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55 changes: 51 additions & 4 deletions README.md
Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,7 @@
<a href="https://github.com/psf/black">
<img src="https://img.shields.io/badge/code%20style-black-000000.svg" alt="Code style: black">
</a>
<a href="https://doi.org/10.5281/zenodo.14296666"><img src="https://zenodo.org/badge/DOI/10.5281/zenodo.14296666.svg" alt="DOI"></a>
</p>

<img src="https://github.com/tis-lab/closed-illustrations/raw/master/logos/sssom-logos/sssom_logo_black_banner.png" />
Expand All @@ -37,9 +38,10 @@ This is a python library and command line toolkit for working with SSSOM. It als
See [documentation](https://mapping-commons.github.io/sssom-py/index.html#)

### Deploy documentation
```shell
make sphinx
make deploy-docs

```console
$ make sphinx
$ make deploy-docs
```

## Schema
Expand All @@ -53,7 +55,7 @@ derivations to JSON-Schema, ShEx, etc.
configuration is stored in [`tox.ini`](tox.ini) in different "environments"
whose headers look like `[testenv:...]`. All tests can be run with:

```shell
```console
$ pip install tox
$ tox
```
Expand All @@ -78,4 +80,49 @@ natural language processing and large-scale knowledge assembly. Their work on SS
DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).

https://indralab.github.io

## Citation

SSSOM itself can be cited with:

```bibtex
@article{10.1093/database/baac035,
author = {Matentzoglu, Nicolas and Balhoff, James P and Bello, Susan M and Bizon, Chris and Brush, Matthew and Callahan, Tiffany J and Chute, Christopher G and Duncan, William D and Evelo, Chris T and Gabriel, Davera and Graybeal, John and Gray, Alasdair and Gyori, Benjamin M and Haendel, Melissa and Harmse, Henriette and Harris, Nomi L and Harrow, Ian and Hegde, Harshad B and Hoyt, Amelia L and Hoyt, Charles T and Jiao, Dazhi and Jiménez-Ruiz, Ernesto and Jupp, Simon and Kim, Hyeongsik and Koehler, Sebastian and Liener, Thomas and Long, Qinqin and Malone, James and McLaughlin, James A and McMurry, Julie A and Moxon, Sierra and Munoz-Torres, Monica C and Osumi-Sutherland, David and Overton, James A and Peters, Bjoern and Putman, Tim and Queralt-Rosinach, Núria and Shefchek, Kent and Solbrig, Harold and Thessen, Anne and Tudorache, Tania and Vasilevsky, Nicole and Wagner, Alex H and Mungall, Christopher J},
title = {A Simple Standard for Sharing Ontological Mappings (SSSOM)},
journal = {Database},
volume = {2022},
pages = {baac035},
year = {2022},
month = {05},
issn = {1758-0463},
doi = {10.1093/database/baac035},
url = {https://doi.org/10.1093/database/baac035},
eprint = {https://academic.oup.com/database/article-pdf/doi/10.1093/database/baac035/43832024/baac035.pdf},
}
```

To cite the SSSOM-py software package specifically, use:

```bibtex
@software{sssom-py,
author = {Harshad Hegde and
Nico Matentzoglu and
Charles Tapley Hoyt and
Chris Mungall and
Joe Flack and
Benjamin M. Gyori and
Damien Goutte-Gattat and
Glass and
Syphax Bouazzouni},
title = {mapping-commons/sssom-py: v0.4.15 release (minor
fixes)
},
month = dec,
year = 2024,
publisher = {Zenodo},
version = {v0.4.15},
doi = {10.5281/zenodo.14296666},
url = {https://doi.org/10.5281/zenodo.14296666},
}
```

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