@article {555, title = {PyCellBase, an efficient python package for easy retrieval of biological data from heterogeneous sources.}, journal = {BMC Bioinformatics}, volume = {20}, year = {2019}, month = {2019 Mar 28}, pages = {159}, abstract = {

BACKGROUND: Biological databases and repositories are incrementing in diversity and complexity over the years. This rapid expansion of current and new sources of biological knowledge raises serious problems of data accessibility and integration. To handle the growing necessity of unification, CellBase was created as an integrative solution. CellBase provides a centralized NoSQL database containing biological information from different and heterogeneous sources. Access to this information is done through a RESTful web service API, which provides an efficient interface to the data.

RESULTS: In this work we present PyCellBase, a Python package that provides programmatic access to the rich RESTful web service API offered by CellBase. This package offers a fast and user-friendly access to biological information without the need of installing any local database. In addition, a series of command-line tools are provided to perform common bioinformatic tasks, such as variant annotation. CellBase data is always available by a high-availability cluster and queries have been tuned to ensure a real-time performance.

CONCLUSION: PyCellBase is an open-source Python package that provides an efficient access to heterogeneous biological information. It allows to perform tasks that require a comprehensive set of knowledge resources, as for example variant annotation. Queries can be easily fine-tuned to retrieve the desired information of particular biological features. PyCellBase offers the convenience of an object-oriented scripting language and provides the ability to integrate the obtained results into other Python applications and pipelines.

}, keywords = {Computational Biology, Databases, Factual, Software, User-Computer Interface}, issn = {1471-2105}, doi = {10.1186/s12859-019-2726-4}, author = {Perez-Gil, Daniel and Lopez, Francisco J and Dopazo, Joaquin and Marin-Garcia, Pablo and Rendon, Augusto and Medina, Ignacio} } @article {387, title = {HGVA: the Human Genome Variation Archive.}, journal = {Nucleic Acids Res}, volume = {45}, year = {2017}, month = {2017 07 03}, pages = {W189-W194}, abstract = {

High-profile genomic variation projects like the 1000 Genomes project or the Exome Aggregation Consortium, are generating a wealth of human genomic variation knowledge which can be used as an essential reference for identifying disease-causing genotypes. However, accessing these data, contrasting the various studies and integrating those data in downstream analyses remains cumbersome. The Human Genome Variation Archive (HGVA) tackles these challenges and facilitates access to genomic data for key reference projects in a clean, fast and integrated fashion. HGVA provides an efficient and intuitive web-interface for easy data mining, a comprehensive RESTful API and client libraries in Python, Java and JavaScript for fast programmatic access to its knowledge base. HGVA calculates population frequencies for these projects and enriches their data with variant annotation provided by CellBase, a rich and fast annotation solution. HGVA serves as a proof-of-concept of the genome analysis developments being carried out by the University of Cambridge together with UK{\textquoteright}s 100 000 genomes project and the National Institute for Health Research BioResource Rare-Diseases, in particular, deploying open-source for Computational Biology (OpenCB) software platform for storing and analyzing massive genomic datasets.

}, keywords = {Genetic Variation, Genome, Human, Humans, Internet, Software, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkx445}, url = {https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkx445}, author = {Lopez, Javier and Coll, Jacobo and Haimel, Matthias and Kandasamy, Swaathi and T{\'a}rraga, Joaqu{\'\i}n and Furio-Tari, Pedro and Bari, Wasim and Bleda, Marta and Rueda, Antonio and Gr{\"a}f, Stefan and Rendon, Augusto and Dopazo, Joaquin and Medina, Ignacio} }