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ORCIDDatabase - The Journal of Biological Databases and Curation, Volume 2024
Volume 2024, January 2024
- Kai Wang
, Bambarendage P. U. Perera, Rachel K. Morgan, Kimberley Sala-Hamrick, Viviana Geron, Laurie K. Svoboda, Christopher Faulk, Dana C. Dolinoy, Maureen A. Sartor:
piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation. - Anmol M. Kiran, Mariem Hanachi, Nihad Alsayed, Meriem Fassatoui, Ovokeraye Achinike-Oduaran, Imane Allali, Suresh Maslamoney, Ayton Meintjes, Lyndon Zass, Jorge Da Rocha, Rym Kefi, Alia Benkahla, Kais Ghedira, Sumir Panji, Nicola J. Mulder, Faisal M. Fadlelmola, Oussema Souiai:
The African Human Microbiome Portal: a public web portal of curated metagenomic metadata. - Ruiqing Wang, Chao Ren, Tian Gao, Hao Li, Xiaochen Bo, Dahai Zhu, Dan Zhang, Hebing Chen, Yong Zhang:
SEPDB: a database of secreted proteins. - Shahin Ramazi, Seyed Amir Hossein Tabatabaei, Elham Khalili, Amirhossein Golshan Nia, Kiomars Motarjem:
Analysis and review of techniques and tools based on machine learning and deep learning for prediction of lysine malonylation sites in protein sequences. - Daniel Walke, Daniel Micheel, Kay Schallert, Thilo Muth, David Broneske, Gunter Saake, Robert Heyer:
The importance of graph databases and graph learning for clinical applications. - Alexander Bach, Florian Raub, Hubert Höfer, Richard Ottermanns, Martina Roß-Nickoll:
ARAapp: filling gaps in the ecological knowledge of spiders using an automated and dynamic approach to analyze systematically collected community data. - Shuchang Xiong, Zhengwen Liu, Xin Yi, Kai Liu, Bingding Huang, Xin Wang:
NanoLAS: a comprehensive nanobody database with data integration, consolidation and application. - Nie Kai, Cai Qingsong, Ma Kejia, Luo Weiwei, Xing Wu, Chen Xuejie, Cai Lixia, Deng Minzi, Yuan-Yuan Yang, Wang Xiaoyan:
An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP). - Qingkang Meng, Yiyang Cai, Kun Zhou, Fei Xu, Diwei Huo, Hongbo Xie, Meini Yu, Denan Zhang, Xiujie Chen:
DAPredict: a database for drug action phenotype prediction. - Correction to: The importance of graph databases and graph learning for clinical applications.
- Correction to: LeishMANIAdb: a comparative resource for Leishmania proteins.
- Tae Jin Lee, Arnav Goyal, Garrett Jones, Joshua Glass, Vishal Doshi, Kathryn Bollinger, Lane Ulrich, Saleh Ahmed, Sai Karthik Kodeboyina, Amy Estes, Marc Töteberg-Harms, Wenbo Zhi, Shruti Sharma, Ashok Sharma:
AHP DB: a reference database of proteins in the human aqueous humor. - Renzo Angles, Mauricio Arenas-Salinas, Roberto García, Ben Ingram:
An optimized relational database for querying structural patterns in proteins. - Serena Baini, Alessio De Biase:
Filling knowledge gaps in insect conservation by leveraging genetic data from public archives. - Kunjulakshmi R, Ambuj Kumar, Keerthana Vinod Kumar, Avik Sengupta, Kavita Kundal, Simran Sharma, Ankita Pawar, Pithani Sai Krishna, Mohammad Alfatah, Sandipan Ray, Bhavana Tiwari, Rahul Kumar:
AagingBase: a comprehensive database of anti-aging peptides. - Zhiwei Zhou, Jingyi Du, Jianhua Wang, Liangyi Liu, M. Gracie Gordon, Chun Jimmie Ye, Joseph E. Powell, Mulin Jun Li, Shuquan Rao:
SingleQ: a comprehensive database of single-cell expression quantitative trait loci (sc-eQTLs) cross human tissues. - Carlos Vega, Marek Ostaszewski, Valentin Grouès, Reinhard Schneider, Venkata P. Satagopam:
BioKC: a collaborative platform for curation and annotation of molecular interactions. - Federica Quaglia, Anastasia Chasapi, Maria Victoria Nugnes, Maria Cristina Aspromonte, Emanuela Leonardi, Damiano Piovesan, Silvio C. E. Tosatto:
Best practices for the manual curation of intrinsically disordered proteins in DisProt. - Fuyuan Zhang, Hongzhe Cao, Helong Si, Jinping Zang, Jingao Dong, Jihong Xing, Kang Zhang:
FGCD: a database of fungal gene clusters related to secondary metabolism. - Puneet K. Singh, Razvan C. Stan:
ThermoPCD: a database of molecular dynamics trajectories of antibody-antigen complexes at physiologic and fever-range temperatures. - Tan Meng, Hanqing Jiao, Yi Zhang, Yi Zhou, Shaoying Chen, Xinrui Wang, Bowen Yang, Jie Sun, Xin Geng, Dilay Hazal Ayhan, Li Guo:
FoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen. - Hongfang Wu, Rongxian Chen, Xuejian Li, Yue Zhang, Jianwei Zhang, Yanbo Yang, Jun Wan, Yang Zhou, Huanchun Chen, Jinquan Li, Runze Li, Geng Zou:
ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides. - Victor Avram, Shweta Yadav, Pranav Sahasrabudhe, Dan Chang, Jing Wang:
IBDTransDB: a manually curated transcriptomic database for inflammatory bowel disease. - Correction to: SEPDB: a database of secreted proteins.
- Subhashini Sivagnanam, Steven Yeu, Kai Lin, S. Sakai, F. Garzon, Kenneth Yoshimoto, Katrina Prantzalos, D. P. Upadhyaya, Amitava Majumdar, Satya S. Sahoo, William W. Lytton:
Towards building a trustworthy pipeline integrating Neuroscience Gateway and Open Science Chain. - Correction to: Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium.
- Bharathram Uppili, Mohammed Faruq:
STRIDE-DB: a comprehensive database for exploration of instability and phenotypic relevance of short tandem repeats in the human genome. - Junkang Wei, Jin Xiao, Siyuan Chen, Licheng Zong, Xin Gao, Yu Li:
ProNet DB: a proteome-wise database for protein surface property representations and RNA-binding profiles. - Darawan Rinchai, Tobias Brummaier, Alexandra A. Marr, Tanwir Habib, Mohammed Toufiq, Tomoshigue Kino, Francois Nosten, Souhaila Al Khodor, Annalisa Terranegra, Rose McGready, Basirudeen Syed Ahamed Kabeer, Damien Chaussabel:
A data browsing application for accessing gene and module-level blood transcriptome profiles of healthy pregnant women from high- and low-resource settings. - Pengyu Du, Yingli Chen, Qianzhong Li, Zhimin Gai, Hui Bai, Luqiang Zhang, Yuxian Liu, Yanni Cao, Yuanyuan Zhai, Wen Jin:
CancerMHL: the database of integrating key DNA methylation, histone modifications and lncRNAs in cancer. - Jorge Novoa, Javier López-Ibáñez, Monica Chagoyen, Juan Antonio Garcia-Ranea, Florencio Pazos:
CoMentG: comprehensive retrieval of generic relationships between biomedical concepts from the scientific literature. - Alexander Kellmann, Max Postema, Joris de Keijser, Pjotr Svetachov, Rebecca C. Wilson, Esther van Enckevort, Morris A. Swertz:
Visualization and exploration of linked data using virtual reality. - Wenhui Zhou, Tao Yang, Liucui Zeng, Jing Chen, Yayu Wang, Xing Guo, Lijin You, Yiqun Liu, Wensi Du, Fan Yang, Cong Hua, Jia Cai, Theo van Hintum, Huan Liu, Ying Gu, Xiaofeng Wei, Tong Wei:
LettuceDB: an integrated multi-omics database for cultivated lettuce. - Laha Ale, Robert Gentleman, Teresa Filshtein Sonmez, Deepayan Sarkar, Christopher Endres:
nhanesA: achieving transparency and reproducibility in NHANES research. - Rahel Paloots, Michael Baudis:
cancercelllines.org - a novel resource for genomic variants in cancer cell lines. - Marija Orlic-Milacic, Karen Rothfels, Lisa Matthews, Adam J. Wright, Bijay Jassal, Veronica Shamovsky, Quang M. Trinh, Marc Gillespie, Cristoffer Sevilla, Krishna Tiwari, Eliot Ragueneau, Chuqiao Gong, Ralf Stephan, Bruce May, Robin Haw, Joel Weiser, Deidre Beavers, Patrick Conley, Henning Hermjakob, Lincoln D. Stein, Peter D'Eustachio, Guanming Wu:
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes. - Jiabei Liu, Yiyi Yu, Mingyue Li, Yixuan Wu, Weijun Chen, Guanru Liu, Lingxian Liu, Jiechun Lin, Chujun Peng, Weijun Sun, Xiaoli Wu, Xin Chen:
PMBC: a manually curated database for prognostic markers of breast cancer. - Alberto García S., Mireia Costa, Alba García-Zarzoso, Oscar Pastor:
CardioHotspots: a database of mutational hotspots for cardiac disorders. 0 - Correction to: ESKtides: a comprehensive database and mining method for ESKAPE phage-derived antimicrobial peptides.
- Yue Liu, Yuhuan Zhou, Xiumei Hu, Wuri Le-Ge, Haoyan Wang, Tao Jiang, Junyi Li, Yang Hu, Yadong Wang:
DIRMC: a database of immunotherapy-related molecular characteristics. - Daniel Faria, Patrícia Eugénio, Marta Contreiras Silva, Laura Balbi, Georges Bedran, Ashwin Adrian Kallor, Susana Nunes, Aleksander Palkowski, Michal Waleron, Javier Antonio Alfaro, Catia Pesquita:
The Immunopeptidomics Ontology (ImPO). - Christophe Jenny, Valentin Guignon, Felip Manyer I Ballester, Max Ruas, Mathieu Rouard:
Collecting and managing in situ banana genetic resources information (Musa spp.) using online resources and citizen science. - Feng Shao, Minzhi Zeng, Xiaofei Xu, Huahao Zhang, Zuogang Peng:
FishTEDB 2.0: an update fish transposable element (TE) database with new functions to facilitate TE research. - Shumin Ren, Lin Yang, Jiale Du, Mengqiao He, Bairong Shen:
DRGKB: a knowledgebase of worldwide diagnosis-related groups' practices for comparison, evaluation and knowledge-guided application. - Eléonore Bettacchioli, Laurent Chiche, Damien Chaussabel, Divi Cornec, Noémie Jourde-Chiche, Darawan Rinchai:
An interactive web application for exploring systemic lupus erythematosus blood transcriptomic diversity. - Tao Wu, Yaopan Hou, Guanghao Xin, Jingyan Niu, Shanshan Peng, Fanfan Xu, Ying Li, Yuling Chen, Yifangfei Yu, Huixue Zhang, Xiaotong Kong, Yuze Cao, Shangwei Ning, Lihua Wang, Junwei Hao:
MSGD: a manually curated database of genomic, transcriptomic, proteomic and drug information for multiple sclerosis. - Yuanyuan Wang, Yexin Yang, Yi Liu, Chao Liu, Meng Xu, Miao Fang, Xidong Mu:
CoSFISH: a comprehensive reference database of COI and 18S rRNA barcodes for fish. - Preeti Choudhary, Zukang Feng, John M. Berrisford, Henry Chao, Yasuyo Ikegawa, Ezra Peisach, Dennis W. Piehl, James Smith, Ahsan Tanweer, Mihaly Varadi, John D. Westbrook, Jasmine Young, Ardan Patwardhan, Kyle L. Morris, Jeffrey C. Hoch, Genji Kurisu, Sameer Velankar, Stephen K. Burley:
PDB NextGen Archive: centralizing access to integrated annotations and enriched structural information by the Worldwide Protein Data Bank. - Correction to: A Terpenoids Database with the Chemical Content as A Novel Agronomic Trait.
- Charlotte Nachtegael, Jacopo De Stefani, Anthony Cnudde, Tom Lenaerts:
DUVEL: an active-learning annotated biomedical corpus for the recognition of oligogenic combinations. - Wenqian Li, Yinliang Chen, Ruofei Yang, Zilong Hu, Shaozhong Wei, Sheng Hu, Xinjun Xiong, Meijuan Wang, Ammar Lubeiny, Xiaohua Li, Minglei Feng, Shuang Dong, Xinlu Xie, Chao Nie, Jingyi Zhang, Yunhao Luo, Yichen Zhou, Ruodi Liu, Jinhai Pan, De-Xin Kong, Xuebo Hu:
A terpenoids database with the chemical content as a novel agronomic trait. - Leho Tedersoo, Mahdieh S. Hosseyni Moghaddam, Vladimir Mikryukov, Ali Hakimzadeh, Mohammad Bahram, R. Henrik Nilsson, Iryna Yatsiuk, Stefan Geisen, Arne Schwelm, Kasia Piwosz, Marko Prous, Sirje Sildever, Dominika Chmolowska, Sonja Rueckert, Pavel Skaloud, Peeter Laas, Marco Tines, Jae-Ho Jung, Ji Hye Choi, Saad Alkahtani, Sten Anslan:
EUKARYOME: the rRNA gene reference database for identification of all eukaryotes. - Ismahene Mesbah, Bianca Habermann, Felix Rico:
MechanoProDB: a web-based database for exploring the mechanical properties of proteins. - Tzu-Hsien Yang, Yu-Huai Yu, Sheng-Hang Wu, Fang-Yuan Chang, Hsiu-Chun Tsai, Ya-Chiao Yang:
DMLS: an automated pipeline to extract the Drosophila modular transcription regulators and targets from massive literature articles. 0 - Yanhong Xiong, Shiyu Li, Yuxuan Zhang, Qianqian Chen, Mengtan Xing, Yong Zhang, Qi Wang:
MechanoBase: a comprehensive database for the mechanics of tissues and cells. - Chong Peng, Xiaofeng Liu, Xiangbo Meng, Congge Chen, Xinming Wu, Lin Bai, Fuping Lu, Fufeng Liu:
IPAD-DB: a manually curated database for experimentally verified inhibitors of proteins associated with Alzheimer's disease.
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