GeMI: interactive interface for transformer-based Genomic Metadata Integration.

ABSTRACT: The Gene Expression Omnibus (GEO) is a public archive containing >4 million digital samples from functional genomics experiments collected over almost two decades. The accompanying metadata describing the experiments suffer from redundancy, inconsistency and incompleteness due to the prevalence of free text and the lack of well-defined data formats and their validation. To remedy this situation, we created Genomic Metadata Integration (GeMI; http://gmql.eu/gemi/), a web application that learns to automatically extract structured metadata (in the form of key-value pairs) from the plain text descriptions of GEO experiments. The extracted information can then be indexed for structured search and used for various downstream data mining activities. GeMI works in continuous interaction with its

SUBMITTER: Serna Garcia G 

PROVIDER: S-EPMC9216561 | biostudies-literature | 2022 Jun

REPOSITORIES: biostudies-literature