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ORCIDDatabase - The Journal of Biological Databases and Curation, Volume 2018
Volume 2018, 2018
- Jasmine Young
, John D. Westbrook, Zukang Feng, Ezra Peisach, Irina Persikova, Raul Sala, Sanchayita Sen, John M. Berrisford, Jawahar Swaminathan, Thomas J. Oldfield, Aleksandras Gutmanas, Reiko Igarashi, David R. Armstrong, Kumaran Baskaran, Li Chen, Minyu Chen, Alice R. Clark, Luigi Di Costanzo, Dimitris Dimitropoulos, Guanghua Gao, Sutapa Ghosh, Swanand P. Gore, Vladimir Guranovic, Pieter M. S. Hendrickx, Brian P. Hudson, Yasuyo Ikegawa, Yumiko Kengaku, Catherine L. Lawson, Yuhe Liang, Lora Mak, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Kayoko Nishiyama, Ardan Patwardhan, Gaurav Sahni, Eduardo Sanz-García, Junko Sato, Monica Sekharan, Chenghua Shao, Oliver S. Smart, Lihua Tan, Glen van Ginkel, Huanwang Yang, Marina Zhuravleva, John L. Markley, Haruki Nakamura, Genji Kurisu, Gerard J. Kleywegt, Sameer Velankar, Helen M. Berman, Stephen K. Burley:
Worldwide Protein Data Bank biocuration supporting open access to high-quality 3D structural biology data. bay002
- Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen:
TISSUES 2.0: an integrative web resource on mammalian tissue expression. bay003
- Liang Chen, Liisa Heikkinen, Changliang Wang, Yang Yang, K. Emily Knott, Garry Wong:
miRToolsGallery: a tag-based and rankable microRNA bioinformatics resources database portal. bay004
- Erzsébet Orosz, Nathalie Van de Wiele, Tamás Emri, Miaomiao Zhou, Vincent Robert, Ronald P. de Vries, István Pócsi:
Fungal Stress Database (FSD)--a repository of fungal stress physiological data. bay009 - Natalie P. Bonvino, Julia Liang, Elizabeth D. McCord, Elena Zafiris, Natalia Benetti, Nancy B. Ray, Andrew Hung, Dimitrios Boskou, Tom C. Karagiannis:
OliveNet™: a comprehensive library of compounds from Olea europaea. bay016 - Dagmar Triebel, Wolfgang Reichert, Simone Bosert, Martin Feulner, Daniel Osieko Okach, Abderachid Slimani, Gerhard Rambold:
A generic workflow for effective sampling of environmental vouchers with UUID assignment and image processing. bax096 - Leonardo Ledesma, Eduardo B. Sandoval, Uriel Cruz-Martínez, Ana María Escalante, Selene Mejía, Paola Moreno-Álvarez, Emiliano Ávila, Erik García, Gerardo Coello, Francisco Torres-Quiroz:
YAAM: Yeast Amino Acid Modifications Database. bax099
- Nico M. Franz, Beckett W. Sterner:
To increase trust, change the social design behind aggregated biodiversity data. bax100
- Yi-Fang Lee, Chien-Yueh Lee, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, Eric Y. Chuang:
CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system. bax101
- Bruno Reis Dotto, Evelise Leis Carvalho, Alexandre Freitas Silva, Filipe Zimmer Dezordi, Paulo Marcos Pinto, Tulio de Lima Campos, Antônio M. Rezende, Gabriel da Luz Wallau:
HTT-DB: new features and updates. bax102
- Randi Vita, James A. Overton, Christopher J. Mungall, Alessandro Sette, Bjoern Peters:
FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability. bax105 - Feng Shao, Jianrong Wang, Hongen Xu, Zuogang Peng:
FishTEDB: a collective database of transposable elements identified in the complete genomes of fish. bax106
- Shuai Yang, Xingwei Zhang, Huayang Li, Yudong Chen, Long Yang:
GAN: a platform of genomics and genetics analysis and application in Nicotiana. bay001
- Randi Vita, James A. Overton, Bjoern Peters:
Identification of errors in the IEDB using ontologies. bay005 - Shobha Sharma, Stacy Ciufo, Elena Starchenko, Dakshesh Darji, Larry Chlumsky, Ilene Karsch-Mizrachi, Conrad L. Schoch:
The NCBI BioCollections Database. bay006
- Stacia R. Engel, Marek S. Skrzypek, Sage T. Hellerstedt, Edith D. Wong, Robert S. Nash, Shuai Weng, Gail Binkley, Travis K. Sheppard, Kalpana Karra, J. Michael Cherry:
Updated regulation curation model at the Saccharomyces Genome Database. bay007
- Idan Gabdank, Esther T. Chan, Jean M. Davidson, Jason A. Hilton, Carrie A. Davis, Ulugbek K. Baymuradov, Aditi K. Narayanan, Kathrina C. Onate, Keenan Graham, Stuart R. Miyasato, Timothy R. Dreszer, J. Seth Strattan, Otto Jolanki, Forrest Tanaka, Benjamin C. Hitz, Cricket A. Sloan, J. Michael Cherry:
Prevention of data duplication for high throughput sequencing repositories. bay008 - Jinying Liu, Yuan Liu, Dan Wang, Mengqi He, Lihong Diao, Zhongyang Liu, Yang Li, Li Tang, Fuchu He, Dong Li, Shuzhen Guo:
AllerGAtlas 1.0: a human allergy-related genes database. bay010
- Kleanthi Lakiotaki, Nikolaos Vorniotakis, Michail Tsagris, Georgios Georgakopoulos, Ioannis Tsamardinos:
BioDataome: a collection of uniformly preprocessed and automatically annotated datasets for data-driven biology. bay011
- Daniela Raciti, Karen Yook, Todd W. Harris, Tim Schedl, Paul W. Sternberg:
Micropublication: incentivizing community curation and placing unpublished data into the public domain. bay013 - Modupeore O. Adetunji, Susan J. Lamont, Carl J. Schmidt:
TransAtlasDB: an integrated database connecting expression data, metadata and variants. bay014
- Qingmin Yang, Yuqi Zhang, Hui Cui, Lanming Chen, Yong Zhao, Yong Lin, Menghuan Zhang, Lu Xie:
dbDEPC 3.0: the database of differentially expressed proteins in human cancer with multi-level annotation and drug indication. bay015 - Yang Yang, Chen Xu, Xingyun Liu, Chao Xu, Yuanyuan Zhang, Li Shen, Mauno Vihinen, Bairong Shen:
NDDVD: an integrated and manually curated Neurodegenerative Diseases Variation Database. bay018 - Sankha Subhra Das, Pritam Saha, Nishant Chakravorty:
miRwayDB: a database for experimentally validated microRNA-pathway associations in pathophysiological conditions. bay023
- Salman Sadullah Usmani, Rajesh Kumar, Vinod Kumar, Sandeep Singh, Gajendra P. S. Raghava:
AntiTbPdb: a knowledgebase of anti-tubercular peptides. bay025 - Wei Wei, Zhanglong Ji, Yupeng He, Kai Zhang, Yuanchi Ha, Qi Li, Lucila Ohno-Machado:
Finding relevant biomedical datasets: the UC San Diego solution for the bioCADDIE Retrieval Challenge. bay017 - Noha S. Tawfik, Marco R. Spruit:
The SNPcurator: literature mining of enriched SNP-disease associations. bay020 - Ankita Singh, Rahul Kaushik, Himani Kuntal, B. Jayaram:
PvaxDB: a comprehensive structural repository of Plasmodium vivax proteome. bay021 - Yasunori Yamamoto, Atsuko Yamaguchi, Andrea Splendiani:
YummyData: providing high-quality open life science data. bay022 - Fei Yi, Zirui Jia, Yao Xiao, Wenjun Ma, Junhui Wang:
SPTEdb: a database for transposable elements in salicaceous plants. bay024
- Oana Palasca, Alberto Santos, Christian Stolte, Jan Gorodkin, Lars Juhl Jensen:
TISSUES 2.0: an integrative web resource on mammalian tissue expression. bay028
- Artur Cieslewicz, Jakub Dutkiewicz, Czeslaw Jedrzejek:
Baseline and extensions approach to information retrieval of complex medical data: Poznan's approach to the bioCADDIE 2016. bax103 - Jin Li, Su-Ping Deng, Gang Wei, Peng Yu:
CITGeneDB: a comprehensive database of human and mouse genes enhancing or suppressing cold-induced thermogenesis validated by perturbation experiments in mice. bay012 - Zhao Li, Jin Li, Peng Yu:
GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata. bay019
Original Article
- Sebastian Köhler:
Improved ontology-based similarity calculations using a study-wise annotation model. bay026
- Sonoko Kinjo, Norikazu Monma, Sadahiko Misu, Norikazu Kitamura, Junichi Imoto, Kazutoshi Yoshitake, Takashi Gojobori, Kazuho Ikeo:
Maser: one-stop platform for NGS big data from analysis to visualization. bay027
- Alan F. McCulloch, Ruy Jáuregui, Paul H. Maclean, Rachael L. Ashby, Roger A. Moraga, Aurélie Laugraud, Rüdiger Bräuning, Ken G. Dodds, John C. McEwan:
An entropy-reducing data representation approach for bioinformatic data. bay029 - Andreina I Castillo, Andrew D. L. Nelson, Asher Haug-Baltzell, Eric Lyons:
A tutorial of diverse genome analysis tools found in the CoGe web-platform using Plasmodium spp. as a model. bay030 - Amel Bekkar, Anne Estreicher, Anne Niknejad, Cristina Casals-Casas, Alan J. Bridge, Ioannis Xenarios, Julien Dorier, Isaac Crespo:
Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation. bay031
- Bifang He, Lixu Jiang, Yaocong Duan, Guoshi Chai, Yewei Fang, Juanjuan Kang, Min Yu, Ning Li, Zhongjie Tang, Pengcheng Yao, Pengcheng Wu, Ratmir Derda, Jian Huang:
Biopanning data bank 2018: hugging next generation phage display. bay032
- Nora Escribano, David Galicia, Arturo H. Ariño:
The tragedy of the biodiversity data commons: a data impediment creeping nigher? bay033
- Ling Liu, Yi Xiong, Hongyun Gao, Dong-Qing Wei, Julie C. Mitchell, Xiaolei Zhu:
dbAMEPNI: a database of alanine mutagenic effects for protein-nucleic acid interactions. bay034 - Maria Kondratova, Nicolas Sompairac, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein:
Signalling maps in cancer research: construction and data analysis. bay036 - David A. Schott, Abhinav G. Vinnakota, John L. Portwood II, Carson M. Andorf, Taner Z. Sen:
SNPversity: a web-based tool for visualizing diversity. bay037 - Jian Wang, Tailang Yin, Xuwen Xiao, Dan He, Zhidong Xue, Xinnong Jiang, Yan Wang:
StraPep: a structure database of bioactive peptides. bay038 - Payam Karisani, Zhaohui S. Qin, Eugene Agichtein:
Probabilistic and machine learning-based retrieval approaches for biomedical dataset retrieval. bax104 - Hartmut Foerster, Aureliano Bombarely, James N. D. Battey, Nicolas Sierro, Nikolai V. Ivanov, Lukas A. Mueller:
SolCyc: a database hub at the Sol Genomics Network (SGN) for the manual curation of metabolic networks in Solanum and Nicotiana specific databases. bay035
- Fulong Yu, Guanxiong Zhang, Aiai Shi, Jing Hu, Feng Li, Xinxin Zhang, Yan Zhang, Jian Huang, Yun Xiao, Xia Li, Shujun Cheng:
LnChrom: a resource of experimentally validated lncRNA-chromatin interactions in human and mouse. bay039
- Saba Ferdous, Andrew C. R. Martin:
AbDb: antibody structure database - a database of PDB-derived antibody structures. bay040 - Inhae Jeong, Namhee Yu, Insu Jang, Yukyung Jun, Minseo Kim, Jinhyuk Choi, Byungwook Lee, Sanghyuk Lee:
GEMiCCL: mining genotype and expression data of cancer cell lines with elaborate visualization. bay041 - Nicola Bordin, Juan Carlos González-Sánchez, Damien P. Devos:
PVCbase: an integrated web resource for the PVC bacterial proteomes. bay042 - Chunyan Fan, Xiujuan Lei, Zengqiang Fang, Qinghua Jiang, Fang-Xiang Wu:
CircR2Disease: a manually curated database for experimentally supported circular RNAs associated with various diseases. bay044 - Samir Gupta, Hayley Dingerdissen, Karen E. Ross, Yu Hu, Cathy H. Wu, Raja Mazumder, K. Vijay-Shanker:
DEXTER: Disease-Expression Relation Extraction from Text. bay045
- Xueli Zhang, Xiao-Feng Sun, Yang Cao, Benchen Ye, Qiliang Peng, Xingyun Liu, Bairong Shen, Hong Zhang:
CBD: a biomarker database for colorectal cancer. bay046 - Junkyoung Choe, Ji-Eun Kim, Bong-Woo Lee, Jeong Hee Lee, Moon Nam, Youn-Il Park, Sung-Hwan Jo:
A comparative synteny analysis tool for target-gene SNP marker discovery: connecting genomics data to breeding in Solanaceae. bay047
- Hong-Jie Dai, Onkar Singh:
SPRENO: a BioC module for identifying organism terms in figure captions. bay048 - Pengbo Wen, Junfeng Xia, Xianbin Cao, Bin Chen, Yinping Tao, Lijun Wu, An Xu, Guoping Zhao:
dbCRSR: a manually curated database for regulation of cancer radiosensitivity. bay049 - Charles Tapley Hoyt, Daniel Domingo-Fernández, Nora Balzer, Anka Güldenpfennig, Martin Hofmann-Apitius:
A systematic approach for identifying shared mechanisms in epilepsy and its comorbidities. bay050 - Smriti Mishra, Mohammad I Shah, Malay Sarkar, Nimisha Asati, Chittaranjan Rout:
ILDgenDB: integrated genetic knowledge resource for interstitial lung diseases (ILDs). bay053 - Jin Li, Su-Ping Deng, Jacob Vieira, James Thomas, Valerio Costa, Ching-San Tseng, Franjo Ivankovic, Alfredo Ciccodicola, Peng Yu:
RBPMetaDB: a comprehensive annotation of mouse RNA-Seq datasets with perturbations of RNA-binding proteins. bay054
- Tingting Zhang, Jiaojiao Miao, Na Han, Yujun Qiang, Wen Zhang:
MPD: a pathogen genome and metagenome database. bay055 - Shruti Beriwal, Nikhil Padhiyar, Deven Bhatt, Prabhakar D. Pandit, Afzal Ansari, Kumari Snehkant Lata, Zuber M. Saiyed, Vibhisha Vaghasia, Priyanka Sharma, Shivarudrappa B. Bhairappanavar, Subhash Soni, Jayashankar Das:
LeptoDB: an integrated database of genomics and proteomics resource of Leptospira. bay057
- Sangrak Lim, Jaewoo Kang:
Chemical-gene relation extraction using recursive neural network. bay060
- Cong Pian, Guang-Le Zhang, Tengfei Tu, Xiangyu Ma, Fei Li:
LncCeRBase: a database of experimentally validated human competing endogenous long non-coding RNAs. bay061
- Yining Liu, Mingyu Luo, Zhaochen Jin, Min Zhao, Hong Qu:
dbLGL: an online leukemia gene and literature database for the retrospective comparison of adult and childhood leukemia genetics with literature evidence. bay062
- Nikita Gupta, Ajeet Singh, Shafaque Zahra, Shailesh Kumar:
PtRFdb: a database for plant transfer RNA-derived fragments. bay063 - Garima Singh, Basharat Bhat, M. S. K. Jayadev, Ch Madhusudhan, Ashutosh Singh:
mutTCPdb: a comprehensive database for genomic variants of a tropical country neglected disease - tropical calcific pancreatitis. bay043 - Fabienne Lambusch, Dagmar Waltemath, Olaf Wolkenhauer, Kurt Sandkuhl, Christian Rosenke, Ron Henkel:
Identifying frequent patterns in biochemical reaction networks: a workflow. bay051 - Lana Yeganova, Won Kim, Donald C. Comeau, W. John Wilbur, Zhiyong Lu:
A Field Sensor: computing the composition and intent of PubMed queries. bay052
- Muhammad Nabeel Asim, Muhammad Wasim, Muhammad Usman Ghani Khan, Waqar Mahmood:
Improved biomedical term selection in pseudo relevance feedback. bay056 - Kabita Tripathy, Balwant Singh, Nisha Singh, Vandna Rai, Gauri Misra, Nagendra Kumar Singh:
A database of wild rice germplasm of Oryza rufipogon species complex from different agro-climatic zones of India. bay058
- Huan Zhang, Asim Ali, Jianing Gao, Rongjun Ban, Xiaohua Jiang, Yuanwei Zhang, Qinghua Shi:
IsopiRBank: a research resource for tracking piRNA isoforms. bay059 - Cheng Zeng, Weihua Zhan, Lei Deng:
SDADB: a functional annotation database of protein structural domains. bay064
- Chen Li, Zhiqiang Rao, Qinghua Zheng, Xiangrong Zhang:
A set of domain rules and a deep network for protein coreference resolution. bay065 - Peter Corbett, John Boyle:
Improving the learning of chemical-protein interactions from literature using transfer learning and specialized word embeddings. bay066
- Wen-Jing Wang, Yu-Mei Wang, Yi Hu, Qin Lin, Rou Chen, Huan Liu, Wen-Ze Cao, Hui-Fang Zhu, Chang Tong, Li Li, Lu-Ying Peng:
HDncRNA: a comprehensive database of non-coding RNAs associated with heart diseases. bay067
- Elton José R. Vasconcelos, Vinícius C. Mesel, Lucas F. daSilva, David S. Pires, Guilherme M. Lavezzo, Adriana S. A. Pereira, Murilo S. Amaral, Sergio Verjovski-Almeida:
Atlas of Schistosoma mansoni long non-coding RNAs and their expression correlation to protein-coding genes. bay068 - Xin Chen, Zhengqiang Miao, Mayur Divate, Zuxianglan Zhao, Edwin Cheung:
KM-express: an integrated online patient survival and gene expression analysis tool for the identification and functional characterization of prognostic markers in breast and prostate cancers. bay069 - Kai Feng, Xi-Lin Hou, Meng-Yao Li, Qian Jiang, Zhi-Sheng Xu, Jie-Xia Liu, Ai-Sheng Xiong:
CeleryDB: a genomic database for celery. bay070 - Huiwei Zhou, Zhuang Liu, Shixian Ning, Yunlong Yang, Chengkun Lang, Yingyu Lin, Kun Ma:
Leveraging prior knowledge for protein-protein interaction extraction with memory network. bay071 - Fei Chen, Jiawei Zhang, Junhao Chen, Xiaojiang Li, Wei Dong, Jian Hu, Meigui Lin, Yanhui Liu, Guowei Li, Zhengjia Wang, Liangsheng Zhang:
realDB: a genome and transcriptome resource for the red algae (phylum Rhodophyta). bay072 - Yifan Peng, Anthony Rios, Ramakanth Kavuluru, Zhiyong Lu:
Extracting chemical-protein relations with ensembles of SVM and deep learning models. bay073 - Wei-Sheng Wu, Yu-Xuan Jiang, Jer-Wei Chang, Yu-Han Chu, Yi-Hao Chiu, Yi-Hong Tsao, Torbjörn E. M. Nordling, Yan Yuan Tseng, Joseph T. Tseng:
HRPDviewer: human ribosome profiling data viewer. bay074
- Lu Zhou, Qingyu Xiao, Jie Bi, Zhen Wang, Yixue Li:
RabGTD: a comprehensive database of rabbit genome and transcriptome. bay075
- Chun-Wei Tung, Shan-Shan Wang:
ChemDIS 2: an update of chemical-disease inference system. bay077
- Aris Fergadis, Christos Baziotis, Dimitris Pappas, Haris Papageorgiou, Alexandros Potamianos:
Hierarchical bi-directional attention-based RNNs for supporting document classification on protein-protein interactions affected by genetic mutations. bay076
- Daniel Longhi Fernandes Pedro, Alan Péricles Rodrigues Lorenzetti, Douglas Silva Domingues, Alexandre Rossi Paschoal:
PlaNC-TE: a comprehensive knowledgebase of non-coding RNAs and transposable elements in plants. bay078 - Aaron M. Cohen, Zackary O. Dunivin, Neil R. Smalheiser:
A probabilistic automated tagger to identify human-related publications. bay079
- Judith Mary Hariprakash, Shamsudheen Karuthedath Vellarikkal, Ankit Verma, Anop Singh Ranawat, Rijith Jayarajan, Rowmika Ravi, Anoop Kumar, Vishal Dixit, Ambily Sivadas, Atul Kumar Kashyap, Vigneshwar Senthivel, Paras Sehgal, Vijayalakshmi Mahadevan, Vinod Scaria, Sridhar Sivasubbu:
SAGE: a comprehensive resource of genetic variants integrating South Asian whole genomes and exomes. bay080 - Longfei Chen, Kun Lang, Shoudong Bi, Jiapeng Luo, Feiling Liu, Xinhai Ye, Jiadan Xu, Kang He, Fei Li, Gongyin Ye, Xuexin Chen:
WaspBase: a genomic resource for the interactions among parasitic wasps, insect hosts and plants. bay081
- Subodh Kumar Mishra, Neha Jain, Uma Shankar, Arpita Tawani, Amit Mishra, Amit Kumar:
SMMDB: a web-accessible database for small molecule modulators and their targets involved in neurological diseases. bay082 - ZiaurRehman Tanoli, Zaid Alam, Markus Vähä-Koskela, Balaguru Ravikumar, Alina Malyutina, Alok Jaiswal, Jing Tang, Krister Wennerberg, Tero Aittokallio:
Drug Target Commons 2.0: a community platform for systematic analysis of drug-target interaction profiles. bay083
- 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. bay084
- Xiao Wen, Lin Gao, Xingli Guo, Xing Li, Xiaotai Huang, Ying Wang, Haifu Xu, Ruijie He, Chenglong Jia, Feixiang Liang:
lncSLdb: a resource for long non-coding RNA subcellular localization. bay085 - Kevin K. Le, Matthew D. Whiteside, James E. Hopkins, Victor P. J. Gannon, Chad R. Laing:
Spfy: an integrated graph database for real-time prediction of bacterial phenotypes and downstream comparative analyses. bay086 - Peter C. Marks, Marc Bigler, Eric B. Alsop, Adrien Vigneron, Bart P. Lomans, Renato de Paula, Brett Geissler, Nicolas Tsesmetzis:
MetaHCR: a web-enabled metagenome data management system for hydrocarbon resources. bay087 - Lisa C. Harper, Jacqueline D. Campbell, Ethalinda K. S. Cannon, Sook Jung, Monica Poelchau, Ramona L. Walls, Carson M. Andorf, Elizabeth Arnaud, Tanya Z. Berardini, Clayton L. Birkett, Steven B. Cannon, James D. Carson, Bradford Condon, Laurel Cooper, Nathan A. Dunn, Christine G. Elsik, Andrew D. Farmer, Stephen P. Ficklin, David M. Grant, Emily S. Grau, Nic Herndon, Zhi-Liang Hu, Jodi L. Humann, Pankaj Jaiswal, Clément Jonquet, Marie-Angélique Laporte, Pierre Larmande, Gerard R. Lazo, Fiona McCarthy, Naama Menda, Christopher J. Mungall, Monica C. Munoz-Torres, Sushma Naithani, Rex T. Nelson, Daureen Nesdill, Carissa A. Park, James M. Reecy, Leonore Reiser, Lacey-Anne Sanderson, Taner Z. Sen, Margaret Staton, Sabarinath Subramaniam, Marcela Karey Tello-Ruiz, Victor Unda, Deepak R. Unni, Liya Wang, Doreen Ware, Jill L. Wegrzyn, Jason Williams, Margaret Woodhouse, Jing Yu, Doreen Main:
AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. bay088
- Roddy Jorquera, Carolina González, Philip T. L. C. Clausen, Bent Petersen, David S. Holmes:
Improved ontology for eukaryotic single-exon coding sequences in biological databases. bay089
- Justin S. Diamond, Yang Zhang:
THE-DB: a threading model database for comparative protein structure analysis of the E. coli K12 and human proteomes. bay090 - Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu:
Assisting document triage for human kinome curation via machine learning. bay091 - Tung Tran, Ramakanth Kavuluru:
An end-to-end deep learning architecture for extracting protein-protein interactions affected by genetic mutations. bay092
- Wenjing Wang, Peng Zhang, Leijie Li, Zhaobin Chen, Weiyang Bai, Guiyou Liu, Liangcai Zhang, Haiyang Jia, Li Li, Yingcui Yu, Mingzhi Liao:
ATD: a comprehensive bioinformatics resource for deciphering the association of autophagy and diseases. bay093 - Nicolas Fiorini, Kathi Canese, Rostyslav Bryzgunov, Ievgeniia Radetska, Asta Gindulyte, Martin Latterner, Vadim Miller, Maxim Osipov, Michael Kholodov, Grisha Starchenko, Evgeny Kireev, Zhiyong Lu:
PubMed Labs: an experimental system for improving biomedical literature search. bay094
- Nik Shazana Nik Mohd Sanusi, Rozana Rosli, Mohd Amin Ab Halim, Kuang-Lim Chan, Jayanthi Nagappan, Norazah Azizi, Nadzirah Amiruddin, Tatiana V. Tatarinova, Eng-Ti Leslie Low:
PalmXplore: oil palm gene database. bay095 - Suwisa Kaewphan, Kai Hakala, Niko Miekka, Tapio Salakoski, Filip Ginter:
Wide-scope biomedical named entity recognition and normalization with CRFs, fuzzy matching and character level modeling. bay096 - Ling Luo, Zhihao Yang, Hongfei Lin, Jian Wang:
Document triage for identifying protein-protein interactions affected by mutations: a neural network ensemble approach. bay097 - Marco Antonio Valenzuela-Escárcega, Özgün Babur, Gus Hahn-Powell, Dane Bell, Thomas Hicks, Enrique Noriega-Atala, Xia Wang, Mihai Surdeanu, Emek Demir, Clayton T. Morrison:
Large-scale automated machine reading discovers new cancer-driving mechanisms. bay098
- Bradford Condon, Abdullah Almsaeed, Ming Chen, Joe West, Margaret Staton:
Tripal Developer Toolkit. bay099
- Ruya Sun, Chunmei Cui, Yuan Zhou, Qinghua Cui:
AGD: Aneurysm Gene Database. bay100
- Muhammad Nabeel Asim, Muhammad Wasim, Muhammad Usman Ghani Khan, Waqar Mahmood, Hafiza Mahnoor Abbasi:
A survey of ontology learning techniques and applications. bay101
- Sijia Liu, Feichen Shen, Ravikumar Komandur Elayavilli, Yanshan Wang, Majid Rastegar-Mojarad, Vipin Chaudhary, Hongfang Liu:
Extracting chemical-protein relations using attention-based neural networks. bay102 - Agnes Kirchhoff, Ulrich Bügel, Eduard Santamaria, Fabian Reimeier, Dominik Röpert, Alexander Tebbje, Anton Güntsch, Fernando Chaves, Karl-Heinz Steinke, Walter G. Berendsohn:
Toward a service-based workflow for automated information extraction from herbarium specimens. bay103 - Julien Gobeill, Pascale Gaudet, Daniel Dopp, Adam Morrone, Indika Kahanda, Yi-Yu Hsu, Chih-Hsuan Wei, Zhiyong Lu, Patrick Ruch:
Overview of the BioCreative VI text-mining services for Kinome Curation Track. bay104
- Nikita Gupta, Shafaque Zahra, Ajeet Singh, Shailesh Kumar:
PVsiRNAdb: a database for plant exclusive virus-derived small interfering RNAs. bay105
- Changhong Yang, Jiarui Li, Qixi Wu, Xiaoxu Yang, August Yue Huang, Jie Zhang, Adam Yongxin Ye, Yanmei Dou, Linlin Yan, Wei-Zhen Zhou, Lei Kong, Meng Wang, Chen Ai, Dechang Yang, Liping Wei:
AutismKB 2.0: a knowledgebase for the genetic evidence of autism spectrum disorder. bay106
- Hao Wang, Hanwei Yan, Huanlong Liu, Rui Liu, Jun Chen, Yan Xiang:
GFDP: the gene family database in poplar. bay107
- Neha Warikoo, Yung-Chun Chang, Wen-Lian Hsu:
LPTK: a linguistic pattern-aware dependency tree kernel approach for the BioCreative VI CHEMPROT task. bay108 - Jongyeun Park, Seung Hyun Ahn, Kwang Moon Cho, Dowoon Gu, Eun-Sook Jang, Sung Wook Chi:
siAbasic: a comprehensive database for potent siRNA-6Ø sequences without off-target effects. bay109
- Alejandro Llanes, Carlos Mario Restrepo, Ricardo Lleonart:
VianniaTopes: a database of predicted immunogenic peptides for Leishmania (Viannia) species. bay111
- Tin-Hang Wong, Grace Wing-Chiu But, Hoi-Yan Wu, Stacey Shun-Kei Tsang, David Tai-Wai Lau, Pang-Chui Shaw:
Medicinal Materials DNA Barcode Database (MMDBD) version 1.5 - one-stop solution for storage, BLAST, alignment and primer design. bay112
- Junhao Chen, Jiawei Zhang, Meigui Lin, Wei Dong, Xinyue Guo, Yang Dong, Zhengjia Wang, Liangsheng Zhang, Fei Chen:
MGH: a genome hub for the medicinal plant maca (Lepidium meyenii). bay113 - Xiang Hu, Wen Chen, Jing Li, Shulan Huang, Xuling Xu, Xuan Zhang, Shuanglin Xiang, Changning Liu:
ZFLNC: a comprehensive and well-annotated database for zebrafish lncRNA. bay114 - Wasila M. Dahdul, Prashanti Manda, Hong Cui, James P. Balhoff, T. Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Todd J. Vision, Paula M. Mabee:
Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems. bay110 - Chia-Jung Yang, Jung-Hsien Chiang:
Gene ontology concept recognition using named concept: understanding the various presentations of the gene functions in biomedical literature. bay115
- Wei-Sheng Wu, Hao-Ping Tu, Yu-Han Chu, Torbjörn E. M. Nordling, Yan Yuan Tseng, Hung-Jiun Liaw:
YHMI: a web tool to identify histone modifications and histone/chromatin regulators from a gene list in yeast. bay116
- Yu Wei, Jinlong Li, Baiqing Li, Chunfeng Ma, Xuanming Xu, Xu Wang, Aqin Liu, Tengfei Du, Zhonghua Wang, Zhangyong Hong, Jianping Lin:
GCDB: a glaucomatous chemogenomics database for in silico drug discovery. bay117 - Cheng-Dong Zhang, Yuan Yang, Huan-Huan Chen, Ting Zhang, Qiang Wang, Yuan Liang, Liang Zhang, Yan Zhou:
RTPDB: a database providing associations between genetic variation or expression and cancer prognosis with radiotherapy-based treatment. bay118
- Sarah E. Hunt, William M. McLaren, Laurent Gil, Anja Thormann, Helen Schuilenburg, Daniel Sheppard, Andrew Parton, Irina M. Armean, Stephen J. Trevanion, Paul Flicek, Fiona Cunningham:
Ensembl variation resources. bay119
- Farrokh Mehryary, Jari Björne, Tapio Salakoski, Filip Ginter:
Potent pairing: ensemble of long short-term memory networks and support vector machine for chemical-protein relation extraction. bay120 - Ruifeng Hu, Yulin Dai, Peilin Jia, Zhongming Zhao:
ANCO-GeneDB: annotations and comprehensive analysis of candidate genes for alcohol, nicotine, cocaine and opioid dependence. bay121 - Qingyu Chen, Nagesh C. Panyam, Aparna Elangovan, Karin Verspoor:
BioCreative VI Precision Medicine Track system performance is constrained by entity recognition and variations in corpus characteristics. bay122 - Shuichi Kawashima, Toshiaki Katayama, Hideki Hatanaka, Tatsuya Kushida, Toshihisa Takagi:
NBDC RDF portal: a comprehensive repository for semantic data in life sciences. bay123 - Niklas Pallast, Frederique Wieters, Marieke Nill, Gereon R. Fink, Markus Aswendt:
Cloud-based relational database for multimodal animal data. bay124 - Marco Necci, Damiano Piovesan, Diego Micheletti, Lisanna Paladin, Alessandro Cestaro, Silvio C. E. Tosatto:
PhytoTypeDB: a database of plant protein inter-cultivar variability and function. bay125 - Charles Tapley Hoyt, Daniel Domingo-Fernández, Martin Hofmann-Apitius:
BEL Commons: an environment for exploration and analysis of networks encoded in Biological Expression Language. bay126 - Marco Necci, Damiano Piovesan, Silvio C. E. Tosatto:
Where differences resemble: sequence-feature analysis in curated databases of intrinsically disordered proteins. bay127 - Jia Ren, Gang Li, Karen Ross, Cecilia N. Arighi, Peter B. McGarvey, Shruti Rao, Julie Cowart, Subha Madhavan, K. Vijay-Shanker, Cathy H. Wu:
iTextMine: integrated text-mining system for large-scale knowledge extraction from the literature. bay128 - Aurore Britan, Isabelle Cusin, Valérie Hinard, Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Daniel Dinis Teixeira, Pierre-André Michel, Patrick Ruch, Pascale Gaudet:
Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. bay129 - Ibrahim Burak Özyurt, Jeffrey S. Grethe:
Foundry: a message-oriented, horizontally scalable ETL system for scientific data integration and enhancement. bay130 - Fei Yi, Juanjuan Ling, Yao Xiao, Hanguo Zhang, Fangqun Ouyang, Junhui Wang:
ConTEdb: a comprehensive database of transposable elements in conifers. bay131
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