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references.bib
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% Generated by Paperpile. Check out https://paperpile.com for more information.
% BibTeX export options can be customized via Settings -> BibTeX.
@ARTICLE{Gargano2024-nj,
title = "The Human Phenotype Ontology in 2024: phenotypes around the world",
author = "Gargano, Michael A and Matentzoglu, Nicolas and Coleman, Ben and
Addo-Lartey, Eunice B and Anagnostopoulos, Anna V and Anderton,
Joel and Avillach, Paul and Bagley, Anita M and Bak{\v s}tein,
Eduard and Balhoff, James P and Baynam, Gareth and Bello, Susan M
and Berk, Michael and Bertram, Holli and Bishop, Somer and Blau,
Hannah and Bodenstein, David F and Botas, Pablo and Boztug, Kaan
and {\v C}ady, Jolana and Callahan, Tiffany J and Cameron,
Rhiannon and Carbon, Seth J and Castellanos, Francisco and
Caufield, J Harry and Chan, Lauren E and Chute, Christopher G and
Cruz-Rojo, Jaime and Dahan-Oliel, No{\'e}mi and Davids, Jon R and
de Dieuleveult, Maud and de Souza, Vinicius and de Vries, Bert B
A and de Vries, Esther and DePaulo, J Raymond and Derfalvi, Beata
and Dhombres, Ferdinand and Diaz-Byrd, Claudia and Dingemans,
Alexander J M and Donadille, Bruno and Duyzend, Michael and
Elfeky, Reem and Essaid, Shahim and Fabrizzi, Carolina and Fico,
Giovanna and Firth, Helen V and Freudenberg-Hua, Yun and
Fullerton, Janice M and Gabriel, Davera L and Gilmour, Kimberly
and Giordano, Jessica and Goes, Fernando S and Moses, Rachel Gore
and Green, Ian and Griese, Matthias and Groza, Tudor and Gu,
Weihong and Guthrie, Julia and Gyori, Benjamin and Hamosh, Ada
and Hanauer, Marc and Hanu{\v s}ov{\'a}, Kate{\v r}ina and He,
Yongqun Oliver and Hegde, Harshad and Helbig, Ingo and
Holasov{\'a}, Kate{\v r}ina and Hoyt, Charles Tapley and Huang,
Shangzhi and Hurwitz, Eric and Jacobsen, Julius O B and Jiang,
Xiaofeng and Joseph, Lisa and Keramatian, Kamyar and King, Bryan
and Knoflach, Katrin and Koolen, David A and Kraus, Megan L and
Kroll, Carlo and Kusters, Maaike and Ladewig, Markus S and
Lagorce, David and Lai, Meng-Chuan and Lapunzina, Pablo and
Laraway, Bryan and Lewis-Smith, David and Li, Xiarong and Lucano,
Caterina and Majd, Marzieh and Marazita, Mary L and
Martinez-Glez, Victor and McHenry, Toby H and McInnis, Melvin G
and McMurry, Julie A and Mihulov{\'a}, Michaela and Millett,
Caitlin E and Mitchell, Philip B and Moslerov{\'a}, Veronika and
Narutomi, Kenji and Nematollahi, Shahrzad and Nevado, Julian and
Nierenberg, Andrew A and {\v C}ajbikov{\'a}, Nikola Nov{\'a}k and
Nurnberger, Jr, John I and Ogishima, Soichi and Olson, Daniel and
Ortiz, Abigail and Pachajoa, Harry and Perez de Nanclares,
Guiomar and Peters, Amy and Putman, Tim and Rapp, Christina K and
Rath, Ana and Reese, Justin and Rekerle, Lauren and Roberts,
Angharad M and Roy, Suzy and Sanders, Stephan J and Schuetz,
Catharina and Schulte, Eva C and Schulze, Thomas G and Schwarz,
Martin and Scott, Katie and Seelow, Dominik and Seitz, Berthold
and Shen, Yiping and Similuk, Morgan N and Simon, Eric S and
Singh, Balwinder and Smedley, Damian and Smith, Cynthia L and
Smolinsky, Jake T and Sperry, Sarah and Stafford, Elizabeth and
Stefancsik, Ray and Steinhaus, Robin and Strawbridge, Rebecca and
Sundaramurthi, Jagadish Chandrabose and Talapova, Polina and
Tenorio Castano, Jair A and Tesner, Pavel and Thomas, Rhys H and
Thurm, Audrey and Turnovec, Marek and van Gijn, Marielle E and
Vasilevsky, Nicole A and Vl{\v c}kov{\'a}, Mark{\'e}ta and
Walden, Anita and Wang, Kai and Wapner, Ron and Ware, James S and
Wiafe, Addo A and Wiafe, Samuel A and Wiggins, Lisa D and
Williams, Andrew E and Wu, Chen and Wyrwoll, Margot J and Xiong,
Hui and Yalin, Nefize and Yamamoto, Yasunori and Yatham, Lakshmi
N and Yocum, Anastasia K and Young, Allan H and Y{\"u}ksel, Zafer
and Zandi, Peter P and Zankl, Andreas and Zarante, Ignacio and
Zvolsk{\'y}, Miroslav and Toro, Sabrina and Carmody, Leigh C and
Harris, Nomi L and Munoz-Torres, Monica C and Danis, Daniel and
Mungall, Christopher J and K{\"o}hler, Sebastian and Haendel,
Melissa A and Robinson, Peter N",
abstract = "The Human Phenotype Ontology (HPO) is a widely used resource that
comprehensively organizes and defines the phenotypic features of
human disease, enabling computational inference and supporting
genomic and phenotypic analyses through semantic similarity and
machine learning algorithms. The HPO has widespread applications
in clinical diagnostics and translational research, including
genomic diagnostics, gene-disease discovery, and cohort
analytics. In recent years, groups around the world have
developed translations of the HPO from English to other
languages, and the HPO browser has been internationalized,
allowing users to view HPO term labels and in many cases synonyms
and definitions in ten languages in addition to English. Since
our last report, a total of 2239 new HPO terms and 49235 new HPO
annotations were developed, many in collaboration with external
groups in the fields of psychiatry, arthrogryposis, immunology
and cardiology. The Medical Action Ontology (MAxO) is a new
effort to model treatments and other measures taken for clinical
management. Finally, the HPO consortium is contributing to
efforts to integrate the HPO and the GA4GH Phenopacket Schema
into electronic health records (EHRs) with the goal of more
standardized and computable integration of rare disease data in
EHRs.",
journal = "Nucleic Acids Res.",
volume = 52,
number = "D1",
pages = "D1333--D1346",
month = jan,
year = 2024,
language = "en"
}
@ARTICLE{Lazarin2014-rz,
title = "Systematic Classification of Disease Severity for Evaluation of
Expanded Carrier Screening Panels",
author = "Lazarin, Gabriel A and Hawthorne, Felicia and Collins, Nicholas S
and Platt, Elizabeth A and Evans, Eric A and Haque, Imran S",
abstract = "Professional guidelines dictate that disease severity is a key
criterion for carrier screening. Expanded carrier screening,
which tests for hundreds to thousands of mutations
simultaneously, requires an objective, systematic means of
describing a given disease's severity to build screening panels.
We hypothesized that diseases with characteristics deemed to be
of highest impact would likewise be rated as most severe, and
diseases with characteristics of lower impact would be rated as
less severe. We describe a pilot test of this hypothesis in which
we surveyed 192 health care professionals to determine the impact
of specific disease phenotypic characteristics on perceived
severity, and asked the same group to rate the severity of
selected inherited diseases. The results support the hypothesis:
we identified four ``Tiers'' of disease characteristics (1-4).
Based on these responses, we developed an algorithm that, based
on the combination of characteristics normally seen in an
affected individual, classifies the disease as Profound, Severe,
Moderate, or Mild. This algorithm allows simple classification of
disease severity that is replicable and not labor intensive.",
journal = "PLoS One",
volume = 9,
number = 12,
pages = "e114391",
month = dec,
year = 2014,
language = "en"
}
@article{
openaiGPT4TechnicalReport2024,
title={GPT-4 Technical Report},
url={http://arxiv.org/abs/2303.08774},
DOI={10.48550/arXiv.2303.08774},
journal={arXiv},
year={2024},
author={OpenAI and Achiam, Josh and Adler, Steven and Agarwal, Sandhini and Ahmad, Lama and Akkaya, Ilge and Aleman, Florencia Leoni and Almeida, Diogo and Altenschmidt, Janko and Altman, Sam and et al.} }
@article{
vanveenAdaptedLargeLanguage2024,
title={Adapted large language models can outperform medical experts in clinical text summarization},
ISSN={1546-170X},
url={https://www.nature.com/articles/s41591-024-02855-5},
DOI={10.1038/s41591-024-02855-5},
journal={Nature Medicine},
publisher={Nature},
author={Van Veen, Dave and Van Uden, Cara and Blankemeier, Louis and Delbrouck, Jean-Benoit and Aali, Asad and Bluethgen, Christian and Pareek, Anuj and Polacin, Malgorzata and Reis, Eduardo Pontes and Seehofnerová, Anna and et al.},
year={2024},
month={Feb},
pages={1–9} }
@article{
singhalLargeLanguageModels2023,
title={Large language models encode clinical knowledge},
ISSN={1476-4687},
url={https://www.nature.com/articles/s41586-023-06291-2},
DOI={10.1038/s41586-023-06291-2},
journal={Nature},
publisher={Nature},
author={Singhal, Karan and Azizi, Shekoofeh and Tu, Tao and Mahdavi, S. Sara and Wei, Jason and Chung, Hyung Won and Scales, Nathan and Tanwani, Ajay and Cole-Lewis, Heather and Pfohl, Stephen and et al.},
year={2023},
month={Jul},
pages={1–9} }
@article{
luoBioGPTGenerativePretrained2022,
title={BioGPT: generative pre-trained transformer for biomedical text generation and mining},
volume={23},
ISSN={1477-4054},
url={https://doi.org/10.1093/bib/bbac409},
DOI={10.1093/bib/bbac409},
number={6},
journal={Briefings in Bioinformatics},
author={Luo, Renqian and Sun, Liai and Xia, Yingce and Qin, Tao and Zhang, Sheng and Poon, Hoifung and Liu, Tie-Yan},
year={2022},
month={Nov},
pages={bbac409} }
@article{
chengExploringPotentialGPT42023,
title={Exploring the Potential of GPT-4 in Biomedical Engineering: The Dawn of a New Era},
volume={51},
ISSN={1573-9686},
DOI={10.1007/s10439-023-03221-1},
number={8},
journal={Annals of Biomedical Engineering},
author={Cheng, Kunming and Guo, Qiang and He, Yongbin and Lu, Yanqiu and Gu, Shuqin and Wu, Haiyang},
year={2023},
month={Aug},
pages={1645–1653} }
@article{
zhangBiomedGPTUnifiedGeneralist2023,
title={BiomedGPT: A Unified and Generalist Biomedical Generative Pre-trained Transformer for Vision, Language, and Multimodal Tasks},
url={http://arxiv.org/abs/2305.17100},
DOI={10.48550/arXiv.2305.17100},
journal={arXiv},
year={2023},
author={Zhang, Kai and Yu, Jun and Yan, Zhiling and Liu, Yixin and Adhikarla, Eashan and Fu, Sunyang and Chen, Xun and Chen, Chen and Zhou, Yuyin and Li, Xiang and et al.} }
@article{
boltonBioMedLM7BParameter2024,
title={BioMedLM: A 2.7B Parameter Language Model Trained On Biomedical Text},
url={http://arxiv.org/abs/2403.18421},
DOI={10.48550/arXiv.2403.18421},
journal={arXiv},
year={2024},
author={Bolton, Elliot and Venigalla, Abhinav and Yasunaga, Michihiro and Hall, David and Xiong, Betty and Lee, Tony and Daneshjou, Roxana and Frankle, Jonathan and Liang, Percy and Carbin, Michael and et al.} }
@article{
guDomainSpecificLanguageModel2021,
title={Domain-Specific Language Model Pretraining for Biomedical Natural Language Processing},
volume={3},
url={https://dl.acm.org/doi/10.1145/3458754},
DOI={10.1145/3458754},
number={1},
journal={ACM Transactions on Computing for Healthcare},
author={Gu, Yu and Tinn, Robert and Cheng, Hao and Lucas, Michael and Usuyama, Naoto and Liu, Xiaodong and Naumann, Tristan and Gao, Jianfeng and Poon, Hoifung},
year={2021},
month={Oct},
pages={2:1–2:23} }
@inproceedings{
shinBioMegatronLargerBiomedical2020,
place={Online},
title={BioMegatron: Larger Biomedical Domain Language Model},
url={https://aclanthology.org/2020.emnlp-main.379},
DOI={10.18653/v1/2020.emnlp-main.379},
booktitle={Proceedings of the 2020 Conference on Empirical Methods in Natural Language Processing (EMNLP)},
publisher={Association for Computational Linguistics},
author={Shin, Hoo-Chang and Zhang, Yang and Bakhturina, Evelina and Puri, Raul and Patwary, Mostofa and Shoeybi, Mohammad and Mani, Raghav},
editor={Webber, Bonnie and Cohn, Trevor and He, Yulan and Liu, Yang},
year={2020},
month={Nov},
pages={4700–4706} }
@article{
mcduffAccurateDifferentialDiagnosis2023,
title={Towards Accurate Differential Diagnosis with Large Language Models},
url={http://arxiv.org/abs/2312.00164},
DOI={10.48550/arXiv.2312.00164},
journal={arXiv},
year={2023},
author={McDuff, Daniel and Schaekermann, Mike and Tu, Tao and Palepu, Anil and Wang, Amy and Garrison, Jake and Singhal, Karan and Sharma, Yash and Azizi, Shekoofeh and Kulkarni, Kavita and et al.} }
@article{
singhalExpertLevelMedicalQuestion2023,
title={Towards Expert-Level Medical Question Answering with Large Language Models},
url={http://arxiv.org/abs/2305.09617},
DOI={10.48550/arXiv.2305.09617},
journal={arXiv},
year={2023},
author={Singhal, Karan and Tu, Tao and Gottweis, Juraj and Sayres, Rory and Wulczyn, Ellery and Hou, Le and Clark, Kevin and Pfohl, Stephen and Cole-Lewis, Heather and Neal, Darlene and et al.} }
@article{
oneilPhenomicsAssistantInterface2024,
title={Phenomics Assistant: An Interface for LLM-based Biomedical Knowledge Graph Exploration},
url={https://www.biorxiv.org/content/10.1101/2024.01.31.578275v1},
DOI={10.1101/2024.01.31.578275},
journal={bioRxiv},
year={2024},
author={O’Neil, Shawn T. and Schaper, Kevin and Elsarboukh, Glass and Reese, Justin T. and Moxon, Sierra A. T. and Harris, Nomi L. and Munoz-Torres, Monica C. and Robinson, Peter N. and Haendel, Melissa A. and Mungall, Christopher J.} }
@article{
labrakBioMistralCollectionOpenSource2024,
title={BioMistral: A Collection of Open-Source Pretrained Large Language Models for Medical Domains},
url={http://arxiv.org/abs/2402.10373},
DOI={10.48550/arXiv.2402.10373},
journal={arXiv},
year={2024},
author={Labrak, Yanis and Bazoge, Adrien and Morin, Emmanuel and Gourraud, Pierre-Antoine and Rouvier, Mickael and Dufour, Richard} }
@article{
noriCanGeneralistFoundation2023,
title={Can Generalist Foundation Models Outcompete Special-Purpose Tuning? Case Study in Medicine},
url={http://arxiv.org/abs/2311.16452},
DOI={10.48550/arXiv.2311.16452},
journal={arXiv},
year={2023},
author={Nori, Harsha and Lee, Yin Tat and Zhang, Sheng and Carignan, Dean and Edgar, Richard and Fusi, Nicolo and King, Nicholas and Larson, Jonathan and Li, Yuanzhi and Liu, Weishung and et al.} }
@inbook{
garagnaniSyndromesAssociatedSyndactyly2013,
place={New York, NY},
title={Syndromes Associated with Syndactyly},
ISBN={978-1-4614-8758-6},
url={https://doi.org/10.1007/978-1-4614-8758-6_14-1},
DOI={10.1007/978-1-4614-8758-6_14-1},
booktitle={The Pediatric Upper Extremity},
publisher={Springer},
author={Garagnani, Lorenzo and Smith, Gillian D.},
editor={Abzug, Joshua M. and Kozin, Scott and Zlotolow, Dan A.},
year={2013},
pages={1–31} }
@article{
gleesonMolarToothSign2004,
title={Molar tooth sign of the midbrain–hindbrain junction: Occurrence in multiple distinct syndromes},
volume={125A},
ISSN={1552-4833},
url={https://onlinelibrary.wiley.com/doi/abs/10.1002/ajmg.a.20437},
DOI={10.1002/ajmg.a.20437},
note={_eprint: https://onlinelibrary.wiley.com/doi/pdf/10.1002/ajmg.a.20437},
number={2},
journal={American Journal of Medical Genetics Part A},
author={Gleeson, Joseph G. and Keeler, Lesley C. and Parisi, Melissa A. and Marsh, Sarah E. and Chance, Phillip F. and Glass, Ian A. and Graham Jr, John M. and Maria, Bernard L. and Barkovich, A. James and Dobyns, William B.},
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pages={125–134} }
@article{
kohlerHumanPhenotypeOntology2021,
title={The Human Phenotype Ontology in 2021},
volume={49},
ISSN={0305-1048},
url={https://doi.org/10.1093/nar/gkaa1043},
DOI={10.1093/nar/gkaa1043},
number={D1},
journal={Nucleic Acids Research},
author={Köhler, Sebastian and Gargano, Michael and Matentzoglu, Nicolas and Carmody, Leigh C and Lewis-Smith, David and Vasilevsky, Nicole A and Danis, Daniel and Balagura, Ganna and Baynam, Gareth and Brower, Amy M and et al.},
year={2021},
month={Jan},
pages={D1207–D1217} }
@article{
garganoHumanPhenotypeOntology2024,
title={The Human Phenotype Ontology in 2024: phenotypes around the world},
volume={52},
ISSN={0305-1048},
url={https://doi.org/10.1093/nar/gkad1005},
DOI={10.1093/nar/gkad1005},
number={D1},
journal={Nucleic Acids Research},
author={Gargano, Michael A and Matentzoglu, Nicolas and Coleman, Ben and Addo-Lartey, Eunice B and Anagnostopoulos, Anna V and Anderton, Joel and Avillach, Paul and Bagley, Anita M and Bakštein, Eduard and Balhoff, James P and et al.},
year={2024},
month={Jan},
pages={D1333–D1346} }
@article{
caufieldStructuredPromptInterrogation2023,
title={Structured prompt interrogation and recursive extraction of semantics (SPIRES): A method for populating knowledge bases using zero-shot learning},
url={http://arxiv.org/abs/2304.02711},
DOI={10.48550/arXiv.2304.02711},
journal={arXiv},
year={2023},
author={Caufield, J. Harry and Hegde, Harshad and Emonet, Vincent and Harris, Nomi L. and Joachimiak, Marcin P. and Matentzoglu, Nicolas and Kim, HyeongSik and Moxon, Sierra A. T. and Reese, Justin T. and Haendel, Melissa A. and et al.} }
@article{
panLargeLanguageModels2023,
title={Large Language Models and Knowledge Graphs: Opportunities and Challenges},
url={http://arxiv.org/abs/2308.06374},
DOI={10.48550/arXiv.2308.06374},
journal={arXiv},
year={2023},
author={Pan, Jeff Z. and Razniewski, Simon and Kalo, Jan-Christoph and Singhania, Sneha and Chen, Jiaoyan and Dietze, Stefan and Jabeen, Hajira and Omeliyanenko, Janna and Zhang, Wen and Lissandrini, Matteo and et al.} }
@article{
putmanMonarchInitiative20242024,
title={The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species},
volume={52},
ISSN={1362-4962},
url={https://europepmc.org/articles/PMC10767791},
DOI={10.1093/nar/gkad1082},
number={D1},
journal={Nucleic acids research},
author={Putman, Tim E and Schaper, Kevin and Matentzoglu, Nicolas and Rubinetti, Vincent P and Alquaddoomi, Faisal S and Cox, Corey and Caufield, J Harry and Elsarboukh, Glass and Gehrke, Sarah and Hegde, Harshad and et al.},
year={2024},
month={Jan},
pages={D938–D949} }
@article{
mungallMonarchInitiativeIntegrative2017a,
title={The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species},
volume={45},
ISSN={0305-1048},
url={https://doi.org/10.1093/nar/gkw1128},
DOI={10.1093/nar/gkw1128},
number={D1},
journal={Nucleic Acids Research},
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pages={D712–D722} }
@article{
ochoaOpenTargetsPlatform2021,
title={Open Targets Platform: supporting systematic drug–target identification and prioritisation},
volume={49},
ISSN={0305-1048},
url={https://doi.org/10.1093/nar/gkaa1027},
DOI={10.1093/nar/gkaa1027},
number={D1},
journal={Nucleic Acids Research},
author={Ochoa, David and Hercules, Andrew and Carmona, Miguel and Suveges, Daniel and Gonzalez-Uriarte, Asier and Malangone, Cinzia and Miranda, Alfredo and Fumis, Luca and Carvalho-Silva, Denise and Spitzer, Michaela and et al.},
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month={Jan},
pages={D1302–D1310} }
@article{
toroDynamicRetrievalAugmented2023,
title={Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI)},
url={http://arxiv.org/abs/2312.10904},
DOI={10.48550/arXiv.2312.10904},
journal={arXiv},
year={2023},
author={Toro, Sabrina and Anagnostopoulos, Anna V. and Bello, Sue and Blumberg, Kai and Cameron, Rhiannon and Carmody, Leigh and Diehl, Alexander D. and Dooley, Damion and Duncan, William and Fey, Petra and et al.} }
@article{
jonesStatisticalInterpretationTerm1972,
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