`sbmltoodejax.biomodels_api`#

This provides several utils functions for accessing the BioModels API as described on https://www.ebi.ac.uk/biomodels/docs/

See also

The biomodels_api code and documentation is copied (and slightly adapated) from the basico repository that is maintained by the COPASI group and under Artistic License 2.0. The original code can be found at copasi/basico

Note

The only (minor) modification with respect to original code is that we deal with special characters in get_content_for_model() using urllib.parse.quote

Examples

# get info for a specific model
info = get_model_info(12)
print(info['name'], info['files']['main'][0]['name'])
# get all files for one model
files = get_files_for_model(12)
print(files['main'][0]['name'])
# get content of specific model
sbml = get_content_for_model(12)
print(sbml)
# search for model
models = search_for_model('repressilator')
for model in models:
   print(model['id'], model['name'], model['format'])

sbmltoodejax.biomodels_api.download_from(url)[source]#

Convenience method reading content from a URL. This convenience method uses urlopen on either python 2.7 or 3.x

Parameters:: url (str) – the url to read from
Returns:: the contents of the URL as str
Return type:: str

sbmltoodejax.biomodels_api.download_json(url)[source]#

Convenience method reading the content of the url as JSON.

Parameters:: url (str) – the url to read from
Returns:: a python object representing the json content loaded
Return type:: dict

sbmltoodejax.biomodels_api.get_content_for_model(model_id, file_name=None)[source]#

Downloads the specified file from biomodels

Parameters:

model_id – either an integer, or a valid model id
file_name – the filename to download (or None, to download the main file)

Returns:

the content of the specified file

sbmltoodejax.biomodels_api.get_files_for_model(model_id)[source]#

Retrieves the json structure for all files for the given biomodel. The structure is of form:

{
    'additional': [
        {'description': 'Auto-generated Scilab file',
         'fileSize': '3873',
         'name': 'BIOMD0000000010.sci'},
         ...
    ],
    'main': [
        {'fileSize': '31568',
         'name': 'BIOMD0000000010_url.xml'
        }
    ]
}

Parameters:: model_id – either an integer, or a valid model id
Returns:: json structure

sbmltoodejax.biomodels_api.get_model_info(model_id)[source]#

Return the model info for the provided model_id.

Parameters:: model_id – either an integer, or a valid model id
Returns:: a python object describing the model

sbmltoodejax.biomodels_api.search_for_model(query, offset=0, num_results=10, sort='id-asc')[source]#

Queries the biomodel database Queries the database, for information about the query system see: https://www.ebi.ac.uk/biomodels-static/jummp-biomodels-help/model_search.html

Example

>>> search_for_model('glycolysis')
[...,
    {
    'format': 'SBML',
    'id': 'BIOMD0000000206',
    'lastModified': '2012-07-04T23:00:00Z',
    'name': 'Wolf2000_Glycolytic_Oscillations',
    'submissionDate': '2008-11-27T00:00:00Z',
    'submitter': 'Harish Dharuri',
    'url': 'https://www.ebi.ac.uk/biomodels/BIOMD0000000206'
    }
]
Note by default, it will include only manually curated models, to obtain Non-curated models you would use:
>>> search_for_model('Hodgkin AND curationstatus:"Non-curated"')
[...,
    {
    'format': 'SBML',
    'id': 'MODEL1006230012',
    'lastModified': '2012-02-02T00:00:00Z'',
    'name': 'Stewart2009_ActionPotential_PurkinjeFibreCells',
    'submissionDate': '2010-06-22T23:00:00Z',
    'submitter': 'Camille Laibe',
    'url': 'https://www.ebi.ac.uk/biomodels/MODEL1006230012'
    }
]

Parameters:

query – the query to use (it will be encoded with quote_plus before send out, so it is safe to use spaces)
offset – offset (defaults to 0)
num_results – number of results to obtain (defaults to 10)
sort – sort criteria to be used (defaults to id-asc)

Returns:

the search result as [{}]

sbmltoodejax.biomodels_api

Contents

sbmltoodejax.biomodels_api#

`sbmltoodejax.biomodels_api`#