extract-publications.py

#!/usr/bin/env python3

import argparse

import yaml

# Read the ontologies.yml file
# collect the first 'publications' entry from each project,
# and write as Markdown.

__author__ = "James A. Overton"


header = """---
layout: doc
title: Publications Related to the OBO Foundry
---

## Papers about the OBO Foundry

[**OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies**](https://academic.oup.com/database/article/doi/10.1093/database/baab069/6410158) **(2021)**.

Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D Diehl, Damion M Dooley, William D Duncan, Nomi L Harris, Melissa A Haendel, Suzanna E Lewis, Darren A Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M Schriml, Barry Smith, Christian J Stoeckert Jr., Nicole A Vasilevsky, Ramona L Walls, Jie Zheng, Christopher J Mungall, Bjoern Peters. *Database*, Volume 2021, baab069, https://doi.org/10.1093/database/baab069

[The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration](http://www.nature.com/nbt/journal/v25/n11/abs/nbt1346.html)

Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L Whetzel, and Suzanna Lewis

*Nature Biotechnology* **25**, 1251 - 1255 (2007)

[Google Scholar list of papers citing The OBO Foundry.](https://scholar.google.ca/scholar?cites=13806088078865650870&as_sdt=2005&sciodt=0,5&hl=en)

### Some Ontology Project Publications (not a complete list)

"""

template = "- {ontology} ({id}): [{title}]({link})\n"


def main():
    parser = argparse.ArgumentParser(description="Extract publication data")
    parser.add_argument(
        "ontologies",
        type=argparse.FileType("r"),
        help="the ontologies YAML file to read",
    )
    parser.add_argument(
        "publications_path", type=str, help="the path to the output file"
    )
    args = parser.parse_args()

    data = yaml.load(args.ontologies, Loader=yaml.SafeLoader)
    publications = []
    for ontology in data["ontologies"]:
        result = {}
        if "title" in ontology:
            result["ontology"] = ontology["title"]
        if "id" in ontology:
            result["id"] = ontology["id"]

        for publication in ontology.get("publications", []):
            if "id" in publication and "title" in publication:
                result["link"] = publication["id"]
                result["title"] = publication["title"]
                break
        if (
            "ontology" in result
            and "id" in result
            and "link" in result
            and "title" in result
        ):
            publications.append(result)

    publications = sorted(publications, key=lambda k: k["ontology"])
    with open(args.publications_path, "w") as output:
        output.write(header)
        for publication in publications:
            output.write(template.format(**publication))


if __name__ == "__main__":
    main()