https://github.com/dd-decaf/id-mapper

ID mapper for biological entities (metabolites, reactions, genes, etc)
https://github.com/dd-decaf/id-mapper

Last synced: 3 months ago
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ID mapper for biological entities (metabolites, reactions, genes, etc)

• Host: GitHub
• URL: https://github.com/dd-decaf/id-mapper
• Owner: DD-DeCaF
• License: apache-2.0
• Created: 2017-01-31T20:36:41.000Z (almost 8 years ago)
• Default Branch: devel
• Last Pushed: 2021-07-21T17:37:48.000Z (over 3 years ago)
• Last Synced: 2023-10-20T19:15:30.909Z (over 1 year ago)
• Language: Python
• Homepage:
• Size: 284 KB
• Stars: 5
• Watchers: 10
• Forks: 1
• Open Issues: 7
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# ID Mapper

[![Build Status](https://travis-ci.org/DD-DeCaF/id-mapper.svg?branch=master)]()

[![Codecov](https://codecov.io/gh/DD-DeCaF/id-mapper/branch/master/graph/badge.svg)](https://codecov.io/gh/DD-DeCaF/id-mapper)

[![DOI](https://zenodo.org/badge/80559780.svg)](https://zenodo.org/badge/latestdoi/80559780)

Based on [MetaNetX](http://www.metanetx.org/). Information about metabolites and reactions is provided by [MNXref namespace](http://www.metanetx.org/mnxdoc/mnxref.html).

An online API service endpoint can be found at https://api.dd-decaf.eu/id-mapper/query.

Example on how to find a match for the chemical with [BIGG](http://bigg.ucsd.edu/) id `nh3` in [BioPath](https://webapps.molecular-networks.com/biopath3/biopath3) database:

```{python}

In [1]: import requests

In [2]: query = {"ids": ["atp"], "db_from": "bigg", "db_to": "kegg", "type": "Metabolite"}

In [3]: requests.post("http://localhost:8000/query", json=query).json()

Out[3]: {"ids": {"atp": ["C00002", "D08646"]}}

```

The graph consists of large amount of connected components. A connected component is considered being one object: a metabolite or a reaction. Search is returning all the elements in the component with `db_to` database name.

![graph](graph.png)

## Development

Download and load the chemical references into the graph database (may take several hours):

```{bash}

curl -O https://www.metanetx.org/cgi-bin/mnxget/mnxref/chem_xref.tsv

docker-compose run --rm web python src/load_chem_xref.py

```

Start the application:

```{bash}

docker-compose up

```

### Updating Python dependencies

To compile a new requirements file and then re-build the service with the new requirements, run:

    make pip-compile build

## License

id-mapper is licensed under the Apache License Version 2.0 (see LICENSE in source directory).