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

- Jornod et al. AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development. Bioinformatics. 2021 oct 30; doi: 10.1093/bioinformatics/btab750.
- XXXXXXXXXXXX. AOP-helpFinder 2.0 : ...

------- 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.

------- WHAT IS AOP-helpFinder web server 2.0 ? -------------

AOP-helpFinder 2.0 is a web server for identification and extraction of associations between 'prototypical stressor - event' and and 'event - event' associations at various level of the biological organization (molecular initiating event (MIE), key event (KE), and adverse outcome (AO)).
The web server AOP-helpFinder 2.0 proposes a new module to identify event-event linkage, and to prioritize them by a classification system, supporting the weight of evidence. For easier interpretation of the results, new visualization options are also available.

For more information please read :
- Jornod et al. AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development. Bioinformatics. 2021 oct 30; doi: 10.1093/bioinformatics/btab750.
- XXXXXXXXXXXX. AOP-helpFinder 2.0 : ...

------- 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


------- STRUCTURE OF THE FOLDER------------


--- A : Prototypical stressor - event search ---

Results-global-stressor-event/

	-> input/
		-> events_file.txt
			- File containing your list of events.
		-> stressors_file.txt
			- File containing your list of stressors.
		-> uid/StressorXXX-uid.txt
			- For each stressor : File containing all PubMed IDs (PMIDs) analyzed by AOP-helpFinder for your stressor-event search.

	-> stressor_event_links.xlsx
			- Distribution of stressor-event links in matrix form. Links are colored according to their Confidence scores.

	-> result_AOP-helpFinder.xlsx 
			- Results for the stressor-event search. The results for all stressors are grouped together in this .xlsx spreadsheet. For each link you have the year, the title of the abstract, the PMID, the name of the stressor and the event found. This file is dynamic : click on the PMID to be forwarded to the corresponding PubMed page. This option is only available if the number of links is strictly lower than : 65 530. If you cannot open this table, please open 'all_stressors.csv' in the 'raw_AOP-helpFinder' folder.

	-> result_AOP-helpFinder_1s1s.xlsx
			- Results for the stressor-event search. The results for each stressor are stored in separate sheets. For each link you have the year, the title of the abstract, the PMID, the name of the stressor and the event found. This file is dynamic : click on the PMID to be forwarded to the corresponding PubMed page. This option is only available if the number of links is strictly lower than : 65 530. If you cannot open this table, please go to 'raw_AOP-helpFinder' folder.

	-> raw_AOP-helpFinder/
		-> StressorXXX.tsv
			- Raw results for the stressor XX. For each link you have the year, the title of the abstract, the PMID and the events found.
		-> all_stressors.csv 
			- Raw results for the stressor-event search. The results for all stressors are grouped together in this .csv spreadsheet. For each link you have the year, the title of the abstract, the PMID, the name of the stressor and the event found.

	-> raw_scoring/
 		-> scoring_stressor-event.tsv
			- Files containing information about the Confidence scores for each pair of stressor-event links.

	-> resume/
		-> resume-XX.txt
			- Resume for the stressor XX with the number of PubMed abstracts, the number of events found, and the total number of links. Then for each found event, the number of associated abstracts.
	
	-> Figures/
		-> distribution_articles.pdf
			- Distribution of the articles according to the number of stressors and events detected.
		-> distribution_events.pdf
			- Distribution of stressor-event links according to the most common events.
		-> distribution_stressors.pdf
			- Distribution of stressor-event links according to the most common stressors.
		-> distribution_scores.pdf
			- Distribution of links according to the Confidence score and number of links. The results are colored according to the Confidence scores of links.
		-> distribution_years.pdf
			- Distribution of articles according to their publication date.
		-> heatmap_total_cs.pdf
			- Distribution of stressor-event links in the form of a heatmap. The results are colored according to the Confidence scores of links.
		-> heatmap_total.pdf
			- Distribution of stressor-event links in the form of a heatmap. The results are colored according to the number of links.

	-> Automated_report.pdf
			- Summary of stressor-event research. Slides containing important information on AOP-helpFinder and stressor-event research (parameters, resume, figures, licenses)

	-> results_tutorial.pdf
			- Gives an example of results provided by AOP-helpFinder (on a test dataset) to guide and help the user in the analysis of his own results.



--- B : Event - event search ---

Results-global-event-event/ 

	-> input/
		-> events_file.txt
			- File containing your list of events.
		-> uid/event-uid_uniq.txt
			- Contains all PubMed IDs (PMIDs) analyzed by AOP-helpFinder for your event-event search

	-> event_event_links.xlsx
			- Distribution of event-event links in matrix form. Links are colored according to their Confidence scores
	
	-> result_AOP-helpFinder.xlsx 
			- Results for the event-event search. For each link you have the year, the title of the abstract, the PMID and the events found. This file is dynamic : click on the PMID to be forwarded to the corresponding PubMed page. This option is only available if the number of links is strictly lower than : 65 530. If you cannot open this table, please go to the 'raw_AOP-helpFinder' folder.
	
	-> raw_AOP-helpFinder/
		-> output-eventevent.tsv
			- Raw results for the event-event search. For each link you have the year, the title of the abstract, the PMID and the events found.
	-> raw_scoring/
 		-> scoring_event-event.tsv
			- Files containing information about the Confidence scores for each pair of event-event links.
	
	-> Figures/
		-> distribution_scores.pdf
			- Distribution of links according to the confidence score and number of links. The results are colored according to the Confidence scores of links.
		-> distribution_years.pdf
			- Distribution of articles according to their publication date.

	-> Automated_report.pdf
		- Summary of stressor-event research. Slides containing important information on AOP-helpFinder and event-event research (parameters, resume, figures, licenses).

	-> results_tutorial.pdf
			- Gives an example of results provided by AOP-helpFinder (on a test dataset) to guide and help the user in the analysis of his own results.
