11 papers · ranked by Valyu relevance
Maria Paasivaara, Philippe Kruchten, Saeid Heshmatisafa, Marko Seppänen
'Marko Seppänen'] Many companies have followed the trend toward exposing their business assets through open (i.e., Web) application programming interfaces (APIs). However, these firms appear to have adopted API technology largely to meet their customers’ needs and demands. The pressures on industries to develop…
Aziz Khan, Anthony Mathelier
JASPAR is a widely used open-access database of curated, non-redundant transcription factor binding profiles. Currently, data from JASPAR can be retrieved as flat files or by using programming language-specific interfaces. Here, we present a programming language-independent application programming interface (API) to…
Chunlei Wu, Adam Mark, Andrew I. Su
Biomedical knowledge is often represented as annotations of biological entities such as genes, genetic variants, diseases, and drugs. For gene annotations, they are fragmented across data repositories like NCBI Entrez, Ensembl, UniProt, and hundreds (or more) of other specialized databases. While the volume and breadth…
Aleksandra Tarkowska, Denise Carvalho-Silva, Charles E. Cook, Edd Turner + 3 more
HTTP defines a set of verbs that can be applied to an endpoint to change the action performed. The most commonly used are ‘GET’ to transfer a current representation of the resource from an endpoint. ‘POST’, ‘PUT’, ‘PATCH’, and ‘DELETE’ (so-called unsafe methods) perform a processing operation, which could be…
Stephen K Woody, David Burdick, Hilmar Lapp, Erich S. Huang
Storing very large amounts of data and delivering them to researchers in an efficient, verifiable, and compliant manner, is one of the major challenges faced by health care providers and researchers in the life sciences. The electronic health record (EHR) at a hospital or clinic currently functions as a silo, and…
George Jones, Amanda E. Wakefield, Jeff Triplett, Kojo Idrissa + 3 more
'James Goebel' 'Dima Kozakov' 'Sandor Vajda'] Within the last few decades, increases in computational resources have contributed enormously to the progress of science and engineering (S & E). To continue making rapid advancements, the S & E community must be able to access computing resources. One way to provide such…
Sebastien Lelong, Xinghua Zhou, Cyrus Afrasiabi, Zhongchao Qian + 9 more
To meet the increased need of making biomedical resources more accessible and reusable, Web APIs or web services have become a common way to disseminate knowledge sources. The BioThings APIs are a collection of high-performance, scalable, annotation as a service APIs that automate the integration of biological…
Bishwa Ghimire, Nicholas Booth, Tapio Lönnberg, Tero Aittokallio + 1 more
Nextflow’s command-line interface has the optional flag -with-trace, which generates an execution tracing file trace.txt for a single pipeline run. Alternatively, Nextflow’s configuration file option (‘trace.enabled = true’) generates the execution tracing file for all pipeline runs as well. The file contains task…
Marc Chakiachvili, Anne-Muriel Arigon Chifolleau, Vincent Lefort
WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely…
Erik Huckvale, Hunter N.B. Moseley
The Kyoto Encyclopedia of Genes and Genomes (KEGG) provides organized genomic, biomolecular, and metabolic information and knowledge that is reasonably current and highly useful for a wide range of analyses and modeling. KEGG follows the principles of data stewardship to be findable, accessible, interoperable, and…
Jiwen Xin, Cyrus Afrasiabi, Sebastien Lelong, Julee Adesara + 3 more
Application Programming Interfaces (APIs) are now widely used to distribute biological data. And many popular biological APIs developed by many different research teams have adopted Javascript Object Notation (JSON) as their primary data format. While usage of a common data format offers significant advantages, that…