BibTeX records: Christian J. Stoeckert Jr.

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@article{DBLP:journals/nar/AmosABBBBBBBBBC22,
  author       = {Beatrice Amos and
                  Cristina Aurrecoechea and
                  Matthieu Barba and
                  Ana Barreto and
                  Evelina Y. Basenko and
                  Wojciech Bazant and
                  Robert Belnap and
                  Ann S. Blevins and
                  Ulrike B{\"{o}}hme and
                  John Brestelli and
                  Brian P. Brunk and
                  Mark J. Caddick and
                  Danielle Callan and
                  Lahcen I. Campbell and
                  Mikkel B. Christensen and
                  George K. Christophides and
                  Kathryn Crouch and
                  Kristina Davis and
                  Jeremy D. DeBarry and
                  Ryan Doherty and
                  Yikun Duan and
                  Michael Dunn and
                  Dave Falke and
                  Steve Fisher and
                  Paul Flicek and
                  Brett Fox and
                  Bindu Gajria and
                  Gloria I. Giraldo{-}Calder{\'{o}}n and
                  Omar S. Harb and
                  Elizabeth Harper and
                  Christiane Hertz{-}Fowler and
                  Mark J. Hickman and
                  Connor Howington and
                  Sufen Hu and
                  Jay C. Humphrey and
                  John Iodice and
                  Andrew R. Jones and
                  John Judkins and
                  Sarah A. Kelly and
                  Jessica C. Kissinger and
                  Dae Kun Kwon and
                  Kristopher Lamoureux and
                  Daniel Lawson and
                  Wei Li and
                  Kallie Lies and
                  Disha Lodha and
                  Jamie Long and
                  Robert M. MacCallum and
                  Gareth Maslen and
                  Mary Ann McDowell and
                  Jaroslaw Nabrzyski and
                  David S. Roos and
                  Samuel S. C. Rund and
                  Stephanie wever Schulman and
                  Achchuthan Shanmugasundram and
                  Vasily Sitnik and
                  Drew Spruill and
                  David Starns and
                  Christian J. Stoeckert Jr. and
                  Sheena Shah Tomko and
                  Haiming Wang and
                  Susanne Warrenfeltz and
                  Robert Wieck and
                  Paul A. Wilkinson and
                  Lin Xu and
                  Jie Zheng},
  title        = {VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics
                  resource center},
  journal      = {Nucleic Acids Res.},
  volume       = {50},
  number       = {{D1}},
  pages        = {898--911},
  year         = {2022},
  url          = {https://doi.org/10.1093/nar/gkab929},
  doi          = {10.1093/NAR/GKAB929},
  timestamp    = {Mon, 05 Feb 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nar/AmosABBBBBBBBBC22.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/JacksonMOVBBCCD21,
  author       = {Rebecca C. Jackson and
                  Nicolas Matentzoglu and
                  James A. Overton and
                  Randi Vita and
                  James P. Balhoff and
                  Pier Luigi Buttigieg and
                  Seth Carbon and
                  M{\'{e}}lanie Courtot and
                  Alexander D. Diehl and
                  Damion M. Dooley and
                  William D. Duncan and
                  Nomi L. Harris and
                  Melissa A. Haendel and
                  Suzanna E. Lewis and
                  Darren A. Natale and
                  David Osumi{-}Sutherland and
                  Alan Ruttenberg and
                  Lynn M. Schriml and
                  Barry Smith and
                  Christian J. Stoeckert Jr. and
                  Nicole A. Vasilevsky and
                  Ramona L. Walls and
                  Jie Zheng and
                  Christopher J. Mungall and
                  Bjoern Peters},
  title        = {{OBO} Foundry in 2021: operationalizing open data principles to evaluate
                  ontologies},
  journal      = {Database J. Biol. Databases Curation},
  volume       = {2021},
  year         = {2021},
  url          = {https://doi.org/10.1093/database/baab069},
  doi          = {10.1093/DATABASE/BAAB069},
  timestamp    = {Tue, 16 Aug 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/biodb/JacksonMOVBBCCD21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/VitaZJDOMBSHKBL21,
  author       = {Randi Vita and
                  Jie Zheng and
                  Rebecca C. Jackson and
                  Damion M. Dooley and
                  James A. Overton and
                  Mark A. Miller and
                  Daniel C. Berrios and
                  Richard H. Scheuermann and
                  Yongqun He and
                  Hande K{\"{u}}{\c{c}}{\"{u}}k{-}McGinty and
                  Mathias Brochhausen and
                  Aisyah Yu Lin and
                  Sagar B. Jain and
                  Marcus C. Chibucos and
                  John Judkins and
                  Michelle G. Giglio and
                  Irene Y. Feng and
                  Gully Burns and
                  Matthew H. Brush and
                  Bjoern Peters and
                  Christian J. Stoeckert Jr.},
  title        = {Standardization of assay representation in the Ontology for Biomedical
                  Investigations},
  journal      = {Database J. Biol. Databases Curation},
  volume       = {2021},
  year         = {2021},
  url          = {https://doi.org/10.1093/database/baab040},
  doi          = {10.1093/DATABASE/BAAB040},
  timestamp    = {Tue, 16 Aug 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/biodb/VitaZJDOMBSHKBL21.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/FreedmanMWS20,
  author       = {Hayden Freedman and
                  Mark A. Miller and
                  Heather Williams and
                  Christian J. Stoeckert Jr.},
  editor       = {Janna Hastings and
                  Frank Loebe},
  title        = {Scaling and Querying a Semantically Rich, Electronic Healthcare Graph},
  booktitle    = {Proceedings of the 11th International Conference on Biomedical Ontologies
                  {(ICBO)} joint with the 10th Workshop on Ontologies and Data in Life
                  Sciences {(ODLS)} and part of the Bolzano Summer of Knowledge (BoSK
                  2020), Virtual conference hosted in Bolzano, Italy, September 17,
                  2020},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {2807},
  pages        = {1--11},
  publisher    = {CEUR-WS.org},
  year         = {2020},
  url          = {https://ceur-ws.org/Vol-2807/paperC.pdf},
  timestamp    = {Fri, 10 Mar 2023 16:22:24 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/FreedmanMWS20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/MillerFS20,
  author       = {Mark A. Miller and
                  Hayden Freedman and
                  Christian J. Stoeckert Jr.},
  editor       = {Janna Hastings and
                  Frank Loebe},
  title        = {A Robust, Self-Training Classifier for Medication Strings, with Quantitative
                  and Semantic Confidence Metrics},
  booktitle    = {Proceedings of the 11th International Conference on Biomedical Ontologies
                  {(ICBO)} joint with the 10th Workshop on Ontologies and Data in Life
                  Sciences {(ODLS)} and part of the Bolzano Summer of Knowledge (BoSK
                  2020), Virtual conference hosted in Bolzano, Italy, September 17,
                  2020},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {2807},
  pages        = {1--12},
  publisher    = {CEUR-WS.org},
  year         = {2020},
  url          = {https://ceur-ws.org/Vol-2807/paperI.pdf},
  timestamp    = {Fri, 10 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/MillerFS20.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/0001JS19,
  author       = {Jie Zheng and
                  John Judkins and
                  Christian J. Stoeckert Jr.},
  editor       = {Alexander D. Diehl and
                  William D. Duncan and
                  Gloria Sanso},
  title        = {OWLmaker: An Application for Generating {OWL} Files from Tabular Text},
  booktitle    = {Proceedings of the 10th International Conference on Biomedical Ontology
                  {(ICBO} 2019), Buffalo, New York, USA, July 30 - August 2, 2019},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {2931},
  pages        = {1--3},
  publisher    = {CEUR-WS.org},
  year         = {2019},
  url          = {https://ceur-ws.org/Vol-2931/ICBO\_2019\_paper\_54.pdf},
  timestamp    = {Fri, 10 Mar 2023 16:22:23 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/0001JS19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/BostES0SB19,
  author       = {Sarah Bost and
                  Niina Eklund and
                  Kaisa Silander and
                  Jie Zheng and
                  Christian J. Stoeckert Jr. and
                  Mathias Brochhausen},
  editor       = {Alexander D. Diehl and
                  William D. Duncan and
                  Gloria Sanso},
  title        = {Mapping Data Annotated with the Minimum Information About BIobank
                  data Sharing {(MIABIS)} 2.0 to the Ontology for Biobanking {(OBIB)}},
  booktitle    = {Proceedings of the 10th International Conference on Biomedical Ontology
                  {(ICBO} 2019), Buffalo, New York, USA, July 30 - August 2, 2019},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {2931},
  pages        = {1--2},
  publisher    = {CEUR-WS.org},
  year         = {2019},
  url          = {https://ceur-ws.org/Vol-2931/ICBO\_2019\_paper\_52.pdf},
  timestamp    = {Fri, 10 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/BostES0SB19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/HeOSDOSRS000SYY19,
  author       = {Yongqun He and
                  Edison Ong and
                  Jennifer Schaub and
                  Frederick Dowd and
                  John F. O'Toole and
                  Anastasios Siapos and
                  Christian G. Reich and
                  Sarah Seager and
                  Ling Wang and
                  Hong Yu and
                  Jie Zheng and
                  Christian J. Stoeckert Jr. and
                  Xiaolin Yang and
                  Sheng Yang and
                  Becky Steck and
                  Christopher Park and
                  Laura Barisoni and
                  Matthias Kretzler and
                  Jonathan Himmelfarb and
                  Ravi Iyengar and
                  Sean D. Mooney},
  editor       = {Alexander D. Diehl and
                  William D. Duncan and
                  Gloria Sanso},
  title        = {{OPMI:} the Ontology of Precision Medicine and Investigation and its
                  Support for Clinical Data and Metadata Representation and Analysis},
  booktitle    = {Proceedings of the 10th International Conference on Biomedical Ontology
                  {(ICBO} 2019), Buffalo, New York, USA, July 30 - August 2, 2019},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {2931},
  pages        = {1--10},
  publisher    = {CEUR-WS.org},
  year         = {2019},
  url          = {https://ceur-ws.org/Vol-2931/ICBO\_2019\_paper\_34.pdf},
  timestamp    = {Fri, 10 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/HeOSDOSRS000SYY19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/MillerS19,
  author       = {Mark A. Miller and
                  Christian J. Stoeckert Jr.},
  editor       = {Alexander D. Diehl and
                  William D. Duncan and
                  Gloria Sanso},
  title        = {A Collaborative, Realism-Based, Electronic Healthcare Graph: Public
                  Data, Common Data Models, and Practical Instantiation},
  booktitle    = {Proceedings of the 10th International Conference on Biomedical Ontology
                  {(ICBO} 2019), Buffalo, New York, USA, July 30 - August 2, 2019},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {2931},
  pages        = {1--10},
  publisher    = {CEUR-WS.org},
  year         = {2019},
  url          = {https://ceur-ws.org/Vol-2931/ICBO\_2019\_paper\_28.pdf},
  timestamp    = {Fri, 10 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/MillerS19.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/OliveiraBCZIFAK18,
  author       = {Francislon S. Oliveira and
                  John Brestelli and
                  Shon Cade and
                  Jie Zheng and
                  John Iodice and
                  Steve Fischer and
                  Cristina Aurrecoechea and
                  Jessica C. Kissinger and
                  Brian P. Brunk and
                  Christian J. Stoeckert Jr. and
                  Gabriel R. Fernandes and
                  David S. Roos and
                  Daniel P. Beiting},
  title        = {MicrobiomeDB: a systems biology platform for integrating, mining and
                  analyzing microbiome experiments},
  journal      = {Nucleic Acids Res.},
  volume       = {46},
  number       = {Database-Issue},
  pages        = {D684--D691},
  year         = {2018},
  url          = {https://doi.org/10.1093/nar/gkx1027},
  doi          = {10.1093/NAR/GKX1027},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/OliveiraBCZIFAK18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/MasciMREO0S018,
  author       = {Anna Maria Masci and
                  Shannon McCall and
                  Alessandro Racioppi and
                  Helena Judge Ellis and
                  Jihad S. Obeid and
                  Barry Smith and
                  Christian J. Stoeckert Jr. and
                  Jie Zheng},
  editor       = {Pankaj Jaiswal and
                  Laurel Cooper and
                  Melissa A. Haendel and
                  Christopher J. Mungall},
  title        = {Standardization of the Histopathology Cancer Report: An Ontological
                  Approach},
  booktitle    = {Proceedings of the 9th International Conference on Biological Ontology
                  {(ICBO} 2018), Corvallis, Oregon, USA, August 7-10, 2018},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {2285},
  publisher    = {CEUR-WS.org},
  year         = {2018},
  url          = {https://ceur-ws.org/Vol-2285/ICBO\_2018\_paper\_10.pdf},
  timestamp    = {Fri, 10 Mar 2023 16:22:24 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/MasciMREO0S018.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/StoeckertBFMW18,
  author       = {Christian J. Stoeckert Jr. and
                  David L. Birtwell and
                  Hayden Freedman and
                  Mark A. Miller and
                  Heather Williams},
  editor       = {Pankaj Jaiswal and
                  Laurel Cooper and
                  Melissa A. Haendel and
                  Christopher J. Mungall},
  title        = {Transforming and Unifying Research with Biomedical Ontologies: The
                  Penn {TURBO} Project},
  booktitle    = {Proceedings of the 9th International Conference on Biological Ontology
                  {(ICBO} 2018), Corvallis, Oregon, USA, August 7-10, 2018},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {2285},
  publisher    = {CEUR-WS.org},
  year         = {2018},
  url          = {https://ceur-ws.org/Vol-2285/ICBO\_2018\_paper\_12.pdf},
  timestamp    = {Fri, 10 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/StoeckertBFMW18.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AurrecoecheaBBB17,
  author       = {Cristina Aurrecoechea and
                  Ana Barreto and
                  Evelina Y. Basenko and
                  John Brestelli and
                  Brian P. Brunk and
                  Shon Cade and
                  Kathryn Crouch and
                  Ryan Doherty and
                  Dave Falke and
                  Steve Fischer and
                  Bindu Gajria and
                  Omar S. Harb and
                  Mark Heiges and
                  Christiane Hertz{-}Fowler and
                  Sufen Hu and
                  John Iodice and
                  Jessica C. Kissinger and
                  Cris Lawrence and
                  Wei Li and
                  Deborah F. Pinney and
                  Jane A. Pulman and
                  David S. Roos and
                  Achchuthan Shanmugasundram and
                  Fatima Silva{-}Franco and
                  Sascha Steinbiss and
                  Christian J. Stoeckert Jr. and
                  Drew Spruill and
                  Haiming Wang and
                  Susanne Warrenfeltz and
                  Jie Zheng},
  title        = {EuPathDB: the eukaryotic pathogen genomics database resource},
  journal      = {Nucleic Acids Res.},
  volume       = {45},
  number       = {Database-Issue},
  pages        = {D581--D591},
  year         = {2017},
  url          = {https://doi.org/10.1093/nar/gkw1105},
  doi          = {10.1093/NAR/GKW1105},
  timestamp    = {Mon, 05 Feb 2024 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nar/AurrecoecheaBBB17.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/BrochhausenZBWM16,
  author       = {Mathias Brochhausen and
                  Jie Zheng and
                  David L. Birtwell and
                  Heather Williams and
                  Anna Maria Masci and
                  Helena Judge Ellis and
                  Christian J. Stoeckert Jr.},
  title        = {OBIB-a novel ontology for biobanking},
  journal      = {J. Biomed. Semant.},
  volume       = {7},
  pages        = {23},
  year         = {2016},
  url          = {https://doi.org/10.1186/s13326-016-0068-y},
  doi          = {10.1186/S13326-016-0068-Y},
  timestamp    = {Thu, 13 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/biomedsem/BrochhausenZBWM16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/ZhengCBRSJAGDSC16,
  author       = {Jie Zheng and
                  Jashon Cade and
                  Brian P. Brunk and
                  David S. Roos and
                  Christian J. Stoeckert Jr. and
                  San James and
                  Emmanuel Arinaitwe and
                  Bryan Greenhouse and
                  Grant Dorsey and
                  Steven Sullivan and
                  Jane M. Carlton and
                  Gabriel Carrasco{-}Escobar and
                  Dionicia Gamboa and
                  Paula Maguina{-}Mercedes and
                  Joseph Vinetz},
  editor       = {Pankaj Jaiswal and
                  Robert Hoehndorf and
                  Cecilia N. Arighi and
                  Austin Meier},
  title        = {Malaria Study Data Integration and Information Retrieval Based on
                  {OBO} Foundry Ontologies},
  booktitle    = {Proceedings of the Joint International Conference on Biological Ontology
                  and BioCreative, Corvallis, Oregon, United States, August 1-4, 2016},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {1747},
  publisher    = {CEUR-WS.org},
  year         = {2016},
  url          = {https://ceur-ws.org/Vol-1747/IT503\_ICBO2016.pdf},
  timestamp    = {Fri, 10 Mar 2023 16:22:23 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/ZhengCBRSJAGDSC16.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhengXSH14,
  author       = {Jie Zheng and
                  Zuoshuang Xiang and
                  Christian J. Stoeckert Jr. and
                  Yongqun He},
  title        = {Ontodog: a web-based ontology community view generation tool},
  journal      = {Bioinform.},
  volume       = {30},
  number       = {9},
  pages        = {1340--1342},
  year         = {2014},
  url          = {https://doi.org/10.1093/bioinformatics/btu008},
  doi          = {10.1093/BIOINFORMATICS/BTU008},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ZhengXSH14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/SarntivijaiLXMDVSPMPLTSMNBHZSPMCSAH14,
  author       = {Sirarat Sarntivijai and
                  Yu Lin and
                  Zuoshuang Xiang and
                  Terrence F. Meehan and
                  Alexander D. Diehl and
                  Uma D. Vempati and
                  Stephan C. Sch{\"{u}}rer and
                  Chao Pang and
                  James Malone and
                  Helen E. Parkinson and
                  Yue Liu and
                  Terue Takatsuki and
                  Kaoru Saijo and
                  Hiroshi Masuya and
                  Yukio Nakamura and
                  Matthew H. Brush and
                  Melissa A. Haendel and
                  Jie Zheng and
                  Christian J. Stoeckert Jr. and
                  Bjoern Peters and
                  Christopher J. Mungall and
                  Thomas E. Carey and
                  David J. States and
                  Brian D. Athey and
                  Yongqun He},
  title        = {{CLO:} The cell line ontology},
  journal      = {J. Biomed. Semant.},
  volume       = {5},
  pages        = {37},
  year         = {2014},
  url          = {https://doi.org/10.1186/2041-1480-5-37},
  doi          = {10.1186/2041-1480-5-37},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/biomedsem/SarntivijaiLXMDVSPMPLTSMNBHZSPMCSAH14.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/Greenfest-AllenMPS13,
  author       = {Emily Greenfest{-}Allen and
                  Jeffrey Malik and
                  James Palis and
                  Christian J. Stoeckert Jr.},
  title        = {Stat and interferon genes identified by network analysis differentially
                  regulate primitive and definitive erythropoiesis},
  journal      = {{BMC} Syst. Biol.},
  volume       = {7},
  pages        = {38},
  year         = {2013},
  url          = {https://doi.org/10.1186/1752-0509-7-38},
  doi          = {10.1186/1752-0509-7-38},
  timestamp    = {Sun, 02 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bmcsb/Greenfest-AllenMPS13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AurrecoecheaBBBCDFGGGGHHHIKKLPPRSSWW13,
  author       = {Cristina Aurrecoechea and
                  Ana Barreto and
                  John Brestelli and
                  Brian P. Brunk and
                  Shon Cade and
                  Ryan Doherty and
                  Steve Fischer and
                  Bindu Gajria and
                  Xin Gao and
                  Alan R. Gingle and
                  Gregory R. Grant and
                  Omar S. Harb and
                  Mark Heiges and
                  Sufen Hu and
                  John Iodice and
                  Jessica C. Kissinger and
                  Eileen T. Kraemer and
                  Wei Li and
                  Deborah F. Pinney and
                  Brian Pitts and
                  David S. Roos and
                  Ganesh Srinivasamoorthy and
                  Christian J. Stoeckert Jr. and
                  Haiming Wang and
                  Susanne Warrenfeltz},
  title        = {EuPathDB: The Eukaryotic Pathogen database},
  journal      = {Nucleic Acids Res.},
  volume       = {41},
  number       = {Database-Issue},
  pages        = {684--691},
  year         = {2013},
  url          = {https://doi.org/10.1093/nar/gks1113},
  doi          = {10.1093/NAR/GKS1113},
  timestamp    = {Wed, 17 Feb 2021 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nar/AurrecoecheaBBBCDFGGGGHHHIKKLPPRSSWW13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/ZhengMS13,
  author       = {Jie Zheng and
                  Elisabetta Manduchi and
                  Christian J. Stoeckert Jr.},
  editor       = {Michel Dumontier and
                  Robert Hoehndorf and
                  Christopher J. O. Baker},
  title        = {Development of an Application Ontology for Beta Cell Genomics Based
                  On the Ontology for Biomedical Investigations},
  booktitle    = {Proceedings of the 4th International Conference on Biomedical Ontology,
                  {ICBO} 2013, Montreal, Canada, July 7-12, 2013},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {1060},
  pages        = {62--67},
  publisher    = {CEUR-WS.org},
  year         = {2013},
  url          = {https://ceur-ws.org/Vol-1060/icbo2013\_submission\_31.pdf},
  timestamp    = {Fri, 10 Mar 2023 16:22:24 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/ZhengMS13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/CourtotZSBR13,
  author       = {M{\'{e}}lanie Courtot and
                  Jie Zheng and
                  Christian J. Stoeckert Jr. and
                  Ryan Remy Brinkman and
                  Alan Ruttenberg},
  editor       = {Michel Dumontier and
                  Robert Hoehndorf and
                  Christopher J. O. Baker},
  title        = {Diagnostic criteria and clinical guidelines standardization to automate
                  case classification},
  booktitle    = {Proceedings of the 4th International Conference on Biomedical Ontology,
                  {ICBO} 2013, Montreal, Canada, July 7-12, 2013},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {1060},
  pages        = {101--104},
  publisher    = {CEUR-WS.org},
  year         = {2013},
  url          = {https://ceur-ws.org/Vol-1060/icbo2013\_submission\_57.pdf},
  timestamp    = {Fri, 10 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/CourtotZSBR13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/BrushZHSPDSH13,
  author       = {Matthew H. Brush and
                  Jie Zheng and
                  Yongqun He and
                  Sirarat Sarntivijai and
                  Bjoern Peters and
                  Alexander D. Diehl and
                  Christian J. Stoeckert Jr. and
                  Melissa A. Haendel},
  editor       = {Michel Dumontier and
                  Robert Hoehndorf and
                  Christopher J. O. Baker},
  title        = {Alignment of Cultured Cell Modeling Across {OBO} Foundry Ontologies:
                  Key Outcomes, Insights},
  booktitle    = {Proceedings of the 4th International Conference on Biomedical Ontology,
                  {ICBO} 2013, Montreal, Canada, July 7-12, 2013},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {1060},
  pages        = {120},
  publisher    = {CEUR-WS.org},
  year         = {2013},
  url          = {https://ceur-ws.org/Vol-1060/icbo2013\_submission\_68.pdf},
  timestamp    = {Fri, 10 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/BrushZHSPDSH13.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/ParikhZLSLTPSCBS12,
  author       = {Priti Parikh and
                  Jie Zheng and
                  Flora J. Logan{-}Klumpler and
                  Christian J. Stoeckert Jr. and
                  Christos Louis and
                  Pantelis Topalis and
                  Anna V. Protasio and
                  Amit P. Sheth and
                  Mark Carrington and
                  Matthew Berriman and
                  Satya Sanket Sahoo},
  title        = {The Ontology for Parasite Lifecycle {(OPL):} towards a consistent
                  vocabulary of lifecycle stages in parasitic organisms},
  journal      = {J. Biomed. Semant.},
  volume       = {3},
  pages        = {5},
  year         = {2012},
  url          = {https://doi.org/10.1186/2041-1480-3-5},
  doi          = {10.1186/2041-1480-3-5},
  timestamp    = {Thu, 14 Oct 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/biomedsem/ParikhZLSLTPSCBS12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/StajichHBBFHKLNPSR12,
  author       = {Jason E. Stajich and
                  Todd W. Harris and
                  Brian P. Brunk and
                  John Brestelli and
                  Steve Fischer and
                  Omar S. Harb and
                  Jessica C. Kissinger and
                  Wei Li and
                  Vishal Nayak and
                  Deborah F. Pinney and
                  Christian J. Stoeckert Jr. and
                  David S. Roos},
  title        = {FungiDB: an integrated functional genomics database for fungi},
  journal      = {Nucleic Acids Res.},
  volume       = {40},
  number       = {Database-Issue},
  pages        = {675--681},
  year         = {2012},
  url          = {https://doi.org/10.1093/nar/gkr918},
  doi          = {10.1093/NAR/GKR918},
  timestamp    = {Sun, 02 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/StajichHBBFHKLNPSR12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/fois/DhamanaskarCZKSM12,
  author       = {Alok Dhamanaskar and
                  Michael E. Cotterell and
                  Jie Zheng and
                  Jessica C. Kissinger and
                  Christian J. Stoeckert Jr. and
                  John A. Miller},
  editor       = {Maureen Donnelly and
                  Giancarlo Guizzardi},
  title        = {Suggestions for Galaxy Workflow Design Using Semantically Annotated
                  Services},
  booktitle    = {Formal Ontology in Information Systems - Proceedings of the Seventh
                  International Conference, {FOIS} 2012, Gray, Austria, July 24-27,
                  2012},
  series       = {Frontiers in Artificial Intelligence and Applications},
  volume       = {239},
  pages        = {29--42},
  publisher    = {{IOS} Press},
  year         = {2012},
  url          = {https://doi.org/10.3233/978-1-61499-084-0-29},
  doi          = {10.3233/978-1-61499-084-0-29},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/conf/fois/DhamanaskarCZKSM12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/ZhengXSH12,
  author       = {Jie Zheng and
                  Zuoshuang Xiang and
                  Christian J. Stoeckert Jr. and
                  Yongqun He},
  editor       = {Ronald Cornet and
                  Robert Stevens},
  title        = {Ontodog: {A} Web-based Ontology Community View Generator},
  booktitle    = {Proceedings of the 3rd International Conference on Biomedical Ontology
                  {(ICBO} 2012), {KR-MED} Series, Graz, Austria, July 21-25, 2012},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {897},
  publisher    = {CEUR-WS.org},
  year         = {2012},
  url          = {https://ceur-ws.org/Vol-897/poster\_13.pdf},
  timestamp    = {Fri, 10 Mar 2023 16:22:23 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/ZhengXSH12.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/FischerABGHKPTKRS11,
  author       = {Steve Fischer and
                  Cristina Aurrecoechea and
                  Brian P. Brunk and
                  Xin Gao and
                  Omar S. Harb and
                  Eileen T. Kraemer and
                  Cary Pennington and
                  Charles Treatman and
                  Jessica C. Kissinger and
                  David S. Roos and
                  Christian J. Stoeckert Jr.},
  title        = {The strategies {WDK:} a graphical search interface and web development
                  kit for functional genomics databases},
  journal      = {Database J. Biol. Databases Curation},
  volume       = {2011},
  year         = {2011},
  url          = {https://doi.org/10.1093/database/bar027},
  doi          = {10.1093/DATABASE/BAR027},
  timestamp    = {Thu, 13 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/biodb/FischerABGHKPTKRS11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/ZhengSMLS11,
  author       = {Jie Zheng and
                  Julia Stoyanovich and
                  Elisabetta Manduchi and
                  Junmin Liu and
                  Christian J. Stoeckert Jr.},
  title        = {AnnotCompute: annotation-based exploration and meta-analysis of genomics
                  experiments},
  journal      = {Database J. Biol. Databases Curation},
  volume       = {2011},
  year         = {2011},
  url          = {https://doi.org/10.1093/database/bar045},
  doi          = {10.1093/DATABASE/BAR045},
  timestamp    = {Thu, 13 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/biodb/ZhengSMLS11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrantFPLSBSHP11,
  author       = {Gregory R. Grant and
                  Michael H. Farkas and
                  Angel D. Pizarro and
                  Nicholas F. Lahens and
                  Jonathan Schug and
                  Brian P. Brunk and
                  Christian J. Stoeckert Jr. and
                  John B. Hogenesch and
                  Eric A. Pierce},
  title        = {Comparative analysis of RNA-Seq alignment algorithms and the RNA-Seq
                  unified mapper {(RUM)}},
  journal      = {Bioinform.},
  volume       = {27},
  number       = {18},
  pages        = {2518--2528},
  year         = {2011},
  url          = {https://doi.org/10.1093/bioinformatics/btr427},
  doi          = {10.1093/BIOINFORMATICS/BTR427},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/GrantFPLSBSHP11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AurrecoecheaBBBCFGGGGHHIKKLNPPPRSSTW11,
  author       = {Cristina Aurrecoechea and
                  Ana Barreto and
                  John Brestelli and
                  Brian P. Brunk and
                  Elisabet V. Caler and
                  Steve Fischer and
                  Bindu Gajria and
                  Xin Gao and
                  Alan R. Gingle and
                  Gregory R. Grant and
                  Omar S. Harb and
                  Mark Heiges and
                  John Iodice and
                  Jessica C. Kissinger and
                  Eileen T. Kraemer and
                  Wei Li and
                  Vishal Nayak and
                  Cary Pennington and
                  Deborah F. Pinney and
                  Brian Pitts and
                  David S. Roos and
                  Ganesh Srinivasamoorthy and
                  Christian J. Stoeckert Jr. and
                  Charles Treatman and
                  Haiming Wang},
  title        = {AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa
                  and Microsporidia species},
  journal      = {Nucleic Acids Res.},
  volume       = {39},
  number       = {Database-Issue},
  pages        = {612--619},
  year         = {2011},
  url          = {https://doi.org/10.1093/nar/gkq1006},
  doi          = {10.1093/NAR/GKQ1006},
  timestamp    = {Sun, 02 Oct 2022 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/AurrecoecheaBBBCFGGGGHHIKKLNPPPRSSTW11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/GuttulaDWMKZS11,
  author       = {Chaitanya Guttula and
                  Alok Dhamanaskar and
                  Rui Wang and
                  John A. Miller and
                  Jessica C. Kissinger and
                  Jie Zheng and
                  Christian J. Stoeckert Jr.},
  editor       = {Olivier Bodenreider and
                  Maryann E. Martone and
                  Alan Ruttenberg},
  title        = {Enriching the Ontology for Biomedical Investigations {(OBI)} to Improve
                  its Suitability for Web Service Annotations},
  booktitle    = {Proceedings of the 2nd International Conference on Biomedical Ontology,
                  Buffalo, NY, USA, July 26-30, 2011},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {833},
  publisher    = {CEUR-WS.org},
  year         = {2011},
  url          = {https://ceur-ws.org/Vol-833/paper37.pdf},
  timestamp    = {Fri, 10 Mar 2023 16:22:24 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/GuttulaDWMKZS11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/ZhengHS11,
  author       = {Jie Zheng and
                  Omar S. Harb and
                  Christian J. Stoeckert Jr.},
  editor       = {Olivier Bodenreider and
                  Maryann E. Martone and
                  Alan Ruttenberg},
  title        = {Ontology Driven Data Collection for EuPathDB},
  booktitle    = {Proceedings of the 2nd International Conference on Biomedical Ontology,
                  Buffalo, NY, USA, July 26-30, 2011},
  series       = {{CEUR} Workshop Proceedings},
  volume       = {833},
  publisher    = {CEUR-WS.org},
  year         = {2011},
  url          = {https://ceur-ws.org/Vol-833/paper13.pdf},
  timestamp    = {Fri, 10 Mar 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/icbo/ZhengHS11.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ShankarPBHLMSWBSSB10,
  author       = {Ravi Shankar and
                  Helen E. Parkinson and
                  Tony Burdett and
                  Emma Hastings and
                  Junmin Liu and
                  Michael Miller and
                  Rashmi Srinivasa and
                  Joseph White and
                  Alvis Brazma and
                  Gavin Sherlock and
                  Christian J. Stoeckert Jr. and
                  Catherine A. Ball},
  title        = {Annotare - a tool for annotating high-throughput biomedical investigations
                  and resulting data},
  journal      = {Bioinform.},
  volume       = {26},
  number       = {19},
  pages        = {2470--2471},
  year         = {2010},
  url          = {https://doi.org/10.1093/bioinformatics/btq462},
  doi          = {10.1093/BIOINFORMATICS/BTQ462},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ShankarPBHLMSWBSSB10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/BrinkmanCDFHLMPPRRSSSTZa10,
  author       = {Ryan Remy Brinkman and
                  M{\'{e}}lanie Courtot and
                  Dirk Derom and
                  Jennifer Fostel and
                  Yongqun He and
                  Phillip W. Lord and
                  James Malone and
                  Helen E. Parkinson and
                  Bj{\"{o}}rn Peters and
                  Philippe Rocca{-}Serra and
                  Alan Ruttenberg and
                  Susanna{-}Assunta Sansone and
                  Larisa N. Soldatova and
                  Christian J. Stoeckert Jr. and
                  Jessica A. Turner and
                  Jie Zheng and
                  et al.},
  title        = {Modeling biomedical experimental processes with {OBI}},
  journal      = {J. Biomed. Semant.},
  volume       = {1},
  number       = {{S-1}},
  pages        = {S7},
  year         = {2010},
  url          = {http://www.jbiomedsem.com/content/1/S1/S7},
  timestamp    = {Thu, 13 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/biomedsem/BrinkmanCDFHLMPPRRSSSTZa10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AurrecoecheaBBFGGGGHHIIKKLMNPPRRSSTTW10,
  author       = {Cristina Aurrecoechea and
                  John Brestelli and
                  Brian P. Brunk and
                  Steve Fischer and
                  Bindu Gajria and
                  Xin Gao and
                  Alan R. Gingle and
                  Gregory R. Grant and
                  Omar S. Harb and
                  Mark Heiges and
                  Frank Innamorato and
                  John Iodice and
                  Jessica C. Kissinger and
                  Eileen T. Kraemer and
                  Wei Li and
                  John A. Miller and
                  Vishal Nayak and
                  Cary Pennington and
                  Deborah F. Pinney and
                  David S. Roos and
                  Chris Ross and
                  Ganesh Srinivasamoorthy and
                  Christian J. Stoeckert Jr. and
                  Ryan Thibodeau and
                  Charles Treatman and
                  Haiming Wang},
  title        = {EuPathDB: a portal to eukaryotic pathogen databases},
  journal      = {Nucleic Acids Res.},
  volume       = {38},
  number       = {Database-Issue},
  pages        = {415--419},
  year         = {2010},
  url          = {https://doi.org/10.1093/nar/gkp941},
  doi          = {10.1093/NAR/GKP941},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/AurrecoecheaBBFGGGGHHIIKKLMNPPRRSSTTW10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AslettAB10,
  author       = {Martin Aslett and
                  Cristina Aurrecoechea and
                  Matthew Berriman and
                  John Brestelli and
                  Brian P. Brunk and
                  Mark Carrington and
                  Daniel P. Depledge and
                  Steve Fischer and
                  Bindu Gajria and
                  Xin Gao and
                  Malcolm J. Gardner and
                  Alan R. Gingle and
                  Gregory R. Grant and
                  Omar S. Harb and
                  Mark Heiges and
                  Christiane Hertz{-}Fowler and
                  Robin Houston and
                  Frank Innamorato and
                  John Iodice and
                  Jessica C. Kissinger and
                  Eileen T. Kraemer and
                  Wei Li and
                  Flora J. Logan and
                  John A. Miller and
                  Siddhartha Mitra and
                  Peter J. Myler and
                  Vishal Nayak and
                  Cary Pennington and
                  Isabelle Phan and
                  Deborah F. Pinney and
                  Gowthaman Ramasamy and
                  Matthew B. Rogers and
                  David S. Roos and
                  Chris Ross and
                  Dhileep Sivam and
                  Deborah F. Smith and
                  Ganesh Srinivasamoorthy and
                  Christian J. Stoeckert Jr. and
                  Sandhya Subramanian and
                  Ryan Thibodeau and
                  Adrian Tivey and
                  Charles Treatman and
                  Giles Velarde and
                  Haiming Wang},
  title        = {TriTrypDB: a functional genomic resource for the Trypanosomatidae},
  journal      = {Nucleic Acids Res.},
  volume       = {38},
  number       = {Database-Issue},
  pages        = {457--462},
  year         = {2010},
  url          = {https://doi.org/10.1093/nar/gkp851},
  doi          = {10.1093/NAR/GKP851},
  timestamp    = {Wed, 17 Feb 2021 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nar/AslettAB10.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AurrecoecheaBBCDFGGGGHHIIKKLMMNPPRRSSTW09,
  author       = {Cristina Aurrecoechea and
                  John Brestelli and
                  Brian P. Brunk and
                  Jane M. Carlton and
                  Jennifer Dommer and
                  Steve Fischer and
                  Bindu Gajria and
                  Xin Gao and
                  Alan R. Gingle and
                  Gregory R. Grant and
                  Omar S. Harb and
                  Mark Heiges and
                  Frank Innamorato and
                  John Iodice and
                  Jessica C. Kissinger and
                  Eileen T. Kraemer and
                  Wei Li and
                  John A. Miller and
                  Hilary G. Morrison and
                  Vishal Nayak and
                  Cary Pennington and
                  Deborah F. Pinney and
                  David S. Roos and
                  Chris Ross and
                  Christian J. Stoeckert Jr. and
                  Steven Sullivan and
                  Charles Treatman and
                  Haiming Wang},
  title        = {GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic
                  protist pathogens \emph{Giardia lamblia} and \emph{Trichomonas vaginalis}},
  journal      = {Nucleic Acids Res.},
  volume       = {37},
  number       = {Database-Issue},
  pages        = {526--530},
  year         = {2009},
  url          = {https://doi.org/10.1093/nar/gkn631},
  doi          = {10.1093/NAR/GKN631},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/AurrecoecheaBBCDFGGGGHHIIKKLMMNPPRRSSTW09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AurrecoecheaBBDFGGGGHHIIKKLMNPPRRSTW09,
  author       = {Cristina Aurrecoechea and
                  John Brestelli and
                  Brian P. Brunk and
                  Jennifer Dommer and
                  Steve Fischer and
                  Bindu Gajria and
                  Xin Gao and
                  Alan R. Gingle and
                  Gregory R. Grant and
                  Omar S. Harb and
                  Mark Heiges and
                  Frank Innamorato and
                  John Iodice and
                  Jessica C. Kissinger and
                  Eileen T. Kraemer and
                  Wei Li and
                  John A. Miller and
                  Vishal Nayak and
                  Cary Pennington and
                  Deborah F. Pinney and
                  David S. Roos and
                  Chris Ross and
                  Christian J. Stoeckert Jr. and
                  Charles Treatman and
                  Haiming Wang},
  title        = {PlasmoDB: a functional genomic database for malaria parasites},
  journal      = {Nucleic Acids Res.},
  volume       = {37},
  number       = {Database-Issue},
  pages        = {539--543},
  year         = {2009},
  url          = {https://doi.org/10.1093/nar/gkn814},
  doi          = {10.1093/NAR/GKN814},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/AurrecoecheaBBDFGGGGHHIIKKLMNPPRRSTW09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/BidautS09,
  author       = {Ghislain Bidaut and
                  Christian J. Stoeckert Jr.},
  editor       = {Russ B. Altman and
                  A. Keith Dunker and
                  Lawrence Hunter and
                  Tiffany Murray and
                  Teri E. Klein},
  title        = {Characterization of Unknown Adult Stem Cell Samples by Large Scale
                  Data Integration and Artificial Neural Networks},
  booktitle    = {Biocomputing 2009: Proceedings of the Pacific Symposium, Kohala Coast,
                  Hawaii, USA, 5-9 January 2009},
  pages        = {356--367},
  year         = {2009},
  url          = {http://psb.stanford.edu/psb-online/proceedings/psb09/bidaut.pdf},
  timestamp    = {Thu, 12 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/conf/psb/BidautS09.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/GajriaBBDFGHIKMPRSWB08,
  author       = {Bindu Gajria and
                  Amit Bahl and
                  John Brestelli and
                  Jennifer Dommer and
                  Steve Fischer and
                  Xin Gao and
                  Mark Heiges and
                  John Iodice and
                  Jessica C. Kissinger and
                  Aaron J. Mackey and
                  Deborah F. Pinney and
                  David S. Roos and
                  Christian J. Stoeckert Jr. and
                  Haiming Wang and
                  Brian P. Brunk},
  title        = {ToxoDB: an integrated \emph{Toxoplasma gondii} database resource},
  journal      = {Nucleic Acids Res.},
  volume       = {36},
  number       = {Database-Issue},
  pages        = {553--556},
  year         = {2008},
  url          = {https://doi.org/10.1093/nar/gkm981},
  doi          = {10.1093/NAR/GKM981},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/GajriaBBDFGHIKMPRSWB08.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AurrecoecheaHWWFRMKSRK07,
  author       = {Cristina Aurrecoechea and
                  Mark Heiges and
                  Haiming Wang and
                  Zhiming Wang and
                  Steve Fischer and
                  Philippa M. Rhodes and
                  John A. Miller and
                  Eileen T. Kraemer and
                  Christian J. Stoeckert Jr. and
                  David S. Roos and
                  Jessica C. Kissinger},
  title        = {ApiDB: integrated resources for the apicomplexan bioinformatics resource
                  center},
  journal      = {Nucleic Acids Res.},
  volume       = {35},
  number       = {Database-Issue},
  pages        = {427--430},
  year         = {2007},
  url          = {https://doi.org/10.1093/nar/gkl880},
  doi          = {10.1093/NAR/GKL880},
  timestamp    = {Sat, 30 Sep 2023 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/AurrecoecheaHWWFRMKSRK07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/MazzarelliBGLMPSWKS07,
  author       = {Joan M. Mazzarelli and
                  John Brestelli and
                  Regina K. Gorski and
                  Junmin Liu and
                  Elisabetta Manduchi and
                  Deborah F. Pinney and
                  Jonathan Schug and
                  Peter White and
                  Klaus H. Kaestner and
                  Christian J. Stoeckert Jr.},
  title        = {EPConDB: a web resource for gene expression related to pancreatic
                  development, beta-cell function and diabetes},
  journal      = {Nucleic Acids Res.},
  volume       = {35},
  number       = {Database-Issue},
  pages        = {751--755},
  year         = {2007},
  url          = {https://doi.org/10.1093/nar/gkl748},
  doi          = {10.1093/NAR/GKL748},
  timestamp    = {Mon, 26 Oct 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/nar/MazzarelliBGLMPSWKS07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dils/SchugMS07,
  author       = {Jonathan Schug and
                  Max Mintz and
                  Christian J. Stoeckert Jr.},
  editor       = {Sarah Cohen Boulakia and
                  Val Tannen},
  title        = {Data Integration and Pattern-Finding in Biological Sequence with TESS's
                  Annotation Grammar and Extraction Language (AnGEL)},
  booktitle    = {Data Integration in the Life Sciences, 4th International Workshop,
                  {DILS} 2007, Philadelphia, PA, USA, June 27-29, 2007, Proceedings},
  series       = {Lecture Notes in Computer Science},
  volume       = {4544},
  pages        = {188--203},
  publisher    = {Springer},
  year         = {2007},
  url          = {https://doi.org/10.1007/978-3-540-73255-6\_16},
  doi          = {10.1007/978-3-540-73255-6\_16},
  timestamp    = {Mon, 16 Sep 2019 15:28:31 +0200},
  biburl       = {https://dblp.org/rec/conf/dils/SchugMS07.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WhetzelPCFFFGHMRSTWJ06,
  author       = {Patricia L. Whetzel and
                  Helen E. Parkinson and
                  Helen C. Causton and
                  Liju Fan and
                  Jennifer Fostel and
                  Gilberto Fragoso and
                  Laurence Game and
                  Mervi Heiskanen and
                  Norman Morrison and
                  Philippe Rocca{-}Serra and
                  Susanna{-}Assunta Sansone and
                  Chris F. Taylor and
                  Joseph White and
                  Christian J. Stoeckert Jr.},
  title        = {The {MGED} Ontology: a resource for semantics-based description of
                  microarray experiments},
  journal      = {Bioinform.},
  volume       = {22},
  number       = {7},
  pages        = {866--873},
  year         = {2006},
  url          = {https://doi.org/10.1093/bioinformatics/btl005},
  doi          = {10.1093/BIOINFORMATICS/BTL005},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/WhetzelPCFFFGHMRSTWJ06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RaynerRSCFHILMMPQSSWWWPSBB06,
  author       = {Tim F. Rayner and
                  Philippe Rocca{-}Serra and
                  Paul T. Spellman and
                  Helen C. Causton and
                  Anna Farne and
                  Ele Holloway and
                  Rafael A. Irizarry and
                  Junmin Liu and
                  Donald Maier and
                  Michael Miller and
                  Kjell Petersen and
                  John Quackenbush and
                  Gavin Sherlock and
                  Christian J. Stoeckert Jr. and
                  Joseph White and
                  Patricia L. Whetzel and
                  Farrell Wymore and
                  Helen E. Parkinson and
                  Ugis Sarkans and
                  Catherine A. Ball and
                  Alvis Brazma},
  title        = {A simple spreadsheet-based, MIAME-supportive format for microarray
                  data: {MAGE-TAB}},
  journal      = {{BMC} Bioinform.},
  volume       = {7},
  pages        = {489},
  year         = {2006},
  url          = {https://doi.org/10.1186/1471-2105-7-489},
  doi          = {10.1186/1471-2105-7-489},
  timestamp    = {Sun, 15 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bmcbi/RaynerRSCFHILMMPQSSWWWPSBB06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ChenMSR06,
  author       = {Feng Chen and
                  Aaron J. Mackey and
                  Christian J. Stoeckert Jr. and
                  David S. Roos},
  title        = {OrthoMCL-DB: querying a comprehensive multi-species collection of
                  ortholog groups},
  journal      = {Nucleic Acids Res.},
  volume       = {34},
  number       = {Database-Issue},
  pages        = {363--368},
  year         = {2006},
  url          = {https://doi.org/10.1093/nar/gkj123},
  doi          = {10.1093/NAR/GKJ123},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/ChenMSR06.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GrantLS05,
  author       = {Gregory R. Grant and
                  Junmin Liu and
                  Christian J. Stoeckert Jr.},
  title        = {A practical false discovery rate approach to identifying patterns
                  of differential expression in microarray data},
  journal      = {Bioinform.},
  volume       = {21},
  number       = {11},
  pages        = {2684--2690},
  year         = {2005},
  url          = {https://doi.org/10.1093/bioinformatics/bti407},
  doi          = {10.1093/BIOINFORMATICS/BTI407},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/GrantLS05.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ManduchiGHLMPWS04,
  author       = {Elisabetta Manduchi and
                  Gregory R. Grant and
                  H. He and
                  Junmin Liu and
                  Matthew D. Mailman and
                  Angel D. Pizarro and
                  Patricia L. Whetzel and
                  Christian J. Stoeckert Jr.},
  title        = {{RAD} and the {RAD} Study-Annotator: an approach to collection, organization
                  and exchange of all relevant information for high-throughput gene
                  expression studies},
  journal      = {Bioinform.},
  volume       = {20},
  number       = {4},
  pages        = {452--459},
  year         = {2004},
  url          = {https://doi.org/10.1093/bioinformatics/btg428},
  doi          = {10.1093/BIOINFORMATICS/BTG428},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ManduchiGHLMPWS04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JonesHWPS04,
  author       = {Andrew R. Jones and
                  Ela Hunt and
                  Jonathan M. Wastling and
                  Angel D. Pizarro and
                  Christian J. Stoeckert Jr.},
  title        = {An object model and database for functional genomics},
  journal      = {Bioinform.},
  volume       = {20},
  number       = {10},
  pages        = {1583--1590},
  year         = {2004},
  url          = {https://doi.org/10.1093/bioinformatics/bth130},
  doi          = {10.1093/BIOINFORMATICS/BTH130},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/JonesHWPS04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LiCFPSSR04,
  author       = {Li Li and
                  Jonathan Crabtree and
                  Steve Fischer and
                  Deborah F. Pinney and
                  Christian J. Stoeckert Jr. and
                  L. David Sibley and
                  David S. Roos},
  title        = {ApiEST-DB: analyzing clustered {EST} data of the apicomplexan parasites},
  journal      = {Nucleic Acids Res.},
  volume       = {32},
  number       = {Database-Issue},
  pages        = {326--328},
  year         = {2004},
  url          = {https://doi.org/10.1093/nar/gkh112},
  doi          = {10.1093/NAR/GKH112},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/LiCFPSSR04.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BahlBCFGGGGKLLMMPRSSW03,
  author       = {Amit Bahl and
                  Brian P. Brunk and
                  Jonathan Crabtree and
                  Martin J. Fraunholz and
                  Bindu Gajria and
                  Gregory R. Grant and
                  Hagai Ginsburg and
                  Dinesh Gupta and
                  Jessica C. Kissinger and
                  Philip Labo and
                  Li Li and
                  Matthew D. Mailman and
                  Arthur J. Milgram and
                  David S. Pearson and
                  David S. Roos and
                  Jonathan Schug and
                  Christian J. Stoeckert Jr. and
                  Patricia L. Whetzel},
  title        = {PlasmoDB: the Plasmodium genome resource. {A} database integrating
                  experimental and computational data},
  journal      = {Nucleic Acids Res.},
  volume       = {31},
  number       = {1},
  pages        = {212--215},
  year         = {2003},
  url          = {https://doi.org/10.1093/nar/gkg081},
  doi          = {10.1093/NAR/GKG081},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/BahlBCFGGGGKLLMMPRSSW03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/omics/Jr03,
  author       = {Christian J. Stoeckert Jr.},
  title        = {Common Objects: Think Global, Act Local},
  journal      = {{OMICS}},
  volume       = {7},
  number       = {1},
  pages        = {103--104},
  year         = {2003},
  url          = {https://doi.org/10.1089/153623103322006715},
  doi          = {10.1089/153623103322006715},
  timestamp    = {Thu, 28 Nov 2019 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/omics/Jr03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/BallSPRBCCGHHRSSSTBQ02,
  author       = {Catherine A. Ball and
                  Gavin Sherlock and
                  Helen E. Parkinson and
                  Philippe Rocca{-}Serra and
                  Catherine Brooksbank and
                  Helen C. Causton and
                  Duccio Cavalieri and
                  Terry Gaasterland and
                  Pascal Hingamp and
                  Frank C. P. Holstege and
                  Martin Ringwald and
                  Paul T. Spellman and
                  Christian J. Stoeckert Jr. and
                  Jason E. Stewart and
                  Ronald C. Taylor and
                  Alvis Brazma and
                  John Quackenbush},
  title        = {An open letter to the scientific journals},
  journal      = {Bioinform.},
  volume       = {18},
  number       = {11},
  pages        = {1409},
  year         = {2002},
  url          = {https://doi.org/10.1093/bioinformatics/18.11.1409},
  doi          = {10.1093/BIOINFORMATICS/18.11.1409},
  timestamp    = {Tue, 28 Feb 2023 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/BallSPRBCCGHHRSSSTBQ02.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/isb/DavidsonS02,
  author       = {Susan B. Davidson and
                  Christian J. Stoeckert Jr.},
  title        = {In memory of Vadim Aleksandrovich Ratner},
  journal      = {Silico Biol.},
  volume       = {2},
  number       = {4},
  pages        = {523--524},
  year         = {2002},
  url          = {http://content.iospress.com/articles/in-silico-biology/isb00070},
  timestamp    = {Thu, 20 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/isb/DavidsonS02.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/BahlBCCDFGGHKLLMMRSS03,
  author       = {Amit Bahl and
                  Brian P. Brunk and
                  Ross L. Coppel and
                  Jonathan Crabtree and
                  Sharon J. Diskin and
                  Martin J. Fraunholz and
                  Gregory R. Grant and
                  Dinesh Gupta and
                  Robert L. Huestis and
                  Jessica C. Kissinger and
                  Philip Labo and
                  Li Li and
                  Shannon K. McWeeney and
                  Arthur J. Milgram and
                  David S. Roos and
                  Jonathan Schug and
                  Christian J. Stoeckert Jr.},
  title        = {PlasmoDB: the Plasmodium genome resource. An integrated database providing
                  tools for accessing, analyzing and mapping expression and sequence
                  data (both finished and unfinished)},
  journal      = {Nucleic Acids Res.},
  volume       = {30},
  number       = {1},
  pages        = {87--90},
  year         = {2002},
  url          = {https://doi.org/10.1093/nar/30.1.87},
  doi          = {10.1093/NAR/30.1.87},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/BahlBCCDFGGHKLLMMRSS03.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/StoeckertPMGBCSSO01,
  author       = {Christian J. Stoeckert Jr. and
                  Angel D. Pizarro and
                  Elisabetta Manduchi and
                  M. Gibson and
                  Brian P. Brunk and
                  Jonathan Crabtree and
                  Jonathan Schug and
                  Shai Shen{-}Orr and
                  G. Christian Overton},
  title        = {A relational schema for both array-based and {SAGE} gene expression
                  experiments},
  journal      = {Bioinform.},
  volume       = {17},
  number       = {4},
  pages        = {300--308},
  year         = {2001},
  url          = {https://doi.org/10.1093/bioinformatics/17.4.300},
  doi          = {10.1093/BIOINFORMATICS/17.4.300},
  timestamp    = {Fri, 09 Apr 2021 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/StoeckertPMGBCSSO01.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ibmsj/DavidsonCBSTOJ01,
  author       = {Susan B. Davidson and
                  Jonathan Crabtree and
                  Brian P. Brunk and
                  Jonathan Schug and
                  Val Tannen and
                  G. Christian Overton and
                  Christian J. Stoeckert Jr.},
  title        = {K2/Kleisli and {GUS:} Experiments in integrated access to genomic
                  data sources},
  journal      = {{IBM} Syst. J.},
  volume       = {40},
  number       = {2},
  pages        = {512--531},
  year         = {2001},
  url          = {https://doi.org/10.1147/sj.402.0512},
  doi          = {10.1147/SJ.402.0512},
  timestamp    = {Fri, 13 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/ibmsj/DavidsonCBSTOJ01.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ManduchiGMOSSS00,
  author       = {Elisabetta Manduchi and
                  Gregory R. Grant and
                  Steven E. McKenzie and
                  G. Christian Overton and
                  Saul Surrey and
                  Christian J. Stoeckert Jr.},
  title        = {Generation of patterns from gene expression data by assigning confidence
                  to differentially expressed genes},
  journal      = {Bioinform.},
  volume       = {16},
  number       = {8},
  pages        = {685--698},
  year         = {2000},
  url          = {https://doi.org/10.1093/bioinformatics/16.8.685},
  doi          = {10.1093/BIOINFORMATICS/16.8.685},
  timestamp    = {Mon, 02 Mar 2020 00:00:00 +0100},
  biburl       = {https://dblp.org/rec/journals/bioinformatics/ManduchiGMOSSS00.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/isb/DavidsonS00,
  author       = {Susan B. Davidson and
                  Christian J. Stoeckert Jr.},
  title        = {In Memory of Chris Overton},
  journal      = {Silico Biol.},
  volume       = {1},
  pages        = {S27--S28},
  year         = {2000},
  url          = {http://content.iospress.com/articles/in-silico-biology/isb00021},
  timestamp    = {Thu, 20 Aug 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/isb/DavidsonS00.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/StoeckertSBO99,
  author       = {Christian J. Stoeckert Jr. and
                  Fidel Salas and
                  Brian P. Brunk and
                  G. Christian Overton},
  title        = {EpoDB: a prototype database for the analysis of genes expressed during
                  vertebrate erythropoiesis},
  journal      = {Nucleic Acids Res.},
  volume       = {27},
  number       = {1},
  pages        = {200--203},
  year         = {1999},
  url          = {https://doi.org/10.1093/nar/27.1.200},
  doi          = {10.1093/NAR/27.1.200},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/StoeckertSBO99.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SalasHBSO98,
  author       = {Fidel Salas and
                  Juergen Haas and
                  Brian P. Brunk and
                  Christian J. Stoeckert Jr. and
                  G. Christian Overton},
  title        = {EpoDB: a database of genes expressed during vertebrate erythropoiesis},
  journal      = {Nucleic Acids Res.},
  volume       = {26},
  number       = {1},
  pages        = {288--289},
  year         = {1998},
  url          = {https://doi.org/10.1093/nar/26.1.288},
  doi          = {10.1093/NAR/26.1.288},
  timestamp    = {Sun, 17 May 2020 01:00:00 +0200},
  biburl       = {https://dblp.org/rec/journals/nar/SalasHBSO98.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/SalasOHS96,
  author       = {Fidel Salas and
                  G. Christian Overton and
                  Juergen Haas and
                  Christian J. Stoeckert Jr.},
  title        = {EpoDB: An Erythropoiesis Gene Expression Database/Knowledge Base},
  booktitle    = {Proceedings of the German Conference on Bioinformatics, {GCB} 1996,
                  Leipzig, Germany, September 30 - October 2, 1996},
  pages        = {40--45},
  year         = {1996},
  timestamp    = {Sat, 07 Sep 2019 11:59:23 +0200},
  biburl       = {https://dblp.org/rec/conf/gcb/SalasOHS96.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/gcb/SalasHOS96,
  author       = {Fidel Salas and
                  Juergen Haas and
                  G. Christian Overton and
                  Christian J. Stoeckert Jr.},
  editor       = {Ralf Hofest{\"{a}}dt and
                  Thomas Lengauer and
                  Markus L{\"{o}}ffler and
                  Dietmar Schomburg},
  title        = {EpoDB: An Erythropoiesis Gene Expression Database in Progress},
  booktitle    = {Bioinformatics, German Conference on Bioinformatics, Leipzig, Germany,
                  September 30 - October 2, 1996, Selected Papers},
  series       = {Lecture Notes in Computer Science},
  volume       = {1278},
  pages        = {52--61},
  publisher    = {Springer},
  year         = {1996},
  url          = {https://doi.org/10.1007/BFb0033203},
  doi          = {10.1007/BFB0033203},
  timestamp    = {Tue, 14 May 2019 10:00:42 +0200},
  biburl       = {https://dblp.org/rec/conf/gcb/SalasHOS96.bib},
  bibsource    = {dblp computer science bibliography, https://dblp.org}
}
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