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ORCIDDatabase - The Journal of Biological Databases and Curation, Volume 2025
Volume 2025, 2025
- Andrew Green
, Carlos Eduardo Ribas, Nancy Ontiveros-Palacios, Sam Griffiths-Jones, Anton I. Petrov, Alex Bateman, Blake A. Sweeney:
LitSumm: large language models for literature summarization of noncoding RNAs. - Correction to: The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study.
- Limin Zhang, Julian R. Starr, Bruce Ford, Anton Reznicek, Yuxuan Zhou, Étienne Léveillé-Bourret, Étienne Lacroix-Carignan, Jacques Cayouette, Tyler W. Smith, Donald Sutherland, Paul Catling, Jeffery M. Saarela, Hong Cui, James A. Macklin:
Helping authors produce FAIR taxonomic data: evaluation of an author-driven phenotype data production prototype. - Yaxuan Hu, Xingli Guo, Yao Yun, Liang Lu, Xiaotai Huang, Songwei Jia:
DisGeNet: a disease-centric interaction database among diseases and various associated genes. - Harshad Hegde, Jennifer Vendetti, Damien Goutte-Gattat, J. Harry Caufield, John B. Graybeal, Nomi L. Harris, Naouel Karam, Christian Kindermann, Nicolas Matentzoglu, James A. Overton, Mark A. Musen, Christopher J. Mungall:
A change language for ontologies and knowledge graphs. - Naina Kumari, Samir Kumar, Anupama Roy, Princy Saini, Sarika Jaiswal, Mir Asif Iquebal, Ulavappa B. Angadi, Dinesh Kumar:
BuffExDb: web-based tissue-specific gene expression resource for breeding and conservation programmes in Bubalus bubalis. - Chunjuan He, Lichang Chen, Juntao Cao, Yuqing Zhong, Zhendong Gao, Weidong Deng, Jiajin Zhang:
BbGSD: Black-boned Sheep Genome SNP Database. - Alexander B. Rogers, Varsha Kale, Germana Baldi, Antton Alberdi, M. Thomas P. Gilbert, Dipayan Gupta, Morten Tønsberg Limborg, Sen Li, Thomas Payne, Bent Petersen, Jacob A. Rasmussen, Lorna J. Richardson, Robert D. Finn:
HoloFood Data Portal: holo-omic datasets for analysing host-microbiota interactions in animal production. - Expression of Concern: DisGeNet: a disease-centric interaction database among diseases and various associated genes.
- Jennifer R. Smith, Marek A. Tutaj, Jyothi Thota, Logan Lamers, Adam C. Gibson, Akhilanand Kundurthi, Varun Reddy Gollapally, Kent C. Brodie, Stacy Zacher, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Monika Tutaj, Mary L. Kaldunski, Mahima Vedi, Wendy M. Demos, Jeffrey L. De Pons, Melinda R. Dwinell, Anne E. Kwitek:
Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database. - Esmaeil Nourani, Evangelia-Mantelena Makri, Xiqing Mao, Sampo Pyysalo, Søren Brunak, Katerina C. Nastou, Lars Juhl Jensen:
LSD600: the first corpus of biomedical abstracts annotated with lifestyle-disease relations. - Sara Sepehri, Anja Heymans, Dinja De Win, Jan Maushagen, Audrey Sanctorum, Christophe Debruyne, Robim M. Rodrigues, Joery De Kock, Vera Rogiers, Olga De Troyer, Tamara Vanhaecke:
The TOXIN knowledge graph: supporting animal-free risk assessment of cosmetics. - Sook Jung, Chun-Huai Cheng, Taein Lee, Katheryn Buble, Jodi L. Humann, Ping Zheng, Jing Yu, Dorrie Main:
Building resource-efficient community databases using open-source software. - Elly Poretsky, Victoria C. Blake, Carson M. Andorf, Taner Z. Sen:
Assessing the performance of generative artificial intelligence in retrieving information against manually curated genetic and genomic data. - Sarah R. Davies:
Working in biocuration: contemporary experiences and perspectives. - Bálint Biró, Zoltán Gál, Zsófia Nagy, Juan Francisco Garcia, Tsend-Ayush Batbold, Orsolya Ivett Hoffmann:
MANUDB: database and application to retrieve and visualize mammalian NUMTs. - Pingping Huang, Weilin Cao, Zhaojun Li, Qingshuai Chen, Guangchao Wang, Bailing Zhou, Jihua Wang:
PotatoBSLnc: a curated repository of potato long noncoding RNAs in response to biotic stress. - Tao Luo, Wen-Kang Shen, Chu-Yu Zhang, Dan-Dan Song, Xiu-Qing Zhang, An-Yuan Guo, Qian Lei:
TcEVdb: a database for T-cell-derived small extracellular vesicles from single-cell transcriptomes. - Fernando Mora-Márquez, Mikel Hurtado, Unai López de Heredia:
gymnotoa-db: a database and application to optimize functional annotation in gymnosperms. - E. L. Tejada-Gutiérrez, Jordi Mateo-Fornés, Francesc Solsona, Rui Alves:
ForestForward: visualizing and accessing integrated world forest data from the last 50 years. - Yan Shao, Yang Gao, Ling-Yu Wu, Shu-Guang Ge, Peng-Bo Wen:
TumorAgDB1.0: tumor neoantigen database platform. - Xiaomin Zhang, Zhongyi Lei, Jiarong Zhang, Tingting Yang, Xian Liu, Jiguo Xue, Ming Ni:
AnnCovDB: a manually curated annotation database for mutations in SARS-CoV-2 spike protein. - Takayuki Suzuki, Hidemasa Bono:
Pipeline to explore information on genome editing using large language models and genome editing meta-database. - Correction to: CardioHotspots: a database of mutational hotspots for cardiac disorders.
- Lei Gong, Fufeng Liu, Chuanxi Zhang, Yongfan Ming, Yulan Mou, Zhaoting Yuan, Haiming Jiang, Bei Gao, Fuping Lu, Lujia Zhang:
LICEDB: light industrial core enzyme database for industrial applications and AI enzyme design. - Thomas C. Wiegers, Allan Peter Davis, Jolene Wiegers, Daniela Sciaky, Fern Barkalow, Brent Wyatt, Melissa Strong, Roy McMorran, Sakib Abrar, Carolyn J. Mattingly:
Integrating AI-powered text mining from PubTator into the manual curation workflow at the Comparative Toxicogenomics Database. - Naama Menda, Bryan J. Ellerbrock, Christiano C. Simoes, Srikanth Kumar Karaikal, Christine Nyaga, Mirella Flores-Gonzalez, Isaak Y. Tecle, David Lyon, Afolabi Agbona, Paterne A Agre, Prasad Peteti, Violet Akech, Amos Asiimwe, Eglantine Fauvelle, Karima Meghar, Thierry Tran, Dominique Dufour, Laurel Cooper, Marie-Angélique Laporte, Elizabeth Arnaud, Lukas A Mueller:
Post-composing ontology terms for efficient phenotyping in plant breeding. - Swier Garst, Andre Dekker, Marcel J. T. Reinders:
A comprehensive experimental comparison between federated and centralized learning. - Tzu-Hsien Yang, Xiang-Wei Li, Yuan-Han Lee, Shang-Yi Lu, Wei-Sheng Wu, Heng-Chi Lee:
mirTarCLASH: a comprehensive miRNA target database based on chimeric read-based experiments. - Mireia Costa, Alberto García S., Oscar Pastor:
VarGuideAtlas: a repository of variant interpretation guidelines. - Sharon Wei, Kapeel Chougule, Andrew Olson, Zhenyuan Lu, Marcela K. Tello-Ruiz, Vivek Kumar, Sunita Kumari, Lifang Zhang, Audra Olson, Catherine Kim, Nick Gladman, Doreen Ware:
GrameneOryza: a comprehensive resource for Oryza genomes, genetic variation, and functional data. - Takahide Matsushima, Yuki Naito, Tomoki Chiba, Ryota Kurimoto, Keiko Itano, Koji Ochiai, Koichi Takahashi, Naoki Goshima, Hiroshi Asahara:
Localizatome: a database for stress-dependent subcellular localization changes in proteins. - Sarthak Joshi, Shailendu Mohapatra, Dhwani Kumar, Adwait Joshi, Meenakshi S. Iyer, Ramanathan Sowdhamini:
GenDiS3 database: census on the prevalence of protein domain superfamilies of known structure in the entire sequence database. - Brian M. Mack, Matthew D. Lebar:
AFED, a comprehensive resource for Aspergillus flavus gene expression profiling. - Milind Chauhan, Amisha Gupta, Ritu Tomer, Gajendra P. S. Raghava:
CancerPPD2: an updated repository of anticancer peptides and proteins. - Boyan Gong, Sida Li, Yifan Chen, Liya Liu, Ralf Hofestädt, Ming Chen:
STCDB4ND: a signal transduction classification database for neurological diseases. - Jiaojiao Zhao, Min Wu, Meihua Wan, Xue Li, Jie Li, Qin Liu, Minghao Xiong, Mengjie Tu, Jun Zhou, Shilin Li, Jie Zhang, Jiangping Fu, Yin Zhang, Chungang Zhao, Litong Qin, Xue Yang, Hong Zhao, Yan Zhang, Fanxin Zeng:
MIPD: Molecules, Imagings, and Clinical Phenotype Integrated Database. - Annarita Marrano, Leyla Cabugos, Alenka Hafner, Beant Kapoor, John McNamara, Megan O'donnell, Leonore Reiser, Marcela Karey Tello-Ruiz, Huiting Zhang, Margaret Staton:
A teaching and training framework to promote findable, accessible, interoperable, and reusable data generation in agriculture. - Jaehyeon Oh, Hwang-Weon Jeong, Il Pyung Ahn, Seon-Hwa Bae, Sung Mi Kim, Eunhee Kim, Su Jung Ra, Jinjeong Lee, Hyeyeon Choi, Young-Joo Seol:
CPDMS: a database system for crop physiological disorder management. - An Phan, Parnal Joshi, Claus Kadelka, Iddo Friedberg:
A longitudinal analysis of function annotations of the human proteome reveals consistently high biases. - Gabrielle Rigutto, Cliona M. McHale, Ettayapuram Ramaprasad Azhagiya Singam, Iemaan Rana, Luoping Zhang, Martyn T. Smith:
Mapping assays to the key characteristics of carcinogens to support decision-making. - Wilailack Meesawad, Jen-Chieh Han, Chun-Yu Hsueh, Yu Zhang, Hsi-Chuan Hung, Richard Tzong-Han Tsai:
Enhancing biomedical relation extraction through data-centric and preprocessing-robust ensemble learning approach. - Alexander Kellmann, Sander van den Hoek, Max Postema, W. T. Kars Maassen, Brenda S. Hijmans, Marije van der Geest, K. Joeri van der Velde, Esther van Enckevort, Morris A. Swertz:
An exploratory study combining Virtual Reality and Semantic Web for life science research using Graph2VR. - Muhammad Nabeel Asim, Tayyaba Asif, Faiza Hassan, Andreas Dengel:
Protein Sequence Analysis landscape: A Systematic Review of Task Types, Databases, Datasets, Word Embeddings Methods, and Language Models. - Fang-Yi Su, Gia-Han Ngo, Ben Phan, Jung-Hsien Chiang:
CAS: enhancing implicit constrained data augmentation with semantic enrichment for biomedical relation extraction and beyond.
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