ArticleGigaScience2020
Machado: Open source genomics data integration framework.
Article in GigaScience, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- Transcriptomics, proteomics, and metabolomics interventions prompt crop improvement against metal(loid) toxicity.Plant cell reports · 2024Review
- A Secure and Reusable Software Architecture for Supporting Online Data Harmonization.Proceedings : ... IEEE International Conference on Big Data. IEEE International Conference on Big Data · 2021Article
- Plant Co-expression Annotation Resource: a web server for identifying targets for genetically modified crop breeding pipelines.BMC bioinformatics · 2021Article
- Advances in "Omics" Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants.Frontiers in plant science · 2021Review
- Machado: Open source genomics data integration framework.GigaScience · 2020Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenome projects and multiomics experiments generate huge volumes of data that must be stored, mined, and transformed into useful knowledge. All this information is supposed to be accessible and, if possible, browsable afterwards. Computational biologists have been dealing with this scenario for more than a decade and have been implementing software and databases to meet this challenge. The GMOD's (Generic Model Organism Database) biological relational database schema, known as Chado, is one of the few successful open source initiatives; it is widely adopted and many software packages are able to connect to it.
findingsWe have been developing an open source software package named Machado, a genomics data integration framework implemented in Python, to enable research groups to both store and visualize genomics data. The framework relies on the Chado database schema and, therefore, should be very intuitive for current developers to adopt it or have it running on top of already existing databases. It has several data-loading tools for genomics and transcriptomics data and also for annotation results from tools such as BLAST, InterproScan, OrthoMCL, and LSTrAP. There is an API to connect to JBrowse, and a web visualization tool is implemented using Django Views and Templates. The Haystack library integrated with the ElasticSearch engine was used to implement a Google-like search, i.e., single auto-complete search box that provides fast results and filters.
conclusionMachado aims to be a modern object-relational framework that uses the latest Python libraries to produce an effective open source resource for genomics research.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.