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ORCIDDatabase - The Journal of Biological Databases and Curation, Volume 2012
Volume 2012, 2012
- Allan Peter Davis, Robin J. Johnson, Kelley Lennon-Hopkins, Daniela Sciaky
, Michael C. Rosenstein, Thomas C. Wiegers, Carolyn J. Mattingly:
Targeted journal curation as a method to improve data currency at the Comparative Toxicogenomics Database. - Donghui Li, Tanya Z. Berardini, Robert J. Muller, Eva Huala:
Building an efficient curation workflow for the Arabidopsis literature corpus. - Dina Vishnyakova, Emilie Pasche, Patrick Ruch:
Using binary classification to prioritize and curate articles for the Comparative Toxicogenomics Database. - Catalina O. Tudor, Cecilia N. Arighi, Qinghua Wang, Cathy H. Wu, K. Vijay-Shanker:
The eFIP system for text mining of protein interaction networks of phosphorylated proteins. - Harold J. Drabkin, Judith A. Blake:
Manual Gene Ontology annotation workflow at the Mouse Genome Informatics Database. - Thomas C. Wiegers, Allan Peter Davis, Carolyn J. Mattingly:
Collaborative biocuration - text-mining development task for document prioritization for curation. - Lakshmi R. Pillai, Philippe Chouvarine, Catalina O. Tudor, Carl J. Schmidt, K. Vijay-Shanker, Fiona M. McCarthy:
Developing a biocuration workflow for AgBase, a non-model organism database. - Peter McQuilton:
Opportunities for text mining in the FlyBase genetic literature curation workflow. - Kimberly Van Auken, Petra Fey, Tanya Z. Berardini, Robert J. Dodson, Laurel Cooper, Donghui Li, Juancarlos Chan, Yuling Li, Siddhartha Basu, Hans-Michael Müller, Rex L. Chisholm, Eva Huala, Paul W. Sternberg:
Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. - Chih-Hsuan Wei, Bethany R. Harris, Donghui Li, Tanya Z. Berardini, Eva Huala, Hung-Yu Kao, Zhiyong Lu:
Accelerating literature curation with text-mining tools: a case study of using PubTator to curate genes in PubMed abstracts. - Sun Kim, Won Kim, Chih-Hsuan Wei, Zhiyong Lu, W. John Wilbur:
Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information. - Zhiyong Lu, Lynette Hirschman:
Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II. - Margarida Julià-Sapé, Miguel Lurgi, Mariola Mier, Francesc Estanyol, Xavier Rafael Palou, Ana-Paula Candiota, Anna Barceló, Alina García, M. Carmen Martínez-Bisbal, Rubén Ferrer-Luna, Àngel Moreno-Torres, Bernardo Celda, Carles Arús:
Strategies for annotation and curation of translational databases: the eTUMOUR project. - Pascale Gaudet, Cecilia N. Arighi, Frederic B. Bastian, Alex Bateman, Judith A. Blake, J. Michael Cherry, Peter D'Eustachio, Robert D. Finn, Michelle G. Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica C. Munoz-Torres, Darren A. Natale, Claire O'Donovan, B. F. Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul N. Schofield, Granger G. Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy H. Wu, Jasmine Young, Raja Mazumder:
Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference. - Tao Lu, Bo Yao, Chi Zhang:
DFVF: database of fungal virulence factors. - Georgios V. Gkoutos, Paul N. Schofield, Robert Hoehndorf:
The Units Ontology: a tool for integrating units of measurement in science. - Tanya Z. Berardini, Donghui Li, Robert J. Muller, Raymond Chetty, Larry Ploetz, Shanker Singh, April Wensel, Eva Huala:
Assessment of community-submitted ontology annotations from a novel database-journal partnership. - Christina Chandras, Michael Zouberakis, Ekaterina Salimova, Damian Smedley, Nadia A. Rosenthal, Vassilis Aidinis:
CreZOO - the European virtual repository of Cre and other targeted conditional driver strains. - Andreas Braun, Bettina Halwachs, Martina Geier, Katrin Weinhandl, Michael Guggemos, Jan Marienhagen, Anna Joëlle Ruff, Ulrich Schwaneberg, Vincent Rabin, Daniel E. Torres Pazmiño, Gerhard G. Thallinger, Anton Glieder:
MuteinDB: the mutein database linking substrates, products and enzymatic reactions directly with genetic variants of enzymes. - Aurélie Névéol, W. John Wilbur, Zhiyong Lu:
Improving links between literature and biological data with text mining: a case study with GEO, PDB and MEDLINE. - Stephanie M. Bunt, Gary Grumbling, Helen I. Field, Steven J. Marygold, Nicholas H. Brown, Gillian H. Millburn:
Directly e-mailing authors of newly published papers encourages community curation. - Daniel G. Jamieson, Martin Gerner, Farzaneh Sarafraz, Goran Nenadic, David L. Robertson:
Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database. - Fabio Rinaldi, Simon Clematide, Yael Garten, Michelle Whirl Carrillo, Li Gong, Joan M. Hebert, Katrin Sangkuhl, Caroline F. Thorn, Teri E. Klein, Russ B. Altman:
Using ODIN for a PharmGKB revalidation experiment. - Lynette Hirschman, Gully A. P. C. Burns, Martin Krallinger, Cecilia N. Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-aryamontri, Karen G. Dowell, Eva Huala, Anália Lourenço, Robert S. Nash, Anne-Lise Veuthey, Thomas C. Wiegers, Andrew G. Winter:
Text mining for the biocuration workflow. - Teresa K. Attwood, Alain Coletta, Gareth Muirhead, Athanasia Pavlopoulou, Peter B. Philippou, Ivan Popov, Carlos Romá-Mateo, Athina Theodosiou, Alex L. Mitchell:
The PRINTS database: a fine-grained protein sequence annotation and analysis resource - its status in 2012. - Ambarish Nag, Tatiana V. Karpinets, Christopher H. Chang, Maor Bar-Peled:
Enhancing a Pathway-Genome Database (PGDB) to capture subcellular localization of metabolites and enzymes: the nucleotide-sugar biosynthetic pathways of Populus trichocarpa. - Martin Krallinger, Florian Leitner, Miguel Vazquez, David Salgado, Christophe Marcelle, Mike Tyers, Alfonso Valencia, Andrew Chatr-aryamontri:
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience. - William Spooner, Ken Youens-Clark, Daniel M. Staines, Doreen Ware:
GrameneMart: the BioMart data portal for the Gramene project. - Sudheer Tumu, Ashish Patil, William Towns, Madhu Dyavaiah, Thomas J. Begley:
The gene-specific codon counting database: a genome-based catalog of one-, two-, three-, four- and five-codon combinations present in Saccharomyces cerevisiae genes. - Alper Uzun, Alyse Laliberte, Jeremy Parker, Caroline Andrew, Emily Winterrowd, Surendra Sharma, Sorin Istrail, James Padbury:
dbPTB: a database for preterm birth. - Sarah W. Burge, Elizabeth Kelly, David Lonsdale, Prudence Mutowo-Meullenet, Craig McAnulla, Alex L. Mitchell, Amaia Sangrador-Vegas, Siew-Yit Yong, Nicola J. Mulder, Sarah Hunter:
Manual GO annotation of predictive protein signatures: the InterPro approach to GO curation. - Kevin L. Childs, Kranti Konganti, C. Robin Buell:
The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species. - Adam Frankish, Jonathan M. Mudge, Mark Thomas, Jennifer L. Harrow:
The importance of identifying alternative splicing in vertebrate genome annotation. - Stanley J. F. Laulederkind, Marek Tutaj, Mary Shimoyama, G. Thomas Hayman, Timothy Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Jeff de Pons, Melinda R. Dwinell, Howard J. Jacob:
Ontology searching and browsing at the Rat Genome Database. - Qinghua Wang, Cecilia N. Arighi, Benjamin L. King, Shawn W. Polson, James Vincent, Chuming Chen, Hongzhan Huang, Brewster F. Kingham, Shallee T. Page, Marc Farnum Rendino, William Kelley Thomas, Daniel W. Udwary, Cathy H. Wu:
Community annotation and bioinformatics workforce development in concert - Little Skate Genome Annotation Workshops and Jamborees. - Myra K. Derbyshire, Christopher J. Lanczycki, Stephen H. Bryant, Aron Marchler-Bauer:
Annotation of functional sites with the Conserved Domain Database. - Anita E. Bandrowski, Jonathan Cachat, Yuling Li, Hans-Michael Müller, Paul W. Sternberg, Paolo Ciccarese, Tim Clark, Luis N. Marenco, Rixin Wang, Vadim Astakhov, Jeffrey S. Grethe, Maryann E. Martone:
A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework. - Attila Csordas, David Ovelleiro, Rui Wang, Joseph M. Foster, Daniel Rios, Juan Antonio Vizcaíno, Henning Hermjakob:
PRIDE: Quality control in a proteomics data repository. - Rama Balakrishnan, Julie Park, Kalpana Karra, Benjamin C. Hitz, Gail Binkley, Eurie L. Hong, Julie M. Sullivan, Gos Micklem, J. Michael Cherry:
YeastMine - an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit. - Rafal Rak, Andrew Rowley, William J. Black, Sophia Ananiadou:
Argo: an integrative, interactive, text mining-based workbench supporting curation. - Nicholas A. Stover, Ravinder S. Punia, Michael S. Bowen, Steven B. Dolins, Theodore G. Clark:
Tetrahymena genome database Wiki: a community-maintained model organism database. - Julie Park, Maria C. Costanzo, Rama Balakrishnan, J. Michael Cherry, Eurie L. Hong:
CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations. - Benjamin M. Good, Erik L. Clarke, Salvatore Loguercio, Andrew I. Su:
Building a biomedical semantic network in Wikipedia with Semantic Wiki Links. - Susan M. Bello, Joel E. Richardson, Allan Peter Davis, Thomas C. Wiegers, Carolyn J. Mattingly, Mary E. Dolan, Cynthia L. Smith, Judith A. Blake, Janan T. Eppig:
Disease model curation improvements at Mouse Genome Informatics. - Jane E. Loveland, James G. R. Gilbert, Ed Griffiths, Jennifer L. Harrow:
Community gene annotation in practice. - Rachel A. Harte, Catherine M. Farrell, Jane E. Loveland, Marie-Marthe Suner, Laurens G. Wilming, Bronwen L. Aken, Daniel Barrell, Adam Frankish, Craig Wallin, Steve Searle, Mark Diekhans, Jennifer L. Harrow, Kim D. Pruitt:
Tracking and coordinating an international curation effort for the CCDS Project. - Jose Cruz-Toledo, Maureen McKeague, Xueru Zhang, Amanda Giamberardino, Erin McConnell, Tariq Francis, Maria C. DeRosa, Michel Dumontier:
Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments. - Terry F. Hayamizu, Sherri de Coronado, Gilberto Fragoso, Nicholas Sioutos, James A. Kadin, Martin Ringwald:
The mouse-human anatomy ontology mapping project. - Allan Peter Davis, Thomas C. Wiegers, Michael C. Rosenstein, Carolyn J. Mattingly:
MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database. - Esther T. Chan, J. Michael Cherry:
Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report. - Ruth Y. Eberhardt, Daniel H. Haft, Marco Punta, Maria Jesus Martin, Claire O'Donovan, Alex Bateman:
AntiFam: a tool to help identify spurious ORFs in protein annotation. - Nicole A. Vasilevsky, Tenille Johnson, Karen Corday, Carlo Torniai, Matthew H. Brush, Erik Segerdell, Melanie Wilson, Chris Shaffer, David Robinson, Melissa A. Haendel:
Research resources: curating the new eagle-i discovery system. - Sarah W. Burge, Teresa K. Attwood, Alex Bateman, Tanya Z. Berardini, J. Michael Cherry, Claire O'Donovan, Ioannis Xenarios, Pascale Gaudet:
Biocurators and Biocuration: surveying the 21st century challenges.
- Nobuyoshi Sugaya, Satoru Kanai, Toshio Furuya:
Dr. PIAS 2.0: an update of a database of predicted druggable protein-protein interactions. - Joseph A. Rothwell, Mireia Urpi-Sarda, Maria Boto-Ordoñez, Craig Knox, Rafael Llorach, Roman Eisner, Joseph A. Cruz, Vanessa Neveu, David S. Wishart, Claudine Manach, Cristina Andres-Lacueva, Augustin Scalbert:
Phenol-Explorer 2.0: a major update of the Phenol-Explorer database integrating data on polyphenol metabolism and pharmacokinetics in humans and experimental animals.
- Julia Feichtinger, Ramsay J. McFarlane, Lee D. Larcombe:
CancerMA: a web-based tool for automatic meta-analysis of public cancer microarray data. - Victor Zeng, Cassandra G. Extavour:
ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species. - Slawek Mazur, Gabor Csucs, Karol Kozak:
RNAiAtlas: a database for RNAi (siRNA) libraries and their specificity. - Benoît Vanderperre, Jean-François Lucier, Xavier Roucou:
HAltORF: a database of predicted out-of-frame alternative open reading frames in human. - Peter H. Thorpe, John C. Dittmar, Rodney Rothstein:
ScreenTroll: a searchable database to compare genome-wide yeast screens. - Tien-Dao Luu, Alin-Mihai Rusu, Vincent Walter, Raymond Ripp, Luc Moulinier, Jean Muller, Thierry Toursel, Julie Dawn Thompson, Olivier Poch, Hoan Nguyen:
MSV3d: database of human MisSense variants mapped to 3D protein structure. - Ankur Gautam, Harinder Singh, Atul Tyagi, Kumardeep Chaudhary, Rahul Kumar, Pallavi Kapoor, G. P. S. Raghava:
CPPsite: a curated database of cell penetrating peptides.
- Cathy H. Wu, Cecilia N. Arighi, Kevin Bretonnel Cohen, Lynette Hirschman, Martin Krallinger, Zhiyong Lu, Carolyn J. Mattingly, Alfonso Valencia, Thomas C. Wiegers, W. John Wilbur:
BioCreative-2012 Virtual Issue. - Pascale Gaudet, Raja Mazumder:
Biocuration Virtual Issue 2012.
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