Literature DB >> 25593347

The 2015 Nucleic Acids Research Database Issue and molecular biology database collection.

Michael Y Galperin1, Daniel J Rigden2, Xosé M Fernández-Suárez3.   

Abstract

The 2015 Nucleic Acids Research Database Issue contains 172 papers that include descriptions of 56 new molecular biology databases, and updates on 115 databases whose descriptions have been previously published in NAR or other journals. Following the classification that has been introduced last year in order to simplify navigation of the entire issue, these articles are divided into eight subject categories. This year's highlights include RNAcentral, an international community portal to various databases on noncoding RNA; ValidatorDB, a validation database for protein structures and their ligands; SASBDB, a primary repository for small-angle scattering data of various macromolecular complexes; MoonProt, a database of 'moonlighting' proteins, and two new databases of protein-protein and other macromolecular complexes, ComPPI and the Complex Portal. This issue also includes an unusually high number of cancer-related databases and other databases dedicated to genomic basics of disease and potential drugs and drug targets. The size of NAR online Molecular Biology Database Collection, http://www.oxfordjournals.org/nar/database/a/, remained approximately the same, following the addition of 74 new resources and removal of 77 obsolete web sites. The entire Database Issue is freely available online on the Nucleic Acids Research web site (http://nar.oxfordjournals.org/). Published by Oxford University Press on behalf of Nucleic Acids Research 2014. This work is written by (a) US Government employee(s) and is in the public domain in the US.

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Mesh:

Year:  2015        PMID: 25593347      PMCID: PMC4383995          DOI: 10.1093/nar/gku1241

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN: 0305-1048            Impact factor:   16.971


  50 in total

1.  SASBDB, a repository for biological small-angle scattering data.

Authors:  Erica Valentini; Alexey G Kikhney; Gianpietro Previtali; Cy M Jeffries; Dmitri I Svergun
Journal:  Nucleic Acids Res       Date:  2014-10-28       Impact factor: 16.971

2.  MultitaskProtDB: a database of multitasking proteins.

Authors:  Sergio Hernández; Gabriela Ferragut; Isaac Amela; JosepAntoni Perez-Pons; Jaume Piñol; Angel Mozo-Villarias; Juan Cedano; Enrique Querol
Journal:  Nucleic Acids Res       Date:  2013-11-18       Impact factor: 16.971

3.  IMGT®, the international ImMunoGeneTics information system® 25 years on.

Authors:  Marie-Paule Lefranc; Véronique Giudicelli; Patrice Duroux; Joumana Jabado-Michaloud; Géraldine Folch; Safa Aouinti; Emilie Carillon; Hugo Duvergey; Amélie Houles; Typhaine Paysan-Lafosse; Saida Hadi-Saljoqi; Souphatta Sasorith; Gérard Lefranc; Sofia Kossida
Journal:  Nucleic Acids Res       Date:  2014-11-05       Impact factor: 19.160

4.  The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements.

Authors:  Adrian M Altenhoff; Nives Škunca; Natasha Glover; Clément-Marie Train; Anna Sueki; Ivana Piližota; Kevin Gori; Bartlomiej Tomiczek; Steven Müller; Henning Redestig; Gaston H Gonnet; Christophe Dessimoz
Journal:  Nucleic Acids Res       Date:  2014-11-15       Impact factor: 16.971

5.  Genome3D: exploiting structure to help users understand their sequences.

Authors:  Tony E Lewis; Ian Sillitoe; Antonina Andreeva; Tom L Blundell; Daniel W A Buchan; Cyrus Chothia; Domenico Cozzetto; José M Dana; Ioannis Filippis; Julian Gough; David T Jones; Lawrence A Kelley; Gerard J Kleywegt; Federico Minneci; Jaina Mistry; Alexey G Murzin; Bernardo Ochoa-Montaño; Matt E Oates; Marco Punta; Owen J L Rackham; Jonathan Stahlhacke; Michael J E Sternberg; Sameer Velankar; Christine Orengo
Journal:  Nucleic Acids Res       Date:  2014-10-27       Impact factor: 16.971

6.  DBTSS as an integrative platform for transcriptome, epigenome and genome sequence variation data.

Authors:  Ayako Suzuki; Hiroyuki Wakaguri; Riu Yamashita; Shin Kawano; Katsuya Tsuchihara; Sumio Sugano; Yutaka Suzuki; Kenta Nakai
Journal:  Nucleic Acids Res       Date:  2014-11-05       Impact factor: 16.971

7.  BioModels: ten-year anniversary.

Authors:  Vijayalakshmi Chelliah; Nick Juty; Ishan Ajmera; Raza Ali; Marine Dumousseau; Mihai Glont; Michael Hucka; Gaël Jalowicki; Sarah Keating; Vincent Knight-Schrijver; Audald Lloret-Villas; Kedar Nath Natarajan; Jean-Baptiste Pettit; Nicolas Rodriguez; Michael Schubert; Sarala M Wimalaratne; Yangyang Zhao; Henning Hermjakob; Nicolas Le Novère; Camille Laibe
Journal:  Nucleic Acids Res       Date:  2014-11-20       Impact factor: 16.971

8.  lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs.

Authors:  Xiu Cheng Quek; Daniel W Thomson; Jesper L V Maag; Nenad Bartonicek; Bethany Signal; Michael B Clark; Brian S Gloss; Marcel E Dinger
Journal:  Nucleic Acids Res       Date:  2014-10-20       Impact factor: 16.971

9.  The RCSB Protein Data Bank: views of structural biology for basic and applied research and education.

Authors:  Peter W Rose; Andreas Prlić; Chunxiao Bi; Wolfgang F Bluhm; Cole H Christie; Shuchismita Dutta; Rachel Kramer Green; David S Goodsell; John D Westbrook; Jesse Woo; Jasmine Young; Christine Zardecki; Helen M Berman; Philip E Bourne; Stephen K Burley
Journal:  Nucleic Acids Res       Date:  2014-11-26       Impact factor: 19.160

10.  Pfam: the protein families database.

Authors:  Robert D Finn; Alex Bateman; Jody Clements; Penelope Coggill; Ruth Y Eberhardt; Sean R Eddy; Andreas Heger; Kirstie Hetherington; Liisa Holm; Jaina Mistry; Erik L L Sonnhammer; John Tate; Marco Punta
Journal:  Nucleic Acids Res       Date:  2013-11-27       Impact factor: 16.971

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  18 in total

1.  Public data sources to support systems toxicology applications.

Authors:  Allan Peter Davis; Jolene Wiegers; Thomas C Wiegers; Carolyn J Mattingly
Journal:  Curr Opin Toxicol       Date:  2019-03-11

2.  PyMine: a PyMOL plugin to integrate and visualize data for drug discovery.

Authors:  Rajan Chaudhari; Zhijun Li
Journal:  BMC Res Notes       Date:  2015-10-01

Review 3.  Databases for Microbiologists.

Authors:  Igor B Zhulin
Journal:  J Bacteriol       Date:  2015-05-26       Impact factor: 3.490

4.  KaBOB: ontology-based semantic integration of biomedical databases.

Authors:  Kevin M Livingston; Michael Bada; William A Baumgartner; Lawrence E Hunter
Journal:  BMC Bioinformatics       Date:  2015-04-23       Impact factor: 3.169

5.  From data repositories to submission portals: rethinking the role of domain-specific databases in CollecTF.

Authors:  Sefa Kılıç; Dinara M Sagitova; Shoshannah Wolfish; Benoit Bely; Mélanie Courtot; Stacy Ciufo; Tatiana Tatusova; Claire O'Donovan; Marcus C Chibucos; Maria J Martin; Ivan Erill
Journal:  Database (Oxford)       Date:  2016-04-25       Impact factor: 3.451

Review 6.  Non-coding yet non-trivial: a review on the computational genomics of lincRNAs.

Authors:  Travers Ching; Jayson Masaki; Jason Weirather; Lana X Garmire
Journal:  BioData Min       Date:  2015-12-22       Impact factor: 2.522

7.  Wikidata as a semantic framework for the Gene Wiki initiative.

Authors:  Sebastian Burgstaller-Muehlbacher; Andra Waagmeester; Elvira Mitraka; Julia Turner; Tim Putman; Justin Leong; Chinmay Naik; Paul Pavlidis; Lynn Schriml; Benjamin M Good; Andrew I Su
Journal:  Database (Oxford)       Date:  2016-03-17       Impact factor: 3.451

8.  Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base.

Authors:  Alejandro Rodríguez-Iglesias; Alejandro Rodríguez-González; Alistair G Irvine; Ane Sesma; Martin Urban; Kim E Hammond-Kosack; Mark D Wilkinson
Journal:  Front Plant Sci       Date:  2016-05-12       Impact factor: 5.753

9.  Generation of open biomedical datasets through ontology-driven transformation and integration processes.

Authors:  María Del Carmen Legaz-García; José Antonio Miñarro-Giménez; Marcos Menárguez-Tortosa; Jesualdo Tomás Fernández-Breis
Journal:  J Biomed Semantics       Date:  2016-06-03

10.  Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat.

Authors:  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; Joanna L Sharman; Michael Spedding; Konstantinos D Tsirigos; Ake Vastermark; Gerrit Vriend
Journal:  Database (Oxford)       Date:  2015-07-11       Impact factor: 3.451

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