sssom 0.4.19

Operations on SSSOM mapping tables

Python Utilities for SSSOM

A Python library and command line interface (CLI) for working with SSSOM (Simple Standard for Sharing Ontology Mappings).

Getting Started

A SSSOM TSV can be parsed with

import sssom

# other SSSOM files can be found on https://mapping-commons.github.io
url = "https://raw.githubusercontent.com/mapping-commons/mh_mapping_initiative/master/mappings/mp_hp_eye_impc.sssom.tsv"

# TSV can be parsed into a mapping set dataframe object,
# which includes a pandas DataFrame, a curies.Converter,
# and metadata
msdf = sssom.parse_tsv(url)

# SSSOM comes with several "write" functions
sssom.write_tsv(msdf, "test.tsv")
sssom.write_json(msdf, "test.json")
sssom.write_owl(msdf, "test.owl")
sssom.write_rdf(msdf, "test.ttl")

[!WARNING]
The export formats (json, rdf) of sssom-py are not yet finalised! Expect changes in future releases.

Documentation

See documentation

Deploy documentation

$ make sphinx
$ make deploy-docs

Schema

See the schema/ folder for source schema in YAML, plus derivations to JSON-Schema, ShEx, etc.

Testing

tox is similar to make, but specific for Python software projects. Its configuration is stored in tox.ini in different "environments" whose headers look like [testenv:...]. All tests can be run with:

$ pip install tox
$ tox

A specific environment can be run using the -e flag, such as tox -e lint to run the linting environment.

Outstanding Contributors

Outstanding contributors are groups and institutions that have helped with organising the SSSOM Python package's development, providing funding, advice and infrastructure. We are very grateful for all your contribution - the project would not exist without you!

Harvard Medical School

The INDRA Lab, a part of the Laboratory of Systems Pharmacology and the Harvard Program in Therapeutic Science (HiTS), is interested in natural language processing and large-scale knowledge assembly. Their work on SSSOM is funded by the DARPA Young Faculty Award W911NF2010255 (PI: Benjamin M. Gyori).

https://indralab.github.io

Citation

SSSOM itself can be cited with:

@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:

@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},
}