Database - The Journal of Biological Databases and Curation, Volume 2017

Volume 2017, 2017

Original Articles

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  Tian Li, Guo-Qing Pan, Charles R. Vossbrinck, Jin-Shan Xu, Chunfeng Li, Jie Chen, Meng-Xian Long, Ming Yang, Xiaofei Xu, Chen Xu, Bettina A. Debrunner-Vossbrinck, Zeyang Zhou:
  SilkPathDB: a comprehensive resource for the study of silkworm pathogens. bax001
• 
  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:
  Outreach and online training services at the Saccharomyces Genome Database. bax002
• 
  Anton Güntsch, Roger Hyam, Gregor Hagedorn, Simon Chagnoux, Dominik Röpert, Ana Casino, Gabi Droege, Falko Glöckler, Karsten Gödderz, Quentin Groom, Jana Hoffmann, Ayco Holleman, Matús Kempa, Hanna Koivula, Karol Marhold, Nicky Nicolson, Vincent S. Smith, Dagmar Triebel:
  Actionable, long-term stable and semantic web compatible identifiers for access to biological collection objects. bax003
• 
  Junko Yabuzaki:
  Carotenoids Database: structures, chemical fingerprints and distribution among organisms. bax004

Database Tool

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  João Carneiro, Adriana Resende, Filipe Pereira:
  The HIV oligonucleotide database (HIVoligoDB). bax005

Original Articles

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  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:
  Biocuration in the structure-function linkage database: the anatomy of a superfamily. bax006
• 
  Chris Armit, Bill Hill, Shanmugasundaram Venkataraman, Kenneth McLeod, Albert Burger, Richard A. Baldock:
  The 'straight mouse': defining anatomical axes in 3D embryo models. bax010
• 
  Sage T. Hellerstedt, Robert S. Nash, Shuai Weng, Kelley M. Paskov, Edith D. Wong, Kalpana Karra, Stacia R. Engel, J. Michael Cherry:
  Curated protein information in the Saccharomyces genome database. bax011
• 
  Fabio Rinaldi, Oscar Lithgow-Serrano, Socorro Gama-Castro, Hilda Solano-Lira, Alejandra López-Fuentes, Luis Muñiz-Rascado, Cecilia Ishida-Gutiérrez, Carlos-Francisco Méndez-Cruz, Julio Collado-Vides:
  Strategies towards digital and semi-automated curation in RegulonDB. bax012

Meeting Report

• 
  Randi Vita, James A. Overton, Alessandro Sette, Bjoern Peters:
  Better living through ontologies at the Immune Epitope Database. bax014

Database Tool

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  Sankha Subhra Das, Mithun James, Sandip Paul, Nishant Chakravorty:
  miRnalyze: an interactive database linking tool to unlock intuitive microRNA regulation of cell signaling pathways. bax015

Database Update

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  Simon Jon McIlroy, Rasmus Hansen Kirkegaard, Bianca McIlroy, Marta Nierychlo, Jannie Munk Kristensen, Søren Michael Karst, Mads Albertsen, Per Halkjær Nielsen:
  MiDAS 2.0: an ecosystem-specific taxonomy and online database for the organisms of wastewater treatment systems expanded for anaerobic digester groups. bax016

Original Articles

• 
  Lutz Suhrbier, Wolf-Henning Kusber, Okka Tschöpe, Anton Güntsch, Walter G. Berendsohn:
  AnnoSys - implementation of a generic annotation system for schema-based data using the example of biodiversity collection data. bax018

Database Update

• 
  Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew R. Laird, Ian Longden, Glenn Proctor, Steve Searle, Daniel M. Staines, Kieron R. Taylor, Alessandro Vullo, Andrew D. Yates, Daniel R. Zerbino, Paul Flicek:
  Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation. bax020

Original Articles

• 
  Mohamed Reda Bouadjenek, Karin Verspoor, Justin Zobel:
  Literature consistency of bioinformatics sequence databases is effective for assessing record quality. bax021
• 
  Hedvig Tordai, Kristóf Jakab, Gergely Gyimesi, Kinga András, Anna Brózik, Balázs Sarkadi, Tamás Hegedüs:
  ABCMdb reloaded: updates on mutations in ATP binding cassette proteins. bax023
• 
  Rezarta Islamaj Dogan, Sun Kim, Andrew Chatr-aryamontri, Christie S. Chang, Rose Oughtred, Jennifer M. Rust, W. John Wilbur, Donald C. Comeau, Kara Dolinski, Mike Tyers:
  The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions. baw147

Technical Report

• 
  Connor Wytko, Brian Soto, Stephen P. Ficklin:
  blend4php: a PHP API for galaxy. baw154

Original Articles

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  K. E. Ravikumar, Majid Rastegar-Mojarad, Hongfang Liu:
  BELMiner: adapting a rule-based relation extraction system to extract biological expression language statements from bio-medical literature evidence sentences. baw156

Database Tool

• 
  Aitor Blanco-Míguez, Alberto Gutiérrez-Jácome, Florentino Fdez-Riverola, Anália Lourenço, Borja Sánchez:
  MAHMI database: a comprehensive MetaHit-based resource for the study of the mechanism of action of the human microbiota. baw157
• 
  Mario Deng, Johannes Brägelmann, Ivan Kryukov, Nuno Saraiva-Agostinho, Sven Perner:
  FirebrowseR: an R client to the Broad Institute's Firehose Pipeline. baw160

Original Articles

• 
  Qingyu Chen, Justin Zobel, Karin Verspoor:
  Duplicates, redundancies and inconsistencies in the primary nucleotide databases: a descriptive study. baw163
• 
  James C. Wallace, Jesse A. Port, Marissa N. Smith, Elaine M. Faustman:
  FARME DB: a functional antibiotic resistance element database. baw165
• 
  Ferhat Aydin, Zehra Melce Hüsünbeyi, Arzucan Özgür:
  Automatic query generation using word embeddings for retrieving passages describing experimental methods. baw166
• 
  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:
  RAIN: RNA-protein Association and Interaction Networks. baw167
• 
  Michal Wojciech Szczesniak, Michal Kabza, Justyna A. Karolak, Malgorzata Rydzanicz, Dorota M. Nowak, Barbara Ginter-Matuszewska, Piotr Polakowski, Rafal Ploski, Jacek P. Szaflik, Marzena Gajecka:
  KTCNlncDB - a first platform to investigate lncRNAs expressed in human keratoconus and non-keratoconus corneas. baw168

Database Tool

• 
  Fay-Wei Li, Catherine A. Rushworth, James B. Beck, Michael D. Windham:
  Boechera microsatellite website: an online portal for species identification and determination of hybrid parentage. baw169
• 
  Junyang Yue, Danfeng Zhang, Rongjun Ban, Xiaojing Ma, Danyang Chen, Guangwei Li, Jia Liu, Michael Wisniewski, Samir Droby, Yongsheng Liu:
  PCPPI: a comprehensive database for the prediction of Penicillium-crop protein-protein interactions. baw170

Original Articles

• 
  Ana Rosa Cortázar, José A. Oguiza, Ana M. Aransay, José Luis Lavín:
  VerSeDa: vertebrate secretome database. baw171
• 
  Cyrielle Gasc, Antony Constantin, Faouzi Jaziri, Pierre Peyret:
  OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture. baw172

Erratum

• 
  RAIN: RNA-protein Association and Interaction Networks. bax007

Original Article

• 
  Roberto Vera Alvarez, Newton Medeiros Vidal, Gina A. Garzón-Martínez, Luz S. Barrero, David Landsman, Leonardo Mariño-Ramírez:
  Workflow and web application for annotating NCBI BioProject transcriptome data. bax008
• 
  Steven T. Hill, Ramcharan Sudarsanam, John Henning, David Hendrix:
  HopBase: a unified resource for Humulus genomics. bax009

Erratum

• 
  Fabio Rinaldi, Oscar Lithgow-Serrano, Socorro Gama-Castro, Hilda Solano-Lira, Alejandra López-Fuentes, Luis Muñiz-Rascado, Cecilia Ishida-Gutiérrez, Carlos-Francisco Méndez-Cruz, Julio Collado-Vides:
  Erratum: Strategies towards digital and semi-automated curation in RegulonDB. bax012

Database tool

• 
  Zhenzhen Xu, Jing Liu, Wanchao Ni, Zhen Peng, Yue Guo, Wuwei Ye, Fang Huang, Xianggui Zhang, Peng Xu, Qi Guo, Xinlian Shen, Jianchang Du:
  GrTEdb: the first web-based database of transposable elements in cotton (Gossypium raimondii). bax013

Original Article

• 
  Xiangying Jiang, Martin Ringwald, Judith A. Blake, Hagit Shatkay:
  Effective biomedical document classification for identifying publications relevant to the mouse Gene Expression Database (GXD). bax017
• 
  Víctor Suárez-Paniagua, Isabel Segura-Bedmar, Paloma Martínez:
  Exploring convolutional neural networks for drug-drug interaction extraction. bax019
• 
  Guillaume Postic, Yassine Ghouzam, Catherine Etchebest, Jean-Christophe Gelly:
  TMPL: a database of experimental and theoretical transmembrane protein models positioned in the lipid bilayer. bax022
• 
  Jinghang Gu, Fuqing Sun, Longhua Qian, Guodong Zhou:
  Chemical-induced disease relation extraction via convolutional neural network. bax024
• 
  Tim E. Putman, Sebastien Lelong, Sebastian Burgstaller-Muehlbacher, Andra Waagmeester, Colin M. Diesh, Nathan A. Dunn, Monica C. Munoz-Torres, Gregory S. Stupp, Chunlei Wu, Andrew I. Su, Benjamin M. Good:
  WikiGenomes: an open web application for community consumption and curation of gene annotation data in Wikidata. bax025
• 
  Mathurin Dorel, Eric Viara, Emmanuel Barillot, Andrei Yu. Zinovyev, Inna Kuperstein:
  NaviCom: a web application to create interactive molecular network portraits using multi-level omics data. bax026
• 
  Honghan Wu, Anika Oellrich, Christine Girges, Bernard de Bono, Tim J. P. Hubbard, Richard J. B. Dobson:
  Automated PDF highlighting to support faster curation of literature for Parkinson's and Alzheimer's disease. bax027
• 
  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:
  GeneHancer: genome-wide integration of enhancers and target genes in GeneCards. bax028
• 
  Yalbi Itzel Balderas-Martínez, Fabio Rinaldi, Gabriela Contreras, Hilda Solano-Lira, Mishael Sánchez-Pérez, Julio Collado-Vides, Moisés Selman, Annie Pardo:
  Improving biocuration of microRNAs in diseases: a case study in idiopathic pulmonary fibrosis. bax030
• 
  Taner Z. Sen, Bremen L. Braun, David A. Schott, John L. Portwood II, Mary L. Schaeffer, Lisa C. Harper, Jack M. Gardiner, Ethalinda K. S. Cannon, Carson M. Andorf:
  Surveying the Maize community for their diversity and pedigree visualization needs to prioritize tool development and curation. bax031
• 
  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, David C. Farrow, David Hunter, Taylar Morgan, Kayla Shore, Victoria Guzman, Allison Izsak, Danielle E. Dixon, Andrew Cridge, Liliana M. Cano, Xiaolong Cao, Haobo Jiang, Nan Leng, Shannon Johnson, Brandi L. Cantarel, Stephen Richards, Adam C. English, Robert G. Shatters, Christopher P. Childers, Mei-Ju Chen, Wayne B. Hunter, Michelle Cilia, Lukas A. Mueller, Monica C. Munoz-Torres, David Nelson, Monica Poelchau, Joshua B. Benoit, Helen Wiersma-Koch, Tom D'Elia, Susan J. Brown:
  Improved annotation of the insect vector of citrus greening disease: biocuration by a diverse genomics community. bax032
• 
  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:
  TriatoKey: a web and mobile tool for biodiversity identification of Brazilian triatomine species. bax033

Technical Report

• 
  Matthias P. Gerstl, Michael Hanscho, David E. Ruckerbauer, Jürgen Zanghellini, Nicole Borth:
  CHOmine: an integrated data warehouse for CHO systems biology and modeling. bax034

Original Article

• 
  Matheus Eloy Franco, Tamires Aparecida Bitencourt, Mozart Marins, Ana Lúcia Fachin:
  In silico characterization of tandem repeats in Trichophyton rubrum and related dermatophytes provides new insights into their role in pathogenesis. bax035

Corrigendum

• 
  Lutz Suhrbier, Wolf-Henning Kusber, Okka Tschöpe, Anton Güntsch, Walter G. Berendsohn:
  AnnoSys - implementation of a generic annotation system for schema-based data using the example of biodiversity collection data. bax036

Original Article

• 
  Yanjun Xu, Haixiu Yang, Tan Wu, Qun Dong, Zeguo Sun, Desi Shang, Feng Li, Yingqi Xu, Fei Su, Siyao Liu, Yunpeng Zhang, Xia Li:
  BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases. bax037

Database update

• 
  Wojciech Rosikiewicz, Michal Kabza, Jan Kosinski, Joanna Ciomborowska-Basheer, Magdalena R. Kubiak, Izabela Makalowska:
  RetrogeneDB-a database of plant and animal retrocopies. bax038

Database tool

• 
  Richard J. Challis, Sujai Kumar, Lewis Stevens, Mark L. Blaxter:
  GenomeHubs: simple containerized setup of a custom Ensembl database and web server for any species. bax039

Original Article

• 
  Luc Mottin, Emilie Pasche, Julien Gobeill, Valentine Rech de Laval, Anne Gleizes, Pierre-André Michel, Amos Bairoch, Pascale Gaudet, Patrick Ruch:
  Triage by ranking to support the curation of protein interactions. bax040

Database tool

• 
  Sony Malhotra, Grace Mugumbate, Tom L. Blundell, Alicia P. Higueruelo:
  TIBLE: a web-based, freely accessible resource for small-molecule binding data for mycobacterial species. bax041

Original Article

• 
  Steve Lefever, Jasper Anckaert, Pieter-Jan Volders, Manuel Luypaert, Jo Vandesompele, Pieter Mestdagh:
  decodeRNA - predicting non-coding RNA functions using guilt-by-association. bax042
• 
  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, Miguel Angel Mayer, Sandra Montagud-Romero, Roser Nadal, Jordi Ortiz, Francisco Javier Pavon, Ezequiel Perez, Marta Rodríguez-Arias, Antonia Serrano, Marta Torrens, Vincent Warnault, Ferran Sanz, Laura I. Furlong:
  Text mining and expert curation to develop a database on psychiatric diseases and their genes. bax043

Database tool

• 
  Yueqiong Ni, Kasper Jensen, Irene Kouskoumvekaki, Gianni Panagiotou:
  NutriChem 2.0: exploring the effect of plant-based foods on human health and drug efficacy. bax044

Corrigendum

• 
  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:
  Biocuration in the structure-function linkage database: the anatomy of a superfamily. bax045

Database tool

• 
  Max Ruas, Valentin Guignon, Guilhem Sempéré, Julie Sardos, Yann Hueber, H. Duvergey, Alain Andrieu, Richard Chase, Christophe Jenny, Tom Hazekamp, Brian M. Irish, K. Jelali, J. Adeka, Tomás Ayala-Silva, C. P. Chao, Jeff W. Daniells, B. Dowiya, B. Effa effa, L. Gueco, L. Herradura, L. Ibobondji, E. Kempenaers, J. Kilangi, S. Muhangi, P. Ngo Xuan, J. Paofa, Claudie Pavis, Deless Thiémélé, Colette Tossou, Jeffrey Sandoval, Asti Sutanto, G. Vangu Paka, Guilian Yi, Ines van den houwe, Nicolas Roux, Mathieu Rouard:
  MGIS: managing banana (Musa spp.) genetic resources information and high-throughput genotyping data. bax046
• 
  Felipe Torres, Raúl Arias-Carrasco, José C. Caris-Maldonado, Aldina Barral, Vinicius Maracaja-Coutinho, Artur T. L. De Queiroz:
  LeishDB: a database of coding gene annotation and non-coding RNAs in Leishmania braziliensis. bax047

Original Article

• 
  Zhongyin Zhou, Aimin Li, Newton Otieno Otecko, Yan-Hu Liu, David M. Irwin, Lu Wang, Adeniyi C. Adeola, Junying Zhang, Hai-Bing Xie, Ya-Ping Zhang:
  PigVar: a database of pig variations and positive selection signatures. bax048
• 
  Marek S. Wiewiórka, Dawid P. Wysakowicz, Michal J. Okoniewski, Tomasz Gambin:
  Benchmarking distributed data warehouse solutions for storing genomic variant information. bax049

Corrigendum

• 
  Lei Sheng, Haiyang Jiang, Hanwei Yan, Xiaoyu Li, Yongxiang Lin, Hui Ye, Beijiu Cheng:
  MGFD: the maize gene families database. bax050

Database tool

• 
  Yaxin Chen, Mijuan Shi, Wanting Zhang, Yingyin Cheng, Yaping Wang, Xiaoqin Xia:
  The Grass Carp Genome Database (GCGD): an online platform for genome features and annotations. bax051
• 
  Ming Chen, Nathan Henry, Abdullah Almsaeed, Xiao Zhou, Jill L. Wegrzyn, Stephen P. Ficklin, Margaret Staton:
  New extension software modules to enhance searching and display of transcriptome data in Tripal databases. bax052

Database update

• 
  Christian Hinske, Felipe R. C. dos Santos, Daniel T. Ohara, Lucila Ohno-Machado, Simone Kreth, Pedro A. F. Galante:
  MiRIAD update: using alternative polyadeniylation, protein interaction network analysis and additional species to enhance exploration of the role of intragenic miRNAs and their host genes. bax053

Original Article

• 
  Bülent Arman Aksoy, Vlado Dancík, Kenneth Smith, Jessica N. Mazerik, Zhou Ji, Benjamin E. Gross, Olga Nikolova, Nadia Jaber, Andrea Califano, Stuart L. Schreiber, Daniela S. Gerhard, Leandro Hermida, Subhashini Jagu, Chris Sander, Aris Floratos, Paul A. Clemons:
  CTD2 Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network. bax054

Database tool

• 
  Sajjad Janfaza, Maryam Banan Nojavani, Babak Khorsand, Maryam Nikkhah, Javad Zahiri:
  Cancer Odor Database (COD): a critical databank for cancer diagnosis research. bax055

Original Article

• 
  Antony Scerri, John Kuriakose, Amit Ajit Deshmane, Mark Stanger, Peter Cotroneo, Rebekah Moore, Raj Naik, Anita de Waard:
  Elsevier's approach to the bioCADDIE 2016 Dataset Retrieval Challenge. bax056

Database tool

• 
  Xing Chen, Ya-Zhou Sun, De-Hong Zhang, Jian-Qiang Li, Guiying Yan, Ji-Yong An, Zhu-Hong You:
  NRDTD: a database for clinically or experimentally supported non-coding RNAs and drug targets associations. bax057
• 
  John A. Choi, John J. Wyrick:
  RegulatorDB: a resource for the analysis of yeast transcriptional regulation. bax058

Original Article

• 
  Wei Hu, Honglei Qiu, Jiacheng Huang, Michel Dumontier:
  BioSearch: a semantic search engine for Bio2RDF. bax059
• 
  Keith A. Jolley, James E. Bray, Martin C. J. Maiden:
  A RESTful application programming interface for the PubMLST molecular typing and genome databases. bax060
• 
  Trevor Cohen, Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, George Alter, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Hua Xu:
  A publicly available benchmark for biomedical dataset retrieval: the reference standard for the 2016 bioCADDIE dataset retrieval challenge. bax061
• 
  Mohamed Reda Bouadjenek, Karin Verspoor:
  Multi-field query expansion is effective for biomedical dataset retrieval. bax062
• 
  Rajan Pandey, Pawan Kumar, Dinesh Gupta:
  KiPho: malaria parasite kinome and phosphatome portal. bax063
• 
  Luís Campos, Vasco Pedro, Francisco M. Couto:
  Impact of translation on named-entity recognition in radiology texts. bax064
• 
  Theodore B. Wright, David Ball, William R. Hersh:
  Query expansion using MeSH terms for dataset retrieval: OHSU at the bioCADDIE 2016 dataset retrieval challenge. bax065
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  Kiran Kadam, Rajiv Karbhal, V. K. Jayaraman, Sangeeta Sawant, Urmila Kulkarni-Kale:
  AllerBase: a comprehensive allergen knowledgebase. bax066
• 
  Nadav Topaz, Nazia Mojib, Aroon T. Chande, Julia Kubanek, I. King Jordan:
  RampDB: a web application and database for the exploration and prediction of receptor activity modifying protein interactions. bax067

Perspective/Opinion

• 
  Kirk Roberts, Anupama E. Gururaj, Xiaoling Chen, Saeid Pournejati, William R. Hersh, Dina Demner-Fushman, Lucila Ohno-Machado, Trevor Cohen, Hua Xu:
  Information retrieval for biomedical datasets: the 2016 bioCADDIE dataset retrieval challenge. bax068

Database tool

• 
  I-Man Ng, Jia-Hsin Huang, Shang-Chi Tsai, Huai-Kuang Tsai:
  IsoPlot: a database for comparison of mRNA isoforms in fruit fly and mosquitoes. bax069

Original Article

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  Carlos-Francisco Méndez-Cruz, Socorro Gama-Castro, Citlalli Mejía-Almonte, Marco Polo Castillo-Villalba, Luis Muñiz-Rascado, Julio Collado-Vides:
  First steps in automatic summarization of transcription factor properties for RegulonDB: classification of sentences about structural domains and regulated processes. bax070

Database update

• 
  Jin Li, Ching-San Tseng, Antonio Federico, Franjo Ivankovic, Yi-Shuian Huang, Alfredo Ciccodicola, Maurice S. Swanson, Peng Yu:
  SFMetaDB: a comprehensive annotation of mouse RNA splicing factor RNA-Seq datasets. bax071

Original Article

• 
  Barbara Robbertse, Pooja K. Strope, Priscila Chaverri, Romina Gazis, Stacy Ciufo, Michael Domrachev, Conrad L. Schoch:
  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. bax072
• 
  S. M. Niaz Arifin, Gregory R. Madey, Alexander Vyushkov, Benoit Raybaud, Thomas R. Burkot, Frank H. Collins:
  An online analytical processing multi-dimensional data warehouse for malaria data. bax073

Database update

• 
  Parul Kudtarkar, R. Andrew Cameron:
  Echinobase: an expanding resource for echinoderm genomic information. bax074

Original Article

• 
  Antonella Zanzi, Jann Th. Martinsohn:
  FishTrace: a genetic catalogue of European fishes. bax075
• 
  Anuradha Surendra, Miroslava Cuperlovic-Culf:
  Database of resistance related metabolites in Wheat Fusarium head blight Disease (MWFD). bax076
• 
  Ankit Sharma, Vrushali Deshpande, Madankumar Ghatge, Rajani Kanth Vangala:
  In-Cardiome: integrated knowledgebase for coronary artery disease enabling translational research. bax077
• 
  Asma N. Cheema, Samantha L. Rosenthal, M. Ilyas Kamboh:
  Proficiency of data interpretation: identification of signaling SNPs/specific loci for coronary artery disease. bax078

Database tool

• 
  Leandro Costa Nascimento, Marcela Mendes Salazar, Jorge Lepikson-Neto, Eduardo Leal Oliveira Camargo, Lucas Salera Parreiras, Gonçalo Amarante Guimarães Pereira, Marcelo Falsarella Carazzolle:
  EUCANEXT: an integrated database for the exploration of genomic and transcriptomic data from Eucalyptus species. bax079

Technical Report

• 
  Jonas Hausen, Björn Scholz-Starke, Ulrich Burkhardt, Stephan Lesch, Sebastian Rick, David Russell, Martina Roß-Nickoll, Richard Ottermanns:
  Edaphostat: interactive ecological analysis of soil organism occurrences and preferences from the Edaphobase data warehouse. bax080

Original Article

• 
  Ruoyao Ding, Emmanuel Boutet, Damien Lieberherr, Michel Schneider, Michael Tognolli, Cathy H. Wu, K. Vijay-Shanker, Cecilia N. Arighi:
  eGenPub, a text mining system for extending computationally mapped bibliography for UniProt Knowledgebase by capturing centrality. bax081
• 
  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:
  Biomarker identification of hepatocellular carcinoma using a methodical literature mining strategy. bax082
• 
  Douglas Teodoro, Luc Mottin, Julien Gobeill, Arnaud Gaudinat, Thérèse Vachon, Patrick Ruch:
  Improving average ranking precision in user searches for biomedical research datasets. bax083
• 
  Ya-Zhou Sun, De-Hong Zhang, Zhong Ming, Jian-Qiang Li, Xing Chen:
  DLREFD: a database providing associations of long non-coding RNAs, environmental factors and phenotypes. bax084
• 
  Wei-Sheng Wu, Pin-Han Chen, Tsung-Te Chen, Yan Yuan Tseng:
  YGMD: a repository for yeast cooperative transcription factor sets and their target gene modules. bax085

Database update

• 
  Suzanne M. Paley, Peter D. Karp:
  Update notifications for the BioCyc collection of databases. bax086

Original Article

• 
  Michael Bada, Nicole A. Vasilevsky, William A. Baumgartner Jr., Melissa A. Haendel, Lawrence E. Hunter:
  Gold-standard ontology-based anatomical annotation in the CRAFT Corpus. bax087
• 
  Pedro Sernadela, José Luís Oliveira:
  A semantic-based workflow for biomedical literature annotation. bax088

Database tool

• 
  Peijing Zhang, Xianwen Meng, Hongjun Chen, Yongjing Liu, Jitong Xue, Yincong Zhou, Ming Chen:
  PlantCircNet: a database for plant circRNA-miRNA-mRNA regulatory networks. bax089

Original Article

• 
  Martín Pérez-Pérez, Gael Pérez Rodríguez, Florentino Fdez-Riverola, Anália Lourenço:
  Collaborative relation annotation and quality analysis in Markyt environment. bax090
• 
  Yanshan Wang, Majid Rastegar-Mojarad, Ravikumar Komandur Elayavilli, Hongfang Liu:
  Leveraging word embeddings and medical entity extraction for biomedical dataset retrieval using unstructured texts. bax091

Database tool

• 
  Sook Jung, Taein Lee, Chun-Huai Cheng, Stephen P. Ficklin, Jing Yu, Jodi L. Humann, Dorrie Main:
  Extension modules for storage, visualization and querying of genomic, genetic and breeding data in Tripal databases. bax092

Original Article

• 
  Tasnia Tahsin, Davy Weissenbacher, Demetrius Jones-Shargani, Daniel Magee, Matteo Vaiente, Graciela Gonzalez, Matthew Scotch:
  Named entity linking of geospatial and host metadata in GenBank for advancing biomedical research. bax093
• 
  Yuan Liu, Mengqi He, Dan Wang, Lihong Diao, Jinying Liu, Li Tang, Shuzhen Guo, Fuchu He, Dong Li:
  HisgAtlas 1.0: a human immunosuppression gene database. bax094

Database tool

• 
  Peng Ding, Xin Yan, Zhihong Liu, Jiewen Du, Yunfei Du, Yutong Lu, Di Wu, Yuehua Xu, Huihao Zhou, Qiong Gu, Jun Xu:
  PTS: a pharmaceutical target seeker. bax095

Original Article

• 
  Zhonghai Fang, Yichen Yang, Yanshi Hu, Ming D. Li, Ju Wang:
  GRONS: a comprehensive genetic resource of nicotine and smoking. bax097
• 
  Nor Afiqah-Aleng, Sarahani Harun, Mohd Rusman Arief A.-Rahman, Nor Azlan Nor Muhammad, Zeti-Azura Mohamed-Hussein:
  PCOSBase: a manually curated database of polycystic ovarian syndrome. bax098