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ORCIDDatabase - The Journal of Biological Databases and Curation, Volume 2023
Volume 2023, 2023
- Dena Salehipour, Kirsten M. Farncombe
, Veronica Andric, Safa Ansar, Sean Delong, Eric Li, Samantha Macpherson, Sarah Ridd, Deborah I. Ritter, Courtney Thaxton, Raymond H. Kim:
Developing a disease-specific annotation protocol for VHL gene curation using Hypothes.is. - Ming Hao, Yue Qi, Rongji Xu, Kangqi Zhao, Mingqing Li, Yongyan Shan, Tian Xia, Kun Yang, Wuyang Hasi, Cong Zhang, Daowei Li, Yi Wang, Peng Wang, Hongyu Kuang:
ENCD: a manually curated database of experimentally supported endocrine system disease and lncRNA associations. - Zahra Fathifar, Leila Kalankesh, Alireza Ostadrahimi, Reza Ferdousi:
New approaches in developing medicinal herbs databases. - Supratim Mukherjee, Galina Ovchinnikova, Dimitri Stamatis, Cindy Tianqing Li, I-Min A. Chen, Nikos Kyrpides, T. B. K. Reddy:
Standardized naming of microbiome samples in Genomes OnLine Database. - Davy Weissenbacher, Karen O'Connor, Siddharth Rawal, Yu Zhang, Richard Tzong-Han Tsai, Timothy A. Miller, Dongfang Xu, Carol Anderson, Bo Liu, Qing Han, Jinfeng Zhang, Igor Kulev, Berkay Köprü, Raul Rodriguez-Esteban, Elif Ozkirimli, Ammer Ayach, Roland Roller, Stephen R. Piccolo, Peijin Han, V. G. Vinod Vydiswaran, Ramya Tekumalla, Juan M. Banda, Parsa Bagherzadeh, Sabine Bergler, João Figueira Silva, Tiago Almeida, Paloma Martínez, Renzo M. Rivera Zavala, Chen-Kai Wang, Hong-Jie Dai, Luis Alberto Robles Hernandez, Graciela Gonzalez-Hernandez:
Automatic Extraction of Medication Mentions from Tweets - Overview of the BioCreative VII Shared Task 3 Competition. - Akanksha Arora, Dashleen Kaur, Sumeet Patiyal, Dilraj Kaur, Ritu Tomer, Gajendra P. S. Raghava:
SalivaDB - a comprehensive database for salivary biomarkers in humans. - Jarjapu Mahita, Brendan Ha, Anais Gambiez, Sharon L. Schendel, Haoyang Li, Kathryn M. Hastie, S. Moses Dennison, Kan Li, Natalia Kuzmina, Sivakumar Periasamy, Alexander Bukreyev, Jennifer E. Munt, Mary Osei-Twum, Caroline Atyeo, James A. Overton, Randi Vita, Hector Guzman-Orozco, Marcus Mendes, Mari Kojima, Peter J. Halfmann, Yoshihiro Kawaoka, Galit Alter, Luc Gagnon, Ralph S. Baric, Georgia D. Tomaras, Tim Germann, Daniel Bedinger, Jason A. Greenbaum, Erica Ollmann Saphire, Bjoern Peters:
Coronavirus Immunotherapeutic Consortium Database. - Xueping Quan, Weijing Cai, Chenghang Xi, Chunxiao Wang, Linghua Yan:
AIMedGraph: a comprehensive multi-relational knowledge graph for precision medicine. - Giacomo B. Marino, Megan L. Wojciechowicz, Daniel J. B. Clarke, Maxim V. Kuleshov, Zhuorui Xie, Minji Jeon, Alexander Lachmann, Avi Ma'ayan:
lncHUB2: aggregated and inferred knowledge about human and mouse lncRNAs. - Dorotea Dudas, Ulrike Wittig, Maja Rey, Andreas Weidemann, Wolfgang Müller:
Improved insights into the SABIO-RK database via visualization. - Olivia Garland, Mariia Radaeva, Mohit Pandey, Artem Cherkasov, Nada Lallous:
PurificationDB: database of purification conditions for proteins. - Muriel Rabone, Tammy Horton, Daniel O. B. Jones, Erik Simon-Lledó, Adrian G. Glover:
A review of the International Seabed Authority database DeepData from a biological perspective: challenges and opportunities in the UN Ocean Decade. - Tuan Nguyen, Robert Malina, Ilias Mokas, Antonis Papakonstantinou, Orestes Polyzos, Maarten P. M. Vanhove:
WASP: the World Archives of Species Perception. - Jimin Pei, Qian Cong:
AFTM: a database of transmembrane regions in the human proteome predicted by AlphaFold. - Chengxin Zhang, Anna Marie Pyle:
PDC: a highly compact file format to store protein 3D coordinates. - Emilie Pasche, Anaïs Mottaz, Julien Gobeill, Pierre-André Michel, Déborah Caucheteur, Nona Naderi, Patrick Ruch:
Assessing the use of supplementary materials to improve genomic variant discovery. - Robert Leaman, Rezarta Islamaj, Virginia Adams, Mohammed Alliheedi, João Rafael Almeida, Rui Antunes, Robert Bevan, Yung-Chun Chang, Arslan Erdengasileng, Matthew Hodgskiss, Ryuki Ida, Hyunjae Kim, Keqiao Li, Robert E. Mercer, Lukrécia Mertová, Ghadeer Mobasher, Hoo-Chang Shin, Mujeen Sung, Tomoki Tsujimura, Wen-Chao Yeh, Zhiyong Lu:
Chemical identification and indexing in full-text articles: an overview of the NLM-Chem track at BioCreative VII. - J. Allen Baron, Lynn M. Schriml:
Assessing resource use: a case study with the Human Disease Ontology. - Muhammad Rashid, Mohd. Adib Omar, Tapan Kumar Mohanta:
FungiProteomeDB: a database for the molecular weight and isoelectric points of the fungal proteomes. - Rachana Dande, Ramasubbu Sankararamakrishnan:
dbAQP-SNP: a database of missense single-nucleotide polymorphisms in human aquaporins. - Yongmei Wang, Peng Wang, Yongheng Zhang, Siyi Yao, Zhipeng Xu, Youhua Zhang:
TRSRD: a database for research on risky substances in tea using natural language processing and knowledge graph-based techniques. - Zhi-Liang Hu, Carissa A. Park, James M. Reecy:
A combinatorial approach implementing new database structures to facilitate practical data curation management of QTL, association, correlation and heritability data on trait variants. - Correction to: Standardized naming of microbiome samples in Genomes OnLine Database.
- Angela L. Riffo-Campos, Juan Domingo, Esther Durá:
OncoCardioDB: a public and curated database of molecular information in onco-cardiology/cardio-oncology. - Alexander Kellmann, Pauline Lanting, Lude Franke, David van Enckevort, Morris A. Swertz:
Semi-automatic translation of medicine usage data (in Dutch, free-text) from Lifelines COVID-19 questionnaires to ATC codes. - Zhengpeng Zeng, Jiamin Hu, Miyuan Cao, Bingbing Li, Xiting Wang, Feng Yu, Longfei Mao:
MantaID: a machine learning-based tool to automate the identification of biological database IDs. - Mario S. Valdés-Tresanco, Mario E. Valdés-Tresanco, Esteban Molina-Abad, Ernesto Moreno:
NbThermo: a new thermostability database for nanobodies. - Dorian Kariuki, Kesava Asam, Bradley E. Aouizerat, Kimberly A Lewis, Jose C. Florez, Elena Flowers:
Review of databases for experimentally validated human microRNA-mRNA interactions. - Shashwat Deepali Nagar, I. King Jordan, Leonardo Mariño-Ramírez:
The landscape of health disparities in the UK Biobank. - Arman Edalatmand, Andrew G. McArthur:
CARD*Shark: automated prioritization of literature curation for the Comprehensive Antibiotic Resistance Database. - Walter Arancio, Nicolina Sciaraffa, Claudia Coronnello:
MBS: a genome browser annotation track for high-confident microRNA binding sites in whole human transcriptome. - Raphaël Flores, Cécile Huneau, Laura Burlot, Mathilde Lainé, Erik Kimmel, Cyril Pommier, Michael Alaux, Anne-Françoise Adam-Blondon, Caroline Pont, Hadi Quesneville, Jérôme Salse:
SyntenyViewer: a comparative genomics-driven translational research tool. - Zhi-Hui Luo, Meng-Wei Shi, Yuan Zhang, Dan-Yang Wang, Yi-Bo Tong, Xue-Ling Pan, Shanshan Cheng:
CenhANCER: a comprehensive cancer enhancer database for primary tissues and cell lines. - Yuhao Chi, Ruicheng Qi, Yue Zhou, Huige Tong, Hanbo Jin, Christoph W. Turck, Wei-Hua Chen, Guang-Zhong Wang:
scBrainMap: a landscape for cell types and associated genetic markers in the brain. - Abhishek Khatri, Aman Thakur, Ayush Lepcha, Vishal Acharya, Rakshak Kumar:
IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2). - Yi Jing, Baiyang Feng, Jing Gao, Jin Li, Ganghui Zhou, Zhihong Sun, Yufei Wang:
BLAB2CancerKD: a knowledge graph database focusing on the association between lactic acid bacteria and cancer, but beyond. - Grigory Ryabykh, S. V. Kuznetsov, Y. D. Korostelev, A. I. Sigorskikh, A. A. Zharikova, Andrey A. Mironov:
RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome. - Shalini Chaudhary, Yibing Wu, Doug Strongman, Yan Wang:
CIGAF - a database and interactive platform for insect-associated trichomycete fungi. - Pauline Brochet, Jean-Christophe Mouren, Laurent Hannouche, Fabrice Lopez, Benoît Ballester, Edecio Cunha-Neto, Lionel Spinelli, Christophe Chevillard:
ChagasDB: 80 years of publicly available data on the molecular host response to Trypanosoma cruzi infection in a single database. - Ruben De Blaere, Kévin Lievens, Dieter Van Hassel, Victor Deklerck, Tom De Mil, Wannes Hubau, Joris Van Acker, Nils Bourland, Jan Verwaeren, Jan Van den Bulcke, Hans Beeckman:
SmartWoodID - an image collection of large end-grain surfaces to support wood identification systems. - Ana Julia Velez Rueda, Franco Leonardo Bulgarelli, Nicolas Palopoli, Gustavo D. Parisi:
CaviDB: a database of cavities and their features in the structural and conformational space of proteins. - Nianhang Chen, Rong Zhang, Tao Zeng, Xuting Zhang, Ruibo Wu:
Developing TeroENZ and TeroMAP modules for the terpenome research platform TeroKit. - Darius Linge, Marius Gedgaudas, Andrius Merkys, Vytautas Petrauskas, Antanas Vaitkus, Algirdas Grybauskas, Vaida Paketuryte, Asta Zubriene, Audrius Zaksauskas, Aurelija Mickeviciute, Joana Smirnoviene, Lina Baranauskiene, Edita Capkauskaite, Virginija Dudutiene, Ernestas Urniezius, Aleksandras Konovalovas, Egidijus Kazlauskas, Kirill Shubin, Helgi B. Schiöth, Wen-Yih Chen, John E. Ladbury, Saulius Grazulis, Daumantas Matulis:
PLBD: protein-ligand binding database of thermodynamic and kinetic intrinsic parameters. - Raghunandan Wable, Achuth Suresh Nair, Anirudh Pappu, Widnie Pierre-Louis, Habiba Abdelhalim, Khushbu Patel, Dinesh Mendhe, Shreyas Bolla, Sahil Mittal, Zeeshan Ahmed:
Integrated ACMG-approved genes and ICD codes for the translational research and precision medicine. - Liskin Swint-Kruse, Larissa L. Dougherty, Braelyn Page, Tiffany Wu, Pierce T. O'Neil, Charulata B. Prasannan, Cody Timmons, Qingling Tang, Daniel Joseph Parente, Shwetha Sreenivasan, Todd Holyoak, Aron W. Fenton:
PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. - Jingtian Xu, Can Zhu, Minzeng Su, Sida Li, Haoyu Chao, Ming Chen:
CropGF: a comprehensive visual platform for crop gene family mining and analysis. - Shahid Ullah, Wajeeha Rahman, Farhan Ullah, Anees Ullah, Gulzar Ahmad, Muhammad Ijaz, Hameed Ullah, Zilong Zheng, Tianshun Gao:
AVPCD: a plant-derived medicine database of antiviral phytochemicals for cancer, Covid-19, malaria and HIV. - Tao Wu, Jing Chen, Kaixuan Diao, Guangshuai Wang, Jinyu Wang, Huizi Yao, Xue-Song Liu:
Neodb: a comprehensive neoantigen database and discovery platform for cancer immunotherapy. - Matt J. Thorstensen, Alyssa M. Weinrauch, William S. Bugg, Ken M. Jeffries, W. Gary Anderson:
Tissue-specific transcriptomes reveal potential mechanisms of microbiome heterogeneity in an ancient fish. - Bernardo Estevam, Carlos A. Matos, Clévio Nóbrega:
PolyQ Database - an integrated database on polyglutamine diseases. - Sergio Romero-Tapiador, Blanca Lacruz-Pleguezuelos, Ruben Tolosana, Gala Freixer, Roberto Daza, Cristina M. Fernández-Díaz, Elena Aguilar-Aguilar, Jorge Fernández-Cabezas, Silvia Cruz-Gil, Susana Molina, Maria Carmen Crespo, Teresa Laguna, Laura Judith Marcos-Zambrano, Rubén Vera-Rodríguez, Julian Fiérrez, Ana Ramírez de Molina, Javier Ortega-Garcia, Isabel Espinosa-Salinas, Aythami Morales, Enrique Carrillo-de Santa Pau:
AI4FoodDB: a database for personalized e-Health nutrition and lifestyle through wearable devices and artificial intelligence. - Andrzej Zielezinski, Wojciech Dobrychlop, Wojciech M. Karlowski:
TRGdb: a universal resource for the exploration of taxonomically restricted genes in bacteria. - Young Jin Noh, Hae In Lee, Ji-Hye Choi, Seong-Ho Cho, Yoon Hui Yi, Ji Hyun Lim, Eun Been Myung, Ye Ju Shin, Hyo Jin Shin, Hyun Goo Woo:
CCIDB: a manually curated cell-cell interaction database with cell context information. - Noam Hadar, Grisha Weintraub, Ehud Gudes, Shlomi Dolev, Ohad S. Birk:
GeniePool: genomic database with corresponding annotated samples based on a cloud data lake architecture. - Qinyun Cai, Zhou Zhang, Xiaolong Cui, Chang Zeng, Jiabin Cai, Jiajun Cai, Kai Wu, Xu Zhang, Yixiang Shi, Zoe Arvanitakis, Marc A Bissonnette, Brian C.-H. Chiu, Shi-Yuan Cheng, Chuan He, Wei Zhang:
PETCH-DB: a Portal for Exploring Tissue-specific and Complex disease-associated 5-Hydroxymethylcytosines. - Pietro Pinoli, Arif Canakoglu, Stefano Ceri, Matteo Chiara, Erika Ferrandi, Luca Minotti, Anna Bernasconi:
VariantHunter: a method and tool for fast detection of emerging SARS-CoV-2 variants. - Jian Hu, Baisha Huang, Hao Yin, Kaijie Qi, Yuanyuan Jia, Zhihua Xie, Yuan Gao, Hongxiang Li, Qionghou Li, Zewen Wang, Ying Zou, Shaoling Zhang, Xin Qiao:
PearMODB: a multiomics database for pear (Pyrus) genomics, genetics and breeding study. - Correction to: RNA-Chrom: a manually curated analytical database of RNA-chromatin interactome.
- Merve Gül Turan, Mehmet Emin Orhan, Sebiha Cevik, Oktay I. Kaplan:
CiliaMiner: an integrated database for ciliopathy genes and ciliopathies. - Gustavo Henrique Cervi, Cecilia Dias Flores, Claudia Elizabeth Thompson:
The MetaGens algorithm for metagenomic database lossy compression and subject alignment. - Yunchi Zhu, Chengda Tong, Zuohan Zhao, Zuhong Lu:
MineProt: a stand-alone server for structural proteome curation. 0 - Wonjin Yoon, Sean S. Yi, Richard Jackson, Hyunjae Kim, Sunkyu Kim, Jaewoo Kang:
Biomedical relation extraction with knowledge base-refined weak supervision. - Eva Viesi, Davide S. Sardina, Ugo Perricone, Rosalba Giugno:
APDB: a database on air pollutant characterization and similarity prediction. - Beckett W. Sterner, Steve Elliott, Edward E. Gilbert, Nico M. Franz:
Unified and pluralistic ideals for data sharing and reuse in biodiversity. - Simona Panni, Kalpana Panneerselvam, Pablo Porras, Margaret J. Duesbury, Livia Perfetto, Luana Licata, Henning Hermjakob, Sandra E. Orchard:
The landscape of microRNA interaction annotation: analysis of three rare disorders as a case study. - Minghui Piao, Ke Feng, Xinyu Liu, Xuefeng Bai, Yuqi Zheng, Meiling Sun, Peng Zhao, Yani Wang, Xiaofang Ban, Jie Xiong, Chengyu Shi, Li Meng, Yuxin Liu, Li Yu, Jing Li, Shan Zhong, Xinjian Jiang, Yu Chen, Xin Sun, Yan Zheng, Jinwei Tian:
AgingReG: a curated database of aging regulatory relationships in humans. - Asma Sindhoo Nangraj, Saima Sipy, Abbas Khan, Gurudeeban Selvaraj, Abdulrahman Alshammari, Mark E. Casida, Dong-Qing Wei:
ESOMIR: a curated database of biomarker genes and miRNAs associated with esophageal cancer. - Shailima Rampogu, Mohammed Rafi Shaik, Merajuddin Khan, Mujeeb Khan, Tae Hwan Oh, Baji Shaik:
CBPDdb: a curated database of compounds derived from Coumarin-Benzothiazole-Pyrazole. - Chengzheng Tai, Hongjun Li, Jing Zhang:
BCEDB: a linear B-cell epitopes database for SARS-CoV-2. - Stefano Marchesin, Laura Menotti, Fabio Giachelle, Gianmaria Silvello, Omar Alonso:
Building a large gene expression-cancer knowledge base with limited human annotations. - Ana Petrus, Tobias Wildi, Stefanie Müller:
Preproject 'Swiss Virtual Natural History Collection'. - Jordi Ribera-Altimir, Gerard Llorach Tó, Joan Sala-Coromina, Joan Baptista Company, Eve Galimany:
Fisheries data management systems in the NW Mediterranean: from data collection to web visualization. - Weiping Wang, Jiming Hu, Han Li, Jun Yan, Xiaoyong Sun:
PlantIntronDB: a database for plant introns that host functional elements. - Blanca Lacruz-Pleguezuelos, Oscar Piette, Marco Garranzo, David Pérez-Serrano, Jelena Milesevic, Isabel Espinosa-Salinas, Ana Ramírez de Molina, Teresa Laguna, Enrique Carrillo-de Santa Pau:
FooDrugs: a comprehensive food-drug interactions database with text documents and transcriptional data. - Shatabdi Sen, Margaret Woodhouse, John L. Portwood II, Carson M. Andorf:
Maize Feature Store: A centralized resource to manage and analyze curated maize multi-omics features for machine learning applications. - Kavya Singh, Harshit Maurya, Parthasarathi Singh, Pujarani Panda, Amit Kumar Behera, Arshad Jamal, Ganesh Eslavath, Somesh Mohapatra, Harsh Chauhan, Deepak Sharma:
DISPEL: database for ascertaining the best medicinal plants to cure human diseases. - Correction to: H3ABioNet genomic medicine and microbiome data portals hackathon proceedings.
- Mateusz Jundzill, Riccardo Spott, Mara Lohde, Martin Hölzer, Adrian Viehweger, Christian Brandt:
Managing and monitoring a pandemic: showcasing a practical approach for the genomic surveillance of SARS-CoV-2. - Robin Bramley, Stephen Howe, Haralambos Marmanis:
Notes on the data quality of bibliographic records from the MEDLINE database. - Quan Xu, Yueyue Liu, Dawei Sun, Xiaoqian Huang, Feihong Li, Jincheng Zhai, Yang Li, Qiming Zhou, Niansong Qian, Beifang Niu:
OncoCTMiner: streamlining precision oncology trial matching via molecular profile analysis. - Gábor E. Tusnády, András Zeke, Zsofia E. Kalman, Marie Fatoux-Ardore, Sylvie Ricard-Blum, Toby J. Gibson, Laszlo Dobson:
LeishMANIAdb: a comparative resource for Leishmania proteins. - Ivan Merelli, Stefano Beretta, Daniela Cesana, Alessandro Gennari, Fabrizio Benedicenti, Giulio Spinozzi, Daniele Cesini, Eugenio Montini, Daniele D'Agostino, Andrea Calabria:
InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration. - Carlos Pintado-Grima, Oriol Bárcenas, Valentín Iglesias, Jaime Santos, Zoe Manglano-Artuñedo, Irantzu Pallarès, Michal Burdukiewicz, Salvador Ventura:
aSynPEP-DB: a database of biogenic peptides for inhibiting α-synuclein aggregation. - Jennifer L. Clarke, Laurel D. Cooper, Monica F. Poelchau, Tanya Z. Berardini, Justin Elser, Andrew D. Farmer, Stephen P. Ficklin, Sunita Kumari, Marie-Angélique Laporte, Rex T. Nelson, Rie Sadohara, Peter Selby, Anne E. Thessen, Brandon Whitehead, Taner Z. Sen:
Data sharing and ontology use among agricultural genetics, genomics, and breeding databases and resources of the Agbiodata Consortium. - Cecilia H. Deng, Sushma Naithani, Sunita Kumari, Irene Cobo-Simón, Elsa H. Quezada-Rodríguez, Mária Skrabisová, Nick Gladman, Melanie J. Correll, Akeem Babatunde Sikiru, Olusola O. Afuwape, Annarita Marrano, Ines Rebollo, Wentao Zhang, Sook Jung:
Genotype and phenotype data standardization, utilization and integration in the big data era for agricultural sciences. - Antonio Miranda-Escalada, Farrokh Mehryary, Jouni Luoma, Darryl Estrada-Zavala, Luis Gascó, Sampo Pyysalo, Alfonso Valencia, Martin Krallinger:
Overview of DrugProt task at BioCreative VII: data and methods for large-scale text mining and knowledge graph generation of heterogenous chemical-protein relations. - Chun Fu, Yaojun Yang:
iCAZyGFADB: an insect CAZyme and gene function annotation database. - Ni He, Danyang Li, Fanfan Xu, Jingnan Jin, Lifang Li, Liting Tian, Biying Chen, Xiaoju Li, Shangwei Ning, Lihua Wang, Jianjian Wang:
LncPCD: a manually curated database of experimentally supported associations between lncRNA-mediated programmed cell death and diseases. - Parva Kumar Sharma, Hanin Ibrahim Ahmed, Matthias Heuberger, Dal-Hoe Koo, Jesus Quiroz-Chavez, Laxman Adhikari, John Raupp, Stéphane Cauet, Nathalie Rodde, Charlotte Cravero, Caroline Callot, Inderjit Singh Yadav, Nagarajan Kathiresan, Naveenkumar Athiyannan, Ricardo H. Ramirez-Gonzalez, Cristobal Uauy, Thomas Wicker, Michael Abrouk, Yong Q. Gu, Jesse Poland, Simon G. Krattinger, Gerard R. Lazo, Vijay K. Tiwari:
An online database for einkorn wheat to aid in gene discovery and functional genomics studies. - Bide Zhang, Vanessa Lage-Rupprecht, Philipp Wegner, Astghik Sargsyan, Stephan Gebel, Marc Jacobs, Jürgen Klein, Martin Hofmann-Apitius, Alpha Tom Kodamullil:
Design of the formalized and integrated Alzheimer's Disease Ontology and its application in retrieving textual data via text mining.
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