4.1.1.1.1.2. datanator.api.query package

4.1.1.1.1.2.1. Submodules

4.1.1.1.1.2.2. datanator.api.query.dna_protein_interactions module

Author:Saahith Pochiraju <saahith116@gmail.com> Date:2017-09-28 Copyright:2017, Karr Lab License:MIT

class datanator.api.query.dna_protein_interactions.DNAtoProteinInteractionQuery(taxon=None, max_taxon_dist=None, taxon_dist_scale=None, include_variants=False, temperature=37.0, temperature_std=1.0, ph=7.5, ph_std=0.3, cache_dirname=None)

Bases: datanator.core.data_query.CachedDataSourceQueryGenerator

Queries DNA reigons for relevant proteins

get_observed_result(DnaSpecie)

Find observed concentrations for the metabolite or similar metabolites

NOTE: Currently there are no Gene objects in common schema models. When added this query will be updated to input models.Gene and output data_model.ProteinSpecie

Parameters:specie (data_model.DnaSpecie) – species to find data for Returns:list of observed_result Return type:list of data_model.Observable

get_protein_by_DNA_sequence(sequence, select=<class 'datanator.core.models.ProteinSubunit'>)

NOTE: Currently there are no Gene objects in common schema models. When added this query will be updated to input models.Gene and output data_model.ProteinSpecie

Parameters:sequence (data_model.DnaSpecie.sequence) – sequence of DNA segment Returns:Returns the query for a protein, sequence position, and score Return type:list of tuple

class datanator.api.query.dna_protein_interactions.ProteintoDNAInteractionQuery(taxon=None, max_taxon_dist=None, taxon_dist_scale=None, include_variants=False, temperature=37.0, temperature_std=1.0, ph=7.5, ph_std=0.3, cache_dirname=None)

Bases: datanator.core.data_query.CachedDataSourceQueryGenerator

Queries Proteins for their DNA

get_DNA_by_protein(protein, select=<class 'datanator.core.models.DNABindingData'>)

Parameters:protein (models.ProteinSubunit) – protein subunit to find data for Returns:list of versions queries for DNA binding observed for similar proteins Return type:list of sqlalchemy.orm.query.Query

get_observed_result(protein)

Find the DNA binding motif for a given protein

Parameters:protein (models.ProteinSubunit) – protein subunit to find data for Returns:list of observables Return type:list of data_model.Observable

4.1.1.1.1.2.3. datanator.api.query.metabolite_concentrations module

Author:Jonathan Karr <jonrkarr@gmail.com> Author:Saahith Pochiraju <saahith116@gmail.com> Date:2017-05-16 Copyright:2017, Karr Lab License:MIT

class datanator.api.query.metabolite_concentrations.MetaboliteConcentrationQuery(taxon=None, max_taxon_dist=None, taxon_dist_scale=None, include_variants=False, temperature=37.0, temperature_std=1.0, ph=7.5, ph_std=0.3, cache_dirname=None)

Bases: datanator.core.data_query.CachedDataSourceQueryGenerator

Finds relevant concentration observations for metabolites

get_concentration_by_structure(inchi, only_formula_and_connectivity=True, select=<class 'datanator.core.models.Concentration'>)

Parameters:inchi (str) – inchi structure to find concentrations Returns:query for matching concentration rows Return type:sqlalchemy.orm.query.Query

get_observed_result(metabolite)

Find observed concentrations for the metabolite or similar metabolites

Parameters:metabolite (models.Metabolite) – metabolite to find data for Returns:list of relevant observations Return type:list of data_model.ObservedValue

4.1.1.1.1.2.4. datanator.api.query.protein_abundance module

Author:Saahith Pochiraju <saahith116@gmail.com> Date:2017-09-12 Copyright:2017, Karr Lab License:MIT

class datanator.api.query.protein_abundance.ProteinAbundanceQuery(taxon=None, max_taxon_dist=None, taxon_dist_scale=None, include_variants=False, temperature=37.0, temperature_std=1.0, ph=7.5, ph_std=0.3, cache_dirname=None)

Bases: datanator.core.data_query.CachedDataSourceQueryGenerator

Finds relevant concentration observations for proteins

get_abundance_by_entrez(entrez_id, select=<class 'datanator.core.models.AbundanceData'>)

Find the abundance from uniprot

Parameters:entrez_id (str) – NCBI entrez id for a given protein Returns:query for matching abundance rows Return type:sqlalchemy.orm.query.Query

get_abundance_by_gene_name(gene_name, select=<class 'datanator.core.models.AbundanceData'>)

Find the abundance from gene_name

Parameters:gene_name (str) – gene name for a given protein Returns:query for matching abundance rows Return type:sqlalchemy.orm.query.Query

get_abundance_by_length(length, select=<class 'datanator.core.models.AbundanceData'>)

Find the abundance from uniprot

Parameters:length (str) – number of amino acids in a protein Returns:query for matching abundance rows Return type:sqlalchemy.orm.query.Query

get_abundance_by_mass(mass, select=<class 'datanator.core.models.AbundanceData'>)

Find the abundance from uniprot

Parameters:mass (int) – mass of a protein Returns:query for matching abundance rows Return type:sqlalchemy.orm.query.Query

get_abundance_by_sequence(sequence, select=<class 'datanator.core.models.AbundanceData'>)

Find the abundance from uniprot

Parameters:sequence (str) – amino acid sequence for a given protein Returns:query for matching abundance rows Return type:sqlalchemy.orm.query.Query

get_abundance_by_uniprot(uniprot, select=<class 'datanator.core.models.AbundanceData'>)

Find the abundance from a uniprot id

Parameters:uniprot (str) – protein id from Uniprot Database Returns:query for matching abundance rows Return type:sqlalchemy.orm.query.Query

get_observed_result(protein)

Find the observed values for protein abundance

Parameters:protein (models.ProteinSubunit) – Protein Subunit to find data for Returns:list of relevant observed values Return type:list of data_model.ObservedValue

4.1.1.1.1.2.5. datanator.api.query.protein_protein_interactions module

Author:Saahith Pochiraju <saahith116@gmail.com> Date:2018-05-10 Copyright:2017, Karr Lab License:MIT

class datanator.api.query.protein_protein_interactions.ProteinInteractionandComplexQuery(taxon=None, max_taxon_dist=None, taxon_dist_scale=None, include_variants=False, temperature=37.0, temperature_std=1.0, ph=7.5, ph_std=0.3, cache_dirname=None)

Bases: datanator.core.data_query.CachedDataSourceQueryGenerator

Queries Proteins to find Interactions with other Proteins

get_interaction_by_subunit(uniprot, select=<class 'datanator.core.models.ProteinInteraction'>)

Get interactions that were observed for a given uniprot id

Parameters:uniprot (str) – uniprot id to search for Returns:query for protein interactions that contain the uniprot_id Return type:sqlalchemy.orm.query.Query

get_known_complex_by_subunit(uniprot, select=<class 'datanator.core.models.ProteinComplex'>)

Get known complexes that were observed for a given uniprot id subunit

Parameters:uniprot (str) – uniprot id to search for Returns:query for protein complexes that contain the uniprot_id Return type:sqlalchemy.orm.query.Query

get_observable_complex(protein_subunit)

Get known protein complex that were observed for a given subunit

Parameters:protein_subunit (models.ProteinSubunit) – subunit to find complex for Returns:list of Protein Complexes Return type:list of data_model.ObservedSpecie

get_observable_interactions(protein_subunit)

Get known protein interactions that were observed for a given subunit

Parameters:protein_subunit (models.ProteinSubunit) – subunit to find interactions for Returns:list of Observed Protein Interactions Return type:list of data_model.ObservedInteraction

get_observable_subunits(protein_complex)

Get known protein subunit that were observed for a given protein complex

Parameters:protein_subunit (models.ProteinComplex) – complex to find subunits for Returns:list of Protein Subunits Return type:list of data_model.ObservedSpecie

get_observed_result(component)

Get known observed interactions, complexes, or subunits for a given component

Parameters:component (models.ProteinSubunit) or (models.ProteinComplex) – subunit or complex to find interactions for Returns:list of Protein Interactions Return type:list of data_model.SpecieInteraction

get_subunits_by_known_complex(complex_name, select=<class 'datanator.core.models.ProteinSubunit'>)

Get known protein subunits that were observed for a given complex

Parameters:complex_name (str) – complex to find subunits for Returns:query for protein subunits that are within the given protein complex Return type:sqlalchemy.orm.query.Query

4.1.1.1.1.2.6. datanator.api.query.reaction_kinetics module

Author:Yosef Roth <yosefdroth@gmail.com> Author:Jonathan Karr <jonrkarr@gmail.com> Author:Saahith Pochiraju <saahith116@gmail.com> Date:2017-05-16 Copyright:2017, Karr Lab License:MIT

class datanator.api.query.reaction_kinetics.ReactionKineticsQuery(taxon=None, max_taxon_dist=None, taxon_dist_scale=None, include_variants=False, temperature=37.0, temperature_std=1.0, ph=7.5, ph_std=0.3, cache_dirname=None)

Bases: datanator.core.data_query.CachedDataSourceQueryGenerator

Finds relevant kinetics observations for reactions

1. Find kinetics observed for the reaction or similar reactions

1. Find kinetics observed for the reaction

1. Find the metabolite(s) of each participant
2. Find the reaction(s) which contain all of these metabolites
3. Find the kinetic laws associated with these reactions

2. Find kinetics observed for similar reactions

1. Find kinetics observed for the assigned EC number(s)
2. Find kinetics observed for EC number(s) predicted by tools such as E-zyme

2. Filter out observations from disimilar genetic and environmental conditions and rank the remaing observations by their similarity to the desired genetic and environmental conditions
3. Calculate a statistical representation of the relevant observations

convert_rxn_to_data_model(reaction_list)

Converts SQL model reaction into a Obj Model based data_model reaction

:param reaction_list list of models.Reaction: ): list of reaction participants

Returns:a cohesive reaction data object Return type:data_model.Reaction

get_kinetic_laws_by_ec_numbers(ec_numbers, match_levels=4, select=<class 'datanator.core.models.KineticLaw'>)

Get kinetic laws which have one of a list of EC numbers or, optionally, belong to one of a list of EC classes.

Parameters:

• ec_numbers (list of str) – EC numbers to search for
• match_levels (int) – number of EC levels that the EC number must match

Returns:

query for matching kinetic laws

Return type:

sqlalchemy.orm.query.Query

get_kinetic_laws_by_metabolite(metabolite, role='reactant', select=<class 'datanator.core.models.KineticLaw'>)

Get kinetic laws that contain a structure in role role

Parameters:

• structure (str) – InChI structure or formula and connectivity layers to search for
• only_formula_and_connectivity (bool, optional) – if True, find kinetic laws which contain species with the same InChI formula and connectivity layers
• role (str, optional) – role (reactant, or product) to search for species

Returns:

query for kinetic laws that contain the structure in role role

Return type:

sqlalchemy.orm.query.Query

get_kinetic_laws_by_participants(participants, only_formula_and_connectivity=False, include_water_hydrogen=False, select=<class 'datanator.core.models.KineticLaw'>)

Get kinetic laws with the participants participants

Parameters:

• participants (list of data_model.ReactionParticipant) – list of reaction participants
• only_formula_and_connectivity (bool, optional) – if True, find kinetic laws which contain species with the same InChI formula and connectivity layers
• include_water_hydrogen (bool, optional) – if True, restrict kinetic laws based on their water, hydroxide, and hydrogen participants

Returns:

a list kinetic laws that contain all of the participants

Return type:

list of models.KineticLaw

get_kinetic_laws_by_reaction(reaction, select=<class 'datanator.core.models.KineticLaw'>)

Get kinetic laws that were observed for similar reactions (same participants or same EC class)

Parameters:reaction (data_model.Reaction) – reaction to find data for Returns:a list kinetic laws that contain all of the participants Return type:list of models.KineticLaw

get_kinetic_laws_by_structure(structure, only_formula_and_connectivity=False, role='reactant', select=<class 'datanator.core.models.KineticLaw'>)

Get kinetic laws that contain a structure in role role

Parameters:

• structure (str) – InChI structure or formula and connectivity layers to search for
• only_formula_and_connectivity (bool, optional) – if True, find kinetic laws which contain species with the same InChI formula and connectivity layers
• role (str, optional) – role (reactant, or product) to search for species

Returns:

query for kinetic laws that contain the structure in role role

Return type:

sqlalchemy.orm.query.Query

get_metabolites_by_structure(inchi, only_formula_and_connectivity=False, select=<class 'datanator.core.models.Metabolite'>)

Get metabolites with the same structure. Optionally, get metabolites which only have the same core empirical formula and core atom connecticity (i.e. same InChI formula and connectivity layers).

Parameters:

• inchi (str) – molecule structure in InChI format
• only_formula_and_connectivity (bool, optional) – if True, get metabolites which only have the same core empirical formula and core atom connecticity. if False, get metabolites with the identical structure.

Returns:

query for matching metabolites

Return type:

sqlalchemy.orm.query.Query

get_observed_result(reaction)

Find observed kinetics for the reaction or similar reactions TODO: Add compartment infomrmation

1. Find kinetics observed for the reaction

1. Find the metabolite(s) of each participant
2. Find the reaction(s) which contain all of these metabolites
3. Find the kinetic laws associated with these reactions

2. Find kinetics observed for similar reactions

1. Find kinetics observed for the assigned EC number(s)
2. Find kinetics observed for EC number(s) predicted by tools such as E-zyme

Parameters:reaction (data_model.Reaction) – reaction to find data for Returns:list of relevant observed values Return type:list of data_model.ObservedValue

get_reaction_by_kinetic_law_id(id)

get_reaction_by_metabolite(metabolite, select=<class 'datanator.core.models.Reaction'>)

Get reaction that contains the metabolite role models.Metabolite

Parameters:structure (models.Metabolite) – InChI structure or formula and connectivity layers to search for Returns:reaction to find data for Return type:data_model.Reaction

4.1.1.1.1.2.7. datanator.api.query.text_search module

Test of common schema

Author:Saahith Pochiraju <saahith116@gmail.com> Date:2017-12-18 Copyright:2017, Karr Lab License:MIT

class datanator.api.query.text_search.TextSearchSession(db_cache_dirname='/root/project')

Bases: object

Represents a text search through the database grabbing relevant information

db_cache_dirname

path location for DB

Type:str

return_search(string)

Collects and creates dictionary of all Database objects coming up in a full text search for related string

Parameters:( (string) – obj :str): item to be searched for Returns:List of ranked collected items from text search dict_db_models (dict): Dictionary of collected items from text search Return type:list_db_models (list)

4.1.1.1.1.2.8. Module contents