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ORCIDBibTeX records: Chris Mungall
@article{DBLP:journals/bib/WrightWMCRSPJGRYSM24,
author = {Adam Wright and
Mark D. Wilkinson and
Christopher J. Mungall and
Scott Cain and
Stephen Richards and
Paul W. Sternberg and
Ellen Provin and
Jonathan L. Jacobs and
Scott Geib and
Daniela Raciti and
Karen Yook and
Lincoln Stein and
David C. Molik},
title = {{FAIR} Header Reference genome: a TRUSTworthy standard},
journal = {Briefings Bioinform.},
volume = {25},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bib/bbae122},
doi = {10.1093/BIB/BBAE122},
timestamp = {Sat, 04 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/WrightWMCRSPJGRYSM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CaufieldHEHJMKMRHRM24,
author = {J. Harry Caufield and
Harshad Hegde and
Vincent Emonet and
Nomi L. Harris and
Marcin P. Joachimiak and
Nicolas Matentzoglu and
Hyeongsik Kim and
Sierra A. T. Moxon and
Justin T. Reese and
Melissa A. Haendel and
Peter N. Robinson and
Christopher J. Mungall},
title = {Structured Prompt Interrogation and Recursive Extraction of Semantics
{(SPIRES):} a method for populating knowledge bases using zero-shot
learning},
journal = {Bioinform.},
volume = {40},
number = {3},
year = {2024},
url = {https://doi.org/10.1093/bioinformatics/btae104},
doi = {10.1093/BIOINFORMATICS/BTAE104},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaufieldHEHJMKMRHRM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijmi/ChanCRHSHVSMHMRH24,
author = {Lauren E. Chan and
Elena Casiraghi and
Justin T. Reese and
Quaker E. Harmon and
Kevin Schaper and
Harshad Hegde and
Giorgio Valentini and
Charles Schmitt and
Alison A. Motsinger{-}Reif and
Janet E. Hall and
Christopher J. Mungall and
Peter N. Robinson and
Melissa A. Haendel},
title = {Predicting nutrition and environmental factors associated with female
reproductive disorders using a knowledge graph and random forests},
journal = {Int. J. Medical Informatics},
volume = {187},
pages = {105461},
year = {2024},
url = {https://doi.org/10.1016/j.ijmedinf.2024.105461},
doi = {10.1016/J.IJMEDINF.2024.105461},
timestamp = {Fri, 19 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijmi/ChanCRHSHVSMHMRH24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/midm/GrozaCGBHRMR24,
author = {Tudor Groza and
J. Harry Caufield and
Dylan Gration and
Gareth Baynam and
Melissa A. Haendel and
Peter N. Robinson and
Christopher J. Mungall and
Justin T. Reese},
title = {An evaluation of {GPT} models for phenotype concept recognition},
journal = {{BMC} Medical Informatics Decis. Mak.},
volume = {24},
number = {1},
pages = {30},
year = {2024},
url = {https://doi.org/10.1186/s12911-024-02439-w},
doi = {10.1186/S12911-024-02439-W},
timestamp = {Tue, 13 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/midm/GrozaCGBHRMR24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/sebd/CavalleriGPMCRM24,
author = {Emanuele Cavalleri and
Mauricio Soto Gomez and
Ali Pashaeibarough and
Dario Malchiodi and
J. Harry Caufield and
Justin T. Reese and
Christopher J. Mungall and
Peter N. Robinson and
Elena Casiraghi and
Giorgio Valentini and
Marco Mesiti},
editor = {Maurizio Atzori and
Paolo Ciaccia and
Michelangelo Ceci and
Federica Mandreoli and
Donato Malerba and
Manuela Sanguinetti and
Antonio Pellicani and
Federico Motta},
title = {Initial achievements in relation extraction from RNA-focused scientific
papers},
booktitle = {Proceedings of the 32nd Symposium of Advanced Database Systems, Villasimius,
Italy, June 23rd to 26th, 2024},
series = {{CEUR} Workshop Proceedings},
volume = {3741},
pages = {61--69},
publisher = {CEUR-WS.org},
year = {2024},
url = {https://ceur-ws.org/Vol-3741/paper53.pdf},
timestamp = {Wed, 21 Aug 2024 22:46:00 +0200},
biburl = {https://dblp.org/rec/conf/sebd/CavalleriGPMCRM24.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2404-03044,
author = {Marcin P. Joachimiak and
Mark A. Miller and
J. Harry Caufield and
Ryan Ly and
Nomi L. Harris and
Andrew J. Tritt and
Christopher J. Mungall and
Kristofer E. Bouchard},
title = {The Artificial Intelligence Ontology: LLM-assisted construction of
{AI} concept hierarchies},
journal = {CoRR},
volume = {abs/2404.03044},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2404.03044},
doi = {10.48550/ARXIV.2404.03044},
eprinttype = {arXiv},
eprint = {2404.03044},
timestamp = {Mon, 13 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2404-03044.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2406-00063,
author = {Matthew Avaylon and
Ryan Ly and
Andrew J. Tritt and
Benjamin K. Dichter and
Kristofer E. Bouchard and
Christopher J. Mungall and
Oliver R{\"{u}}bel},
title = {Methods for Linking Data to Online Resources and Ontologies with Applications
to Neurophysiology},
journal = {CoRR},
volume = {abs/2406.00063},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2406.00063},
doi = {10.48550/ARXIV.2406.00063},
eprinttype = {arXiv},
eprint = {2406.00063},
timestamp = {Thu, 04 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2406-00063.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2406-02623,
author = {Kathleen R. Mullen and
Imke Tammen and
Nicolas A. Matentzoglu and
Marius Mather and
Christopher J. Mungall and
Melissa A. Haendel and
Frank W. Nicholas and
Sabrina Toro and
the Vertebrate Breed Ontology Consortium},
title = {The Vertebrate Breed Ontology: Towards Effective Breed Data Standardization},
journal = {CoRR},
volume = {abs/2406.02623},
year = {2024},
url = {https://doi.org/10.48550/arXiv.2406.02623},
doi = {10.48550/ARXIV.2406.02623},
eprinttype = {arXiv},
eprint = {2406.02623},
timestamp = {Wed, 24 Jul 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2406-02623.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KarlebachCSCHRMVR23,
author = {Guy Karlebach and
Leigh Carmody and
Jagadish Chandrabose Sundaramurthi and
Elena Casiraghi and
Peter Hansen and
Justin T. Reese and
Christopher J. Mungall and
Giorgio Valentini and
Peter N. Robinson},
title = {An expectation-maximization framework for comprehensive prediction
of isoform-specific functions},
journal = {Bioinform.},
volume = {39},
number = {4},
year = {2023},
url = {https://doi.org/10.1093/bioinformatics/btad132},
doi = {10.1093/BIOINFORMATICS/BTAD132},
timestamp = {Sat, 08 Jun 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/KarlebachCSCHRMVR23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/ChanTDMSGVMRMH23,
author = {Lauren E. Chan and
Anne E. Thessen and
William D. Duncan and
Nicolas Matentzoglu and
Charles Schmitt and
Cynthia J. Grondin and
Nicole A. Vasilevsky and
Julie A. McMurry and
Peter N. Robinson and
Christopher J. Mungall and
Melissa A. Haendel},
title = {The Environmental Conditions, Treatments, and Exposures Ontology {(ECTO):}
connecting toxicology and exposure to human health and beyond},
journal = {J. Biomed. Semant.},
volume = {14},
number = {1},
pages = {3},
year = {2023},
url = {https://doi.org/10.1186/s13326-023-00283-x},
doi = {10.1186/S13326-023-00283-X},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/ChanTDMSGVMRMH23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ncs/CappellettiFCRC23,
author = {Luca Cappelletti and
Tommaso Fontana and
Elena Casiraghi and
Vida Ravanmehr and
Tiffany J. Callahan and
Carlos Cano and
Marcin P. Joachimiak and
Christopher J. Mungall and
Peter N. Robinson and
Justin T. Reese and
Giorgio Valentini},
title = {{GRAPE} for fast and scalable graph processing and random-walk-based
embedding},
journal = {Nat. Comput. Sci.},
volume = {3},
number = {6},
pages = {552--568},
year = {2023},
url = {https://doi.org/10.1038/s43588-023-00465-8},
doi = {10.1038/S43588-023-00465-8},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ncs/CappellettiFCRC23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/om2/MatentzogluBCGG23,
author = {Nicolas Matentzoglu and
Ian Braun and
Anita R. Caron and
Damien Goutte{-}Gattat and
Benjamin M. Gyori and
Nomi L. Harris and
Emily Hartley and
Harshad B. Hegde and
Sven Hertling and
Charles Tapley Hoyt and
Hyeongsik Kim and
Huanyu Li and
James A. McLaughlin and
C{\'{a}}ssia Trojahn and
Nicole A. Vasilevsky and
Christopher J. Mungall},
editor = {Pavel Shvaiko and
J{\'{e}}r{\^{o}}me Euzenat and
Ernesto Jim{\'{e}}nez{-}Ruiz and
Oktie Hassanzadeh and
C{\'{a}}ssia Trojahn},
title = {A simple standard for ontological mappings 2023: updates on data model,
collaborations and tooling},
booktitle = {Proceedings of the 18th International Workshop on Ontology Matching
co-located with the 22nd International Semantic Web Conference {(ISWC}
2023), Athens, Greece, November 7, 2023},
series = {{CEUR} Workshop Proceedings},
volume = {3591},
pages = {73--78},
publisher = {CEUR-WS.org},
year = {2023},
url = {https://ceur-ws.org/Vol-3591/om2023\_STpaper3.pdf},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/om2/MatentzogluBCGG23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2302-10800,
author = {J. Harry Caufield and
Tim E. Putman and
Kevin Schaper and
Deepak R. Unni and
Harshad Hegde and
Tiffany J. Callahan and
Luca Cappelletti and
Sierra A. T. Moxon and
Vida Ravanmehr and
Seth Carbon and
Lauren E. Chan and
Katherina Cortes and
Kent A. Shefchek and
Glass Elsarboukh and
James P. Balhoff and
Tommaso Fontana and
Nicolas Matentzoglu and
Richard M. Bruskiewich and
Anne E. Thessen and
Nomi L. Harris and
Monica C. Munoz{-}Torres and
Melissa A. Haendel and
Peter N. Robinson and
Marcin P. Joachimiak and
Christopher J. Mungall and
Justin T. Reese},
title = {KG-Hub - Building and Exchanging Biological Knowledge Graphs},
journal = {CoRR},
volume = {abs/2302.10800},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2302.10800},
doi = {10.48550/ARXIV.2302.10800},
eprinttype = {arXiv},
eprint = {2302.10800},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2302-10800.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2304-02711,
author = {J. Harry Caufield and
Harshad Hegde and
Vincent Emonet and
Nomi L. Harris and
Marcin P. Joachimiak and
Nicolas Matentzoglu and
HyeongSik Kim and
Sierra A. T. Moxon and
Justin T. Reese and
Melissa A. Haendel and
Peter N. Robinson and
Christopher J. Mungall},
title = {Structured prompt interrogation and recursive extraction of semantics
{(SPIRES):} {A} method for populating knowledge bases using zero-shot
learning},
journal = {CoRR},
volume = {abs/2304.02711},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2304.02711},
doi = {10.48550/ARXIV.2304.02711},
eprinttype = {arXiv},
eprint = {2304.02711},
timestamp = {Tue, 18 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2304-02711.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2305-13338,
author = {Marcin P. Joachimiak and
J. Harry Caufield and
Nomi L. Harris and
Hyeongsik Kim and
Christopher J. Mungall},
title = {Gene Set Summarization using Large Language Models},
journal = {CoRR},
volume = {abs/2305.13338},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2305.13338},
doi = {10.48550/ARXIV.2305.13338},
eprinttype = {arXiv},
eprint = {2305.13338},
timestamp = {Tue, 06 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2305-13338.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2307-05727,
author = {Tiffany J. Callahan and
Ignacio J. Tripodi and
Adrianne L. Stefanski and
Luca Cappelletti and
Sanya Bathla Taneja and
Jordan M. Wyrwa and
Elena Casiraghi and
Nicolas A. Matentzoglu and
Justin T. Reese and
Jonathan C. Silverstein and
Charles Tapley Hoyt and
Richard D. Boyce and
Scott A. Malec and
Deepak R. Unni and
Marcin P. Joachimiak and
Peter N. Robinson and
Christopher J. Mungall and
Emanuele Cavalleri and
Tommaso Fontana and
Giorgio Valentini and
Marco Mesiti and
Lucas A. Gillenwater and
Brook E. Santangelo and
Nicole A. Vasilevsky and
Robert Hoehndorf and
Tellen D. Bennett and
Patrick B. Ryan and
George Hripcsak and
Michael G. Kahn and
Michael Bada and
William A. Baumgartner Jr. and
Lawrence E. Hunter},
title = {An Open-Source Knowledge Graph Ecosystem for the Life Sciences},
journal = {CoRR},
volume = {abs/2307.05727},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2307.05727},
doi = {10.48550/ARXIV.2307.05727},
eprinttype = {arXiv},
eprint = {2307.05727},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2307-05727.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2309-17169,
author = {Tudor Groza and
J. Harry Caufield and
Dylan Gration and
Gareth Baynam and
Melissa A. Haendel and
Peter N. Robinson and
Chris Mungall and
Justin T. Reese},
title = {An evaluation of {GPT} models for phenotype concept recognition},
journal = {CoRR},
volume = {abs/2309.17169},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2309.17169},
doi = {10.48550/ARXIV.2309.17169},
eprinttype = {arXiv},
eprint = {2309.17169},
timestamp = {Tue, 17 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2309-17169.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2310-03666,
author = {Nicolas Matentzoglu and
J. Harry Caufield and
Harshad B. Hegde and
Justin T. Reese and
Sierra A. T. Moxon and
Hyeongsik Kim and
Nomi L. Harris and
Melissa A. Haendel and
Christopher J. Mungall},
title = {MapperGPT: Large Language Models for Linking and Mapping Entities},
journal = {CoRR},
volume = {abs/2310.03666},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2310.03666},
doi = {10.48550/ARXIV.2310.03666},
eprinttype = {arXiv},
eprint = {2310.03666},
timestamp = {Thu, 19 Oct 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2310-03666.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2311-05042,
author = {Oluwamayowa O. Amusat and
Harshad Hegde and
Christopher J. Mungall and
Anna Giannakou and
Neil P. Byers and
Dan Gunter and
Kjiersten Fagnan and
Lavanya Ramakrishnan},
title = {Automated Annotation of Scientific Texts for ML-based Keyphrase Extraction
and Validation},
journal = {CoRR},
volume = {abs/2311.05042},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2311.05042},
doi = {10.48550/ARXIV.2311.05042},
eprinttype = {arXiv},
eprint = {2311.05042},
timestamp = {Tue, 14 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2311-05042.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2312-10904,
author = {Sabrina Toro and
Anna V. Anagnostopoulos and
Sue Bello and
Kai Blumberg and
Rhiannon Cameron and
Leigh Carmody and
Alexander D. Diehl and
Damion M. Dooley and
William D. Duncan and
Petra Fey and
Pascale Gaudet and
Nomi L. Harris and
Marcin P. Joachimiak and
Leila Kiani and
Tiago Lubiana and
Monica C. Munoz{-}Torres and
Shawn T. O'Neil and
David Osumi{-}Sutherland and
Aleix Puig and
Justin P. Reese and
Leonore Reiser and
Sofia M. C. Robb and
Troy Ruemping and
James Seager and
Eric Sid and
Raymund Stefancsik and
Magalie Weber and
Valerie Wood and
Melissa A. Haendel and
Christopher J. Mungall},
title = {Dynamic Retrieval Augmented Generation of Ontologies using Artificial
Intelligence {(DRAGON-AI)}},
journal = {CoRR},
volume = {abs/2312.10904},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2312.10904},
doi = {10.48550/ARXIV.2312.10904},
eprinttype = {arXiv},
eprint = {2312.10904},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2312-10904.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/Crecy-LagardHAB22,
author = {Val{\'{e}}rie de Cr{\'{e}}cy{-}Lagard and
Rocio Amorin de Hegedus and
Cecilia N. Arighi and
Jill Babor and
Alex Bateman and
Ian Blaby and
Crysten Blaby{-}Haas and
Alan J. Bridge and
Stephen K. Burley and
Stacey Cleveland and
Lucy J. Colwell and
Ana Conesa and
Christian Dallago and
Antoine Danchin and
Anita de Waard and
Adam Deutschbauer and
Raquel Dias and
Yousong Ding and
Gang Fang and
Iddo Friedberg and
John Gerlt and
Joshua Goldford and
Mark Gorelik and
Benjamin M. Gyori and
Christopher S. Henry and
Geoffrey Hutinet and
Marshall Jaroch and
Peter D. Karp and
Liudmyla Kondratova and
Zhiyong Lu and
Aron Marchler{-}Bauer and
Maria Jesus Martin and
Claire D. McWhite and
Gaurav D. Moghe and
Paul Monaghan and
Anne Morgat and
Christopher J. Mungall and
Darren A. Natale and
William C. Nelson and
Se{\'{a}}n I. O'Donoghue and
Christine A. Orengo and
Katherine H. O'Toole and
Predrag Radivojac and
Colbie Reed and
Richard J. Roberts and
Dmitri Rodionov and
Irina A. Rodionova and
Jeffrey DePons and
Lana Saleh and
Gloria M. Sheynkman and
Fran{\c{c}}oise Thibaud{-}Nissen and
Paul D. Thomas and
Peter Uetz and
David Vallenet and
Erica Watson Carter and
Peter Weigele and
Valerie Wood and
Elisha M. Wood{-}Charlson and
Jin Xu},
title = {A roadmap for the functional annotation of protein families: a community
perspective},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022},
url = {https://doi.org/10.1093/database/baac062},
doi = {10.1093/DATABASE/BAAC062},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/Crecy-LagardHAB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/MatentzogluBBBB22,
author = {Nicolas Matentzoglu and
James P. Balhoff and
Susan M. Bello and
Chris Bizon and
Matthew H. Brush and
Tiffany J. Callahan and
Christopher G. Chute and
William D. Duncan and
Chris T. A. Evelo and
Davera Gabriel and
John Graybeal and
Alasdair J. G. Gray and
Benjamin M. Gyori and
Melissa A. Haendel and
Henriette Harmse and
Nomi L. Harris and
Ian Harrow and
Harshad Hegde and
Amelia L. Hoyt and
Charles Tapley Hoyt and
Dazhi Jiao and
Ernesto Jim{\'{e}}nez{-}Ruiz and
Simon Jupp and
Hyeongsik Kim and
Sebastian K{\"{o}}hler and
Thomas Liener and
Qinqin Long and
James Malone and
James A. McLaughlin and
Julie A. McMurry and
Sierra A. T. Moxon and
Monica C. Munoz{-}Torres and
David Osumi{-}Sutherland and
James A. Overton and
Bjoern Peters and
Tim E. Putman and
N{\'{u}}ria Queralt{-}Rosinach and
Kent A. Shefchek and
Harold Solbrig and
Anne E. Thessen and
Tania Tudorache and
Nicole A. Vasilevsky and
Alex H. Wagner and
Christopher J. Mungall},
title = {A Simple Standard for Sharing Ontological Mappings {(SSSOM)}},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022},
url = {https://doi.org/10.1093/database/baac035},
doi = {10.1093/DATABASE/BAAC035},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/MatentzogluBBBB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/MatentzogluGTBC22,
author = {Nicolas Matentzoglu and
Damien Goutte{-}Gattat and
Shawn Zheng Kai Tan and
James P. Balhoff and
Seth Carbon and
Anita R. Caron and
William D. Duncan and
Joe E. Flack and
Melissa A. Haendel and
Nomi L. Harris and
William R. Hogan and
Charles Tapley Hoyt and
Rebecca C. Jackson and
Hyeongsik Kim and
H{\"{u}}seyin Kir and
Martin Larralde and
Julie A. McMurry and
James A. Overton and
Bjoern Peters and
Clare Pilgrim and
Raymund Stefancsik and
Sofia M. C. Robb and
Sabrina Toro and
Nicole A. Vasilevsky and
Ramona L. Walls and
Christopher J. Mungall and
David Osumi{-}Sutherland},
title = {Ontology Development Kit: a toolkit for building, maintaining and
standardizing biomedical ontologies},
journal = {Database J. Biol. Databases Curation},
volume = {2022},
number = {2022},
year = {2022},
url = {https://doi.org/10.1093/database/baac087},
doi = {10.1093/DATABASE/BAAC087},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/MatentzogluGTBC22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/NadendlaJMQMOHG22,
author = {Suvarna Nadendla and
Rebecca C. Jackson and
James B. Munro and
Federica Quaglia and
B{\'{a}}lint M{\'{e}}sz{\'{a}}ros and
Dustin Olley and
Elizabeth T. Hobbs and
Stephen M. Goralski and
Marcus C. Chibucos and
Christopher J. Mungall and
Silvio C. E. Tosatto and
Ivan Erill and
Michelle G. Giglio},
title = {{ECO:} the Evidence and Conclusion Ontology, an update for 2022},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {1515--1521},
year = {2022},
url = {https://doi.org/10.1093/nar/gkab1025},
doi = {10.1093/NAR/GKAB1025},
timestamp = {Fri, 10 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/NadendlaJMQMOHG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/semweb/MatentzogluFGHH22,
author = {Nicolas Matentzoglu and
Joe E. Flack and
John Graybeal and
Nomi L. Harris and
Harshad B. Hegde and
Charles Tapley Hoyt and
Hyeongsik Kim and
Sabrina Toro and
Nicole A. Vasilevsky and
Christopher J. Mungall},
editor = {Pavel Shvaiko and
J{\'{e}}r{\^{o}}me Euzenat and
Ernesto Jim{\'{e}}nez{-}Ruiz and
Oktie Hassanzadeh and
C{\'{a}}ssia Trojahn},
title = {A simple standard for ontological mappings 2022: updates of data model
and outlook},
booktitle = {Proceedings of the 17th International Workshop on Ontology Matching
{(OM} 2022) co-located with the 21th International Semantic Web Conference
{(ISWC} 2022), Hangzhou, China, held as a virtual conference, October
23, 2022},
series = {{CEUR} Workshop Proceedings},
volume = {3324},
pages = {61--66},
publisher = {CEUR-WS.org},
year = {2022},
url = {https://ceur-ws.org/Vol-3324/om2022\_LTpaper6.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:07 +0100},
biburl = {https://dblp.org/rec/conf/semweb/MatentzogluFGHH22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2203-13906,
author = {Deepak R. Unni and
Sierra A. T. Moxon and
Michael Bada and
Matthew H. Brush and
Richard M. Bruskiewich and
Paul A. Clemons and
Vlado Danc{\'{\i}}k and
Michel Dumontier and
Karamarie Fecho and
Gustavo Glusman and
Jennifer J. Hadlock and
Nomi L. Harris and
Arpita Joshi and
Tim E. Putman and
Guangrong Qin and
Stephen A. Ramsey and
Kent A. Shefchek and
Harold Solbrig and
Karthik Soman and
Anne E. Thessen and
Melissa A. Haendel and
Chris Bizon and
Christopher J. Mungall},
title = {Biolink Model: {A} Universal Schema for Knowledge Graphs in Clinical,
Biomedical, and Translational Science},
journal = {CoRR},
volume = {abs/2203.13906},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2203.13906},
doi = {10.48550/ARXIV.2203.13906},
eprinttype = {arXiv},
eprint = {2203.13906},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2203-13906.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2207-02056,
author = {Nicolas Matentzoglu and
Damien Goutte{-}Gattat and
Shawn Zheng Kai Tan and
James P. Balhoff and
Seth Carbon and
Anita R. Caron and
William D. Duncan and
Joe E. Flack and
Melissa A. Haendel and
Nomi L. Harris and
William R. Hogan and
Charles Tapley Hoyt and
Rebecca C. Jackson and
Hyeongsik Kim and
H{\"{u}}seyin Kir and
Martin Larralde and
Julie A. McMurry and
James A. Overton and
Bjoern Peters and
Clare Pilgrim and
Raymund Stefancsik and
Sofia M. C. Robb and
Sabrina Toro and
Nicole A. Vasilevsky and
Ramona L. Walls and
Christopher J. Mungall and
David Osumi{-}Sutherland},
title = {Ontology Development Kit: a toolkit for building, maintaining, and
standardising biomedical ontologies},
journal = {CoRR},
volume = {abs/2207.02056},
year = {2022},
url = {https://doi.org/10.48550/arXiv.2207.02056},
doi = {10.48550/ARXIV.2207.02056},
eprinttype = {arXiv},
eprint = {2207.02056},
timestamp = {Thu, 15 Sep 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2207-02056.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/bioinformatics/ToureVALOBCCdFG21,
author = {Vasundra Tour{\'{e}} and
Steven Vercruysse and
Marcio Luis Acencio and
Ruth C. Lovering and
Sandra E. Orchard and
Glyn Bradley and
Cristina Casals{-}Casas and
Claudine Chaouiya and
Noemi del{-}Toro and
{\AA}smund Flobak and
Pascale Gaudet and
Henning Hermjakob and
Charles Tapley Hoyt and
Luana Licata and
Astrid L{\ae}greid and
Christopher J. Mungall and
Anne Niknejad and
Simona Panni and
Livia Perfetto and
Pablo Porras and
Dexter Pratt and
Julio Saez{-}Rodriguez and
Denis Thieffry and
Paul D. Thomas and
D{\'{e}}nes T{\"{u}}rei and
Martin Kuiper},
title = {The Minimum Information about a Molecular Interaction CAusal STatement
{(MI2CAST)}},
journal = {Bioinform.},
volume = {36},
number = {24},
pages = {5712--5718},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btaa622},
doi = {10.1093/BIOINFORMATICS/BTAA622},
timestamp = {Sat, 09 Apr 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ToureVALOBCCdFG21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/GoodAHMCBATMBD21,
author = {Benjamin M. Good and
Kimberly Van Auken and
David P. Hill and
Huaiyu Mi and
Seth Carbon and
James P. Balhoff and
Laurent{-}Philippe Albou and
Paul D. Thomas and
Christopher J. Mungall and
Judith A. Blake and
Peter D'Eustachio},
title = {Reactome and the Gene Ontology: digital convergence of data resources},
journal = {Bioinform.},
volume = {37},
number = {19},
pages = {3343--3348},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab325},
doi = {10.1093/BIOINFORMATICS/BTAB325},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/GoodAHMCBATMBD21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fbinf/HuCEABCDDFFFHHJ21,
author = {Bin Hu and
Shane Canon and
Emiley A. Eloe{-}Fadrosh and
Fnu Anubhav and
Michal Babinski and
Yuri Corilo and
Karen Davenport and
William D. Duncan and
Kjiersten Fagnan and
Mark Flynn and
Brian Foster and
David Hays and
Marcel Huntemann and
Elais Player Jackson and
Julia Kelliher and
Po{-}E Li and
Chien{-}Chi Lo and
Douglas Mans and
Lee Ann McCue and
Nigel Mouncey and
Christopher J. Mungall and
Paul D. Piehowski and
Samuel O. Purvine and
Montana Smith and
Neha Jacob Varghese and
Donald Winston and
Yan Xu and
Patrick S. G. Chain},
title = {Challenges in Bioinformatics Workflows for Processing Microbiome Omics
Data at Scale},
journal = {Frontiers Bioinform.},
volume = {1},
year = {2021},
url = {https://doi.org/10.3389/fbinf.2021.826370},
doi = {10.3389/FBINF.2021.826370},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fbinf/HuCEABCDDFFFHHJ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/0001GMCLVDBBBCC21,
author = {Sebastian K{\"{o}}hler and
Michael A. Gargano and
Nicolas Matentzoglu and
Leigh Carmody and
David Lewis{-}Smith and
Nicole A. Vasilevsky and
Daniel Danis and
Ganna Balagura and
Gareth Baynam and
Amy M. Brower and
Tiffany J. Callahan and
Christopher G. Chute and
Johanna L. Est and
Peter D. Galer and
Shiva Ganesan and
Matthias Griese and
Matthias Haimel and
Julia Pazmandi and
Marc Hanauer and
Nomi L. Harris and
Michael Hartnett and
Maximilian Hastreiter and
Fabian Hauck and
Yongqun He and
Tim Jeske and
Hugh Kearney and
Gerhard Kindle and
Christoph Klein and
Katrin Knoflach and
Roland Krause and
David Lagorce and
Julie A. McMurry and
Jillian A. Miller and
Monica C. Munoz{-}Torres and
Rebecca L. Peters and
Christina K. Rapp and
Ana Rath and
Shahmir A. Rind and
Avi Z. Rosenberg and
Michael M. Segal and
Markus G. Seidel and
Damian Smedley and
Tomer Talmy and
Yarlalu Thomas and
Samuel A. Wiafe and
Julie Xian and
Zafer Y{\"{u}}ksel and
Ingo Helbig and
Christopher J. Mungall and
Melissa A. Haendel and
Peter N. Robinson},
title = {The Human Phenotype Ontology in 2021},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D1207--D1217},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1043},
doi = {10.1093/NAR/GKAA1043},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/0001GMCLVDBBBCC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CarbonDGUHMBCDH21,
author = {Seth Carbon and
Eric Douglass and
Benjamin M. Good and
Deepak R. Unni and
Nomi L. Harris and
Christopher J. Mungall and
Siddartha Basu and
Rex L. Chisholm and
Robert J. Dodson and
Eric Hartline and
Petra Fey and
Paul D. Thomas and
Laurent{-}Philippe Albou and
Dustin Ebert and
Michael J. Kesling and
Huaiyu Mi and
Anushya Muruganujan and
Xiaosong Huang and
Tremayne Mushayahama and
Sandra A. LaBonte and
Deborah A. Siegele and
Giulia Antonazzo and
Helen Attrill and
Nick H. Brown and
Phani V. Garapati and
Steven J. Marygold and
Vitor Trovisco and
Gilberto dos Santos and
Kathleen Falls and
Christopher J. Tabone and
Pinglei Zhou and
Joshua L. Goodman and
Victor B. Strelets and
Jim Thurmond and
Penelope Garmiri and
Rizwan Ishtiaq and
Milagros Rodr{\'{\i}}guez{-}L{\'{o}}pez and
Marcio Luis Acencio and
Martin Kuiper and
Astrid L{\ae}greid and
Colin Logie and
Ruth C. Lovering and
Barbara Kramarz and
Shirin C. C. Saverimuttu and
Sandra M. Pinheiro and
Heather Gunn and
Renzhi Su and
Katherine E. Thurlow and
Marcus C. Chibucos and
Michelle G. Giglio and
Suvarna Nadendla and
James B. Munro and
Rebecca C. Jackson and
Margaret J. Duesbury and
Noemi del{-}Toro and
Birgit H. M. Meldal and
Kalpana Paneerselvam and
Livia Perfetto and
Pablo Porras and
Sandra E. Orchard and
Anjali Shrivastava and
Hsin{-}Yu Chang and
Robert D. Finn and
Alex L. Mitchell and
Neil D. Rawlings and
Lorna J. Richardson and
Amaia Sangrador{-}Vegas and
Judith A. Blake and
Karen R. Christie and
Mary E. Dolan and
Harold J. Drabkin and
David P. Hill and
Li Ni and
Dmitry M. Sitnikov and
Midori A. Harris and
Stephen G. Oliver and
Kim Rutherford and
Valerie Wood and
Jaqueline Hayles and
J{\"{u}}rg B{\"{a}}hler and
Elizabeth R. Bolton and
Jeffrey DePons and
Melinda R. Dwinell and
G. Thomas Hayman and
Mary L. Kaldunski and
Anne E. Kwitek and
Stanley J. F. Laulederkind and
Cody Plasterer and
Marek Tutaj and
Mahima Vedi and
Shur{-}Jen Wang and
Peter D'Eustachio and
Lisa Matthews and
James P. Balhoff and
Suzi A. Aleksander and
Michael J. Alexander and
J. Michael Cherry and
Stacia R. Engel and
Felix Gondwe and
Kalpana Karra and
Stuart R. Miyasato and
Robert S. Nash and
Matt Simison and
Marek S. Skrzypek and
Shuai Weng and
Edith D. Wong and
Marc Feuermann and
Pascale Gaudet and
Anne Morgat and
Erica Bakker and
Tanya Z. Berardini and
Leonore Reiser and
Shabari Subramaniam and
Eva Huala and
Cecilia N. Arighi and
Andrea H. Auchincloss and
Kristian B. Axelsen and
Ghislaine Argoud{-}Puy and
Alex Bateman and
Marie{-}Claude Blatter and
Emmanuel Boutet and
Emily Bowler and
Lionel Breuza and
Alan J. Bridge and
Ramona Britto and
Hema Bye{-}A{-}Jee and
Cristina Casals{-}Casas and
Elisabeth Coudert and
Paul Denny and
Anne Estreicher and
Maria Livia Famiglietti and
George E. Georghiou and
Arnaud Gos and
Nadine Gruaz{-}Gumowski and
Emma Hatton{-}Ellis and
Chantal Hulo and
Alexandr Ignatchenko and
Florence Jungo and
Kati Laiho and
Philippe Le Mercier and
Damien Lieberherr and
Antonia Lock and
Yvonne Lussi and
Alistair MacDougall and
Michele Magrane and
Maria Jesus Martin and
Patrick Masson and
Darren A. Natale and
Nevila Hyka{-}Nouspikel and
Ivo Pedruzzi and
Lucille Pourcel and
Sylvain Poux and
Sangya Pundir and
Catherine Rivoire and
Elena Speretta and
Shyamala Sundaram and
Nidhi Tyagi and
Kate Warner and
Rossana Zaru and
Cathy H. Wu and
Alexander D. Diehl and
Juancarlos Chan and
Christian A. Grove and
Raymond Y. N. Lee and
Hans{-}Michael M{\"{u}}ller and
Daniela Raciti and
Kimberly Van Auken and
Paul W. Sternberg and
Matthew Berriman and
Michael Paulini and
Kevin L. Howe and
Sibyl Gao and
Adam Wright and
Lincoln Stein and
Douglas G. Howe and
Sabrina Toro and
Monte Westerfield and
Pankaj Jaiswal and
Laurel Cooper and
Justin Elser},
title = {The Gene Ontology resource: enriching a GOld mine},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D325--D334},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1113},
doi = {10.1093/NAR/GKAA1113},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CarbonDGUHMBCDH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/patterns/ReeseUCCRCSGBFB21,
author = {Justin T. Reese and
Deepak R. Unni and
Tiffany J. Callahan and
Luca Cappelletti and
Vida Ravanmehr and
Seth Carbon and
Kent A. Shefchek and
Benjamin M. Good and
James P. Balhoff and
Tommaso Fontana and
Hannah Blau and
Nicolas Matentzoglu and
Nomi L. Harris and
Monica C. Munoz{-}Torres and
Melissa A. Haendel and
Peter N. Robinson and
Marcin P. Joachimiak and
Christopher J. Mungall},
title = {{KG-COVID-19:} {A} Framework to Produce Customized Knowledge Graphs
for {COVID-19} Response},
journal = {Patterns},
volume = {2},
number = {1},
pages = {100155},
year = {2021},
url = {https://doi.org/10.1016/j.patter.2020.100155},
doi = {10.1016/J.PATTER.2020.100155},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/patterns/ReeseUCCRCSGBFB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/ChanVTMDMH21,
author = {Lauren E. Chan and
Nicole A. Vasilevsky and
Anne E. Thessen and
Nicolas Matentzoglu and
William D. Duncan and
Christopher J. Mungall and
Melissa A. Haendel},
editor = {Janna Hastings and
Adrien Barton},
title = {A Semantic Model Leveraging Pattern-based Ontology Terms to Bridge
Environmental Exposures and Health Outcomes},
booktitle = {Proceedings of the International Conference on Biomedical Ontologies
2021 co-located with the Workshop on Ontologies for the Behavioural
and Social Sciences (OntoBess 2021) as part of the Bolzano Summer
of Knowledge {(BOSK} 2021), Bozen-Bolzano, Italy, 16-18 September,
2021},
series = {{CEUR} Workshop Proceedings},
volume = {3073},
pages = {48--55},
publisher = {CEUR-WS.org},
year = {2021},
url = {https://ceur-ws.org/Vol-3073/paper5.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:23 +0100},
biburl = {https://dblp.org/rec/conf/icbo/ChanVTMDMH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/VasilevskyTMJHR21,
author = {Nicole A. Vasilevsky and
Sabrina Toro and
Nicolas Matentzoglu and
Dazhi Jiao and
Melissa A. Haendel and
Peter N. Robinson and
Christopher J. Mungall},
editor = {Janna Hastings and
Adrien Barton},
title = {Reclassification of Infectious Disease in the Mondo Disease Ontology},
booktitle = {Proceedings of the International Conference on Biomedical Ontologies
2021 co-located with the Workshop on Ontologies for the Behavioural
and Social Sciences (OntoBess 2021) as part of the Bolzano Summer
of Knowledge {(BOSK} 2021), Bozen-Bolzano, Italy, 16-18 September,
2021},
series = {{CEUR} Workshop Proceedings},
volume = {3073},
pages = {104--109},
publisher = {CEUR-WS.org},
year = {2021},
url = {https://ceur-ws.org/Vol-3073/paper14.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/VasilevskyTMJHR21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/JoachimiakHDRCT21,
author = {Marcin P. Joachimiak and
Harshad Hegde and
William D. Duncan and
Justin T. Reese and
Luca Cappelletti and
Anne E. Thessen and
Christopher J. Mungall},
editor = {Janna Hastings and
Adrien Barton},
title = {KG-Microbe: {A} Reference Knowledge-Graph and Platform for Harmonized
Microbial Information},
booktitle = {Proceedings of the International Conference on Biomedical Ontologies
2021 co-located with the Workshop on Ontologies for the Behavioural
and Social Sciences (OntoBess 2021) as part of the Bolzano Summer
of Knowledge {(BOSK} 2021), Bozen-Bolzano, Italy, 16-18 September,
2021},
series = {{CEUR} Workshop Proceedings},
volume = {3073},
pages = {131--133},
publisher = {CEUR-WS.org},
year = {2021},
url = {https://ceur-ws.org/Vol-3073/paper19.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/JoachimiakHDRCT21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/DuncanAABBBBCCC21,
author = {William D. Duncan and
Faiza Ahmed and
Fnu Anubhav and
Jeffrey Baumes and
Jonathan Beezley and
Mark Borkum and
Lisa M. Bramer and
Shane Canon and
Patrick S. G. Chain and
Danielle Christianson and
Yuri Corilo and
Karen Davenport and
Brandon Davis and
Meghan Drake and
Kjiersten Fagnan and
Mark Flynn and
David Hays and
Bin Hu and
Marcel Huntemann and
Julia Kelliher and
Sofya Lebedeva and
Po{-}E Li and
Mary Lipton and
Chien{-}Chi Lo and
Douglas Mans and
Stanton Martin and
Lee Ann McCue and
David Millard and
Kayd Miller and
Nigel Mouncey and
Paul D. Piehowski and
Elais Player Jackson and
Anastasiya Prymolenna and
Samuel O. Purvine and
T. B. K. Reddy and
Rachel Richardson and
Migun Shakya and
Montana Smith and
Jagadish Chandrabose Sundaramurthi and
Mark A. Miller and
Deepak R. Unni and
Pajau Vangay and
Bruce Wilson and
Donald Winston and
Elisha M. Wood{-}Charlson and
Yan Xu and
Emiley A. Eloe{-}Fadrosh and
Christopher J. Mungall},
editor = {Janna Hastings and
Adrien Barton},
title = {Leveraging Ontologies within the National Microbiome Data Collaborative},
booktitle = {Proceedings of the International Conference on Biomedical Ontologies
2021 co-located with the Workshop on Ontologies for the Behavioural
and Social Sciences (OntoBess 2021) as part of the Bolzano Summer
of Knowledge {(BOSK} 2021), Bozen-Bolzano, Italy, 16-18 September,
2021},
series = {{CEUR} Workshop Proceedings},
volume = {3073},
pages = {141--143},
publisher = {CEUR-WS.org},
year = {2021},
url = {https://ceur-ws.org/Vol-3073/paper22.pdf},
timestamp = {Fri, 15 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/DuncanAABBBBCCC21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/MillerJM21,
author = {Mark A. Miller and
Rebecca C. Jackson and
Christopher J. Mungall},
editor = {Janna Hastings and
Adrien Barton},
title = {Bringing Schemas to the Schemaless},
booktitle = {Proceedings of the International Conference on Biomedical Ontologies
2021 co-located with the Workshop on Ontologies for the Behavioural
and Social Sciences (OntoBess 2021) as part of the Bolzano Summer
of Knowledge {(BOSK} 2021), Bozen-Bolzano, Italy, 16-18 September,
2021},
series = {{CEUR} Workshop Proceedings},
volume = {3073},
pages = {144--147},
publisher = {CEUR-WS.org},
year = {2021},
url = {https://ceur-ws.org/Vol-3073/paper23.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/MillerJM21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/MoxonSUJBBVDHMB21,
author = {Sierra A. T. Moxon and
Harold Solbrig and
Deepak R. Unni and
Dazhi Jiao and
Richard M. Bruskiewich and
James P. Balhoff and
Gaurav Vaidya and
William D. Duncan and
Harshad Hegde and
Mark Miller and
Matthew H. Brush and
Nomi L. Harris and
Melissa A. Haendel and
Christopher J. Mungall},
editor = {Janna Hastings and
Adrien Barton},
title = {The Linked Data Modeling Language (LinkML): {A} General-Purpose Data
Modeling Framework Grounded in Machine-Readable Semantics},
booktitle = {Proceedings of the International Conference on Biomedical Ontologies
2021 co-located with the Workshop on Ontologies for the Behavioural
and Social Sciences (OntoBess 2021) as part of the Bolzano Summer
of Knowledge {(BOSK} 2021), Bozen-Bolzano, Italy, 16-18 September,
2021},
series = {{CEUR} Workshop Proceedings},
volume = {3073},
pages = {148--151},
publisher = {CEUR-WS.org},
year = {2021},
url = {https://ceur-ws.org/Vol-3073/paper24.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/MoxonSUJBBVDHMB21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2110-06196,
author = {Luca Cappelletti and
Tommaso Fontana and
Elena Casiraghi and
Vida Ravanmehr and
Tiffany J. Callahan and
Marcin P. Joachimiak and
Christopher J. Mungall and
Peter N. Robinson and
Justin T. Reese and
Giorgio Valentini},
title = {GraPE: fast and scalable Graph Processing and Embedding},
journal = {CoRR},
volume = {abs/2110.06196},
year = {2021},
url = {https://arxiv.org/abs/2110.06196},
eprinttype = {arXiv},
eprint = {2110.06196},
timestamp = {Fri, 22 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-2110-06196.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2112-07051,
author = {Nicolas Matentzoglu and
James P. Balhoff and
Susan M. Bello and
Chris Bizon and
Matthew H. Brush and
Tiffany J. Callahan and
Christopher G. Chute and
William D. Duncan and
Chris T. A. Evelo and
Davera Gabriel and
John Graybeal and
Alasdair J. G. Gray and
Benjamin M. Gyori and
Melissa A. Haendel and
Henriette Harmse and
Nomi L. Harris and
Ian Harrow and
Harshad Hegde and
Amelia L. Hoyt and
Charles Tapley Hoyt and
Dazhi Jiao and
Ernesto Jim{\'{e}}nez{-}Ruiz and
Simon Jupp and
Hyeongsik Kim and
Sebastian K{\"{o}}hler and
Thomas Liener and
Qinqin Long and
James Malone and
James A. McLaughlin and
Julie A. McMurry and
Sierra A. T. Moxon and
Monica C. Munoz{-}Torres and
David Osumi{-}Sutherland and
James A. Overton and
Bjoern Peters and
Tim E. Putman and
N{\'{u}}ria Queralt{-}Rosinach and
Kent A. Shefchek and
Harold Solbrig and
Anne E. Thessen and
Tania Tudorache and
Nicole A. Vasilevsky and
Alex H. Wagner and
Christopher J. Mungall},
title = {A Simple Standard for Sharing Ontological Mappings {(SSSOM)}},
journal = {CoRR},
volume = {abs/2112.07051},
year = {2021},
url = {https://arxiv.org/abs/2112.07051},
eprinttype = {arXiv},
eprint = {2112.07051},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2112-07051.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/datasci/OvertonCM20,
author = {James A. Overton and
Michael Cuffaro and
Christopher J. Mungall},
title = {String of PURLs - frugal migration and maintenance of persistent identifiers},
journal = {Data Sci.},
volume = {3},
number = {1},
pages = {3--13},
year = {2020},
url = {https://doi.org/10.3233/ds-190022},
doi = {10.3233/DS-190022},
timestamp = {Thu, 16 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/datasci/OvertonCM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AgapiteAAAAABBB20,
author = {Julie Agapite and
Laurent{-}Philippe Albou and
Suzi A. Aleksander and
Joanna Argasinska and
Valerio Arnaboldi and
Helen Attrill and
Susan M. Bello and
Judith A. Blake and
Olin Blodgett and
Yvonne M. Bradford and
Carol J. Bult and
Scott Cain and
Brian R. Calvi and
Seth Carbon and
Juancarlos Chan and
Wen J. Chen and
J. Michael Cherry and
Jae{-}Hyoung Cho and
Karen R. Christie and
Madeline A. Crosby and
Jeff de Pons and
Mary E. Dolan and
Gilberto dos Santos and
Barbara Dunn and
Nathan A. Dunn and
Anne E. Eagle and
Dustin Ebert and
Stacia R. Engel and
David Fashena and
Ken Frazer and
Sibyl Gao and
Felix Gondwe and
Joshua L. Goodman and
L. Sian Gramates and
Christian A. Grove and
Todd W. Harris and
Marie{-}Claire Harrison and
Douglas G. Howe and
Kevin L. Howe and
Sagar Jha and
James A. Kadin and
Thomas C. Kaufman and
Patrick Kalita and
Kalpana Karra and
Ranjana Kishore and
Stanley J. F. Laulederkind and
Raymond Y. N. Lee and
Kevin A. MacPherson and
Steven J. Marygold and
Beverley Matthews and
Gillian H. Millburn and
Stuart R. Miyasato and
Sierra A. T. Moxon and
Hans{-}Michael M{\"{u}}ller and
Christopher J. Mungall and
Anushya Muruganujan and
Tremayne Mushayahama and
Robert S. Nash and
Patrick Ng and
Michael Paulini and
Norbert Perrimon and
Christian Pich and
Daniela Raciti and
Joel E. Richardson and
Matthew Russell and
Susan Russo Gelbart and
Leyla Ruzicka and
Kevin Schaper and
Mary Shimoyama and
Matt Simison and
Cynthia L. Smith and
David R. Shaw and
Ajay Shrivatsav and
Marek S. Skrzypek and
Jennifer R. Smith and
Paul W. Sternberg and
Christopher J. Tabone and
Paul D. Thomas and
Jyothi Thota and
Sabrina Toro and
Monika Tomczuk and
Marek Tutaj and
Monika Tutaj and
Jose{-}Maria Urbano and
Kimberly Van Auken and
Ceri E. Van Slyke and
Shur{-}Jen Wang and
Shuai Weng and
Monte Westerfield and
Gary Williams and
Edith D. Wong and
Adam Wright and
Karen Yook},
title = {Alliance of Genome Resources Portal: unified model organism research
platform},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D650--D658},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz813},
doi = {10.1093/NAR/GKZ813},
timestamp = {Mon, 03 Jan 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/AgapiteAAAAABBB20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ShefchekHGMUBKC20,
author = {Kent A. Shefchek and
Nomi L. Harris and
Michael A. Gargano and
Nicolas Matentzoglu and
Deepak R. Unni and
Matthew H. Brush and
Dan Keith and
Tom Conlin and
Nicole A. Vasilevsky and
Xingmin Aaron Zhang and
James P. Balhoff and
Larry Babb and
Susan M. Bello and
Hannah Blau and
Yvonne M. Bradford and
Seth Carbon and
Leigh Carmody and
Lauren E. Chan and
Valentina Cipriani and
Alayne Cuzick and
Maria G. Della Rocca and
Nathan A. Dunn and
Shahim Essaid and
Petra Fey and
Christian A. Grove and
Jean{-}Philippe F. Gourdine and
Ada Hamosh and
Midori A. Harris and
Ingo Helbig and
Maureen E. Hoatlin and
Marcin P. Joachimiak and
Simon Jupp and
Kenneth B. Lett and
Suzanna E. Lewis and
Craig McNamara and
Zo{\"{e}} May Pendlington and
Clare Pilgrim and
Tim E. Putman and
Vida Ravanmehr and
Justin T. Reese and
Erin Rooney Riggs and
Sofia M. C. Robb and
Paola Roncaglia and
James Seager and
Erik Segerdell and
Morgan Similuk and
Andrea L. Storm and
Courtney Thaxon and
Anne E. Thessen and
Julius O. B. Jacobsen and
Julie A. McMurry and
Tudor Groza and
Sebastian K{\"{o}}hler and
Damian Smedley and
Peter N. Robinson and
Christopher J. Mungall and
Melissa A. Haendel and
Monica C. Munoz{-}Torres and
David Osumi{-}Sutherland},
title = {The Monarch Initiative in 2019: an integrative data and analytic platform
connecting phenotypes to genotypes across species},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D704--D715},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz997},
doi = {10.1093/NAR/GKZ997},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ShefchekHGMUBKC20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/patterns/ArnaudLKALMCJKS20,
author = {Elizabeth Arnaud and
Marie{-}Ang{\'{e}}lique Laporte and
Soonho Kim and
C{\'{e}}line Aubert and
Sabina Leonelli and
Berta Miro and
Laurel Cooper and
Pankaj Jaiswal and
Gideon Kruseman and
Rosemary Shrestha and
Pier Luigi Buttigieg and
Christopher J. Mungall and
Julian Pietragalla and
Afolabi Agbona and
Jacqueline Muliro and
Jeffrey Detras and
Vilma Hualla and
Abhishek Rathore and
Roma Rani Das and
Ibnou Dieng and
Guillaume Bauchet and
Naama Menda and
Cyril Pommier and
Felix Shaw and
David Lyon and
Leroy Mwanzia and
Henry Juarez and
Enrico Bonaiuti and
Brian Chiputwa and
Oluremi Olatunbosun and
Sandrine Auzoux and
Esther Dzal{\'{e}} Yeumo and
Lukas A. Mueller and
Kevin A. T. Silverstein and
Alexandra Lafargue and
Erick Antezana and
Medha Devare and
Brian King},
title = {The Ontologies Community of Practice: {A} {CGIAR} Initiative for Big
Data in Agrifood Systems},
journal = {Patterns},
volume = {1},
number = {7},
pages = {100105},
year = {2020},
url = {https://doi.org/10.1016/j.patter.2020.100105},
doi = {10.1016/J.PATTER.2020.100105},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/patterns/ArnaudLKALMCJKS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ThessenWVSWBBMM20,
author = {Anne E. Thessen and
Ramona L. Walls and
Lars Vogt and
Jessica Singer and
Robert Warren and
Pier Luigi Buttigieg and
James P. Balhoff and
Christopher J. Mungall and
Deborah L. McGuinness and
Brian J. Stucky and
Matthew J. Yoder and
Melissa A. Haendel},
title = {Transforming the study of organisms: Phenomic data models and knowledge
bases},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {11},
year = {2020},
url = {https://doi.org/10.1371/journal.pcbi.1008376},
doi = {10.1371/JOURNAL.PCBI.1008376},
timestamp = {Mon, 05 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ploscb/ThessenWVSWBBMM20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/CooperLEBSMAJ20,
author = {Laurel Cooper and
Marie{-}Ang{\'{e}}lique Laporte and
Justin Elser and
Victoria Carollo Blake and
Taner Z. Sen and
Chris Mungall and
Elizabeth Arnaud and
Pankaj Jaiswal},
editor = {Janna Hastings and
Frank Loebe},
title = {The Plant Trait Ontology Links Wheat Traits for Crop Improvement and
Genomics (short paper)},
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--2},
publisher = {CEUR-WS.org},
year = {2020},
url = {https://ceur-ws.org/Vol-2807/abstractT.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:24 +0100},
biburl = {https://dblp.org/rec/conf/icbo/CooperLEBSMAJ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/VasilevskyEMHHR20,
author = {Nicole A. Vasilevsky and
Shahim Essaid and
Nicolas Matentzoglu and
Nomi L. Harris and
Melissa A. Haendel and
Peter N. Robinson and
Christopher J. Mungall},
editor = {Janna Hastings and
Frank Loebe},
title = {Mondo Disease Ontology: Harmonizing Disease Concepts Across the World
(short paper)},
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--2},
publisher = {CEUR-WS.org},
year = {2020},
url = {https://ceur-ws.org/Vol-2807/abstractY.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/VasilevskyEMHHR20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/JacksonBDHMO19,
author = {Rebecca C. Jackson and
James P. Balhoff and
Eric Douglass and
Nomi L. Harris and
Christopher J. Mungall and
James A. Overton},
title = {{ROBOT:} {A} Tool for Automating Ontology Workflows},
journal = {{BMC} Bioinform.},
volume = {20},
number = {1},
pages = {407:1--407:10},
year = {2019},
url = {https://doi.org/10.1186/s12859-019-3002-3},
doi = {10.1186/S12859-019-3002-3},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/JacksonBDHMO19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KohlerCVJDGGHMM19,
author = {Sebastian K{\"{o}}hler and
Leigh Carmody and
Nicole A. Vasilevsky and
Julius O. B. Jacobsen and
Daniel Danis and
Jean{-}Philippe F. Gourdine and
Michael A. Gargano and
Nomi L. Harris and
Nicolas Matentzoglu and
Julie A. McMurry and
David Osumi{-}Sutherland and
Valentina Cipriani and
James P. Balhoff and
Tom Conlin and
Hannah Blau and
Gareth Baynam and
Richard Palmer and
Dylan Gratian and
Hugh J. S. Dawkins and
Michael Segal and
Anna C. Jansen and
Ahmed Muaz and
Willie H. Chang and
Jenna Bergerson and
Stanley J. F. Laulederkind and
Zafer Y{\"{u}}ksel and
Sergi Beltran and
Alexandra F. Freeman and
Panagiotis I. Sergouniotis and
Daniel Durkin and
Andrea L. Storm and
Marc Hanauer and
Michael Brudno and
Susan M. Bello and
Murat Sincan and
Kayli Rageth and
Matthew T. Wheeler and
Renske Oegema and
Halima Lourghi and
Maria G. Della Rocca and
Rachel Thompson and
Francisco Castellanos and
James Priest and
Charlotte Cunningham{-}Rundles and
Ayushi Hegde and
Ruth C. Lovering and
Catherine Hajek and
Annie Olry and
Luigi Notarangelo and
Morgan Similuk and
Xingmin Aaron Zhang and
David G{\'{o}}mez{-}Andr{\'{e}}s and
Hanns Lochm{\"{u}}ller and
H{\'{e}}l{\`{e}}ne Dollfus and
Sergio Rosenzweig and
Shruti Marwaha and
Ana Rath and
Kathleen Sullivan and
Cynthia L. Smith and
Joshua D. Milner and
Doroth{\'{e}}e Leroux and
Cornelius F. Boerkoel and
Amy Klion and
Melody C. Carter and
Tudor Groza and
Damian Smedley and
Melissa A. Haendel and
Chris Mungall and
Peter N. Robinson},
title = {Expansion of the Human Phenotype Ontology {(HPO)} knowledge base and
resources},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D1018--D1027},
year = {2019},
url = {https://doi.org/10.1093/nar/gky1105},
doi = {10.1093/NAR/GKY1105},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KohlerCVJDGGHMM19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/GiglioTNMOBMSGH19,
author = {Michelle G. Giglio and
Rebecca Tauber and
Suvarna Nadendla and
James B. Munro and
Dustin Olley and
Shoshannah Ball and
Elvira Mitraka and
Lynn M. Schriml and
Pascale Gaudet and
Elizabeth T. Hobbs and
Ivan Erill and
Deborah A. Siegele and
James C. Hu and
Chris Mungall and
Marcus C. Chibucos},
title = {ECO, the Evidence {\&} Conclusion Ontology: community standard
for evidence information},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D1186--D1194},
year = {2019},
url = {https://doi.org/10.1093/nar/gky1036},
doi = {10.1093/NAR/GKY1036},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/GiglioTNMOBMSGH19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/npjdm/ZhangYVGCCDJRPC19,
author = {Xingmin Aaron Zhang and
Amy Yates and
Nicole A. Vasilevsky and
Jean{-}Philippe F. Gourdine and
Tiffany J. Callahan and
Leigh C. Carmody and
Daniel Danis and
Marcin P. Joachimiak and
Vida Ravanmehr and
Emily R. Pfaff and
James Champion and
Kimberly Robasky and
Hao Xu and
Karamarie Fecho and
Nephi A. Walton and
Richard L. Zhu and
Justin Ramsdill and
Christopher J. Mungall and
Sebastian K{\"{o}}hler and
Melissa A. Haendel and
Clement J. McDonald and
Daniel J. Vreeman and
David B. Peden and
Tellen D. Bennett and
James A. Feinstein and
Blake Martin and
Adrianne L. Stefanski and
Lawrence E. Hunter and
Christopher G. Chute and
Peter N. Robinson},
title = {Semantic integration of clinical laboratory tests from electronic
health records for deep phenotyping and biomarker discovery},
journal = {npj Digit. Medicine},
volume = {2},
year = {2019},
url = {https://doi.org/10.1038/s41746-019-0110-4},
doi = {10.1038/S41746-019-0110-4},
timestamp = {Fri, 08 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/npjdm/ZhangYVGCCDJRPC19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/CarmodyZVMMR19,
author = {Leigh C. Carmody and
Xingmin Aaron Zhang and
Nicole A. Vasilevsky and
Christopher J. Mungall and
Nicolas Matentzoglu and
Peter N. Robinson},
editor = {Alexander D. Diehl and
William D. Duncan and
Gloria Sanso},
title = {Medical Action Ontology (MAxO)},
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},
publisher = {CEUR-WS.org},
year = {2019},
url = {https://ceur-ws.org/Vol-2931/ICBO\_2019\_paper\_60.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:23 +0100},
biburl = {https://dblp.org/rec/conf/icbo/CarmodyZVMMR19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/VitaOMSP18,
author = {Randi Vita and
James A. Overton and
Christopher J. Mungall and
Alessandro Sette and
Bjoern Peters},
title = {{FAIR} principles and the {IEDB:} short-term improvements and a long-term
vision of OBO-foundry mediated machine-actionable interoperability},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bax105},
year = {2018},
url = {https://doi.org/10.1093/database/bax105},
doi = {10.1093/DATABASE/BAX105},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/VitaOMSP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/HarperCCJPWAABB18,
author = {Lisa C. Harper and
Jacqueline D. Campbell and
Ethalinda K. S. Cannon and
Sook Jung and
Monica Poelchau and
Ramona L. Walls and
Carson M. Andorf and
Elizabeth Arnaud and
Tanya Z. Berardini and
Clayton L. Birkett and
Steven B. Cannon and
James D. Carson and
Bradford Condon and
Laurel Cooper and
Nathan A. Dunn and
Christine G. Elsik and
Andrew D. Farmer and
Stephen P. Ficklin and
David M. Grant and
Emily S. Grau and
Nic Herndon and
Zhi{-}Liang Hu and
Jodi L. Humann and
Pankaj Jaiswal and
Cl{\'{e}}ment Jonquet and
Marie{-}Ang{\'{e}}lique Laporte and
Pierre Larmande and
Gerard R. Lazo and
Fiona McCarthy and
Naama Menda and
Christopher J. Mungall and
Monica C. Munoz{-}Torres and
Sushma Naithani and
Rex T. Nelson and
Daureen Nesdill and
Carissa A. Park and
James M. Reecy and
Leonore Reiser and
Lacey{-}Anne Sanderson and
Taner Z. Sen and
Margaret Staton and
Sabarinath Subramaniam and
Marcela Karey Tello{-}Ruiz and
Victor Unda and
Deepak R. Unni and
Liya Wang and
Doreen Ware and
Jill L. Wegrzyn and
Jason Williams and
Margaret Woodhouse and
Jing Yu and
Doreen Main},
title = {AgBioData consortium recommendations for sustainable genomics and
genetics databases for agriculture},
journal = {Database J. Biol. Databases Curation},
volume = {2018},
pages = {bay088},
year = {2018},
url = {https://doi.org/10.1093/database/bay088},
doi = {10.1093/DATABASE/BAY088},
timestamp = {Tue, 25 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/HarperCCJPWAABB18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/MatentzogluMMS18,
author = {Nicolas Matentzoglu and
James Malone and
Chris Mungall and
Robert Stevens},
title = {{MIRO:} guidelines for minimum information for the reporting of an
ontology},
journal = {J. Biomed. Semant.},
volume = {9},
number = {1},
pages = {6:1--6:13},
year = {2018},
url = {https://doi.org/10.1186/s13326-017-0172-7},
doi = {10.1186/S13326-017-0172-7},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/MatentzogluMMS18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CooperMLEMSCCD018,
author = {Laurel Cooper and
Austin Meier and
Marie{-}Ang{\'{e}}lique Laporte and
Justin Elser and
Chris Mungall and
Brandon T. Sinn and
Dario Cavaliere and
Seth Carbon and
Nathan A. Dunn and
Barry Smith and
Botong Qu and
Justin Preece and
Eugene Zhang and
Sinisa Todorovic and
Georgios V. Gkoutos and
John H. Doonan and
Dennis W. Stevenson and
Elizabeth Arnaud and
Pankaj Jaiswal},
title = {The Planteome database: an integrated resource for reference ontologies,
plant genomics and phenomics},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D1168--D1180},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx1152},
doi = {10.1093/NAR/GKX1152},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/CooperMLEMSCCD018.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/MabeeBDLMV18,
author = {Paula M. Mabee and
James P. Balhoff and
Wasila M. Dahdul and
Hilmar Lapp and
Christopher J. Mungall and
Todd J. Vision},
editor = {Pankaj Jaiswal and
Laurel Cooper and
Melissa A. Haendel and
Christopher J. Mungall},
title = {Reasoning over Anatomical Homology in the Phenoscape {KB}},
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\_62.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:24 +0100},
biburl = {https://dblp.org/rec/conf/icbo/MabeeBDLMV18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/TauberBDMO18,
author = {Rebecca Tauber and
James P. Balhoff and
Eric Douglass and
Chris Mungall and
James A. Overton},
editor = {Pankaj Jaiswal and
Laurel Cooper and
Melissa A. Haendel and
Christopher J. Mungall},
title = {Standardizing Ontology Workflows Using {ROBOT}},
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\_46.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/TauberBDMO18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/semweb/BalhoffGCM18,
author = {James P. Balhoff and
Benjamin M. Good and
Seth Carbon and
Chris Mungall},
editor = {Marieke van Erp and
Medha Atre and
Vanessa L{\'{o}}pez and
Kavitha Srinivas and
Carolina Fortuna},
title = {Arachne: an {OWL} {RL} Reasoner Applied to Gene Ontology Causal Activity
Models (and Beyond)},
booktitle = {Proceedings of the {ISWC} 2018 Posters {\&} Demonstrations, Industry
and Blue Sky Ideas Tracks co-located with 17th International Semantic
Web Conference {(ISWC} 2018), Monterey, USA, October 8th - to - 12th,
2018},
series = {{CEUR} Workshop Proceedings},
volume = {2180},
publisher = {CEUR-WS.org},
year = {2018},
url = {https://ceur-ws.org/Vol-2180/paper-05.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:03 +0100},
biburl = {https://dblp.org/rec/conf/semweb/BalhoffGCM18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/icbo/2018,
editor = {Pankaj Jaiswal and
Laurel Cooper and
Melissa A. Haendel and
Christopher J. Mungall},
title = {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},
urn = {urn:nbn:de:0074-2285-4},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/2018.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/artmed/ElhananOMLMP17,
author = {Gai Elhanan and
Christopher Ochs and
Jos{\'{e}} L. V. Mejino Jr. and
Hao Liu and
Christopher J. Mungall and
Yehoshua Perl},
title = {From {SNOMED} {CT} to Uberon: Transferability of evaluation methodology
between similarly structured ontologies},
journal = {Artif. Intell. Medicine},
volume = {79},
pages = {9--14},
year = {2017},
url = {https://doi.org/10.1016/j.artmed.2017.05.002},
doi = {10.1016/J.ARTMED.2017.05.002},
timestamp = {Tue, 26 Mar 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/artmed/ElhananOMLMP17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HolmesM17,
author = {Ian H. Holmes and
Christopher J. Mungall},
title = {BioMake: a {GNU} make-compatible utility for declarative workflow
management},
journal = {Bioinform.},
volume = {33},
number = {21},
pages = {3502--3504},
year = {2017},
url = {https://doi.org/10.1093/bioinformatics/btx306},
doi = {10.1093/BIOINFORMATICS/BTX306},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HolmesM17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/Osumi-Sutherland17,
author = {David Osumi{-}Sutherland and
M{\'{e}}lanie Courtot and
James P. Balhoff and
Christopher J. Mungall},
title = {Dead simple {OWL} design patterns},
journal = {J. Biomed. Semant.},
volume = {8},
number = {1},
pages = {18:1--18:7},
year = {2017},
url = {https://doi.org/10.1186/s13326-017-0126-0},
doi = {10.1186/S13326-017-0126-0},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/Osumi-Sutherland17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/OngXZLLZMCRH17,
author = {Edison Ong and
Zuoshuang Xiang and
Bin Zhao and
Yue Liu and
Yu Lin and
Jie Zheng and
Chris Mungall and
M{\'{e}}lanie Courtot and
Alan Ruttenberg and
Yongqun He},
title = {Ontobee: {A} linked ontology data server to support ontology term
dereferencing, linkage, query and integration},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D347--D352},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw918},
doi = {10.1093/NAR/GKW918},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/OngXZLLZMCRH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/MungallM0BBBCCD17,
author = {Christopher J. Mungall and
Julie A. McMurry and
Sebastian K{\"{o}}hler and
James P. Balhoff and
Charles D. Borromeo and
Matthew H. Brush and
Seth Carbon and
Tom Conlin and
Nathan A. Dunn and
Mark Engelstad and
Erin Foster and
Jean{-}Philippe F. Gourdine and
Julius O. B. Jacobsen and
Dan Keith and
Bryan Laraway and
Suzanna E. Lewis and
Jeremy NguyenXuan and
Kent A. Shefchek and
Nicole A. Vasilevsky and
Zhou Yuan and
Nicole L. Washington and
Harry Hochheiser and
Tudor Groza and
Damian Smedley and
Peter N. Robinson and
Melissa A. Haendel},
title = {The Monarch Initiative: an integrative data and analytic platform
connecting phenotypes to genotypes across species},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D712--D722},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw1128},
doi = {10.1093/NAR/GKW1128},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/MungallM0BBBCCD17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LizioHANKSMAMML17,
author = {Marina Lizio and
Jayson Harshbarger and
Imad Abugessaisa and
Shuei Noguchi and
Atsushi Kondo and
Jessica Severin and
Chris Mungall and
David J. Arenillas and
Anthony Mathelier and
Yulia A. Medvedeva and
Andreas Lennartsson and
Finn Drabl{\o}s and
Jordan A. Ramilowski and
Owen J. L. Rackham and
Julian Gough and
Robin Andersson and
Albin Sandelin and
Hans Ienasescu and
Hiromasa Ono and
Hidemasa Bono and
Yoshihide Hayashizaki and
Piero Carninci and
Alistair R. R. Forrest and
Takeya Kasukawa and
Hideya Kawaji},
title = {Update of the {FANTOM} web resource: high resolution transcriptome
of diverse cell types in mammals},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D737--D743},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw995},
doi = {10.1093/NAR/GKW995},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/LizioHANKSMAMML17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/0001VEFMABBBBBB17,
author = {Sebastian K{\"{o}}hler and
Nicole A. Vasilevsky and
Mark Engelstad and
Erin Foster and
Julie A. McMurry and
S{\'{e}}gol{\`{e}}ne Aym{\'{e}} and
Gareth Baynam and
Susan M. Bello and
Cornelius F. Boerkoel and
Kym M. Boycott and
Michael Brudno and
Orion J. Buske and
Patrick F. Chinnery and
Valentina Cipriani and
Laureen E. Connell and
Hugh J. S. Dawkins and
Laura E. DeMare and
Andrew Devereau and
Bert B. A. de Vries and
Helen V. Firth and
Kathleen Freson and
Daniel Greene and
Ada Hamosh and
Ingo Helbig and
Courtney Hum and
Johanna J{\"{a}}hn and
Roger James and
Roland Krause and
Stanley J. F. Laulederkind and
Hanns Lochm{\"{u}}ller and
Gholson J. Lyon and
Soichi Ogishima and
Annie Olry and
Willem H. Ouwehand and
Nikolas Pontikos and
Ana Rath and
Franz Schaefer and
Richard H. Scott and
Michael Segal and
Panagiotis I. Sergouniotis and
Richard Sever and
Cynthia L. Smith and
Volker Straub and
Rachel Thompson and
Catherine Turner and
Ernest Turro and
Marijcke W. M. Veltman and
Tom Vulliamy and
Jing Yu and
Julie von Ziegenweidt and
Andreas Zankl and
Stephan Z{\"{u}}chner and
Tomasz Zemojtel and
Julius O. B. Jacobsen and
Tudor Groza and
Damian Smedley and
Christopher J. Mungall and
Melissa A. Haendel and
Peter N. Robinson},
title = {The Human Phenotype Ontology in 2017},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D865--D876},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw1039},
doi = {10.1093/NAR/GKW1039},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/0001VEFMABBBBBB17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/BalhoffBCCFHMRV17,
author = {James P. Balhoff and
Matthew H. Brush and
Laura Christopherson and
Sherri de Coronado and
Gilberto Fragoso and
Melissa A. Haendel and
Christopher J. Mungall and
Kimberly Robasky and
Nicole A. Vasilevsky and
Lawrence W. Wright},
editor = {Matthew Horridge and
Phillip Lord and
Jennifer D. Warrender},
title = {Tailoring the {NCI} Thesaurus for Use in The {OBO} Library},
booktitle = {Proceedings of the 8th International Conference on Biomedical Ontology
{(ICBO} 2017), Newcastle-upon-Tyne, United Kingdom, September 13th
- 15th, 2017},
series = {{CEUR} Workshop Proceedings},
volume = {2137},
publisher = {CEUR-WS.org},
year = {2017},
url = {https://ceur-ws.org/Vol-2137/ws\_ONCONTO\_paper\_4.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:24 +0100},
biburl = {https://dblp.org/rec/conf/icbo/BalhoffBCCFHMRV17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/VasilevskyBMO0B17,
author = {Nicole A. Vasilevsky and
James P. Balhoff and
Christopher J. Mungall and
David Osumi{-}Sutherland and
Sebastian K{\"{o}}hler and
Susan M. Bello and
Cynthia L. Smith and
Peter N. Robinson and
Melissa A. Haendel},
editor = {Matthew Horridge and
Phillip Lord and
Jennifer D. Warrender},
title = {Aligning the Human Phenotype and Mammalian Phenotype Ontology using
Dead Simple Ontology Design Patterns},
booktitle = {Proceedings of the 8th International Conference on Biomedical Ontology
{(ICBO} 2017), Newcastle-upon-Tyne, United Kingdom, September 13th
- 15th, 2017},
series = {{CEUR} Workshop Proceedings},
volume = {2137},
publisher = {CEUR-WS.org},
year = {2017},
url = {https://ceur-ws.org/Vol-2137/paper\_22.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/VasilevskyBMO0B17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/MungallH17,
author = {Christopher J. Mungall and
Ian H. Holmes},
title = {WTFgenes: What's The Function of these genes? Static sites for model-based
gene set analysis},
journal = {F1000Research},
volume = {6},
pages = {423},
year = {2017},
url = {https://doi.org/10.12688/f1000research.11175.1},
doi = {10.12688/F1000RESEARCH.11175.1},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/MungallH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/HillDBMRB16,
author = {David P. Hill and
Peter D'Eustachio and
Tanya Z. Berardini and
Christopher J. Mungall and
Nikolai Renedo and
Judith A. Blake},
title = {Modeling biochemical pathways in the gene ontology},
journal = {Database J. Biol. Databases Curation},
volume = {2016},
year = {2016},
url = {https://doi.org/10.1093/database/baw126},
doi = {10.1093/DATABASE/BAW126},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/HillDBMRB16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/BollemanMSBDBBH16,
author = {Jerven T. Bolleman and
Christopher J. Mungall and
Francesco Strozzi and
Joachim Baran and
Michel Dumontier and
Raoul Jean Pierre Bonnal and
Robert M. Buels and
Robert Hoehndorf and
Takatomo Fujisawa and
Toshiaki Katayama and
Peter J. A. Cock},
title = {{FALDO:} a semantic standard for describing the location of nucleotide
and protein feature annotation},
journal = {J. Biomed. Semant.},
volume = {7},
pages = {39},
year = {2016},
url = {https://doi.org/10.1186/s13326-016-0067-z},
doi = {10.1186/S13326-016-0067-Z},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/BollemanMSBDBBH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/DiehlMBBDDHORSS16,
author = {Alexander D. Diehl and
Terrence F. Meehan and
Yvonne M. Bradford and
Matthew H. Brush and
Wasila M. Dahdul and
David S. Dougall and
Yongqun He and
David Osumi{-}Sutherland and
Alan Ruttenberg and
Sirarat Sarntivijai and
Ceri E. Van Slyke and
Nicole A. Vasilevsky and
Melissa A. Haendel and
Judith A. Blake and
Christopher J. Mungall},
title = {The Cell Ontology 2016: enhanced content, modularization, and ontology
interoperability},
journal = {J. Biomed. Semant.},
volume = {7},
pages = {44},
year = {2016},
url = {https://doi.org/10.1186/s13326-016-0088-7},
doi = {10.1186/S13326-016-0088-7},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/biomedsem/DiehlMBBDDHORSS16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/ButtigiegPLSWM16,
author = {Pier Luigi Buttigieg and
Evangelos Pafilis and
Suzanna E. Lewis and
Mark P. Schildhauer and
Ramona L. Walls and
Christopher J. Mungall},
title = {The environment ontology in 2016: bridging domains with increased
scope, semantic density, and interoperation},
journal = {J. Biomed. Semant.},
volume = {7},
pages = {57},
year = {2016},
url = {https://doi.org/10.1186/s13326-016-0097-6},
doi = {10.1186/S13326-016-0097-6},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/ButtigiegPLSWM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/ButtigiegJWM16,
author = {Pier Luigi Buttigieg and
Mark Jensen and
Ramona L. Walls and
Christopher J. Mungall},
editor = {Pankaj Jaiswal and
Robert Hoehndorf and
Cecilia N. Arighi and
Austin Meier},
title = {Environmental Semantics for Sustainable Development in an Interconnected
Biosphere},
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/IT201\_ICBO2016.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:23 +0100},
biburl = {https://dblp.org/rec/conf/icbo/ButtigiegJWM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/CooperMEPXKQZTJ16,
author = {Laurel Cooper and
Austin Meier and
Justin Elser and
Justin Preece and
Xu Xu and
Ryan Kitchen and
Botong Qu and
Eugene Zhang and
Sinisa Todorovic and
Pankaj Jaiswal and
Marie{-}Ang{\'{e}}lique Laporte and
Elizabeth Arnaud and
Seth Carbon and
Chris Mungall and
Barry Smith and
Georgios V. Gkoutos and
John H. Doonan},
editor = {Pankaj Jaiswal and
Robert Hoehndorf and
Cecilia N. Arighi and
Austin Meier},
title = {The Planteome Project},
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/IT406-IP35\_ICBO2016.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/CooperMEPXKQZTJ16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/CourtotMM16,
author = {M{\'{e}}lanie Courtot and
James Malone and
Chris Mungall},
editor = {Pankaj Jaiswal and
Robert Hoehndorf and
Cecilia N. Arighi and
Austin Meier},
title = {Ten Simple Rules for Biomedical Ontology Development},
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/IT404\_ICBO2016.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/CourtotMM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/LaporteVCMMJA16,
author = {Marie{-}Ang{\'{e}}lique Laporte and
L{\'{e}}o Valette and
Laurel Cooper and
Chris Mungall and
Austin Meier and
Pankaj Jaiswal and
Elizabeth Arnaud},
editor = {Pankaj Jaiswal and
Robert Hoehndorf and
Cecilia N. Arighi and
Austin Meier},
title = {Comparison of Ontology Mapping Techniques to Map Plant Trait 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/IP17\_ICBO2016.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/LaporteVCMMJA16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/QuDZEJCM16,
author = {Botong Qu and
Jaden Diefenbaugh and
Eugene Zhang and
Justin Elser and
Pankaj Jaiswal and
Seth Carbon and
Christopher J. Mungall},
editor = {Pankaj Jaiswal and
Robert Hoehndorf and
Cecilia N. Arighi and
Austin Meier},
title = {Planteome Gene Annotation Enrichment Analysis},
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/IP31\_ICBO2016.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/QuDZEJCM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/VasilevskyEFMR016,
author = {Nicole A. Vasilevsky and
Mark Engelstad and
Erin Foster and
Chris Mungall and
Peter N. Robinson and
Sebastian K{\"{o}}hler and
Melissa A. Haendel},
editor = {Pankaj Jaiswal and
Robert Hoehndorf and
Cecilia N. Arighi and
Austin Meier},
title = {Enhancing the Human Phenotype Ontology for Use by the Layperson},
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/IT402\_ICBO2016.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/VasilevskyEFMR016.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/MandaMBLV16,
author = {Prashanti Manda and
Christopher J. Mungall and
James P. Balhoff and
Hilmar Lapp and
Todd J. Vision},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein and
Marylyn D. Ritchie},
title = {Investigating the Importance of Anatomical Homology for Cross-Species
Phenotype Comparisons Using Semantic Similarity},
booktitle = {Biocomputing 2016: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 4-8, 2016},
pages = {132--143},
year = {2016},
url = {http://psb.stanford.edu/psb-online/proceedings/psb16/manda.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/MandaMBLV16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {Warren A. Kibbe and
Cesar Arze and
Victor Felix and
Elvira Mitraka and
Evan Bolton and
Gang Fu and
Christopher J. Mungall and
Janos X. Binder and
James Malone and
Drashtti Vasant and
Helen E. Parkinson and
Lynn M. Schriml},
title = {Disease Ontology 2015 update: an expanded and updated database of
human diseases for linking biomedical knowledge through disease data},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Database-Issue},
pages = {1071--1078},
year = {2015},
url = {https://doi.org/10.1093/nar/gku1011},
doi = {10.1093/NAR/GKU1011},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KibbeAFMBFMBMVPS15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/OvertonDEOM15,
author = {James A. Overton and
Heiko Dietze and
Shahim Essaid and
David Osumi{-}Sutherland and
Christopher J. Mungall},
editor = {Francisco M. Couto and
Janna Hastings},
title = {{ROBOT:} {A} command-line tool for ontology development},
booktitle = {Proceedings of the International Conference on Biomedical Ontology,
{ICBO} 2015, Lisbon, Portugal, July 27-30, 2015},
series = {{CEUR} Workshop Proceedings},
volume = {1515},
publisher = {CEUR-WS.org},
year = {2015},
url = {https://ceur-ws.org/Vol-1515/demo6.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:24 +0100},
biburl = {https://dblp.org/rec/conf/icbo/OvertonDEOM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/ChibucosMBCHWBLG14,
author = {Marcus C. Chibucos and
Christopher J. Mungall and
Rama Balakrishnan and
Karen R. Christie and
Rachael P. Huntley and
Owen White and
Judith A. Blake and
Suzanna E. Lewis and
Michelle G. Giglio},
title = {Standardized description of scientific evidence using the Evidence
Ontology {(ECO)}},
journal = {Database J. Biol. Databases Curation},
volume = {2014},
year = {2014},
url = {https://doi.org/10.1093/database/bau075},
doi = {10.1093/DATABASE/BAU075},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/ChibucosMBCHWBLG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/HaendelBBBBBCDDDHILMNRSM14,
author = {Melissa A. Haendel and
James P. Balhoff and
Frederic B. Bastian and
David C. Blackburn and
Judith A. Blake and
Yvonne M. Bradford and
Aur{\'{e}}lie Comte and
Wasila M. Dahdul and
Thomas Dececchi and
Robert E. Druzinsky and
Terry F. Hayamizu and
Nizar Ibrahim and
Suzanna E. Lewis and
Paula M. Mabee and
Anne Niknejad and
Marc Robinson{-}Rechavi and
Paul C. Sereno and
Christopher J. Mungall},
title = {Unification of multi-species vertebrate anatomy ontologies for comparative
biology in Uberon},
journal = {J. Biomed. Semant.},
volume = {5},
pages = {21},
year = {2014},
url = {https://doi.org/10.1186/2041-1480-5-21},
doi = {10.1186/2041-1480-5-21},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/HaendelBBBBBCDDDHILMNRSM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/DahdulCMMOWH14,
author = {Wasila M. Dahdul and
Hong Cui and
Paula M. Mabee and
Christopher J. Mungall and
David Osumi{-}Sutherland and
Ramona L. Walls and
Melissa A. Haendel},
title = {Nose to tail, roots to shoots: spatial descriptors for phenotypic
diversity in the Biological Spatial Ontology},
journal = {J. Biomed. Semant.},
volume = {5},
pages = {34},
year = {2014},
url = {https://doi.org/10.1186/2041-1480-5-34},
doi = {10.1186/2041-1480-5-34},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/DahdulCMMOWH14.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/biomedsem/ThackerDKVSHM14,
author = {Robert W. Thacker and
Maria D{\'{\i}}az and
Adeline Kerner and
R{\'{e}}gine Vignes{-}Lebbe and
Erik Segerdell and
Melissa A. Haendel and
Christopher J. Mungall},
title = {The Porifera Ontology {(PORO):} enhancing sponge systematics with
an anatomy ontology},
journal = {J. Biomed. Semant.},
volume = {5},
pages = {39},
year = {2014},
url = {https://doi.org/10.1186/2041-1480-5-39},
doi = {10.1186/2041-1480-5-39},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/ThackerDKVSHM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/DietzeBFHLORM14,
author = {Heiko Dietze and
Tanya Z. Berardini and
Rebecca E. Foulger and
David P. Hill and
Jane Lomax and
David Osumi{-}Sutherland and
Paola Roncaglia and
Christopher J. Mungall},
title = {TermGenie - {A} web application for pattern-based ontology class generation},
journal = {J. Biomed. Semant.},
volume = {5},
pages = {48},
year = {2014},
url = {https://doi.org/10.1186/2041-1480-5-48},
doi = {10.1186/2041-1480-5-48},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/DietzeBFHLORM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/OellrichKWMLHRS14,
author = {Anika Oellrich and
Sebastian K{\"{o}}hler and
Nicole L. Washington and
Chris Mungall and
Suzanna Lewis and
Melissa A. Haendel and
Peter N. Robinson and
Damian Smedley},
title = {The influence of disease categories on gene candidate predictions
from model organism phenotypes},
journal = {J. Biomed. Semant.},
volume = {5},
number = {{S-1}},
pages = {S4},
year = {2014},
url = {https://doi.org/10.1186/2041-1480-5-S1-S4},
doi = {10.1186/2041-1480-5-S1-S4},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/OellrichKWMLHRS14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/HuntleyHABCDDFHKLLLMSAWM14,
author = {Rachael P. Huntley and
Midori A. Harris and
Yasmin Alam{-}Faruque and
Judith A. Blake and
Seth Carbon and
Heiko Dietze and
Emily C. Dimmer and
Rebecca E. Foulger and
David P. Hill and
Varsha K. Khodiyar and
Antonia Lock and
Jane Lomax and
Ruth C. Lovering and
Prudence Mutowo{-}Meullenet and
Tony Sawford and
Kimberly Van Auken and
Valerie Wood and
Christopher J. Mungall},
title = {A method for increasing expressivity of Gene Ontology annotations
using a compositional approach},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {155},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-155},
doi = {10.1186/1471-2105-15-155},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/HuntleyHABCDDFHKLLLMSAWM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ecoi/PoelenSM14,
author = {Jorrit H. Poelen and
James D. Simons and
Chris Mungall},
title = {Global biotic interactions: An open infrastructure to share and analyze
species-interaction datasets},
journal = {Ecol. Informatics},
volume = {24},
pages = {148--159},
year = {2014},
url = {https://doi.org/10.1016/j.ecoinf.2014.08.005},
doi = {10.1016/J.ECOINF.2014.08.005},
timestamp = {Sat, 22 Feb 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/ecoi/PoelenSM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KohlerDM14,
author = {Sebastian K{\"{o}}hler and
Sandra C. Doelken and
Christopher J. Mungall and
Sebastian Bauer and
Helen V. Firth and
Isabelle Bailleul{-}Forestier and
Graeme C. M. Black and
Danielle L. Brown and
Michael Brudno and
Jennifer Campbell and
David R. FitzPatrick and
Janan T. Eppig and
Andrew P. Jackson and
Kathleen Freson and
Marta G{\^{\i}}rdea and
Ingo Helbig and
Jane A. Hurst and
Johanna J{\"{a}}hn and
Laird G. Jackson and
Anne M. Kelly and
David H. Ledbetter and
Sahar Mansour and
Christa L. Martin and
Celia Moss and
Andrew D. Mumford and
Willem H. Ouwehand and
Soo{-}Mi Park and
Erin Rooney Riggs and
Richard H. Scott and
Sanjay Sisodiya and
Steven Van Vooren and
Ronald J. Wapner and
Andrew O. M. Wilkie and
Caroline F. Wright and
Anneke T. Vulto{-}van Silfhout and
Nicole de Leeuw and
Bert B. A. de Vries and
Nicole L. Washington and
Cynthia L. Smith and
Monte Westerfield and
Paul N. Schofield and
Barbara J. Ruef and
Georgios V. Gkoutos and
Melissa A. Haendel and
Damian Smedley and
Suzanna E. Lewis and
Peter N. Robinson},
title = {The Human Phenotype Ontology project: linking molecular biology and
disease through phenotype data},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {966--974},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1026},
doi = {10.1093/NAR/GKT1026},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KohlerDM14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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author = {The Fantom Consortium and
RIKEN PMII and
RIKEN CLST (DGT) and
Alistair R. R. Forrest and
Hideya Kawaji and
Michael Rehli and
J. Kenneth Baillie and
Michiel J. L. de Hoon and
Vanja Haberle and
Timo Lassmann and
Ivan V. Kulakovskiy and
Marina Lizio and
Masayoshi Itoh and
Robin Andersson and
Christopher J. Mungall and
Terrence F. Meehan and
Sebastian Schmeier and
Nicolas Bertin and
Mette J{\o}rgensen and
Emmanuel Dimont and
Erik Arner and
Christian Schmidl and
Ulf Schaefer and
Yulia A. Medvedeva and
Charles Plessy and
Morana Vitezic and
Jessica Severin and
Colin A. M. Semple and
Yuri Ishizu and
Robert S. Young and
Margherita Francescatto and
Intikhab Alam and
Davide Albanese and
Gabriel M. Altschuler and
Takahiro Arakawa and
John A. C. Archer and
Peter Arner and
Magda Babina and
Sarah Rennie and
Piotr J. Balwierz and
Anthony G. Beckhouse and
Swati Pradhan{-}Bhatt and
Judith A. Blake and
Antje Blumenthal and
Beatrice Bodega and
Alessandro Bonetti and
James Briggs and
Frank Brombacher and
A. Maxwell Burroughs and
Andrea Califano and
Carlo V. Cannistraci and
Daniel Carbajo and
Yun Chen and
Marco Chierici and
Yari Ciani and
Hans Clevers and
Emiliano Dalla and
Carrie A. Davis and
Michael Detmar and
Alexander D. Diehl and
Taeko Dohi and
Finn Drabl{\o}s and
Albert S. B. Edge and
Matthias Edinger and
Karl Ekwall and
Mitsuhiro Endoh and
Hideki Enomoto and
Michela Fagiolini and
Lynsey Fairbairn and
Hai Fang and
Mary C. Farach{-}Carson and
Geoffrey J. Faulkner and
Alexander V. Favorov and
Malcolm E. Fisher and
Martin C. Frith and
Rie Fujita and
Shiro Fukuda and
Cesare Furlanello and
Masaaki Furuno and
Jun{-}ichi Furusawa and
Teunis B. Geijtenbeek and
Andrew P. Gibson and
Thomas R. Gingeras and
Daniel Goldowitz and
Julian Gough and
Sven Guhl and
Reto Guler and
Stefano Gustincich and
Thomas J. Ha and
Masahide Hamaguchi and
Mitsuko Hara and
Matthias Harbers and
Jayson Harshbarger and
Akira Hasegawa and
Yuki Hasegawa and
Takehiro Hashimoto and
Meenhard Herlyn and
Kelly J. Hitchens and
Shannan J. Ho Sui and
Oliver M. Hofmann and
Ilka Hoof and
Fumi Hori and
Lukasz Huminiecki and
Kei Iida and
Tomokatsu Ikawa and
Boris R. Jankovic and
Hui Jia and
Anagha Joshi and
Giuseppe Jurman and
Bogumil Kaczkowski and
Chieko Kai and
Kaoru Kaida and
Ai Kaiho and
Kazuhiro Kajiyama and
Mutsumi Kanamori{-}Katayama and
Artem S. Kasianov and
Takeya Kasukawa and
Shintaro Katayama and
Sachi Kato and
Shuji Kawaguchi and
Hiroshi Kawamoto and
Yuki I. Kawamura and
Tsugumi Kawashima and
Judith S. Kempfle and
Tony J. Kenna and
Juha Kere and
Levon M. Khachigian and
Toshio Kitamura and
S. Peter Klinken and
Alan J. Knox and
Miki Kojima and
Soichi Kojima and
Naoto Kondo and
Haruhiko Koseki and
Shigeo Koyasu and
Sarah Krampitz and
Atsutaka Kubosaki and
Andrew T. Kwon and
Jeroen F. J. Laros and
Weonju Lee and
Andreas Lennartsson and
Kang Li and
Berit Lilje and
Leonard Lipovich and
Alan Mackay{-}Sim and
Ri{-}ichiroh Manabe and
Jessica Cara Mar and
Benoit Marchand and
Anthony Mathelier and
Niklas Mejhert and
Alison M. Meynert and
Yosuke Mizuno and
David A. de Lima Morais and
Hiromasa Morikawa and
Mitsuru Morimoto and
Kazuyo Moro and
Efthymios Motakis and
Hozumi Motohashi and
Christine Mummery and
Mitsuyoshi Murata and
Sayaka Nagao{-}Sato and
Yutaka Nakachi and
Fumio Nakahara and
Toshiyuki Nakamura and
Yukio Nakamura and
Kenichi Nakazato and
Erik van Nimwegen and
Noriko Ninomiya and
Hiromi Nishiyori and
Shohei Noma and
Tadasuke Nozaki and
Soichi Ogishima and
Naganari Ohkura and
Hiroko Ohmiya and
Hiroshi Ohno and
Mitsuhiro Ohshima and
Mariko Okada{-}Hatakeyama and
Yasushi Okazaki and
Valerio Orlando and
Dmitry A. Ovchinnikov and
Arnab Pain and
Robert Passier and
Margaret Patrikakis and
Helena Persson and
Silvano Piazza and
James G. D. Prendergast and
Owen J. L. Rackham and
Jordan A. Ramilowski and
Mamoon Rashid and
Timothy Ravasi and
Patrizia Rizzu and
Marco Roncador and
Sugata Roy and
Morten B. Rye and
Eri Saijyo and
Antti Sajantila and
Akiko Saka and
Shimon Sakaguchi and
Mizuho Sakai and
Hiroki Sato and
Hironori Sato and
Suzana Savvi and
Alka Saxena and
Claudio Schneider and
Erik A. Schultes and
Gundula G. Schulze{-}Tanzil and
Anita Schwegmann and
Thierry Sengstag and
Guojun Sheng and
Hisashi Shimoji and
Yishai Shimoni and
Jay W. Shin and
Christophe Simon and
Daisuke Sugiyama and
Takaaki Sugiyama and
Masanori Suzuki and
Naoko Suzuki and
Rolf K. Swoboda and
Peter A. C. 't Hoen and
Michihira Tagami and
Naoko Takahashi and
Jun Takai and
Hiroshi Tanaka and
Hideki Tatsukawa and
Zuotian Tatum and
Mark Thompson and
Hiroo Toyoda and
Tetsuro Toyoda and
Eivind Valen and
Marc van de Wetering and
Linda M. van den Berg and
Roberto Verardo and
Dipti Vijayan and
Ilya E. Vorontsov and
Wyeth W. Wasserman and
Shoko Watanabe and
Christine A. Wells and
Louise N. Winteringham and
Ernst Wolvetang and
Emily J. Wood and
Yoko Yamaguchi and
Masayuki Yamamoto and
Misako Yoneda and
Yohei Yonekura and
Shigehiro Yoshida and
Susan E. Zabierowski and
Peter G. Zhang and
Xiaobei Zhao and
Silvia Zucchelli and
Kim M. Summers and
Harukazu Suzuki and
Carsten O. Daub and
Jun Kawai and
Peter Heutink and
Winston Hide and
Tom C. Freeman and
Boris Lenhard and
Vladimir B. Bajic and
Martin S. Taylor and
Vsevolod J. Makeev and
Albin Sandelin and
David A. Hume and
Piero Carninci and
Yoshihide Hayashizaki},
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journal = {Nat.},
volume = {507},
number = {7493},
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year = {2014},
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timestamp = {Tue, 21 Feb 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nature/ConsortiumFKRB14.bib},
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@inproceedings{DBLP:conf/owled/MungallDO14,
author = {Chris Mungall and
Heiko Dietze and
David Osumi{-}Sutherland},
editor = {C. Maria Keet and
Valentina A. M. Tamma},
title = {Use of {OWL} within the Gene Ontology},
booktitle = {Proceedings of the 11th International Workshop on {OWL:} Experiences
and Directions {(OWLED} 2014) co-located with 13th International Semantic
Web Conference on {(ISWC} 2014), Riva del Garda, Italy, October 17-18,
2014},
series = {{CEUR} Workshop Proceedings},
volume = {1265},
pages = {25--36},
publisher = {CEUR-WS.org},
year = {2014},
url = {https://ceur-ws.org/Vol-1265/owled2014\_submission\_5.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:02 +0100},
biburl = {https://dblp.org/rec/conf/owled/MungallDO14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/SmedleyOKRWRLM13,
author = {Damian Smedley and
Anika Oellrich and
Sebastian K{\"{o}}hler and
Barbara J. Ruef and
Monte Westerfield and
Peter N. Robinson and
Suzanna Lewis and
Christopher J. Mungall},
title = {PhenoDigm: analyzing curated annotations to associate animal models
with human diseases},
journal = {Database J. Biol. Databases Curation},
volume = {2013},
year = {2013},
url = {https://doi.org/10.1093/database/bat025},
doi = {10.1093/DATABASE/BAT025},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/SmedleyOKRWRLM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/ArangurenFAMGW13,
author = {Mikel Ega{\~{n}}a Aranguren and
Jesualdo Tom{\'{a}}s Fern{\'{a}}ndez{-}Breis and
Erick Antezana and
Chris Mungall and
Alejandro Rodr{\'{\i}}guez Gonz{\'{a}}lez and
Mark D. Wilkinson},
title = {OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as
part of bioinformatics workflows},
journal = {J. Biomed. Semant.},
volume = {4},
pages = {2},
year = {2013},
url = {https://doi.org/10.1186/2041-1480-4-2},
doi = {10.1186/2041-1480-4-2},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/ArangurenFAMGW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/RoncagliaMHBFIDML13,
author = {Paola Roncaglia and
Maryann E. Martone and
David P. Hill and
Tanya Z. Berardini and
Rebecca E. Foulger and
Fahim T. Imam and
Harold J. Drabkin and
Christopher J. Mungall and
Jane Lomax},
title = {The Gene Ontology {(GO)} Cellular Component Ontology: integration
with {SAO} (Subcellular Anatomy Ontology) and other recent developments},
journal = {J. Biomed. Semant.},
volume = {4},
pages = {20},
year = {2013},
url = {https://doi.org/10.1186/2041-1480-4-20},
doi = {10.1186/2041-1480-4-20},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/RoncagliaMHBFIDML13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/ButtigiegMSML13,
author = {Pier Luigi Buttigieg and
Norman Morrison and
Barry Smith and
Christopher J. Mungall and
Suzanna E. Lewis},
title = {The environment ontology: contextualising biological and biomedical
entities},
journal = {J. Biomed. Semant.},
volume = {4},
pages = {43},
year = {2013},
url = {https://doi.org/10.1186/2041-1480-4-43},
doi = {10.1186/2041-1480-4-43},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/ButtigiegMSML13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MeehanVMDHBD13,
author = {Terrence F. Meehan and
Nicole A. Vasilevsky and
Christopher J. Mungall and
David S. Dougall and
Melissa A. Haendel and
Judith A. Blake and
Alexander D. Diehl},
title = {Ontology based molecular signatures for immune cell types via gene
expression analysis},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {263},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-263},
doi = {10.1186/1471-2105-14-263},
timestamp = {Thu, 16 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/MeehanVMDHBD13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/fini/MaynardMLIM13,
author = {Sarah Maynard and
Christopher J. Mungall and
Suzanna E. Lewis and
Fahim T. Imam and
Maryann E. Martone},
title = {A knowledge based approach to matching human neurodegenerative disease
and animal models},
journal = {Frontiers Neuroinformatics},
volume = {7},
pages = {7},
year = {2013},
url = {https://doi.org/10.3389/fninf.2013.00007},
doi = {10.3389/FNINF.2013.00007},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/fini/MaynardMLIM13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/BrushMWH13,
author = {Matthew H. Brush and
Chris Mungall and
Nicole L. Washington and
Melissa A. Haendel},
editor = {Michel Dumontier and
Robert Hoehndorf and
Christopher J. O. Baker},
title = {What's in a Genotype?: An Ontological Characterization for Integration
of Genetic Variation Data},
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 = {105--108},
publisher = {CEUR-WS.org},
year = {2013},
url = {https://ceur-ws.org/Vol-1060/icbo2013\_submission\_60.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:24 +0100},
biburl = {https://dblp.org/rec/conf/icbo/BrushMWH13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Osumi-SutherlandRMNRJA12,
author = {David Osumi{-}Sutherland and
Simon Reeve and
Christopher J. Mungall and
Fabian Neuhaus and
Alan Ruttenberg and
Gregory S. X. E. Jefferis and
J. Douglas Armstrong},
title = {A strategy for building neuroanatomy ontologies},
journal = {Bioinform.},
volume = {28},
number = {9},
pages = {1262--1269},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts113},
doi = {10.1093/BIOINFORMATICS/BTS113},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Osumi-SutherlandRMNRJA12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Osumi-SutherlandRMNRJA12a,
author = {David Osumi{-}Sutherland and
Simon Reeve and
Christopher J. Mungall and
Fabian Neuhaus and
Alan Ruttenberg and
Gregory S. X. E. Jefferis and
J. Douglas Armstrong},
title = {A strategy for building neuroanatomy ontologies},
journal = {Bioinform.},
volume = {28},
number = {15},
pages = {2091},
year = {2012},
url = {https://doi.org/10.1093/bioinformatics/bts353},
doi = {10.1093/BIOINFORMATICS/BTS353},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/Osumi-SutherlandRMNRJA12a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ThomasWMLB12,
author = {Paul D. Thomas and
Valerie Wood and
Christopher J. Mungall and
Suzanna E. Lewis and
Judith A. Blake},
title = {On the Use of Gene Ontology Annotations to Assess Functional Similarity
among Orthologs and Paralogs: {A} Short Report},
journal = {PLoS Comput. Biol.},
volume = {8},
number = {2},
year = {2012},
url = {https://doi.org/10.1371/journal.pcbi.1002386},
doi = {10.1371/JOURNAL.PCBI.1002386},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ThomasWMLB12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/WallsCMMCSJ12,
author = {Ramona L. Walls and
Hong Cui and
James A. Macklin and
Chris Mungall and
Laurel Cooper and
Dennis W. Stevenson and
Pankaj Jaiswal},
editor = {Ronald Cornet and
Robert Stevens},
title = {Mapping of glossary terms from the Flora of North America to the Plant
Ontology enhances both resources},
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\_6.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:23 +0100},
biburl = {https://dblp.org/rec/conf/icbo/WallsCMMCSJ12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ao/HoehndorfBBDEKMRSWZL11,
author = {Robert Hoehndorf and
Colin R. Batchelor and
Thomas Bittner and
Michel Dumontier and
Karen Eilbeck and
Rob Knight and
Chris Mungall and
Jane S. Richardson and
Jesse Stombaugh and
Eric Westhof and
Craig L. Zirbel and
Neocles Leontis},
title = {The {RNA} Ontology {(RNAO):} An ontology for integrating {RNA} sequence
and structure data},
journal = {Appl. Ontology},
volume = {6},
number = {1},
pages = {53--89},
year = {2011},
url = {https://doi.org/10.3233/AO-2011-0082},
doi = {10.3233/AO-2011-0082},
timestamp = {Sun, 28 May 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ao/HoehndorfBBDEKMRSWZL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biomedsem/TirmiziAMMSSM11,
author = {Syed Hamid Tirmizi and
Stuart Aitken and
Dilvan A. Moreira and
Chris Mungall and
Juan F. Sequeda and
Nigam H. Shah and
Daniel P. Miranker},
title = {Mapping between the {OBO} and {OWL} ontology languages},
journal = {J. Biomed. Semant.},
volume = {2},
number = {{S-1}},
pages = {S3},
year = {2011},
url = {http://www.jbiomedsem.com/content/2/S1/S3},
timestamp = {Thu, 13 Aug 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biomedsem/TirmiziAMMSSM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MeehanMACBMD11,
author = {Terrence F. Meehan and
Anna Maria Masci and
Amina Abdulla and
Lindsay G. Cowell and
Judith A. Blake and
Christopher J. Mungall and
Alexander D. Diehl},
title = {Logical Development of the Cell Ontology},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {6},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-6},
doi = {10.1186/1471-2105-12-6},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MeehanMACBMD11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/KohlerBMCSSGR11,
author = {Sebastian K{\"{o}}hler and
Sebastian Bauer and
Chris Mungall and
Gabriele Carletti and
Cynthia L. Smith and
Paul N. Schofield and
Georgios V. Gkoutos and
Peter N. Robinson},
title = {Improving ontologies by automatic reasoning and evaluation of logical
definitions},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {418},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-418},
doi = {10.1186/1471-2105-12-418},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/KohlerBMCSSGR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/DiehlABCGGMMMNPPSYZM11,
author = {Alexander D. Diehl and
Alison Deckhut Augustine and
Judith A. Blake and
Lindsay G. Cowell and
Elizabeth S. Gold and
Timothy A. Gondr{\'{e}}{-}Lewis and
Anna Maria Masci and
Terrence F. Meehan and
Penelope A. Morel and
Anastasia Nijnik and
Bjoern Peters and
Bali Pulendran and
Richard H. Scheuermann and
Q. Alison Yao and
Martin S. Zand and
Christopher J. Mungall},
title = {Hematopoietic cell types: Prototype for a revised cell ontology},
journal = {J. Biomed. Informatics},
volume = {44},
number = {1},
pages = {75--79},
year = {2011},
url = {https://doi.org/10.1016/j.jbi.2010.01.006},
doi = {10.1016/J.JBI.2010.01.006},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/DiehlABCGGMMMNPPSYZM11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/MungallBBDIHHL11,
author = {Christopher J. Mungall and
Michael Bada and
Tanya Z. Berardini and
Jennifer I. Deegan and
Amelia Ireland and
Midori A. Harris and
David P. Hill and
Jane Lomax},
title = {Cross-product extensions of the Gene Ontology},
journal = {J. Biomed. Informatics},
volume = {44},
number = {1},
pages = {80--86},
year = {2011},
url = {https://doi.org/10.1016/j.jbi.2010.02.002},
doi = {10.1016/J.JBI.2010.02.002},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/MungallBBDIHHL11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jbi/MungallBE11,
author = {Christopher J. Mungall and
Colin R. Batchelor and
Karen Eilbeck},
title = {Evolution of the Sequence Ontology terms and relationships},
journal = {J. Biomed. Informatics},
volume = {44},
number = {1},
pages = {87--93},
year = {2011},
url = {https://doi.org/10.1016/j.jbi.2010.03.002},
doi = {10.1016/J.JBI.2010.03.002},
timestamp = {Tue, 16 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jbi/MungallBE11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/CourtotMBR11,
author = {M{\'{e}}lanie Courtot and
Chris Mungall and
Ryan Remy Brinkman and
Alan Ruttenberg},
editor = {Olivier Bodenreider and
Maryann E. Martone and
Alan Ruttenberg},
title = {Building the {OBO} Foundry - One Policy at a Time},
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/paper72.pdf},
timestamp = {Fri, 10 Mar 2023 16:22:24 +0100},
biburl = {https://dblp.org/rec/conf/icbo/CourtotMBR11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/MeehanMBD11,
author = {Terrence F. Meehan and
Christopher J. Mungall and
Judith A. Blake and
Alexander D. Diehl},
editor = {Olivier Bodenreider and
Maryann E. Martone and
Alan Ruttenberg},
title = {Gene Ontology Signatures for Immune Cell-Types Inferred by Gene Expression
Analysis},
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/paper41.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/MeehanMBD11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/MeehanMD11,
author = {Terrence F. Meehan and
Christopher J. Mungall and
Alexander D. Diehl},
editor = {Olivier Bodenreider and
Maryann E. Martone and
Alan Ruttenberg},
title = {Revising the Cell Ontology},
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/paper2.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/MeehanMD11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/MungallABCCCCDEEGKILMMTTTTWH11,
author = {Chris Mungall and
David Anderson and
Anita E. Bandrowski and
Brian A. Canada and
Andrew Chatr{-}aryamontri and
Keith C. Cheng and
P. Michael Conn and
Kara Dolinski and
Mark H. Ellisman and
Janan T. Eppig and
Jeffrey S. Grethe and
Joseph W. Kemnitz and
Shawn Iadonato and
Stephen D. Larson and
Charles Magness and
Maryann E. Martone and
Mike Tyers and
Carlo Torniai and
Olga G. Troyanskaya and
Judith Turner and
Monte Westerfield and
Melissa A. Haendel},
editor = {Olivier Bodenreider and
Maryann E. Martone and
Alan Ruttenberg},
title = {An Ontology-Based Approach to Linking Model Organisms and Resources
to Human Diseases},
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/paper43.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/MungallABCCCCDEEGKILMMTTTTWH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/MungallHIMMOTD11,
author = {Christopher J. Mungall and
Melissa A. Haendel and
Amelia Ireland and
Shahid Manzoor and
Terry Meehan and
David Osumi{-}Sutherland and
Carlo Torniai and
Alexander D. Diehl},
editor = {Olivier Bodenreider and
Maryann E. Martone and
Alan Ruttenberg},
title = {Modularization for the Cell Ontology},
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/paper71.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/MungallHIMMOTD11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icbo/XiangMRH11,
author = {Zuoshuang Xiang and
Chris Mungall and
Alan Ruttenberg and
Yongqun He},
editor = {Olivier Bodenreider and
Maryann E. Martone and
Alan Ruttenberg},
title = {Ontobee: {A} Linked Data Server and Browser for Ontology Terms},
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/paper48.pdf},
timestamp = {Fri, 10 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/icbo/XiangMRH11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/owled/Mungall11,
author = {Chris Mungall},
editor = {Michel Dumontier and
M{\'{e}}lanie Courtot},
title = {Posh - The Prolog {OWL} Shell},
booktitle = {Proceedings of the 8th International Workshop on {OWL:} Experiences
and Directions {(OWLED} 2011), San Francisco, California, USA, June
5-6, 2011},
series = {{CEUR} Workshop Proceedings},
volume = {796},
publisher = {CEUR-WS.org},
year = {2011},
url = {https://ceur-ws.org/Vol-796/owled2011\_submission\_15.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:02 +0100},
biburl = {https://dblp.org/rec/conf/owled/Mungall11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ClarkDM10,
author = {Jennifer I. Deegan and
Emily C. Dimmer and
Christopher J. Mungall},
title = {Formalization of taxon-based constraints to detect inconsistencies
in annotation and ontology development},
journal = {{BMC} Bioinform.},
volume = {11},
pages = {530},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-530},
doi = {10.1186/1471-2105-11-530},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ClarkDM10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/AntezanaVMMK10,
author = {Erick Antezana and
Aravind Venkatesan and
Chris Mungall and
Vladimir Mironov and
Martin Kuiper},
title = {ONTO-ToolKit: enabling bio-ontology engineering via Galaxy},
journal = {{BMC} Bioinform.},
volume = {11},
number = {{S-12}},
pages = {S8},
year = {2010},
url = {https://doi.org/10.1186/1471-2105-11-S12-S8},
doi = {10.1186/1471-2105-11-S12-S8},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/AntezanaVMMK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/CarbonIMSML09,
author = {Seth Carbon and
Amelia Ireland and
Christopher J. Mungall and
Shengqiang Shu and
Brad Marshall and
Suzanna Lewis},
title = {AmiGO: online access to ontology and annotation data},
journal = {Bioinform.},
volume = {25},
number = {2},
pages = {288--289},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btn615},
doi = {10.1093/BIOINFORMATICS/BTN615},
timestamp = {Fri, 30 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/CarbonIMSML09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MasciADLMSSC09,
author = {Anna Maria Masci and
Cecilia N. Arighi and
Alexander D. Diehl and
Anne E. Lieberman and
Chris Mungall and
Richard H. Scheuermann and
Barry Smith and
Lindsay G. Cowell},
title = {An improved ontological representation of dendritic cells as a paradigm
for all cell types},
journal = {{BMC} Bioinform.},
volume = {10},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-70},
doi = {10.1186/1471-2105-10-70},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MasciADLMSSC09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/SchoberSLKLMTRS09,
author = {Daniel Schober and
Barry Smith and
Suzanna E. Lewis and
Waclaw Kusnierczyk and
Jane Lomax and
Chris Mungall and
Chris F. Taylor and
Philippe Rocca{-}Serra and
Susanna{-}Assunta Sansone},
title = {Survey-based naming conventions for use in {OBO} Foundry ontology
development},
journal = {{BMC} Bioinform.},
volume = {10},
year = {2009},
url = {https://doi.org/10.1186/1471-2105-10-125},
doi = {10.1186/1471-2105-10-125},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/SchoberSLKLMTRS09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iclp/Mungall09,
author = {Chris Mungall},
editor = {Patricia M. Hill and
David Scott Warren},
title = {Experiences Using Logic Programming in Bioinformatics},
booktitle = {Logic Programming, 25th International Conference, {ICLP} 2009, Pasadena,
CA, USA, July 14-17, 2009. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5649},
pages = {1--21},
publisher = {Springer},
year = {2009},
url = {https://doi.org/10.1007/978-3-642-02846-5\_1},
doi = {10.1007/978-3-642-02846-5\_1},
timestamp = {Fri, 27 Dec 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/iclp/Mungall09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/semweb/VassiliadisWM08,
author = {Vangelis Vassiliadis and
Jan Wielemaker and
Chris Mungall},
editor = {Rinke Hoekstra and
Peter F. Patel{-}Schneider},
title = {Processing {OWL2} Ontologies using Thea: An Application of Logic Programming},
booktitle = {Proceedings of the 5th International Workshop on {OWL:} Experiences
and Directions {(OWLED} 2009), Chantilly, VA, United States, October
23-24, 2009},
series = {{CEUR} Workshop Proceedings},
volume = {529},
publisher = {CEUR-WS.org},
year = {2009},
url = {https://ceur-ws.org/Vol-529/owled2009\_submission\_43.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:05 +0100},
biburl = {https://dblp.org/rec/conf/semweb/VassiliadisWM08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/swat4ls/TirmiziAMMSSM09,
author = {Syed Hamid Tirmizi and
Stuart Aitken and
Dilvan A. Moreira and
Chris Mungall and
Juan F. Sequeda and
Nigam H. Shah and
Daniel P. Miranker},
editor = {M. Scott Marshall and
Albert Burger and
Paolo Romano and
Adrian Paschke and
Andrea Splendiani},
title = {{OBO} {\&} {OWL:} Roundtrip Ontology Transformations},
booktitle = {Proceedings of the Workshop on Semantic Web Applications and Tools
for Life Sciences, Amsterdam, The Netherlands, November 20, 2009},
series = {{CEUR} Workshop Proceedings},
volume = {559},
publisher = {CEUR-WS.org},
year = {2009},
url = {https://ceur-ws.org/Vol-559/Paper6.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:02 +0100},
biburl = {https://dblp.org/rec/conf/swat4ls/TirmiziAMMSSM09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/YandellMSMMWR08,
author = {Mark Yandell and
Barry Moore and
Fidel Salas and
Chris Mungall and
Andrew MacBride and
Charles White and
Martin G. Reese},
title = {Genome-Wide Analysis of Human Disease Alleles Reveals That Their Locations
Are Correlated in Paralogous Proteins},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {11},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000218},
doi = {10.1371/JOURNAL.PCBI.1000218},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/YandellMSMMWR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/owled/BadaMH08,
author = {Michael Bada and
Chris Mungall and
Lawrence Hunter},
editor = {Catherine Dolbear and
Alan Ruttenberg and
Ulrike Sattler},
title = {A Call for an Abductive Reasoning Feature in OWL-Reasoning Tools toward
Ontology Quality Control},
booktitle = {Proceedings of the Fifth {OWLED} Workshop on {OWL:} Experiences and
Directions, collocated with the 7th International Semantic Web Conference
(ISWC-2008), Karlsruhe, Germany, October 26-27, 2008},
series = {{CEUR} Workshop Proceedings},
volume = {432},
publisher = {CEUR-WS.org},
year = {2008},
url = {https://ceur-ws.org/Vol-432/owled2008eu\_submission\_44.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:02 +0100},
biburl = {https://dblp.org/rec/conf/owled/BadaMH08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@incollection{DBLP:series/cb/HaendelNOMMM008,
author = {Melissa A. Haendel and
Fabian Neuhaus and
David Osumi{-}Sutherland and
Paula M. Mabee and
Jos{\'{e}} L. V. Mejino Jr. and
Chris Mungall and
Barry Smith},
editor = {Albert Burger and
Duncan Davidson and
Richard A. Baldock},
title = {{CARO} - The Common Anatomy Reference Ontology},
booktitle = {Anatomy Ontologies for Bioinformatics, Principles and Practice},
series = {Computational Biology},
volume = {6},
pages = {327--349},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-1-84628-885-2\_16},
doi = {10.1007/978-1-84628-885-2\_16},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/series/cb/HaendelNOMMM008.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dagstuhl/WashingtonGMAGWHL08,
author = {Nicole L. Washington and
M. Gibson and
Chris Mungall and
Michael Ashburner and
Georgios V. Gkoutos and
Monte Westerfield and
Melissa A. Haendel and
Suzanna E. Lewis},
editor = {Michael Ashburner and
Ulf Leser and
Dietrich Rebholz{-}Schuhmann},
title = {{NLP} and Phenotypes: using Ontologies to link Human Diseases to Animal
Models},
booktitle = {Ontologies and Text Mining for Life Sciences: Current Status and Future
Perspectives, 24.03. - 28.03.2008},
series = {Dagstuhl Seminar Proceedings},
volume = {08131},
publisher = {Internationales Begegnungs- und Forschungszentrum f{\"{u}}r Informatik
(IBFI), Schloss Dagstuhl, Germany},
year = {2008},
url = {http://drops.dagstuhl.de/opus/volltexte/2008/1514},
timestamp = {Thu, 10 Jun 2021 13:02:07 +0200},
biburl = {https://dblp.org/rec/conf/dagstuhl/WashingtonGMAGWHL08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/MungallE07,
author = {Chris Mungall and
David B. Emmert},
title = {A Chado case study: an ontology-based modular schema for representing
genome-associated biological information},
booktitle = {Proceedings 15th International Conference on Intelligent Systems for
Molecular Biology {(ISMB)} {\&} 6th European Conference on Computational
Biology (ECCB), Vienna, Austria, July 21-25, 2007},
pages = {337--346},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm189},
doi = {10.1093/BIOINFORMATICS/BTM189},
timestamp = {Fri, 27 Dec 2019 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/MungallE07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/owled/Mungall07,
author = {Chris Mungall},
editor = {Christine Golbreich and
Aditya Kalyanpur and
Bijan Parsia},
title = {Representing Phenotypes in {OWL}},
booktitle = {Proceedings of the {OWLED} 2007 Workshop on {OWL:} Experiences and
Directions, Innsbruck, Austria, June 6-7, 2007},
series = {{CEUR} Workshop Proceedings},
volume = {258},
publisher = {CEUR-WS.org},
year = {2007},
url = {https://ceur-ws.org/Vol-258/paper29.pdf},
timestamp = {Fri, 10 Mar 2023 16:23:02 +0100},
biburl = {https://dblp.org/rec/conf/owled/Mungall07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/YandellMSPKHLR06,
author = {Mark Yandell and
Chris Mungall and
Chris Smith and
Simon Prochnik and
Joshua S. Kaminker and
George Hartzell and
Suzanna Lewis and
Gerald M. Rubin},
title = {Large-Scale Trends in the Evolution of Gene Structures within 11 Animal
Genomes},
journal = {PLoS Comput. Biol.},
volume = {2},
number = {3},
year = {2006},
url = {https://doi.org/10.1371/journal.pcbi.0020015},
doi = {10.1371/JOURNAL.PCBI.0020015},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/YandellMSPKHLR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HuMLPNBSLBHA01,
author = {Jian Hu and
Chris Mungall and
Andy Law and
Richard Papworth and
J. Paul Nelson and
Alison Brown and
Irene Simpson and
Shirley Leckie and
David W. Burt and
Alan L. Hillyard and
Alan L. Archibald},
title = {The ARKdb: genome databases for farmed and other animals},
journal = {Nucleic Acids Res.},
volume = {29},
number = {1},
pages = {106--110},
year = {2001},
url = {https://doi.org/10.1093/nar/29.1.106},
doi = {10.1093/NAR/29.1.106},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HuMLPNBSLBHA01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HuMNA98,
author = {Jian Hu and
Chris Mungall and
David Nicholson and
Alan L. Archibald},
title = {Design and implementation of a CORBA-based genome mapping system prototype},
journal = {Bioinform.},
volume = {14},
number = {2},
pages = {112--120},
year = {1998},
url = {https://doi.org/10.1093/bioinformatics/14.2.112},
doi = {10.1093/BIOINFORMATICS/14.2.112},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HuMNA98.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/dexaw/HuNMHA96,
author = {Jian Hu and
David Nicholson and
Chris Mungall and
Alan L. Hillyard and
Alan L. Archibald},
editor = {Roland Wagner and
Helmut Thoma},
title = {WebinTool: {A} Generic Web to Database Interface Building Tool},
booktitle = {Seventh International Workshop on Database and Expert Systems Applications,
{DEXA} '96, Zurich, Switzerland, September 9-10, 1996},
pages = {285--290},
publisher = {{IEEE} Computer Society},
year = {1996},
url = {https://doi.org/10.1109/DEXA.1996.558323},
doi = {10.1109/DEXA.1996.558323},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/dexaw/HuNMHA96.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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