SlideShare a Scribd company logo
TOXTREE:
                            TOXIC HAZARD ESTIMATION BY DECISION TREE APPROACH
                                                                                                          Nina Jeliazkova a, Silvia Lapennab, Andrew Worthb
                                                                                                 a) Ideaconsult Ltd, 4 A. Kanchev str., Sofia 1000, Bulgaria, jeliazkova.nina@gmail.com
                                                                                                 b) European Commission, Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, Italy

                                                                                                                                                                                                                  Toxtree citations
                                                                             • Toxtree is a flexible and user-friendly open-source application [1].                                            70

                                                                             • Places chemicals into categories and predicts various kinds of toxic effect,                                    60
                                                                                                                                                                                               50

                                                                               mostly by applying structural alerts, arranged in a decision tree fashion.                                      40
                                                                                                                                                                                               30

                                                                             • Available at http://toxtree.sourceforge.net                                                                     20
                                                                                                                                                                                               10

                                                                             • Initially commissioned by the European Commission’s Joint Research Centre.                                       0
                                                                                                                                                                                                    2006   2007    2008    2009     2010      2011          2012


                                                                             • The first version (v. 1.0) was released in 2005. It implemented the                                                                Toxtree usage map

                                                                               Cramer structural rules for estimating the threshold of toxicological concern.                                                       Toxtree citations

                                                                             • More than 10 major releases since 2005.                                                                         70

                                                                                                                                                                                               60

                                                                             • Input: SDF, MOL, SMILES, XLS, CSV, CML, structure diagram editor (since v. 1.0),                                50


                                                                               InChI, chemical names (since 2.2.0), chemical identifier lookup via remote OpenTox
                                                                                                                                                                                               40

                                                                                                                                                                                               30


                                                                               web service (since 2.5.0).                                                                                      20

                                                                                                                                                                                               10

                                                                             • The latest version Toxtree 2.5.1 includes 15 prediction modules:                                                 0
                                                                                                                                                                                                    2006   2007     2008     2009      2010          2011          2012




                                                                             • Cramer rules & Cramer rules with extensions
                                                                             • Verhaar scheme
                                                                             • Modified Verhaar scheme for predicting toxicity mode of action
                                                                             • Skin irritation (BfR rules) and Eye irritation (BfR rules)
                                                                             • Benigni / Bossa rule base for mutagenicity and carcinogenicity
                                                                             • START biodegradation and persistence
                                                                             • Structural alerts for identification of Michael acceptors;
                                                                             • Structural alerts for skin sensitization
                                                                             • Kroes Threshold of Toxicological Concern Decision tree
                                                                             • SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and
                                                                               metabolites prediction;
                                                                             • Structural alerts for the in vivo micronucleus assay in rodents (ISSMIC)
                                                                             • Structural alerts for Functional Group Identification (ISSFUNC)
                                                                             • Structural alerts for protein binding

                                                                             A key feature of Toxtree is the transparent reporting of the rationale underlying
                                                                             each prediction. This is supported by keeping track of the path through the
                                                                             decision tree and reporting the result of applying the rules. Since version 2.1.0
                                                                             (2010), Toxtree supports structural alerts highlighting.
                                                                             Some of the prediction modules also use descriptor calculation procedures and
                                                                             QSAR models. The SMARTCyp plugin was extended in 2011 to enable metabolite
                                                                             predictions, in addition to predicting sites of metabolism.
                                                                             Besides being used as downloadable standalone application, Toxtree was reported
                                                                             to be embedded in various workflow systems and exposed as a web service as
                                                                             early as 2007. Since 2010, Toxtree has been available as an OpenTox API
                                                                             compatible web service and also embedded in the online application
                                                                             http://toxpredict.org .

                                                                                                Application to publicly available datasets
                                                                              Chemical structures and data from various sources have been imported into the
                                                                              Ambit database [2,3] and made available via the OpenTox REST API interface.
                                                                              Toxtree modules are available as OpenTox API compliant models.
                          For developers                                                         ECHA Preregistration list                                                         Plant Protection Products
• Designed with flexible capabilities for future extensions.
• Provides a core platform, implementing the user interface and
  common functionalities as input and output, and standardized Java
  interfaces for the prediction modules.
• This architecture allows the development of prediction modules to
  concentrate on the model specifics, and facilitates the collaboration of
  independent developers.
• Toxtree modules have been developed by the JRC in collaboration with
  various consultants.
• You could develop the next toxicity prediction module!




                                                                                                     Structural alerts for acyl   Verhaar scheme for                                  Structural alerts for acyl              Verhaar scheme for
                                                                                 Cramer rules        transfer agents              toxicity mode of action   Cramer rules              transfer agents                         toxicity mode of action




Frequently Asked Questions:
http://toxtree.sourceforge.net/faq.html#K2
Q: How to run Toxtree predictions from (Java) code and embed Toxtree
into my software?
A1: Java standalone example
• Toxtree and CDK dependencies are available via Apache Maven
   repository. Example code available.
A2: REST web service - via OpenTox API
http://opentox.org/dev/apis/api-1.2                                                                                                                                                   Structural alerts for the
• Toxtree modules are available as OpenTox REST API web services. The                                                                                                                 in vivo micronucleus
   example assumes your dataset is uploaded to an OpenTox dataset                                                                                           START biodegradation      assay in rodents
   service. The dataset service accepts common chemical data formats
   for upload via HTTP POST calls.
                                                                             References
 [1] Patlewicz G, Jeliazkova N, Safford RJ, Worth AP, Aleksiev B. (2008) An evaluation of the implementation of the Cramer classification scheme
 in the Toxtree software. SAR QSAR Environ Res. ;19(5-6):495-524.
 [2] Jeliazkova N., Jeliazkov V. AMBIT RESTful web services: an implementation of the OpenTox application programming interface, Journal of
 Cheminformatics 2011, 3:18, doi:10.1186/1758-2946-3-18.
 [3] OpenTox D3.4 Report on Final Database http://opentox.org/data/documents/development/opentoxreports/opentoxreportd34

More Related Content

Recently uploaded

Cell Therapy Expansion and Challenges in Autoimmune Disease
Cell Therapy Expansion and Challenges in Autoimmune DiseaseCell Therapy Expansion and Challenges in Autoimmune Disease
Cell Therapy Expansion and Challenges in Autoimmune Disease
Health Advances
 
Top Travel Vaccinations in Manchester
Top Travel Vaccinations in ManchesterTop Travel Vaccinations in Manchester
Top Travel Vaccinations in Manchester
NX Healthcare
 
pharmacology for dummies free pdf download.pdf
pharmacology for dummies free pdf download.pdfpharmacology for dummies free pdf download.pdf
pharmacology for dummies free pdf download.pdf
KerlynIgnacio
 
Alzheimer’s Disease Case Conference: Gearing Up for the Expanding Role of Neu...
Alzheimer’s Disease Case Conference: Gearing Up for the Expanding Role of Neu...Alzheimer’s Disease Case Conference: Gearing Up for the Expanding Role of Neu...
Alzheimer’s Disease Case Conference: Gearing Up for the Expanding Role of Neu...
PVI, PeerView Institute for Medical Education
 
The Nervous and Chemical Regulation of Respiration
The Nervous and Chemical Regulation of RespirationThe Nervous and Chemical Regulation of Respiration
The Nervous and Chemical Regulation of Respiration
MedicoseAcademics
 
NARCOTICS- POLICY AND PROCEDURES FOR ITS USE
NARCOTICS- POLICY AND PROCEDURES FOR ITS USENARCOTICS- POLICY AND PROCEDURES FOR ITS USE
NARCOTICS- POLICY AND PROCEDURES FOR ITS USE
Dr. Ahana Haroon
 
SENSORY NEEDS B.SC. NURSING SEMESTER II.
SENSORY NEEDS B.SC. NURSING SEMESTER II.SENSORY NEEDS B.SC. NURSING SEMESTER II.
SENSORY NEEDS B.SC. NURSING SEMESTER II.
KULDEEP VYAS
 
What are the different types of Dental implants.
What are the different types of Dental implants.What are the different types of Dental implants.
What are the different types of Dental implants.
Gokuldas Hospital
 
10 Benefits an EPCR Software should Bring to EMS Organizations
10 Benefits an EPCR Software should Bring to EMS Organizations   10 Benefits an EPCR Software should Bring to EMS Organizations
10 Benefits an EPCR Software should Bring to EMS Organizations
Traumasoft LLC
 
Ophthalmic drugs latest. Xxxxxxzxxxxxx.pdf
Ophthalmic drugs latest. Xxxxxxzxxxxxx.pdfOphthalmic drugs latest. Xxxxxxzxxxxxx.pdf
Ophthalmic drugs latest. Xxxxxxzxxxxxx.pdf
MuhammadMuneer49
 
Demystifying Fallopian Tube Blockage- Grading the Differences and Implication...
Demystifying Fallopian Tube Blockage- Grading the Differences and Implication...Demystifying Fallopian Tube Blockage- Grading the Differences and Implication...
Demystifying Fallopian Tube Blockage- Grading the Differences and Implication...
FFragrant
 
Physical demands in sports - WCSPT Oslo 2024
Physical demands in sports - WCSPT Oslo 2024Physical demands in sports - WCSPT Oslo 2024
Physical demands in sports - WCSPT Oslo 2024
Torstein Dalen-Lorentsen
 
Breast cancer: Post menopausal endocrine therapy
Breast cancer: Post menopausal endocrine therapyBreast cancer: Post menopausal endocrine therapy
Breast cancer: Post menopausal endocrine therapy
Dr. Sumit KUMAR
 
Nano-gold for Cancer Therapy chemistry investigatory project
Nano-gold for Cancer Therapy chemistry investigatory projectNano-gold for Cancer Therapy chemistry investigatory project
Nano-gold for Cancer Therapy chemistry investigatory project
SIVAVINAYAKPK
 
How to Control Your Asthma Tips by gokuldas hospital.
How to Control Your Asthma Tips by gokuldas hospital.How to Control Your Asthma Tips by gokuldas hospital.
How to Control Your Asthma Tips by gokuldas hospital.
Gokuldas Hospital
 
CHEMOTHERAPY_RDP_CHAPTER 1_ANTI TB DRUGS.pdf
CHEMOTHERAPY_RDP_CHAPTER 1_ANTI TB DRUGS.pdfCHEMOTHERAPY_RDP_CHAPTER 1_ANTI TB DRUGS.pdf
CHEMOTHERAPY_RDP_CHAPTER 1_ANTI TB DRUGS.pdf
rishi2789
 
Histololgy of Female Reproductive System.pptx
Histololgy of Female Reproductive System.pptxHistololgy of Female Reproductive System.pptx
Histololgy of Female Reproductive System.pptx
AyeshaZaid1
 
Pollen and Fungal allergy: aeroallergy.pdf
Pollen and Fungal allergy: aeroallergy.pdfPollen and Fungal allergy: aeroallergy.pdf
Pollen and Fungal allergy: aeroallergy.pdf
Chulalongkorn Allergy and Clinical Immunology Research Group
 
Promoting Wellbeing - Applied Social Psychology - Psychology SuperNotes
Promoting Wellbeing - Applied Social Psychology - Psychology SuperNotesPromoting Wellbeing - Applied Social Psychology - Psychology SuperNotes
Promoting Wellbeing - Applied Social Psychology - Psychology SuperNotes
PsychoTech Services
 
Test bank for karp s cell and molecular biology 9th edition by gerald karp.pdf
Test bank for karp s cell and molecular biology 9th edition by gerald karp.pdfTest bank for karp s cell and molecular biology 9th edition by gerald karp.pdf
Test bank for karp s cell and molecular biology 9th edition by gerald karp.pdf
rightmanforbloodline
 

Recently uploaded (20)

Cell Therapy Expansion and Challenges in Autoimmune Disease
Cell Therapy Expansion and Challenges in Autoimmune DiseaseCell Therapy Expansion and Challenges in Autoimmune Disease
Cell Therapy Expansion and Challenges in Autoimmune Disease
 
Top Travel Vaccinations in Manchester
Top Travel Vaccinations in ManchesterTop Travel Vaccinations in Manchester
Top Travel Vaccinations in Manchester
 
pharmacology for dummies free pdf download.pdf
pharmacology for dummies free pdf download.pdfpharmacology for dummies free pdf download.pdf
pharmacology for dummies free pdf download.pdf
 
Alzheimer’s Disease Case Conference: Gearing Up for the Expanding Role of Neu...
Alzheimer’s Disease Case Conference: Gearing Up for the Expanding Role of Neu...Alzheimer’s Disease Case Conference: Gearing Up for the Expanding Role of Neu...
Alzheimer’s Disease Case Conference: Gearing Up for the Expanding Role of Neu...
 
The Nervous and Chemical Regulation of Respiration
The Nervous and Chemical Regulation of RespirationThe Nervous and Chemical Regulation of Respiration
The Nervous and Chemical Regulation of Respiration
 
NARCOTICS- POLICY AND PROCEDURES FOR ITS USE
NARCOTICS- POLICY AND PROCEDURES FOR ITS USENARCOTICS- POLICY AND PROCEDURES FOR ITS USE
NARCOTICS- POLICY AND PROCEDURES FOR ITS USE
 
SENSORY NEEDS B.SC. NURSING SEMESTER II.
SENSORY NEEDS B.SC. NURSING SEMESTER II.SENSORY NEEDS B.SC. NURSING SEMESTER II.
SENSORY NEEDS B.SC. NURSING SEMESTER II.
 
What are the different types of Dental implants.
What are the different types of Dental implants.What are the different types of Dental implants.
What are the different types of Dental implants.
 
10 Benefits an EPCR Software should Bring to EMS Organizations
10 Benefits an EPCR Software should Bring to EMS Organizations   10 Benefits an EPCR Software should Bring to EMS Organizations
10 Benefits an EPCR Software should Bring to EMS Organizations
 
Ophthalmic drugs latest. Xxxxxxzxxxxxx.pdf
Ophthalmic drugs latest. Xxxxxxzxxxxxx.pdfOphthalmic drugs latest. Xxxxxxzxxxxxx.pdf
Ophthalmic drugs latest. Xxxxxxzxxxxxx.pdf
 
Demystifying Fallopian Tube Blockage- Grading the Differences and Implication...
Demystifying Fallopian Tube Blockage- Grading the Differences and Implication...Demystifying Fallopian Tube Blockage- Grading the Differences and Implication...
Demystifying Fallopian Tube Blockage- Grading the Differences and Implication...
 
Physical demands in sports - WCSPT Oslo 2024
Physical demands in sports - WCSPT Oslo 2024Physical demands in sports - WCSPT Oslo 2024
Physical demands in sports - WCSPT Oslo 2024
 
Breast cancer: Post menopausal endocrine therapy
Breast cancer: Post menopausal endocrine therapyBreast cancer: Post menopausal endocrine therapy
Breast cancer: Post menopausal endocrine therapy
 
Nano-gold for Cancer Therapy chemistry investigatory project
Nano-gold for Cancer Therapy chemistry investigatory projectNano-gold for Cancer Therapy chemistry investigatory project
Nano-gold for Cancer Therapy chemistry investigatory project
 
How to Control Your Asthma Tips by gokuldas hospital.
How to Control Your Asthma Tips by gokuldas hospital.How to Control Your Asthma Tips by gokuldas hospital.
How to Control Your Asthma Tips by gokuldas hospital.
 
CHEMOTHERAPY_RDP_CHAPTER 1_ANTI TB DRUGS.pdf
CHEMOTHERAPY_RDP_CHAPTER 1_ANTI TB DRUGS.pdfCHEMOTHERAPY_RDP_CHAPTER 1_ANTI TB DRUGS.pdf
CHEMOTHERAPY_RDP_CHAPTER 1_ANTI TB DRUGS.pdf
 
Histololgy of Female Reproductive System.pptx
Histololgy of Female Reproductive System.pptxHistololgy of Female Reproductive System.pptx
Histololgy of Female Reproductive System.pptx
 
Pollen and Fungal allergy: aeroallergy.pdf
Pollen and Fungal allergy: aeroallergy.pdfPollen and Fungal allergy: aeroallergy.pdf
Pollen and Fungal allergy: aeroallergy.pdf
 
Promoting Wellbeing - Applied Social Psychology - Psychology SuperNotes
Promoting Wellbeing - Applied Social Psychology - Psychology SuperNotesPromoting Wellbeing - Applied Social Psychology - Psychology SuperNotes
Promoting Wellbeing - Applied Social Psychology - Psychology SuperNotes
 
Test bank for karp s cell and molecular biology 9th edition by gerald karp.pdf
Test bank for karp s cell and molecular biology 9th edition by gerald karp.pdfTest bank for karp s cell and molecular biology 9th edition by gerald karp.pdf
Test bank for karp s cell and molecular biology 9th edition by gerald karp.pdf
 

Featured

How Race, Age and Gender Shape Attitudes Towards Mental Health
How Race, Age and Gender Shape Attitudes Towards Mental HealthHow Race, Age and Gender Shape Attitudes Towards Mental Health
How Race, Age and Gender Shape Attitudes Towards Mental Health
ThinkNow
 
AI Trends in Creative Operations 2024 by Artwork Flow.pdf
AI Trends in Creative Operations 2024 by Artwork Flow.pdfAI Trends in Creative Operations 2024 by Artwork Flow.pdf
AI Trends in Creative Operations 2024 by Artwork Flow.pdf
marketingartwork
 
Skeleton Culture Code
Skeleton Culture CodeSkeleton Culture Code
Skeleton Culture Code
Skeleton Technologies
 
PEPSICO Presentation to CAGNY Conference Feb 2024
PEPSICO Presentation to CAGNY Conference Feb 2024PEPSICO Presentation to CAGNY Conference Feb 2024
PEPSICO Presentation to CAGNY Conference Feb 2024
Neil Kimberley
 
Content Methodology: A Best Practices Report (Webinar)
Content Methodology: A Best Practices Report (Webinar)Content Methodology: A Best Practices Report (Webinar)
Content Methodology: A Best Practices Report (Webinar)
contently
 
How to Prepare For a Successful Job Search for 2024
How to Prepare For a Successful Job Search for 2024How to Prepare For a Successful Job Search for 2024
How to Prepare For a Successful Job Search for 2024
Albert Qian
 
Social Media Marketing Trends 2024 // The Global Indie Insights
Social Media Marketing Trends 2024 // The Global Indie InsightsSocial Media Marketing Trends 2024 // The Global Indie Insights
Social Media Marketing Trends 2024 // The Global Indie Insights
Kurio // The Social Media Age(ncy)
 
Trends In Paid Search: Navigating The Digital Landscape In 2024
Trends In Paid Search: Navigating The Digital Landscape In 2024Trends In Paid Search: Navigating The Digital Landscape In 2024
Trends In Paid Search: Navigating The Digital Landscape In 2024
Search Engine Journal
 
5 Public speaking tips from TED - Visualized summary
5 Public speaking tips from TED - Visualized summary5 Public speaking tips from TED - Visualized summary
5 Public speaking tips from TED - Visualized summary
SpeakerHub
 
ChatGPT and the Future of Work - Clark Boyd
ChatGPT and the Future of Work - Clark Boyd ChatGPT and the Future of Work - Clark Boyd
ChatGPT and the Future of Work - Clark Boyd
Clark Boyd
 
Getting into the tech field. what next
Getting into the tech field. what next Getting into the tech field. what next
Getting into the tech field. what next
Tessa Mero
 
Google's Just Not That Into You: Understanding Core Updates & Search Intent
Google's Just Not That Into You: Understanding Core Updates & Search IntentGoogle's Just Not That Into You: Understanding Core Updates & Search Intent
Google's Just Not That Into You: Understanding Core Updates & Search Intent
Lily Ray
 
How to have difficult conversations
How to have difficult conversations How to have difficult conversations
How to have difficult conversations
Rajiv Jayarajah, MAppComm, ACC
 
Introduction to Data Science
Introduction to Data ScienceIntroduction to Data Science
Introduction to Data Science
Christy Abraham Joy
 
Time Management & Productivity - Best Practices
Time Management & Productivity -  Best PracticesTime Management & Productivity -  Best Practices
Time Management & Productivity - Best Practices
Vit Horky
 
The six step guide to practical project management
The six step guide to practical project managementThe six step guide to practical project management
The six step guide to practical project management
MindGenius
 
Beginners Guide to TikTok for Search - Rachel Pearson - We are Tilt __ Bright...
Beginners Guide to TikTok for Search - Rachel Pearson - We are Tilt __ Bright...Beginners Guide to TikTok for Search - Rachel Pearson - We are Tilt __ Bright...
Beginners Guide to TikTok for Search - Rachel Pearson - We are Tilt __ Bright...
RachelPearson36
 
Unlocking the Power of ChatGPT and AI in Testing - A Real-World Look, present...
Unlocking the Power of ChatGPT and AI in Testing - A Real-World Look, present...Unlocking the Power of ChatGPT and AI in Testing - A Real-World Look, present...
Unlocking the Power of ChatGPT and AI in Testing - A Real-World Look, present...
Applitools
 
12 Ways to Increase Your Influence at Work
12 Ways to Increase Your Influence at Work12 Ways to Increase Your Influence at Work
12 Ways to Increase Your Influence at Work
GetSmarter
 
ChatGPT webinar slides
ChatGPT webinar slidesChatGPT webinar slides
ChatGPT webinar slides
Alireza Esmikhani
 

Featured (20)

How Race, Age and Gender Shape Attitudes Towards Mental Health
How Race, Age and Gender Shape Attitudes Towards Mental HealthHow Race, Age and Gender Shape Attitudes Towards Mental Health
How Race, Age and Gender Shape Attitudes Towards Mental Health
 
AI Trends in Creative Operations 2024 by Artwork Flow.pdf
AI Trends in Creative Operations 2024 by Artwork Flow.pdfAI Trends in Creative Operations 2024 by Artwork Flow.pdf
AI Trends in Creative Operations 2024 by Artwork Flow.pdf
 
Skeleton Culture Code
Skeleton Culture CodeSkeleton Culture Code
Skeleton Culture Code
 
PEPSICO Presentation to CAGNY Conference Feb 2024
PEPSICO Presentation to CAGNY Conference Feb 2024PEPSICO Presentation to CAGNY Conference Feb 2024
PEPSICO Presentation to CAGNY Conference Feb 2024
 
Content Methodology: A Best Practices Report (Webinar)
Content Methodology: A Best Practices Report (Webinar)Content Methodology: A Best Practices Report (Webinar)
Content Methodology: A Best Practices Report (Webinar)
 
How to Prepare For a Successful Job Search for 2024
How to Prepare For a Successful Job Search for 2024How to Prepare For a Successful Job Search for 2024
How to Prepare For a Successful Job Search for 2024
 
Social Media Marketing Trends 2024 // The Global Indie Insights
Social Media Marketing Trends 2024 // The Global Indie InsightsSocial Media Marketing Trends 2024 // The Global Indie Insights
Social Media Marketing Trends 2024 // The Global Indie Insights
 
Trends In Paid Search: Navigating The Digital Landscape In 2024
Trends In Paid Search: Navigating The Digital Landscape In 2024Trends In Paid Search: Navigating The Digital Landscape In 2024
Trends In Paid Search: Navigating The Digital Landscape In 2024
 
5 Public speaking tips from TED - Visualized summary
5 Public speaking tips from TED - Visualized summary5 Public speaking tips from TED - Visualized summary
5 Public speaking tips from TED - Visualized summary
 
ChatGPT and the Future of Work - Clark Boyd
ChatGPT and the Future of Work - Clark Boyd ChatGPT and the Future of Work - Clark Boyd
ChatGPT and the Future of Work - Clark Boyd
 
Getting into the tech field. what next
Getting into the tech field. what next Getting into the tech field. what next
Getting into the tech field. what next
 
Google's Just Not That Into You: Understanding Core Updates & Search Intent
Google's Just Not That Into You: Understanding Core Updates & Search IntentGoogle's Just Not That Into You: Understanding Core Updates & Search Intent
Google's Just Not That Into You: Understanding Core Updates & Search Intent
 
How to have difficult conversations
How to have difficult conversations How to have difficult conversations
How to have difficult conversations
 
Introduction to Data Science
Introduction to Data ScienceIntroduction to Data Science
Introduction to Data Science
 
Time Management & Productivity - Best Practices
Time Management & Productivity -  Best PracticesTime Management & Productivity -  Best Practices
Time Management & Productivity - Best Practices
 
The six step guide to practical project management
The six step guide to practical project managementThe six step guide to practical project management
The six step guide to practical project management
 
Beginners Guide to TikTok for Search - Rachel Pearson - We are Tilt __ Bright...
Beginners Guide to TikTok for Search - Rachel Pearson - We are Tilt __ Bright...Beginners Guide to TikTok for Search - Rachel Pearson - We are Tilt __ Bright...
Beginners Guide to TikTok for Search - Rachel Pearson - We are Tilt __ Bright...
 
Unlocking the Power of ChatGPT and AI in Testing - A Real-World Look, present...
Unlocking the Power of ChatGPT and AI in Testing - A Real-World Look, present...Unlocking the Power of ChatGPT and AI in Testing - A Real-World Look, present...
Unlocking the Power of ChatGPT and AI in Testing - A Real-World Look, present...
 
12 Ways to Increase Your Influence at Work
12 Ways to Increase Your Influence at Work12 Ways to Increase Your Influence at Work
12 Ways to Increase Your Influence at Work
 
ChatGPT webinar slides
ChatGPT webinar slidesChatGPT webinar slides
ChatGPT webinar slides
 

TOXTREE: TOXIC HAZARD ESTIMATION BY A DECISION TREE APPROACH

  • 1. TOXTREE: TOXIC HAZARD ESTIMATION BY DECISION TREE APPROACH Nina Jeliazkova a, Silvia Lapennab, Andrew Worthb a) Ideaconsult Ltd, 4 A. Kanchev str., Sofia 1000, Bulgaria, jeliazkova.nina@gmail.com b) European Commission, Joint Research Centre, Via E. Fermi 2749, 21027 Ispra, Italy Toxtree citations • Toxtree is a flexible and user-friendly open-source application [1]. 70 • Places chemicals into categories and predicts various kinds of toxic effect, 60 50 mostly by applying structural alerts, arranged in a decision tree fashion. 40 30 • Available at http://toxtree.sourceforge.net 20 10 • Initially commissioned by the European Commission’s Joint Research Centre. 0 2006 2007 2008 2009 2010 2011 2012 • The first version (v. 1.0) was released in 2005. It implemented the Toxtree usage map Cramer structural rules for estimating the threshold of toxicological concern. Toxtree citations • More than 10 major releases since 2005. 70 60 • Input: SDF, MOL, SMILES, XLS, CSV, CML, structure diagram editor (since v. 1.0), 50 InChI, chemical names (since 2.2.0), chemical identifier lookup via remote OpenTox 40 30 web service (since 2.5.0). 20 10 • The latest version Toxtree 2.5.1 includes 15 prediction modules: 0 2006 2007 2008 2009 2010 2011 2012 • Cramer rules & Cramer rules with extensions • Verhaar scheme • Modified Verhaar scheme for predicting toxicity mode of action • Skin irritation (BfR rules) and Eye irritation (BfR rules) • Benigni / Bossa rule base for mutagenicity and carcinogenicity • START biodegradation and persistence • Structural alerts for identification of Michael acceptors; • Structural alerts for skin sensitization • Kroes Threshold of Toxicological Concern Decision tree • SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction; • Structural alerts for the in vivo micronucleus assay in rodents (ISSMIC) • Structural alerts for Functional Group Identification (ISSFUNC) • Structural alerts for protein binding A key feature of Toxtree is the transparent reporting of the rationale underlying each prediction. This is supported by keeping track of the path through the decision tree and reporting the result of applying the rules. Since version 2.1.0 (2010), Toxtree supports structural alerts highlighting. Some of the prediction modules also use descriptor calculation procedures and QSAR models. The SMARTCyp plugin was extended in 2011 to enable metabolite predictions, in addition to predicting sites of metabolism. Besides being used as downloadable standalone application, Toxtree was reported to be embedded in various workflow systems and exposed as a web service as early as 2007. Since 2010, Toxtree has been available as an OpenTox API compatible web service and also embedded in the online application http://toxpredict.org . Application to publicly available datasets Chemical structures and data from various sources have been imported into the Ambit database [2,3] and made available via the OpenTox REST API interface. Toxtree modules are available as OpenTox API compliant models. For developers ECHA Preregistration list Plant Protection Products • Designed with flexible capabilities for future extensions. • Provides a core platform, implementing the user interface and common functionalities as input and output, and standardized Java interfaces for the prediction modules. • This architecture allows the development of prediction modules to concentrate on the model specifics, and facilitates the collaboration of independent developers. • Toxtree modules have been developed by the JRC in collaboration with various consultants. • You could develop the next toxicity prediction module! Structural alerts for acyl Verhaar scheme for Structural alerts for acyl Verhaar scheme for Cramer rules transfer agents toxicity mode of action Cramer rules transfer agents toxicity mode of action Frequently Asked Questions: http://toxtree.sourceforge.net/faq.html#K2 Q: How to run Toxtree predictions from (Java) code and embed Toxtree into my software? A1: Java standalone example • Toxtree and CDK dependencies are available via Apache Maven repository. Example code available. A2: REST web service - via OpenTox API http://opentox.org/dev/apis/api-1.2 Structural alerts for the • Toxtree modules are available as OpenTox REST API web services. The in vivo micronucleus example assumes your dataset is uploaded to an OpenTox dataset START biodegradation assay in rodents service. The dataset service accepts common chemical data formats for upload via HTTP POST calls. References [1] Patlewicz G, Jeliazkova N, Safford RJ, Worth AP, Aleksiev B. (2008) An evaluation of the implementation of the Cramer classification scheme in the Toxtree software. SAR QSAR Environ Res. ;19(5-6):495-524. [2] Jeliazkova N., Jeliazkov V. AMBIT RESTful web services: an implementation of the OpenTox application programming interface, Journal of Cheminformatics 2011, 3:18, doi:10.1186/1758-2946-3-18. [3] OpenTox D3.4 Report on Final Database http://opentox.org/data/documents/development/opentoxreports/opentoxreportd34