The bio-centric ORM

The pdm_utils bio-centric ORM is designed to process data that has been stored/retrieved in a MySQL database, GenBank-formatted flat files, PhagesDB, etc. Data is parsed from GenBank-formatted flat files using BioPython. Data is parsed from PhagesDB using the PhagesDB API. As a result, some pdm_utils objects contain attributes that directly map to each of these different data structures.

Refer to the brief introductory library tutorial to coding with the pdm_utils library.

Below is a map of how genome-level data is stored within these data structures:

pdm_utils object.attribute	MySQL table.column	GenBank flat file BioPython object.attribute	PhagesDB API dictionary
Genome.id	phage.PhageID	SeqRecord.id OR user-selected	dictionary[“phage_name”]
Genome.name	phage.Name	SeqRecord.name OR user-selected	dictionary[“phage_name”]
Genome.seq	phage.Sequence	SeqRecord.seq	dictionary[“fasta_file”]
Genome.length	phage.Length	SeqRecord.seq	dictionary[“fasta_file”]
Genome.gc	phage.GC	SeqRecord.seq	dictionary[“fasta_file”]
Genome.cluster	phage.Cluster	N/A	dictionary[“pcluster”][“cluster”]
Genome.subcluster	phage.Subcluster	N/A	dictionary[“psubcluster”][“subcluster”]
Genome.accession	phage.Accession	SeqRecord.annotations[“accessions”][0]	dictionary[“genbank_accession”]
Genome.host_genus	phage.HostGenus	SeqRecord.annotations[“source”] OR [“organism”] OR [“description”] OR user-selected	dictionary[“isolation_host”][“genus”]
Genome.date	phage.DateLastModified	SeqRecord.annotations[“date”]	N/A
Genome.annotation_status	phage.Status	N/A	N/A
Genome.retrieve_record	phage.RetrieveRecord	N/A	N/A
Genome.annotation_author	phage.AnnotationAuthor	N/A	N/A
Genome.description	N/A	SeqRecord.description	dictionary[“fasta_file”]
Genome.source	N/A	SeqRecord.annotations[“source”]	N/A
Genome.organism	N/A	SeqRecord.annotations[“organism”]	N/A
Genome.authors	N/A	Reference.authors (from SeqRecord.annotations[“references”])	N/A
Genome.filename	N/A	N/A	dictionary[“fasta_file”]

Below is a map of how CDS-level data is stored within these data structures:

pdm_utils object.attribute	MySQL table.column	GenBank flat file BioPython object.attribute	PhagesDB API dictionary
Cds.id	gene.GeneID	N/A	N/A
Cds.name	gene.Name	SeqFeature qualifiers	N/A
Cds.genome_id	gene.PhageID	N/A	N/A
Cds.start	gene.Start	SeqFeature.location.start OR end	N/A
Cds.stop	gene.Stop	SeqFeature.location.start OR end	N/A
Cds.coordinate_format	N/A	N/A	N/A
Cds.orientation	gene.Orientation	SeqFeature.strand	N/A
Cds.parts	N/A	SeqFeature.location.parts	N/A
Cds.seq	N/A	N/A	N/A
Cds.length	gene.Length	SeqFeature.location.start AND end	N/A
Cds.translation	gene.Translation	SeqFeature.qualifiers[“translation”][0]	N/A
Cds.translation_length	N/A	SeqFeature.qualifiers[“translation”][0]	N/A
Cds.translation_table	N/A	SeqFeature.qualifiers[“transl_table”][0]	N/A
Cds.locus_tag	gene.LocusTag	SeqFeature.qualifiers[“locus_tag”][0]	N/A
Cds.description	gene.Notes	SeqFeature.qualifiers[“product”] OR [“function”] OR [“note”]	N/A
Cds.gene	N/A	SeqFeature.qualifiers[“gene”][0]	N/A
Cds.product	N/A	SeqFeature.qualifiers[“product”][0]	N/A
Cds.function	N/A	SeqFeature.qualifiers[“function”][0]	N/A
Cds.note	N/A	SeqFeature.qualifiers[“note”][0]	N/A
Cds.seqfeature	N/A	SeqFeature	N/A
N/A	gene.DomainStatus	N/A	N/A

Below is a map of how tRNA-level data is stored within these data structures:

pdm_utils object.attribute	MySQL table.column	GenBank flat file BioPython object.attribute	PhagesDB API dictionary
Trna.id	trna.GeneID	N/A	N/A
Trna.name	trna.Name	SeqFeature qualifiers	N/A
Trna.genome_id	trna.PhageID	N/A	N/A
Trna.start	trna.Start	SeqFeature.location.start OR end	N/A
Trna.stop	trna.Stop	SeqFeature.location.start OR end	N/A
Trna.coordinate_format	N/A	N/A	N/A
Trna.orientation	trna.Orientation	SeqFeature.strand	N/A
Trna.parts	N/A	SeqFeature.location.parts	N/A
Trna.length	trna.Length	SeqFeature.location.start AND end	N/A
Trna.locus_tag	trna.LocusTag	SeqFeature.qualifiers[“locus_tag”][0]	N/A
Trna.note	trna.Note	SeqFeature.qualifiers[“note”][0]	N/A
Trna.seqfeature	N/A	SeqFeature	N/A
Trna.amino_acid	trna.AminoAcid	SeqFeature.qualifiers[“product”][0]	N/A
Trna.anticodon	trna.Anticodon	SeqFeature.qualifiers[“note”][0]	N/A
Trna.structure	trna.Structure	N/A	N/A
Trna.use	trna.Source	N/A	N/A
Trna.product	N/A	SeqFeature.qualifiers[“product”][0]	N/A
Trna.gene	N/A	SeqFeature.qualifiers[“gene”][0]	N/A

Below is a map of how tmRNA-level data is stored within these data structures:

pdm_utils object.attribute	MySQL table.column	GenBank flat file BioPython object.attribute	PhagesDB API dictionary
Tmrna.id	tmrna.GeneID	N/A	N/A
Tmrna.name	tmrna.Name	SeqFeature qualifiers	N/A
Tmrna.genome_id	tmrna.PhageID	N/A	N/A
Tmrna.start	tmrna.Start	SeqFeature.location.start OR end	N/A
Tmrna.stop	tmrna.Stop	SeqFeature.location.start OR end	N/A
Tmrna.coordinate_format	N/A	N/A	N/A
Tmrna.orientation	tmrna.Orientation	SeqFeature.strand	N/A
Tmrna.parts	N/A	SeqFeature.location.parts	N/A
Tmrna.length	tmrna.Length	SeqFeature.location.start AND end	N/A
Tmrna.locus_tag	tmrna.LocusTag	SeqFeature.qualifiers[“locus_tag”][0]	N/A
Tmrna.note	tmrna.Note	SeqFeature.qualifiers[“note”][0]	N/A
Tmrna.seqfeature	N/A	SeqFeature	N/A
Tmrna.gene	N/A	SeqFeature.qualifiers[“gene”][0]	N/A
Tmrna.peptide_tag	tmrna.PeptideTag	SeqFeature.qualifiers[“note”][0]	N/A

GenBank-formatted flat files contain a Source feature. Although this data is not stored within the MySQL database, it is parsed and evaluated for quality when the genome is imported into the database. Below is a map of how Source-level data is stored within these data structures:

pdm_utils object.attribute	MySQL table.column	GenBank flat file BioPython object.attribute	PhagesDB API dictionary
Source.id	N/A	N/A	N/A
Source.name	N/A	N/A	N/A
Source.seqfeature	N/A	SeqFeature	N/A
Source.start	N/A	SeqFeature.location.start OR end	N/A
Source.stop	N/A	SeqFeature.location.start OR end	N/A
Source.organism	N/A	SeqFeature.qualifiers[“organism”][0]	N/A
Source.host	N/A	SeqFeature.qualifiers[“host”][0]	N/A
Source.lab_host	N/A	SeqFeature.qualifiers[“lab_host”][0]	N/A