introduction - european commissionec.europa.eu/environment/chemicals/lab_animals/pdf/go3r... ·...
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Introduction - Go3R project - How can “semantic” tools help searching?
How is the Go3R search engine built to retrieve 3Rs information?
Search examples Outlook
Using Go3R to collect 3Rs information
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Go3R - semantic search engine on 3Rs methods
Project funded by German Federal Ministry for Research
and Education (BMBF) (2009-2012)
Pilot study funded by BfR (2007-2009)
Sustainment and maintenance (2012 onwards)
developed by Transinsight (since 2005)
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BMBF project: Go3R - semantic search engine to avoid animal testing in regulatory toxicity testing REACH Registration dossiers: Information on substance properties • Collection of all available existing data • Before compiling new data:
Information on 3Rs methods • Animal testing only as a last resort
>> Directive 2010/63/EU
How can Go3R search engine help avoiding animal testing?
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How can semantic tools help searching?
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Jaguar
behavior
engine
Semantic tools “understand” and sort information by comparing text to underlying expert knowledge
CAR
CAT textmining
textmining
Jaguar 3000 rpm
engine
prey eyes
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Semantic tools: Underlying expert knowledge: Ontology = “Mind map“ with concepts, terms and synonyms
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Example: “eye irritation” • eye irritancy • ocular irritancy • irritating to the eye, irritant to the eye • irritant / irritating reactions on [rabbit] eyes • adverse effects on eyes • conjunctival reactions • corneal lesion, corneal opacity • ocular damage • ocular safety
Formulation search query > outcome of search? No: Go3R terms automatically include synonyms
…Synonyms: Never underestimate the authors’ linguistic imagination
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How is Go3R built to “understand” & sort information? www.Go3R.org
box for search queries, searching in PubMed and Toxnet
Sci. Consult. – Animal Welfare
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How is Go3R built to “understand” & sort information? www.Go3R.org
personal settings
topic-related table of contents
underlying expert knowledge is used to build “table of contents” presented alongside search retrieval
author-related table of contents
database-, affiliation- and journal-related table of contents
time-related table of contents
Sci. Consult. – Animal Welfare
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How is Go3R built to “understand” & sort information?
7,147 documents retrieved
list of documents, relevant terms highlighted in green
box for search queries; using Go3R terms automatically includes synonyms and subordinate terms
“table of contents”
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How is Go3R built to “understand” & sort information?
different levels of terms and subordinate terms
ontology branch in vitro test systems
“table of contents”
ontology branch “animal experiments”
Go3R compares terms in title & abstract to terms in ontology and sorts documents accordingly
not shown: further ontology branches for in vitro endpoints, in vitro endpoint detection methods, validation of test methods, etc.
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Finding relevant “topic” in table of contents…
…too complicated?
also because relevant information spread out over different ontology branches
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Further processing of underlying expert knowledge
Goal: for a given test substance, automatically sort all toxicity data into respective IUCLID endpoint categories
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How: BASF literature for registration dossiers as “gold standard”
- one-by-one manual evaluation of TI / AB - recognize relevant terms - process into underlying “search term phrase” - supplementary to textmining
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How: BASF literature for registration dossiers as “gold standard”
- one-by-one manual evaluation of TI / AB - recognize relevant terms - process into underlying “search term phrase” - supplementary to textmining
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IUCLID 7.4.1 – Skin sensitisation
IUCLID 7.1.2 - Dermal absorption
IUCLID 7.6.1 – (In vitro) genotoxicity
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IUCLID 7.2.1 – (Acute oral) toxicity
IUCLID 7.3.1 – Skin irritation; (test substance?)
IUCLID 7.5.3 – Repeated-dose inhalation toxicity
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7.3.2. Eye irritation “In Vivo Test Methods, Eye Irritation"[go3r] OR "3Rs in Eye Irritation Testing"[go3r]
“Eye Irritation"[go3r] OR “Eye Corrosivity"[go3r]
7.8.2. Developmental toxicity / teratogenicity (“Developmental Toxicity"[go3r] OR "Prenatal Developmental Toxicity"[go3r] OR Embryotoxicity[go3r] OR Teratogenicity[go3r] OR "Developmental Neurotoxicity"[go3r] OR "Ovarian Toxicity"[go3r]) NOT fish[go3r] NOT "Daphnia magna"[go3r] NOT Amphibian[go3r]
“Neonatal Exposure"[go3r] OR “Prenatal Exposure"[go3r] OR “Juvenile Exposure"[go3r] OR “Maternal Weight Gain"[go3r] OR “Weaning"[go3r] OR "Gestational Exposure"[go3r]
("Prenatal Developmental Toxicity Study"[go3r] OR "Developmental Neurotoxicity Study"[go3r]) NOT Fish[go3r] NOT "Daphnia Magna"[go3r] NOT Amphibian[go3r]
("Congenital, Hereditary, and Neonatal Diseases and Abnormalities"[go3r] OR "Pregnancy Complications"[go3r] OR "Embryonic Structures"[go3r] OR "Developmental Biology"[go3r] OR "Embryo-Related Endpoints"[go3r] OR "Embryonic and Fetal Development"[go3r]) NOT "Fetal Blood"[go3r]
Examples – just for show!
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more than 50,000 documents retrieved
Search query “Formaldehyde”
Go3R: Retrieving toxicological data for a given test substance
relevant documents are sorted in accordance to respective IUCLID endpoints
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Go3R: Retrieving toxicological data for a given test substance
IUCLID 7.6.1 Genetic toxicity in vitro
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How well does Go3R address the challenge to collect information under REACH?
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Underlying search term phrases too broad: too many insignificant documents
Underlying search term phrases too narrow: too many significant documents missing
Find the right balance:
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Go3R: Sorting into IUCLID categories
IUCLID category Substance 1 Substance 2 Substance 3
7.1 toxicokinetics 88 % 7.2 acute toxicity 75 % - 60% 7.3 irritation / corrosion 75 % 88% 7.4 sensitisation - 71% - 7.5 repeated dose toxicity 57% 33% 7.6 genetic toxicity 7.7 carcinogenicity 7.8 reprodct./develop. toxicity 67% 95% 7.9.1 neurotoxicity - 7.9.2 immunotoxicity - - 7.9.3 other investigations 79% 67% 85% 7.10 human data 44% 92% 83% Total 71% 85% 89%
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Go3R: Retrieving information on 3Rs methods
BMBF project Go3R:
Searching for 3Rs alternatives in regulatory testing (REACH)
- concrete animals test (possibly required by law) - specific endpoint - specific alternative test method(s), if available - or, e.g., in vitro study addressing given endpoint
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“skin sensitisation“ > “replacement methods”
Go3R: Retrieving information on 3Rs methods
search query “sensitisation”
automatic 3Rs signet
3Rs methods sorted by area of use
“skin sensitisation“ > “reduction / refinement methods”
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Go3R: PubMed & Toxnet not enough? Go3R-Web
Google search higher ranking for 170 selected 3Rs websites
e.g. TSAR, ICCVAM, ECVAM, AltTox, AltWeb information on • test protocols • validation • regulatory acceptance
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BMBF Project Go3R
• Established to be used in the context of REACH • Toxicological data and information 3Rs methods • Currently searching in PubMed and Toxnet • Can be adapted to search in other databases • Can be adapted to search in in-house databases • Ontology and search queries require continuous
processing and updating • Ontology: unfinished branches for further topics
other than regulatory toxicology
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Go3R: Retrieving information on 3Rs methods
Additional task:
Searching for 3Rs alternatives in fundamental research - as a rule, animal experiments not standardised - animal experiment developed for specific project? - application of 3Rs possibly not by specific method, - but by “measures“, i.e. protocol changes, techniques
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Go3R: 3Rs information in fundamental research “higher level” table of contents for 3Rs methods & techniques for topics other than regulatory toxicology
including a number of terms, e.g.
“Telemetry“
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Go3R: 3Rs information in fundamental research
search query “asthma”
list of cells and cell lines used > overview in vitro studies
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Go3R: 3Rs information in fundamental research list of cells and cell lines used > overview in vitro studies
search query “asthma“, filtered
for “human epithelial cells“
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Go3R: 3Rs information in fundamental research search query
“Interleukin-1”
overview “Diseases & Symptoms” (MeSH)
here: “Immune System Diseases”
filtered for “Diabetes Mellitus, Type 1“
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How can Go3R assist in searching for 3Rs methods and measures in areas other than regulatory toxicity?
Intelligent table of contents incomplete for non-toxicological methods, techniques, and “measures“ (BMBF Project: regulatory toxicology)
Nevertheless, also in areas other than regulatory toxicity, Go3R already allows obtaining an overview for general search queries
and narrowing these down with the help of selected topic-related terms (either Go3R terms or own terms)
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Conclusion
We appreciate your feedback
• What are you searching for? • How do you want to find it? • What are your experiences in searching for 3Rs
methods? • Cooperation to expand Go3R to include detailed
information relating to fundamental research?
Thank you for your attention!