Volume 2017

2017

EISSN 1758-0463

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Volume 2017, 2017

Original Article

The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions

Rezarta Islamaj Doğan, Sun Kim, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer Rust, W. John Wilbur, Donald C. Comeau, Kara Dolinski, Mike Tyers

Database, Volume 2017, 2017, baw147, https://doi.org/10.1093/database/baw147

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BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences

K.E. Ravikumar, Majid Rastegar-Mojarad, Hongfang Liu

Database, Volume 2017, 2017, baw156, https://doi.org/10.1093/database/baw156

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Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study

Qingyu Chen, Justin Zobel, Karin Verspoor

Database, Volume 2017, 2017, baw163, https://doi.org/10.1093/database/baw163

FARME DB: a functional antibiotic resistance element database

James C. Wallace, Jesse A. Port, Marissa N. Smith, Elaine M. Faustman

Database, Volume 2017, 2017, baw165, https://doi.org/10.1093/database/baw165

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Automatic query generation using word embeddings for retrieving passages describing experimental methods

Ferhat Aydın, Zehra Melce Hüsünbeyi, Arzucan Özgür

Database, Volume 2017, 2017, baw166, https://doi.org/10.1093/database/baw166

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RAIN: RNA–protein Association and Interaction Networks

Alexander Junge, Jan C. Refsgaard, Christian Garde, Xiaoyong Pan, Alberto Santos, Ferhat Alkan, Christian Anthon, Christian von Mering, Christopher T. Workman, Lars Juhl Jensen, Jan Gorodkin

Database, Volume 2017, 2017, baw167, https://doi.org/10.1093/database/baw167

KTCNlncDB—a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas

Michał W. Szcześniak, Michal Kabza, Justyna A. Karolak, Malgorzata Rydzanicz, Dorota M. Nowak, Barbara Ginter-Matuszewska, Piotr Polakowski, Rafal Ploski, Jacek P. Szaflik, Marzena Gajecka

Database, Volume 2017, 2017, baw168, https://doi.org/10.1093/database/baw168

VerSeDa: vertebrate secretome database

Ana R. Cortazar, José A. Oguiza, Ana M. Aransay, José L. Lavín

Database, Volume 2017, 2017, baw171, https://doi.org/10.1093/database/baw171

OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture

Cyrielle Gasc, Antony Constantin, Faouzi Jaziri, Pierre Peyret

Database, Volume 2017, 2017, baw172, https://doi.org/10.1093/database/baw172

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SilkPathDB: a comprehensive resource for the study of silkworm pathogens

Tian Li, Guo-Qing Pan, Charles R. Vossbrinck, Jin-Shan Xu, Chun-Feng Li, Jie Chen, Meng-Xian Long, Ming Yang, Xiao-Fei Xu, Chen Xu, Bettina A. Debrunner-Vossbrinck, Ze-Yang Zhou

Database, Volume 2017, 2017, bax001, https://doi.org/10.1093/database/bax001

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Outreach and online training services at the Saccharomyces Genome Database

Kevin A. MacPherson, Barry Starr, Edith D. Wong, Kyla S. Dalusag, Sage T. Hellerstedt, Olivia W. Lang, Robert S. Nash, Marek S. Skrzypek, Stacia R. Engel, J. Michael Cherry

Database, Volume 2017, 2017, bax002, https://doi.org/10.1093/database/bax002

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Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects

Anton Güntsch, Roger Hyam, Gregor Hagedorn, Simon Chagnoux, Dominik Röpert, Ana Casino, Gabi Droege, Falko Glöckler, Karsten Gödderz, Quentin Groom, Jana Hoffmann, Ayco Holleman, Matúš Kempa, Hanna Koivula, Karol Marhold, Nicky Nicolson, Vincent S. Smith, Dagmar Triebel

Database, Volume 2017, 2017, bax003, https://doi.org/10.1093/database/bax003

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Carotenoids Database: structures, chemical fingerprints and distribution among organisms

Junko Yabuzaki

Database, Volume 2017, 2017, bax004, https://doi.org/10.1093/database/bax004

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Biocuration in the structure–function linkage database: the anatomy of a superfamily

Gemma L. Holliday, Shoshana D. Brown, Eyal Akiva, David Mischel, Michael A. Hicks, John H. Morris, Conrad C. Huang, Elaine C. Meng, Scott C.-H. Pegg, Thomas E. Ferrin, Patricia C. Babbitt

Database, Volume 2017, 2017, bax006, https://doi.org/10.1093/database/bax006

Workflow and web application for annotating NCBI BioProject transcriptome data

Roberto Vera Alvarez, Newton Medeiros Vidal, Gina A. Garzón-Martínez, Luz S. Barrero, David Landsman, Leonardo Mariño-Ramírez

Database, Volume 2017, 2017, bax008, https://doi.org/10.1093/database/bax008

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HopBase: a unified resource for Humulus genomics

Steven T. Hill, Ramcharan Sudarsanam, John Henning, David Hendrix

Database, Volume 2017, 2017, bax009, https://doi.org/10.1093/database/bax009

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The ‘straight mouse’: defining anatomical axes in 3D embryo models

Chris Armit, Bill Hill, S. Venkataraman, Kenneth McLeod, Albert Burger, Richard Baldock

Database, Volume 2017, 2017, bax010, https://doi.org/10.1093/database/bax010

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Curated protein information in the Saccharomyces genome database

Sage T. Hellerstedt, Robert S. Nash, Shuai Weng, Kelley M. Paskov, Edith D. Wong, Kalpana Karra, Stacia R. Engel, J. Michael Cherry

Database, Volume 2017, 2017, bax011, https://doi.org/10.1093/database/bax011

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Strategies towards digital and semi-automated curation in RegulonDB

Fabio Rinaldi, Oscar Lithgow, Socorro Gama-Castro, Hilda Solano, Alejandra López-Fuentes, Luis José Muñiz Rascado, Cecilia Ishida-Gutiérrez, Carlos-Francisco Méndez-Cruz, Julio Collado-Vides

Database, Volume 2017, 2017, bax012, https://doi.org/10.1093/database/bax012

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Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD)

Xiangying Jiang, Martin Ringwald, Judith Blake, Hagit Shatkay

Database, Volume 2017, 2017, bax017, https://doi.org/10.1093/database/bax017

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AnnoSys—implementation of a generic annotation system for schema-based data using the example of biodiversity collection data

L. Suhrbier, W.-H. Kusber, O. Tschöpe, A. Güntsch, W. G. Berendsohn

Database, Volume 2017, 2017, bax018, https://doi.org/10.1093/database/bax018

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Exploring convolutional neural networks for drug–drug interaction extraction

Víctor Suárez-Paniagua, Isabel Segura-Bedmar, Paloma Martínez

Database, Volume 2017, 2017, bax019, https://doi.org/10.1093/database/bax019

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Literature consistency of bioinformatics sequence databases is effective for assessing record quality

Mohamed Reda Bouadjenek, Karin Verspoor, Justin Zobel

Database, Volume 2017, 2017, bax021, https://doi.org/10.1093/database/bax021

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TMPL: a database of experimental and theoretical transmembrane protein models positioned in the lipid bilayer

Guillaume Postic, Yassine Ghouzam, Catherine Etchebest, Jean-Christophe Gelly

Database, Volume 2017, 2017, bax022, https://doi.org/10.1093/database/bax022

ABCMdb reloaded: updates on mutations in ATP binding cassette proteins

Hedvig Tordai, Kristóf Jakab, Gergely Gyimesi, Kinga András, Anna Brózik, Balázs Sarkadi, Tamás Hegedűs

Database, Volume 2017, 2017, bax023, https://doi.org/10.1093/database/bax023

Chemical-induced disease relation extraction via convolutional neural network

Jinghang Gu, Fuqing Sun, Longhua Qian, Guodong Zhou

Database, Volume 2017, 2017, bax024, https://doi.org/10.1093/database/bax024

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WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata

Tim E. Putman, Sebastien Lelong, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Colin Diesh, Nathan Dunn, Monica Munoz-Torres, Gregory S. Stupp, Chunlei Wu, Andrew I. Su, Benjamin M. Good

Database, Volume 2017, 2017, bax025, https://doi.org/10.1093/database/bax025

NaviCom: a web application to create interactive molecular network portraits using multi-level omics data

Mathurin Dorel, Eric Viara, Emmanuel Barillot, Andrei Zinovyev, Inna Kuperstein

Database, Volume 2017, 2017, bax026, https://doi.org/10.1093/database/bax026

Automated PDF highlighting to support faster curation of literature for Parkinson’s and Alzheimer’s disease

Honghan Wu, Anika Oellrich, Christine Girges, Bernard de Bono, Tim J.P. Hubbard, Richard J.B. Dobson

Database, Volume 2017, 2017, bax027, https://doi.org/10.1093/database/bax027

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards

Simon Fishilevich, Ron Nudel, Noa Rappaport, Rotem Hadar, Inbar Plaschkes, Tsippi Iny Stein, Naomi Rosen, Asher Kohn, Michal Twik, Marilyn Safran, Doron Lancet, Dana Cohen

Database, Volume 2017, 2017, bax028, https://doi.org/10.1093/database/bax028

Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis

Yalbi Itzel Balderas-Martínez, Fabio Rinaldi, Gabriela Contreras, Hilda Solano-Lira, Mishael Sánchez-Pérez, Julio Collado-Vides, Moisés Selman, Annie Pardo

Database, Volume 2017, 2017, bax030, https://doi.org/10.1093/database/bax030

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, Carson M. Andorf

Database, Volume 2017, 2017, bax031, https://doi.org/10.1093/database/bax031

Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community

Surya Saha, Prashant S Hosmani, Krystal Villalobos-Ayala, Sherry Miller, Teresa Shippy, Mirella Flores, Andrew Rosendale, Chris Cordola, Tracey Bell, Hannah Mann, Gabe DeAvila, Daniel DeAvila, Zachary Moore, Kyle Buller, Kathryn Ciolkevich, Samantha Nandyal, Robert Mahoney, Joshua Van Voorhis, Megan Dunlevy … Susan J Brown

Database, Volume 2017, 2017, bax032, https://doi.org/10.1093/database/bax032

TriatoKey: a web and mobile tool for biodiversity identification of Brazilian triatomine species

Luciana Márcia de Oliveira, Raissa Nogueira de Brito, Paul Anderson Souza Guimarães, Rômulo Vitor Mastrângelo Amaro dos Santos, Liléia Gonçalves Diotaiuti, Rita de Cássia Moreira de Souza, Jeronimo Conceição Ruiz

Database, Volume 2017, 2017, bax033, https://doi.org/10.1093/database/bax033

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In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis

Matheus Eloy Franco, Tamires Aparecida Bitencourt, Mozart Marins, Ana Lúcia Fachin

Database, Volume 2017, 2017, bax035, https://doi.org/10.1093/database/bax035

BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases

Yanjun Xu, Haixiu Yang, Tan Wu, Qun Dong, Zeguo Sun, Desi Shang, Feng Li, Yingqi Xu, Fei Su, Siyao Liu, Yunpeng Zhang, Xia Li

Database, Volume 2017, 2017, bax037, https://doi.org/10.1093/database/bax037

Triage by ranking to support the curation of protein interactions

Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Pierre-André Michel, Amos Bairoch, Pascale Gaudet, Patrick Ruch

Database, Volume 2017, 2017, bax040, https://doi.org/10.1093/database/bax040

decodeRNA— predicting non-coding RNA functions using guilt-by-association

Steve Lefever, Jasper Anckaert, Pieter-Jan Volders, Manuel Luypaert, Jo Vandesompele, Pieter Mestdagh

Database, Volume 2017, 2017, bax042, https://doi.org/10.1093/database/bax042

Text mining and expert curation to develop a database on psychiatric diseases and their genes

Alba Gutiérrez-Sacristán, Àlex Bravo, Marta Portero-Tresserra, Olga Valverde, Antonio Armario, M.C. Blanco-Gandía, Adriana Farré, Lierni Fernández-Ibarrondo, Francina Fonseca, Jesús Giraldo, Angela Leis, Anna Mané, M.A. Mayer, Sandra Montagud-Romero, Roser Nadal, Jordi Ortiz, Francisco Javier Pavon, Ezequiel Jesús Perez, Marta Rodríguez-Arias … Laura I. Furlong

Database, Volume 2017, 2017, bax043, https://doi.org/10.1093/database/bax043

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PigVar: a database of pig variations and positive selection signatures

Zhong-Yin Zhou, Aimin Li, Newton O Otecko, Yan-Hu Liu, David M Irwin, Lu Wang, Adeniyi C Adeola, Junying Zhang, Hai-Bing Xie, Ya-Ping Zhang

Database, Volume 2017, 2017, bax048, https://doi.org/10.1093/database/bax048

Benchmarking distributed data warehouse solutions for storing genomic variant information

Marek S. Wiewiórka, Dawid P. Wysakowicz, Michał J. Okoniewski, Tomasz Gambin

Database, Volume 2017, 2017, bax049, https://doi.org/10.1093/database/bax049

CTD² Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network

Bülent Arman Aksoy, Vlado Dančík, Kenneth Smith, Jessica N. Mazerik, Zhou Ji, Benjamin Gross, Olga Nikolova, Nadia Jaber, Andrea Califano, Stuart L. Schreiber, Daniela S. Gerhard, Leandro C. Hermida, Subhashini Jagu, Chris Sander, Aris Floratos, Paul A. Clemons

Database, Volume 2017, 2017, bax054, https://doi.org/10.1093/database/bax054

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Elsevier’s approach to the bioCADDIE 2016 Dataset Retrieval Challenge

Antony Scerri, John Kuriakose, Amit Ajit Deshmane, Mark Stanger, Peter Cotroneo, Rebekah Moore, Raj Naik, Anita de Waard

Database, Volume 2017, 2017, bax056, https://doi.org/10.1093/database/bax056

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BioSearch: a semantic search engine for Bio2RDF

Wei Hu, Honglei Qiu, Jiacheng Huang, Michel Dumontier

Database, Volume 2017, 2017, bax059, https://doi.org/10.1093/database/bax059

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A RESTful application programming interface for the PubMLST molecular typing and genome databases

Keith A. Jolley, James E. Bray, Martin C. J. Maiden

Database, Volume 2017, 2017, bax060, https://doi.org/10.1093/database/bax060

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A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge

Trevor Cohen, Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, George Alter, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Hua Xu

Database, Volume 2017, 2017, bax061, https://doi.org/10.1093/database/bax061

Multi-field query expansion is effective for biomedical dataset retrieval

Mohamed Reda Bouadjenek, Karin Verspoor

Database, Volume 2017, 2017, bax062, https://doi.org/10.1093/database/bax062

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KiPho: malaria parasite kinome and phosphatome portal

Rajan Pandey, Pawan Kumar, Dinesh Gupta

Database, Volume 2017, 2017, bax063, https://doi.org/10.1093/database/bax063

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Impact of translation on named-entity recognition in radiology texts

Luís Campos, Vasco Pedro, Francisco Couto

Database, Volume 2017, 2017, bax064, https://doi.org/10.1093/database/bax064

Query expansion using MeSH terms for dataset retrieval: OHSU at the bioCADDIE 2016 dataset retrieval challenge

Theodore B Wright, David Ball, William Hersh

Database, Volume 2017, 2017, bax065, https://doi.org/10.1093/database/bax065

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AllerBase: a comprehensive allergen knowledgebase

Kiran Kadam, Rajiv Karbhal, V. K. Jayaraman, Sangeeta Sawant, Urmila Kulkarni-Kale

Database, Volume 2017, 2017, bax066, https://doi.org/10.1093/database/bax066

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RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions

Nadav Topaz, Nazia Mojib, Aroon T. Chande, Julia Kubanek, I. King Jordan

Database, Volume 2017, 2017, bax067, https://doi.org/10.1093/database/bax067

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First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes

Carlos-Francisco Méndez-Cruz, Socorro Gama-Castro, Citlalli Mejía-Almonte, Marco-Polo Castillo-Villalba, Luis-José Muñiz-Rascado, Julio Collado-Vides

Database, Volume 2017, 2017, bax070, https://doi.org/10.1093/database/bax070

Improving taxonomic accuracy for fungi in public sequence databases: applying ‘one name one species’ in well-defined genera with Trichoderma/Hypocrea as a test case

Barbara Robbertse, Pooja K Strope, Priscila Chaverri, Romina Gazis, Stacy Ciufo, Michael Domrachev, Conrad L Schoch

Database, Volume 2017, 2017, bax072, https://doi.org/10.1093/database/bax072

An online analytical processing multi-dimensional data warehouse for malaria data

S M Niaz Arifin, Gregory R Madey, Alexander Vyushkov, Benoit Raybaud, Thomas R Burkot, Frank H Collins

Database, Volume 2017, 2017, bax073, https://doi.org/10.1093/database/bax073

FishTrace: a genetic catalogue of European fishes

Antonella Zanzi, Jann Th Martinsohn

Database, Volume 2017, 2017, bax075, https://doi.org/10.1093/database/bax075

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Database of resistance related metabolites in Wheat Fusarium head blight Disease (MWFD)

Anuradha Surendra, Miroslava Cuperlovic-Culf

Database, Volume 2017, 2017, bax076, https://doi.org/10.1093/database/bax076

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In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research

Ankit Sharma, Vrushali Deshpande, Madankumar Ghatge, Rajani Kanth Vangala

Database, Volume 2017, 2017, bax077, https://doi.org/10.1093/database/bax077

Proficiency of data interpretation: identification of signaling SNPs/specific loci for coronary artery disease

Asma N Cheema, Samantha L Rosenthal, M Ilyas Kamboh

Database, Volume 2017, 2017, bax078, https://doi.org/10.1093/database/bax078

eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality

Ruoyao Ding, Emmanuel Boutet, Damien Lieberherr, Michel Schneider, Michael Tognolli, Cathy H Wu, K Vijay-Shanker, Cecilia N Arighi

Database, Volume 2017, 2017, bax081, https://doi.org/10.1093/database/bax081

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Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy

Nai-Wen Chang, Hong-Jie Dai, Yung-Yu Shih, Chi-Yang Wu, Mira Anne C Dela Rosa, Rofeamor P Obena, Yu-Ju Chen, Wen-Lian Hsu, Yen-Jen Oyang

Database, Volume 2017, 2017, bax082, https://doi.org/10.1093/database/bax082

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Improving average ranking precision in user searches for biomedical research datasets

Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch

Database, Volume 2017, 2017, bax083, https://doi.org/10.1093/database/bax083

DLREFD: a database providing associations of long non-coding RNAs, environmental factors and phenotypes

Ya-Zhou Sun, De-Hong Zhang, Zhong Ming, Jian-Qiang Li, Xing Chen

Database, Volume 2017, 2017, bax084, https://doi.org/10.1093/database/bax084

YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules

Wei-Sheng Wu, Pin-Han Chen, Tsung-Te Chen, Yan-Yuan Tseng

Database, Volume 2017, 2017, bax085, https://doi.org/10.1093/database/bax085

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Gold-standard ontology-based anatomical annotation in the CRAFT Corpus

Michael Bada, Nicole Vasilevsky, William A Baumgartner, Jr, Melissa Haendel, Lawrence E Hunter

Database, Volume 2017, 2017, bax087, https://doi.org/10.1093/database/bax087

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A semantic-based workflow for biomedical literature annotation

Pedro Sernadela, José Luís Oliveira

Database, Volume 2017, 2017, bax088, https://doi.org/10.1093/database/bax088

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Collaborative relation annotation and quality analysis in Markyt environment

Martín Pérez-Pérez, Gael Pérez-Rodríguez, Florentino Fdez-Riverola, Anália Lourenço

Database, Volume 2017, 2017, bax090, https://doi.org/10.1093/database/bax090

Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts

Yanshan Wang, Majid Rastegar-Mojarad, Ravikumar Komandur-Elayavilli, Hongfang Liu

Database, Volume 2017, 2017, bax091, https://doi.org/10.1093/database/bax091

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Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research

Tasnia Tahsin, Davy Weissenbacher, Demetrius Jones-Shargani, Daniel Magee, Matteo Vaiente, Graciela Gonzalez, Matthew Scotch

Database, Volume 2017, 2017, bax093, https://doi.org/10.1093/database/bax093

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HisgAtlas 1.0: a human immunosuppression gene database

Yuan Liu, Mengqi He, Dan Wang, Lihong Diao, Jinying Liu, Li Tang, Shuzhen Guo, Fuchu He, Dong Li

Database, Volume 2017, 2017, bax094, https://doi.org/10.1093/database/bax094

GRONS: a comprehensive genetic resource of nicotine and smoking

Zhonghai Fang, Yichen Yang, Yanshi Hu, Ming D Li, Ju Wang

Database, Volume 2017, 2017, bax097, https://doi.org/10.1093/database/bax097

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PCOSBase: a manually curated database of polycystic ovarian syndrome

Nor Afiqah-Aleng, Sarahani Harun, Mohd Rusman Arief A-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein

Database, Volume 2017, 2017, bax098, https://doi.org/10.1093/database/bax098

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Technical Report

blend4php: a PHP API for galaxy

Connor Wytko, Brian Soto, Stephen P. Ficklin

Database, Volume 2017, 2017, baw154, https://doi.org/10.1093/database/baw154

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CHOmine: an integrated data warehouse for CHO systems biology and modeling

Matthias P. Gerstl, Michael Hanscho, David E. Ruckerbauer, Jürgen Zanghellini, Nicole Borth

Database, Volume 2017, 2017, bax034, https://doi.org/10.1093/database/bax034

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Edaphostat: interactive ecological analysis of soil organism occurrences and preferences from the Edaphobase data warehouse

Jonas Hausen, Björn Scholz-Starke, Ulrich Burkhardt, Stephan Lesch, Sebastian Rick, David Russell, Martina Roß-Nickoll, Richard Ottermanns

Database, Volume 2017, 2017, bax080, https://doi.org/10.1093/database/bax080

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Database Tool

MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota

Aitor Blanco-Míguez, Alberto Gutiérrez-Jácome, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez

Database, Volume 2017, 2017, baw157, https://doi.org/10.1093/database/baw157

FirebrowseR: an R client to the Broad Institute’s Firehose Pipeline

Mario Deng, Johannes Brägelmann, Ivan Kryukov, Nuno Saraiva-Agostinho, Sven Perner

Database, Volume 2017, 2017, baw160, https://doi.org/10.1093/database/baw160

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Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage

Fay-Wei Li, Catherine A. Rushworth, James B. Beck, Michael D. Windham

Database, Volume 2017, 2017, baw169, https://doi.org/10.1093/database/baw169

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PCPPI: a comprehensive database for the prediction of Penicillium–crop protein–protein interactions

Junyang Yue, Danfeng Zhang, Rongjun Ban, Xiaojing Ma, Danyang Chen, Guangwei Li, Jia Liu, Michael Wisniewski, Samir Droby, Yongsheng Liu

Database, Volume 2017, 2017, baw170, https://doi.org/10.1093/database/baw170

The HIV oligonucleotide database (HIVoligoDB)

João Carneiro, Adriana Resende, Filipe Pereira

Database, Volume 2017, 2017, bax005, https://doi.org/10.1093/database/bax005

GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii)

Zhenzhen Xu, Jing Liu, Wanchao Ni, Zhen Peng, Yue Guo, Wuwei Ye, Fang Huang, Xianggui Zhang, Peng Xu, Qi Guo, Xinlian Shen, Jianchang Du

Database, Volume 2017, 2017, bax013, https://doi.org/10.1093/database/bax013

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miRnalyze: an interactive database linking tool to unlock intuitive microRNA regulation of cell signaling pathways

Sankha Subhra Das, Mithun James, Sandip Paul, Nishant Chakravorty

Database, Volume 2017, 2017, bax015, https://doi.org/10.1093/database/bax015

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GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species

Richard J. Challis, Sujai Kumar, Lewis Stevens, Mark Blaxter

Database, Volume 2017, 2017, bax039, https://doi.org/10.1093/database/bax039

TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species

Sony Malhotra, Grace Mugumbate, Tom L. Blundell, Alicia P. Higueruelo

Database, Volume 2017, 2017, bax041, https://doi.org/10.1093/database/bax041

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NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy

Yueqiong Ni, Kasper Jensen, Irene Kouskoumvekaki, Gianni Panagiotou

Database, Volume 2017, 2017, bax044, https://doi.org/10.1093/database/bax044

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MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data

Max Ruas, V. Guignon, G. Sempere, J. Sardos, Y. Hueber, H. Duvergey, A. Andrieu, R. Chase, C. Jenny, T. Hazekamp, B. Irish, K. Jelali, J. Adeka, T. Ayala-Silva, C.P. Chao, J. Daniells, B. Dowiya, B. Effa effa, L. Gueco … M. Rouard

Database, Volume 2017, 2017, bax046, https://doi.org/10.1093/database/bax046

LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis

Felipe Torres, Raúl Arias-Carrasco, José C. Caris-Maldonado, Aldina Barral, Vinicius Maracaja-Coutinho, Artur T. L. De Queiroz

Database, Volume 2017, 2017, bax047, https://doi.org/10.1093/database/bax047

The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations

Yaxin Chen, Mijuan Shi, Wanting Zhang, Yingyin Cheng, Yaping Wang, Xiao-Qin Xia

Database, Volume 2017, 2017, bax051, https://doi.org/10.1093/database/bax051

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New extension software modules to enhance searching and display of transcriptome data in Tripal databases

Ming Chen, Nathan Henry, Abdullah Almsaeed, Xiao Zhou, Jill Wegrzyn, Stephen Ficklin, Margaret Staton

Database, Volume 2017, 2017, bax052, https://doi.org/10.1093/database/bax052

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Cancer Odor Database (COD): a critical databank for cancer diagnosis research

Sajjad Janfaza, Maryam Banan Nojavani, Babak Khorsand, Maryam Nikkhah, Javad Zahiri

Database, Volume 2017, 2017, bax055, https://doi.org/10.1093/database/bax055

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NRDTD: a database for clinically or experimentally supported non-coding RNAs and drug targets associations

Xing Chen, Ya-Zhou Sun, De-Hong Zhang, Jian-Qiang Li, Gui-Ying Yan, Ji-Yong An, Zhu-Hong You

Database, Volume 2017, 2017, bax057, https://doi.org/10.1093/database/bax057

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RegulatorDB: a resource for the analysis of yeast transcriptional regulation

John A. Choi, John J. Wyrick

Database, Volume 2017, 2017, bax058, https://doi.org/10.1093/database/bax058

IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes

I-Man Ng, Jia-Hsin Huang, Shang-Chi Tsai, Huai-Kuang Tsai

Database, Volume 2017, 2017, bax069, https://doi.org/10.1093/database/bax069

EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species

Leandro Costa Nascimento, Marcela Mendes Salazar, Jorge Lepikson-Neto, Eduardo Leal Oliveira Camargo, Lucas Salera Parreiras, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle

Database, Volume 2017, 2017, bax079, https://doi.org/10.1093/database/bax079

PlantCircNet: a database for plant circRNA–miRNA–mRNA regulatory networks

Peijing Zhang, Xianwen Meng, Hongjun Chen, Yongjing Liu, Jitong Xue, Yincong Zhou, Ming Chen

Database, Volume 2017, 2017, bax089, https://doi.org/10.1093/database/bax089

Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases

Sook Jung, Taein Lee, Chun-Huai Cheng, Stephen Ficklin, Jing Yu, Jodi Humann, Dorrie Main

Database, Volume 2017, 2017, bax092, https://doi.org/10.1093/database/bax092

PTS: a pharmaceutical target seeker

Peng Ding, Xin Yan, Zhihong Liu, Jiewen Du, Yunfei Du, Yutong Lu, Di Wu, Yuehua Xu, Huihao Zhou, Qiong Gu, Jun Xu

Database, Volume 2017, 2017, bax095, https://doi.org/10.1093/database/bax095

Erratum

RAIN: RNA–protein Association and Interaction Networks

Database, Volume 2017, 2017, bax007, https://doi.org/10.1093/database/bax007

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Strategies towards digital and semi-automated curation in RegulonDB

Fabio Rinaldi, Oscar Lithgow, Socorro Gama-Castro, Hilda Solano, Alejandra López-Fuentes, Luis José Muñiz Rascado, Cecilia Ishida-Gutiérrez, Carlos-Francisco Méndez-Cruz, Julio Collado-Vides

Database, Volume 2017, 2017, bax012, https://doi.org/10.1093/database/bax029

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Meeting Report

Better living through ontologies at the Immune Epitope Database

Randi Vita, James A. Overton, Alessandro Sette, Bjoern Peters

Database, Volume 2017, 2017, bax014, https://doi.org/10.1093/database/bax014

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Database Update

MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups

Simon Jon McIlroy, Rasmus Hansen Kirkegaard, Bianca McIlroy, Marta Nierychlo, Jannie Munk Kristensen, Søren Michael Karst, Mads Albertsen, Per Halkjær Nielsen

Database, Volume 2017, 2017, bax016, https://doi.org/10.1093/database/bax016

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation

Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew Laird, Ian Longden, Glenn Proctor, Steve Searle, Daniel Staines, Kieron Taylor, Alessandro Vullo, Andrew Yates, Daniel Zerbino, Paul Flicek

Database, Volume 2017, 2017, bax020, https://doi.org/10.1093/database/bax020

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RetrogeneDB–a database of plant and animal retrocopies

Wojciech Rosikiewicz, Michał Kabza, Jan G. Kosiński, Joanna Ciomborowska-Basheer, Magdalena R. Kubiak, Izabela Makałowska

Database, Volume 2017, 2017, bax038, https://doi.org/10.1093/database/bax038

MiRIAD update: using alternative polyadenylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes

Ludwig C. Hinske, Felipe R. C. dos Santos, Daniel T. Ohara, Lucila Ohno-Machado, Simone Kreth, Pedro A. F. Galante

Database, Volume 2017, 2017, bax053, https://doi.org/10.1093/database/bax053

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SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets

Jin Li, Ching-San Tseng, Antonio Federico, Franjo Ivankovic, Yi-Shuian Huang, Alfredo Ciccodicola, Maurice S. Swanson, Peng Yu

Database, Volume 2017, 2017, bax071, https://doi.org/10.1093/database/bax071

Echinobase: an expanding resource for echinoderm genomic information

Parul Kudtarkar, R. Andrew Cameron

Database, Volume 2017, 2017, bax074, https://doi.org/10.1093/database/bax074

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Update notifications for the BioCyc collection of databases

Suzanne Paley, Peter D Karp

Database, Volume 2017, 2017, bax086, https://doi.org/10.1093/database/bax086

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Corrigendum

AnnoSys—implementation of a generic annotation system for schema-based data using the example of biodiversity collection data

L. Suhrbier, W.-H. Kusber, O. Tschöpe, A. Güntsch, W. G. Berendsohn

Database, Volume 2017, 2017, bax036, https://doi.org/10.1093/database/bax036

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Biocuration in the structure–function linkage database: the anatomy of a superfamily

Gemma L. Holliday, Shoshana D. Brown, Eyal Akiva, David Mischel, Michael A. Hicks, John H. Morris, Conrad C. Huang, Elaine C. Meng, Scott C.-H. Pegg, Thomas E. Ferrin, Patricia C. Babbitt

Database, Volume 2017, 2017, bax045, https://doi.org/10.1093/database/bax045