DATABASE is pleased to have published the following articles originating from International Biocuration conferences. The articles were subject to the journal’s normal peer review process, and are collected together here as a ‘virtual issue’.

The goal of the Biocuration Conferences is ‘to create a forum for curators and developers of biological databases to discuss their work, promote collaborations, and foster a sense of community in this very active and growing area of research’. Visit the website for more information.

• Biocuration 2020
• Biocuration 2019
• Biocuration 2018
• Biocuration 2017
• Biocuration 2016
• Biocuration 2015
• Biocuration 2014
• Biocuration 2013
• Biocuration 2012
• Biocuration 2009

Biocuration 2020

Bioinformatics tools developed to support BioCompute Objects 
Janisha A Patel, Dennis A Dean, Charles Hadley King, Nan Xiao, Soner Koc, Ekaterina Minina, Anton Golikov, Phillip Brooks, Robel Kahsay, Rahi Navelkar, Manisha Ray, Dave Roberson, Chris Armstrong, Raja Mazumder, Jonathon Keeney
Database, Volume 2021, 2021, baab008, doi:10.1093/database/baab008

Automated generation of gene summaries at the Alliance of Genome Resources
Ranjana Kishore, Valerio Arnaboldi, Ceri E Van Slyke, Juancarlos Chan, Robert S Nash, Jose M Urbano, Mary E Dolan, Stacia R Engel, Mary Shimoyama, Paul W Sternberg, the Alliance of Genome Resources
Database, Volume 2020, 2020, baaa037, doi:10.1093/database/baaa037

Community curation in PomBase: enabling fission yeast experts to provide detailed, standardized, sharable annotation from research publications 
Antonia Lock, Midori A Harris, Kim Rutherford, Jacqueline Hayles, Valerie Wood
Database, Volume 2020, 2020, baaa028, doi:10.1093/database/baaa028

UPCLASS: a deep learning-based classifier for UniProtKB entry publications 
Douglas Teodoro, Julien Knafou, Nona Naderi, Emilie Pasche, Julien Gobeill, Cecilia N Arighi, Patrick Ruch
Database, Volume 2020, 2020, baaa026, doi:10.1093/database/baaa026

Integrating image caption information into biomedical document classification in support of biocuration 
Xiangying Jiang, Pengyuan Li, James Kadin, Judith A Blake, Martin Ringwald, Hagit Shatkay
Database, Volume 2020, 2020, baaa024, doi:10.1093/database/baaa024

A structured model for immune exposures 
Randi Vita, James A Overton, Patrick Dunn, Kei-Hoi Cheung, Steven H Kleinstein, Alessandro Sette, Bjoern Peters
Database, Volume 2020, 2020, baaa016, doi:10.1093/database/baaa016

Structured reviews for data and knowledge-driven research 
Núria Queralt-Rosinach, Gregory S Stupp, Tong Shu Li, Michael Mayers, Maureen E Hoatlin, Matthew Might, Benjamin M Good, Andrew I Su
Database, Volume 2020, 2020, baaa015, doi:10.1093/database/baaa015

Geographic assessment of cancer genome profiling studies 
Paula Carrio-Cordo, Elise Acheson, Qingyao Huang, Michael Baudis
Database, Volume 2020, 2020, baaa009, doi:10.1093/database/baaa009

Incorporation of a unified protein abundance dataset into the Saccharomyces genome database 
Robert S Nash, Shuai Weng, Kalpana Karra, Edith D Wong, Stacia R Engel, J Michael Cherry, SGD Project
Database, Volume 2020, 2020, baaa008, doi:10.1093/database/baaa008

Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase 
Valerio Arnaboldi, Daniela Raciti, Kimberly Van Auken, Juancarlos N Chan, Hans-Michael Müller, Paul W Sternberg
Database, Volume 2020, 2020, baaa006, doi:10.1093/database/baaa006

GXD’s RNA-Seq and Microarray Experiment Search: using curated metadata to reliably find mouse expression studies of interest 
Constance M Smith, James A Kadin, Richard M Baldarelli, Jonathan S Beal, Olin Blodgett, Sharon C Giannatto, Joel E Richardson, Martin Ringwald
Database, Volume 2020, 2020, baaa002, doi:10.1093/database/baaa002

RESTful API for iPTMnet: a resource for protein post-translational modification network discovery 
Sachin Gavali, Julie Cowart, Chuming Chen, Karen E Ross, Cecilia Arighi, Cathy H Wu
Database, Volume 2020, 2020, baz157, doi:10.1093/database/baz157

Biocuration 2019

ccPDB 2.0: an updated version of datasets created and compiled from Protein Data Bank
Piyush Agrawal, Sumeet Patiyal, Rajesh Kumar, Vinod Kumar, Harinder Singh, Pawan Kumar Raghav, and Gajendra P S Raghava
Database, Volume 2019, 1 January 2019, bay142, doi: 10.1093/database/bay142

Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase
Phani V Garapati, Jingyao Zhang, Alix J Rey, and Steven J Marygold
Database, Volume 2019, 1 January 2019, bay144, doi:10.1093/database/bay144

Involving community in genes and pathway curation
Sushma Naithani, Parul Gupta, Justin Preece, Priyanka Garg, Valerie Fraser, Lillian K Padgitt-Cobb, Matthew Martin, Kelly Vining, and Pankaj Jaiswal
Database, Volume 2019, 1 January 2019, bay146, doi: 10.1093/database/bay146

APID database: redefining protein-protein interaction experimental evidences and binary interactomes
Diego Alonso-López, Francisco J Campos-Laborie, Miguel A Gutiérrez, Luke Lambourne, Michael A Calderwood, Marc Vidal, and Javier De Las Rivas
Database, Volume 2019, 1 January 2019, baz005, doi: 10.1093/database/baz005

Annotation of gene product function from high-throughput studies using the Gene Ontology
Helen Attrill, Pascale Gaudet, Rachael P Huntley, Ruth C Lovering, Stacia R Engel, Sylvain Poux, Kimberly M Van Auken, George Georghiou, Marcus C Chibucos, Tanya Z Berardini, Valerie Wood, Harold Drabkin, Petra Fey, Penelope Garmiri, Midori A Harris, Tony Sawford, Leonore Reiser, Rebecca Tauber, Sabrina Toro, and The Gene Ontology Consortium
Database, Volume 2019, 1 January 2019, baz007, doi: 10.1093/database/baz007

Integration of macromolecular complex data into the Saccharomyces Genome Database
Edith D Wong, Marek S Skrzypek, Shuai Weng, Gail Binkley, Birgit H M Meldal, Livia Perfetto, Sandra E Orchard, Stacia R Engel, J Michael Cherry, and the SGD Project
Database, Volume 2019, 1 January 2019, baz008, doi: 10.1093/database/baz008

Using deep learning to identify translational research in genomic medicine beyond bench to bedside
Yi-Yu Hsu, Mindy Clyne, Chih-Hsuan Wei, Muin J Khoury, and Zhiyong Lu
Database, Volume 2019, 1 January 2019, baz010, doi: 10.1093/database/baz010

ImmunoSPdb: an archive of immunosuppressive peptides
Salman Sadullah Usmani, Piyush Agrawal, Manika Sehgal, Pradeep Kumar Patel, and Gajendra P S Raghava
Database, Volume 2019, 1 January 2019, baz012, doi: 10.1093/database/baz012

RiceMetaSysB: a database of blast and bacterial blight responsive genes in rice and its utilization in identifying key blast-resistant WRKY genes
V Sureshkumar, Bipratip Dutta, Vishesh Kumar, G Prakash, Dwijesh C Mishra, K K Chaturvedi, Anil Rai, Amitha Mithra Sevanthi, and Amolkumar U Solanke
Database, Volume 2019, 1 January 2019, baz015, doi: 10.1093/database/baz015

Increased interactivity and improvements to the Gigascience database, GigaDB
Si Zhe Xiao, Chris Armit, Scott Edmunds, Laurie Goodman, Peter Li, Mary Ann Tuli, and Christopher Ian Hunter
Database, Volume 2019, 1 January 2019, baz016, doi: 10.1093/database/baz016

Ontology based text mining of gene-phenotype associations: application to candidate gene prediction
Şenay Kafkas, and Robert Hoehndorf
Database, Volume 2019, 1 January 2019, baz019, doi: 10.1093/database/baz019

PIRSitePredict for protein functional site prediction using position-specific rules
Chuming Chen, Qinghua Wang, Hongzhan Huang, Cholanayakanahalli R Vinayaka, John S Garavelli, Cecilia N Arighi, Darren A Natale, and Cathy H Wu
Database, Volume 2019, 1 January 2019, baz026, doi: 10.1093/database/baz026

Biocuration 2018

FAIR principles and the IEDB: short-term improvements and a long-term vision of OBO-foundry mediated machine-actionable interoperability
Randi Vita, James A Overton, Christopher J Mungall, Alessandro Sette, and Bjoern Peters
Database, Volume 2018, 1 January 2018, bax105, doi: 10.1093/database/bax105

Identification of errors in the IEDB using ontologies
Randi Vita, James A Overton, and Bjoern Peters
Database, Volume 2018, 1 January 2018, bay005, doi: 10.1093/database/bay005

Updated regulation curation model at the Saccharomyces Genome Database
Stacia R Engel, Marek S Skrzypek, Sage T Hellerstedt, Edith D Wong, Robert S Nash, Shuai Weng, Gail Binkley, Travis K Sheppard, Kalpana Karra, and J Michael Cherry
Database, Volume 2018, 1 January 2018, bay007, doi: 10.1093/database/bay007

Prevention of data duplication for high throughput sequencing repositories
Idan Gabdank, Esther T Chan, Jean M Davidson, Jason A Hilton, Carrie A Davis, Ulugbek K Baymuradov, Aditi Narayanan, Kathrina C Onate, Keenan Graham, Stuart R Miyasato, Timothy R Dreszer, J Seth Strattan, Otto Jolanki, Forrest Y Tanaka, Benjamin C Hitz, Cricket A Sloan, and J Michael Cherry
Database, Volume 2018, 1 January 2018, bay008, doi: 10.1093/database/bay008

CITGeneDB: a comprehensive database of human and mouse genes enhancing or suppressing cold-induced thermogenesis validated by perturbation experiments in mice
Jin Li, Su-Ping Deng, Gang Wei, and Peng Yu
Database, Volume 2018, 1 January 2018, bay012, doi: 10.1093/database/bay012

Micropublication: incentivizing community curation and placing unpublished data into the public domain
Daniela Raciti, Karen Yook, Todd W Harris, Tim Schedl, and Paul W Sternberg
Database, Volume 2018, 1 January 2018, bay013, doi: 10.1093/database/bay013

GEOMetaCuration: a web-based application for accurate manual curation of Gene Expression Omnibus metadata
Zhao Li, Jin Li, and Peng Yu
Database, Volume 2018, 1 January 2018, bay019, doi: 10.1093/database/bay019

Expert curation for building network-based dynamical models: a case study on atherosclerotic plaque formation
Amel Bekkar, Anne Estreicher, Anne Niknejad, Cristina Casals-Casas, Alan Bridge, Ioannis Xenarios, Julien Dorier and Isaac Crespo.
Database, Volume 2018, 1 January 2018, bay031, doi: 10.1093/database/bay031

Signalling maps in cancer research: construction and data analysis
Maria Kondratova, Nicolas Sompairac, Emmanuel Barillot, Andrei Zinovyev, and Inna Kuperstein
Database, Volume 2018, 1 January 2018, bay036, doi: 10.1093/database/bay036

A set of domain rules and a deep network for protein coreference resolution
Chen Li, Zhiqiang Rao, Qinghua Zheng and Xiangrong Zhang.
Database, Volume 2018, 1 January 2018, bay065, doi: 10.1093/database/bay065

Annotation of phenotypes using ontologies: a gold standard for the training and evaluation of natural language processing systems
Wasila Dahdul, Prashanti Manda, Hong Cui, James P Balhoff, T Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Todd Vision and Paula M Mabee
Database, Volume 2018, 1 January 2018, bay110, doi: 10.1093/database/bay110

Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt
Aurore Britan, Isabelle Cusin, Valérie Hinard, Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Daniel Teixeira, Pierre-André Michel, Patrick Ruch and Pascale Gaudet
Database, Volume 2018, 1 January 2018, bay129, doi: 10.1093/database/bay129

Biocuration 2017

The tenth International Biocuration Conference, Stanford University, Palo Alto, California, USA, March 26-29, 2017 (papers submitted to and selected by DATABASE).

Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation
Taner Z. Sen, Bremen L. Braun, David A. Schott, John L. Portwood, II, Mary L. Schaeffer, Lisa C. Harper, Jack M. Gardiner, Ethalinda K. Cannon and Carson M. Andorf
Database, Volume 2017, 1 January 2017, bax031, doi: 10.1093/database/bax031

Outreach and online training services at the Saccharomyces Genome Database
Kevin MacPherson, Barry Starr, Edith Wong, Kyla Dalusag, Sage Hellerstedt, Olivia Lang, Robert Nash, Marek Skrzypek, Stacia Engel, and J. Cherry
Database Vol. 2016, baw002 doi:10.1093/database/baw002

Biocuration in the Structure-Function Linkage Database: The Anatomy of a Superfamily
Gemma Holliday, Shoshana Brown, Eyal Akiva, David Mischel, Michael Hicks, John Morris, Conrad Huang, Elaine Meng, Scott Pegg, Tom Ferrin, and Patricia Babbitt
Database Vol. 2016, baw006 doi:10.1093/database/baw006

 

Biocuration 2016

The Ninth International Biocuration Conference, Campus Biotech, Geneva, Switzerland, April 10-14, 2016 (papers submitted to and selected by DATABASE).

The UniProtKB guide to the human proteome
Lionel Breuza, Sylvain Poux, Anne Estreicher, Maria Livia Famiglietti, Michele Magrane, Michael Tognolli, Alan Bridge, Delphine Baratin and Nicole Redaschi
Database Vol. 2016, bav120 doi:10.1093/database/bav120

DemaDb: an integrated dematiaceous fungal genomes database
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 and Kee Peng Ng
Database Vol. 2016, baw008 doi:10.1093/database/baw008

Principles of metadata organization at the ENCODE data coordination center
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 and J. Michael Cherry
Database Vol. 2016, baw001 doi:10.1093/database/baw001

Wikidata as a semantic framework for the Gene Wiki initiative
Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Elvira Mitraka, Julia Turner, Tim Putman, Justin Leong, Chinmay Naik, Paul Pavlidis, Lynn Schriml, Benjamin M Good and Andrew I Su
Database Vol. 2016, baw015 doi:10.1093/database/baw015

Sustainable funding for biocuration: The Arabidopsis Information Resource (TAIR) as a case study of a subscription-based funding model
Leonore Reiser, Tanya Z. Berardini, Donghui Li, Robert Muller, Emily M. Strait, Qian Li, Yarik Mezheritsky, Andrey Vetushko and Eva Huala
Database Vol. 2016, baw018 doi:10.1093/database/baw018

From one to many: expanding the Saccharomyces cerevisiae reference genome panel
Stacia R. Engel, Shuai Weng, Gail Binkley, Kelley Paskov, Giltae Song and J. Michael Cherry
Database Vol. 2016, baw020 doi:10.1093/database/baw020

GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations
Amaia Sangrador-Vegas, Alex L. Mitchell, Hsin-Yu Chang, Siew-Yit Yong and Robert D. Finn
Database Vol. 2016, baw027 doi:10.1093/database/baw027

The Disease Portals, disease–gene annotation and the RGD disease ontology at the Rat Genome Database
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 and Mary Shimoyama
Database Vol. 2016, baw034 doi:10.1093/database/baw034

Centralizing content and distributing labor: a community model for curating the very long tail of microbial genomes
Tim E. Putman, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Chunlei Wu, Andrew I. Su and Benjamin M. Good
Database Vol. 2016, baw028 doi:10.1093/database/baw028

Discovering biomedical semantic relations in PubMed queries for information retrieval and database curation
Chung-Chi Huang and Zhiyong Lu
Database Vol. 2016, baw025 doi:10.1093/database/baw025

ICEPO: the ion channel electrophysiology ontology
V. Hinard, A. Britan, J.S. Rougier, A. Bairoch, H. Abriel and P. Gaudet
Database Vol. 2016, baw017 doi:10.1093/database/baw017

PGP repository: a plant phenomics and genomics data publication infrastructure
Daniel Arend, Astrid Junker, Uwe Scholz, Danuta Schüler, Juliane Wylie and Matthias Lange
Database Vol. 2016, baw033 doi:10.1093/database/baw033

Improving HIV proteome annotation: new features of BioAfrica HIV Proteomics Resource
Megan Druce, Chantal Hulo, Patrick Masson, Paula Sommer, Ioannis Xenarios, Philippe Le Mercier and Tulio De Oliveira
Database Vol. 2016, baw045 doi:10.1093/database/baw045

From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF
Sefa Kılıç, Dinara M. Sagitova, Shoshannah Wolfish, Benoit Bely, Mélanie Courtot, Stacy Ciufo, Tatiana Tatusova, Claire O’Donovan, Marcus C. Chibucos, Maria J. Martin and Ivan Erill
Database Vol. 2016, baw055 doi:10.1093/database/baw055

BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences
Peter McQuilton, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Milo Thurston, Allyson Lister, Eamonn Maguire, and Susanna-Assunta Sansone
Database Vol. 2016, baw075 doi:10.1093/database/baw075

Predicting structured metadata from unstructured metadata
Lisa Posch, Maryam Panahiazar, Michel Dumontier, and Olivier Gevaert
Database Vol. 2016, baw080 doi:10.1093/database/baw080

neXtA₅: Accelerating Annotation of Articles via Automated Approaches in neXtProt
Luc Mottin, Julien Gobeill, Emilie Pasche, Pierre-André Michel, Isabelle Cusin, Pascale Gaudet, and Patrick Ruch
Database Vol. 2016, baw098 doi:10.1093/database/baw098

Automated Detection of Discourse Segment and Experimental Types from Cancer Pathway Results Sections
Gully Burns, Pradeep Dasigi, Anita de Waard, and Eduard Hovy
Database Vol. 2016, baw122 doi:10.1093/database/baw122

 

Biocuration 2015

The Eighth International Biocuration Conference, Beijing Institute of Genomics, China, April 23-26, 2015 (papers submitted to and selected by DATABASE).

Deep Question Answering for protein annotation
Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Dina Vishnyakova, Pascale Gaudet, Amos Bairoch and Patrick Ruch
Database Vol. 2015, bav081 doi:10.1093/database/bav081

Comprehensive comparative homeobox gene annotation in human and mouse
Laurens G. Wilming, Veronika Boychenko and Jennifer L. Harrow
Database Vol. 2015, bav091 doi:10.1093/database/bav091

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases
Shweta Bagewadi, Subash Adhikari, Anjani Dhrangadhariya, Afroza Khanam Irin, Christian Ebeling, Aishwarya Alex Namasivayam, Matthew Page, Martin Hofmann-Apitius and Philipp Senger
Database Vol. 2015, bav099 doi:10.1093/database/bav099

Developing the eHistology Atlas
Lorna Richardson, Liz Graham, Julie Moss, Nick Burton, Yogmatee Roochun, Chris Armit and Richard A. Baldock
Database Vol. 2015, bav105
doi:10.1093/database/bav105

An update of miRNASNP database for better SNP selection by GWAS data, miRNA expression and online tools
Jing Gong, Chunjie Liu, Wei Liu, Yuliang Wu, Zhaowu Ma, Hu Chen and An-Yuan Guo
Database Vol. 2015, bav029 doi:10.1093/database/bav029

The Confidence Information Ontology: a step towards a standard for asserting confidence in annotations
Frederic B. Bastian, Marcus C. Chibucos, Pascale Gaudet, Michelle Giglio, Gemma L. Holliday, Hong Huang, Suzanna E. Lewis, Anne Niknejad, Sandra Orchard, Sylvain Poux, Nives Skunca and Marc Robinson-Rechavi
Database Vol. 2015, bav043 doi:10.1093/database/bav043

Construction of biological networks from unstructured information based on a semi-automated curation workflow
Justyna Szostak, Sam Ansari, Sumit Madan, Juliane Fluck, Marja Talikka, Anita Iskandar, Hector De Leon, Martin Hofmann-Apitius, Manuel C. Peitsch and Julia Hoeng
Database Vol. 2015, bav057 doi:10.1093/database/bav057

EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A
Andrew Ndhlovu, Pierre M. Durand and Scott Hazelhurst
Database Vol. 2015, bav065 doi:10.1093/database/bav065

dbPPT: a comprehensive database of protein phosphorylation in plants
Han Cheng, Wankun Deng, Yongbo Wang, Jian Ren, Zexian Liu and Yu Xue
Database Vol. 2014, bau121 doi:10.1093/database/bau121

PhenoMiner: a quantitative phenotype database for the laboratory rat, Rattus norvegicus. Application in hypertension and renal disease
Shur-Jen Wang, Stanley J. F. Laulederkind, G. Thomas Hayman, Victoria Petri, Weisong Liu, Jennifer R. Smith, Rajni Nigam, Melinda R. Dwinell and Mary Shimoyama
Database Vol. 2015, bau128 doi:10.1093/database/bau128

OntoMate: a text-mining tool aiding curation at the Rat Genome Database
Weisong Liu, Stanley J. F. Laulederkind, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Jennifer R. Smith, Jeff De Pons, Melinda R. Dwinell and Mary Shimoyama
Database Vol. 2015, bau129 doi:10.1093/database/bau129

Construction of phosphorylation interaction networks by text mining of full-length articles using the eFIP system
Catalina O. Tudor, Karen E. Ross, Gang Li, K. Vijay-Shanker, Cathy H. Wu and Cecilia N. Arighi
Database Vol. 2015, bav020 doi:10.1093/database/bav020

BioXpress: An integrated RNA-seq derived gene expression database for pan-cancer analysis
Quan Wan, Hayley Dingerdissen, Yu Fan, Naila Gulzar, Yang Pan, Tsung-Jung Wu, Cheng Yan, Haichen Zhang and Raja Mazumder
Database Vol. 2015, bav019 doi:10.1093/database/bav019

mycoCLAP, the database for characterized lignocellulose-active proteins of fungal origin: resource and text mining curation support
Kimchi Strasser, Erin McDonnell, Carol Nyaga, Min Wu, Sherry Wu, Hayda Almeida, Marie-Jean Meurs, Leila Kosseim, Justin Powlowski, Greg Butler and Adrian Tsang
Database Vol. 2015, bav008 doi:10.1093/database/bav008

Improving the consistency of domain annotation within the Conserved Domain Database
Myra K. Derbyshire, Noreen R. Gonzales, Shennan Lu, Jane He, Gabriele H. Marchler, Zhouxi Wang and Aron Marchler-Bauer
Database Vol. 2015, bav012 doi:10.1093/database/bav012

Shared Resources, shared costs – leveraging biocuration resources
Sandra Orchard and Henning Hermjakob
Database Vol. 2015, bav009 doi:10.1093/database/bav009

Ontology application and use at the ENCODE DCC
Venkat S. Malladi, Drew T. Erickson, Nikhil R. Podduturi, Laurence D. Rowe, Esther T. Chan, Jean M. Davidson, Benjamin C. Hitz, Marcus Ho, Brian T. Lee, Stuart Miyasato, Gregory R. Roe, Matt Simison, Cricket A. Sloan, J. Seth Strattan, Forrest Tanaka, W. James Kent, J. Michael Cherry and Eurie L. Hong
Database Vol. 2015, bav010 doi:10.1093/database/bav010

Generating a focused view of disease ontology cancer terms for pan-cancer data integration and analysis
Tsung-Jung Wu, Lynn M. Schriml, Qing-Rong Chen, Maureen Colbert, Daniel J. Crichton, Richard Finney, Ying Hu, Warren A. Kibbe, Heather Kincaid, Daoud Meerzaman, Elvira Mitraka, Yang Pan, Krista M. Smith, Sudhir Srivastava, Sari Ward, Cheng Yan and Raja Mazumder
Database Vol. 2015, bav032 doi:10.1093/database/bav032

Small molecule annotation for the Protein Data Bank
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 and Marina A. Zhuravleva
Database Vol. 2015, bau116 doi:10.1093/database/bau116

dbPSP: a curated database for protein phosphorylation sites in prokaryotes
Zhicheng Pan, Bangshan Wang, Ying Zhang, Yongbo Wang, Shahid Ullah, Ren Jian, Zexian Liu and Yu Xue
Database Vol. 2015, bav031 doi:10.1093/database/bav031

 

Biocuration 2014

The Seventh International Biocuration Conference, University of Toronto in Toronto, Canada, April 6-9, 2014 (papers submitted to and selected by DATABASE).

The eGenVar data management system—cataloguing and sharing sensitive data and metadata for the life sciences
Sabry Razick, Rok Močnik, Laurent F. Thomas, Einar Ryeng, Finn Drabløs, and Pål Sætrom
Database Vol. 2014, bau02;7 doi: 10.1093/database/bau027

Expert curation in UniProtKB: a case study on dealing with conflicting and erroneous data
Sylvain Poux, Michele Magrane, Cecilia N. Arighi, Alan Bridge, Claire O’Donovan, Kati Laiho, and The UniProt Consortium
Database 2014: bau016 doi:10.1093/database/bau016

Linking tissues to phenotypes using gene expression profiles
Anika Oellrich, Sanger Mouse Genetics Project, and Damian Smedley

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE)
Tsung-Jung Wu, Amirhossein Shamsaddini, Yang Pan, Krista Smith, Daniel J. Crichton, Vahan Simonyan, and Raja Mazumder
Database 2014: bau022 doi:10.1093/database/bau022

GigaDB: promoting data dissemination and reproducibility
Tam P. Sneddon, Xiao Si Zhe, Scott C. Edmunds, Peter Li, Laurie Goodman, and Christopher I. Hunter
Database 2014: bau018 doi:10.1093/database/bau018

 

Biocuration 2013

The Sixth International Biocuration Conference, Churchill College, Cambridge, UK, April 7–10, 2013 (papers submitted to and selected by DATABASE).

PhenoMiner: quantitative phenotype curation at the rat genome database
Stanley J. F. Laulederkind, Weisong Liu, Jennifer R. Smith, G. Thomas Hayman, Shur-Jen Wang, Rajni Nigam, Victoria Petri, Timothy F. Lowry, Jeff de Pons, Melinda R. Dwinell, and Mary Shimoyama
Database Vol. 2013, bat015; doi:10.1093/database/bat015

MalaCards: an integrated compendium for diseases and their annotation
Noa Rappaport, Noam Nativ, Gil Stelzer, Michal Twik, Yaron Guan-Golan, Tsippi Iny Stein, Iris Bahir, Frida Belinky, C. Paul Morrey, Marilyn Safran, and Doron Lancet
Database Vol. 2013, bat018; doi:10.1093/database/bat018

The HUPO proteomics standards initiative - mass spectrometry controlled vocabulary
Gerhard Mayer, Luisa Montecchi-Palazzi, David Ovelleiro, Andrew R. Jones, Pierre-Alain Binz, Eric W. Deutsch, Matthew Chambers, Marius Kallhardt, Fredrik Levander, James Shofstahl, Sandra Orchard, Juan Antonio Vizcaíno, Henning Hermjakob, Christian Stephan, Helmut E. Meyer, and Martin Eisenacher
Database Vol. 2013, bat009; doi:10.1093/database/bat009

Annotating the biomedical literature for the human variome
Karin Verspoor, Antonio Jimeno Yepes, Lawrence Cavedon, Tara McIntosh, Asha Herten-Crabb, Zoë Thomas, and John-Paul Plazzer
Database Vol. 2013, bat019; doi:10.1093/database/bat019

A database for curating the associations between killer cell immunoglobulin-like receptors and diseases in worldwide populations
Louise Y. C. Takeshita, Faviel F. Gonzalez-Galarza, Eduardo J. M. dos Santos, Maria Helena T. Maia, Mushome M. Rahman, Syed M. S. Zain, Derek Middleton, and Andrew R. Jones
Database Vol. 2013, bat021; doi:10.1093/database/bat021

Identification and prioritization of novel uncharacterized peptidases for biochemical characterization
Neil D. Rawlings
Database Vol. 2013, bat022; doi:10.1093/database/bat022

Biological Database of Images and Genomes: Tools for community annotations linking image and genomic information
Andrew T Oberlin, Dominika A Jurkovic, Mitchell F Balish, and Iddo Friedberg
Database Vol. 2013, bat016; doi:10.1093/database/bat016

Uncovering hidden duplicated content in public transcriptomics data
Marta Rosikiewicz, Aurélie Comte, Anne Niknejad, Marc Robinson-Rechavi, and Frederic B. Bastian
Database Vol. 2013, bat010; doi:10.1093/database/bat010

The MetaboLights repository: curation challenges in metabolomics
Reza M. Salek, Kenneth Haug, Pablo Conesa, Janna Hastings, Mark Williams, Tejasvi Mahendraker, Eamonn Maguire, Alejandra N. González-Beltrán, Philippe Rocca-Serra, Susanna-Assunta Sansone, and Christoph Steinbeck
Database Vol. 2013, bat029; doi:10.1093/database/bat029

Towards the Collaborative Curation of the Registry underlying identifiers.org
Nick Juty, Nicolas Le Novère, Henning Hermjakob, and Camille Laibe
Database Vol. 2013, bat017; doi:10.1093/database/bat017

PhenoDigm: analyzing curated annotations to associate animal models with human diseases
Damian Smedley, Anika Oellrich, Sebastian Köhler, Barbara Ruef, Sanger Mouse Genetics Project, Monte Westerfield, Peter Robinson, Suzanna Lewis, and Christopher Mungall
Database Vol. 2013, bat025; doi:10.1093/database/bat025

The challenge of increasing Pfam coverage of the human proteome
Jaina Mistry, Penny Coggill, Ruth Y. Eberhardt, Antonio Deiana, Andrea Giansanti, Robert D. Finn, Alex Bateman, and Marco Punta
Database Vol. 2013, bat023; doi:10.1093/database/bat023

PCorral—interactive mining of protein interactions from MEDLINE
Chen Li, Antonio Jimeno-Yepes, Miguel Arregui, Harald Kirsch, and Dietrich Rebholz-Schuhmann
Database Vol. 2013, bat030; doi:10.1093/database/bat030

The YeastGenome app: the Saccharomyces Genome Database at your fingertips
Edith D. Wong, Kalpana Karra, Benjamin C. Hitz, Eurie L. Hong, and J. Michael Cherry
Database Vol. 2013, bat004; doi:10.1093/database/bat004

The new modern era of yeast genomics: community sequencing and the resulting annotation of multiple Saccharomyces cerevisiae strains at the Saccharomyces Genome Database
Stacia R. Engel and J. Michael Cherry
Database Vol. 2013, bat012; doi:10.1093/database/bat012

The Protein Model Portal — a comprehensive resource for protein structure and model information
Juergen Haas, Steven Roth, Konstantin Arnold, Florian Kiefer, Tobias Schmidt, Lorenza Bordoli, and Torsten Schwede
Database Vol. 2013, bat031; doi:10.1093/database/bat031

 

Biocuration 2012

The Fifth International Biocuration Conference, Washington, DC, April 2–4, 2012 (papers submitted to and selected by DATABASE).

Editorial: Biocuration Virtual Issue 2012
Pascale Gaudet and Raja Mazumder
Database Vol. 2012, bas011; doi:10.1093/database/bas011

Recent advances in biocuration: Meeting Report from the fifth International Biocuration Conference
Pascale Gaudet, Cecilia Arighi, Frederic Bastian, Alex Bateman, Judith A. Blake, Michael J. Cherry, Peter D’Eustachio, Robert Finn, Michelle Giglio, Lynette Hirschman, Renate Kania, William Klimke, Maria Jesus Martin, Ilene Karsch-Mizrachi, Monica Munoz-Torres, Darren Natale, Claire O’Donovan, Francis Ouellette, Kim D. Pruitt, Marc Robinson-Rechavi, Susanna-Assunta Sansone, Paul Schofield, Granger Sutton, Kimberly Van Auken, Sona Vasudevan, Cathy Wu, Jasmine Young, and Raja Mazumder
Database Vol. 2012, bas036; doi:10.1093/database/bas036

Community annotation and bioinformatics workforce development in concert—Little Skate Genome Annotation Workshops and Jamborees
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 and the North East Bioinformatics Collaborative Curation Team
Database Vol. 2012, bar064; doi:10.1093/database/bar064

Annotation of functional sites with the Conserved Domain Database
Myra K. Derbyshire, Christopher J. Lanczycki, Stephen H. Bryant and Aron Marchler-Bauer
Database Vol. 2012, bar058; doi:10.1093/database/bar058

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework
A. E. Bandrowski, J. Cachat, Y. Li, H. M. Mu¨ ller, P. W. Sternberg, P. Ciccarese, T. Clark, L. Marenco, R. Wang, V. Astakhov, J. S. Grethe and M. E. Martone
Database Vol. 2012, bas005; doi:10.1093/database/bas005

PRIDE: Quality control in a proteomics data repository
Attila Csordas, David Ovelleiro, Rui Wang, Joseph M. Foster, Daniel Ríos, Juan Antonio Vizcaíno and Henning Hermjakob
Database Vol. 2012, bas004; doi:10.1093/database/bas004

YeastMine — an integrated data warehouse for Saccharomyces cerevisiae data as a multipurpose tool-kit
Rama Balakrishnan, Julie Park, Kalpana Karra, Benjamin C. Hitz, Gail Binkley, Eurie L. Hong, Julie Sullivan, Gos Micklem and J. Michael Cherry
Database Vol. 2012, bar062; doi:10.1093/database/bar062

Argo: an integrative, interactive, text mining-based workbench supporting curation
Rafal Rak, Andrew Rowley, William Black and Sophia Ananiadou
Database Vol. 2012, bas010; doi:10.1093/database/bas010

Tetrahymena genome database Wiki: a community-maintained model organism database
Nicholas A. Stover, Ravinder S. Punia, Michael S. Bowen, Steven B. Dolins and Theodore G. Clark
Database Vol. 2012, bas007; doi:10.1093/database/bas007

CvManGO, a method for leveraging computational predictions to improve literature-based Gene Ontology annotations
Julie Park, Maria C. Costanzo, Rama Balakrishnan, J. Michael Cherry and Eurie L. Hong
Database Vol. 2012, bas001; doi:10.1093/database/bas001

Building a biomedical semantic network in Wikipedia with Semantic Wiki Links
Benjamin M. Good, Erik L. Clarke, Salvatore Loguercio and Andrew I. Su
Database Vol. 2012, bar060; doi:10.1093/database/bar060

Disease model curation improvements at Mouse Genome Informatics
Susan M. Bello, Joel E. Richardson, Allan P. Davis, Thomas C. Wiegers, Carolyn J. Mattingly, Mary E. Dolan, Cynthia L. Smith, Judith A. Blake and Janan T. Eppig
Database Vol. 2012, bar063; doi:10.1093/database/bar063

Community gene annotation in practice
Jane E. Loveland, James G.R. Gilbert, Ed Griffiths and Jennifer L. Harrow
Database Vol. 2012, bas009; doi:10.1093/database/bas009

Tracking and coordinating an international curation effort for the CCDS Project
Rachel A. Harte, Catherine M. Farrell, Jane E. Loveland, Marie-Marthe Suner, Laurens Wilming, Bronwen Aken, Daniel Barrell, Adam Frankish, Craig Wallin, Steve Searle, Mark Diekhans, Jennifer Harrow and Kim D. Pruitt
Database Vol. 2012, bas008; doi:10.1093/database/bas008

Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments
Jose Cruz-Toledo, Maureen McKeague, Xueru Zhang, Amanda Giamberardino, Erin McConnell, Tariq Francis, Maria C. DeRosa and Michel Dumontier
Database Vol. 2012, bas006; doi:10.1093/database/bas006

The mouse–human anatomy ontology mapping project
Terry F. Hayamizu, Sherri de Coronado, Gilberto Fragoso, Nicholas Sioutos, James A. Kadin and Martin Ringwald
Database Vol. 2012, bar066; doi:10.1093/database/bar066

MEDIC: a practical disease vocabulary used at the Comparative Toxicogenomics Database
Allan Peter Davis, Thomas C. Wiegers, Michael, C. Rosenstein and Carolyn J. Mattingly
Database Vol. 2012, bar065; doi:10.1093/database/bar065

Considerations for creating and annotating the budding yeast Genome Map at SGD: a progress report
Esther T. Chan and J. Michael Cherry
Database Vol. 2012, bar057; doi:10.1093/database/bar057

AntiFam: a tool to help identify spurious ORFs in protein annotation
Ruth Y. Eberhardt, Daniel H. Haft, Marco Punta, Maria Martin, Claire O’Donovan and Alex Bateman
Database Vol. 2012, bas003; doi:10.1093/database/bas003

Research resources: curating the new eagle-i discovery system
Nicole Vasilevsky, Tenille Johnson, Karen Corday, Carlo Torniai, Matthew Brush, Erik Segerdell, Melanie Wilson, Chris Shaffer, David Robinson and Melissa Haendel
Database Vol. 2012, bar067; doi:10.1093/database/bar067

Biocurators and Biocuration: surveying the 21st century challenges
Sarah Burge, Teresa K. Attwood, Alex Bateman, Tanya Z. Berardini, Michael Cherry, Claire O’Donovan, Ioannis Xenarios and Pascale Gaudet
Database Vol. 2012, bar059; doi:10.1093/database/bar059

Ontology searching and browsing at the Rat Genome Database
Stanley J. F. Laulederkind, Marek Tutaj, Mary Shimoyama, G. Thomas Hayman, Timothy F. Lowry, Rajni Nigam, Victoria Petri, Jennifer R. Smith, Shur-Jen Wang, Jeff de Pons, Melinda R. Dwinell and Howard J. Jacob
Database Vol. 2012, bas016; doi:10.1093/database/bas016

The importance of identifying alternative splicing in vertebrate genome annotation
Adam Frankish, Jonathan M. Mudge, Mark Thomas and Jennifer Harrow
Database Vol. 2012, bas014; doi:10.1093/database/bas014

How to link ontologies and protein–protein interactions to literature: text-mining approaches and the BioCreative experience
Martin Krallinger, Florian Leitner, Miguel Vazquez, David Salgado, Christophe Marcelle, Mike Tyers, Alfonso Valencia, and Andrew Chatr-aryamontri
Database Vol. 2012, bas017; doi:10.1093/database/bas017

Text mining for the biocuration workflow
Lynette Hirschman, Gully A. P. C Burns, Martin Krallinger, Cecilia Arighi, K. Bretonnel Cohen, Alfonso Valencia, Cathy H. Wu, Andrew Chatr-Aryamontri, Karen G. Dowell, Eva Huala, Anália Lourenço, Robert Nash, Anne-Lise Veuthey, Thomas Wiegers, and Andrew G. Winter
Database Vol. 2012, bas020; doi:10.1093/database/bas020

Using ODIN for a PharmGKB revalidation experiment
Fabio Rinaldi, Simon Clematide, Yael Garten, Michelle Whirl-Carrillo, Li Gong, Joan M. Hebert, Katrin Sangkuhl, Caroline F. Thorn, Teri E. Klein, and Russ B. Altman
Database Vol. 2012, bas021; doi:10.1093/database/bas021

Towards semi-automated curation: using text mining to recreate the HIV-1, human protein interaction database
Daniel G. Jamieson, Martin Gerner, Farzaneh Sarafraz, Goran Nenadic, and David L. Robertson
Database Vol. 2012, bas023; doi:10.1093/database/bas023

 

Biocuration 2009

The third International Biocurator Conference, Berlin, Germany, April 16–19, 2009 (papers submitted to and selected by DATABASE).

Meeting report: a workshop on Best Practices in Genome Annotation
Ramana Madupu, Lauren M. Brinkac, Jennifer Harrow, Laurens G. Wilming, Ulrike Böhme, Philippe Lamesch, and Linda I. Hannick
Database Vol. 2010, baq001; doi:10.1093/database/baq001

MicroScope: a platform for microbial genome annotation and comparative genomics
D. Vallenet, S. Engelen, D. Mornico, S. Cruveiller, L. Fleury, A. Lajus, Z. Rouy, D. Roche, G. Salvignol, C. Scarpelli, and C. Médigue
Database Vol. 2009, bap021; doi:10.1093/database/bap021

Collaborative annotation of genes and proteins between UniProtKB/Swiss-Prot and dictyBase
P. Gaudet, L. Lane, P. Fey, A. Bridge, S. Poux, A. Auchincloss, K. Axelsen, S. Braconi Quintaje, E. Boutet, P. Brown, E. Coudert, R.S. Datta, W.C. de Lima, T. de Oliveira Lima, S. Duvaud, N. Farriol-Mathis, S. Ferro Rojas, M. Feuermann, A. Gateau, U. Hinz, C. Hulo, J. James, S. Jimenez, F. Jungo, G. Keller, P. Lemercier, D. Lieberherr, M. Moinat, A. Nikolskaya, I. Pedruzzi, C. Rivoire, B. Roechert, M. Schneider, E. Stanley, M. Tognolli, K. Sjölander, L. Bougueleret, R.L. Chisholm, and A. Bairoch
Database Vol. 2009, bap016; doi:10.1093/database/bap016

Integrating text mining into the MGI biocuration workflow
K.G. Dowell, M.S. McAndrews-Hill, D.P. Hill, H.J. Drabkin, and J.A. Blake
Database Vol. 2009, bap019; doi:10.1093/database/bap019

QuickGO: A user tutorial for the web-based Gene Ontology browser
Rachael P. Huntley, David Binns, Emily Dimmer, Daniel Barrell, Claire O’Donovan, and Rolf Apweiler
Database Vol. 2009, bap010; doi:10.1093/database/bap010

A large and accurate collection of peptidase cleavages in the MEROPS database
Neil D. Rawlings
Database Vol. 2009, bap015; doi:10.1093/database/bap015

PDBWiki: added value through community annotation of the Protein Data Bank
Henning Stehr, Jose M. Duarte, Michael Lappe, Jong Bhak, and Dan M. Bolser
Database Vol. 2010, baq009; doi:10.1093/database/baq009