Skip to main content

Table 1 Models

From: miRMaid: a unified programming interface for microRNA data resources

Model Description Attributes Relationships
Precursor The miRNA precursor, processed from longer primary transcripts by endonucleases. name, accession, description, sequence, comment Mature,GenomeContext, GenomePosition, Paper, PrecursorCluster, Species, PrecursorFamily
Mature The mature miRNA, processed from the miRNA precursor by Dicer. name, accession, evidence, experiment, similarity, sequence Precursor, SeedFamily
Species The taxonomic species having miRNAs encoded in the genome. abbreviation, name, division, taxonomy, genome_assembly Precursor
PrecursorFamily The miRBase grouping of precursors into families. name, accession, description Precursor
GenomeContext Other gene models overlapping the miRNA precursor in genome. overlap_sense, overlap_type, transcript_source, transcript_name Precursor
GenomePosition The position of the miRNA precursor in the genome. xsome, contig_start, contig_end, strand Precursor
PrecursorCluster (*) A grouping of precursors occurring close to each other in the genome - presumably transcribed together. Name Precursor
SeedFamily (*) A grouping of mature miRNAs based on the 6mer seed (bases 2-7) or 7mer seed (bases 2-8). name, sequence Mature
Paper Papers related to the annotation and identification of a miRNA as reported in miRBase. medline, title, author, journal Precursor
  1. miRMaid data models: miRMaid restructures data in miRBase to yield a set of core data models. The data for the two models highlighted with a (*) is not readily available from miRBase data but is automatically computed when miRMaid is deployed. Each model is semantically related and connected to other models as listed in the last column of the table. Relationships highlighted in bold denote a 'many' relationship: a species has 'many' miRNA precursors, while a miRNA precursor is only related to 'one' species. The attributes and relations on each data object can be accessed in an object-oriented manner (see Figure 5 for an example).