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Database - The Journal of Biological Databases and Curation, Volume 2016
Volume 2016, 2016
- Rayda Ben Ayed
, Hanen Ben Hassen
OGDD (Olive Genetic Diversity Database): a microsatellite markers' genotypes database of worldwide olive trees for cultivar identification and virgin olive oil traceability. - Xingyan Kuang, Andi Dhroso, Jing Ginger Han, Chi-Ren Shyu, Dmitry Korkin:
DOMMINO 2.0: integrating structurally resolved protein-, RNA-, and DNA-mediated macromolecular interactions. - Jens Kringelum, Sonny Kim Kjærulff, Søren Brunak
ChemProt-3.0: a global chemical biology diseases mapping.
- Mayrolin García Morales, Barbara D. Denno, Douglass R. Miller, Gary L. Miller, Yair Ben-Dov, Nate B. Hardy:
ScaleNet: a literature-based model of scale insect biology and systematics. - Daniel R. Zerbino
Ensembl regulation resources. - Javier Herrero
Ensembl comparative genomics resources. - Lei Sheng, Haiyang Jiang, Hanwei Yan, Xiaoyu Li, Yongxiang Lin, Hui Ye, Beijiu Cheng:
MGFD: the maize gene families database.
- Petra ten Hoopen
Value, but high costs in post-deposition data curation. - Martin Dugas
Portal of medical data models: information infrastructure for medical research and healthcare. - Gabriele Dröge, Till Töpfer:
The Corvids Literature Database - 500 years of ornithological research from a crow's perspective. - Xiaowei Xie, Wenbin Ma
CCSI: a database providing chromatin-chromatin spatial interaction information. - Adam D. DePriest
Regulators of Androgen Action Resource: a one-stop shop for the comprehensive study of androgen receptor action. - Subodh Kumar Mishra
NALDB: nucleic acid ligand database for small molecules targeting nucleic acid. - Evangelos Pafilis, Pier Luigi Buttigieg
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. - Lionel Breuza
The UniProtKB guide to the human proteome. - Miguel Pignatelli, Albert J. Vilella, Matthieu Muffato
ncRNA orthologies in the vertebrate lineage. - Wonjun Choi, Chan-Hun Choi, Young-Ran Kim, Seon-Jong Kim, Chang-Su Na, Hyunju Lee
HerDing: herb recommendation system to treat diseases using genes and chemicals. - Jiaxin Wu, Mengmeng Wu, Lianshuo Li, Zhuo Liu
dbWGFP: a database and web server of human whole-genome single nucleotide variants and their functional predictions. - Daniel K. Manter, Matthew Korsa, Caleb Tebbe, Jorge A. Delgado:
myPhyloDB: a local web server for the storage and analysis of metagenomic data. - Marie Jeanne Basse, Stéphane Betzi, Xavier Morelli
2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions. - Naresh Sahebrao Nagpure, Ajey Kumar Pathak, Rameshwar Pati
Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms. - Chen Li
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. - Yi-An Chen, Lokesh P. Tripathi
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. - G. Thomas Hayman, Stanley J. F. Laulederkind, Jennifer R. Smith, Shur-Jen Wang, Victoria Petri, Rajni Nigam, Marek Tutaj, Jeff de Pons, Melinda R. Dwinell, Mary Shimoyama:
The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database. - Alexander Miguel Monzon
CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state. - Alper Uzun
dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes. - Eurie L. Hong, Cricket A. Sloan, Esther T. Chan
Principles of metadata organization at the ENCODE data coordination center. - Moritz Emanuel Beber
Effect of database drift on network topology and enrichment analyses: a case study for RegulonDB. - Chee Sian Kuan, Su Mei Yew, Chai Ling Chan, Yue Fen Toh, Kok Wei Lee, Wei-Hien Cheong, Wai-Yan Yee, Chee-Choong Hoh, Soon-Joo Yap, Kee-Peng Ng:
DemaDb: an integrated dematiaceous fungal genomes database. - Graham L. Cromar, Anthony Zhao, Xuejian Xiong, Lakshmipuram S. Swapna, Noeleen Loughran, Hongyan Song, John Parkinson
PhyloPro2.0: a database for the dynamic exploration of phylogenetically conserved proteins and their domain architectures across the Eukarya. - Sook Jung, Taein Lee, Stephen P. Ficklin
Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. - Eli J. Draizen, Alexey K. Shaytan
HistoneDB 2.0: a histone database with variants - an integrated resource to explore histones and their variants. - Sebastian Burgstaller-Muehlbacher
Wikidata as a semantic framework for the Gene Wiki initiative. - Frédéric Rimet
R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. - Leonore Reiser
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. - Chen Li
KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. - Stacia R. Engel
From one to many: expanding the Saccharomyces cerevisiae reference genome panel. - Vahan Simonyan, Konstantin Chumakov, Hayley Dingerdissen, William J. Faison, Scott Goldweber, Anton Golikov, Naila Gulzar
High-performance integrated virtual environment (HIVE): a robust infrastructure for next-generation sequence data analysis. - Yi Shen, Heming Yao, Ao Li, Minghui Wang:
CSCdb: a cancer stem cells portal for markers, related genes and functional information. - Amaia Sangrador-Vegas
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. - Chih-Hsuan Wei
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. - Tiago Henrique Trojahn
HNdb: an integrated database of gene and protein information on head and neck squamous cell carcinoma. - Chung-Chi Huang, Zhiyong Lu:
Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation. - Che-Wei Chang, Chai-Wei Chou, Darby Tien-Hao Chang:
CCProf: exploring conformational change profile of proteins. - Jun Xu, Yonghui Wu, Yaoyun Zhang, Jingqi Wang, Hee-Jin Lee, Hua Xu:
CD-REST: a system for extracting chemical-induced disease relation in literature. - Tim E. Putman
Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes. - Lei Chen, Peng Ai, Jinfeng Zhang, Qiming Deng, Shiquan Wang, Shuangcheng Li, Jun Zhu, Ping Li, Ai-ping Zheng:
RSIADB, a collective resource for genome and transcriptome analyses in Rhizoctonia solani AG1 IA. - Meik Kunz, Chunguang Liang, Santosh Nilla, Alexander Cecil
The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development. - Anoop Kishor Singh Gurjar, Abhijeet Singh Panwar, Rajinder Gupta
PmiRExAt: plant miRNA expression atlas database and web applications. - Rahul Agarwal
CoReCG: a comprehensive database of genes associated with colon-rectal cancer. - Yajing Hao
NPInter v3.0: an upgraded database of noncoding RNA-associated interactions. - Sefa Kiliç, Dinara M. Sagitova, Shoshannah Wolfish, Benoit Bely
From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF. - Simon Fishilevich, Shahar Zimmerman, Asher Kohn, Tsippi Iny Stein, Tsviya Olender, Eugene Kolker, Marilyn Safran, Doron Lancet:
Genic insights from integrated human proteomics in GeneCards. - Jinghang Gu
Chemical-induced disease relation extraction with various linguistic features. - Valérie Hinard, Aurore Britan, J. S. Rougier, Amos Bairoch
ICEPO: the ion channel electrophysiology ontology. - Girolamo Giudice
ATtRACT - a database of RNA-binding proteins and associated motifs. - Alison Callahan, Saminda Abeyruwan, Hassan Al-Ali
RegenBase: a knowledge base of spinal cord injury biology for translational research. - Daniel M. Lowe, Noel M. O'Boyle
Efficient chemical-disease identification and relationship extraction using Wikipedia to improve recall. - Kyubum Lee
BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations. - Christopher Hardt
ToxDB: pathway-level interpretation of drug-treatment data. - Xiaoxiao Yun, Lili Xia, Bixia Tang, Hui Zhang, Feifei Li, Zhihua Zhang:
3CDB: a manually curated database of chromosome conformation capture data. - Ewoud Pons
Extraction of chemical-induced diseases using prior knowledge and textual information. - Huiwei Zhou, Huijie Deng, Long Chen, Yunlong Yang, Chen Jia
Exploiting syntactic and semantics information for chemical-disease relation extraction. - Megan Druce, Chantal Hulo, Patrick Masson
Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. - Yaoyun Zhang, Jun Xu, Hui Chen
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. - Tong Shu Li, Àlex Bravo
A crowdsourcing workflow for extracting chemical-induced disease relations from free text. - Daniel Arend
PGP repository: a plant phenomics and genomics data publication infrastructure. - Alexey I. Kuzmenkov
Kalium: a database of potassium channel toxins from scorpion venom. - Karina Yusim, Hyejin Yoon, Brian T. Foley
Integrated sequence and immunology filovirus database at Los Alamos. - Van-Nui Nguyen, Kai-Yao Huang, Julia Tzu-Ya Weng, K. Robert Lai, Tzong-Yi Lee:
UbiNet: an online resource for exploring the functional associations and regulatory networks of protein ubiquitylation. - Saber A. Akhondi, Ewoud Pons
Chemical entity recognition in patents by combining dictionary-based and statistical approaches. - Javier Herrero
Ensembl comparative genomics resources. - Sook Jung, Taein Lee, Stephen P. Ficklin, Jing Yu, Chun-Huai Cheng, Dorrie Main:
Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. - Gurpreet S. Ghattaoraya
A web resource for mining HLA associations with adverse drug reactions: HLA-ADR. - Soheil Moosavinasab, Jeremy Patterson
'RE: fine drugs': an interactive dashboard to access drug repurposing opportunities. - Patrice Baa-Puyoulet, Nicolas Parisot
ArthropodaCyc: a CycADS powered collection of BioCyc databases to analyse and compare metabolism of arthropods. - Po-Ju Yao, Ren-Hua Chung:
GESDB: a platform of simulation resources for genetic epidemiology studies. - Giltae Song
Integration of new alternative reference strain genome sequences into the Saccharomyces genome database. - Dennis J. Pelletier, Thomas C. Wiegers, Ahmed Enayetallah, C. Kibbey, Mark Gosink
ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings. - Jiao Li
BioCreative V CDR task corpus: a resource for chemical disease relation extraction. - Yifan Peng
BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. - Po-Ting Lai
BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text. - Robert Leaman, Chih-Hsuan Wei
Mining chemical patents with an ensemble of open systems. - Olivier Sallou, Paula Duek Roggli
PepPSy: a web server to prioritize gene products in experimental and biocuration workflows. - Mary Shimoyama, Jennifer R. Smith, Jeff de Pons, Marek Tutaj, Pawjai Khampang, Wenzhou Hong, Christy B. Erbe, Garth D. Ehrlich
The Chinchilla Research Resource Database: resource for an otolaryngology disease model. - Shu-Fen Li, Guo-Jun Zhang
DPTEdb, an integrative database of transposable elements in dioecious plants. - Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Hongfang Liu:
BELTracker: evidence sentence retrieval for BEL statements. - Riza Theresa Batista-Navarro
Argo: enabling the development of bespoke workflows and services for disease annotation. - Firoj Alam, Anna Corazza, Alberto Lavelli, Roberto Zanoli:
A knowledge-poor approach to chemical-disease relation extraction. - Peter McQuilton
BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences. - Lisa Posch, Maryam Panahiazar, Michel Dumontier, Olivier Gevaert
Predicting structured metadata from unstructured metadata. - Eugene Baulin
URS DataBase: universe of RNA structures and their motifs. - So Nakagawa
gEVE: a genome-based endogenous viral element database provides comprehensive viral protein-coding sequences in mammalian genomes. - Miguel A. Ibarra-Arellano, Adrián I. Campos-González
Abasy Atlas: a comprehensive inventory of systems, global network properties and systems-level elements across bacteria. - Hong-Jie Dai, Chu-Hsien Su, Po-Ting Lai
MET network in PubMed: a text-mined network visualization and curation system. - Wei-Sheng Wu, Fu-Jou Lai, Bor-Wen Tu, Darby Tien-Hao Chang:
CoopTFD: a repository for predicted yeast cooperative transcription factor pairs. - Chen Li, Jeremy Nagel, Steve G. Androulakis, Christopher J. Lupton, Jiangning Song
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. - Na Han, Yujun Qiang, Wen Zhang:
ANItools web: a web tool for fast genome comparison within multiple bacterial strains. - Roddy Jorquera, Rodrigo Ortiz, Francisco Ossandón, Juan Pablo Cárdenas
SinEx DB: a database for single exon coding sequences in mammalian genomes. - Àlex Bravo
Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text. - Bronwen L. Aken, Sarah C. Ayling, Daniel Barrell
The Ensembl gene annotation system. - Mais G. Ammari, Cathy R. Gresham, Fiona M. McCarthy
HPIDB 2.0: a curated database for host-pathogen interactions. - Haodi Li, Buzhou Tang, Qingcai Chen, Kai Chen, Xiaolong Wang, Baohua Wang, Zhe Wang:
HITSZ_CDR: an end-to-end chemical and disease relation extraction system for BioCreative V. - Sushil Tripathi, Steven Vercruysse
Gene regulation knowledge commons: community action takes care of DNA binding transcription factors. - Hsin-Chun Lee, Yi-Yu Hsu, Hung-Yu Kao:
AuDis: an automatic CRF-enhanced disease normalization in biomedical text. - Sérgio Matos
Mining clinical attributes of genomic variants through assisted literature curation in Egas. - Tian Tian, Qi You, Liwei Zhang, Xin Yi, Hengyu Yan, Wenying Xu, Zhen Su
SorghumFDB: sorghum functional genomics database with multidimensional network analysis. - Miji Choi, Haibin Liu, William A. Baumgartner Jr., Justin Zobel, Karin Verspoor
Coreference resolution improves extraction of Biological Expression Language statements from texts. - Luc Mottin
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. - Andrew D. Rouillard
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. - Deepika Singh
A comprehensive view of the web-resources related to sericulture. - Lisa Posch, Maryam Panahiazar, Michel Dumontier
Predicting structured metadata from unstructured metadata. - Bhawna V. S. Bonthala
PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes. - Fabio Rinaldi
BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language. - Pawan Upadhyay
TMC-SNPdb: an Indian germline variant database derived from whole exome sequences. - Imad Abugessaisa
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. - Hoang-Quynh Le
Sieve-based coreference resolution enhances semi-supervised learning model for chemical-induced disease relation extraction. - Yu Rang Park, Jae-Jung Kim, Young Jo Yoon, Young-Kwang Yoon, Ha Yeong Koo, Young Mi Hong, Gi Young Jang, Soo-Yong Shin, Jong-Keuk Lee:
Establishment of Kawasaki disease database based on metadata standard. - Hong-Jie Dai, Onkar Singh, Jitendra Jonnagaddala
NTTMUNSW BioC modules for recognizing and normalizing species and gene/protein mentions. - Haijun Liu
MODEM: multi-omics data envelopment and mining in maize. - Chong Chen, Yi Jiang, Chenyang Xu, Xinting Liu
Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders. - Peter D. Karp:
How much does curation cost? - Jitendra Jonnagaddala
Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion. - Lynette Hirschman, Karën Fort
Crowdsourcing and curation: perspectives from biology and natural language processing. - Soo-Yong Shin, Sun Kim, W. John Wilbur, Dongseop Kwon:
BioC viewer: a web-based tool for displaying and merging annotations in BioC. - Jeremy D. Edwards
Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data. - Navneet Tomar, Akhilesh Mishra
Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes. - Yung-Chun Chang
PIPE: a protein-protein interaction passage extraction module for BioCreative challenge. - Martín Pérez-Pérez
The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge. - Juliane Fluck
Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL). - Eduardo Andrés León
DDRprot: a database of DNA damage response-related proteins. - Gully A. P. C. Burns, Pradeep Dasigi, Anita de Waard
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. - Qinghua Wang, Shabbir Syed-Abdul
Overview of the interactive task in BioCreative V. - Matsuyuki Shirota, Kengo Kinoshita:
Discrepancies between human DNA, mRNA and protein reference sequences and their relation to single nucleotide variants in the human population. - David P. Hill, Peter D'Eustachio
Modeling biochemical pathways in the gene ontology. - Magdalena Krochmal
PeptiCKDdb - peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease. - Sun Kim, Rezarta Islamaj Dogan
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. - Zeeshan Ahmed
Mining biomedical images towards valuable information retrieval in biomedical and life sciences. - Luis N. Marenco, Rixin Wang, Robert A. McDougal, Tsviya Olender, Michal Twik, Elspeth A. Bruford, Xinyi Liu, Jian Zhang
ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. - Tze King Tan
PGD: a pangolin genome hub for the research community. - Gabriele Dröge, Katharine Barker
The Global Genome Biodiversity Network (GGBN) Data Standard specification. - Giovanni Mazzocco
3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale. - Nadav Brandes, Dan Ofer
ASAP: a machine learning framework for local protein properties. - Sumit Madan, Sven Hodapp, Philipp Senger, Sam Ansari, Justyna Szostak, Julia Hoeng, Manuel C. Peitsch
The BEL information extraction workflow (BELIEF): evaluation in the BioCreative V BEL and IAT track. - Hoang-Quynh Le, Mai-Vu Tran, Thanh Hai Dang, Quang-Thuy Ha
Sieve-based coreference resolution enhances semi-supervised learning model for chemical-induced disease relation extraction. - Zeeshan Ahmed
Mining biomedical images towards valuable information retrieval in biomedical and life sciences. - Elena Denisenko, Daniel Ho
IRNdb: the database of immunologically relevant non-coding RNAs. - Olukemi O. Ifeonu, Raphael Simon, Sharon M. Tennant, Abhineet S. Sheoran, Maria C. Daly, Victor Felix, Jessica C. Kissinger
Cryptosporidium hominis gene catalog: a resource for the selection of novel Cryptosporidium vaccine candidates. - Qikang Wei, Tao Chen, Ruifeng Xu, Yulan He
Disease named entity recognition by combining conditional random fields and bidirectional recurrent neural networks. - Richard Tzong-Han Tsai
NERChem: adapting NERBio to chemical patents via full-token features and named entity feature with chemical sub-class composition. - Mark Gosink
ToxReporter: viewing the genome through the eyes of a toxicologist. - Piotr Przybyla
Text mining resources for the life sciences. - Hans Ienasescu, Kang Li, Robin Andersson
On-the-fly selection of cell-specific enhancers, genes, miRNAs and proteins across the human body using SlideBase. - Matej Stano, Gabor Beke, Lubos Klucar
viruSITE - integrated database for viral genomics. - Yi Jin Liew
Reefgenomics.Org - a repository for marine genomics data. - Allison Piovesan
GeneBase 1.1: a tool to summarize data from NCBI gene datasets and its application to an update of human gene statistics. - Yunfeng Qi, Dadong Wang, Daying Wang, Taicheng Jin, Liping Yang, Hui Wu, Yaoyao Li, Jing Zhao, Fengping Du, Mingxia Song, Renjun Wang:
HEDD: the human epigenetic drug database. - Min-Jin Han
iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects. - Marc Feuermann, Pascale Gaudet
Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes. - Wei-Ting Liu, Chia-Chun Yang, Rong-Kuen Chen, Woei-Shyuan Jwo, Chih-Wen Wu, Wen-Yen Ting, Dah-Pyng Shung, Chun-Chi Liu, Jeremy J. W. Chen
RiceATM: a platform for identifying the association between rice agronomic traits and miRNA expression. - Borisas Bursteinas, Ramona Britto
Minimizing proteome redundancy in the UniProt Knowledgebase. - Paula Jorge
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow. - Markus J. Ankenbrand
TBro: visualization and management of de novo transcriptomes. - Robert P. Guralnick, Paula F. Zermoglio
The importance of digitized biocollections as a source of trait data and a new VertNet resource. - Sonu Kumar
CaspNeuroD: a knowledgebase of predicted caspase cleavage sites in human proteins related to neurodegenerative diseases.
- Peter D. Karp:
Crowd-sourcing and author submission as alternatives to professional curation. - Ayush Singhal, Robert Leaman, Natalie L. Catlett, Thomas Lemberger, Johanna R. McEntyre
Pressing needs of biomedical text mining in biocuration and beyond: opportunities and challenges. - Peter D. Karp:
Crowd-sourcing and author submission as alternatives to professional curation. baw149
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