aop-wiki resource description framework2019/07/08 · aop-wiki are blobs of plain text difficult...
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www.openrisknet.org
OpenRiskNet: Open e-Infrastructure to Support Data Sharing, Knowledge Integration and in silico Analysis and Modelling in Risk Assessment
Project Number 731075
AOP-Wiki Resource Description Framework
Marvin Martens - Maastricht University
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www.openrisknet.org
OpenRiskNet case study: AOPLink
Problem: ● AOP-Wiki are blobs of plain text● Difficult to extract information (accessibility)● Impossible to harmonize with other databases (interoperability)
Solution: semantic modeling of the content of the database, including ontological annotations and persistent identifiers
Experimental data Adverse Outcome Pathways
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www.openrisknet.org
https://aopwiki.org/aops/38
Adverse Outcome Pathway:- Abstract- Background- Applicability- Key Events- Key Event Relationships- Stressors- Assessment
Key Event Relationship:- Description- Biological plausibility- Empirical evidence- Uncertainties- Quantitative understanding- Applicability - Taxonomy - Life stage - Sex
AOPs in AOP-Wiki contain a lot of information
3
Stressor:- Chemical - CAS - DSStox - InchiKey - Names- Evidence- Description
Stressor:- Chemical - CAS - DSStox - InchiKey - Names- Evidence- Description
Stressor:- Chemical - CAS - DSStox - InchiKey - Names- Evidence- Description Key Event:
- Description- Method- Key Event components - Biological process - Biological object - Biological action- Applicability - Taxonomy - Life stage - Sex
Key Event:- Description- Method- Key Event components - Biological process - Biological object - Biological action- Applicability - Taxonomy - Life stage - Sex
Key Event:- Description- Method- Key Event components - Biological process - Biological object - Biological action- Applicability - Taxonomy - Life stage - Sex
Key Event:- Description- Method- Key Event components - Biological process - Biological object - Biological action- Applicability - Taxonomy - Life stage - Sex
Key Event:- Description- Method- Key Event components - Biological process - Biological object - Biological action- Applicability - Taxonomy - Life stage - Sex
Key Event:- Description- Method- Key Event components - Biological process - Biological object - Biological action- Applicability - Taxonomy - Life stage - Sex
Key Event Relationship:- Description- Biological plausibility- Empirical evidence- Uncertainties- Quantitative understanding- Applicability - Taxonomy - Life stage - Sex
Key Event Relationship:- Description- Biological plausibility- Empirical evidence- Uncertainties- Quantitative understanding- Applicability - Taxonomy - Life stage - Sex
Key Event Relationship:- Description- Biological plausibility- Empirical evidence- Uncertainties- Quantitative understanding- Applicability - Taxonomy - Life stage - Sex
Key Event Relationship:- Description- Biological plausibility- Empirical evidence- Uncertainties- Quantitative understanding- Applicability - Taxonomy - Life stage - Sex
Key Event Relationship:- Description- Biological plausibility- Empirical evidence- Uncertainties- Quantitative understanding- Applicability - Taxonomy - Life stage - Sex
Key Event Relationship:- Description- Biological plausibility- Empirical evidence- Uncertainties- Quantitative understanding- Applicability - Taxonomy - Life stage - Sex
Key Event:- Description- Method- Key Event components - Biological process - Biological object - Biological action- Applicability - Taxonomy - Life stage - Sex
Adverse Outcome Pathway:- Abstract- Background- Applicability- Key Events- Key Event Relationships- Stressors- Assessment
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Existing links in the AOP-Wiki
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Eleven central components in the data dumps
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All components are connected through identifiers
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Adding meaningful context to links using ontologies
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Increased accessibility and interoperability
Accessibility
● Allows custom queries● Query for distant relationships
Interoperability● Uses of ontologies and persistent identifiers
○ Links to external databases / knowledge sources○ Standard vocabulary within AOP domain (e.g. the AOP Ontology)
● Integration in systematic, reproducible workflows● Easy links to external databases
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Thank you for your attention!
Webinar “Connecting AOPs, knowledge and data with AOPLink workflows” on July 15th, 4PM CEST, organized by OpenRiskNet (https://openrisknet.org/events/70/)
Previous webinar “Identification and linking of data related to AOPWiki” (https://openrisknet.org/events/59/)
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Improved accessibility: examples
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From an AOP, give me all measurement methods.For AOP 12, print me all KE IDs, KE names, and measurement methods text
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Find AOPs and their MIEs from searching by CAS-RN. By single CAS-RN: 107-18-6:
By list of CAS-RN: 107-18-6, 103-90-2, 83-79-4 (no limit)
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Get chemical identifiers for a certain chemical
For CAS-RN 107-18-6, external identifiers for ChEBI, HMDB, ChemSpider, etc.
For CAS-RN 107-18-6, find identifiers for ChEBI
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Search AOPs by ChEBI Identifier
With one of the ChEBI IDs found earlier: CHEBI:16605
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Linking all AOs and MIEs Give me all Molecular Initiating Events that lead to a particular Adverse Outcome: Learning and memory impairment (KE ID 341)
Give me all Adverse Outcomes that can be the result of a particular Molecular Initiating Event: AhR activation (KE ID 18)
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Get chemicals that could lead to a particular Key Event.
In this case, for the Adverse Outcome: Learning and memory impairment
Also possible for any MIE or intermediate KE