{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T16:03:16Z","timestamp":1763740996859,"version":"3.45.0"},"posted":{"date-parts":[[2018,7,3]]},"reference-count":0,"publisher":"F1000 Research Ltd","license":[{"start":{"date-parts":[[2018,7,3]],"date-time":"2018-07-03T00:00:00Z","timestamp":1530576000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"abstract":"<ns3:p>The Plant miRNA Service, under development at the ELIXIR PT Node, will provide a novel approach to processing miRNA data. MiRNAs are a class of non-coding small RNAs which repress target gene expression posttranscriptionally. Since miRNAs have important regulatory roles during plant growth and development, adaptation to the environment and response to pathogen, a repository integrating existing information on miRNAs and their role in gene expression regulation, along with new miRNA data, in a searchable repository will represent an important resource for plant bioinformatics. The Plant miRNA service will automatically generate structured data derived from raw NGS data. The process starts by prompting \u00a0researchers with descriptive metadata at the beginning of the data submission process using terms from a controlled vocabulary. The Plant miRNA Service then executes the MiRPursuit information pipeline to subject the data to cleaning operations to reduce noise, add annotations from previous experiments and provenance information.<\/ns3:p>\n                <ns3:p>The coupling of RNA-seq data with the stored miRNA data from related experiments enables the generation of miRNA-gene graphs, where the node weights are their expressions. These graphs are then used to predict miRNA targets and infer their respective functions using \u00a0machine learning algorithms.<\/ns3:p>\n                <ns3:p>The Plant miRNA Service will provide the miRNA Plant community with additional tools aimed at dealing with model and non-model species, providing novel query and visualization tools to generate new knowledge. Researchers interested in miRNA data will be able to query their metadata and view it through a genome browser or the miRNA-gene graph, a new viewport to miRNA data providing validated targets and functions.<\/ns3:p>","DOI":"10.7490\/f1000research.1115759.1","type":"posted-content","created":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T15:42:08Z","timestamp":1763739728000},"source":"Crossref","is-referenced-by-count":0,"title":["Building the Plant miRNA Service"],"prefix":"10.7490","author":[{"given":"Bruno V.","family":"Costa","sequence":"first","affiliation":[]},{"given":"In\u00eas","family":"Chaves","sequence":"additional","affiliation":[]},{"given":"C\u00e9lia M.","family":"Miguel","sequence":"additional","affiliation":[]},{"given":"M\u00e1rio J.","family":"Silva","sequence":"additional","affiliation":[]}],"member":"2560","container-title":[],"original-title":[],"deposited":{"date-parts":[[2025,11,21]],"date-time":"2025-11-21T15:42:16Z","timestamp":1763739736000},"score":1,"resource":{"primary":{"URL":"https:\/\/f1000research.com\/posters\/7-998"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,7,3]]},"references-count":0,"URL":"https:\/\/doi.org\/10.7490\/f1000research.1115759.1","relation":{},"subject":[],"published":{"date-parts":[[2018,7,3]]},"subtype":"other"}}