Query

Contents

• Query
  • Examples
  • Methods by examples
  • Properties
  • Query Manager Reference

Examples

For all string parameters you can use % as wildcard (please check the documentation below). All methods have a parameter limit which allows to limit the number of results and as_df which allows to return a pandas.DataFrame.

Initialize query object

import pyuniprot
pyuniprot.update(taxids=[9606,10090,10116]) # human, mouse, rat update
query = pyuniprot.query()

Methods by examples

search for …

human proteins with gene name ‘TP53’ (taxid=9606)

>>> query.entry(gene_name='TP53', taxid=9606)
[Cellular tumor antigen p53]

human proteins with recommended full name starts with ‘Myeloid cell surface’ (use % at the end)

>>> query.entry(recommended_full_name='Myeloid cell surface%', taxid=9606)
[Myeloid cell surface antigen CD33]

find all UniProt entries where the recommended full name contains ‘CD33’ (% at the start and end of search term) and return as pandas.DataFrame

>>> results = query.entry(name='%CD33%', taxid=9606, as_df=True)
# get first 2 lines of results with columns 'name','recommended_full_name', 'taxid'
>>> my_results_as_data_frame.ix[:2,('name','recommended_full_name', 'taxid')]
          name                     recommended_full_name  taxid
0   CD33_HUMAN         Myeloid cell surface antigen CD33   9606
1  CCD33_HUMAN  Coiled-coil domain-containing protein 33   9606

find entries by a list of gene names

>>> query.entry(name=('TREM2_HUMAN', 'CD33_HUMAN'))
[Myeloid cell surface antigen CD33, Triggering receptor expressed on myeloid cells 2]

If an attribute ends of an s it a clear hint that this is an 1:n or n:m relationship like keywords. There could be several proteins linked to a keyword, but also several keywords are linked to one protein. Next lines of code shows how to query for all proteins linked to the keyword ‘Neurodegenaration’ and returns the gene names.

>>> results = query.entry(keywords='Neurodegeneration')
>>> len(results) # number of results
322
>>> [x.gene_name for x in results][:3] # show only the first 2 gene names
['CHMP1A', 'CLN3', 'COQ8A']

Every element in the list represents a pyuniprot.manager.models.Entry instance:

>>> first_protein = results[0] # fetch first result
>>> type(first_protein)
pyuniprot.manager.models.Entry
>>> first_protein
Charged multivesicular body protein 1a
# get first 3 of all other keywords to this protein
>>> first_protein.keywords[:3]
[Reference proteome:KW-1185, Coiled coil:KW-0175, Repressor:KW-0678]

Properties

q.gene_forms
q.interaction_actions
q.actions
q.pathways

Query Manager Reference