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ORCIDDatabase - The Journal of Biological Databases and Curation, Volume 2021
Volume 2021, January 2021
- Xuzhen Li
, Zhi Li, Quankuan Shen, Yunbin Pan, Xiao Dong, Zetan Xu, Shengchang Duan, Yunfei Li, Yuan Du, Shanshan Chen, Zhaocheng Ma, Yang Dong:
HGFDB: a collective database of helmeted guinea fowl genomics. - Marie Lefebvre, Alban Gaignard, Maxime Folschette, Jérémie Bourdon, Carito Guziolowski:
Large-scale regulatory and signaling network assembly through linked open data. - Lauren E. Chan, Nicole A. Vasilevsky, Anne E. Thessen, Julie A. McMurry, Melissa A. Haendel:
The landscape of nutri-informatics: a review of current resources and challenges for integrative nutrition research. - Xi Chen, Yang Mei, Mengyao Chen, Dong Jing, Yumin He, Feiling Liu, Kang He, Fei Li:
InSexBase: an annotated genomic resource of sex chromosomes and sex-biased genes in insects. - Roddy Jorquera, Carolina González, Philip T. L. C. Clausen, Bent Petersen, David S. Holmes:
SinEx DB 2.0 update 2020: database for eukaryotic single-exon coding sequences. - Vasundra Touré, John Zobolas, Martin Kuiper, Steven Vercruysse:
CausalBuilder: bringing the MI2CAST causal interaction annotation standard to the curator. - Yifan Shao, Haoru Li, Jinghang Gu, Longhua Qian, Guodong Zhou:
Extraction of causal relations based on SBEL and BERT model. - Nathaniel Lim, Stepan Tesar, Manuel Belmadani, Guillaume Poirier-Morency, Burak Ogan Mancarci, Jordan Sicherman, Matthew Jacobson, Justin Leong, Patrick Tan, Paul Pavlidis:
Curation of over 10 000 transcriptomic studies to enable data reuse. - Pascal Jézéquel, Wilfried Gouraud, Fadoua Ben Azzouz, Catherine Guérin-Charbonnel, Philippe P. Juin, Hamza Lasla, Mario Campone:
bc-GenExMiner 4.5: new mining module computes breast cancer differential gene expression analyses. - Ching-chia Yang, Kakeru Yokoi, Kimiko Yamamoto, Akiya Jouraku:
An update of KAIKObase, the silkworm genome database. - Wen-Ping Guo, Xiao-Bao Ding, Jie Jin, Hai-bo Zhang, Qiao-lei Yang, Peng-Cheng Chen, Heng Yao, Li Ruan, Yu-Tian Tao, Xin Chen:
HIR V2: a human interactome resource for the biological interpretation of differentially expressed genes via gene set linkage analysis. - Zhongyan Li, Siyu Chen, Jhih-Hua Jhong, Yuxuan Pang, Kai-Yao Huang, Shangfu Li, Tzong-Yi Lee:
UbiNet 2.0: a verified, classified, annotated and updated database of E3 ubiquitin ligase-substrate interactions. - Jing Chen, Xingyun Liu, Li Shen, Yuxin Lin, Bairong Shen:
CMBD: a manually curated cancer metabolic biomarker knowledge database. - Shaikh Farhad Hossain, Ming Huang, Naoaki Ono, Aki Morita, Shigehiko Kanaya, Md. Altaf-Ul-Amin:
Development of a biomarker database toward performing disease classification and finding disease interrelations. - Lindy Edwards, Rebecca C. Jackson, James A. Overton, Randi Vita, Nina Blazeska, Bjoern Peters, Alessandro Sette:
An immunologically friendly classification of non-peptidic ligands. - Janisha A. Patel, Dennis A. Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Y. Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson, Chris Armstrong, Raja Mazumder, Jonathon Keeney:
Bioinformatics tools developed to support BioCompute Objects. - Pedro Matos-Filipe, António J. Preto, Panagiotis I. Koukos, Joana Mourão, Alexandre M. J. J. Bonvin, Irina S. Moreira:
MENSAdb: a thorough structural analysis of membrane protein dimers. - Valerio Arnaboldi, Jae-Hyoung Cho, Paul W. Sternberg:
Wormicloud: a new text summarization tool based on word clouds to explore the C. elegans literature. - Shahin Ramazi, Javad Zahiri:
Post-translational modifications in proteins: resources, tools and prediction methods. - Faisal M. Fadlelmola, Kais Ghedira, Yosr Hamdi, Mariem Hanachi, Fouzia Radouani, Imane Allali, Anmol M. Kiran, Lyndon Zass, Nihad Alsayed, Meriem Fassatoui, Chaimae Samtal, Samah Ahmed, Jorge Da Rocha, Souad Chaqsare, Reem M. Sallam, Melek Chaouch, Mohammed Farahat, Alfred Ssekagiri, Ziyaad Parker, Mai Adil, Michael Turkson, Aymen Benchaalia, Alia Benkahla, Sumir Panji, Samar Kamal Kassim, Oussema Souiai, Nicola J. Mulder:
H3ABioNet genomic medicine and microbiome data portals hackathon proceedings. - Abbas Khan, Taimoor Khan, Syed Nouman Nasir, Syed Shujait Ali, Muhammad Suleman, Muhammad Rizwan, Muhammad Waseem, Shahid Ali, Xia Zhao, Dong-Qing Wei:
BC-TFdb: a database of transcription factor drivers in breast cancer. - András Hatos, Federica Quaglia, Damiano Piovesan, Silvio C. E. Tosatto:
APICURON: a database to credit and acknowledge the work of biocurators. - Eryk Kropiwnicki, John Erol Evangelista, Daniel J. Stein, Daniel J. B. Clarke, Alexander Lachmann, Maxim V. Kuleshov, Minji Jeon, Kathleen M. Jagodnik, Avi Ma'ayan:
Drugmonizome and Drugmonizome-ML: integration and abstraction of small molecule attributes for drug enrichment analysis and machine learning. - Adam R. Klie, Brian Tsui, Shamim Mollah, Dylan Skola, Michelle Dow, Chun-Nan Hsu, Hannah Carter:
Increasing metadata coverage of SRA BioSample entries using deep learning-based named entity recognition. - Manica Balant, Airy Gras, Francisco Gálvez, Teresa Garnatje, Joan Vallès, Daniel Vitales:
CANNUSE, a database of traditional Cannabis uses - an opportunity for new research. - Farhat Khan, Aleksandar Radovanovic, Takashi Gojobori, Mandeep Kaur:
IBDDB: a manually curated and text-mining-enhanced database of genes involved in inflammatory bowel disease. - Tzu-Hsien Yang, Chung-Yu Wang, Hsiu-Chun Tsai, Cheng-Tse Liu:
Human IRES Atlas: an integrative platform for studying IRES-driven translational regulation in humans. - Ádám Nagy, Balázs Ligeti, János Szebeni, Sándor Pongor, Balazs Györffy:
COVIDOUTCOME - estimating COVID severity based on mutation signatures in the SARS-CoV-2 genome. - Sebastien A. Choteau, Audrey Wagner, Philippe Pierre, Lionel Spinelli, Christine Brun:
MetamORF: a repository of unique short open reading frames identified by both experimental and computational approaches for gene and metagene analyses. - Saoirse Foley, Carolyn Ku, Brad Arshinoff, Vaneet Lotay, Kamran Karimi, Peter D. Vize, Veronica F. Hinman:
Integration of 1: 1 orthology maps and updated datasets into Echinobase.
Volume 2021, April 2021
- Sook Jung, Chun-Huai Cheng, Katheryn Buble, Taein Lee, Jodi L. Humann, Jing Yu, James Crabb, Heidi Hough, Dorrie Main:
Tripal MegaSearch: a tool for interactive and customizable query and download of big data.
Volume 2021, May 2021
- Santiago Timón-Reina, Mariano Rincón, Rafael Martínez-Tomás:
An overview of graph databases and their applications in the biomedical domain. - Liliana Andrés-Hernández, Razlin Azman Halimi, Ramil Mauleon, Sean Mayes, Abdul Baten, Graham J. King:
Challenges for FAIR-compliant description and comparison of crop phenotype data with standardized controlled vocabularies. - Sanchari Pradhan, Subrata Das, Animesh K. Singh, Chitrarpita Das, Analabha Basu, Partha P. Majumder, Nidhan K. Biswas:
dbGENVOC: database of GENomic Variants of Oral Cancer, with special reference to India. - Claudio Zanettini, Mohamed Omar, Wikum Dinalankara, Eddie Luidy Imada, Elizabeth Colantuoni, Giovanni Parmigiani, Luigi Marchionni:
covid19census: U.S. and Italy COVID-19 metrics and other epidemiological data. - Debarati Roychowdhury, Samir Gupta, Xihan Qin, Cecilia N. Arighi, K. Vijay-Shanker:
emiRIT: a text-mining-based resource for microRNA information. - Yunqing Liu, Yunchi Zhu, Chunpeng He, Zuhong Lu:
BENviewer: a gene interaction network visualization server based on graph embedding model. - Reza Zolfaghari Emameh, Seyed Nezamedin Hosseini, Seppo Parkkila:
Application of beta and gamma carbonic anhydrase sequences as tools for identification of bacterial contamination in the whole genome sequence of inbred Wuzhishan minipig (Sus scrofa) annotated in databases.
Volume 2021, June 2021
- Geoffrey Fell, Robert A. Redd, Alyssa M. Vanderbeek, Rifaquat Rahman, Bill Louv, Jon McDunn, Andrea Arfè, Brian M. Alexander, Steffen Ventz, Lorenzo Trippa:
KMDATA: a curated database of reconstructed individual patient-level data from 153 oncology clinical trials. - Kirill Borziak, Irena Parvanova, Joseph Finkelstein:
ReMeDy: a platform for integrating and sharing published stem cell research data with a focus on iPSC trials. - Yekai Zhou, Hongjun Chen, Sida Li, Ming Chen:
mPPI: a database extension to visualize structural interactome in a one-to-many manner. - Limin Zhang, Xingyi Yang, Zuleima Cota, Hong Cui, Bruce Ford, Hsin-liang Oliver Chen, James A. Macklin, Anton Reznicek, Julian R. Starr:
Which methods are the most effective in enabling novice users to participate in ontology creation? A usability study.
Volume 2021, July 2021
- Yang Cao, Qingyang Dong, Dan Wang, Ying Liu, Pengcheng Zhang, Xiaobo Yu, Chao Niu:
TIDB: a comprehensive database of trained immunity. - Paula Duek Roggli, Camille Mary, Monique Zahn-Zabal, Amos Bairoch, Lydie Lane:
Functionathon: a manual data mining workflow to generate functional hypotheses for uncharacterized human proteins and its application by undergraduate students. - Min Zhao, Yining Liu, Hong Qu:
circExp database: an online transcriptome platform for human circRNA expressions in cancers. - Randi Vita, Jie Zheng, Rebecca C. Jackson, Damion M. Dooley, James A. Overton, Mark A. Miller, Daniel C. Berrios, Richard H. Scheuermann, Yongqun He, Hande Küçük-McGinty, Mathias Brochhausen, Aisyah Yu Lin, Sagar B. Jain, Marcus C. Chibucos, John Judkins, Michelle G. Giglio, Irene Y. Feng, Gully Burns, Matthew H. Brush, Bjoern Peters, Christian J. Stoeckert Jr.:
Standardization of assay representation in the Ontology for Biomedical Investigations. - Qingyao Huang, Paula Carrio-Cordo, Bo Gao, Rahel Paloots, Michael Baudis:
The Progenetix oncogenomic resource in 2021. - Amrita Chattopadhyay, Zi Han Teoh, Chi-Yun Wu, Jyh-Ming Jimmy Juang, Liang-Chuan Lai, Mong-Hsun Tsai, Chia-Hsin Wu, Tzu-Pin Lu, Eric Y. Chuang:
CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer. - Gauri S. Mittal, Anu R. I, Aastha Vatsyayan, Kavita Pandhare, Vinod Scaria:
MUSTARD - a comprehensive resource of mutation-specific therapies in cancer. - Florian Malard, Eugenia Wulff-Fuentes, Rex R. Berendt, Guillaume Didier, Stéphanie Olivier-Van Stichelen:
Automatization and self-maintenance of the O-GlcNAcome catalog: a smart scientific database.
Volume 2021, August 2021
- Junyi Liu, Siyu Liu, Chenzhe Liu, Yaping Zhang, Yuliang Pan, Zixiang Wang, Jiacheng Wang, Ting Wen, Lei Deng:
Nabe: an energetic database of amino acid mutations in protein-nucleic acid binding interfaces. - Sook Jung, Taein Lee, Ksenija Gasic, B. Todd Campbell, Jing Yu, Jodi L. Humann, Sushan Ru, Daniel Edge-Garza, Heidi Hough, Dorrie Main:
The Breeding Information Management System (BIMS): an online resource for crop breeding. - Mahmoud Ahmed, Deok Ryong Kim:
LINPS: a database for cancer-cell-specific perturbations of biological networks. - Thomas R. Beatman, Katherine M. Buckley, Gregory A. Cary, Veronica F. Hinman, Charles A. Ettensohn:
A nomenclature for echinoderm genes.
Volume 2021, September 2021
- Cristofer Quiroz, Yasna Barrera Saavedra, Benjamín Armijo-Galdames, Juan Amado-Hinojosa, Alvaro Olivera-Nappa, Anamaria Sanchez-Daza, David Medina-Ortiz:
Peptipedia: a user-friendly web application and a comprehensive database for peptide research supported by Machine Learning approach. - Jiangyong Qu, Yanran Xu, Yutong Cui, Sen Wu, Lijun Wang, Xiumei Liu, Zhikai Xing, Xiaoyu Guo, Shanshan Wang, Ruoran Li, Xiaoyue Sun, Xiang Li, Xiyue Wang, Tao Liu, Xumin Wang:
MODB: a comprehensive mitochondrial genome database for Mollusca. - Rohit Satyam, Malik Yousef, Sahar Qazi, Adil Manzoor Bhat, Khalid Raza:
COVIDium: a COVID-19 resource compendium.
Volume 2021, October 2021
- Dan Shao, Lan Huang, Yan Wang, Xueteng Cui, Yufei Li, Yao Wang, Qin Ma, Wei Du, Juan Cui:
HBFP: a new repository for human body fluid proteome. - Rebecca C. Jackson, Nicolas Matentzoglu, James A. Overton, Randi Vita, James P. Balhoff, Pier Luigi Buttigieg, Seth Carbon, Mélanie Courtot, Alexander D. Diehl, Damion M. Dooley, William D. Duncan, Nomi L. Harris, Melissa A. Haendel, Suzanna E. Lewis, Darren A. Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M. Schriml, Barry Smith, Christian J. Stoeckert Jr., Nicole A. Vasilevsky, Ramona L. Walls, Jie Zheng, Christopher J. Mungall, Bjoern Peters:
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies. - Shirin C. C. Saverimuttu, Barbara Kramarz, Milagros Rodríguez-López, Penelope Garmiri, Helen Attrill, Katherine E. Thurlow, Marios Makris, Sandra M. Pinheiro, Sandra E. Orchard, Ruth C. Lovering:
Gene Ontology curation of the blood-brain barrier to improve the analysis of Alzheimer's and other neurological diseases. - Marie Deckers, Julien Van Braeckel, Kevin Vanneste, Dieter Deforce, Marie-Alice Fraiture, Nancy H. C. Roosens:
Food Enzyme Database (FEDA): a web application gathering information about food enzyme preparations available on the European market. - Stano Pekár, Jonas O. Wolff, Ludmila Cernecká, Klaus Birkhofer, Stefano Mammola, Elizabeth C. Lowe, Caroline S. Fukushima, Marie E. Herberstein, Adam Kucera, Bruno A. Buzatto, El Aziz Djoudi, Marc Domenech, Alison Vanesa Enciso, Yolanda M. G. Piñanez Espejo, Sara Febles, Luis F. García, Thiago Gonçalves-Souza, Marco Isaia, Denis Lafage, Eva Líznarová, Nuria Macías-Hernández, Ivan Magalhães, Jagoba Malumbres-Olarte, Ondrej Michálek, Peter Michalik, Radek Michalko, Filippo Milano, Ana Munévar, Wolfgang Nentwig, Giuseppe Nicolosi, Christina J. Painting, Julien Pétillon, Elena Piano, Kaïna Privet, Martín J. Ramírez, Cândida Ramos, Milan Rezác, Aurélien Ridel, Vlastimil Ruzicka, Irene Santos, Lenka Sentenská, Leilani Walker, Kaja Wierucka, Gustavo Andres Zurita, Pedro Cardoso:
The World Spider Trait database: a centralized global open repository for curated data on spider traits. - Cristiano Galletti, Patricia Mirela Bota, Baldo Oliva, Narcis Fernandez-Fuentes:
Mining drug-target and drug-adverse drug reaction databases to identify target-adverse drug reaction relationships. - Na Wu, Asha J. Dissanayake, Ishara S. Manawasinghe, Achala R. Rathnayaka, Jian-Kui Liu, Alan j. l Phillips, Itthayakorn Promputtha, Kevin D. Hyde:
https://botryosphaeriales.org/, an online platform for up-to-date classification and account of taxa of Botryosphaeriales. - Taimoor Khan, Abbas Khan, Dong-Qing Wei:
MMV-db: vaccinomics and RNA-based therapeutics database for infectious hemorrhagic fever-causing mammarenaviruses.
Volume 2021, November 2021
- Isaac Arnold Emerson, Kiran Kumar Chitluri:
DCMP: database of cancer mutant protein domains. - Jing Wu, Min Zhao, Tao Li, Jinxiu Sun, Qi Chen, Chengliang Yin, Zhilong Jia, Chenghui Zhao, Gui Lin, Yuan Ni, Guotong Xie, Jinlong Shi, Kunlun He:
HFIP: an integrated multi-omics data and knowledge platform for the precision medicine of heart failure. - Katarzyna Nowis, Paulina Jackowiak, Marek Figlerowicz, Anna Philips:
At-C-RNA database, a one-stop source for information on circRNAs in Arabidopsis thaliana in a unified format. - Shintaro Akiyama, Sayuri Higaki, Takahiro Ochiya, Kouichi Ozaki, Shumpei Niida, Daichi Shigemizu:
JAMIR-eQTL: Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types. - Mikolaj Dziurzynski, Przemyslaw Decewicz, Mateusz Iskra, Zofia Bakula, Tomasz Jagielski:
Prototheca-ID: a web-based application for molecular identification of Prototheca species. - Kamran Karimi, Sergei Agalakov, Cheryl A. Telmer, Thomas R. Beatman, Troy J. Pells, Bradley I. M. Arshinoff, Carolyn Ku, Saoirse Foley, Veronica F. Hinman, Charles A. Ettensohn, Peter D. Vize:
Classifying domain-specific text documents containing ambiguous keywords. - Karsten Klein, Dimitar Garkov, Sina Rütschlin, Thomas Böttcher, Falk Schreiber:
QSDB - a graphical Quorum Sensing Database. - Bo Liu, Qingfeng Zhang, Jingou Wang, Shumin Cao, Zhiyuan Zhou, Zexian Liu, Han Cheng:
iCAV: an integrative database of cancer-associated viruses. - Noha S. Tawfik, Marco R. Spruit:
Corrigendum to: the SNPcurator: literature mining of enriched SNP-disease associations. - Karsten Klein, Dimitar Garkov, Sina Rütschlin, Thomas Böttcher, Falk Schreiber:
Corrigendum to: QSDB - a graphical Quorum Sensing Database. - Anna Bernasconi, Luca Cilibrasi, Ruba Al Khalaf, Tommaso Alfonsi, Stefano Ceri, Pietro Pinoli, Arif Canakoglu:
EpiSurf: metadata-driven search server for analyzing amino acid changes within epitopes of SARS-CoV-2 and other viral species.
Volume 2021, December 2021
- Tavis K. Anderson, Blake Inderski, Diego G. Diel, Benjamin M. Hause, Elizabeth G. Porter, Travis Clement, Eric A. Nelson, Jianfa Bai, Jane Christopher-Hennings, Phillip C. Gauger, Jianqiang Zhang, Karen M. Harmon, Rodger Main, Kelly Lager, Kay Faaberg:
The United States Swine Pathogen Database: integrating veterinary diagnostic laboratory sequence data to monitor emerging pathogens of swine. - Xiaoshun Shi, Ruidong Li, Jianxue Zhai, Allen Menglin Chen, Kailing Huang, Zhouxia Zheng, Zhuona Chen, Xiaoyin Dong, Xiguang Liu, Di Lu, Siyang Feng, Dingwei Diao, Pengfei Ren, Zhaoguo Liu, Grant Morahan, Kaican Cai:
The first comprehensive database of germline pathogenic variants in East Asian cancer patients. - Mubashar Raza, Lei Cai, Muhammad Waseem Abbasi, Marium Tariq, Nalin N. Wijayawardene:
https: //www.fungiofpakistan.com: a continuously updated online database of fungi in Pakistan.
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