stormlovetao/pomelo

Corpus POMELO annotated with FDI

POMELO

POMELO Corpus

639 Medline abstracts annotated with Food-Drug Interactions

Version: 1.0 Creation Date: March 24, 2021 Realease Date: March 24, 2021

Authors:

Thierry Hamon, [email protected] (corresponding author), Vincent Tabanou, Fleur Mougin, Natalia Grabar, Frantz Thiessard

1. Corpus Description

POMELO is a corpus of 639 titles and abstracts issued from The MEDLINE bibliographical base [1]. Citations related to food-drug interactions has been collected from MEDLINE in December 2013 with the following query:

("FOOD DRUG INTERACTIONS"[MH] OR "FOOD DRUG INTERACTIONS*") AND ("adverse effects*")

This corpus is called POMELO, namely grapefruit in French, because has been built and annotated during the French MESHS-funded project POMELO.

The titles and abstracts has been manually annotated in order to make explicit the information on food/drug interactions. The annotation schema is described in [6]. Two experts have been involved in the annotation process: one resident and one medical doctor. The annotation has been done mainly by the resident, who was helped by the medical doctor when facing difficult situations. The annotation has been performed with the BRAT software [2,3].

2. Repository Structure

POMELO/README.md Current readme file

POMELO/corpus Directory containing the corpus in text format and the annotations in Brat format [3], but also the brat configuration files (annotation.conf, tools.conf, visual.conf)

3. Acknowledgements

If you use the POMELO corpus, please cite the following paper:

Thierry Hamon and Vincent Tabanou and Fleur Mougin and Natalia Grabar and Frantz Thiessard. POMELO: Medline corpus with manually annotated food-drug interactions. Proceedings of Biomedical NLP Workshop associated with RANLP 2017. pages 73-80. September 2017. Varna, Bulgaria

This work was supported by the MESH emergent project POMELO [4] and Agence Nationale de la Recherche through the grant ANR-16-CE23-0012 France (project MIAM) [5].

The BibTeX citation is:

@InProceedings{Hamon&al2017b,
  author = 	 {Thierry Hamon and Vincent Tabanou and Fleur Mougin and Natalia Grabar and Frantz Thiessard},
  title = 	 {POMELO: Medline corpus with manually annotated food-drug interactions},
  booktitle =    {Proceedings of Biomedical NLP Workshop associated with RANLP 2017},
  year = 	 {2017},
  pages = 	 {73-80},
  month = 	 {September},
  address = 	 {Varna, Bulgaria},
}

4. License

This work (the annotations) is licensed under the Creative Commons Zero v1.0 Universal.

5. References

[1] https://pubmed.ncbi.nlm.nih.gov/

[2] Pontus Stenetorp, Sampo Pyysalo, Goran Topić, Tomoko Ohta, Sophia Ananiadou, and Jun’ichi Tsujii. 2012. brat: a web-based tool for nlp-assisted text annotation. In Proceedings of the Demonstrations at the 13th Conference of the European Chapter of the Association for Computational Linguistics. Association for Computa- tional Linguistics, Avignon, France, pages 102–107. http://www.aclweb.org/anthology/E12-2021.

[3] http://brat.nlplab.org/

[4] http://natalia.grabar.free.fr/POMELO/

[5] https://miam.limsi.fr/

[6] Thierry Hamon and Vincent Tabanou and Fleur Mougin and Natalia Grabar and Frantz Thiessard. POMELO: Medline corpus with manually annotated food-drug interactions. Proceedings of Biomedical NLP Workshop associated with RANLP 2017. pages 73-80. September 2017. Varna, Bulgaria