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ORCIDDatabase - The Journal of Biological Databases and Curation, Volume 2014
Volume 2014, 2014
- Kathrin Poos, Jan Smida
, Michaela Nathrath, Doris Maugg, Daniel Baumhoer, Anna Neumann, Eberhard Korsching:
Structuring osteosarcoma knowledge: an osteosarcoma-gene association database based on literature mining and manual annotation. - Pierrick Craveur, Joseph Rebehmed, Alexandre G. de Brevern:
PTM-SD: a database of structurally resolved and annotated posttranslational modifications in proteins. - Maria Chaley, Vladimir Kutyrkin, Gayane Tulbasheva, Elena Teplukhina, Nafisa Nazipova:
HeteroGenome: database of genome periodicity. - Yifan Peng, Catalina O. Tudor, Manabu Torii, Cathy H. Wu, K. Vijay-Shanker:
iSimp in BioC standard format: enhancing the interoperability of a sentence simplification system. - Yongmin Kim, Jaeyoung Choi, Hyeyoung Lee, Gir-Won Lee, Yong-Hwan Lee, Doil Choi:
dbCRY: a Web-based comparative and evolutionary genomics platform for blue-light receptors. - Leandro G. Radusky, Lucas A. Defelipe, Esteban Lanzarotti, F. Javier Luque, Xavier Barril, Marcelo A. Marti, Adrian Gustavo Turjanski:
TuberQ: a Mycobacterium tuberculosis protein druggability database. - Faouzi Jaziri, Nicolas Parisot, Anis Abid, Jérémie Denonfoux, Céline Ribière, Cyrielle Gasc, Delphine Boucher, Jean-François Brugère, Antoine Mahul, David R. C. Hill, Eric Peyretaillade, Pierre Peyret:
PhylOPDb: a 16S rRNA oligonucleotide probe database for prokaryotic identification. - Juan Miguel Cejuela, Peter McQuilton, Laura Ponting, Steven J. Marygold, Raymund Stefancsik, Gillian H. Millburn, Burkhard Rost:
tagtog: interactive and text-mining-assisted annotation of gene mentions in PLOS full-text articles. - Alinda Nagy, László Patthy:
FixPred: a resource for correction of erroneous protein sequences. - Sabry Razick, Rok Mocnik, Laurent F. Thomas, Einar Ryeng, Finn Drabløs, Pål Sætrom:
The eGenVar data management system - cataloguing and sharing sensitive data and metadata for the life sciences. - Enyu Dai, Xuexin Yu, Yan Zhang, Fanlin Meng, Shuyuan Wang, Xinyi Liu, Dianming Liu, Jing Wang, Xia Li, Wei Jiang:
EpimiR: a database of curated mutual regulation between miRNAs and epigenetic modifications. - Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Crichton, Vahan Simonyan, Raja Mazumder:
A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE). - Lihong Chen, Bo Liu, Jian Yang, Qi Jin:
DBatVir: the database of bat-associated viruses. - Anika Oellrich, Damian Smedley:
Linking tissues to phenotypes using gene expression profiles. - Tam P. Sneddon, Sizhe Xiao, Scott C. Edmunds, Peter Li, Laurie Goodman, Christopher I. Hunter:
GigaDB: promoting data dissemination and reproducibility. - Sylvain Poux, Michele Magrane, Cecilia N. Arighi, Alan J. Bridge, Claire O'Donovan, Kati Laiho:
Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data. - Tzu-Hsien Yang, Chung-Ching Wang, Yu-Chao Wang, Wei-Sheng Wu:
YTRP: a repository for yeast transcriptional regulatory pathways. - Filip Claes, Dmitry Kuznetsov, Robin Liechti, Sophie von Dobschütz, Bao Dinh Truong, Anne Gleizes, Daniele Conversa, Alessandro Colonna, Ettore Demaio, Sabina Ramazzotto, Fairouz Larfaoui, Julio Pinto, Philippe Le Mercier, Ioannis Xenarios, Gwenaelle Dauphin:
The EMPRES-i genetic module: a novel tool linking epidemiological outbreak information and genetic characteristics of influenza viruses. - Hansheng Zhao, Zhenhua Peng, Benhua Fei, Lubin Li, Tao Hu, Zhimin Gao, Zehui Jiang:
BambooGDB: a bamboo genome database with functional annotation and an analysis platform. - Janos X. Binder, Sune Pletscher-Frankild, Kalliopi Tsafou, Christian Stolte, Seán I. O'Donoghue, Reinhard Schneider, Lars Juhl Jensen:
COMPARTMENTS: unification and visualization of protein subcellular localization evidence. - Margherita Scarpato, Roberta Esposito, Daniela Evangelista, Marianna Aprile, Maria Rosaria Ambrosio, Claudia Angelini, Alfredo Ciccodicola, Valerio Costa:
AnaLysis of Expression on human chromosome 21, ALE-HSA21: a pilot integrated web resource. - Jun Zhong, Jyoti Sharma, Rajesh Raju, Shyam Mohan Palapetta, T. S. Keshava Prasad, Tai-Chung Huang, Akinori Yoda, Jeffrey W. Tyner, Diederik van Bodegom, David M. Weinstock, Steven F. Ziegler, Akhilesh Pandey:
TSLP signaling pathway map: a platform for analysis of TSLP-mediated signaling. - Paulo R. Pagliosa, João G. Doria, Dairana Misturini, Mariana B. P. Otegui, Mariana S. Oortman, Wilson A. Weis, Larisse Faroni-Perez, Alexandre P. Alves, Mauricio G. Camargo, A. Cecília Z. Amaral, Antonio C. Marques, Paulo C. Lana:
NONATObase: a database for Polychaeta (Annelida) from the Southwestern Atlantic Ocean. - Antonio Jimeno-Yepes, Karin Verspoor:
Literature mining of genetic variants for curation: quantifying the importance of supplementary material. - Justen Manasa, Richard Lessells, Theresa Rossouw, Kevindra Naidu, Cloete Van Vuuren, Dominique Goedhals, Gert van Zyl, Armand Bester, Andrew Skingsley, Katharine Stott, Siva Danaviah, Terusha Chetty, Lavanya Singh, Pravi Moodley, Collins Iwuji, Nuala McGrath, Christopher J. Seebregts, Tulio de Oliveira:
Southern African Treatment Resistance Network (SATuRN) RegaDB HIV drug resistance and clinical management database: supporting patient management, surveillance and research in southern Africa. - Michele Tinti, Fábio Madeira, Gavuthami Murugesan, Gerta Hoxhaj, Rachel Toth, Carol MacKintosh:
ANIA: ANnotation and Integrated Analysis of the 14-3-3 interactome. - Yu Jiang, Can Lin, Weiyi Meng, Clement T. Yu, Aaron M. Cohen, Neil R. Smalheiser:
Rule-based deduplication of article records from bibliographic databases. - Kandarp Rakeshkumar Joshi, Heena Dhiman, Vinod Scaria:
tbvar: a comprehensive genome variation resource for Mycobacterium tuberculosis. - Hongbo Liu, Rangfei Zhu, Jie Lv, Hongjuan He, Lin Yang, Zhijun Huang, Jianzhong Su, Yan Zhang, Shihuan Yu, Qiong Wu:
DevMouse, the mouse developmental methylome database and analysis tools.
- Noa Godin, Jerry Eichler:
aglgenes, a curated and searchable database of archaeal N-glycosylation pathway components. - Praveen Anand, Deepesh Nagarajan, Sumanta Mukherjee, Nagasuma R. Chandra:
PLIC: protein-ligand interaction clusters. - Julio C. Bolívar, Fabian Machens, Yuri Brill, Artyom Romanov, Lorenz Bülow, Reinhard Hehl:
'In silico expression analysis', a novel PathoPlant web tool to identify abiotic and biotic stress conditions associated with specific cis-regulatory sequences. - Avnika A. Ruparelia, Johanna E. Simkin, David Salgado, Donald F. Newgreen, Gabriel G. Martins, Robert J. Bryson-Richardson:
The quail anatomy portal. - Julia Feichtinger, Ramsay J. McFarlane, Lee D. Larcombe:
CancerEST: a web-based tool for automatic meta-analysis of public EST data. - Guanglan Zhang, Angelika Riemer, Derin B. Keskin, Lou Chitkushev, Ellis L. Reinherz, Vladimir Brusic:
HPVdb: a data mining system for knowledge discovery in human papillomavirus with applications in T cell immunology and vaccinology. - Cao Nguyen, Abdul Baten, Grant Morahan:
Comparison of sequence variants in transcriptomic control regions across 17 mouse genomes. - Yungang Xu, Maozu Guo, Xiaoyan Liu, Chun-yu Wang, Yang Liu:
SoyFN: a knowledge database of soybean functional networks. - Valentine Rech de Laval, Gilbert Deléage, Abdel Aouacheria, Christophe Combet:
BCL2DB: database of BCL-2 family members and BH3-only proteins. - Meghna Singh, Deeksha Bhartiya, Jayant Maini, Meenakshi Sharma, Angom Ramcharan Singh, Subburaj Kadarkaraisamy, Rajiv Rana, Ankit Sabharwal, Srishti Nanda, Aravindhakshan Ramachandran, Ashish Mittal, Shruti Kapoor, Paras Sehgal, Zainab Asad, Kriti Kaushik, Shamsudheen Karuthedath Vellarikkal, Divya Jagga, Muthulakshmi Muthuswami, Rajendra K. Chauhan, Elvin Leonard, Ruby Priyadarshini, Mahantappa Halimani, Sunny Malhotra, Ashok Patowary, Harinder Vishwakarma, Prateek Rakeshkumar Joshi, Vivek Bhardwaj, Arijit Bhaumik, Bharat Bhatt, Aamod Jha, Aalok Kumar, Prerna Budakoti, Mukesh Kumar Lalwani, Rajeshwari Meli, Saakshi Jalali, Kandarp Joshi, Koustav Pal, Heena Dhiman, Saurabh V. Laddha, Vaibhav Jadhav, Naresh Singh, Vikas Pandey, Chetana Sachidanandan, Stephen C. Ekker, Eric W. Klee, Vinod Scaria, Sridhar Sivasubbu:
The Zebrafish GenomeWiki: a crowdsourcing approach to connect the long tail for zebrafish gene annotation. - Hamed Heydari, Naresh V. R. Mutha, Mahafizul Imran Mahmud, Cheuk C. Siow, Wei Yee Wee, Guat Jah Wong, Amir Hessam Yazdi, Mia Yang Ang, Siew Woh Choo:
StaphyloBase: a specialized genomic resource for the staphylococcal research community. - Weiqi Tang, Liying Yu, Weiyi He, Guang Yang, Fushi Ke, Simon W. Baxter, Shijun You, Carl J. Douglas, Minsheng You:
DBM-DB: the diamondback moth genome database.
- Kai-Yao Huang, Hsin-Yi Wu, Yi-Ju Chen, Cheng-Tsung Lu, Min-Gang Su, Yun-Chung Hsieh, Chih-Ming Tsai, Kuo-I Lin, Hsien-Da Huang, Tzong-Yi Lee, Yu-Ju Chen:
RegPhos 2.0: an updated resource to explore protein kinase-substrate phosphorylation networks in mammals. - Jing Li, Jia Jia, Hong Li, Jian Yu, Han Sun, Ying He, Daqing Lv, Xiaojuan Yang, Michael O. Glocker, Liang-Xiao Ma, Jiabei Yang, Ling Li, Wei Li, Guoqing Zhang, Qian Liu, Yixue Li, Lu Xie:
SysPTM 2.0: an updated systematic resource for post-translational modification. - Agnel Praveen Joseph, Prashant Shingate, Atul Kumar Upadhyay, Ramanathan Sowdhamini:
3PFDB+: improved search protocol and update for the identification of representatives of protein sequence domain families. - Omer An, Vera Pendino, Matteo D'Antonio, Emanuele Ratti, Marco Gentilini, Francesca D. Ciccarelli:
NCG 4.0: the network of cancer genes in the era of massive mutational screenings of cancer genomes. - John Christian Gaby, Daniel H. Buckley:
A comprehensive aligned nifH gene database: a multipurpose tool for studies of nitrogen-fixing bacteria. - Stephan Pabinger, René Snajder, Timo Hardiman, Michaela Willi, Andreas Dander, Zlatko Trajanoski:
MEMOSys 2.0: an update of the bioinformatics database for genome-scale models and genomic data. - Suresh B. Mudunuri, Sujan Patnana, Hampapathalu A. Nagarajaram:
MICdb3.0: a comprehensive resource of microsatellite repeats from prokaryotic genomes.
- Cecilia N. Arighi, Cathy H. Wu, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Alfonso Valencia, Zhiyong Lu, W. John Wilbur, Thomas C. Wiegers:
BioCreative-IV virtual issue.
- Han Cheng, Wankun Deng, Yongbo Wang, Jian Ren, Zexian Liu, Yu Xue:
dbPPT: a comprehensive database of protein phosphorylation in plants. - Sangita Kumari, Sachin Pundhir, Piyush Priya, Ganga Jeena, Ankita Punetha, Konika Chawla, Zohra Firdos Jafaree, Subhasish Mondal, Gitanjali Yadav:
EssOilDB: a database of essential oils reflecting terpene composition and variability in the plant kingdom. - Ruchika Sahajpal, Gaurav Kandoi, Heena Dhiman, Sweety Raj, Vinod Scaria, Deeksha Bhartiya, Yasha Hasija:
HGV&TB: a comprehensive online resource on human genes and genetic variants associated with tuberculosis. - Yi Wang, Roger Thilmony, Yunjun Zhao, Guoping Chen, Yong Qiang Gu:
AIM: a comprehensive Arabidopsis interactome module database and related interologs in plants. - Abhishikha Srivastava, Neelja Singhal, Manisha Goel, Jugsharan Singh Virdi, Manish Kumar:
CBMAR: a comprehensive β-lactamase molecular annotation resource. - Márcia Duarte, Ruy Jáuregui, Ramiro Vilchez-Vargas, Howard Junca, Dietmar H. Pieper:
AromaDeg, a novel database for phylogenomics of aerobic bacterial degradation of aromatics. - Naveen Sharma, Mohammad Samir Farooqi, Krishna Kumar Chaturvedi, Shashi Bhushan Lal, Monendra Grover, Anil Rai, Pankaj Pandey:
The Halophile Protein Database. - Sanchayita Sen, Jasmine Young, John M. Berrisford, Minyu Chen, Matthew J. Conroy, Shuchismita Dutta, Luigi Di Costanzo, Guanghua Gao, Sutapa Ghosh, Brian P. Hudson, Reiko Igarashi, Yumiko Kengaku, Yuhe Liang, Ezra Peisach, Irina Persikova, Abhik Mukhopadhyay, Buvaneswari Coimbatore Narayanan, Gaurav Sahni, Junko Sato, Monica Sekharan, Chenghua Shao, Lihua Tan, Marina Zhuravleva:
Small molecule annotation for the Protein Data Bank. - Yanpeng Li, Hong Yu:
A robust data-driven approach for gene ontology annotation. - Peng Zhang, Xiaohui Si, Geir Skogerbø, Jiajia Wang, Dongya Cui, Yongxing Li, Xubin Sun, Li Liu, Baofa Sun, Runsheng Chen, Shunmin He, Da-Wei Huang:
piRBase: a web resource assisting piRNA functional study. - Jennifer D'Souza, Vincent Ng:
Knowledge-rich temporal relation identification and classification in clinical notes. - Aditi Kapil, Piyush Kant Rai, Asheesh Shanker:
ChloroSSRdb: a repository of perfect and imperfect chloroplastic simple sequence repeats (cpSSRs) of green plants. - Abid Qureshi, Nishant Thakur, Isha Monga, Anamika Thakur, Manoj Kumar:
VIRmiRNA: a comprehensive resource for experimentally validated viral miRNAs and their targets. - Romain Chebrek, Sylvain Léonard, Alexandre G. de Brevern, Jean-Christophe Gelly:
PolyprOnline: polyproline helix II and secondary structure assignment database. - Emmanouil Athanasiadis, Kyriaki Antonopoulou, Foteini Chatzinasiou, Christina M. Lill, Marilena M. Bourdakou, Argiris Sakellariou, Katerina Kypreou, Irene Stefanaki, Evangelos Evangelou, John P. A. Ioannidis, Lars Bertram, Alexander J. Stratigos, George M. Spyrou:
A Web-based database of genetic association studies in cutaneous melanoma enhanced with network-driven data exploration tools. - Julien Rey, Patrick Deschavanne, Pierre Tufféry:
BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes. - Salim Bougouffa, Aleksandar Radovanovic, Magbubah Essack, Vladimir B. Bajic:
DEOP: a database on osmoprotectants and associated pathways. - Gregory Vey, Trevor C. Charles:
MetaProx: the database of metagenomic proximons. - Adam Ameur, Ignas Bunikis, Stefan Enroth, Ulf Gyllensten:
CanvasDB: a local database infrastructure for analysis of targeted- and whole genome re-sequencing projects. - Zhi-Sheng Xu, Hua-Wei Tan, Feng Wang, Xi-Lin Hou, Ai-Sheng Xiong:
CarrotDB: a genomic and transcriptomic database for carrot. - Christopher Wilks, Melissa S. Cline, Erich Weiler, Mark Diekhans, Brian Craft, Christy Martin, Daniel Murphy, Howdy Pierce, John Black, Donavan Nelson, Brian Litzinger, Thomas Hatton, Lori Maltbie, Michael Ainsworth, Patrick Allen, Linda Rosewood, Elizabeth Mitchell, Bradley Smith, Jim Warner, John Groboske, Haifang Telc, Daniel Wilson, Brian Sanford, Hannes Schmidt, David Haussler, Daniel Maltbie:
The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. - Abdullah Ercument Cicek, Xinjian Qi, Ali Cakmak, Stephen R. Johnson, Xu Han, Sami Alshalwi, Zehra Meral Özsoyoglu, Gultekin Özsoyoglu:
An online system for metabolic network analysis. - Qingzhou Zhang, Bo Yang, Xujiao Chen, Jing Xu, Changlin Mei, Zhiguo Mao:
Renal Gene Expression Database (RGED): a relational database of gene expression profiles in kidney disease. - John D. Burger, Emily Doughty, Ritu Khare, Chih-Hsuan Wei, Rajashree Mishra, John S. Aberdeen, David Tresner-Kirsch, Ben Wellner, Maricel G. Kann, Zhiyong Lu, Lynette Hirschman:
Hybrid curation of gene-mutation relations combining automated extraction and crowdsourcing. - Ruijie Zhang, Meiwei Luan, Zhenwei Shang, Lian Duan, Guoping Tang, Miao Shi, Wenhua Lv, Hongjie Zhu, Jin Li, Hongchao Lv, Mingming Zhang, Guiyou Liu, He Chen, Yongshuai Jiang:
RADB: a database of rheumatoid arthritis-related polymorphisms. - Mengyuan Fan, Hong Sang Low, Markus R. Wenk, Limsoon Wong:
A semi-automated methodology for finding lipid-related GO terms. - Ehsan Emadzadeh, Azadeh Nikfarjam, Rachel E. Ginn, Graciela Gonzalez-Hernandez:
Unsupervised gene function extraction using semantic vectors. - Julien Gobeill, Emilie Pasche, Dina Vishnyakova, Patrick Ruch:
Closing the loop: from paper to protein annotation using supervised Gene Ontology classification. - Dongqing Zhu, Dingcheng Li, Ben Carterette, Hongfang Liu:
Integrating information retrieval with distant supervision for Gene Ontology annotation. - Hong-Jie Dai, Johnny Chi-Yang Wu, Josan Wei-San Lin, Aaron James F. Reyes, Mira Anne C. dela Rosa, Syed Abdul Shabbir, Richard Tzong-Han Tsai, Wen-Lian Hsu:
LiverCancerMarkerRIF: a liver cancer biomarker interactive curation system combining text mining and expert annotations. - Yuqing Mao, Kimberly Van Auken, Donghui Li, Cecilia N. Arighi, Peter McQuilton, G. Thomas Hayman, Susan Tweedie, Mary L. Schaeffer, Stanley J. F. Laulederkind, Shur-Jen Wang, Julien Gobeill, Patrick Ruch, Anh Tuan Luu, Jung-Jae Kim, Jung-Hsien Chiang, Yu-De Chen, Chia-Jung Yang, Hongfang Liu, Dongqing Zhu, Yanpeng Li, Hong Yu, Ehsan Emadzadeh, Graciela Gonzalez, Jian-Ming Chen, Hong-Jie Dai, Zhiyong Lu:
Overview of the gene ontology task at BioCreative IV. - Gert Van Peer, Steve Lefever, Jasper Anckaert, Anneleen Beckers, Ali Rihani, Alan Van Goethem, Pieter-Jan Volders, Fjoralba Zeka, Maté Ongenaert, Pieter Mestdagh, Jo Vandesompele:
miRBase Tracker: keeping track of microRNA annotation changes. - Mia Yang Ang, Hamed Heydari, Nick S. Jakubovics, Mahafizul Imran Mahmud, Avirup Dutta, Wei Yee Wee, Guat Jah Wong, Naresh V. R. Mutha, Shi Yang Tan, Siew Woh Choo:
FusoBase: an online Fusobacterium comparative genomic analysis platform. - Michaela Matthes, Martin Preusse, Jingzhong Zhang, Julia Schechter, Daniela Mayer, Bernd Lentes, Fabian J. Theis, Nilima Prakash, Wolfgang Wurst, Dietrich Trümbach:
Mouse IDGenes: a reference database for genetic interactions in the developing mouse brain. - Manas Ranjan Dikhit, Kanhu Charan Moharana, Bikash R. Sahoo, Ganesh Chandra Sahoo, Pradeep Das:
LeishMicrosatDB: open source database of repeat sequences detected in six fully sequenced Leishmania genomes. - Manabu Torii, Gang Li, Zhiwen Li, Rose Oughtred, Francesca Diella, Irem Çelen, Cecilia N. Arighi, Hongzhan Huang, K. Vijay-Shanker, Cathy H. Wu:
RLIMS-P: an online text-mining tool for literature-based extraction of protein phosphorylation information. - Kimberly Van Auken, Mary L. Schaeffer, Peter McQuilton, Stanley J. F. Laulederkind, Donghui Li, Shur-Jen Wang, G. Thomas Hayman, Susan Tweedie, Cecilia N. Arighi, James Done, Hans-Michael Müller, Paul W. Sternberg, Yuqing Mao, Chih-Hsuan Wei, Zhiyong Lu:
BC4GO: a full-text corpus for the BioCreative IV GO task. - Ritu Khare, Chih-Hsuan Wei, Yuqing Mao, Robert Leaman, Zhiyong Lu:
tmBioC: improving interoperability of text-mining tools with BioC. - Sören Müller, Lukas Rycak, Fabian Afonso-Grunz, Peter Winter, Adam M. Zawada, Ewa Damrath, Jessica Scheider, Juliane Schmäh, Ina Koch, Günter Kahl, Björn Rotter:
APADB: a database for alternative polyadenylation and microRNA regulation events. - Marcus C. Chibucos, Christopher J. Mungall, Rama Balakrishnan, Karen R. Christie, Rachael P. Huntley, Owen White, Judith A. Blake, Suzanna E. Lewis, Michelle G. Giglio:
Standardized description of scientific evidence using the Evidence Ontology (ECO). - Dongseop Kwon, Sun Kim, Soo-Yong Shin, Andrew Chatr-aryamontri, W. John Wilbur:
Assisting manual literature curation for protein-protein interactions using BioQRator. - Rafal Rak, Riza Theresa Batista-Navarro, Andrew Rowley, Jacob Carter, Sophia Ananiadou:
Text-mining-assisted biocuration workflows in Argo. - Baoshan Ma, Jinyan Huang, Liming Liang:
RTeQTL: Real-Time Online Engine for Expression Quantitative Trait Loci Analyses. - Vincent J. Henry, Anita E. Bandrowski, Anne-Sophie Pepin, Bruno J. Gonzalez, Arnaud Desfeux:
OMICtools: an informative directory for multi-omic data analysis. - Kwanjeera Wanichthanarak, Intawat Nookaew, Dina Petranovic:
yStreX: yeast stress expression database. - Rafal Rak, Riza Theresa Batista-Navarro, Jacob Carter, Andrew Rowley, Sophia Ananiadou:
Processing biological literature with customizable Web services supporting interoperable formats. - Donald C. Comeau, Riza Theresa Batista-Navarro, Hong-Jie Dai, Rezarta Islamaj Dogan, Antonio Jimeno-Yepes, Ritu Khare, Zhiyong Lu, Hernani Marques, Carolyn J. Mattingly, Mariana L. Neves, Yifan Peng, Rafal Rak, Fabio Rinaldi, Richard Tzong-Han Tsai, Karin Verspoor, Thomas C. Wiegers, Cathy H. Wu, W. John Wilbur:
BioC interoperability track overview. - Conrad L. Schoch, Barbara Robbertse, Vincent Robert, Duong Vu, Gianluigi Cardinali, Laszlo Irinyi, Wieland Meyer, R. Henrik Nilsson, Karen Hughes, Andrew N. Miller, Paul M. Kirk, Kessy Abarenkov, M. Catherine Aime, Hiran A. Ariyawansa, Martin Bidartondo, Teun Boekhout, Bart Buyck, Qing Cai, Jie Chen, Ana Crespo, Pedro W. Crous, Ulrike Damm, Z. Wilhelm De Beer, Bryn T. M. Dentinger, Pradeep K. Divakar, Margarita Dueñas, Nicolas Feau, Katerina Fliegerova, Miguel A. García, Zai-Wei Ge, Gareth W. Griffith, Johannes Z. Groenewald, Marizeth Groenewald, Martin Grube, Marieka Gryzenhout, Cécile Gueidan, Liangdong Guo, Sarah Hambleton, Richard C. Hamelin, Karen Hansen, Valérie Hofstetter, Seung-Beom Hong, Jos Houbraken, Kevin D. Hyde, Patrik Inderbitzin, Peter R. Johnston, Samantha C. Karunarathna, Urmas Kõljalg, Gábor M. Kovács, Ekaphan Kraichak, Krisztina Krizsan, Cletus P. Kurtzman, Karl-Henrik Larsson, Steven Leavitt, Peter M. Letcher, Kare Liimatainen, Jian-Kui Liu, D. Jean Lodge, Janet Jennifer Luangsa-ard, H. Thorsten Lumbsch, Sajeewa S. N. Maharachchikumbura, Dimuthu Manamgoda, María P. Martín, Andrew M. Minnis, Jean-Marc Moncalvo, Giuseppina Mulè, Karen K. Nakasone, Tuula Niskanen, Ibai Olariaga, Tamás Papp, Tamás Petkovits, Raquel Pino-Bodas, Martha J. Powell, Huzefa A. Raja, Dirk Redecker, J. M. Sarmiento-Ramirez, Keith A. Seifert, Bhushan Shrestha, Soili Stenroos, Benjamin Stielow, Sung-Oui Suh, Kazuaki Tanaka, Leho Tedersoo, M. Teresa Telleria, Dhanushka Udayanga, Wendy A. Untereiner, Javier Diéguez Uribeondo, Krishna V. Subbarao, Csaba Vágvölgyi, Cobus M. Visagie, Kerstin Voigt, Donald M. Walker, Bevan S. Weir, Michael Weiß, Nalin N. Wijayawardene, Michael J. Wingfield, J. P. Xu, Zhu L. Yang, Ning Zhang, Wen-Ying Zhuang, Scott Federhen:
Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi. - Wanli Liu, Rezarta Islamaj Dogan, Dongseop Kwon, Hernani Marques, Fabio Rinaldi, W. John Wilbur, Donald C. Comeau:
BioC implementations in Go, Perl, Python and Ruby. - Steven Jupe, Bijay Jassal, Mark Williams, Guanming Wu:
A controlled vocabulary for pathway entities and events. - Shunping Huang, James Holt, Chia-Yu Kao, Leonard McMillan, Wei Wang:
A novel multi-alignment pipeline for high-throughput sequencing data. - Donald C. Comeau, Haibin Liu, Rezarta Islamaj Dogan, W. John Wilbur:
Natural language processing pipelines to annotate BioC collections with an application to the NCBI disease corpus. - Ingrid M. Keseler, Marek S. Skrzypek, Deepika Weerasinghe, Albert Y. Chen, Carol A. Fulcher, Gene-Wei Li, Kimberly C. Lemmer, Katherine M. Mladinich, Edmond D. Chow, Gavin Sherlock, Peter D. Karp:
Curation accuracy of model organism databases. - Wen Wei, Yuan-Nong Ye, Sen Luo, Yan-Yan Deng, Dan Lin, Feng-Biao Guo:
IFIM: a database of integrated fitness information for microbial genes. - Thomas C. Wiegers, Allan Peter Davis, Carolyn J. Mattingly:
Web services-based text-mining demonstrates broad impacts for interoperability and process simplification. - Rezarta Islamaj Dogan, Donald C. Comeau, Lana Yeganova, W. John Wilbur:
Finding abbreviations in biomedical literature: three BioC-compatible modules and four BioC-formatted corpora. - Yitzhak Friedman, Solange Karsenty, Michal Linial:
miRror-Suite: decoding coordinated regulation by microRNAs. - Socorro Gama-Castro, Fabio Rinaldi, Alejandra López-Fuentes, Yalbi Itzel Balderas-Martínez, Simon Clematide, Tilia Renate Ellendorff, Alberto Santos-Zavaleta, Hernani Marques-Madeira, Julio Collado-Vides:
Assisted curation of regulatory interactions and growth conditions of OxyR in E. coli K-12. - Maria Taboada, Hadriana Rodríguez, Diego Martínez Hernández, María Pardo, María Jesús Sobrido:
Automated semantic annotation of rare disease cases: a case study.
- Franco L. Simonetti, Cristian Tornador, Nuria Nabau-Moretó, Miguel A. Molina-Vila, Cristina Marino Buslje:
Kin-Driver: a database of driver mutations in protein kinases. - Zan Zhang, Chuanlin Yin, Ying Liu, Wencai Jie, Wenjie Lei, Fei Li:
iPathCons and iPathDB: an improved insect pathway construction tool and the database. - Ludwig Christian G. Hinske, Gustavo S. França, Hugo A. M. Torres, Daniel T. Ohara, Camila Miranda Lopes-Ramos, Jens Heyn, Luiz F. L. Reis, Lucila Ohno-Machado, Simone Kreth, Pedro A. F. Galante:
miRIAD - integrating microRNA inter- and intragenic data. - Jonathan R. Karr, Nolan C. Phillips, Markus W. Covert:
WholeCellSimDB: a hybrid relational/HDF database for whole-cell model predictions. - Zeeshan Ahmed, Saman Zeeshan, Claudia Huber, Michael Hensel, Dietmar Schomburg, Richard Münch, Eva Eylert, Wolfgang Eisenreich, Thomas Dandekar:
'Isotopo' a database application for facile analysis and management of mass isotopomer data. - Alexander Ekstrom, Rahil Taujale, Nathan McGinn, Yanbin Yin:
PlantCAZyme: a database for plant carbohydrate-active enzymes. - Chuanlin Yin, Ying Liu, Jinding Liu, Huamei Xiao, Shuiqing Huang, Yongjun Lin, Zhaojun Han, Fei Li:
ChiloDB: a genomic and transcriptome database for an important rice insect pest Chilo suppressalis. - Xia Ran, Wei-Jun Cai, Xiu-Feng Huang, Qi Liu, Fan Lu, Jia Qu, Jinyu Wu, Zi-Bing Jin:
'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration. - Chun-Wei Tung, Ying-Chi Lin, Hsun-Shuo Chang, Chia-Chi Wang, Ih-Sheng Chen, Jhao-Liang Jheng, Jih-Heng Li:
TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants. - Divya Mehta, Priya Anand, Vineet Kumar, Anshika Joshi, Deepika Mathur, Sandeep Singh, Abhishek Tuknait, Kumardeep Chaudhary, Shailendra K. Gautam, Ankur Gautam, Grish C. Varshney, Gajendra P. S. Raghava:
ParaPep: a web resource for experimentally validated antiparasitic peptide sequences and their structures. - Tian Li, Xiwu Qi, Qiwei Zeng, Zhonghuai Xiang, Ningjia He:
MorusDB: a resource for mulberry genomics and genome biology. - David Campos, Jóni Lourenço, Sérgio Matos, José Luís Oliveira:
Egas: a collaborative and interactive document curation platform.
- Yanbin Liu, Qiang Wei, Guisheng Yu, Wanxia Gai, Yongquan Li, Xin Chen:
DCDB 2.0: a major update of the drug combination database. - Jittima Piriyapongsa, Chaiwat Bootchai, Chumpol Ngamphiw, Sissades Tongsima:
microPIR2: a comprehensive database for human-mouse comparative study of microRNA-promoter interactions. - Kamran Karimi, Peter D. Vize:
The Virtual Xenbase: transitioning an online bioinformatics resource to a private cloud. - Sònia Garcia, Francisco Gálvez, Airy Gras, Ales Kovarík, Teresa Garnatje:
Plant rDNA database: update and new features. - Vincenzo Lomonaco, Riccardo Martoglia, Federica Mandreoli, Laura Anderlucci, Warren Emmett, Silvio Bicciato, Cristian Taccioli:
UCbase 2.0: ultraconserved sequences database (2014 update).
- Xia Ran, Wei-Jun Cai, Xiu-Feng Huang, Qi Liu, Fan Lu, Jia Qu, Jinyu Wu, Zi-Bing Jin:
'RetinoGenetics': a comprehensive mutation database for genes related to inherited retinal degeneration.
- Julien Rey, Patrick Deschavanne, Pierre Tufféry:
BactPepDB: a database of predicted peptides from a exhaustive survey of complete prokaryote genomes.
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