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ORCIDDatabase - The Journal of Biological Databases and Curation, Volume 2019
Volume 2019, 2019
- Toshiaki Katayama
, Shuichi Kawashima, Shinobu Okamoto, Yuki Moriya, Hirokazu Chiba, Yuki Naito, Takatomo Fujisawa, Hiroshi Mori, Toshihisa Takagi:
TogoGenome/TogoStanza: modularized Semantic Web genome database. bay132 - Suwen Liu, Wei Cheng, Longhua Qian, Guodong Zhou:
Combining relation extraction with function detection for BEL statement extraction. bay133
- Abigail J. Heithoff, Steven A. Totusek, Duc Le, Lucas Barwick, Gary Gensler, Donald R. Franklin, Allison C. Dye, Sanjit Pandey, Seth Sherman, Chittibabu Guda, Howard S. Fox:
The integrated National NeuroAIDS Tissue Consortium database: a rich platform for neuroHIV research. bay134
- Ajeet Singh, Shafaque Zahra, Durdam Das, Shailesh Kumar:
AtFusionDB: a database of fusion transcripts in Arabidopsis thaliana. bay135 - Muhammad Riaz Khan, Ihtisham Bukhari, Ranjha Khan, Hafiz Muhammad Jafar Hussain, Mian Wu, Rick Francis Thorne, Jinming Li, Guangzhi Liu:
TP53LNC-DB, the database of lncRNAs in the p53 signalling network. bay136 - José Garcia-Pelaez, David Rodriguez, Roberto Medina-Molina, Gerardo Garcia-Rivas, Carlos Jerjes-Sánchez, Victor Trevino:
PubTerm: a web tool for organizing, annotating and curating genes, diseases, molecules and other concepts from PubMed records. bay137
- Pei-Yau Lung, Zhe He, Tingting Zhao, Disa Yu, Jinfeng Zhang:
Extracting chemical-protein interactions from literature using sentence structure analysis and feature engineering. bay138 - Zena Cai, Ya Cui, Zhiying Tan, Gaihua Zhang, Zhongyang Tan, Xinlei Zhang, Yousong Peng:
RAEdb: a database of enhancers identified by high-throughput reporter assays. bay140 - Ran Kang, Yiming Zhang, Qingqing Huang, Junhua Meng, Ruofan Ding, Yunjian Chang, Lili Xiong, Zhiyun Guo:
EnhancerDB: a resource of transcriptional regulation in the context of enhancers. bay141
- Piyush Agrawal, Sumeet Patiyal, Rajesh Kumar, Vinod Kumar, Harinder Singh, Pawan Kumar Raghav, Gajendra P. S. Raghava:
ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank. bay142
- Neil R. Smalheiser, Mengqi Luo, Sidharth Addepalli, Xiaokai Cui:
A manual corpus of annotated main findings of clinical case reports. bay143
- Phani V. Garapati, Jingyao Zhang, Alix J. Rey, Steven J. Marygold:
Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase. bay144
- Guocai Chen, Juan Camilo Ramírez, Nan Deng, Xing Qiu, Canglin Wu, W. Jim Zheng, Hulin Wu:
Restructured GEO: restructuring Gene Expression Omnibus metadata for genome dynamics analysis. bay145
- Sushma Naithani, Parul Gupta, Justin Preece, Priyanka Garg, Valerie Fraser, Lillian K. Padgitt-Cobb, Matthew Martin, Kelly Vining, Pankaj Jaiswal:
Involving community in genes and pathway curation. bay146
- Martyna Nowacka, Pietro Boccaletto, Elzbieta Jankowska, Tomasz Jarzynka, Janusz M. Bujnicki, Stanislaw Dunin-Horkawicz:
RRMdb - an evolutionary-oriented database of RNA recognition motif sequences. bay148 - Saber A. Akhondi, Hinnerk Rey, Markus Schwörer, Michael Maier, John P. Toomey, Heike Nau, Gabriele Ilchmann, Mark Sheehan, Matthias Irmer, Claudia Bobach, Marius A. Doornenbal, Michelle Gregory, Jan A. Kors:
Automatic identification of relevant chemical compounds from patents. baz001 - Gerhard Rambold, Pelin Yilmaz, Janno Harjes, Sabrina Klaster, Veronica Sanz, Anton Link, Frank Oliver Glöckner, Dagmar Triebel:
Meta-omics data and collection objects (MOD-CO): a conceptual schema and data model for processing sample data in meta-omics research. baz002
- Xianwen Meng, Dahui Hu, Peijing Zhang, Qi Chen, Ming Chen:
CircFunBase: a database for functional circular RNAs. baz003
- Alberto Grand, Emanuele Geda, Andrea Mignone, Andrea Bertotti, Alessandro Fiori:
One tool to find them all: a case of data integration and querying in a distributed LIMS platform. baz004 - Diego Alonso-López, Francisco J. Campos-Laborie, Miguel A. Gutiérrez, Luke Lambourne, Michael A. Calderwood, Marc Vidal, Javier De Las Rivas:
APID database: redefining protein-protein interaction experimental evidences and binary interactomes. baz005 - Sam M. Ireland, Andrew C. R. Martin:
ZincBind - the database of zinc binding sites. baz006 - Helen Attrill, Pascale Gaudet, Rachael P. Huntley, Ruth C. Lovering, Stacia R. Engel, Sylvain Poux, Kimberly M. Van Auken, George E. Georghiou, Marcus C. Chibucos, Tanya Z. Berardini, Valerie Wood, Harold J. Drabkin, Petra Fey, Penelope Garmiri, Midori A. Harris, Tony Sawford, Leonore Reiser, Rebecca Tauber, Sabrina Toro, The Gene Ontology Consortium:
Annotation of gene product function from high-throughput studies using the Gene Ontology. baz007 - Edith D. Wong, Marek S. Skrzypek, Shuai Weng, Gail Binkley, Birgit H. M. Meldal, Livia Perfetto, Sandra E. Orchard, Stacia R. Engel, J. Michael Cherry, SGD Project:
Integration of macromolecular complex data into the Saccharomyces Genome Database. baz008 - Hee-Ju Yu, Seunghoon Baek, Young-Joon Lee, Ara Cho, Jeong-Hwan Mun:
The radish genome database (RadishGD): an integrated information resource for radish genomics. baz009 - Yi-Yu Hsu, Mindy Clyne, Chih-Hsuan Wei, Muin J. Khoury, Zhiyong Lu:
Using deep learning to identify translational research in genomic medicine beyond bench to bedside. baz010
- Gaole An, Jiaqi Sun, Chao Ren, Zhangyi Ouyang, Lingyun Zhu, Xiaochen Bo, Shaoliang Peng, Wenjie Shu:
LIVE: a manually curated encyclopedia of experimentally validated interactions of lncRNAs. baz011 - Salman Sadullah Usmani, Piyush Agrawal, Manika Sehgal, Pradeep Kumar Patel, Gajendra P. S. Raghava:
ImmunoSPdb: an archive of immunosuppressive peptides. baz012
- Ryan Barrett, Cynthia L. Neben, Anjali D. Zimmer, Gilad Mishne, Wendy McKennon, Alicia Y. Zhou, Jeremy Ginsberg:
A scalable, aggregated genotypic-phenotypic database for human disease variation. baz013 - Shur-Jen Wang, Stanley J. F. Laulederkind, Yiqing Zhao, G. Thomas Hayman, Jennifer R. Smith, Monika Tutaj, Jyothi Thota, Marek Tutaj, Matthew J. Hoffman, Elizabeth R. Bolton, Jeffrey DePons, Melinda R. Dwinell, Mary Shimoyama:
Integrated curation and data mining for disease and phenotype models at the Rat Genome Database. baz014 - V. Sureshkumar, Bipratip Dutta, Vishesh Kumar, G. Prakash, Dwijesh Chandra Mishra, K. K. Chaturvedi, Anil Rai, Amitha Mithra S. V., Amolkumar U. Solanke:
RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes. baz015
- Sizhe Xiao, Chris Armit, Scott C. Edmunds, Laurie Goodman, Peter Li, Mary Ann Tuli, Christopher I. Hunter:
Increased interactivity and improvements to the GigaScience database, GigaDB. baz016
- Michael Farnum, Mathangi Ashok, Daniel Kowalski, Fang Du, Lalit Mohanty, Paul Konstant, Joseph Ciervo, Victor S. Lobanov, Dimitris K. Agrafiotis:
A cross-source, system-agnostic solution for clinical data review. baz017 - Jinding Liu, Dongbo Wang, Yinna Su, Kun Lang, Rongjing Duan, Yufeng Wu, Fei Ma, Shuiqing Huang:
FairBase: a comprehensive database of fungal A-to-I RNA editing. baz018 - Anastasia A. Nikitina, Alexey A. Orlov, Liubov I. Kozlovskaya, Vladimir A. Palyulin, Dmitry I. Osolodkin:
Enhanced taxonomy annotation of antiviral activity data from ChEMBL. bay139
- Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Chih-Hsuan Wei, Donald C. Comeau, Rui Antunes, Sérgio Matos, Qingyu Chen, Aparna Elangovan, Nagesh C. Panyam, Karin Verspoor, Hongfang Liu, Yanshan Wang, Zhuang Liu, Berna Altinel, Zehra Melce Hüsünbeyi, Arzucan Özgür, Aris Fergadis, Chen-Kai Wang, Hong-Jie Dai, Tung Tran, Ramakanth Kavuluru, Ling Luo, Albert Steppi, Jinfeng Zhang, Jinchan Qu, Zhiyong Lu:
Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. bay147 - Senay Kafkas, Robert Hoehndorf:
Ontology based text mining of gene-phenotype associations: application to candidate gene prediction. baz019 - Wanwen Zeng, Xu Min, Rui Jiang:
EnDisease: a manually curated database for enhancer-disease associations. baz020 - Sarahani Harun, Muhammad Redha Abdullah Zawawi, Mohd Rusman Arief A.-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein:
SuCComBase: a manually curated repository of plant sulfur-containing compounds. baz021
- Swagata Pahari, Lexuan Sun, Emil Alexov:
PKAD: a database of experimentally measured pKa values of ionizable groups in proteins. baz024
- Tian Li, Xiaofei Xu, Hui-Hui Du, Li Li, Neng-Zhang Li, Zeyang Zhou, Yuan-Yi Peng:
PamulDB: a comprehensive genomic resource for the study of human- and animal-pathogenic Pasteurella multocida. baz025 - Chuming Chen, Qinghua Wang, Hongzhan Huang, Cholanayakanahalli R. Vinayaka, John S. Garavelli, Cecilia N. Arighi, Darren A. Natale, Cathy H. Wu:
PIRSitePredict for protein functional site prediction using position-specific rules. baz026
- Zhi-Wei Guo, Chen Xie, Kun Li, Xiang-Ming Zhai, Geng-Xi Cai, Xue-Xi Yang, Ying-Song Wu:
SELER: a database of super-enhancer-associated lncRNA- directed transcriptional regulation in human cancers. baz027
- Wentao Yang, Chuanqi Jiang, Ying Zhu, Kai Chen, Guangying Wang, Dong-Xia Yuan, Wei Miao, Jie Xiong:
Tetrahymena Comparative Genomics Database (TCGD): a community resource for Tetrahymena. baz029 - Hong-Jie Dai, Chen-Kai Wang, Nai-Wen Chang, Ming-Siang Huang, Jitendra Jonnagaddala, Feng-Duo Wang, Wen-Lian Hsu:
Statistical principle-based approach for recognizing and normalizing microRNAs described in scientific literature. baz030 - Kevin Correia, Shi M. Yu, Radhakrishnan Mahadevan:
AYbRAH: a curated ortholog database for yeasts and fungi spanning 600 million years of evolution. baz022 - Evi Berchtold, Gergely Csaba, Ralf Zimmer:
YESdb: integrative analysis of environmental stress in yeast. baz023
- Pritha Ghosh, Teerna Bhattacharyya, Oommen K. Mathew, Ramanathan Sowdhamini:
PASS2 version 6: a database of structure-based sequence alignments of protein domain superfamilies in accordance with SCOPe. baz028 - Catarina Nunes, Isa Mestre, Adriana Marcelo, Rebekah Koppenol, Carlos A. Matos, Clévio Nóbrega:
MSGP: the first database of the protein components of the mammalian stress granules. baz031 - Eric Yang, Jeremy D. Scheff, Shih C. Shen, Michael Farnum, James Sefton, Victor S. Lobanov, Dimitris K. Agrafiotis:
A late-binding, distributed, NoSQL warehouse for integrating patient data from clinical trials. baz032
- Sarah J. Vancuren, Janet E. Hill:
Update on cpnDB: a reference database of chaperonin sequences. baz033
- Surya Saha, Prashant S. Hosmani, Krystal Villalobos-Ayala, Sherry Miller, Teresa Shippy, Mirella Flores, Andrew Rosendale, Chris Cordola, Tracey Bell, Hannah Mann, Gabe DeAvila, Daniel DeAvila, Zachary Moore, Kyle Buller, Kathryn Ciolkevich, Samantha Nandyal, Robert Mahoney, Joshua Van Voorhis, Megan Dunlevy, David C. Farrow, David Hunter, Taylar Morgan, Kayla Shore, Victoria Guzman, Allison Izsak, Danielle E. Dixon, Andrew Cridge, Liliana M. Cano, Xiaolong Cao, Haobo Jiang, Nan Leng, Shannon Johnson, Brandi L. Cantarel, Stephen Richards, Adam C. English, Robert G. Shatters, Christopher P. Childers, Mei-Ju Chen, Wayne B. Hunter, Michelle Cilia, Lukas A. Mueller, Monica C. Munoz-Torres, David Nelson, Monica Poelchau, Joshua B. Benoit, Helen Wiersma-Koch, Tom D'Elia, Susan J. Brown:
Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. baz035
- Jason A. Bubier, David P. Hill, Gaurab Mukherjee, Timothy Reynolds, Erich J. Baker, Alexander Berger, Jake Emerson, Judith A. Blake, Elissa J. Chesler:
Curating gene sets: challenges and opportunities for integrative analysis. baz036
- Taylor Falk, Nic Herndon, Emily S. Grau, Sean Buehler, Peter Richter, Sumaira Zaman, Eliza M. Baker, Risharde Ramnath, Stephen P. Ficklin, Margaret Staton, Frank Alex Feltus, Sook Jung, Doreen Main, Jill L. Wegrzyn:
Growing and cultivating the forest genomics database, TreeGenes. baz043
- Gully A. Burns, Xiangci Li, Nanyun Peng:
Building deep learning models for evidence classification from the open access biomedical literature. baz034 - Yiqing Zhao, Jennifer R. Smith, Shur-Jen Wang, Melinda R. Dwinell, Mary Shimoyama:
Quantitative phenotype analysis to identify, validate and compare rat disease models. baz037 - Michael Farnum, Lalit Mohanty, Mathangi Ashok, Paul Konstant, Joseph Ciervo, Victor S. Lobanov, Dimitris K. Agrafiotis:
A dimensional warehouse for integrating operational data from clinical trials. baz039 - Maria Livia Famiglietti, Anne Estreicher, Lionel Breuza, Sylvain Poux, Nicole Redaschi, Ioannis Xenarios, Alan J. Bridge:
An enhanced workflow for variant interpretation in UniProtKB/Swiss-Prot improves consistency and reuse in ClinVar. baz040
- Meenakshi S. Iyer, Kartik Bhargava, Murugavel Pavalam, Ramanathan Sowdhamini:
GenDiS database update with improved approach and features to recognize homologous sequences of protein domain superfamilies. baz042 - Ben Scott, Edward Baker, Matt Woodburn, Sarah Vincent, Helen Hardy, Vincent S. Smith:
The Natural History Museum Data Portal. baz038 - Tim E. Putman, Kevin Hybiske, Derek Jow, Cyrus Afrasiabi, Sebastien Lelong, Marco Alvarado Cano, Chunlei Wu, Andrew I. Su:
ChlamBase: a curated model organism database for the Chlamydia research community. baz041
- Paulo Muniz de Ávila, Diego Cesar Valente e Silva, Paulo Cesar de Melo Bernardo, Ramon Gustavo Teodoro Marques da Silva, Ana Lúcia Fachin, Mozart Marins, Edilson Carlos Caritá:
CANCROX: a cross-species cancer therapy database. baz044 - Xiangying Jiang, Martin Ringwald, Judith A. Blake, Cecilia N. Arighi, Gongbo Zhang, Hagit Shatkay:
An effective biomedical document classification scheme in support of biocuration: addressing class imbalance. baz045 - Oscar Franzén, Li-Ming Gan, Johan L. M. Björkegren:
PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. baz046 - Jan Jelínek, David Hoksza, Jan Hajic Jr., Jan Pesek, Jan Drozen, Tomás Hladík, Michal Klimpera, Jirí Vohradský, Josef Pánek:
rPredictorDB: a predictive database of individual secondary structures of RNAs and their formatted plots. baz047
- Jonathan McMillan, Zhaolian Lu, Judith S. Rodríguez, Tae-Hyuk Ahn, Zhenguo Lin:
YeasTSS: an integrative web database of yeast transcription start sites. baz048
- Malo Le Boulch, Patrice Déhais, Sylvie Combes, Géraldine Pascal:
The MACADAM database: a MetAboliC pAthways DAtabase for Microbial taxonomic groups for mining potential metabolic capacities of archaeal and bacterial taxonomic groups. baz049
- Bo Su, Zhuang Qian, Tianshu Li, Yuwei Zhou, Aloysius Wong:
PlantMP: a database for moonlighting plant proteins. baz050
- Shobha Sharma, Stacy Ciufo, Elena Starchenko, Dakshesh Darji, Larry Chlumsky, Ilene Karsch-Mizrachi, Conrad L. Schoch:
The NCBI BioCollections Database. baz057
- Ying Wang, Yueqian Wang, Shuangkuai Wang, Yuantao Tong, Ling Jin, Hui Zong, Rongbin Zheng, Jinxuan Yang, Zeyu Zhang, En Ouyang, Mengyan Zhou, Xiaoyan Zhang:
GIDB: a knowledge database for the automated curation and multidimensional analysis of molecular signatures in gastrointestinal cancer. baz051
- Kai Wang, Chong Wang, Baohuan Guo, Kun Song, Chuanhong Shi, Xin Jiang, Keyi Wang, Yacong Tan, Lequn Wang, Lin Wang, Jiangjiao Li, Ying Li, Yu Cai, Hongwei Zhao, Xiaoyong Sun:
CropCircDB: a comprehensive circular RNA resource for crops in response to abiotic stress. baz053
- Yijia Zhang, Hongfei Lin, Zhihao Yang, Jian Wang, Yuanyuan Sun:
Chemical-protein interaction extraction via contextualized word representations and multihead attention. baz054 - Leiming You, Jiaqi Chi, Shengfeng Huang, Ting Yu, Guangrui Huang, Yuchao Feng, Xiaopu Sang, Xinhui Gao, Ting'an Li, Zirui Yue, Aijie Liu, Shangwu Chen, Anlong Xu:
LanceletDB: an integrated genome database for lancelet, comparing domain types and combination in orthologues among lancelet and other species. baz056 - Daniel Domingo-Fernández, Allison Provost, Alpha Tom Kodamullil, Josep Marín-Llaó, Heather Lasseter, Kristophe Diaz, Nikolaos P. Daskalakis, Lee Lancashire, Martin Hofmann-Apitius, Magali Haas:
PTSD Biomarker Database: deep dive metadatabase for PTSD biomarkers, visualizations and analysis tools. baz081 - Thidarat Rujirawat, Preecha Patumcharoenpol, Weerayuth Kittichotirat, Theerapong Krajaejun:
Oomycete Gene Table: an online database for comparative genomic analyses of the oomycete microorganisms. baz082 - Dilraj Kaur, Sumeet Patiyal, Neelam Sharma, Salman Sadullah Usmani, Gajendra P. S. Raghava:
PRRDB 2.0: a comprehensive database of pattern-recognition receptors and their ligands. baz076 - Jakub Juracka, Martin Srejber, Michaela Melikova, Václav Bazgier, Karel Berka:
MolMeDB: Molecules on Membranes Database. baz078 - Geng-Ming Hu, M. K. Secario, Chi-Ming Chen:
SeQuery: an interactive graph database for visualizing the GPCR superfamily. baz073 - Dongliang Yu, Jiangjie Lu, Weishan Shao, Xiaoxia Ma, Tian Xie, Hidetaka Ito, Tingzhang Wang, Min Xu, Huizhong Wang, Yijun Meng:
MepmiRDB: a medicinal plant microRNA database. baz070 - Zhiyuan Zhang, Guozhong Chen, Jun Hu, Wajid Hussain, Fenxia Fan, Yalin Yang, Zhigang Zhou, Xiaodong Fang, Jun Zhu, Wei-Hua Chen, Zhi Liu:
Mr.Vc: a database of microarray and RNA-seq of Vibrio cholerae. baz069 - Ben Fan, Cong Wang, Xiaolei Ding, Bingyao Zhu, Xiaofeng Song, Rainer Borriss:
AmyloWiki: an integrated database for Bacillus velezensis FZB42, the model strain for plant growth-promoting Bacilli. baz071 - Qingyu Liu, Yanning Cai, Haiquan Xiong, Yiyun Deng, Xianhua Dai:
CCRDB: a cancer circRNAs-related database and its application in hepatocellular carcinoma-related circRNAs. baz063 - Charles Tapley Hoyt, Daniel Domingo-Fernández, Rana Aldisi, Lingling Xu, Kristian Kolpeja, Sandra Spalek, Esther Wollert, John A. Bachman, Benjamin M. Gyori, Patrick Greene, Martin Hofmann-Apitius:
Re-curation and rational enrichment of knowledge graphs in Biological Expression Language. baz068 - Keeley Collins, Kun Zhao, Chen Jiao, Chenxi Xu, Xiaofeng Cai, Xiaoli Wang, Chenhui Ge, Shaojun Dai, Quanxi Wang, Quanhua Wang, Zhangjun Fei, Yi Zheng:
SpinachBase: a central portal for spinach genomics. baz072 - Shaini Joseph, Smita D. Mahale:
Endometriosis Knowledgebase: a gene-based resource on endometriosis. baz062 - Marcos Martínez Romero, Martin J. O'Connor, Attila L. Egyedi, Debra Willrett, Josef Hardi, John B. Graybeal, Mark A. Musen:
Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. baz059 - Fiona M. McCarthy, Ken Pendarvis, Amanda M. Cooksey, Cathy R. Gresham, Matt Bomhoff, Sean Davey, Eric Lyons, Tad S. Sonstegard, Susan M. Bridges, Shane C. Burgess:
Chickspress: a resource for chicken gene expression. baz058 - Rahul Singh Jasrotia, Pramod Kumar Yadav, Mir Asif Iquebal, S. B. Bhatt, Vasu Arora, Ulavappa B. Angadi, Rukam Singh Tomar, Sarika Jaiswal, Anil Rai, Dinesh Kumar:
VigSatDB: genome-wide microsatellite DNA marker database of three species of Vigna for germplasm characterization and improvement. baz055
- Victoria C. Blake, Margaret Woodhouse, Gerard R. Lazo, Sarah G. Odell, Charlene P. Wight, Nicholas A Tinker, Yi Wang, Yong Q. Gu, Clayton L. Birkett, Jean-Luc Jannink, Dave E. Matthews, David L. Hane, Steve L. Michel, Eric Yao, Taner Z. Sen:
GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. baz065
- Anil Kumar Nalini Chandran, Sunok Moon, Yo-Han Yoo, Yoon-Shil Gho, Peijian Cao, Rita Sharma, Manoj K. Sharma, Pamela C. Ronald, Kihong Jung:
A web-based tool for the prediction of rice transcription factor function. baz061 - Judith Pérez-Granado, Janet Piñero González, Laura Inés Furlong:
ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer. baz060
- Tim E. Putman, Kevin Hybiske, Derek Jow, Cyrus Afrasiabi, Sebastien Lelong, Marco Alvarado Cano, Gregory S. Stupp, Andra Waagmeester, Benjamin M. Good, Chunlei Wu, Andrew I. Su:
ChlamBase: a curated model organism database for the Chlamydia research community. baz091 - Cong Pian, Guang-Le Zhang, Tengfei Tu, Xiangyu Ma, Fei Li:
LncCeRBase: a database of experimentally validated human competing endogenous long non-coding RNAs. baz090
- Jian Liu, Mo Yang, Lei Zhang, Weijun Zhou:
An effective biomedical data migration tool from resource description framework to JSON. baz088 - Chien-Yueh Lee, Amrita Chattopadhyay, Li-Mei Chiang, Jyh-Ming Jimmy Juang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang:
VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases. baz075 - Minglei Yang, Wenliang Zhang, Guocai Yao, Haiyue Zhang, Weizhong Li:
Combined alignments of sequences and domains characterize unknown proteins with remotely related protein search PSISearch2D. baz092 - Shawna Spoor, Chun-Huai Cheng, Lacey-Anne Sanderson, Bradford Condon, Abdullah Almsaeed, Ming Chen, Anthony Bretaudeau, Helena Rasche, Sook Jung, Dorrie Main, Kirstin E. Bett, Margaret Staton, Jill L. Wegrzyn, F. Alex Feltus, Stephen P. Ficklin:
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. baz077 - Iman Almansour, Mazen Alhagri, Rahaf Alfares, Manal Alshehri, Razan Bakhashwain, Ahmed Maarouf:
IRAM: virus capsid database and analysis resource. baz079 - Enyu Dai, Hao Zhang, Xu Zhou, Qian Song, Di Li, Lei Luo, Xinyu Xu, Wei Jiang, Hong Ling:
MycoResistance: a curated resource of drug resistance molecules in Mycobacteria. baz074 - Susie S. Y. Huang, Fatima Al Ali, Sabri Boughorbel, Mohammed Toufiq, Damien Chaussabel, Mathieu Garand:
A curated collection of transcriptome datasets to investigate the molecular mechanisms of immunoglobulin E-mediated atopic diseases. baz066 - Andrea Mignone, Alberto Grand, Alessandro Fiori, Enzo Medico, Andrea Bertotti:
Semalytics: a semantic analytics platform for the exploration of distributed and heterogeneous cancer data in translational research. baz080 - Kristine K. Dennis, Karan Uppal, Ken H. Liu, Chunyu Ma, Bill Liang, Young-Mi Go, Dean P. Jones:
Phytochelatin database: a resource for phytochelatin complexes of nutritional and environmental metals. baz083 - Rezarta Islamaj Dogan, W. John Wilbur, Natalie Xie, Noreen R. Gonzales, Narmada Thanki, Roxanne A. Yamashita, Chanjuan Zheng, Aron Marchler-Bauer, Zhiyong Lu:
PubMed Text Similarity Model and its application to curation efforts in the Conserved Domain Database. baz064
- Jochen T. Bick, Shuqin Zeng, Mark D. Robinson, Susanne E. Ulbrich, Stefan Bauersachs:
Mammalian Annotation Database for improved annotation and functional classification of Omics datasets from less well-annotated organisms. baz086
- Azhar Muhammad, Ramay Waheed, Nauman Ali Khan, Hong Jiang, Xiaoyuan Song:
piRDisease v1.0: a manually curated database for piRNA associated diseases. baz052
- Rebekah H. Griesenauer, Constantino Schillebeeckx, Michael S. Kinch:
CDEK: Clinical Drug Experience Knowledgebase. baz087 - Nan Lu, Tianqing Zhu, Fangqun Ouyang, Yan Xia, Qingfen Li, Zirui Jia, Jiwen Hu, Juanjuan Ling, Wenjun Ma, Guijuan Yang, Hanguo Zhang, Lisheng Kong, Junhui Wang:
PICEAdatabase: a web database for Picea omics and phenotypic information. baz089 - Lars Vogt, Roman Baum, Philipp Bhatty, Christian Köhler, Sandra A. Meid, Björn Quast, Peter Grobe:
SOCCOMAS: a FAIR web content management system that uses knowledge graphs and that is based on semantic programming. baz067
- Zhongjie Tang, ShaoQi Chen, Ang Chen, Bifang He, Yuwei Zhou, Guoshi Chai, Feng-Biao Guo, Jian Huang:
CasPDB: an integrated and annotated database for Cas proteins from bacteria and archaea. baz093
- Lingfeng Mao, Meihong Chen, Qinjie Chu, Lei Jia, Most Humaira Sultana, Dongya Wu, Xiangdong Kong, Jie Qiu, Chu-Yu Ye, Qian-Hao Zhu, Xi Chen, Longjiang Fan:
RiceRelativesGD: a genomic database of rice relatives for rice research. baz110
- Rahila Sardar, Abhinav Kaushik, Rajan Pandey, Asif Mohmmed, Shakir Ali, Dinesh Gupta:
ApicoTFdb: the comprehensive web repository of apicomplexan transcription factors and transcription-associated co-factors. baz094
- Yaw Nti-Addae, Dave Matthews, Victor Jun M. Ulat, Raza Syed, Guilhem Sempéré, Adrien Pétel, Jon Renner, Pierre Larmande, Valentin Guignon, Elizabeth Jones, Kelly Robbins:
Benchmarking database systems for Genomic Selection implementation. baz096 - Andrea Hatlen, Mohab Helmy, Antonio Marco:
PopTargs: a database for studying population evolutionary genetics of human microRNA target sites. baz102 - Leo William Norval, Stefan Daniel Krämer, Mingjie Gao, Tobias Herz, Jianyu Li, Christin Rath, Johannes Wöhrle, Stefan Günther, Günter Roth:
KOFFI and Anabel 2.0 - a new binding kinetics database and its integration in an open-source binding analysis software. baz101 - Justyna Jarczak, Jakub Lach, P. Borówka, Mariusz Galka, Mateusz Bucko, Blazej Marciniak, Dominik Strapagiel:
BioSCOOP - Biobank Sample Communication Protocol. New approach for the transfer of information between biobanks. baz105 - Daniel Vitales, Pol Fernández, Teresa Garnatje, Sònia Garcia:
Progress in the study of genome size evolution in Asteraceae: analysis of the last update. baz098 - Céline Bourdon, Philippe Bardou, Etienne Aujean, Sandrine Le Guillou, Gwenola Tosser-Klopp, Fabienne Le Provost:
RumimiR: a detailed microRNA database focused on ruminant species. baz099 - Sumit Madan, Justyna Szostak, Ravikumar Komandur Elayavilli, Richard Tzong-Han Tsai, Mehdi Ali, Longhua Qian, Majid Rastegar-Mojarad, Julia Hoeng, Juliane Fluck:
The extraction of complex relationships and their conversion to biological expression language (BEL) overview of the BioCreative VI (2017) BEL track. baz084 - Zhihong Liu, Jiewen Du, Jiansong Fang, Yulong Yin, Guohuan Xu, Liwei Xie:
DeepScreening: a deep learning-based screening web server for accelerating drug discovery. baz104 - Katheryn Buble, Sook Jung, Jodi L. Humann, Jing Yu, Chun-Huai Cheng, Taein Lee, Stephen P. Ficklin, Heidi Hough, Bradford Condon, Margaret E. Staton, Jill L. Wegrzyn, Dorrie Main:
Tripal MapViewer: A tool for interactive visualization and comparison of genetic maps. baz100
- Sickle Cell Disease Ontology Working Group:
The Sickle Cell Disease Ontology: enabling universal sickle cell-based knowledge representation. baz118 - Jessica Schuster, Michael Superdock, Anthony Agudelo, Paul Stey, James Padbury, Indra Neil Sarkar, Alper Uzun:
Machine learning approach to literature mining for the genetics of complex diseases. baz124 - Changcheng You, Kai Zhu, Qiuhua Zhang, Jnglong Yan, Yufu Wang, Jing Li:
ODNA: a manually curated database of noncoding RNAs associated with orthopedics. baz126 - Alessandro La Ferlita, Salvatore Alaimo, Dario Veneziano, Giovanni Nigita, Veronica Balatti, Carlo Maria Croce, Alfredo Ferro, Alfredo Pulvirenti:
Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer. baz115 - Zhiqiang Gan, Houjin Zhang:
PMBD: a Comprehensive Plastics Microbial Biodegradation Database. baz119 - Rodrigo Arenas-Galnares, Sergio Castillo-Lara, Vasileios Toulis, Daniel Boloc, Roser Gonzàlez-Duarte, Gemma Marfany, Josep F. Abril:
RPGeNet v2.0: expanding the universe of retinal disease gene interactions network. baz120 - Christopher R. Norman, Elizabeth Gargon, Mariska M. G. Leeflang, Aurélie Névéol, Paula R. Williamson:
Evaluation of an automatic article selection method for timelier updates of the Comet Core Outcome Set database. baz109 - Ana Claudia Sima, Tarcisio Mendes de Farias, Erich Zbinden, Maria Anisimova, Manuel Gil, Heinz Stockinger, Kurt Stockinger, Marc Robinson-Rechavi, Christophe Dessimoz:
Enabling semantic queries across federated bioinformatics databases. baz106 - Rui Zhang, Fangfang Ge, Huayang Li, Yudong Chen, Ying Zhao, Ying Gao, Zhiguo Liu, Long Yang:
PCIR: a database of Plant Chloroplast Inverted Repeats. baz127 - Chaoying Zhan, Manhong Shi, Rongrong Wu, Hongxin He, Xingyun Liu, Bairong Shen:
MIRKB: a myocardial infarction risk knowledge base. baz125 - Rick E. Masonbrink, Tom R. Maier, Arun S. Seetharam, Parijat S. Juvale, Levi Baber, Thomas J. Baum, Andrew J. Severin:
SCNBase: a genomics portal for the soybean cyst nematode (Heterodera glycines). baz111 - Sana Akhter, Harpreet Kaur, Piyush Agrawal, Gajendra P. S. Raghava:
RareLSD: a manually curated database of lysosomal enzymes associated with rare diseases. baz112 - Marcin J. Skwark, Pedro Henrique Monteiro Torres, Liviu Copoiu, Bridget Bannerman-Chukualim, R. Andres Floto, Tom L. Blundell:
Mabellini: a genome-wide database for understanding the structural proteome and evaluating prospective antimicrobial targets of the emerging pathogen Mycobacterium abscessus. baz113 - Gorjan Popovski, Barbara Korousic-Seljak, Tome Eftimov:
FoodBase corpus: a new resource of annotated food entities. baz121 - Gianfranco Politano, Stefano Di Carlo, Alfredo Benso:
'One DB to rule them all' - the RING: a Regulatory INteraction Graph combining TFs, genes/proteins, SNPs, diseases and drugs. baz108 - Peter Brown, RELISH Consortium, Yaoqi Zhou:
Large expert-curated database for benchmarking document similarity detection in biomedical literature search. baz085 - Roberto Martín-Hernández, Guillermo Reglero, José M. Ordovás, Alberto Dávalos:
NutriGenomeDB: a nutrigenomics exploratory and analytical platform. baz097 - Ana Julia Velez Rueda, Nicolas Palopoli, Matías Zacarías, Leandro Matías Sommese, Gustavo D. Parisi:
ProtMiscuity: a database of promiscuous proteins. baz103 - Rui Antunes, Sérgio Matos:
Extraction of chemical-protein interactions from the literature using neural networks and narrow instance representation. baz095
- Jean-Philippe F. Gourdine, Matthew H. Brush, Nicole A. Vasilevsky, Kent A. Shefchek, Sebastian Köhler, Nicolas Matentzoglu, Monica C. Munoz-Torres, Julie A. McMurry, Xingmin Aaron Zhang, Peter N. Robinson, Melissa A. Haendel:
Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery. baz114 - Martin Neidnicht, Daniela Mittermüller, Katharina Effenberger-Neidnicht:
A new unbiased and highly automated approach to find new prognostic markers in preclinical research. baz107
- Clara Amid, Nima Pakseresht, Nicole Silvester, Suran Jayathilaka, Ole Lund, Lukasz D. Dynovski, Bálint Á Pataki, Dávid Visontai, Basil Britto Xavier, Blaise T. F. Alako, Ariane Belka, Jose L. B. Cisneros, Matthew Cotten, George B. Haringhuizen, Peter W. Harrison, Dirk Höper, Sam Holt, Camilla Hundahl, Abdulrahman Hussein, Rolf S. Kaas, Xin Liu, Rasko Leinonen, Surbhi Malhotra-Kumar, David F. Nieuwenhuijse, Nadim Rahman, Carolina dos S. Ribeiro, Jeffrey E. Skiby, Dennis Schmitz, József Stéger, János M. Szalai-Gindl, Martin Christen Frølund Thomsen, Simone M. Cacciò, István Csabai, Annelies Kroneman, Marion Koopmans, Frank Aarestrup, Guy Cochrane:
The COMPARE Data Hubs. baz136 - Chengyu Wang, Fan Yang, Tingting Chen, Qi Dong, Zhangxiang Zhao, Yaoyao Liu, Bo Chen, Haihai Liang, Huike Yang, Yunyan Gu:
RHPCG: a database of the Regulation of the Hippo Pathway in Cancer Genome. baz135 - Pim Bongaerts, Gonzalo Perez-Rosales, Veronica Z. Radice, Gal Eyal, Andrea Gori, Erika Gress, Nicholas M. Hammerman, Alejandra Hernandez-Agreda, Jack Laverick, Paul Muir, Hudson Pinheiro, Richard L. Pyle, Luiz Rocha, Joseph A. Turner, Ryan Booker:
Mesophotic.org: a repository for scientific information on mesophotic ecosystems. baz140 - Zhenglin Zhu, Zhufen Guan, Gexin Liu, Yawang Wang, Ze Zhang:
SGID: a comprehensive and interactive database of the silkworm. baz134 - Weijun Zhou, Zhi Qu, Chao-Yang Song, Yang Sun, An-Li Lai, Ma-Yao Luo, Yu-Zhe Ying, Hu Meng, Zhao Liang, Yan-Jie He, Yu-Hua Li, Jian Liu:
NeoPeptide: an immunoinformatic database of T-cell-defined neoantigens. baz128 - Quentin Groom, Mathias Dillen, Helen Hardy, Sarah Phillips, Luc Willemse, Zhengzhe Wu:
Improved standardization of transcribed digital specimen data. baz129 - Arif Canakoglu, Anna Bernasconi, Andrea Colombo, Marco Masseroli, Stefano Ceri:
GenoSurf: metadata driven semantic search system for integrated genomic datasets. baz132 - Lei Zheng, Shenghui Huang, Nengjiang Mu, Haoyue Zhang, Jiayu Zhang, Yu Chang, Lei Yang, Yongchun Zuo:
RAACBook: a web server of reduced amino acid alphabet for sequence-dependent inference by using Chou's five-step rule. baz131 - Ganesh Panzade, Indu Gangwar, Supriya Awasthi, Nitesh Sharma, Ravi Shankar:
Plant Regulomics Portal (PRP): a comprehensive integrated regulatory information and analysis portal for plant genomes. baz130 - Tao Chen, Mingfen Wu, Hexi Li:
A general approach for improving deep learning-based medical relation extraction using a pre-trained model and fine-tuning. baz116
- Nikhil P. Damle, Maja Köhn:
The human DEPhOsphorylation Database DEPOD: 2019 update. baz133
- Abhijeet Singh, Bettina Müller, Hans-Henrik Fuxelius, Anna Schnürer:
AcetoBase: a functional gene repository and database for formyltetrahydrofolate synthetase sequences. baz142 - Muniba Faiza, Dongming Lan, Shengfeng Huang, Yonghua Wang:
UPObase: an online database of unspecific peroxygenases. baz122
- Guilherme Viteri, Lisa Matthews, Thawfeek M. Varusai, Marc Gillespie, Marija Milacic, Justin Cook, Joel Weiser, Solomon Shorser, Konstantinos Sidiropoulos, Antonio Fabregat, Robin Haw, Guanming Wu, Lincoln Stein, Peter D'Eustachio, Henning Hermjakob:
Reactome and ORCID - fine-grained credit attribution for community curation. baz123
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