Ecosyste.ms: Awesome
An open API service indexing awesome lists of open source software.
https://github.com/maurosilber/biomodels
Python library to download and cache models from BioModels
https://github.com/maurosilber/biomodels
biomodels combine omex sbml sed-ml
Last synced: 3 months ago
JSON representation
Python library to download and cache models from BioModels
- Host: GitHub
- URL: https://github.com/maurosilber/biomodels
- Owner: maurosilber
- License: mit
- Created: 2023-09-21T13:21:15.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2024-02-03T23:10:01.000Z (about 1 year ago)
- Last Synced: 2024-08-10T23:12:53.974Z (6 months ago)
- Topics: biomodels, combine, omex, sbml, sed-ml
- Language: Python
- Homepage:
- Size: 30.3 KB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
README
# BioModels
`biomodels` is a Python library to download models from [BioModels](https://www.ebi.ac.uk/biomodels/).
Models are cached locally in the OS user cache directory,
so they will not be redownloaded every time.
## Usage
### Get model metadata
The first time we download a file,
it will let us know that it is being downloaded
and cached locally.
```python
>>> import biomodels
>>> metadata = biomodels.get_metadata("BIOMD0000000012") # doctest: +SKIP
Downloading data from 'https://www.ebi.ac.uk/biomodels/model/files/BIOMD0000000012?format=json' to file '.../Caches/biomodels/model/files/BIOMD0000000012'.
SHA256 hash of downloaded file: ...
Use this value as the 'known_hash' argument of 'pooch.retrieve' to ensure that the file hasn't changed if it is downloaded again in the future.
```
Later, this file will get fetched from the local cache,
instead of being redownloaded.
```python
>>> metadata = biomodels.get_metadata("BIOMD12") # no need to input the leading zeros
>>> metadata
name description size
-- --------------------------- ----------------------------------- ------
0 BIOMD0000000012_url.xml main 46274
1 BIOMD0000000012-biopax2.owl Auto-generated BioPAX (Level 2) 16748
2 BIOMD0000000012-biopax3.owl Auto-generated BioPAX (Level 3) 23577
3 BIOMD0000000012.m Auto-generated Octave file 4994
4 BIOMD0000000012.pdf Auto-generated PDF file 205156
5 BIOMD0000000012.png Auto-generated Reaction graph (PNG) 39018
6 BIOMD0000000012.sci Auto-generated Scilab file 154
7 BIOMD0000000012.svg Auto-generated Reaction graph (SVG) 35750
8 BIOMD0000000012.vcml Auto-generated VCML file 60183
9 BIOMD0000000012.xpp Auto-generated XPP file 4114
10 BIOMD0000000012_urn.xml Auto-generated SBML file with URNs 47097
```
### Get a particular file
To get a particular file,
you can either pass the filename and model_id:
```python
>>> biomodels.get_file("BIOMD0000000012_url.xml", model_id="BIOMD12")
PosixPath('/biomodels/model/download/BIOMD0000000012/BIOMD0000000012_url.xml')
```
or choose one from the metadata:
```python
>>> path = biomodels.get_file(metadata[0])
>>> path
PosixPath('/biomodels/model/download/BIOMD0000000012/BIOMD0000000012_url.xml')
```
Then, you can use that `Path` object to load the file:
```python
>>> print(path.read_text())
...
```
### Get COMBINE archive
If you are interested in all the model files,
it might be better to download the COMBINE archive,
which is a compressed file (260KB vs 500KB for this small model):
```python
>>> omex = biomodels.get_omex("BIOMD12")
>>> omex
location format master
-- --------------------------- --------------------------------------------------------------------- --------
0 https://identifiers.org/combine.specifications/omex False
1 BIOMD0000000012-biopax2.owl https://identifiers.org/combine.specifications/biopax.level-2 False
2 BIOMD0000000012-biopax3.owl https://identifiers.org/combine.specifications/biopax.level-3 False
3 BIOMD0000000012.m https://purl.org/NET/mediatypes/application/x.unknown False
4 BIOMD0000000012.pdf https://purl.org/NET/mediatypes/application/pdf False
5 BIOMD0000000012.png https://purl.org/NET/mediatypes/image/png False
6 BIOMD0000000012.sci https://purl.org/NET/mediatypes/application/x.unknown False
7 BIOMD0000000012.svg https://purl.org/NET/mediatypes/application/xml False
8 BIOMD0000000012.vcml https://purl.org/NET/mediatypes/application/xml False
9 BIOMD0000000012.xpp https://purl.org/NET/mediatypes/application/x.unknown False
10 BIOMD0000000012_manual.png https://purl.org/NET/mediatypes/image/png False
11 BIOMD0000000012_manual.svg https://purl.org/NET/mediatypes/application/xml False
12 BIOMD0000000012_url.xml https://identifiers.org/combine.specifications/sbml.level-2.version-3 True
13 BIOMD0000000012_urn.xml https://identifiers.org/combine.specifications/sbml.level-2.version-3 False
14 manifest.xml https://identifiers.org/combine.specifications/omex-manifest False
15 metadata.rdf https://identifiers.org/combine.specifications/omex-metadata False
```
We can select a particular file by indexing:
```python
>>> content = omex[12]
>>> content
Content(location='BIOMD0000000012_url.xml', format='https://identifiers.org/combine.specifications/sbml.level-2.version-3', master=True)
```
Then,
you can get a `zipfile.Path` object with the `Content.path` attribute,
and read the contents from the OMEX file:
```python
>>> print(content.path.read_text())
...
```
## Installation
```
pip install biomodels
```
## Development
We are using pytest for testing,
and pre-commit hooks to format and lint the codebase.
To easily set-up a development environment,
run the following commands:
```
git clone https://github.com/maurosilber/biomodels
cd biomodels
conda env create --file environment-dev.yml
pre-commit install
```
which assume you have git and conda preinstalled.