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We implemented an annotation algorithm that integrates knowledge from diverse biological databases to characterize each RNA-seq read.
Thus, it was essential to this effort to implement a new approach to integrate diverse biological databases (9).
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BioMart is a generic scalable system which provides unified access to biological data archived in the diverse and geographically disparate biological databases through a central portal [ 15, 16].
The diverse biological knowledge distilled from multiple external databases has been expanded, updated, and integrated into a flexible single database called the Library of Knowledge Integration (LOKI) that we will continue to expand with additional database sources over time.
This task is performed manually by curators of databases specialized in diverse biological domains, ranging from cellular phenotypes and tissue anatomy to gene function.
Biological databases are developed for diverse purposes, encompass various types of data at heterogeneous coverage and are curated at different levels with different methods, so that there are accordingly several different criteria applicable to database classification.
The ontology has been applied in diverse applications such as annotation of chemicals in biological databases for pathways, interactions, and systems biology models [7 9]; chemical text mining [10]; formalising the chemistry underlying biological ontologies [11]; semantic similarity [12]; and metabolome prediction [13].
Pathways from different databases have similar descriptions yet diverse biological processes, indicating variation in their ability to share similar functional characteristics.
The EcoliNet server (http://www.inetbio.org/ecolinet) provides not only public prediction tools but also a database of cofunctional associations between E. coli genes, derived from diverse biological data.
When classified by the Gene Ontology (GO) database it was shown that these gene sets contain representatives of diverse biological pathways.
HyBrow consists of a modeling framework with the ability to accommodate diverse biological information sources, an event-based ontology for representing biological processes at different levels of detail, a database to query information in the ontology, and programs to perform hypothesis design and evaluation.
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