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ORCIDBibTeX records: Nomi L. Harris
@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 = {Mon, 01 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/CaufieldHEHJMKMRHRM24.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-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-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, 16 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2312-10904.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}
}
@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/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 = {Fri, 15 Mar 2024 00:00:00 +0100},
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/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 16:22:23 +0100},
biburl = {https://dblp.org/rec/conf/icbo/MoxonSUJBBVDHMB21.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/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}
}
@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 16:22:24 +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/ploscb/DunnUDMHYRHEL19,
author = {Nathan A. Dunn and
Deepak R. Unni and
Colin M. Diesh and
Monica C. Munoz{-}Torres and
Nomi L. Harris and
Eric Yao and
Helena Rasche and
Ian H. Holmes and
Christine G. Elsik and
Suzanna E. Lewis},
title = {Apollo: Democratizing genome annotation},
journal = {PLoS Comput. Biol.},
volume = {15},
number = {2},
year = {2019},
url = {https://doi.org/10.1371/journal.pcbi.1006790},
doi = {10.1371/JOURNAL.PCBI.1006790},
timestamp = {Fri, 09 Apr 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/DunnUDMHYRHEL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/HarrisWCCHLFT18,
author = {Nomi L. Harris and
Heather Wiencko and
Brad Chapman and
Peter J. A. Cock and
Karsten Hokamp and
Hilmar Lapp and
Christopher J. Fields and
Bastian Greshake Tzovaras},
title = {The 2018 Bioinformatics Open Source Conference {(GCCBOSC} 2018)},
journal = {F1000Research},
volume = {7},
pages = {1309},
year = {2018},
url = {https://doi.org/10.12688/f1000research.15936.1},
doi = {10.12688/F1000RESEARCH.15936.1},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/HarrisWCCHLFT18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/HarrisCCFHLMTW17,
author = {Nomi L. Harris and
Peter J. A. Cock and
Brad Chapman and
Christopher J. Fields and
Karsten Hokamp and
Hilmar Lapp and
Monica C. Munoz{-}Torres and
Bastian Greshake Tzovaras and
Heather Wiencko},
title = {The 2017 Bioinformatics Open Source Conference {(BOSC)}},
journal = {F1000Research},
volume = {6},
pages = {1858},
year = {2017},
url = {https://doi.org/10.12688/f1000research.12929.1},
doi = {10.12688/F1000RESEARCH.12929.1},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/HarrisCCFHLMTW17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/HarrisCLCDFHM16,
author = {Nomi L. Harris and
Peter J. A. Cock and
Hilmar Lapp and
Brad Chapman and
Rob Davey and
Christopher J. Fields and
Karsten Hokamp and
Monica C. Munoz{-}Torres},
title = {The 2015 Bioinformatics Open Source Conference {(BOSC} 2015)},
journal = {PLoS Comput. Biol.},
volume = {12},
number = {2},
year = {2016},
url = {https://doi.org/10.1371/journal.pcbi.1004691},
doi = {10.1371/JOURNAL.PCBI.1004691},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/HarrisCLCDFHM16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/HarrisCCFHLMW16,
author = {Nomi L. Harris and
Peter J. A. Cock and
Brad Chapman and
Christopher J. Fields and
Karsten Hokamp and
Hilmar Lapp and
Monica C. Munoz{-}Torres and
Heather Wiencko},
title = {The 2016 Bioinformatics Open Source Conference {(BOSC)}},
journal = {F1000Research},
volume = {5},
pages = {2464},
year = {2016},
url = {https://doi.org/10.12688/f1000research.9663.1},
doi = {10.12688/F1000RESEARCH.9663.1},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/HarrisCCFHLMW16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HarrisCCGHL15,
author = {Nomi L. Harris and
Peter J. A. Cock and
Brad A. Chapman and
Jeremy Goecks and
Hans{-}Rudolf Hotz and
Hilmar Lapp},
title = {The Bioinformatics Open Source Conference {(BOSC)} 2013},
journal = {Bioinform.},
volume = {31},
number = {2},
pages = {299--300},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btu413},
doi = {10.1093/BIOINFORMATICS/BTU413},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HarrisCCGHL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/MollerABBBCCGHHKKKPPQSSSSSSSTTGKC14,
author = {Steffen M{\"{o}}ller and
Enis Afgan and
Michael Banck and
Raoul Jean Pierre Bonnal and
Timothy Booth and
John Chilton and
Peter J. A. Cock and
Markus Gumbel and
Nomi L. Harris and
Richard C. G. Holland and
Mat{\'{u}}s Kalas and
L{\'{a}}szl{\'{o}} Kaj{\'{a}}n and
Eri Kibukawa and
David R. Powell and
Pjotr Prins and
Jacqueline Quinn and
Olivier Sallou and
Francesco Strozzi and
Torsten Seemann and
Clare Sloggett and
Stian Soiland{-}Reyes and
William Spooner and
Sascha Steinbiss and
Andreas Tille and
Anthony J. Travis and
Roman Guimera and
Toshiaki Katayama and
Brad A. Chapman},
title = {Community-driven development for computational biology at Sprints,
Hackathons and Codefests},
journal = {{BMC} Bioinform.},
volume = {15},
number = {{S-14}},
pages = {S7},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-S14-S7},
doi = {10.1186/1471-2105-15-S14-S7},
timestamp = {Wed, 07 Dec 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/MollerABBBCCGHHKKKPPQSSSSSSSTTGKC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/LeeHGCL09,
author = {Ed Lee and
Nomi L. Harris and
Mark Gibson and
Raymond Chetty and
Suzanna Lewis},
title = {Apollo: a community resource for genome annotation editing},
journal = {Bioinform.},
volume = {25},
number = {14},
pages = {1836--1837},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp314},
doi = {10.1093/BIOINFORMATICS/BTP314},
timestamp = {Thu, 09 Jul 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/LeeHGCL09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/StatesHH93,
author = {David J. States and
Nomi L. Harris and
Lawrence Hunter},
editor = {Lawrence Hunter and
David B. Searls and
Jude W. Shavlik},
title = {Computationally Efficient Cluster Representation in Molecular Sequence
Megaclassification},
booktitle = {Proceedings of the 1st International Conference on Intelligent Systems
for Molecular Biology, Bethesda, MD, USA, July 1993},
pages = {387--394},
publisher = {{AAAI}},
year = {1993},
url = {http://www.aaai.org/Library/ISMB/1993/ismb93-045.php},
timestamp = {Thu, 13 Dec 2012 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/StatesHH93.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/aaai/HarrisHS92,
author = {Nomi L. Harris and
Lawrence Hunter and
David J. States},
editor = {William R. Swartout},
title = {Mega-Classification: Discovering Motifs in Massive Datastreams},
booktitle = {Proceedings of the 10th National Conference on Artificial Intelligence,
San Jose, CA, USA, July 12-16, 1992},
pages = {837--842},
publisher = {{AAAI} Press / The {MIT} Press},
year = {1992},
url = {http://www.aaai.org/Library/AAAI/1992/aaai92-129.php},
timestamp = {Mon, 04 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/aaai/HarrisHS92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icml/HunterHS92,
author = {Lawrence Hunter and
Nomi L. Harris and
David J. States},
editor = {Derek H. Sleeman and
Peter Edwards},
title = {Efficient Classification of Massive, Unsegmented Datastreams},
booktitle = {Proceedings of the Ninth International Workshop on Machine Learning
{(ML} 1992), Aberdeen, Scotland, UK, July 1-3, 1992},
pages = {224--232},
publisher = {Morgan Kaufmann},
year = {1992},
url = {https://doi.org/10.1016/b978-1-55860-247-2.50034-6},
doi = {10.1016/B978-1-55860-247-2.50034-6},
timestamp = {Mon, 16 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icml/HunterHS92.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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