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ORCIDDatabase - 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 A. 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 Duek Roggli, 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. - Riza Theresa Batista-Navarro, Jacob Carter, Sophia Ananiadou:
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, 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 Syed-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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