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Volume 2015;  2015

Database Tool

FR database 1.0: a resource focused on fruit development and ripening
Junyang Yue, Xiaojing Ma, Rongjun Ban, Qianli Huang, Wenjie Wang, Jia Liu, Yongsheng Liu
Database (Oxford) 2015; 2015: bav002. Published online 2015 Feb 27. doi: 10.1093/database/bav002
PMCID:
PMC4343184
Abstract Article PDF–850K
MnTEdb, a collective resource for mulberry transposable elements
Bi Ma, Tian Li, Zhonghuai Xiang, Ningjia He
Database (Oxford) 2015; 2015: bav004. Published online 2015 Feb 27. doi: 10.1093/database/bav004
PMCID:
PMC4343074
Abstract Article PDF–1.1M
PreDREM: a database of predicted DNA regulatory motifs from 349 human cell and tissue samples
Yiyu Zheng, Xiaoman Li, Haiyan Hu
Database (Oxford) 2015; 2015: bav007. Published online 2015 Feb 27. doi: 10.1093/database/bav007
PMCID:
PMC4343075
Abstract Article PDF–1.2M
TeloPIN: a database of telomeric proteins interaction network in mammalian cells
Zhenhua Luo, Zhiming Dai, Xiaowei Xie, Xuyang Feng, Dan Liu, Zhou Songyang, Yuanyan Xiong
Database (Oxford) 2015; 2015: bav018. Published online 2015 Mar 18. doi: 10.1093/database/bav018
PMCID:
PMC4365144
Abstract Article PDF–877K
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, Raja Mazumder
Database (Oxford) 2015; 2015: bav019. Published online 2015 Mar 28. doi: 10.1093/database/bav019
PMCID:
PMC4377087
Abstract Article PDF–872K
The Listeria monocytogenes strain 10403S BioCyc database
Renato H. Orsi, Teresa M. Bergholz, Martin Wiedmann, Kathryn J. Boor
Database (Oxford) 2015; 2015: bav027. Published online 2015 Mar 28. doi: 10.1093/database/bav027
PMCID:
PMC4377088
Abstract Article PDF–1.9M
DisGeNET: a discovery platform for the dynamical exploration of human diseases and their genes
Janet Piñero, Núria Queralt-Rosinach, Àlex Bravo, Jordi Deu-Pons, Anna Bauer-Mehren, Martin Baron, Ferran Sanz, Laura I. Furlong
Database (Oxford) 2015; 2015: bav028. Published online 2015 Apr 15. doi: 10.1093/database/bav028
PMCID:
PMC4397996
Abstract Article PDF–2.3M
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, Raja Mazumder
Database (Oxford) 2015; 2015: bav032. Published online 2015 Apr 4. doi: 10.1093/database/bav032
PMCID:
PMC4385274
Abstract Article PDF–1.2M
miRGate: a curated database of human, mouse and rat miRNA–mRNA targets
Eduardo Andrés-León, Daniel González Peña, Gonzalo Gómez-López, David G. Pisano
Database (Oxford) 2015; 2015: bav035. Published online 2015 Apr 8. doi: 10.1093/database/bav035
PMCID:
PMC4390609
Abstract Article PDF–521K
NeuroPep: a comprehensive resource of neuropeptides
Yan Wang, Mingxia Wang, Sanwen Yin, Richard Jang, Jian Wang, Zhidong Xue, Tao Xu
Database (Oxford) 2015; 2015: bav038. Published online 2015 Apr 29. doi: 10.1093/database/bav038
PMCID:
PMC4414954
Abstract Article PDF–719K
CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization
Silvia Frias, Kenneth Bryan, Fiona S. L. Brinkman, David J. Lynn
Database (Oxford) 2015; 2015: bav041. Published online 2015 May 7. doi: 10.1093/database/bav041
PMCID:
PMC4423409
Abstract Article PDF–527K
DroughtDB: an expert-curated compilation of plant drought stress genes and their homologs in nine species
Svenja Alter, Kai C. Bader, Manuel Spannagl, Yu Wang, Eva Bauer, Chris-Carolin Schön, Klaus F. X. Mayer
Database (Oxford) 2015; 2015: bav046. Published online 2015 May 15. doi: 10.1093/database/bav046
PMCID:
PMC4433318
Abstract Article PDF–837K
GeneStoryTeller: a mobile app for quick and comprehensive information retrieval of human genes
Stergiani V. Eleftheriou, Marilena M. Bourdakou, Emmanouil I. Athanasiadis, George M. Spyrou
Database (Oxford) 2015; 2015: bav048. Published online 2015 Jun 8. doi: 10.1093/database/bav048
PMCID:
PMC4460399
Abstract Article PDF–650K
HCSD: the human cancer secretome database
Amir Feizi, Amir Banaei-Esfahani, Jens Nielsen
Database (Oxford) 2015; 2015: bav051. Published online 2015 Jun 13. doi: 10.1093/database/bav051
PMCID:
PMC4480035
Abstract Article PDF–1.4M
Drug-Path: a database for drug-induced pathways
Hui Zeng, Chengxiang Qiu, Qinghua Cui
Database (Oxford) 2015; 2015: bav061. Published online 2015 Jun 30. doi: 10.1093/database/bav061
PMCID:
PMC4485432
Abstract Article PDF–572K
OCDB: a database collecting genes, miRNAs and drugs for obsessive-compulsive disorder
Anna P. Privitera, Rosario Distefano, Hugo A. Wefer, Alfredo Ferro, Alfredo Pulvirenti, Rosalba Giugno
Database (Oxford) 2015; 2015: bav069. Published online 2015 Jul 29. doi: 10.1093/database/bav069
PMCID:
PMC4519680
Abstract Article PDF–1.0M
Database of RNA binding protein expression and disease dynamics (READ DB)
Seyedsasan Hashemikhabir, Yaseswini Neelamraju, Sarath Chandra Janga
Database (Oxford) 2015; 2015: bav072. Published online 2015 Jul 25. doi: 10.1093/database/bav072
PMCID:
PMC4515031
Abstract Article PDF–467K
Carbohydrate Structure Database: tools for statistical analysis of bacterial, plant and fungal glycomes
K.S. Egorova, A.N. Kondakova, Ph.V. Toukach
Database (Oxford) 2015; 2015: bav073. Published online 2015 Sep 3. doi: 10.1093/database/bav073
PMCID:
PMC4559136
Abstract Article PDF–4.2M
MESSI: metabolic engineering target selection and best strain identification tool
Kang Kang, Jun Li, Boon Leong Lim, Gianni Panagiotou
Database (Oxford) 2015; 2015: bav076. Published online 2015 Aug 8. doi: 10.1093/database/bav076
PMCID:
PMC4529744
Abstract Article PDF–692K
CicArVarDB: SNP and InDel database for advancing genetics research and breeding applications in chickpea
Dadakhalandar Doddamani, Aamir W. Khan, Mohan A. V. S. K Katta, Gaurav Agarwal, Mahendar Thudi, Pradeep Ruperao, David Edwards, Rajeev K. Varshney
Database (Oxford) 2015; 2015: bav078. Published online 2015 Aug 18. doi: 10.1093/database/bav078
PMCID:
PMC4541373
Abstract Article PDF–907K
Co-LncRNA: investigating the lncRNA combinatorial effects in GO annotations and KEGG pathways based on human RNA-Seq data
Zheng Zhao, Jing Bai, Aiwei Wu, Yuan Wang, Jinwen Zhang, Zishan Wang, Yongsheng Li, Juan Xu, Xia Li
Database (Oxford) 2015; 2015: bav082. Published online 2015 Sep 10. doi: 10.1093/database/bav082
PMCID:
PMC4565967
Abstract Article PDF–1.1M
BaMBa: towards the integrated management of Brazilian marine environmental data
Pedro Milet Meirelles, Luiz M. R. Gadelha, Jr, Ronaldo Bastos Francini-Filho, Rodrigo Leão de Moura, Gilberto Menezes Amado-Filho, Alex Cardoso Bastos, Rodolfo Pinheiro da Rocha Paranhos, Carlos Eduardo Rezende, Jean Swings, Eduardo Siegle, Nils Edvin Asp Neto, Sigrid Neumann Leitão, Ricardo Coutinho, Marta Mattoso, Paulo S. Salomon, Rogério A.B. Valle, Renato Crespo Pereira, Ricardo Henrique Kruger, Cristiane Thompson, Fabiano L. Thompson
Database (Oxford) 2015; 2015: bav088. Published online 2015 Oct 10. doi: 10.1093/database/bav088
PMCID:
PMC4600340
Abstract Article PDF–696K
CRCDA—Comprehensive resources for cancer NGS data analysis
Manonanthini Thangam, Ramesh Kumar Gopal
Database (Oxford) 2015; 2015: bav092. Published online 2015 Oct 8. doi: 10.1093/database/bav092
PMCID:
PMC4597977
Abstract Article PDF–546K
WaspAtlas: a Nasonia vitripennis gene database and analysis platform
Nathaniel J. Davies, Eran Tauber
Database (Oxford) 2015; 2015: bav103. Published online 2015 Oct 9. doi: 10.1093/database/bav103
PMCID:
PMC4599445
Abstract Article PDF–898K
SymbioGenomesDB: a database for the integration and access to knowledge on host–symbiont relationships
Mariana Reyes-Prieto, Carlos Vargas-Chávez, Amparo Latorre, Andrés Moya
Database (Oxford) 2015; 2015: bav109. Published online 2015 Nov 25. doi: 10.1093/database/bav109
PMCID:
PMC4659445
Abstract Article PDF–1.6M
ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases
Teresia M. Buza, Sherman W. Jack, Halid Kirunda, Margaret L. Khaitsa, Mark L. Lawrence, Stephen Pruett, Daniel G. Peterson
Database (Oxford) 2015; 2015: bav110. Published online 2015 Nov 18. doi: 10.1093/database/bav110
PMCID:
PMC4651161
Abstract Article PDF–1.1M
Kiwifruit Information Resource (KIR): a comparative platform for kiwifruit genomics
Junyang Yue, Jian Liu, Rongjun Ban, Wei Tang, Lin Deng, Zhangjun Fei, Yongsheng Liu
Database (Oxford) 2015; 2015: bav113. Published online 2015 Dec 9. doi: 10.1093/database/bav113
PMCID:
PMC4674624
Abstract Article PDF–872K
ProtoBug: functional families from the complete proteomes of insects
Nadav Rappoport, Michal Linial
Database (Oxford) 2015; 2015: bau122. Published online 2015 Apr 24. doi: 10.1093/database/bau122
PMCID:
PMC4408594
Abstract Article PDF–1.1M
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, Mary Shimoyama
Database (Oxford) 2015; 2015: bau129. Published online 2015 Jan 25. doi: 10.1093/database/bau129
PMCID:
PMC4305386
Abstract Article PDF–939K
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study
J. M. Villaveces, R. C. Jiménez, P. Porras, N. del-Toro, M. Duesbury, M. Dumousseau, S. Orchard, H. Choi, P. Ping, N. C. Zong, M. Askenazi, B. H. Habermann, Henning Hermjakob
Database (Oxford) 2015; 2015: bau131. Published online 2015 Feb 3. doi: 10.1093/database/bau131
PMCID:
PMC4316181
Abstract Article PDF–687K

Database Update

SCAN database: facilitating integrative analyses of cytosine modification and expression QTL
Wei Zhang, Eric R. Gamazon, Xu Zhang, Anuar Konkashbaev, Cong Liu, Keely L. Szilágyi, M. Eileen Dolan, Nancy J. Cox
Database (Oxford) 2015; 2015: bav025. Published online 2015 Mar 26. doi: 10.1093/database/bav025
PMCID:
PMC4375357
Abstract Article PDF–595K
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, An-Yuan Guo
Database (Oxford) 2015; 2015: bav029. Published online 2015 Apr 15. doi: 10.1093/database/bav029
PMCID:
PMC4397995
Abstract Article PDF–969K
ChloroMitoSSRDB 2.00: more genomes, more repeats, unifying SSRs search patterns and on-the-fly repeat detection
Gaurav Sablok, G. V. Padma Raju, Suresh B. Mudunuri, Ratna Prabha, Dhananjaya P. Singh, Vesselin Baev, Galina Yahubyan, Peter J. Ralph, Nicola La Porta
Database (Oxford) 2015; 2015: bav084. Published online 2015 Sep 25. doi: 10.1093/database/bav084
PMCID:
PMC4584093
Abstract Article PDF–691K
Brassica database (BRAD) version 2.0: integrating and mining Brassicaceae species genomic resources
Xiaobo Wang, Jian Wu, Jianli Liang, Feng Cheng, Xiaowu Wang
Database (Oxford) 2015; 2015: bav093. Published online 2015 Nov 20. doi: 10.1093/database/bav093
PMCID:
PMC4653866
Abstract Article PDF–910K
LymPHOS 2.0: an update of a phosphosite database of primary human T cells
Tien Dung Nguyen, Oriol Vidal-Cortes, Oscar Gallardo, Joaquin Abian, Montserrat Carrascal
Database (Oxford) 2015; 2015: bav115. Published online 2015 Dec 23. doi: 10.1093/database/bav115
PMCID:
PMC4691341
Abstract Article PDF–1.5M
HitPredict version 4: comprehensive reliability scoring of physical protein–protein interactions from more than 100 species
Yosvany López, Kenta Nakai, Ashwini Patil
Database (Oxford) 2015; 2015: bav117. Published online 2015 Dec 21. doi: 10.1093/database/bav117
PMCID:
PMC4691340
Abstract Article PDF–989K

Meeting Report

Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat
Patricia C. Babbitt, Pantelis G. Bagos, Amos Bairoch, Alex Bateman, Arnaud Chatonnet, Mark Jinan Chen, David J. Craik, Robert D. Finn, David Gloriam, Daniel H. Haft, Bernard Henrissat, Gemma L. Holliday, Vignir Isberg, Quentin Kaas, David Landsman, Nicolas Lenfant, Gerard Manning, Nozomi Nagano, Narayanaswamy Srinivasan, Claire O’Donovan, Kim D. Pruitt, Ramanathan Sowdhamini, Neil D. Rawlings, Milton H. Saier, Jr., Joanna L. Sharman, Michael Spedding, Konstantinos D. Tsirigos, Ake Vastermark, Gerrit Vriend
Database (Oxford) 2015; 2015: bav063. Published online 2015 Jul 11. doi: 10.1093/database/bav063
PMCID:
PMC4499208
Abstract Article PDF–624K

Original Articles

EcoliNet: a database of cofunctional gene network for Escherichia coli
Hanhae Kim, Jung Eun Shim, Junha Shin, Insuk Lee
Database (Oxford) 2015; 2015: bav001. Published online 2015 Feb 2. doi: 10.1093/database/bav001
PMCID:
PMC4314589
Abstract Article PDF–915K

Database Tool

LocSigDB: a database of protein localization signals
Simarjeet Negi, Sanjit Pandey, Satish M. Srinivasan, Akram Mohammed, Chittibabu Guda
Database (Oxford) 2015; 2015: bav003. Published online 2015 Feb 27. doi: 10.1093/database/bav003
PMCID:
PMC4343182
Abstract Article PDF–1.0M
Automatic concept recognition using the Human Phenotype Ontology reference and test suite corpora
Tudor Groza, Sebastian Köhler, Sandra Doelken, Nigel Collier, Anika Oellrich, Damian Smedley, Francisco M Couto, Gareth Baynam, Andreas Zankl, Peter N. Robinson
Database (Oxford) 2015; 2015: bav005. Published online 2015 Feb 27. doi: 10.1093/database/bav005
PMCID:
PMC4343077
Abstract Article PDF–923K
PathCards: multi-source consolidation of human biological pathways
Frida Belinky, Noam Nativ, Gil Stelzer, Shahar Zimmerman, Tsippi Iny Stein, Marilyn Safran, Doron Lancet
Database (Oxford) 2015; 2015: bav006. Published online 2015 Feb 27. doi: 10.1093/database/bav006
PMCID:
PMC4343183
Abstract Article PDF–1.3M
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, Adrian Tsang
Database (Oxford) 2015; 2015: bav008. Published online 2015 Mar 8. doi: 10.1093/database/bav008
PMCID:
PMC4352688
Abstract Article PDF–1.1M
Shared resources, shared costs—leveraging biocuration resources
Sandra Orchard, Henning Hermjakob
Database (Oxford) 2015; 2015: bav009. Published online 2015 Mar 16. doi: 10.1093/database/bav009
PMCID:
PMC4360620
Abstract Article PDF–770K
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, Eurie L. Hong
Database (Oxford) 2015; 2015: bav010. Published online 2015 Mar 16. doi: 10.1093/database/bav010
PMCID:
PMC4360730
Abstract Article PDF–1.1M
RNABP COGEST: a resource for investigating functional RNAs
Sohini Bhattacharya, Shriyaa Mittal, Swati Panigrahi, Purshotam Sharma, Preethi S. P., Rahul Paul, Sukanya Halder, Antarip Halder, Dhananjay Bhattacharyya, Abhijit Mitra
Database (Oxford) 2015; 2015: bav011. Published online 2015 Mar 16. doi: 10.1093/database/bav011
PMCID:
PMC4360618
Abstract Article PDF–774K
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, Aron Marchler-Bauer
Database (Oxford) 2015; 2015: bav012. Published online 2015 Mar 11. doi: 10.1093/database/bav012
PMCID:
PMC4356950
Abstract Article PDF–1.4M
EpiDBase: a manually curated database for small molecule modulators of epigenetic landscape
Saurabh Loharch, Isha Bhutani, Kamal Jain, Pawan Gupta, Debendra K. Sahoo, Raman Parkesh
Database (Oxford) 2015; 2015: bav013. Published online 2015 Mar 16. doi: 10.1093/database/bav013
PMCID:
PMC4360624
Abstract Article PDF–1.0M
LMPID: A manually curated database of linear motifs mediating protein–protein interactions
Debasree Sarkar, Tanmoy Jana, Sudipto Saha
Database (Oxford) 2015; 2015: bav014. Published online 2015 Mar 16. doi: 10.1093/database/bav014
PMCID:
PMC4360622
Abstract Article PDF–895K
Colorectal cancer drug target prediction using ontology-based inference and network analysis
Cui Tao, Jingchun Sun, W. Jim Zheng, Junjie Chen, Hua Xu
Database (Oxford) 2015; 2015: bav015. Published online 2015 Mar 26. doi: 10.1093/database/bav015
PMCID:
PMC4375358
Abstract Article PDF–608K
Scaling drug indication curation through crowdsourcing
Ritu Khare, John D. Burger, John S. Aberdeen, David W. Tresner-Kirsch, Theodore J. Corrales, Lynette Hirchman, Zhiyong Lu
Database (Oxford) 2015; 2015: bav016. Published online 2015 Mar 22. doi: 10.1093/database/bav016
PMCID:
PMC4369375
Abstract Article PDF–1.1M
PTGBase: an integrated database to study tandem duplicated genes in plants
Jingyin Yu, Tao Ke, Sadia Tehrim, Fengming Sun, Boshou Liao, Wei Hua
Database (Oxford) 2015; 2015: bav017. Published online 2015 Mar 22. doi: 10.1093/database/bav017
PMCID:
PMC4369376
Abstract Article PDF–865K
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, Cecilia N. Arighi
Database (Oxford) 2015; 2015: bav020. Published online 2015 Mar 31. doi: 10.1093/database/bav020
PMCID:
PMC4381107
Abstract Article PDF–2.2M
GBIS: the information system of the German Genebank
Markus Oppermann, Stephan Weise, Claudia Dittmann, Helmut Knüpffer
Database (Oxford) 2015; 2015: bav021. Published online 2015 May 7. doi: 10.1093/database/bav021
PMCID:
PMC4423411
Abstract Article PDF–1.1M
Comprehensive data resources and analytical tools for pathological association of aminoacyl tRNA synthetases with cancer
Ji-Hyun Lee, Sungyong You, Do Young Hyeon, Byeongsoo Kang, Hyerim Kim, Kyoung Mii Park, Byungwoo Han, Daehee Hwang, Sunghoon Kim
Database (Oxford) 2015; 2015: bav022. Published online 2015 Mar 29. doi: 10.1093/database/bav022
PMCID:
PMC4377328
Abstract Article PDF–1.9M
LOTUS-DB: an integrative and interactive database for Nelumbo nucifera study
Kun Wang, Jiao Deng, Rebecca Njeri Damaris, Mei Yang, Liming Xu, Pingfang Yang
Database (Oxford) 2015; 2015: bav023. Published online 2015 Mar 27. doi: 10.1093/database/bav023
PMCID:
PMC4383347
Abstract Article PDF–1.5M
Standard development at the Human Variome Project
Timothy D. Smith, Mauno Vihinen
Database (Oxford) 2015; 2015: bav024. Published online 2015 Mar 26. doi: 10.1093/database/bav024
PMCID:
PMC4375356
Abstract Article PDF–287K
CHOPIN: a web resource for the structural and functional proteome of Mycobacterium tuberculosis
Bernardo Ochoa-Montaño, Nishita Mohan, Tom L. Blundell
Database (Oxford) 2015; 2015: bav026. Published online 2015 Mar 31. doi: 10.1093/database/bav026
PMCID:
PMC4381106
Abstract Article PDF–471K
Causal biological network database: a comprehensive platform of causal biological network models focused on the pulmonary and vascular systems
Stéphanie Boué, Marja Talikka, Jurjen Willem Westra, William Hayes, Anselmo Di Fabio, Jennifer Park, Walter K. Schlage, Alain Sewer, Brett Fields, Sam Ansari, Florian Martin, Emilija Veljkovic, Renee Kenney, Manuel C. Peitsch, Julia Hoeng
Database (Oxford) 2015; 2015: bav030. Published online 2015 Apr 17. doi: 10.1093/database/bav030
PMCID:
PMC4401337
Abstract Article PDF–2.2M
dbPSP: a curated database for protein phosphorylation sites in prokaryotes
Zhicheng Pan, Bangshan Wang, Ying Zhang, Yongbo Wang, Shahid Ullah, Ren Jian, Zexian Liu, Yu Xue
Database (Oxford) 2015; 2015: bav031. Published online 2015 Apr 3. doi: 10.1093/database/bav031
PMCID:
PMC4385273
Abstract Article PDF–1.5M
BioSurfDB: knowledge and algorithms to support biosurfactants and biodegradation studies
Jorge S. Oliveira, Wydemberg Araújo, Ana Isabela Lopes Sales, Alaine de Brito Guerra, Sinara Carla da Silva Araújo, Ana Tereza Ribeiro de Vasconcelos, Lucymara F. Agnez-Lima, Ana Teresa Freitas
Database (Oxford) 2015; 2015: bav033. Published online 2015 Mar 31. doi: 10.1093/database/bav033
PMCID:
PMC4381105
Abstract Article PDF–322K
Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature
Guocai Chen, Jieyi Zhao, Trevor Cohen, Cui Tao, Jingchun Sun, Hua Xu, Elmer V. Bernstam, Andrew Lawson, Jia Zeng, Amber M. Johnson, Vijaykumar Holla, Ann M. Bailey, Humberto Lara-Guerra, Beate Litzenburger, Funda Meric-Bernstam, W. Jim Zheng
Database (Oxford) 2015; 2015: bav034. Published online 2015 Apr 8. doi: 10.1093/database/bav034
PMCID:
PMC4390608
Abstract Article PDF–1.1M
Follicle Online: an integrated database of follicle assembly, development and ovulation
Juan Hua, Bo Xu, Yifan Yang, Rongjun Ban, Furhan Iqbal, Howard J Cooke, Yuanwei Zhang, Qinghua Shi
Database (Oxford) 2015; 2015: bav036. Published online 2015 Apr 29. doi: 10.1093/database/bav036
PMCID:
PMC4414955
Abstract Article PDF–1.0M
PEIMAN 1.0: Post-translational modification Enrichment, Integration and Matching ANalysis
Payman Nickchi, Mohieddin Jafari, Shiva Kalantari
Database (Oxford) 2015; 2015: bav037. Published online 2015 Apr 23. doi: 10.1093/database/bav037
PMCID:
PMC4408379
Abstract Article PDF–1.7M
novPTMenzy: a database for enzymes involved in novel post-translational modifications
Shradha Khater, Debasisa Mohanty
Database (Oxford) 2015; 2015: bav039. Published online 2015 Apr 29. doi: 10.1093/database/bav039
PMCID:
PMC4414956
Abstract Article PDF–1.7M
Moving the mountain: analysis of the effort required to transform comparative anatomy into computable anatomy
Wasila Dahdul, T. Alexander Dececchi, Nizar Ibrahim, Hilmar Lapp, Paula Mabee
Database (Oxford) 2015; 2015: bav040. Published online 2015 May 13. doi: 10.1093/database/bav040
PMCID:
PMC4429748
Abstract Article PDF–628K
AtmiRNET: a web-based resource for reconstructing regulatory networks of Arabidopsis microRNAs
Chia-Hung Chien, Yi-Fan Chiang-Hsieh, Yi-An Chen, Chi-Nga Chow, Nai-Yun Wu, Ping-Fu Hou, Wen-Chi Chang
Database (Oxford) 2015; 2015: bav042. Published online 2015 May 13. doi: 10.1093/database/bav042
PMCID:
PMC4429749
Abstract Article PDF–1.6M
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, Marc Robinson-Rechavi
Database (Oxford) 2015; 2015: bav043. Published online 2015 May 9. doi: 10.1093/database/bav043
PMCID:
PMC4425939
Abstract Article PDF–688K
GermlncRNA: a unique catalogue of long non-coding RNAs and associated regulations in male germ cell development
Alfred Chun-Shui Luk, Huayan Gao, Sizhe Xiao, Jinyue Liao, Daxi Wang, Jiajie Tu, Owen M. Rennert, Wai-Yee Chan, Tin-Lap Lee
Database (Oxford) 2015; 2015: bav044. Published online 2015 May 16. doi: 10.1093/database/bav044
PMCID:
PMC4433719
Abstract Article PDF–1.4M
MIsoMine: a genome-scale high-resolution data portal of expression, function and networks at the splice isoform level in the mouse
Hong-Dong Li, Gilbert S. Omenn, Yuanfang Guan
Database (Oxford) 2015; 2015: bav045. Published online 2015 May 7. doi: 10.1093/database/bav045
PMCID:
PMC4423410
Abstract Article PDF–1.0M
GraP: platform for functional genomics analysis of Gossypium raimondii
Liwei Zhang, Jinyan Guo, Qi You, Xin Yi, Yi Ling, Wenying Xu, Jinping Hua, Zhen Su
Database (Oxford) 2015; 2015: bav047. Published online 2015 May 16. doi: 10.1093/database/bav047
PMCID:
PMC4433718
Abstract Article PDF–1.4M
An Ebola virus-centered knowledge base
Maulik R. Kamdar, Michel Dumontier
Database (Oxford) 2015; 2015: bav049. Published online 2015 Jun 8. doi: 10.1093/database/bav049
PMCID:
PMC4460400
Abstract Article PDF–1.2M
A general concept for consistent documentation of computational analyses
Peter Ebert, Fabian Müller, Karl Nordström, Thomas Lengauer, Marcel H. Schulz
Database (Oxford) 2015; 2015: bav050. Published online 2015 Jun 8. doi: 10.1093/database/bav050
PMCID:
PMC4460408
Abstract Article PDF–1017K
dbHiMo: a web-based epigenomics platform for histone-modifying enzymes
Jaeyoung Choi, Ki-Tae Kim, Aram Huh, Seomun Kwon, Changyoung Hong, Fred O. Asiegbu, Junhyun Jeon, Yong-Hwan Lee
Database (Oxford) 2015; 2015: bav052. Published online 2015 Jun 8. doi: 10.1093/database/bav052
PMCID:
PMC4460409
Abstract Article PDF–793K
kpath: integration of metabolic pathway linked data
Ismael Navas-Delgado, María Jesús García-Godoy, Esteban López-Camacho, Maciej Rybinski, Armando Reyes-Palomares, Miguel Ángel Medina, José F. Aldana-Montes
Database (Oxford) 2015; 2015: bav053. Published online 2015 Jun 8. doi: 10.1093/database/bav053
PMCID:
PMC4460419
Abstract Article PDF–1.0M
BioAcoustica: a free and open repository and analysis platform for bioacoustics
Edward Baker, Ben W. Price, S. D. Rycroft, Jon Hill, Vincent S. Smith
Database (Oxford) 2015; 2015: bav054. Published online 2015 Jun 8. doi: 10.1093/database/bav054
PMCID:
PMC4460420
Abstract Article PDF–1.3M
CrisprGE: a central hub of CRISPR/Cas-based genome editing
Karambir Kaur, Himani Tandon, Amit Kumar Gupta, Manoj Kumar
Database (Oxford) 2015; 2015: bav055. Published online 2015 Jun 27. doi: 10.1093/database/bav055
PMCID:
PMC4483309
Abstract Article PDF–632K
Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications
Tamás Hegedűs, Pururawa Mayank Chaubey, György Várady, Edit Szabó, Hajnalka Sarankó, Lia Hofstetter, Bernd Roschitzki, Bruno Stieger, Balázs Sarkadi
Database (Oxford) 2015; 2015: bav056. Published online 2015 Jun 13. doi: 10.1093/database/bav056
PMCID:
PMC4480073
Abstract Article PDF–465K
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, Julia Hoeng
Database (Oxford) 2015; 2015: bav057. Published online 2015 Jun 16. doi: 10.1093/database/bav057
PMCID:
PMC5630939
Abstract Article PDF–5.2M
Pre_GI: a global map of ontological links between horizontally transferred genomic islands in bacterial and archaeal genomes
Rian Pierneef, Louis Cronje, Oliver Bezuidt, Oleg N. Reva
Database (Oxford) 2015; 2015: bav058. Published online 2015 Jun 16. doi: 10.1093/database/bav058
PMCID:
PMC5630688
Abstract Article PDF–653K
G4RNA: an RNA G-quadruplex database
Jean-Michel Garant, Mikael J. Luce, Michelle S. Scott, Jean-Pierre Perreault
Database (Oxford) 2015; 2015: bav059. Published online 2015 Jun 16. doi: 10.1093/database/bav059
PMCID:
PMC5630937
Abstract Article PDF–546K
SInCRe—structural interactome computational resource for Mycobacterium tuberculosis
Rahul Metri, Sridhar Hariharaputran, Gayatri Ramakrishnan, Praveen Anand, Upadhyayula S. Raghavender, Bernardo Ochoa-Montaño, Alicia P. Higueruelo, Ramanathan Sowdhamini, Nagasuma R. Chandra, Tom L. Blundell, Narayanaswamy Srinivasan
Database (Oxford) 2015; 2015: bav060. Published online 2015 Jun 30. doi: 10.1093/database/bav060
PMCID:
PMC4485431
Abstract Article PDF–771K
MiDAS: the field guide to the microbes of activated sludge
Simon Jon McIlroy, Aaron Marc Saunders, Mads Albertsen, Marta Nierychlo, Bianca McIlroy, Aviaja Anna Hansen, Søren Michael Karst, Jeppe Lund Nielsen, Per Halkjær Nielsen
Database (Oxford) 2015; 2015: bav062. Published online 2015 Jun 27. doi: 10.1093/database/bav062
PMCID:
PMC4483311
Abstract Article PDF–669K
BEAN 2.0: an integrated web resource for the identification and functional analysis of type III secreted effectors
Xiaobao Dong, Xiaotian Lu, Ziding Zhang
Database (Oxford) 2015; 2015: bav064. Published online 2015 Jun 27. doi: 10.1093/database/bav064
PMCID:
PMC4483310
Abstract Article PDF–923K
EvoDB: a database of evolutionary rate profiles, associated protein domains and phylogenetic trees for PFAM-A
Andrew Ndhlovu, Pierre M. Durand, Scott Hazelhurst
Database (Oxford) 2015; 2015: bav065. Published online 2015 Jul 2. doi: 10.1093/database/bav065
PMCID:
PMC4492416
Abstract Article PDF–572K
toxoMine: an integrated omics data warehouse for Toxoplasma gondii systems biology research
David B. Rhee, Matthew McKnight Croken, Kevin R. Shieh, Julie Sullivan, Gos Micklem, Kami Kim, Aaron Golden
Database (Oxford) 2015; 2015: bav066. Published online 2015 Jun 30. doi: 10.1093/database/bav066
PMCID:
PMC4485433
Abstract Article PDF–1.2M
EpiFactors: a comprehensive database of human epigenetic factors and complexes
Yulia A. Medvedeva, Andreas Lennartsson, Rezvan Ehsani, Ivan V. Kulakovskiy, Ilya E. Vorontsov, Pouda Panahandeh, Grigory Khimulya, Takeya Kasukawa, The FANTOM Consortium, Finn Drabløs
Database (Oxford) 2015; 2015: bav067. Published online 2015 Jul 7. doi: 10.1093/database/bav067
PMCID:
PMC4494013
Abstract Article PDF–655K
Human metabolic atlas: an online resource for human metabolism
Natapol Pornputtapong, Intawat Nookaew, Jens Nielsen
Database (Oxford) 2015; 2015: bav068. Published online 2015 Jul 23. doi: 10.1093/database/bav068
PMCID:
PMC4513696
Abstract Article PDF–601K
Curcumin Resource Database
Anil Kumar, Hasnahana Chetia, Swagata Sharma, Debajyoti Kabiraj, Narayan Chandra Talukdar, Utpal Bora
Database (Oxford) 2015; 2015: bav070. Published online 2015 Jul 25. doi: 10.1093/database/bav070
PMCID:
PMC4516778
Abstract Article PDF–1013K
SHIELD: an integrative gene expression database for inner ear research
Jun Shen, Déborah I. Scheffer, Kelvin Y. Kwan, David P. Corey
Database (Oxford) 2015; 2015: bav071. Published online 2015 Jul 23. doi: 10.1093/database/bav071
PMCID:
PMC4513695
Abstract Article PDF–578K
The National NeuroAIDS Tissue Consortium (NNTC) Database: an integrated database for HIV-related studies
Matyas F. Cserhati, Sanjit Pandey, James J. Beaudoin, Lorena Baccaglini, Chittibabu Guda, Howard S. Fox
Database (Oxford) 2015; 2015: bav074. Published online 2015 Jul 30. doi: 10.1093/database/bav074
PMCID:
PMC4520230
Abstract Article PDF–1.2M
Phytochemica: a platform to explore phytochemicals of medicinal plants
Shivalika Pathania, Sai Mukund Ramakrishnan, Ganesh Bagler
Database (Oxford) 2015; 2015: bav075. Published online 2015 Aug 8. doi: 10.1093/database/bav075
PMCID:
PMC4529746
Abstract Article PDF–1.2M
MetazSecKB: the human and animal secretome and subcellular proteome knowledgebase
John Meinken, Gary Walker, Chester R. Cooper, Xiang Jia Min
Database (Oxford) 2015; 2015: bav077. Published online 2015 Aug 8. doi: 10.1093/database/bav077
PMCID:
PMC4529745
Abstract Article PDF–464K
FlyVar: a database for genetic variation in Drosophila melanogaster
Fei Wang, Lichun Jiang, Yong Chen, Nele A. Haelterman, Hugo J. Bellen, Rui Chen
Database (Oxford) 2015; 2015: bav079. Published online 2015 Aug 18. doi: 10.1093/database/bav079
PMCID:
PMC4541374
Abstract Article PDF–444K
MicRhoDE: a curated database for the analysis of microbial rhodopsin diversity and evolution
Dominique Boeuf, Stéphane Audic, Loraine Brillet-Guéguen, Christophe Caron, Christian Jeanthon
Database (Oxford) 2015; 2015: bav080. Published online 2015 Aug 18. doi: 10.1093/database/bav080
PMCID:
PMC4539915
Abstract Article PDF–1.0M
Deep Question Answering for protein annotation
Julien Gobeill, Arnaud Gaudinat, Emilie Pasche, Dina Vishnyakova, Pascale Gaudet, Amos Bairoch, Patrick Ruch
Database (Oxford) 2015; 2015: bav081. Published online 2015 Sep 16. doi: 10.1093/database/bav081
PMCID:
PMC4572360
Abstract Article PDF–584K
LncReg: a reference resource for lncRNA-associated regulatory networks
Zhong Zhou, Yi Shen, Muhammad Riaz Khan, Ao Li
Database (Oxford) 2015; 2015: bav083. Published online 2015 Sep 10. doi: 10.1093/database/bav083
PMCID:
PMC4565966
Abstract Article PDF–744K
DENdb: database of integrated human enhancers
Haitham Ashoor, Dimitrios Kleftogiannis, Aleksandar Radovanovic, Vladimir B. Bajic
Database (Oxford) 2015; 2015: bav085. Published online 2015 Sep 5. doi: 10.1093/database/bav085
PMCID:
PMC4560934
Abstract Article PDF–617K
FARE-CAFE: a database of functional and regulatory elements of cancer-associated fusion events
Praveen Kumar Korla, Jack Cheng, Chien-Hung Huang, Jeffrey J. P. Tsai, Yu-Hsuan Liu, Nilubon Kurubanjerdjit, Wen-Tsong Hsieh, Huey-Yi Chen, Ka-Lok Ng
Database (Oxford) 2015; 2015: bav086. Published online 2015 Sep 16. doi: 10.1093/database/bav086
PMCID:
PMC4684693
Abstract Article PDF–1.7M
Connecting proteins with drug-like compounds: Open source drug discovery workflows with BindingDB and KNIME
George Nicola, Michael R. Berthold, Michael P. Hedrick, Michael K. Gilson
Database (Oxford) 2015; 2015: bav087. Published online 2015 Sep 16. doi: 10.1093/database/bav087
PMCID:
PMC4572361
Abstract Article PDF–1.2M
SORTA: a system for ontology-based re-coding and technical annotation of biomedical phenotype data
Chao Pang, Annet Sollie, Anna Sijtsma, Dennis Hendriksen, Bart Charbon, Mark de Haan, Tommy de Boer, Fleur Kelpin, Jonathan Jetten, Joeri K. van der Velde, Nynke Smidt, Rolf Sijmons, Hans Hillege, Morris A. Swertz
Database (Oxford) 2015; 2015: bav089. Published online 2015 Sep 17. doi: 10.1093/database/bav089
PMCID:
PMC4574036
Abstract Article PDF–796K
Comprehensive comparative homeobox gene annotation in human and mouse
Laurens G. Wilming, Veronika Boychenko, Jennifer L. Harrow
Database (Oxford) 2015; 2015: bav091. Published online 2015 Sep 25. doi: 10.1093/database/bav091
PMCID:
PMC4584094
Abstract Article PDF–2.1M
Sample data processing in an additive and reproducible taxonomic workflow by using character data persistently linked to preserved individual specimens
Norbert Kilian, Tilo Henning, Patrick Plitzner, Andreas Müller, Anton Güntsch, Ben C. Stöver, Kai F. Müller, Walter G. Berendsohn, Thomas Borsch
Database (Oxford) 2015; 2015: bav094. Published online 2015 Sep 30. doi: 10.1093/database/bav094
PMCID:
PMC4589695
Abstract Article PDF–1.9M
RegNetwork: an integrated database of transcriptional and post-transcriptional regulatory networks in human and mouse
Zhi-Ping Liu, Canglin Wu, Hongyu Miao, Hulin Wu
Database (Oxford) 2015; 2015: bav095. Published online 2015 Sep 30. doi: 10.1093/database/bav095
PMCID:
PMC4589691
Abstract Article PDF–1.7M
MGDB: a comprehensive database of genes involved in melanoma
Di Zhang, Rongrong Zhu, Hanqian Zhang, Chun-Hou Zheng, Junfeng Xia
Database (Oxford) 2015; 2015: bav097. Published online 2015 Sep 30. doi: 10.1093/database/bav097
PMCID:
PMC4589692
Abstract Article PDF–1.1M
miRSponge: a manually curated database for experimentally supported miRNA sponges and ceRNAs
Peng Wang, Hui Zhi, Yunpeng Zhang, Yue Liu, Jizhou Zhang, Yue Gao, Maoni Guo, Shangwei Ning, Xia Li
Database (Oxford) 2015; 2015: bav098. Published online 2015 Sep 30. doi: 10.1093/database/bav098
PMCID:
PMC4589693
Abstract Article PDF–968K
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, Philipp Senger
Database (Oxford) 2015; 2015: bav099. Published online 2015 Oct 15. doi: 10.1093/database/bav099
PMCID:
PMC4608514
Abstract Article PDF–1.0M
ProPepper: a curated database for identification and analysis of peptide and immune-responsive epitope composition of cereal grain protein families
Angéla Juhász, Réka Haraszi, Csaba Maulis
Database (Oxford) 2015; 2015: bav100. Published online 2015 Oct 8. doi: 10.1093/database/bav100
PMCID:
PMC4597978
Abstract Article PDF–1.9M
JRC GMO-Amplicons: a collection of nucleic acid sequences related to genetically modified organisms
Mauro Petrillo, Alexandre Angers-Loustau, Peter Henriksson, Laura Bonfini, Alex Patak, Joachim Kreysa
Database (Oxford) 2015; 2015: bav101. Published online 2015 Sep 30. doi: 10.1093/database/bav101
PMCID:
PMC4589694
Abstract Article PDF–1.3M
MtiBase: a database for decoding microRNA target sites located within CDS and 5′UTR regions from CLIP-Seq and expression profile datasets
Zhi-Wei Guo, Chen Xie, Jian-Rong Yang, Jun-Hao Li, Jian-Hua Yang, Limin Zheng
Database (Oxford) 2015; 2015: bav102. Published online 2015 Oct 21. doi: 10.1093/database/bav102
PMCID:
PMC4614282
Abstract Article PDF–847K
PhenoMiner: from text to a database of phenotypes associated with OMIM diseases
Nigel Collier, Tudor Groza, Damian Smedley, Peter N. Robinson, Anika Oellrich, Dietrich Rebholz-Schuhmann
Database (Oxford) 2015; 2015: bav104. Published online 2015 Oct 27. doi: 10.1093/database/bav104
PMCID:
PMC4622021
Abstract Article PDF–1.3M
Developing the eHistology Atlas
Lorna Richardson, Liz Graham, Julie Moss, Nick Burton, Yogmatee Roochun, Chris Armit, Richard A. Baldock
Database (Oxford) 2015; 2015: bav105. Published online 2015 Oct 24. doi: 10.1093/database/bav105
PMCID:
PMC4618478
Abstract Article PDF–746K
Differential ligand-signaling network of CCL19/CCL21-CCR7 system
Rajesh Raju, Sachin Gadakh, Priyanka Gopal, Bijesh George, Jayshree Advani, Sowmya Soman, T. S. K. Prasad, Reshmi Girijadevi
Database (Oxford) 2015; 2015: bav106. Published online 2015 Oct 26. doi: 10.1093/database/bav106
PMCID:
PMC4620938
Abstract Article PDF–566K
MAPanalyzer: a novel online tool for analyzing microtubule-associated proteins
Yuan Zhou, Shiping Yang, Tonglin Mao, Ziding Zhang
Database (Oxford) 2015; 2015: bav108. Published online 2015 Nov 13. doi: 10.1093/database/bav108
PMCID:
PMC4644220
Abstract Article PDF–845K
SBMDb: first whole genome putative microsatellite DNA marker database of sugarbeet for bioenergy and industrial applications
Mir Asif Iquebal, Sarika Jaiswal, U.B. Angadi, Gaurav Sablok, Vasu Arora, Sunil Kumar, Anil Rai, Dinesh Kumar
Database (Oxford) 2015; 2015: bav111. Published online 2015 Dec 7. doi: 10.1093/database/bav111
PMCID:
PMC4672366
Abstract Article PDF–481K
ONRLDB—manually curated database of experimentally validated ligands for orphan nuclear receptors: insights into new drug discovery
Ravikanth Nanduri, Isha Bhutani, Arun Kumar Somavarapu, Sahil Mahajan, Raman Parkesh, Pawan Gupta
Database (Oxford) 2015; 2015: bav112. Published online 2015 Nov 4. doi: 10.1093/database/bav112
PMCID:
PMC4669993
Abstract Article PDF–2.4M
Biocuration with insufficient resources and fixed timelines
Raul Rodriguez-Esteban
Database (Oxford) 2015; 2015: bav116. Published online 2015 Dec 23. doi: 10.1093/database/bav116
PMCID:
PMC4691339
Abstract Article PDF–424K
Determining similarity of scientific entities in annotation datasets
Guillermo Palma, Maria-Esther Vidal, Eric Haag, Louiqa Raschid, Andreas Thor
Database (Oxford) 2015; 2015: bau123. Published online 2015 Feb 27. doi: 10.1093/database/bau123
PMCID:
PMC4343076
Abstract Article PDF–1.2M
Fishing for data and sorting the catch: assessing the data quality, completeness and fitness for use of data in marine biogeographic databases
Leen Vandepitte, Samuel Bosch, Lennert Tyberghein, Filip Waumans, Bart Vanhoorne, Francisco Hernandez, Olivier De Clerck, Jan Mees
Database (Oxford) 2015; 2015: bau125. Published online 2015 Jan 28. doi: 10.1093/database/bau125
PMCID:
PMC4309024
Abstract Article PDF–837K
CyanOmics: an integrated database of omics for the model cyanobacterium Synechococcus sp. PCC 7002
Yaohua Yang, Jie Feng, Tao Li, Feng Ge, Jindong Zhao
Database (Oxford) 2015; 2015: bau127. Published online 2015 Jan 28. doi: 10.1093/database/bau127
PMCID:
PMC4309022
Abstract Article PDF–600K
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, Mary Shimoyama
Database (Oxford) 2015; 2015: bau128. Published online 2015 Jan 28. doi: 10.1093/database/bau128
PMCID:
PMC4309021
Abstract Article PDF–1.0M
Combining computational models, semantic annotations and simulation experiments in a graph database
Ron Henkel, Olaf Wolkenhauer, Dagmar Waltemath
Database (Oxford) 2015; 2015: bau130. Published online 2015 Mar 8. doi: 10.1093/database/bau130
PMCID:
PMC4352687
Abstract Article PDF–1.3M
Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach
Philippe Rocca-Serra, Ramona Walls, Jacob Parnell, Rachel Gallery, Jie Zheng, Susanna-Assunta Sansone, Alejandra Gonzalez-Beltran
Database (Oxford) 2015; 2015: bau132. Published online 2015 Jan 28. doi: 10.1093/database/bau132
PMCID:
PMC4309925
Abstract Article PDF–693K

Review

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges
Saikat Chowdhury, Ram Rup Sarkar
Database (Oxford) 2015; 2015: bau126. Published online 2015 Jan 28. doi: 10.1093/database/bau126
PMCID:
PMC4309023
Abstract Article PDF–1.9M

Corrigendum

Automated semantic annotation of rare disease cases: a case study
Maria Taboada, Hadriana Rodríguez, Diego Martínez, María Pardo, María Jesús Sobrido
Database (Oxford) 2015; 2015: bav107. Published online 2015 Nov 13. doi: 10.1093/database/bav107
Corrects:
Database (Oxford). 2014; 2014: bau045.
PMCID:
PMC4644219
Correction PDF–159K
Articles from Database: The Journal of Biological Databases and Curation are provided here courtesy of Oxford University Press
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