README.md
# Mandos
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The “kitchen sink” preprocessing tool for chemical screens:
**Fetch knowledge on compounds from public databases, squeezing it all into a consistent form.**
Mandos extracts ~30 annotation types, including:
- mechanisms of action (MOAs), binding activity, classifications, pathways involved, gene expression effects,
- disease indications, clinical trials, drug–drug interactions, co-occurring literature terms,
- legal statuses, LD50, health hazards, acute exposure effects, physical properties, ...
Output in CSV files is summarized as _semantic triples_,
such as `alprazolam inactive at BK receptor`, with additional data (e.g. EC50 or clinical phase).
It can also fetch annotations for structurally similar compounds.
### 💡 Common uses
It’s a preprocessing tool for algorithms and data analysis on chemical screens.
_Example uses:_
- What distinguishes your screening hits pharmacologically?
- What distinguishes groups from a multidimensional screen?
- Build a training set for machine learning.
- Make sure your results aren’t explained by something like solubility.
These tasks are often performed with just [ATC codes](https://www.ema.europa.eu/en/glossary/atc-code)
or binding to [ChEMBL](https://www.ebi.ac.uk/chembl/) targets.
But if your compounds lack ATC codes, or binding annotations – or don’t correlate with binding –
you can compare against far more pharmacological variables, such as GO terms and literature co-occurrences.
You can also get targets like `GABA-A receptor; anion channel` rather than specific GABA-A subunits and complexes.
### 🎨 Example
Use Mandos as a Python API or command-line tool.
To search just the mechanism of action for alprazolam:
```bash
echo "VREFGVBLTWBCJP-UHFFFAOYSA-N" > compounds.txt
mandos chembl:mechanism compounds.txt
```
The following info is perhaps enough to get started, but a lot is done behind-the-scenes.
**[See the docs 📚](https://mandos-chem.readthedocs.io/en/latest/)** for more.
**Input:** compounds.txt is a line-by-line list of
[InChI Keys](https://en.wikipedia.org/wiki/International_Chemical_Identifier#InChIKey)
Pass type-specific command-line options like `--taxa vertebrata`,
or run multiple searches with `mandos :search compounds.txt searches.toml`.
(See: [example config file](https://github.com/dmyersturnbull/mandos/blob/main/mandos/resources/ags_example.toml))
`mandos <type> --help` will show and briefly explain the options.
**Output:** 10 columns shared between all files, plus type-specific columns.
The consistent columns are: _record_id_, _inchikey_, _compound_id_, _compound_name_,
_predicate_, _object_id_, _object_name_, _weight_, _search_key_, _data_source_, and _universal_id_.
Additional columns include EC50, original name, species, clinical phase, etc.
Some example output:
(_Columns were dropped and renamed for display._)
```
comp. ID comp. name predicate name object ID object name
--------- ---------- ----------------------------- ------------- ------------------------------
CHEMBL661 alprazolam positive allosteric modulator CHEMBL2093872 GABA-A receptor; anion channel
CHEMBL661 alprazolam activity at CHEMBL2096986 Cholecystokinin receptor
CHEMBL661 alprazolam phase-3 trial for D012559 Schizophrenia
CHEMBL661 alprazolam phase-4 trial for D016584 Panic Disorder
CHEMBL661 alprazolam has ATC L3 code N05B anxiolytics
CHEMBL661 alprazolam has ATC L4 code N05BA Benzodiazepine derivatives
PC218 alprazolam has GHS symbol H302 Harmful if swallowed
PC218 alprazolam has acute effect - behavioral: euphoria
PC218 alprazolam DDI with PC65016 amprenavir
PC218 alprazolam therapeutic for D001008 Anxiety Disorders
PC218 alprazolam enriched for term - anxiolytic
PC218 alprazolam co-occurs with drug PC134664 Benzodiazepine
PC218 alprazolam co-occurs with gene 1.14.14.1 Monoamine Oxidase
PC218 alprazolam co-occurs with disease D016584 Panic Disorder
PC218 alprazolam interacts with gene - CYP3A4
PC218 alprazolam positive allosteric modulator GABRA1 GABA(A) Receptor
PC218 alprazolam inactive at KCNMB4 BK Channel
PC218 alprazolam active at AR androgen receptor
PC218 alprazolam is of class CHEBI:22720 benzodiazepine
PC218 alprazolam has DEA schedule 4 Schedule IV
. . . . .
. . . . .
. . . . .
```
### Misc commands
Besides specific searches like chembl:mechanism, disease.ctd:mesh, etc.:
- :search
- :export:tax-tree
- :cache
- :concat
- :filter
- :filter:taxa
- :export:copy
- :export:state
- :export:reify
- :calc:scores
- :calc:matrix
- :calc:matrix-concordance
### 🍁 Contributing
Mandos is licensed under the [Apache License, version 2.0](https://www.apache.org/licenses/LICENSE-2.0).
[New issues](https://github.com/dmyersturnbull/mandos/issues) and pull requests are welcome.
Please refer to the [contributing guide](https://github.com/dmyersturnbull/mandos/blob/master/CONTRIBUTING.md).
Generated with [Tyrannosaurus](https://github.com/dmyersturnbull/tyrannosaurus).