Schema to represent a knowledge base to build models of eukaryotes

Author:: Yin Hoon Chew <yinhoon.chew@mssm.edu>
Date:: 2018-09-10
Copyright:: 2018, Karr Lab
License:: MIT

3.2.4. Module Contents¶

3.2.4.1. Classes¶

`ActivityLevel`	Activity level of regulatory element
`RegulationType`	Type of regulation between a regulatory element and a gene
`RegulatoryDirection`	The direction of regulation
`TranscriptType`	Type of transcript
`LocusAttribute`	Start and end coordinates attribute
`RegDirectionAttribute`	Regulatory direction attribute
`GeneLocus`	Knowledge of a gene
`TranscriptionFactorRegulation`	Transcription factor and the direction of transcriptional regulation
`RegulatoryModule`	Knowledge about regulatory modules
`PtmSite`	Knowledge of protein modification sites
`GenericLocus`	Start and end coordinates of exons and CDSs
`TranscriptSpeciesType`	Knowledge of a transcript (spliced RNA) species
`ProteinSpeciesType`	Knowledge of a protein monomer

class wc_kb.eukaryote.ActivityLevel[source]¶

Bases: enum.Enum

Activity level of regulatory element

active = 1[source]¶

poised = 2[source]¶

repressed = 3[source]¶

inactive = 4[source]¶

na = 5[source]¶

class wc_kb.eukaryote.RegulationType[source]¶

Bases: enum.Enum

Type of regulation between a regulatory element and a gene

proximal = 1[source]¶

distal = 2[source]¶

class wc_kb.eukaryote.RegulatoryDirection[source]¶

Bases: int, enum.Enum

The direction of regulation

activation = 1[source]¶

repression[source]¶

unknown = 0[source]¶

class wc_kb.eukaryote.TranscriptType[source]¶

Bases: enum.Enum

Type of transcript

mRna = 1[source]¶

rRna = 2[source]¶

tRna = 3[source]¶

itRna = 4[source]¶

class wc_kb.eukaryote.LocusAttribute(related_name='', verbose_name='', verbose_related_name='', description='')[source]¶

Bases: obj_tables.ManyToManyAttribute

Start and end coordinates attribute

serialize(coordinates, encoded=None)[source]¶

Serialize related object :param coordinates: a list of instances of GenericLocus Python representation :type coordinates: list of Model :param encoded: dictionary of objects that have already been encoded :type encoded: dict, optional

Returns:: simple Python representation
Return type:: str

deserialize(value, objects, decoded=None)[source]¶

Deserialize value :param value: String representation :type value: str :param objects: dictionary of objects, grouped by model :type objects: dict :param decoded: dictionary of objects that have already been decoded :type decoded: dict, optional

Returns:

tuple of cleaned value: and cleaning error

Return type:

tuple of list of GenericLocus, InvalidAttribute or None

class wc_kb.eukaryote.RegDirectionAttribute(related_name='', verbose_name='', verbose_related_name='', description='')[source]¶

Bases: obj_tables.ManyToManyAttribute

Regulatory direction attribute

serialize(directions, encoded=None)[source]¶

Serialize related object :param directions: a list of instances of TFdirection Python representation :type directions: list of Model :param encoded: dictionary of objects that have already been encoded :type encoded: dict, optional

Returns:: simple Python representation
Return type:: str

deserialize(value, objects, decoded=None)[source]¶

Deserialize value :param value: String representation :type value: str :param objects: dictionary of objects, grouped by model :type objects: dict :param decoded: dictionary of objects that have already been decoded :type decoded: dict, optional

Returns:

tuple of cleaned value: and cleaning error

Return type:

tuple of list of RegDirection, InvalidAttribute or None

class wc_kb.eukaryote.GeneLocus[source]¶

Bases: wc_kb.core.PolymerLocus

Knowledge of a gene

symbol[source]¶

symbol

Type:: str

type[source]¶

type of gene

Type:: GeneType

Related attributes:: transcripts (list of TranscriptSpeciesType): transcripts regulatory_modules (list of RegulatoryModule): regulatory_modules

class Meta[source]¶

Bases: obj_tables.Model.Meta

verbose_name = 'Gene'[source]¶

verbose_name_plural = 'Genes'[source]¶

attribute_order = ('id', 'name', 'synonyms', 'symbol', 'homologs', 'polymer', 'strand', 'start', 'end',...[source]¶

symbol[source]¶

homologs[source]¶

class wc_kb.eukaryote.TranscriptionFactorRegulation[source]¶

Bases: obj_tables.Model

Transcription factor and the direction of transcriptional regulation

transcription_factor[source]¶

transcription factor

Type:: ProteinSpeciesType

direction[source]¶

regulatory direction

Type:: RegulatoryDirection

Related attributes:: regulatory_modules (list of RegulatoryModule): regulatory modules

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('transcription_factor', 'direction')[source]¶

frozen_columns = 1[source]¶

table_format[source]¶

ordering = ('transcription_factor', 'direction')[source]¶

transcription_factor[source]¶

direction[source]¶

static _serialize(transcription_factor_id, direction_name)[source]¶

Generate string representation

Parameters:

transcription_factor_id (str) – transcription factor id
direction_name (str) – regulatory direction name

Returns:

value of primary attribute

Return type:

str

serialize()[source]¶

Generate string representation

Returns:: value of primary attribute
Return type:: str

classmethod deserialize(value, objects)[source]¶

Deserialize value :param value: String representation :type value: str :param objects: dictionary of objects, grouped by model :type objects: dict

Returns:

tuple of cleaned value: and cleaning error

Return type:

tuple of list of TranscriptionFactorRegulation, InvalidAttribute or None

class wc_kb.eukaryote.RegulatoryModule[source]¶

Bases: obj_tables.Model

Knowledge about regulatory modules

id[source]¶

identifier

Type:: str

name[source]¶

name

Type:: str

gene[source]¶

gene

Type:: GeneLocus

promoter[source]¶

promoter ensembl ID

Type:: str

activity[source]¶

cell-type specific activity level

Type:: ActivityLevel

type[source]¶

type of regulation (proximal or distal)

Type:: RegulationType

transcription_factor_regulation[source]¶

transcription factor and direction of regulation

Type:: TranscriptionFactorRegulation

comments[source]¶

comments

Type:: str

references[source]¶

references

Type:: list of Reference

identifiers[source]¶

identifiers

Type:: list of Identifier

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'name', 'gene', 'promoter', 'activity', 'type', 'transcription_factor_regulation',...[source]¶

id[source]¶

name[source]¶

gene[source]¶

promoter[source]¶

activity[source]¶

type[source]¶

transcription_factor_regulation[source]¶

comments[source]¶

references[source]¶

identifiers[source]¶

class wc_kb.eukaryote.PtmSite[source]¶

Bases: wc_kb.core.PolymerLocus

Knowledge of protein modification sites

modified_protein[source]¶

modified protein

Type:: ProteinSpeciesType

type[source]¶

type of modification (phosphorylation, methylation, etc…)

Type:: str

modified_residue[source]¶

residue name and position in protein sequence

Type:: str

fractional_abundance[source]¶

ratio of modified protein abundance

Type:: int

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('id', 'name', 'modified_protein', 'type', 'modified_residue', 'fractional_abundance',...[source]¶

type[source]¶

modified_protein[source]¶

modified_residue[source]¶

fractional_abundance[source]¶

class wc_kb.eukaryote.GenericLocus[source]¶

Bases: obj_tables.Model

Start and end coordinates of exons and CDSs

start[source]¶

start coordinate

Type:: int

end[source]¶

end coordinate

Type:: int

Related attributes:: transcripts (list of TranscriptSpeciesType): transcripts proteins (list of ProteinSpeciesType): proteins

class Meta[source]¶

Bases: obj_tables.Model.Meta

attribute_order = ('start', 'end')[source]¶

table_format[source]¶

ordering = ('start', 'end')[source]¶

start[source]¶

end[source]¶

static _serialize(start, end)[source]¶

Generate string representation

Parameters:

start (int) – start coordinate
end (int) – end coordinate

Returns:

value of primary attribute

Return type:

str

serialize()[source]¶

Generate string representation

Returns:: value of primary attribute
Return type:: str

class wc_kb.eukaryote.TranscriptSpeciesType[source]¶

Bases: wc_kb.core.PolymerSpeciesType

Knowledge of a transcript (spliced RNA) species

gene[source]¶

gene

Type:: GeneLocus

exons[source]¶

exon coordinates

Type:: list of LocusAttribute

type[source]¶

type

Type:: TranscriptType

Related attributes:: protein (ProteinSpeciesType): protein

class Meta[source]¶

Bases: obj_tables.Model.Meta

verbose_name = 'Transcript'[source]¶

verbose_name_plural = 'Transcripts'[source]¶

attribute_order = ('id', 'name', 'gene', 'exons', 'type', 'identifiers', 'references', 'comments')[source]¶

gene[source]¶

exons[source]¶

type[source]¶

get_seq()[source]¶

Get the 5’ to 3’ sequence

Returns:: sequence
Return type:: Bio.Seq.Seq

get_empirical_formula(seq_input=None)[source]¶

Get the empirical formula for a transcript (spliced RNA) species with

5’ monophosphate
Deprotonated phosphate oxygens

\(N_A * AMP + N_C * CMP + N_G * GMP + N_U * UMP - (L-1) * OH\)

Parameters:: seq_input (Bio.Seq.Seq, optional) – if provided, the method will use it instead of reading from fasta file to reduce IO operation
Returns:: empirical formula
Return type:: chem.EmpiricalFormula

get_charge(seq_input=None)[source]¶

Get the charge for a transcript (spliced RNA) species with

5’ monophosphate
Deprotonated phosphate oxygens

\(-L - 1\)

Parameters:: seq_input (Bio.Seq.Seq, optional) – if provided, the method will use it instead of reading from fasta file to reduce IO operation
Returns:: charge
Return type:: int

get_mol_wt(seq_input=None)[source]¶

Get the molecular weight for a transcript (spliced RNA) species with

5’ monophosphate
Deprotonated phosphate oxygens

Parameters:: seq_input (Bio.Seq.Seq, optional) – if provided, the method will use it instead of reading from fasta file to reduce IO operation
Returns:: molecular weight (Da)
Return type:: float

class wc_kb.eukaryote.ProteinSpeciesType[source]¶

Bases: wc_kb.core.PolymerSpeciesType

Knowledge of a protein monomer

uniprot[source]¶

uniprot id

Type:: str

transcript[source]¶

transcript

Type:: TranscriptSpeciesType

coding_regions[source]¶

CDS coordinates

Type:: list of LocusAttribute

Related attributes:: transcription_factor_regulation (list of TranscriptionFactorRegulation): transcription factor regulation ptm_sites (:obj:list` of PtmSite): protein modification sites

class Meta[source]¶

Bases: obj_tables.Model.Meta

verbose_name = 'Protein'[source]¶

verbose_name_plural = 'Proteins'[source]¶

attribute_order = ('id', 'name', 'uniprot', 'transcript', 'coding_regions', 'identifiers', 'references', 'comments')[source]¶

uniprot[source]¶

transcript[source]¶

coding_regions[source]¶

get_seq(table=1, cds=True)[source]¶

Get the 5’ to 3’ sequence

Parameters:

table (int, optional) – NCBI identifier for translation table (default = standard table)
cds (bool, optional) – True indicates the sequence is a complete CDS

Returns:

sequence

Return type:

Bio.Seq.Seq

get_seq_and_start_codon(table=1, cds=True)[source]¶

Get the 5’ to 3’ amino acid sequence and the start codon

Parameters:

table (int, optional) – NCBI identifier for translation table (default = standard table)
cds (bool, optional) – True indicates the sequence is a complete CDS

Returns:

coding RNA sequence that will be translated Bio.Seq.Seq: amino acid sequence Bio.Seq.Seq: start codon

Return type:

Bio.Seq.Seq

get_empirical_formula(table=1, cds=True, seq_input=None)[source]¶

Get the empirical formula

Parameters:

table (int, optional) – NCBI identifier for translation table (default = standard table)
cds (bool, optional) – True indicates the sequence is a complete CDS
seq_input (Bio.Seq.Seq, optional) – if provided, the method will use it instead of reading from fasta file to reduce IO operation

Returns:

empirical formula

Return type:

chem.EmpiricalFormula

get_charge(table=1, cds=True, seq_input=None)[source]¶

Get the charge at physiological pH

Parameters:

table (int, optional) – NCBI identifier for translation table (default = standard table)
cds (bool, optional) – True indicates the sequence is a complete CDS
seq_input (Bio.Seq.Seq, optional) – if provided, the method will use it instead of reading from fasta file to reduce IO operation

Returns:

charge

Return type:

int

get_mol_wt(table=1, cds=True, seq_input=None)[source]¶

Get the molecular weight

Parameters:

table (int, optional) – NCBI identifier for translation table (default = standard table)
cds (bool, optional) – True indicates the sequence is a complete CDS
seq_input (Bio.Seq.Seq, optional) – if provided, the method will use it instead of reading from fasta file to reduce IO operation

Returns:

molecular weight

Return type:

float