Mohamed Helmy; Alexander Crits-Christoph; Gary D. Bader

“ Many journals require a minimum period of at least two years of database maintenance for publication, and funding agencies require sustainable data sharing practices for continued support. Finally, failing to maintain a needed resource that you created can negatively affect your reputation and lead to reduced ability to publish similar work in the future.
Databases aiming for long life are often maintained by major institutions or consortia who employ dedicated staff to maintain content, software, and user support. ”

“ First, use professionally managed hosting resources (e.g., cloud, institutional) , instead of setting up your own web server. Second, if you must run your own server, use virtualization technology, like Docker, to ease system administration and backup tasks. If the server hardware fails, you can bring the system back quickly on another machine. Third, make your database available for download as a set of files or as an all-in-one virtual machine so that the system can be mirrored by others in case the central server is not available. ”

“ Introduction Biological databases are online libraries that contain structured information about living organisms. These databases are indispensable research tools, as they provide convenient, computable access to prior knowledge that is vital for planning future experiments and for discovering new knowledge through data mining—they help us “stand on the shoulders of giants.” ”

“ Use modern technology Most databases are available via an interactive user interface on the web catering to the majority of users. Modern users demand that websites adhere to very high technical and design standards, as is commonplace with websites like Facebook and Google. Websites should have intuitive graphical design and support standard web browsers and operating systems. ”

“ Fourth, promote your database in scientific conferences and meetings. Fifth, monitor online user groups, such as biostars.org, for potential users and let them know about your resource. Sixth, actively use social media to attract new users and keep them up to date with news about your resource [ [38] ] . Using social media can attract many users but requires sustained effort to be effective. ”

“ Don’t reinvent the wheel Creating a high-quality database is a responsibility that involves strong commitment to accurate data collection and regular content and feature updates, not to mention a substantial time investment. ”

“ Web application frameworks, such as Shiny for R and Django for Python, are collections of ready-made packages and tools that enable developers to automatically generate whole websites, thus greatly speeding up the development process and reducing the need for debugging and testing. Furthermore, several modern technologies, such as node.js, enable writing both the client and server side in one language, JavaScript, and come with thousands of packages providing powerful features. ”

“ These users generally require a web interface that facilitates data access and retrieval. On the other hand, computational biologists and software developers generally need multiple channels for accessing data programmatically or in batch for use and integration into their own analysis workflows and software tools. ”

“ For high-quality curated databases, there is currently no replacement for the time consuming curation process; however, crowdsourcing is a promising research area that may already be able to help with certain tasks and, in the future, may greatly improve curation efficiency [ [41] ] . ”

“ Chatonnet, A & Chen, MJ (2015) , Creating a specialist protein resource network: a meeting report for the protein bioinformatics and community resources retreat, vol. 2015, p. bav063, 26284514, pmid:26284514 ↑ Hermjakob, H; Montecchi-Palazzi, L; Bader, G; Wojcik, J; Salwinski, L & Ceol, A (2004) , The HUPO PSI’s molecular interaction format—a community standard for the representation of protein interaction data, vol. 22, pp. 177–83, 14755292, pmid:14755292, DOI 10.1038/nbt926 ↑ Coordinators, NR (2016) , Database resources of the National Center for Biotechnology Information, vol. ”

“ Crowdy, EK & Cho, E (2010) , iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence, vol. 2010, p. baq023, 20940177, pmid:20940177 ↑ Tunkelang, D (2009) , Faceted Search, vol. 1, pp. 1–80 ↑ Safran, M; Dalah, I; Alexander, J; Rosen, N; Iny Stein, T & Shmoish, M (2010) , GeneCards Version 3: the human gene integrator, vol. 2010, p. baq020, 20689021, pmid:20689021 ↑ O’Connor, BD; Day, A; Cain, S; Arnaiz, O; Sperling, L & Stein, LD (2008) , GMODWeb: a web framework for the Generic Model Organism Database, vol. ”