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proccaserra committed Oct 9, 2024
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62 changes: 40 additions & 22 deletions _sources/content/recipes/afterword/people.md

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772 changes: 772 additions & 0 deletions _sources/content/recipes/applied-examples/BIA_submission.md

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Expand Up @@ -204,6 +204,8 @@ This therefore improves **Findability** and **Reusability** of such data.
### What to read next?
- {ref}`fcb-access-aspera`
- {ref}`fcb-find-zenodo`


````{panels}
:column: col-md-4
:body: p-0
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48 changes: 37 additions & 11 deletions _sources/content/recipes/infrastructure/iupac-names.md
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Expand Up @@ -20,34 +20,58 @@

The main purpose of this recipe is:

> To take an IUPAC name and generate an InChIKey
> To take an IUPAC name and generate an InChIKey from it.
---

### Using the OPSIN website

The OPSIN library is an open source tool to parse IUPAC names into chemical graphs {footcite}`Lowe2011Chemical`.

OPSIN has [a website](https://opsin.ch.cam.ac.uk/) where IUPAC names are converted into other representations, including an InChIKey.
The latter is done by the offical InChI library {footcite}`Goodman2021InChI`.

The latter is done by the official InChI library {footcite}`Goodman2021InChI`.

### Automating translations with Google Colab

[Google Colaboratory](https://colab.research.google.com/) (Colab for short) allows us to use Python to automate conversions of IUPAC names.
In Colab we can use [Bacting](https://github.com/egonw/bacting) {footcite}`Willighagen2021`
to access the OPSIN library. We would first download the Bacting libraries and create the Bacting manager objects:

In Colab, we can use [Bacting](https://github.com/egonw/bacting) {footcite}`Willighagen2021`
to access the OPSIN library.

We would first need to set up Colab for Java, Maven, and [scyjava](https://pypi.org/project/scyjava/), followed
by the download of the Bacting libraries and creation of Bacting manager objects.

Java 17 and Maven are installed with the following commands, (with a confirmation which Java is available):

```python
apt-get install openjdk-17-jre-headless maven -qq > /dev/null
import os
os.environ["JAVA_HOME"] = "/usr/lib/jvm/java-17-openjdk-amd64"
update-alternatives --set java /usr/lib/jvm/java-17-openjdk-amd64/bin/java
java -version
```

Scyjava is installed with the following command:

```python
pip install scyjava
```

We can then continue by installing Bacting and setting up the two Bacting managers, `inchi` and `opsin`:

```python
from scyjava import config, jimport
config.endpoints.append('io.github.egonw.bacting:managers-inchi:0.1.0')
config.endpoints.append('io.github.egonw.bacting:managers-opsin:0.1.0')
config.endpoints.append('io.github.egonw.bacting:managers-inchi:0.4.1')
config.endpoints.append('io.github.egonw.bacting:managers-opsin:0.4.1')

inchi_cls = jimport("net.bioclipse.managers.InChIManager")
inchi = inchi_cls(".")
opsin_cls = jimport("net.bioclipse.managers.OpsinManager")
opsin = opsin_cls(".")
```

After that, we use the manager API to parse the IUPAC name and generate an InChI and InChIKey:
After that, we use the manager API to parse the IUPAC name and generate an `InChI` and an `InChIKey`:

```python
anInChI = inchi.generate(opsin.parseIUPACName("methane"))
Expand All @@ -63,11 +87,12 @@ including a button to open the notebook in Colab.
Because Bacting is written in Java and the libraries being available from
[Maven Central](https://search.maven.org/), it also be used in
[Apache Groovy](http://www.groovy-lang.org/) and other Java-based environments.

The above code in Groovy looks like:

```groovy
@Grab(group='io.github.egonw.bacting', module='managers-inchi', version='0.1.0')
@Grab(group='io.github.egonw.bacting', module='managers-opsin', version='0.1.0')
@Grab(group='io.github.egonw.bacting', module='managers-inchi', version='0.4.1')
@Grab(group='io.github.egonw.bacting', module='managers-opsin', version='0.4.1')
workspaceRoot = "."
inchi = new net.bioclipse.managers.InChIManager(workspaceRoot);
Expand All @@ -81,8 +106,9 @@ println "InchIKey: ${anInChI.getKey()}"
## Conclusion

Cheminformatics provides us the tools to parse IUPAC names and convert them to
chemical graph based identifiers, such as the InChIKey. The InChIKey identifier
can be used to find more information about the chemicals represented by the
chemical graph based identifiers, such as the InChIKey.

The InChIKey identifier can be used to find more information about the chemicals represented by the
original IUPAC names.

### What to read next?
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