},
    pages = {288-289},
    year = {2008},
    month = {11},
    abstract = "{AmiGO is a web application that allows users to query, browse and visualize ontologies and related gene product annotation (association) data. AmiGO can be used online at the Gene Ontology (GO) website to access the data provided by the GO Consortium1; it can also be downloaded and installed to browse local ontologies and annotations.2 AmiGO is free open source software developed and maintained by the GO Consortium.Availability:  http://amigo.geneontology.orgDownload:  http://sourceforge.net/projects/geneontology/Contact:  sjcarbon@berkeleybop.org}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btn615},
    url = {https://doi.org/10.1093/bioinformatics/btn615},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/25/2/288/48982949/bioinformatics\_25\_2\_288.pdf},
}

@article{goatools,
  title={GOATOOLS: A Python library for Gene Ontology analyses},
  author={Klopfenstein, DV and Zhang, Liangsheng and Pedersen, Brent S and Ram{\'\i}rez, Fidel and Warwick Vesztrocy, Alex and Naldi, Aur{\'e}lien and Mungall, Christopher J and Yunes, Jeffrey M and Botvinnik, Olga and Weigel, Mark and others},
  journal={Scientific reports},
  volume={8},
  number={1},
  pages={1--17},
  year={2018},
  doi={10.1038/s41598-018-28948-z},
  publisher={Nature Publishing Group}
}

@misc{topGO,
  author = {Alexa, A and Rahnenfuhrer, J},
  title = {topGO: Enrichment Analysis for Gene Ontology},
  year = {2023},
  publisher = {Bioconductor},
  journal = {Bioconductor},
  doi = {10.18129/B9.bioc.topGO},
  url = {https://bioconductor.org/packages/topGO}
}

@article{QuickGO,
    author = {Binns, David and Dimmer, Emily and Huntley, Rachael and Barrell, Daniel and O'Donovan, Claire and Apweiler, Rolf},
    title = "{QuickGO: a web-based tool for Gene Ontology searching}",
    journal = {Bioinformatics},
    volume = {25},
    number = {22},
    pages = {3045-3046},
    year = {2009},
    month = {09},
    abstract = "{Summary: QuickGO is a web-based tool that allows easy browsing of the Gene Ontology (GO) and all associated electronic and manual GO annotations provided by the GO Consortium annotation groups QuickGO has been a popular GO browser for many years, but after a recent redevelopment it is now able to offer a greater range of facilities including bulk downloads of GO annotation data which can be extensively filtered by a range of different parameters and GO slim set generation.Availability and Implementation: QuickGO has implemented in JavaScript, Ajax and HTML, with all major browsers supported. It can be queried online at http://www.ebi.ac.uk/QuickGO. The software for QuickGO is freely available under the Apache 2 licence and can be downloaded from http://www.ebi.ac.uk/QuickGO/installation.htmlContact:  goa@ebi.ac.uk; dbinns@ebi.ac.uk}",
    issn = {1367-4803},
    doi = {10.1093/bioinformatics/btp536},
    url = {https://doi.org/10.1093/bioinformatics/btp536},
    eprint = {https://academic.oup.com/bioinformatics/article-pdf/25/22/3045/48997998/bioinformatics\_25\_22\_3045.pdf},
}

