Authors:
---------
Thomas Jaylet - Université Paris Cité, T3S, INSERM UMR-S 1124, Paris, France
Thibaut Coustillet - Université Paris Cité, T3S, INSERM UMR-S 1124, Paris, France
Florence Jornod - Université Paris Cité, T3S, INSERM UMR-S 1124, Paris, France
Karine Audouze - Université Paris Cité, T3S, INSERM UMR-S 1124, Paris, France

contact: systox@parisdescartes.fr

AOP-helpFinder is provided without any warranty. But if you have any problem please feel free to contact us by e-mail.

HOW TO CITE

If you use AOP-helpFinder, please cite :

for the method(s):

• Carvaillo, J. C., Barouki, R., Coumoul, X., & Audouze, K. (2019). Linking Bisphenol S to Adverse Outcome Pathways Using a Combined Text Mining and Systems Biology Approach. Environmental health perspectives, 127(4), 47005. https://doi.org/10.1289/EHP4200
   
• Jaylet, T., Coustillet, T., Jornod, F., Margaritte-Jeannin, P., & Audouze, K. (2023). AOP-helpFinder 2.0: Integration of an event-event searches module. Environment international, 177, 108017. https://doi.org/10.1016/j.envint.2023.108017

for the webserver:

• Jornod, F., Jaylet, T., Blaha, L., Sarigiannis, D., Tamisier, L., & Audouze, K. (2022). AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development. Bioinformatics (Oxford, England), 38(4), 1173–1175. https://doi.org/10.1093/bioinformatics/btab750
• Jaylet, T., Coustillet, T., Jornod, F., Margaritte-Jeannin, P., & Audouze, K. (2023). AOP-helpFinder 2.0: Integration of an event-event searches module. Environment international, 177, 108017. https://doi.org/10.1016/j.envint.2023.108017

WHAT IS AOP-helpFinder ?

AOP-helpFinder is a tool developed to help AOP development (Jean-Charles Carvaillo: https://github.com/jecarvaill/aop-helpFinder) (Environ Health Perspect. 2019 Apr;127(4):47005).

It is based on text mining and parsing process on scientific abstracts. AOP-helpFinder allows the identification and extraction of associations between 'Prototypical stressor & event' and 'event & event' at various level of the biological organization (molecular initiating event, key event, and adverse outcome) through analysis of abstracts from the PubMed database (https://pubmed.ncbi.nlm.nih.gov/).

AOP-helpFinder was implemented under the H2020 Human Biomonintoring in Europe (HBM4EU) project, Work Package 13.1.
HBM4EU has received funding from the European Union’s H2020 research and innovation programme under grant agreement No 733032.

AOP-helpFinder is freely available at : http://aop-helpfinder-v2.u-paris-sciences.fr/

WHAT IS AOP-helpFinder 2.0 ?

AOP-helpFinder 2.0 is a new version allowing the identification and extraction of associations between 'prototypical stressor - event' and 'event - event' associations at various level of the biological organization (Molecular Initiating Event (MIE), Key Event (KE), and Adverse Outcome (AO)).
 

The new version 2.0 proposes:

1. A new module to identify event-event linkage,
2. A classification system (Confidence Score) to prioritize the relationships in order to support the weight of evidence,
3. New visualization options for easier interpretation of the results,
4. Interactive tables to be forwarded to the PubMed page of articles hosting links for better data curation.

For more information please read :

• Jaylet, T., Coustillet, T., Jornod, F., Margaritte-Jeannin, P., & Audouze, K. (2023). AOP-helpFinder 2.0: Integration of an event-event searches module. Environment international, 177, 108017. https://doi.org/10.1016/j.envint.2023.108017

LICENCE

This software is governed by the CeCILL license under French law and abiding by the rules of distribution of free software. You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL

http://cecill.info/licences/Licence_CeCILL_V2.1-en.txt

AOP-helpFinder figures are governed by CC-by-nc license

How To Use

require for AOP-helpFinder Package Python:

• nltk
• spacy
• pandas
• scipy
• numpy
• pyexcel_ods3
• pubmed_parser (http://github.com/titipata/pubmed_parser)

You need to complete the parameters with completed the param.py file
You will find example file in the example_file folder

$ python3 aophelpfinder.py param.py

$ python3 scoring.py --input (the file from aophelpfinder) --mode (event-event or stressor-event)

Some figures are also available with the different figures scripts.