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ORCIDDatabase - The Journal of Biological Databases and Curation, Volume 2022
Volume 2022, Number 2022, January 2022
- Hong Cui
, Bruce Ford, Julian R. Starr, Anton Reznicek, Limin Zhang, James A. Macklin:
Authors' attitude toward adopting a new workflow to improve the computability of phenotype publications. - Guoshuai Cai, Xuanxuan Yu, Choonhan Youn, Jun Zhou, Feifei Xiao:
SCANNER: a web platform for annotation, visualization and sharing of single cell RNA-seq data. - Andre Brincat, Markus Hofmann:
Automated extraction of genes associated with antibiotic resistance from the biomedical literature. - Jiaxuan Li, Shuai Yang, Xiaojie Yang, Hui Wu, Heng Tang, Long Yang:
PlantGF: an analysis and annotation platform for plant gene families. - David Couvin, Iñaki Cervera-Marzal, Audrey David, Yann Reynaud, Nalin Rastogi:
SITVITBovis - a publicly available database and mapping tool to get an improved overview of animal and human cases caused by Mycobacterium bovis. - Shafi Mahmud, Gobindo Kumar Paul, Suvro Biswas, Taheruzzaman Kazi, Shafquat Mahbub, Mohasana Akter Mita, Shamima Afrose, Ariful Islam, Sheikh Ahaduzzaman, Md. Robiul Hasan, Sharmin Sultana Shimu, Maria Meha Promi, Mobasshir Noor Shehab, Ekhtiar Rahman, Khaled Mahmud Sujon, Md. Wasim Alom, Anik Modak, Shahriar Zaman, Md. Salah Uddin, Talha Bin Emran, Md. Sayeedul Islam, Md. Abu Saleh:
phytochemdb: a platform for virtual screening and computer-aided drug designing.
Volume 2022, February 2022
- Bachir Balech, Anna Sandionigi, Marinella Marzano, Graziano Pesole, Monica Santamaria:
MetaCOXI: an integrated collection of metazoan mitochondrial cytochrome oxidase subunit-I DNA sequences. - Fang Huang, Xia Tang, Bo Ye, Songfeng Wu, Keyue Ding:
PSL-LCCL: a resource for subcellular protein localization in liver cancer cell line SK_HEP1.
Volume 2022, March 2022
- Wendong Li, Ting Sun, Muyang Li, Yufei He, Lin Li, Lu Wang, Haoyu Wang, Jing Li, Hao Wen, Yong Liu, Yifan Chen, Yubo Fan, Beibei Xin, Jing Zhang:
GNIFdb: a neoantigen intrinsic feature database for glioma. - Iman Almansour, Imane Boudellioua:
hCoronavirusesDB: an integrated bioinformatics resource for human coronaviruses. - Qiang Li, Shiyong Ma, Xuelu Zhang, Zhaoyu Zhai, Lu Zhou, Haodong Tao, Yachen Wang, Jianbo Pan:
DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development. - Wafaa M. Rashed, Fatima Adel, Mohamed A. Rezk, Lina Basiouny, Ahmed A. Rezk, Ahmed Abdel Razek:
MicroRNA childhood cancer catalog (M3Cs): a resource for translational bioinformatics toward health informatics in pediatric cancer. - Beverly A. Underwood, Linda Yankie, Eric P. Nawrocki, Vasuki Palanigobu, Sergiy Gotvyanskyy, Vincent D. Calhoun, Michael Kornbluh, Thomas G. Smith, Lydia Fleischmann, Denis Sinyakov, Colleen J. Bollin, Ilene Karsch-Mizrachi:
Rapid automated validation, annotation and publication of SARS-CoV-2 sequences to GenBank. - Zhenyu Yang, Wenjing Yi, Jin Tao, Xiaoqing Liu, Michael Q. Zhang, Guiqian Chen, Qi Dai:
HPVMD-C: a disease-based mutation database of human papillomavirus in China. - Yu-Zhe Sun, Yong-Fei Hu, Yan Zhang, Shu-yi Wei, Bei-Lei Yang, Ying-Ping Xu, Zhi-Li Rong, Dong Wang, Bin Yang:
FibROAD: a manually curated resource for multi-omics level evidence integration of fibrosis research. - Jianyuan Zhou, Yanshang Li, Haotian Cao, Min Yang, Lingyu Chu, Taisong Li, Zhengmin Yu, Rui Yu, Bo Qiu, Qiuyu Wang, Xuecang Li, Jianjun Xie:
CATA: a comprehensive chromatin accessibility database for cancer. - Shahin Ramazi, Neda Mohammadi, Abdollah Allahverdi, Elham Khalili, Parviz Abdolmaleki:
A review on antimicrobial peptides databases and the computational tools. - Neha V. Kalmankar, Murugavel Pavalam, Sowmya Indrakumar, Narayanaswamy Srinivasan, Ramanathan Sowdhamini:
DSDBASE 2.0: updated version of DiSulphide dataBASE, a database on disulphide bonds in proteins. - Henda Merchaoui, Riadh Ksouri, Chedly Abdelly, Mohsen Hanana:
Halophytes.tn: an innovative database for Tunisian halophyte plant identification, distribution and characterization. - Adam J. Wright, Marija Orlic-Milacic, Karen Rothfels, Joel Weiser, Quang M. Trinh, Bijay Jassal, Robin Haw, Lincoln D. Stein:
Evaluating the predictive accuracy of curated biological pathways in a public knowledgebase. - Dhouha Grissa, Alexander Junge, Tudor I. Oprea, Lars Juhl Jensen:
Diseases 2.0: a weekly updated database of disease-gene associations from text mining and data integration. - Nan Deng, Canglin Wu, Ashraf Yaseen, Hulin Wu:
ImmuneData: an integrated data discovery system for immunology data repositories. - Victor Gambarini, Olga Pantos, Joanne M. Kingsbury, Louise Weaver, Kim M. Handley, Gavin Lear:
PlasticDB: a database of microorganisms and proteins linked to plastic biodegradation. - Zsofia E. Kalman, Dániel Dudola, Bálint Mészáros, Zoltán Gáspári, Laszlo Dobson:
PSINDB: the postsynaptic protein-protein interaction database. - Marie Deckers, Julien Van Braekel, Kevin Vanneste, Dieter Deforce, Marie-Alice Fraiture, Nancy H. C. Roosens:
Correction to: FEDA (Food Enzyme Database): a web application gathering information about food enzyme preparations available on the European market. - Chuan Dong, Xin Wang, Cong Ma, Zhi Zeng, Dong-Kai Pu, Shuo Liu, Candy-S. Wu, Shixin Chen, Zixin Deng, Feng-Biao Guo:
Anti-CRISPRdb v2.2: an online repository of anti-CRISPR proteins including information on inhibitory mechanisms, activities and neighbors of curated anti-CRISPR proteins.
Volume 2022, April 2022
- Suresh Panneerselvam, Ruchir Mishra, Colin Berry, Neil Crickmore, Bryony C. Bonning:
BPPRC database: a web-based tool to access and analyse bacterial pesticidal proteins. - Federica Quaglia, Rama Balakrishnan, Susan M. Bello, Nicole A. Vasilevsky:
Conference report: Biocuration 2021 Virtual Conference. - Charlotte Nachtegael, Barbara Gravel, Arnau Dillen, Guillaume Smits, Ann Nowé, Sofia Papadimitriou, Tom Lenaerts:
Scaling up oligogenic diseases research with OLIDA: the Oligogenic Diseases Database. - De-Ping Wei, Eleni Gentekaki, Kevin D. Hyde, Yuan-Pin Xiao, Thatsanee Luangharn, Qing Tian, Yuan-Bing Wang, Saisamorn Lumyong:
https: //invertebratefungi.org/: an expert-curated web-based platform for the identification and classification of invertebrate-associated fungi and fungus-like organisms. - Huiying Qi, Shibin Song, Pingzhang Wang:
ImmuMethy, a database of DNA methylation plasticity at a single cytosine resolution in human blood and immune cells. - Philippe Le Mercier, Jerven T. Bolleman, Edouard De Castro, Elisabeth Gasteiger, Parit Bansal, Andrea H. Auchincloss, Emmanuel Boutet, Lionel Breuza, Cristina Casals-Casas, Anne Estreicher, Marc Feuermann, Damien Lieberherr, Catherine Rivoire, Ivo Pedruzzi, Nicole Redaschi, Alan J. Bridge:
SwissBioPics - an interactive library of cell images for the visualization of subcellular location data. - Teerna Bhattacharyya, Soumya Nayak, Smit Goswami, Vasundhara Gadiyaram, Oommen K. Mathew, Ramanathan Sowdhamini:
PASS2.7: a database containing structure-based sequence alignments and associated features of protein domain superfamilies from SCOPe. - Pengyu Ni, Zhengchang Su:
PCRMS: a database of predicted cis-regulatory modules and constituent transcription factor binding sites in genomes. - Arwin Groenewoud, G. Forn-Cuní, Felix B. Engel, B. Ewa Snaar-Jagalska:
XePhIR: the zebrafish xenograft phenotype interactive repository. - Gaston K. Mazandu, Jade Hotchkiss, Victoria Nembaware, Ambroise Wonkam, Nicola J. Mulder:
The Sickle Cell Disease Ontology: recent development and expansion of the universal sickle cell knowledge representation. - Graciela Gonzalez-Hernandez, Martin Krallinger, Monica A. Muñoz, Raul Rodriguez-Esteban, Özlem Uzuner, Lynette Hirschman:
Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers. - William R. Rolling, Douglas Senalik, Massimo Iorizzo, Shelby Ellison, Allen Van Deynze, Philipp W. Simon:
CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota). - Lihua Liu, Evianne Rovers, Matthieu Schapira:
ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome. - Kuo-Feng Tung, Wen-Chang Lin:
TEx-MST: tissue expression profiles of MANE select transcripts.
Volume 2022, May 2022
- Giulia Agostinetto, Davide Bozzi, Danilo Porro, Maurizio Casiraghi, Massimo Labra, Antonia Bruno:
SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata. - Jie Wang, Min Wu, Xuhui Huang, Li Wang, Sophia Zhang, Hui Liu, Jie Zheng:
SynLethDB 2.0: a web-based knowledge graph database on synthetic lethality for novel anticancer drug discovery. - David C. Molik:
met v1: expanding on old estimations of biodiversity from eDNA with a new database framework. - Sanket Desai, Rohit Mishra, Suhail Ahmad, Supriya Hait, Asim Joshi, Amit Dutt:
TMC-SNPdb 2.0: an ethnic-specific database of Indian germline variants. - Eric Yao, Victoria C. Blake, Laurel Cooper, Charlene P. Wight, Steve L. Michel, H. Busra Cagirici, Gerard R. Lazo, Clayton L. Birkett, David J. Waring, Jean-Luc Jannink, Ian H. Holmes, Amanda J. Waters, David P. Eickholt, Taner Z. Sen:
GrainGenes: a data-rich repository for small grains genetics and genomics. - Nicolas Matentzoglu, James P. Balhoff, Susan M. Bello, Chris Bizon, Matthew H. Brush, Tiffany J. Callahan, Christopher G. Chute, William D. Duncan, Chris T. A. Evelo, Davera Gabriel, John Graybeal, Alasdair J. G. Gray, Benjamin M. Gyori, Melissa A. Haendel, Henriette Harmse, Nomi L. Harris, Ian Harrow, Harshad Hegde, Amelia L. Hoyt, Charles Tapley Hoyt, Dazhi Jiao, Ernesto Jiménez-Ruiz, Simon Jupp, Hyeongsik Kim, Sebastian Köhler, Thomas Liener, Qinqin Long, James Malone, James A. McLaughlin, Julie A. McMurry, Sierra A. T. Moxon, Monica C. Munoz-Torres, David Osumi-Sutherland, James A. Overton, Bjoern Peters, Tim E. Putman, Núria Queralt-Rosinach, Kent A. Shefchek, Harold Solbrig, Anne E. Thessen, Tania Tudorache, Nicole A. Vasilevsky, Alex H. Wagner, Christopher J. Mungall:
A Simple Standard for Sharing Ontological Mappings (SSSOM). - Shijun Zhang, Heng-Yi Wu, Lei Wang, Gongbo Zhang, Luis M. Rocha, Hagit Shatkay, Lang Li:
Translational drug-interaction corpus. - Po Lam Chan, Susana Lauw, Ka Lee Ma, Nelson Kei, Ka Leong Ma, Yiu On Wong, Ho Yan Lam, Yee Yung Ting, Tsz Kwan Yau, Wenyan Nong, Dandan Huang, Yichun Xie, Peter Chi Keung Cheung, Hoi Shan Kwan:
ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics. - Jianhua Li, Xiaotian Yang, Qinjie Chu, Lingjuan Xie, Yuwen Ding, Xiaoxu Xu, Michael P. Timko, Longjiang Fan:
Multi-omics molecular biomarkers and database of osteoarthritis. - Lisa Langnickel, Johannes Darms, Katharina Heldt, Denise Ducks, Juliane Fluck:
Continuous development of the semantic search engine preVIEW: from COVID-19 to long COVID.
Volume 2022, June 2022
- Thabo M. Yates, A. Laine, Jennifer Campbell, David R. FitzPatrick, T. Ian Simpson:
Creation and evaluation of full-text literature-derived, feature-weighted disease models of genetically determined developmental disorders. - Raul Rodriguez-Esteban:
New reasons for biologists to write with a formal language. - Baiyang Feng, Jing Gao:
AnthraxKP: a knowledge graph-based, Anthrax Knowledge Portal mined from biomedical literature. - Abhijeet Singh, Anna Schnürer:
AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters. - Samuele Garda, Freyda Lenihan-Geels, Sebastian Proft, Stefanie Hochmuth, Markus Schuelke, Dominik Seelow, Ulf Leser:
RegEl corpus: identifying DNA regulatory elements in the scientific literature. - Giuseppe Serna Garcia, Michele Leone, Anna Bernasconi, Mark J. Carman:
GeMI: interactive interface for transformer-based Genomic Metadata Integration. - Munetaka Kawamoto, Takashi Kiuchi, Susumu Katsuma:
SilkBase: an integrated transcriptomic and genomic database for Bombyx mori and related species. - Ashley Clayton, Mialy M. DeFelice, Brynn Zalmanek, Jay Hodgson, Caroline Morin, Stockard Simon, Julie A. Bletz, James A. Eddy, Milen Nikolov, Jineta Banerjee, Kalyan C. Vinnakota, Marco Marasca, Kevin J. Boske, Bruce Hoff, Ljubomir Bradic, Yoori Kim, James R. Goss, Robert J. Allaway:
Centralizing neurofibromatosis experimental tool knowledge with the NF Research Tools Database. - Kai-Jie Gu, Chen-Feng Lin, Jun-Jie Wu, Yun-Peng Zhao:
GinkgoDB: an ecological genome database for the living fossil, Ginkgo biloba. - Qiang Li, Shiyong Ma, Xuelu Zhang, Zhaoyu Zhai, Lu Zhou, Haodong Tao, Yachen Wang, Jianbo Pan:
Correction to: DDPD 1.0: a manually curated and standardized database of digital properties of approved drugs for drug-likeness evaluation and drug development. - Zhuoqiao Shen, Minghao Fang, Wujianan Sun, Meifang Tang, Nianping Liu, Lin Zhu, Qian Liu, Bin Li, Ruoming Sun, Yu Shi, Chuang Guo, Jun Lin, Kun Qu:
A transcriptome atlas and interactive analysis platform for autoimmune disease. - Daniele Toti, Gabriele Macari, Enrico Barbierato, Fabio Polticelli:
FGDB: a comprehensive graph database of ligand fragments from the Protein Data Bank.
Volume 2022, July 2022
- Rachel Lyne, Adrián Bazaga, Daniela Butano, Sergio Contrino, Joshua Heimbach, Fengyuan Hu, Alex Kalderimis, Mike Lyne, Kevin Herald Reierskog, Radek Stepan, Julie M. Sullivan, Archie Wise, Yo Yehudi, Gos Micklem:
HumanMine: advanced data searching, analysis and cross-species comparison. - Ling Luo, Po-Ting Lai, Chih-Hsuan Wei, Zhiyong Lu:
A sequence labeling framework for extracting drug-protein relations from biomedical literature. - Tiago Melo Almeida, Rui Antunes, João Figueira Silva, João Rafael Almeida, Sérgio Matos:
Chemical identification and indexing in PubMed full-text articles using deep learning and heuristics. - Tuan-Dung Le, Phuong D. Nguyen, Dmitry Korkin, Thanh Thieu:
PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. - Bin Tan, Saige Xin, Yanshi Hu, Cong Feng, Ming Chen:
LBD: a manually curated database of experimentally validated lymphoma biomarkers. - Giulia Magoga, Giobbe Forni, Matteo Brunetti, Aycan Meral, Alberto Spada, Alessio De Biase, Matteo Montagna:
Curation of a reference database of COI sequences for insect identification through DNA metabarcoding: COins. - Marilyne Summo, Aurore Comte, Guillaume Martin, Pierrick Perelle, Eric M. Weitz, Gaëtan Droc, Mathieu Rouard:
GeMo: a web-based platform for the visualization and curation of genome ancestry mosaics. - Xiaoyan Li, Shunshuai Ma, Wenhui Yan, Yong Wu, Hui Kong, Mingshan Zhang, Xiongjian Luo, Junfeng Xia:
dbBIP: a comprehensive bipolar disorder database for genetic research. - Sheng-Jie Lin, Wen-Chao Yeh, Yu-Wen Chiu, Yung-Chun Chang, Min-Huei Hsu, Yi-Shin Chen, Wen-Lian Hsu:
A BERT-based ensemble learning approach for the BioCreative VII challenges: full-text chemical identification and multi-label classification in PubMed articles. - Nicole Zatorski, David Stein, Rayees Rahman, Ravi Iyengar, Avner Schlessinger:
Structural signatures: a web server for exploring a database of and generating protein structural features from human cell lines and tissues. - Amy L. Olex, Evan French, Peter Burdette, Srilakshmi Sagiraju, Thomas Neumann, Tamas S. Gal, Bridget T. McInnes:
TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4. - Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan J. Bridge, Stephen K. Burley, Stacey Cleveland, Lucy J. Colwell, Ana Conesa, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu:
A roadmap for the functional annotation of protein families: a community perspective. - Harumi Kagiwada, Chie Motono, Katsuhisa Horimoto, Kazuhiko Fukui:
Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements. - Arslan Erdengasileng, Qing Han, Tingting Zhao, Shubo Tian, Xin Sui, Keqiao Li, Wanjing Wang, Jian Wang, Ting Hu, Feng Pan, Yuan Zhang, Jinfeng Zhang:
Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification. - Yinjiaozhi Li, Ruoming Tan, Yang Chen, Zhaojun Liu, Erzhen Chen, Tingting Pan, Hongping Qu:
SC2sepsis: sepsis single-cell whole gene expression database. - Polina Shpilker, John Freeman, Hailey McKelvie, Jill Ashey, Jay-Miguel Fonticella, Hollie Putnam, Jane Greenberg, Lenore Cowen, Alva L. Couch, Noah M. Daniels:
MEDFORD: A human- and machine-readable metadata markup language. - Li Guo, Yuyang Dou, Daoliang Xia, Zibo Yin, Yangyang Xiang, Lulu Luo, Yuting Zhang, Jun Wang, Tingming Liang:
SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis. - Sanchari Sircar, Mayank Musaddi, Nita Parekh:
NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions. - Anfu Tang, Louise Deléger, Robert Bossy, Pierre Zweigenbaum, Claire Nédellec:
Do syntactic trees enhance Bidirectional Encoder Representations from Transformers (BERT) models for chemical-drug relation extraction? - Yu Zhang, Jong Kang Lee, Jen-Chieh Han, Richard Tzong-Han Tsai:
Task reformulation and data-centric approach for Twitter medication name extraction. - Wanying Dou, Hemn Barzan Abdalla, Xu Chen, Changyi Sun, Xuefei Chen, Qiwen Tian, Junyi Wang, Wei Zhou, Wei Chi, Xuan Zhou, Hailv Ye, Chuyun Bi, Xuechen Tian, Yixin Yang, Aloysius Wong:
ProbResist: a database for drug-resistant probiotic bacteria. - Chang Sun, Jipeng Huang, Rong Tang, Minglei Li, Haili Yuan, Yuxiang Wang, Jinmao Wei, Jian Liu:
CPMCP: a database of Chinese patent medicine and compound prescription.
Volume 2022, August 2022
- Zhenfeng Qian, Xuzhen Li, Lilian He, Shujie Gu, Qingqing Shen, Xibing Rao, Rongqiong Zhang, Yining Di, Linyan Xie, Xianhong Wang, Shuying Chen, Yang Dong, Fusheng Li:
EfGD: the Erianthus fulvus genome database. - Qingyu Chen, Alexis Allot, Robert Leaman, Rezarta Islamaj, Jingcheng Du, Li Fang, Wang Kai, Shuo Xu, Yuefu Zhang, Parsa Bagherzadeh, Sabine Bergler, Aakash Bhatnagar, Nidhir Bhavsar, Yung-Chun Chang, Sheng-Jie Lin, Wentai Tang, Hongtong Zhang, Ilija Tavchioski, Senja Pollak, Shubo Tian, Jinfeng Zhang, Yulia Otmakhova, Antonio Jimeno-Yepes, Hang Dong, Honghan Wu, Richard Dufour, Yanis Labrak, Niladri Chatterjee, Kushagri Tandon, Fréjus A. A. Laleye, Loïc Rakotoson, Emmanuele Chersoni, Jinghang Gu, Annemarie Friedrich, Subhash Chandra Pujari, Mariia Chizhikova, Naveen Sivadasan, Saipradeep Vg, Zhiyong Lu:
Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.
Volume 2022, September 2022
- Yiding Geng, Lu Jin, Guangjue Tang, Zhangxiang Zhao, Yunyan Gu, Dan Yang:
LiqBioer: a manually curated database of cancer biomarkers in body fluid. - Orsolya Liska, Balázs Bohár, András Hidas, Tamás Korcsmáros, Balázs Papp, Dávid Fazekas, Eszter Ari:
TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species. - Fan Dai, Jiedan Chen, Ziqian Zhang, Fengjun Liu, Jun Li, Ting Zhao, Yan Hu, Tianzhen Zhang, Lei Fang:
COTTONOMICS: a comprehensive cotton multi-omics database. - Bowen Li, Shanshan Yang, Jinjin Long, Xue Chen, Qianyue Zhang, Lin Ning, Bifang He, Heng Chen, Jian Huang:
AGODB: a comprehensive domain annotation database of argonaute proteins. - Shazia Firdous, Abhirupa Ghosh, Sudipto Saha:
BCSCdb: a database of biomarkers of cancer stem cells. - Hang Hu, Zhenxiao Lu, Haisong Feng, Guojun Chen, Yongmei Wang, Congshan Yang, Zhenyu Yue:
DGPD: a knowledge database of dense granule proteins of the Apicomplexa. - Hyunjae Kim, Mujeen Sung, Wonjin Yoon, Sungjoon Park, Jaewoo Kang:
Full-text chemical identification with improved generalizability and tagging consistency.
Volume 2022, October 2022
- Kiandokht Haddadi, Rana Ahmed Barghout, Radhakrishnan Mahadevan:
KinMod database: a tool for investigating metabolic regulation. - Xi Zhang, Yining Hu, David Roy Smith:
HSDatabase - a database of highly similar duplicate genes from plants, animals, and algae. - Laura Krumpholz, James F. Clarke, Sebastian Polak, Barbara Wisniowska:
An open-access data set of pig skin anatomy and physiology for modelling purposes. - Nicolas Matentzoglu, Damien Goutte-Gattat, Shawn Zheng Kai Tan, James P. Balhoff, Seth Carbon, Anita R. Caron, William D. Duncan, Joe E. Flack, Melissa A. Haendel, Nomi L. Harris, William R. Hogan, Charles Tapley Hoyt, Rebecca C. Jackson, Hyeongsik Kim, Hüseyin Kir, Martin Larralde, Julie A. McMurry, James A. Overton, Bjoern Peters, Clare Pilgrim, Raymund Stefancsik, Sofia M. C. Robb, Sabrina Toro, Nicole A. Vasilevsky, Ramona L. Walls, Christopher J. Mungall, David Osumi-Sutherland:
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. - Andrew Chatr-aryamontri, Lynette Hirschman, Karen E. Ross, Rose Oughtred, Martin Krallinger, Kara Dolinski, Mike Tyers, Tonia Korves, Cecilia N. Arighi:
Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII. - Nadia Brancati, Anna Maria Anniciello, Pushpak Pati, Daniel Riccio, Giosuè Scognamiglio, Guillaume Jaume, Giuseppe De Pietro, Maurizio Di Bonito, Antonio Foncubierta, Gerardo Botti, Maria Gabrani, Florinda Feroce, Maria Frucci:
BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images. - Ling Luo, Chih-Hsuan Wei, Po-Ting Lai, Qingyu Chen, Rezarta Islamaj, Zhiyong Lu:
Assigning species information to corresponding genes by a sequence labeling framework. - Jungeun Kim, Jae-Pil Choi, Min Sun Kim, Jong Bhak:
PharmaKoVariome database for supporting genetic testing.
Volume 2022, November 2022
- Sandeep Kaur, Michael Payne, Lijuan Luo, Sophie Octavia, Mark M. Tanaka, Vitali Sintchenko, Ruiting Lan:
MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens. - Arnaud Delorme, Dung Truong, Choonhan Youn, Subhashini Sivagnanam, Claire Stirm, Kenneth Yoshimoto, Russell A. Poldrack, Amitava Majumdar, Scott Makeig:
NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data. - Jin Li, Jing Gao, Baiyang Feng, Yi Jing:
PlagueKD: a knowledge graph-based plague knowledge database. - Raghav Kataria, Rakesh Kaundal:
TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat - Stem rust host-pathogen interactome. - Jinghang Gu, Emmanuele Chersoni, Xing Wang, Chu-Ren Huang, Longhua Qian, Guodong Zhou:
LitCovid ensemble learning for COVID-19 multi-label classification. - Chengyu Wang, Tingting Chen, Yuchen Mu, Xuan Liang, Kai Xiong, Liqiang Ai, Yunyan Gu, Xingxing Fan, Haihai Liang:
FDRdb: a manually curated database of fibrotic disease-associated RNAome and high-throughput datasets. - Paulina Koscielniak, Paulina Glazinska, Marcin Zadworny:
OakRootRNADB - a consolidated RNA-seq database for coding and noncoding RNA in roots of pedunculate oak (Quercus robur). - Leon Weber, Mario Sänger, Samuele Garda, Fabio Barth, Christoph Alt, Ulf Leser:
Chemical-protein relation extraction with ensembles of carefully tuned pretrained language models. - Jiaqi Chen, Zhengxin Chen, Rufei Chen, Dehua Feng, Tianyi Li, Huirui Han, Xiaoman Bi, Zhenzhen Wang, Kongning Li, Yongsheng Li, Xia Li, Limei Wang, Jin Li:
HCDT: an integrated highly confident drug-target resource. - Adam Valcek, James H. Collier, Alexander Botzki, Charles Van der Henst:
Acinetobase: the comprehensive database and repository of Acinetobacter strains.
Volume 2022, December 2022
- Özge Kart, Alexandre Mestiashvili, Kurt Lachmann, Richard Kwasnicki, Michael Schroeder:
Emati: a recommender system for biomedical literature based on supervised learning. - Rezarta Islamaj, Robert Leaman, David Cissel, Cathleen Coss, Joseph Denicola, Carol Fisher, Rob Guzman, Preeti Gokal Kochar, Nicholas Miliaras, Zoe Punske, Keiko Sekiya, Dorothy Trinh, Deborah Whitman, Susan Schmidt, Zhiyong Lu:
NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles. - Gjorgjina Cenikj, Eva Valencic, Gordana Ispirova, Matevz Ogrinc, Riste Stojanov, Peter Korosec, Ermanno Cavalli, Barbara Korousic-Seljak, Tome Eftimov:
CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources. - Peter D. Karp:
Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation. - Correction to: Acinetobase: the comprehensive database and repository of Acinetobacter strains.
- Daniel K. Manter, Jennifer M. Moore:
CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands.
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