Data Models

PyUniProt uses SQLAlchemy to store the data in the database. Use instance of pyuniprot.manager.query.QueryManager to query the content of the database.

Entity–relationship model:

Contents

• Data Models
  • Entry
  • Accession
  • OtherGeneName
  • Sequence
  • Disease
  • DiseaseComment
  • AlternativeFullName
  • AlternativeShortName
  • Accession
  • Pmid
  • OrganismHost
  • DbReference
  • Feature
  • Function
  • Keyword
  • ECNumber
  • SubcellularLocation
  • TissueSpecificity
  • TissueInReference

Entry

class pyuniprot.manager.models.Entry(**kwargs)

UniProt entry with relations to other models

Query Entry with pyuniprot.manager.query.QueryManager.entry()

Variables:

• dataset (str) – dataset type (SwissProt or TrEMBL)
• created (datetime.datetime) – Date created
• modified (datetime.datetime) – Datemodified
• version (int) – Dataset version
• name (str) – UniProt entry name
• recommended_full_name (str) – Recommended full protein name
• recommended_short_name (str) – Recommended short protein name
• taxid (int) – NCBI taxonomy identifier
• gene_name (str) – Primary gene name
• sequence – 1:1 to Sequence
• accessions (collections.Iterable) – 1:n to Accession
• organism_hosts (collections.Iterable) – 1:n to OrganismHost
• features (collections.Iterable) – 1:n to Feature
• functions (collections.Iterable) – 1:n to Function
• ec_numbers (collections.Iterable) – 1:n to ECNumber
• db_references (collections.Iterable) – 1:n to DbReference
• alternative_full_names (collections.Iterable) – 1:n to AlternativeFullName
• alternative_short_names (collections.Iterable) – 1:n to AlternativeShortName
• disease_comments (collections.Iterable) – 1:n to DiseaseComment
• tissue_specificities (collections.Iterable) – 1:n to TissueSpecificity
• other_gene_names (collections.Iterable) – 1:n to OtherGeneName
• pmids (collections.Iterable) – n:m to Pmid
• keywords (collections.Iterable) – n:m to Keyword
• subcellular_locations (collections.Iterable) – n:m to SubcellularLocation
• tissue_in_references (collections.Iterable) – n:m to TissueInReference

Table view

Links

For more information on UniProt website:

• UniProt entry name
• UniProt protein names
• NCBI taxonomy identifier
• UniProt accession number
• UniProt Sequence annotations
• UniProt functions
• UniProt catalytic activity

Accession

class pyuniprot.manager.models.Accession(**kwargs)

Provides a stable way of identifying UniProtKB entries.

Variables:

• accession (str) – Accession number
• entry (Entry) – Entry object

Table view

Links

More information about alternative names on UniProt help about ‘Accession’

OtherGeneName

class pyuniprot.manager.models.OtherGeneName(**kwargs)

All gene names which are not primary

Query Entry with pyuniprot.manager.query.QueryManager.other_gene_names()

Variables:

• type_ (str) – type of gene name e.g. synonym
• name (str) – gene name
• entry (Entry) – Entry object

Table view

Links

For more information on UniProt website:

• UniProt protein names

Sequence

class pyuniprot.manager.models.Sequence(**kwargs)

Amino acid sequence

Variables:

• sequence (str) – Amino acid sequence
• entry (Entry) – Entry object

Table view

Links

For more information on UniProt website:

• UniProt sequence

Disease

class pyuniprot.manager.models.Disease(**kwargs)

Variables:

• identifier (str) – Disease identifier
• ref_id (str) – Disease reference identifier
• ref_type (str) – Disease reference type
• name (str) – Disease name
• acronym (str) – Disease acronym
• description (str) – Disease description
• disease_comments (str) – 1:n to DiseaseComment

Table view

DiseaseComment

class pyuniprot.manager.models.DiseaseComment(**kwargs)

Disease and comment linked to an entry (protein)

Variables:

• comment (str) – Comment on disease linked to a specific entry
• disease (Disease) – Disease object
• entry (Entry) – Entry object

AlternativeFullName

class pyuniprot.manager.models.AlternativeFullName(**kwargs)

Alternative full name

Variables:

• name (str) – Alternative full name
• entry (Entry) – Entry

Table view

Links

More information about alternative names on UniProt help about ‘Protein names’

AlternativeShortName

class pyuniprot.manager.models.AlternativeShortName(**kwargs)

Alternative short name

Variables:

• name (str) – Alternative short name
• entry (Entry) – Entry

Table view

Links

More information about alternative names on UniProt help about ‘Protein names’

Accession

class pyuniprot.manager.models.Accession(**kwargs)

Provides a stable way of identifying UniProtKB entries.

Variables:

• accession (str) – Accession number
• entry (Entry) – Entry object

Table view

Links

More information about alternative names on UniProt help about ‘Accession’

Pmid

class pyuniprot.manager.models.Pmid(**kwargs)

PMID - The unique identifier assigned to a record when it enters PubMed.

Variables:

• pmid (str) – PubMed identifier
• first (str) – first page of publication
• last (str) – last page of publication
• volume (int) – Volume
• name (str) – Name of Journal
• date (datetime.datetime) – Publication date
• title (str) – Title of publication

Table view

Links

• UniProt publications_section
• PubMed web site of the National Center for Biotechnology Information

OrganismHost

class pyuniprot.manager.models.OrganismHost(**kwargs)

NCBI taxonomy database identifier of the organism host

Variables:

• taxid (int) – NCBI Taxonomy identifier
• entry (Entry) – Entry object

Table view

Links

• NCBI taxonomy website

DbReference

class pyuniprot.manager.models.DbReference(**kwargs)

Cross reference to other databases and information resources

Variables:

• type_ (str) – Type of cross reference
• identifier (str) – Unique identifier of cross reference
• entry (Entry) – Entry object

Table view

Links

• UniProt cross references

Feature

class pyuniprot.manager.models.Feature(**kwargs)

Sequence annotations describe regions or sites of interest in the protein sequence, such as post-translational modifications, binding sites, enzyme active sites, local secondary structure or other characteristics reported in the cited references. In the moment we don’t save the positions. If this is strongly neede contact the PyUniProt team on github.

Variables:

• type_ (str) – Type of feature
• identifier (str) – Feature identifier
• description (str) – Feature description
• entry (Entry) – Entry object

Table view

Links

• UniProt sequence annotation (Features)

Function

class pyuniprot.manager.models.Function(**kwargs)

General description of the function(s) of a protein

Variables:

• text (str) – Decription of function
• entry (Entry) – Entry object

Table view

Links

• UniProt functions

Keyword

class pyuniprot.manager.models.Keyword(**kwargs)

UniProt keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.

Variables:

• name (str) – Keyword
• identifier (str) – Keyword identifier
• entries (list) – list of Entry object

Table view

Links

• UniProt keywords

ECNumber

class pyuniprot.manager.models.ECNumber(**kwargs)

Enzyme Commission number (EC number) is a classification system for enzymes

Variables:

• ec_number (str) – EC number
• entry (Entry) – Entry object

Table view

Links

• UniProt protein names

SubcellularLocation

class pyuniprot.manager.models.SubcellularLocation(**kwargs)

Subcellular location of protein

Variables:

• location (str) – Subcellular location
• entries (list) – list of Entry object

Table view

Links

• UniProt subcellular location

TissueSpecificity

class pyuniprot.manager.models.TissueSpecificity(**kwargs)

Description of the expression of a gene in different tissues

Variables:

• comment (str) – Tissue specificity
• entry (Entry) – Entry object

Table view

Links

• UniProt tissue specificity

TissueInReference

class pyuniprot.manager.models.TissueInReference(**kwargs)

Tissue described in the reference

Variables:entries (list) – list of Entry object

Table view