Works in Database: The Journal of Biological Databases & Curation, 2022, Vol 2022

Results: 117

Correction to: Acinetobase: the comprehensive database and repository of Acinetobacter strains.

Published in:: 2022
Publication type:: Correction Notice

CafeteriaSA corpus: scientific abstracts annotated across different food semantic resources.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac107

By:

Cenikj, Gjorgjina;
Valenčič, Eva;
Ispirova, Gordana;
Ogrinc, Matevž;
Stojanov, Riste;
Korošec, Peter;
Cavalli, Ermanno;
Seljak, Barbara Koroušić;
Eftimov, Tome

Publication type:

Article

Reviewing knowledgebase and database grant proposals in the life sciences: the role of innovation.

Published in:

2022

By:

Karp, Peter D

Publication type:

Editorial

CaRPE: the Carbon Reduction Potential Evaluation tool for building climate mitigation scenarios on US agricultural lands.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac105

By:

Manter, Daniel K;
Moore, Jennifer M

Publication type:

Article

Emati: a recommender system for biomedical literature based on supervised learning.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac104

By:

Kart, Özge;
Mestiashvili, Alexandre;
Lachmann, Kurt;
Kwasnicki, Richard;
Schroeder, Michael

Publication type:

Article

LitCovid ensemble learning for COVID-19 multi-label classification.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac103

By:

Gu, Jinghang;
Chersoni, Emmanuele;
Wang, Xing;
Huang, Chu-Ren;
Qian, Longhua;
Zhou, Guodong

Publication type:

Article

NLM-Chem-BC7: manually annotated full-text resources for chemical entity annotation and indexing in biomedical articles.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac102

By:

Islamaj, Rezarta;
Leaman, Robert;
Cissel, David;
Coss, Cathleen;
Denicola, Joseph;
Fisher, Carol;
Guzman, Rob;
Kochar, Preeti Gokal;
Miliaras, Nicholas;
Punske, Zoe;
Sekiya, Keiko;
Trinh, Dorothy;
Whitman, Deborah;
Schmidt, Susan;
Lu, Zhiyong

Publication type:

Article

HCDT: an integrated highly confident drug–target resource.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac101

By:

Chen, Jiaqi;
Chen, Zhengxin;
Chen, Rufei;
Feng, Dehua;
Li, Tianyi;
Han, Huirui;
Bi, Xiaoman;
Wang, Zhenzhen;
Li, Kongning;
Li, Yongsheng;
Li, Xia;
Wang, Limei;
Li, Jin

Publication type:

Article

PlagueKD: a knowledge graph–based plague knowledge database.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac100

By:

Li, Jin;
Gao, Jing;
Feng, Baiyang;
Jing, Yi

Publication type:

Article

Acinetobase: the comprehensive database and repository of Acinetobacter strains.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac099

By:

Valcek, Adam;
Collier, James;
Botzki, Alexander;
Henst, Charles Van der

Publication type:

Article

Chemical–protein relation extraction with ensembles of carefully tuned pretrained language models.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac098

By:

Weber, Leon;
Sänger, Mario;
Garda, Samuele;
Barth, Fabio;
Alt, Christoph;
Leser, Ulf

Publication type:

Article

OakRootRNADB—a consolidated RNA-seq database for coding and noncoding RNA in roots of pedunculate oak (Quercus robur).

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac097

By:

Kościelniak, Paulina;
Glazińska, Paulina;
Zadworny, Marcin

Publication type:

Article

NEMAR: an open access data, tools and compute resource operating on neuroelectromagnetic data.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac096

By:

Delorme, Arnaud;
Truong, Dung;
Youn, Choonhan;
Sivagnanam, Subhashini;
Stirm, Claire;
Yoshimoto, Kenneth;
Poldrack, Russell A;
Majumdar, Amitava;
Makeig, Scott

Publication type:

Article

FDRdb: a manually curated database of fibrotic disease–associated RNAome and high-throughput datasets.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac095

By:

Wang, Chengyu;
Chen, Tingting;
Mu, Yuchen;
Liang, Xuan;
Xiong, Kai;
Ai, Liqiang;
Gu, Yunyan;
Fan, Xingxing;
Liang, Haihai

Publication type:

Article

MGTdb: a web service and database for studying the global and local genomic epidemiology of bacterial pathogens.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac094

By:

Kaur, Sandeep;
Payne, Michael;
Luo, Lijuan;
Octavia, Sophie;
Tanaka, Mark M;
Sintchenko, Vitali;
Lan, Ruiting

Publication type:

Article

BRACS: A Dataset for BReAst Carcinoma Subtyping in H&E Histology Images.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac093

By:

Brancati, Nadia;
Anniciello, Anna Maria;
Pati, Pushpak;
Riccio, Daniel;
Scognamiglio, Giosuè;
Jaume, Guillaume;
Pietro, Giuseppe De;
Bonito, Maurizio Di;
Foncubierta, Antonio;
Botti, Gerardo;
Gabrani, Maria;
Feroce, Florinda;
Frucci, Maria

Publication type:

Article

PharmaKoVariome database for supporting genetic testing.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac092

By:

Kim, Jungeun;
Choi, Jae-Pil;
Kim, Min Sun;
Bhak, Jong

Publication type:

Article

open-access data set of pig skin anatomy and physiology for modelling purposes.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac091

By:

Krumpholz, Laura;
Clarke, James F;
Polak, Sebastian;
Wiśniowska, Barbara

Publication type:

Article

Assigning species information to corresponding genes by a sequence labeling framework.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac090

By:

Luo, Ling;
Wei, Chih-Hsuan;
Lai, Po-Ting;
Chen, Qingyu;
Islamaj, Rezarta;
Lu, Zhiyong

Publication type:

Article

ChemBioPort: an online portal to navigate the structure, function and chemical inhibition of the human proteome.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac088

By:

Liu, Lihua;
Rovers, Evianne;
Schapira, Matthieu

Publication type:

Article

Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac087

By:

Matentzoglu, Nicolas;
Goutte-Gattat, Damien;
Tan, Shawn Zheng Kai;
Balhoff, James P;
Carbon, Seth;
Caron, Anita R;
Duncan, William D;
Flack, Joe E;
Haendel, Melissa;
Harris, Nomi L;
Hogan, William R;
Hoyt, Charles Tapley;
Jackson, Rebecca C;
Kim, HyeongSik;
Kir, Huseyin;
Larralde, Martin;
McMurry, Julie A;
Overton, James A;
Peters, Bjoern;
Pilgrim, Clare

Publication type:

Article

HSDatabase—a database of highly similar duplicate genes from plants, animals, and algae.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac086

By:

Zhang, Xi;
Hu, Yining;
Smith, David Roy

Publication type:

Article

KinMod database: a tool for investigating metabolic regulation.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac081

By:

Haddadi, Kiandokht;
Barghout, Rana Ahmed;
Mahadevan, Radhakrishnan

Publication type:

Article

SC2sepsis: sepsis single-cell whole gene expression database.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac061

By:

Li, Yinjiaozhi;
Tan, Ruoming;
Chen, Yang;
Liu, Zhaojun;
Chen, Erzhen;
Pan, Tingting;
Qu, Hongping

Publication type:

Article

TEx-MST: tissue expression profiles of MANE select transcripts.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac089

By:

Tung, Kuo-Feng;
Lin, Wen-chang

Publication type:

Article

COTTONOMICS: a comprehensive cotton multi-omics database.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac080

By:

Dai, Fan;
Chen, Jiedan;
Zhang, Ziqian;
Liu, Fengjun;
Li, Jun;
Zhao, Ting;
Hu, Yan;
Zhang, Tianzhen;
Fang, Lei

Publication type:

Article

ProBioQuest: a database and semantic analysis engine for literature, clinical trials and patents related to probiotics.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac059

By:

Chan, Po Lam;
Lauw, Susana;
Ma, Ka Lee;
Kei, Nelson;
Ma, Ka Leong;
Wong, Yiu On;
Lam, Ho Yan;
Ting, Yee Yung;
Yau, Tsz Kwan;
Nong, Wenyan;
Huang, Dandan;
Xie, Yichun;
Cheung, Peter Chi Keung;
Kwan, Hoi Shan

Publication type:

Article

DGPD: a knowledge database of dense granule proteins of the Apicomplexa.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac085

By:

Hu, Hang;
Lu, Zhenxiao;
Feng, Haisong;
Chen, Guojun;
Wang, Yongmei;
Yang, Congshan;
Yue, Zhenyu

Publication type:

Article

Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac084

By:

Chatr-aryamontri, Andrew;
Hirschman, Lynette;
Ross, Karen E;
Oughtred, Rose;
Krallinger, Martin;
Dolinski, Kara;
Tyers, Mike;
Korves, Tonia;
Arighi, Cecilia N

Publication type:

Article

TFLink: an integrated gateway to access transcription factor–target gene interactions for multiple species.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac083

By:

Liska, Orsolya;
Bohár, Balázs;
Hidas, András;
Korcsmáros, Tamás;
Papp, Balázs;
Fazekas, Dávid;
Ari, Eszter

Publication type:

Article

BCSCdb: a database of biomarkers of cancer stem cells.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac082

By:

Firdous, Shazia;
Ghosh, Abhirupa;
Saha, Sudipto

Publication type:

Article

CarrotOmics: a genetics and comparative genomics database for carrot (Daucus carota).

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac079

By:

Rolling, William R;
Senalik, Douglas;
Iorizzo, Massimo;
Ellison, Shelby;
Deynze, Allen Van;
Simon, Philipp W

Publication type:

Article

LiqBioer: a manually curated database of cancer biomarkers in body fluid.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac077

By:

Geng, Yiding;
Jin, Lu;
Tang, Guangjue;
Zhao, Zhangxiang;
Gu, Yunyan;
Yang, Dan

Publication type:

Article

EfGD: the Erianthus fulvus genome database.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac076

By:

Qian, Zhenfeng;
Li, Xuzhen;
He, Lilian;
Gu, Shujie;
Shen, Qingqing;
Rao, Xibing;
Zhang, Rongqiong;
Di, Yining;
Xie, Linyan;
Wang, Xianhong;
Chen, Shuying;
Dong, Yang;
Li, Fusheng

Publication type:

Article

AGODB: a comprehensive domain annotation database of argonaute proteins.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac078

By:

Li, Bowen;
Yang, Shanshan;
Long, Jinjin;
Chen, Xue;
Zhang, Qianyue;
Ning, Lin;
He, Bifang;
Chen, Heng;
Huang, Jian

Publication type:

Article

SLOAD: a comprehensive database of cancer-specific synthetic lethal interactions for precision cancer therapy via multi-omics analysis.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac075

By:

Guo, Li;
Dou, Yuyang;
Xia, Daoliang;
Yin, Zibo;
Xiang, Yangyang;
Luo, Lulu;
Zhang, Yuting;
Wang, Jun;
Liang, Tingming

Publication type:

Article

Full-text chemical identification with improved generalizability and tagging consistency.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac074

By:

Kim, Hyunjae;
Sung, Mujeen;
Yoon, Wonjin;
Park, Sungjoon;
Kang, Jaewoo

Publication type:

Article

CPMCP: a database of Chinese patent medicine and compound prescription.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac073

By:

Sun, Chang;
Huang, Jipeng;
Tang, Rong;
Li, Minglei;
Yuan, Haili;
Wang, Yuxiang;
Wei, Jin-Mao;
Liu, Jian

Publication type:

Article

TopEx: topic exploration of COVID-19 corpora - Results from the BioCreative VII Challenge Track 4.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac063

By:

Olex, Amy L;
French, Evan;
Burdette, Peter;
Sagiraju, Srilakshmi;
Neumann, Thomas;
Gal, Tamas S;
McInnes, Bridget T

Publication type:

Article

Phosprof: pathway analysis database of drug response based on phosphorylation activity measurements.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac072

By:

Kagiwada, Harumi;
Motono, Chie;
Horimoto, Katsuhisa;
Fukui, Kazuhiko

Publication type:

Article

Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac071

By:

Gonzalez-Hernandez, Graciela;
Krallinger, Martin;
Muñoz, Monica;
Rodriguez-Esteban, Raul;
Uzuner, Özlem;
Hirschman, Lynette

Publication type:

Article

Do syntactic trees enhance Bidirectional Encoder Representations from Transformers (BERT) models for chemical–drug relation extraction?

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac070

By:

Tang, Anfu;
Deléger, Louise;
Bossy, Robert;
Zweigenbaum, Pierre;
Nédellec, Claire

Publication type:

Article

Multi-label classification for biomedical literature: an overview of the BioCreative VII LitCovid Track for COVID-19 literature topic annotations.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac069

By:

Chen, Qingyu;
Allot, Alexis;
Leaman, Robert;
Islamaj, Rezarta;
Du, Jingcheng;
Fang, Li;
Wang, Kai;
Xu, Shuo;
Zhang, Yuefu;
Bagherzadeh, Parsa;
Bergler, Sabine;
Bhatnagar, Aakash;
Bhavsar, Nidhir;
Chang, Yung-Chun;
Lin, Sheng-Jie;
Tang, Wentai;
Zhang, Hongtong;
Tavchioski, Ilija;
Pollak, Senja;
Tian, Shubo

Publication type:

Article

TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat—Stem rust host–pathogen interactome.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac068

By:

Kataria, Raghav;
Kaundal, Rakesh

Publication type:

Article

Task reformulation and data-centric approach for Twitter medication name extraction.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac067

By:

Zhang, Yu;
Lee, Jong Kang;
Han, Jen-Chieh;
Tsai, Richard Tzong-Han

Publication type:

Article

ProbResist: a database for drug-resistant probiotic bacteria.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac064

By:

Dou, Wanying;
Abdalla, Hemn Barzan;
Chen, Xu;
Sun, Changyi;
Chen, Xuefei;
Tian, Qiwen;
Wang, Junyi;
Zhou, Wei;
Chi, Wei;
Zhou, Xuan;
Ye, Hailv;
Bi, Chuyun;
Tian, Xuechen;
Yang, Yixin;
Wong, Aloysius

Publication type:

Article

Pre-trained models, data augmentation, and ensemble learning for biomedical information extraction and document classification.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac066

By:

Erdengasileng, Arslan;
Han, Qing;
Zhao, Tingting;
Tian, Shubo;
Sui, Xin;
Li, Keqiao;
Wang, Wanjing;
Wang, Jian;
Hu, Ting;
Pan, Feng;
Zhang, Yuan;
Zhang, Jinfeng

Publication type:

Article

MEDFORD: A human- and machine-readable metadata markup language.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac065

By:

Shpilker, Polina;
Freeman, John;
McKelvie, Hailey;
Ashey, Jill;
Fonticella, Jay-Miguel;
Putnam, Hollie;
Greenberg, Jane;
Cowen, Lenore;
Couch, Alva;
Daniels, Noah M

Publication type:

Article

NetREx: Network-based Rice Expression Analysis Server for abiotic stress conditions.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac060

By:

Sircar, Sanchari;
Musaddi, Mayank;
Parekh, Nita

Publication type:

Article

sequence labeling framework for extracting drug–protein relations from biomedical literature.

Published in:

Database: The Journal of Biological Databases & Curation, 2022, v. 2022, p. 1, doi. 10.1093/database/baac058

By:

Luo, Ling;
Lai, Po-Ting;
Wei, Chih-Hsuan;
Lu, Zhiyong

Publication type:

Article