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Database - The Journal of Biological Databases and Curation, Volume 2016
Volume 2016, 2016
- Rayda Ben Ayed
, Hanen Ben Hassen
, Karim Ennouri
, Riadh Ben Marzoug, Ahmed Rebai
:
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
, Ole Lund
, Tudor I. Oprea
, Olivier Taboureau
:
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
, Nathan Johnson, Thomas Juettemann
, Daniel Sheppard
, Steven P. Wilder
, Ilias Lavidas
, Michael Nuhn
, Emily Perry
, Quentin Raffaillac-Desfosses, Daniel Sobral
, Damian Keefe, Stefan Gräf, Ikhlak Ahmed
, Rhoda Kinsella, Bethan Pritchard, Simon Brent, M. Ridwan Amode, Anne Parker, Stephen J. Trevanion
, Ewan Birney
, Ian Dunham
, Paul Flicek
:
Ensembl regulation resources. - Javier Herrero
, Matthieu Muffato
, Kathryn Beal, Stephen Fitzgerald, Leo Gordon, Miguel Pignatelli, Albert J. Vilella, Stephen M. J. Searle, M. Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha
, Andrew D. Yates
, Paul Flicek
:
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
, Clara Amid
, Pier Luigi Buttigieg
, Evangelos Pafilis, Panos Bravakos, Ana Cerdeño-Tárraga
, Richard Gibson, Tim Kahlke
, Aglaia Legaki, Kada Narayana Murthy, Gabriella Papastefanou, Emiliano Pereira
, Marc Rossello, Ana Luisa Toribio, Guy Cochrane
:
Value, but high costs in post-deposition data curation. - Martin Dugas
, Philipp Neuhaus, Alexandra Meidt, Justin Doods, Michael Storck
, Philipp Bruland, Julian Varghese
:
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
, Songyang Zhou, Zhenhua Luo, Junfeng Huang, Zhiming Dai, Yuanyan Xiong:
CCSI: a database providing chromatin-chromatin spatial interaction information. - Adam D. DePriest
, Michael V. Fiandalo
, Simon Schlanger, Frederike Heemers, James L. Mohler, Song Liu, Hannelore V. Heemers:
Regulators of Androgen Action Resource: a one-stop shop for the comprehensive study of androgen receptor action. - Subodh Kumar Mishra
, Amit Kumar:
NALDB: nucleic acid ligand database for small molecules targeting nucleic acid. - Evangelos Pafilis, Pier Luigi Buttigieg
, Barbra Ferrell
, Emiliano Pereira
, Julia Schnetzer, Christos Arvanitidis
, Lars Juhl Jensen
:
EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation. - Lionel Breuza
, Sylvain Poux
, Anne Estreicher
, Maria Livia Famiglietti, Michele Magrane
, Michael Tognolli
, Alan J. Bridge
, Delphine Baratin, Nicole Redaschi
:
The UniProtKB guide to the human proteome. - Miguel Pignatelli, Albert J. Vilella, Matthieu Muffato
, Leo Gordon, Simon White
, Paul Flicek
, Javier Herrero
:
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
, Wanwen Zeng, Rui Jiang
:
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
, Philippe Roche:
2P2Idb v2: update of a structural database dedicated to orthosteric modulation of protein-protein interactions. - Naresh Sahebrao Nagpure, Ajey Kumar Pathak, Rameshwar Pati
, Iliyas Rashid
, Jyoti Sharma, Shri Prakash Singh, Mahender Singh
, Uttam Kumar Sarkar, Basdeo Kushwaha, Ravindra Kumar, S. Murali:
Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms. - Chen Li
, Jeremy Nagel, Steve G. Androulakis, Jiangning Song
, Ashley M. Buckle
:
PolyQ 2.0: an improved version of PolyQ, a database of human polyglutamine proteins. - Yi-An Chen, Lokesh P. Tripathi
, Kenji Mizuguchi
:
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
, Cristian Oscar Rohr, María Silvina Fornasari, Gustavo D. Parisi
:
CoDNaS 2.0: a comprehensive database of protein conformational diversity in the native state. - Alper Uzun
, Elizabeth W. Triche, Jessica Schuster, Andrew Thomas DeWan
, James Padbury:
dbPEC: a comprehensive literature-based database for preeclampsia related genes and phenotypes. - Eurie L. Hong, Cricket A. Sloan, Esther T. Chan
, Jean M. Davidson, Venkat S. Malladi
, J. Seth Strattan, Benjamin C. Hitz, Idan Gabdank, Aditi K. Narayanan, Marcus Ho
, Brian T. Lee
, Laurence D. Rowe
, Timothy R. Dreszer, Greg R. Roe, Nikhil R. Podduturi, Forrest Tanaka, Jason A. Hilton
, J. Michael Cherry
:
Principles of metadata organization at the ENCODE data coordination center. - Moritz Emanuel Beber
, Georgi Muskhelishvili, Marc-Thorsten Hütt:
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
, Jing Yu, Chun-Huai Cheng, Dorrie Main:
Chado use case: storing genomic, genetic and breeding data of Rosaceae and Gossypium crops in Chado. - Eli J. Draizen, Alexey K. Shaytan
, Leonardo Mariño-Ramírez
, Paul B. Talbert, David Landsman
, Anna R. Panchenko:
HistoneDB 2.0: a histone database with variants - an integrated resource to explore histones and their variants. - Sebastian Burgstaller-Muehlbacher
, Andra Waagmeester
, Elvira Mitraka, Julia Turner, Tim E. Putman
, Justin Leong, Chinmay Naik, Paul Pavlidis
, Lynn M. Schriml
, Benjamin M. Good, Andrew I. Su
:
Wikidata as a semantic framework for the Gene Wiki initiative. - Frédéric Rimet
, Philippe Chaumeil, François Keck
, Lenaïg Kermarrec, Valentin Vasselon
, Maria Kahlert
, Alain Franc, Agnès Bouchez
:
R-Syst::diatom: an open-access and curated barcode database for diatoms and freshwater monitoring. - Leonore Reiser
, Tanya Z. Berardini
, Donghui Li
, Robert J. Muller, Emily M. Strait, Qian Li, Yarik Mezheritsky, Andrey Vetushko, Eva Huala
:
Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model. - Chen Li
, Steve G. Androulakis, Ashley M. Buckle
, Jiangning Song
:
KinetochoreDB: a comprehensive online resource for the kinetochore and its related proteins. - Stacia R. Engel
, Shuai Weng, Gail Binkley, Kelley M. Paskov, Giltae Song
, J. Michael Cherry
:
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
, Konstantinos Karagiannis
, Phuc Vinh Nguyen Lam, Thomas Maudru, Olesja Muravitskaja, Ekaterina Osipova, Yang Pan
, Alexey Pschenichnov, Alexandre Rostovtsev
, Luis V. Santana-Quintero, Krista Smith, Elaine E. Thompson
, Valery Tkachenko, John Torcivia-Rodriguez
, Alin Voskanian, Quan Wan, Jing Wang, Tsung-Jung Wu, Carolyn Wilson, Raja Mazumder
:
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
, Alex L. Mitchell
, Hsin-Yu Chang
, Siew-Yit Yong
, Robert D. Finn
:
GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations. - Chih-Hsuan Wei
, Yifan Peng
, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly
, Jiao Li, Thomas C. Wiegers, Zhiyong Lu:
Assessing the state of the art in biomedical relation extraction: overview of the BioCreative V chemical-disease relation (CDR) task. - Tiago Henrique Trojahn
, Nelson José Freitas da Silveira
, Arthur Henrique Cunha Volpato, Mayra Mataruco Mioto, Ana Carolina Buzzo Stefanini, Adil Bachir Fares, João Gustavo da Silva Castro Andrade, Carolina Masson, Rossana Verónica Mendoza López, Fabio Daumas Nunes
, Luiz Paulo Kowalski
, Patricia Severino
, Eloiza Helena Tajara:
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
, Sebastian Burgstaller-Muehlbacher
, Andra Waagmeester
, Chunlei Wu, Andrew I. Su
, Benjamin M. Good:
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
, Thomas Dandekar:
The drug-minded protein interaction database (DrumPID) for efficient target analysis and drug development. - Anoop Kishor Singh Gurjar, Abhijeet Singh Panwar, Rajinder Gupta
, Shrikant S. Mantri
:
PmiRExAt: plant miRNA expression atlas database and web applications. - Rahul Agarwal
, Binayak Kumar, Msk Jayadev, Dhwani Raghav, Ashutosh Singh
:
CoReCG: a comprehensive database of genes associated with colon-rectal cancer. - Yajing Hao
, Wei Wu
, Hui Li, Jiao Yuan, Jianjun Luo
, Yi Zhao
, Runsheng Chen
:
NPInter v3.0: an upgraded database of noncoding RNA-associated interactions. - Sefa Kiliç, Dinara M. Sagitova, Shoshannah Wolfish, Benoit Bely
, Mélanie Courtot
, Stacy Ciufo, Tatiana A. Tatusova, Claire O'Donovan
, Marcus C. Chibucos
, Maria Jesus Martin
, Ivan Erill
:
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
, Longhua Qian, Guodong Zhou
:
Chemical-induced disease relation extraction with various linguistic features. - Valérie Hinard, Aurore Britan, J. S. Rougier, Amos Bairoch
, Hugues Abriel
, Pascale Gaudet
:
ICEPO: the ion channel electrophysiology ontology. - Girolamo Giudice
, Fátima Sánchez-Cabo, Carlos Torroja Fungairino
, Enrique Lara Pezzi
:
ATtRACT - a database of RNA-binding proteins and associated motifs. - Alison Callahan, Saminda Abeyruwan, Hassan Al-Ali
, Kunie Sakurai, Adam R. Ferguson
, Phillip G. Popovich, Nigam H. Shah, Ubbo Visser
, John L. Bixby, Vance P. Lemmon
:
RegenBase: a knowledge base of spinal cord injury biology for translational research. - Daniel M. Lowe, Noel M. O'Boyle
, Roger A. Sayle:
Efficient chemical-disease identification and relationship extraction using Wikipedia to improve recall. - Kyubum Lee
, Sunwon Lee, Sungjoon Park, Sunkyu Kim, Suhkyung Kim, Kwanghun Choi, Aik Choon Tan
, Jaewoo Kang:
BRONCO: Biomedical entity Relation ONcology COrpus for extracting gene-variant-disease-drug relations. - Christopher Hardt, Moritz Emanuel Beber
, Axel Rasche, Atanas Kamburov, Dennie G. A. J. Hebels, Jos C. S. Kleinjans, Ralf Herwig
:
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
, Benedikt F. H. Becker
, Saber A. Akhondi, Zubair Afzal
, Erik M. van Mulligen
, Jan A. Kors:
Extraction of chemical-induced diseases using prior knowledge and textual information. - Huiwei Zhou, Huijie Deng, Long Chen, Yunlong Yang, Chen Jia
, Degen Huang:
Exploiting syntactic and semantics information for chemical-disease relation extraction. - Megan Druce, Chantal Hulo, Patrick Masson
, Paula Sommer
, Ioannis Xenarios, Philippe Le Mercier
, Tulio de Oliveira:
Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource. - Yaoyun Zhang, Jun Xu, Hui Chen
, Jingqi Wang, Yonghui Wu, Manu Prakasam, Hua Xu:
Chemical named entity recognition in patents by domain knowledge and unsupervised feature learning. - Tong Shu Li, Àlex Bravo
, Laura I. Furlong, Benjamin M. Good, Andrew I. Su
:
A crowdsourcing workflow for extracting chemical-induced disease relations from free text. - Daniel Arend
, Astrid Junker
, Uwe Scholz
, Danuta Schüler
, Juliane Wylie, Matthias Lange
:
PGP repository: a plant phenomics and genomics data publication infrastructure. - Alexey I. Kuzmenkov
, Nikolay A. Krylov
, Anton O. Chugunov
, Eugene V. Grishin, Alexander A. Vassilevski
:
Kalium: a database of potassium channel toxins from scorpion venom. - Karina Yusim, Hyejin Yoon, Brian T. Foley
, Shihai Feng, Jennifer Macke, Mira Dimitrijevic, Werner Abfalterer, James Szinger
, Will Fischer
, Carla Kuiken, Bette T. Korber
:
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
, Zubair Afzal
, Herman van Haagen, Benedikt F. H. Becker
, Kristina M. Hettne
, Erik M. van Mulligen
, Jan A. Kors:
Chemical entity recognition in patents by combining dictionary-based and statistical approaches. - Javier Herrero
, Matthieu Muffato
, Kathryn Beal, Stephen Fitzgerald, Leo Gordon, Miguel Pignatelli, Albert J. Vilella, Stephen M. J. Searle, M. Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha
, Andrew D. Yates
, Paul Flicek
:
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
, Yenal Dundar
, Faviel F. Gonzalez-Galarza, Maria Helena Thomaz Maia
, Eduardo José Melo dos Santos
, Andrea Luciana Soares da Silva, Antony McCabe
, Derek Middleton, Ana Alfirevic, Rumona Dickson, Andrew R. Jones
:
A web resource for mining HLA associations with adverse drug reactions: HLA-ADR. - Soheil Moosavinasab, Jeremy Patterson, Robert Strouse, Majid Rastegar-Mojarad, Kelly Regan
, Philip R. O. Payne
, Yungui Huang, Simon M. Lin:
'RE: fine drugs': an interactive dashboard to access drug repurposing opportunities. - Patrice Baa-Puyoulet, Nicolas Parisot
, Gérard Febvay
, Jaime Huerta-Cepas
, Augusto F. Vellozo, Toni Gabaldón, Federica Calevro
, Hubert Charles
, Stefano Colella
:
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
, Rama Balakrishnan, Gail Binkley, Maria C. Costanzo, Kyla S. Dalusag
, Janos Demeter, Stacia R. Engel
, Sage T. Hellerstedt, Kalpana Karra, Benjamin C. Hitz, Robert S. Nash, Kelley M. Paskov, Travis K. Sheppard
, Marek S. Skrzypek, Shuai Weng, Edith D. Wong, J. Michael Cherry
:
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
, P. Koza-Taylor, Carolyn J. Mattingly
, M. Lawton:
ToxEvaluator: an integrated computational platform to aid the interpretation of toxicology study-related findings. - Jiao Li
, Yueping Sun, Robin J. Johnson, Daniela Sciaky
, Chih-Hsuan Wei
, Robert Leaman, Allan Peter Davis, Carolyn J. Mattingly
, Thomas C. Wiegers, Zhiyong Lu:
BioCreative V CDR task corpus: a resource for chemical disease relation extraction. - Yifan Peng
, Cecilia N. Arighi
, Cathy H. Wu
, K. Vijay-Shanker:
BioC-compatible full-text passage detection for protein-protein interactions using extended dependency graph. - Po-Ting Lai
, Yu-Yan Lo, Ming-Siang Huang, Yu-Cheng Hsiao
, Richard Tzong-Han Tsai
:
BelSmile: a biomedical semantic role labeling approach for extracting biological expression language from text. - Robert Leaman, Chih-Hsuan Wei
, Cherry Zou, Zhiyong Lu:
Mining chemical patents with an ensemble of open systems. - Olivier Sallou, Paula D. Duek
, Thomas A. Darde
, Olivier Collin
, Lydie Lane
, Frédéric Chalmel
:
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
, Lauren O. Bakaletz, Joseph E. Kerschner:
The Chinchilla Research Resource Database: resource for an otolaryngology disease model. - Shu-Fen Li, Guo-Jun Zhang
, Xue-Jin Zhang, Jin-Hong Yuan, Chuan-Liang Deng, Lian-Feng Gu, Wujun Gao:
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. - Firoj Alam, Anna Corazza, Alberto Lavelli, Roberto Zanoli:
A knowledge-poor approach to chemical-disease relation extraction. - Peter McQuilton
, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Milo Thurston, Allyson L. Lister
, Eamonn Maguire, Susanna-Assunta Sansone
:
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
, Victor Yacovlev, Denis Khachko, Sergei A. Spirin
, Mikhail Roytberg:
URS DataBase: universe of RNA structures and their motifs. - So Nakagawa
, Mahoko Ueda Takahashi
:
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
, Luis G. Treviño-Quintanilla, Andreas Tauch, Julio A. Freyre-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
, Ming-Siang Huang, Jitendra Jonnagaddala
, Toni Rose Jue
, Shruti Rao
, Hui-Jou Chou, Marija Milacic
, Onkar Singh, Syed Abdul Shabbir, Wen-Lian Hsu:
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
, Ashley M. Buckle
:
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
, Rene Sepúlveda, Carolina González
, David S. Holmes
:
SinEx DB: a database for single exon coding sequences in mammalian genomes. - Àlex Bravo
, Tong Shu Li, Andrew I. Su
, Benjamin M. Good, Laura I. Furlong:
Combining machine learning, crowdsourcing and expert knowledge to detect chemical-induced diseases in text. - Bronwen L. Aken, Sarah C. Ayling, Daniel Barrell
, Laura Clarke
, Valery Curwen, Susan Fairley
, Julio Fernandez-Banet
, Konstantinos Billis
, Carlos García-Girón
, Thibaut Hourlier
, Kevin Lee Howe
, Andreas Kähäri
, Felix Kokocinski
, Fergal J. Martin
, Daniel N. Murphy
, Rishi Nag
, Magali Ruffier
, Michael Schuster, Y. Amy Tang
, Jan Vogel, Simon White
, Amonida Zadissa
, Paul Flicek
, Stephen M. J. Searle:
The Ensembl gene annotation system. - Mais G. Ammari, Cathy R. Gresham, Fiona M. McCarthy, Bindu Nanduri:
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
, Konika Chawla, Karen R. Christie, Judith A. Blake
, Rachael P. Huntley
, Sandra E. Orchard
, Henning Hermjakob
, Liv Thommesen, Astrid Lægreid, Martin Kuiper:
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
, David Campos, Renato P. Pinho, Raquel M. Silva
, Matthew E. Mort, David N. Cooper, José Luís Oliveira
:
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
, Julien Gobeill
, Emilie Pasche
, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet
, Patrick Ruch
:
neXtA5: accelerating annotation of articles via automated approaches in neXtProt. - Andrew D. Rouillard
, Gregory W. Gundersen, Nicolas F. Fernandez, Zichen Wang
, Caroline D. Monteiro, Michael G. McDermott, Avi Ma'ayan
:
The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins. - Deepika Singh
, Hasnahana Chetia
, Debajyoti Kabiraj, Swagata Sharma, Anil Kumar
, Pragya Sharma
, Manab Deka, Utpal Bora:
A comprehensive view of the web-resources related to sericulture. - Lisa Posch, Maryam Panahiazar, Michel Dumontier
, Olivier Gevaert:
Predicting structured metadata from unstructured metadata. - Bhawna V. S. Bonthala
, M. N. V. Prasad Gajula:
PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes. - Fabio Rinaldi
, Tilia Renate Ellendorff, Sumit Madan, Simon Clematide
, Adrian Van der Lek, Heinz-Theodor Mevissen, Juliane Fluck
:
BioCreative V track 4: a shared task for the extraction of causal network information using the Biological Expression Language. - Pawan Upadhyay
, Nilesh Gardi, Sanket Desai
, Bikram Sahoo, Ankita Singh, Trupti Togar, Prajish Iyer
, Ratnam Prasad, Pratik Chandrani
, Sudeep Gupta, Amit Dutt:
TMC-SNPdb: an Indian germline variant database derived from whole exome sequences. - Imad Abugessaisa
, Hisashi Shimoji, Serkan Sahin, Atsushi Kondo, Jayson Harshbarger, Marina Lizio, Yoshihide Hayashizaki, Piero Carninci
, Alistair R. R. Forrest
, Takeya Kasukawa
, Hideya Kawaji
:
FANTOM5 transcriptome catalog of cellular states based on Semantic MediaWiki. - Hoang-Quynh Le
, Mai-Vu Tran, Thanh Hai Dang, Quang-Thuy Ha
, Nigel Collier
:
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
, Emily Chia-Yu Su:
NTTMUNSW BioC modules for recognizing and normalizing species and gene/protein mentions. - Haijun Liu
, Fan Wang, Yingjie Xiao, Zonglin Tian
, Weiwei Wen, Xuehai Zhang
, Xi Chen, Nannan Liu, Wenqiang Li, Lei Liu, Jie Liu
, Jianbing Yan, Jianxiao Liu:
MODEM: multi-omics data envelopment and mining in maize. - Chong Chen, Yi Jiang, Chenyang Xu, Xinting Liu
, Lin Hu, Yanbao Xiang, Qingshuang Chen, Denghui Chen, Huanzheng Li, Xueqin Xu, Shaohua Tang:
Skeleton Genetics: a comprehensive database for genes and mutations related to genetic skeletal disorders. - Peter D. Karp:
How much does curation cost? - Jitendra Jonnagaddala
, Toni Rose Jue
, Nai-Wen Chang, Hong-Jie Dai:
Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion. - Lynette Hirschman, Karën Fort
, Stéphanie Boué, Nikos Kyrpides
, Rezarta Islamaj Dogan
, Kevin Bretonnel Cohen:
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
, A. M. Baldo, Lukas A. Mueller:
Ricebase: a breeding and genetics platform for rice, integrating individual molecular markers, pedigrees and whole-genome-based data. - Navneet Tomar, Akhilesh Mishra
, Nirotpal Mrinal, B. Jayaram
:
Onco-Regulon: an integrated database and software suite for site specific targeting of transcription factors of cancer genes. - Yung-Chun Chang
, Chun-Han Chu, Yu-Chen Su, Chien Chin Chen
, Wen-Lian Hsu:
PIPE: a protein-protein interaction passage extraction module for BioCreative challenge. - Martín Pérez-Pérez
, Gael Pérez Rodríguez
, Obdulia Rabal
, Miguel Vazquez
, Julen Oyarzabal
, Florentino Fdez-Riverola
, Alfonso Valencia, Martin Krallinger
, Anália Lourenço
:
The Markyt visualisation, prediction and benchmark platform for chemical and gene entity recognition at BioCreative/CHEMDNER challenge. - Juliane Fluck
, Sumit Madan, Sam Ansari, Alpha Tom Kodamullil
, Reagon Karki, Majid Rastegar-Mojarad, Natalie L. Catlett, William Hayes, Justyna Szostak, Julia Hoeng, Manuel C. Peitsch
:
Training and evaluation corpora for the extraction of causal relationships encoded in biological expression language (BEL). - Eduardo Andrés León
, Ildefonso Cases
, Aida Arcas
, Ana M. Rojas
:
DDRprot: a database of DNA damage response-related proteins. - Gully A. P. C. Burns, Pradeep Dasigi, Anita de Waard
, Eduard H. Hovy:
Automated detection of discourse segment and experimental types from the text of cancer pathway results sections. - Qinghua Wang, Shabbir S. Abdul, Lara Almeida, Sophia Ananiadou, Yalbi I. Balderas-Martínez
, Riza Batista-Navarro
, David Campos, Lucy Chilton, Hui-Jou Chou, Gabriela Contreras, Laurel Cooper, Hong-Jie Dai, Barbra Ferrell, Juliane Fluck
, Socorro Gama-Castro, Nancy George, Georgios V. Gkoutos
, Afroza Khanam Irin, Lars Juhl Jensen
, Silvia Jimenez, Toni Rose Jue
, Ingrid M. Keseler, Sumit Madan, Sérgio Matos
, Peter McQuilton
, Marija Milacic
, Matthew E. Mort, Jeyakumar Natarajan, Evangelos Pafilis, Emiliano Pereira
, Shruti Rao
, Fabio Rinaldi
, Karen Rothfels, David Salgado
, Raquel M. Silva
, Onkar Singh, Raymund Stefancsik
, Chu-Hsien Su, Suresh Subramani, Hamsa D. Tadepally, Loukia Tsaprouni, Nicole A. Vasilevsky
, Xiaodong Wang, Andrew Chatr-aryamontri, Stanley J. F. Laulederkind, Sherri Matis-Mitchell, Johanna R. McEntyre
, Sandra E. Orchard
, Sangya Pundir
, Raul Rodriguez-Esteban
, Kimberly Van Auken, Zhiyong Lu, Mary L. Schaeffer, Cathy H. Wu
, Lynette Hirschman, Cecilia N. Arighi
:
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
, Tanya Z. Berardini
, Christopher J. Mungall, Nikolai Renedo, Judith A. Blake
:
Modeling biochemical pathways in the gene ontology. - Magdalena Krochmal
, Marco Fernandes
, Szymon Filip
, Claudia Pontillo, Holger Husi, Jerome Zoidakis, Harald Mischak
, Antonia Vlahou
, Joachim Jankowski:
PeptiCKDdb - peptide- and protein-centric database for the investigation of genesis and progression of chronic kidney disease. - Sun Kim, Rezarta Islamaj Dogan
, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred
, Jennifer M. Rust, Riza Batista-Navarro
, Jacob Carter, Sophia Ananiadou, Sérgio Matos
, André Santos, David Campos, José Luís Oliveira, Onkar Singh, Jitendra Jonnagaddala
, Hong-Jie Dai, Emily Chia-Yu Su, Yung-Chun Chang, Yu-Chen Su, Chun-Han Chu, Chien Chin Chen
, Wen-Lian Hsu, Yifan Peng
, Cecilia N. Arighi
, Cathy H. Wu
, K. Vijay-Shanker, Ferhat Aydin, Zehra Melce Hüsünbeyi, Arzucan Özgür, Soo-Yong Shin, Dongseop Kwon, Kara Dolinski
, Mike Tyers, W. John Wilbur, Donald C. Comeau:
BioCreative V BioC track overview: collaborative biocurator assistant task for BioGRID. - Zeeshan Ahmed
, Saman Zeeshan
, Thomas Dandekar:
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
, Doron Lancet, Gordon M. Shepherd, Chiquito J. Crasto:
ORDB, HORDE, ODORactor and other on-line knowledge resources of olfactory receptor-odorant interactions. - Tze King Tan
, Ka Yun Tan, Ranjeev Hari, Aini Mohamed Yusoff, Guat Jah Wong, Cheuk C. Siow, Naresh V. R. Mutha, Mike Rayko, Aleksey Komissarov, Pavel Dobrynin, Ksenia Krasheninnikova, Gaik Tamazian
, Ian C. Paterson
, Wesley C. Warren, Warren E. Johnson
, Stephen J. O'Brien
, Siew Woh Choo:
PGD: a pangolin genome hub for the research community. - Gabriele Dröge, Katharine Barker
, Ole Seberg, Jonathan Coddington, Erica E. Benson, Walter G. Berendsohn
, Boyke Bunk
, Carol Butler, E. Margaret Casey, John Deck, Markus Döring
, Paul Flemons, Birgit Gemeinholzer
, Anton Güntsch, Tom Hollowell, Patricia Kelbert, Ivaylo Kostadinov, Renzo Kottmann, Rita T. Lawlor
, Chris Lyal, Jacqueline Mackenzie-Dodds, Christopher Meyer, Daniel Mulcahy, Sara Y. Nussbeck
, Éamonn Ó Tuama, Thomas Orrell
, Gitte Petersen
, Tim Robertson, Carola Söhngen, Jamie Whitacre, John Wieczorek, Pelin Yilmaz, Holger Zetzsche, Yong Zhang, Xin Zhou:
The Global Genome Biodiversity Network (GGBN) Data Standard specification. - Giovanni Mazzocco
, Michal Lazniewski, Piotr Migdal, Teresa Szczepinska, Jan P. Radomski, Dariusz Plewczynski
:
3DFlu: database of sequence and structural variability of the influenza hemagglutinin at population scale. - Nadav Brandes, Dan Ofer
, Michal Linial
:
ASAP: a machine learning framework for local protein properties. - Sumit Madan, Sven Hodapp, Philipp Senger, Sam Ansari, Justyna Szostak, Julia Hoeng, Manuel C. Peitsch
, Juliane Fluck
:
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
, Nigel Collier:
Sieve-based coreference resolution enhances semi-supervised learning model for chemical-induced disease relation extraction. - Zeeshan Ahmed
, Saman Zeeshan, Thomas Dandekar:
Mining biomedical images towards valuable information retrieval in biomedical and life sciences. - Elena Denisenko, Daniel Ho
, Ousman Tamgue
, Mumin Ozturk
, Harukazu Suzuki, Frank Brombacher, Reto Guler, Sebastian Schmeier
:
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
, Giovanni Widmer, Myron M. Levine, Saul Tzipori, Joana C. Silva:
Cryptosporidium hominis gene catalog: a resource for the selection of novel Cryptosporidium vaccine candidates. - Qikang Wei, Tao Chen, Ruifeng Xu, Yulan He
, Lin Gui
:
Disease named entity recognition by combining conditional random fields and bidirectional recurrent neural networks. - Richard Tzong-Han Tsai
, Yu-Cheng Hsiao
, Po-Ting Lai
:
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
, Matthew Shardlow, Sophie Aubin, Robert Bossy
, Richard Eckart de Castilho, Stelios Piperidis, John McNaught, Sophia Ananiadou:
Text mining resources for the life sciences. - Hans Ienasescu, Kang Li, Robin Andersson
, Morana Vitezic
, Sarah Rennie
, Yun Chen, Kristoffer Vitting-Seerup
, Emil Lagoni, Mette Boyd, Jette Bornholdt, Michiel J. L. de Hoon
, Hideya Kawaji
, Timo Lassmann
, The Fantom Consortium, Yoshihide Hayashizaki, Alistair R. R. Forrest
, Piero Carninci
, Albin Sandelin
:
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
, Manuel Aranda
, Christian R. Voolstra
:
Reefgenomics.Org - a repository for marine genomics data. - Allison Piovesan
, Maria Caracausi
, Francesca Antonaros, Maria Chiara Pelleri, Lorenza Vitale:
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
, Qiu-Zhong Zhou, Hua-Hao Zhang, Xiaoling Tong
, Cheng Lu, Ze Zhang, Fangyin Dai:
iMITEdb: the genome-wide landscape of miniature inverted-repeat transposable elements in insects. - Marc Feuermann, Pascale Gaudet
, Huaiyu Mi, Suzanna E. Lewis, Paul D. Thomas
:
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
, Benoit Bely
, Andrea H. Auchincloss, Catherine Rivoire
, Nicole Redaschi
, Claire O'Donovan
, Maria Jesus Martin
:
Minimizing proteome redundancy in the UniProt Knowledgebase. - Paula Jorge
, Martín Pérez-Pérez
, Gael Pérez Rodríguez
, Florentino Fdez-Riverola
, Maria Olívia Pereira
, Anália Lourenço
:
Construction of antimicrobial peptide-drug combination networks from scientific literature based on a semi-automated curation workflow. - Markus J. Ankenbrand
, Lorenz Weber, Dirk Becker
, Frank Förster
, Felix Bemm:
TBro: visualization and management of de novo transcriptomes. - Robert P. Guralnick, Paula F. Zermoglio
, John Wieczorek, Raphael LaFrance, David Bloom, Laura Russell
:
The importance of digitized biocollections as a source of trait data and a new VertNet resource. - Sonu Kumar
, Piotr Cieplak:
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
, Shawn W. Polson
, Ioannis Xenarios, Cecilia N. Arighi
, Zhiyong Lu:
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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