Semantic Knowledge Discovery OntoChem IT Solutions
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1 Semantic Knowledge Discovery OntoChem IT Solutions OntoChem IT Solutions GmbH Blücherstr Halle (Saale) Germany Tel Fax: mail: info(at)ontochem.com
2 Get the Gold! Towards automated knowledge mining... OntoChem is creating the equipment! 2
3 Agenda Available ontologies & software Services OCMiner processing pipeline technology Project examples: Extraction of Structure-Property-Relationship data (SPR) Compound bio-profiles and bio-similarity Automated toxicology reports News and Alerts 3
4 Available Ontologies & Software Out-of the box ontologies, taxonomies, vocabularies: Chemistry chemical classes, chemical groups, MolPuzzler, chemformula, alloys... >100 million terms Gene products genes, proteins, cleavage products, peptides, mutants, isoforms > 4 million terms Diseases & Effects diseases (MeSH, SNOMED, ICD10, MedDRA...), physiological effects, pharmacology, cosmetology, nutrition, health, flavors Anatomy, Companies, Geopolitical, Species, Persons, Wikipedia... more than 40 LifeScience taxonomies available 4
5 Available Ontologies & Software Out-of the box software: Ontology editors suited for very large ontologies, first chemistry ontology editor OCMiner enterprise annotation & search engine www-browser GUI for semantic search and report generation company intranet indexing and search service OCMiner web-service (CTD BioCreative IV 2013 Challenge) OntoChem has fastest service! integrated into your IT solution OCMiner hot-folder annotation service for your local PC or workgroup 5
6 Available Ontologies & Software 6
7 Services OntoChem Service Examples: custom topical annotation dictionaries, taxonomies, ontologies (multilingual... high throughput document normalization and standardization (e.g Excel 2.0 documents, table and image extraction...) high quality chemistry annotation, extraction and searching (ChemAxon, Opsin, MolPuzzler, anaphora and table treatment, databases) workflows to extract compound-property facts (search engines, document classification, reactions, SAR & SPR extraction...) exploring the life science knowledge space (triples, N-tuples, databases, chemical reactions, knowledge inference) automated report generation (toxicology reports, compound bioprofiles, concept similarity) scientific trend analytics, news and alert systems 7
8 Agenda Available ontologies & software Services OCMiner processing pipeline technology Project examples: Extraction of Structure-Property-Relationship data (SPR) Compound bio-profiles and bio-similarity Automated toxicology reports News and Alerts 8
9 Flowchart OCMiner UIMA Pipeline OCMiner UIMA Pipeline identify document type document classifier XML detagger language detector normalize text tokenize text picture PDF OCR acronym abbrev detector person annotator document structure domain domain domain annotators annotators annotators 1 n 1 n 1 n Text PDF XML doc Office doc PDF reader XML reader Office reader dictionary cleanup & rule combiner chemistry annotator name-2- structure coordinated entity resolution formula & molpuzzler context handler class/group resolution NE confidence relationship extraction consumer BRAT consumer index consumer XML 9
10 Running OCMiner 10
11 Running OCMiner 11
12 Searching with OCMiner 12
13 Agenda Available ontologies & software Services OCMiner processing pipeline technology Project examples: Extraction of Structure-Property-Relationship data (SPR) Compound bio-profiles and bio-similarity Automated toxicology reports News and Alerts 13
14 Compound Property Data Where is the data? most biological data on compounds is found in tables table normalization / correction needed most physico-chemical data on compounds in experimental part structured understanding of experimental part chemical reactions most SPR relationships are anaphoric label resolution:...compound 3a has a melting point of C... anaphora resolution:...this phenol is a strong antibiotic 14
15 SAR Data in Tables... 15
16 Molecule Puzzler Markush from Tables 16
17 ... Extracted into SDF file or Database 103 compounds, >4000 data points for upload into database 17
18 ...Semantic Property Fact Extraction 18
19 Agenda Available ontologies & software Services OCMiner processing pipeline technology Project examples: Extraction of Structure-Property-Relationship data (SPR) Compound bio-profiles and bio-similarity Automated toxicology reports News and Alerts 19
20 Co-Occurrences 20
21 Knowledge Mining 21
22 Compound Bio-Profiles 22
23 Compound Bio-Similarity 23
24 Agenda Available ontologies & software Services OCMiner processing pipeline technology Project examples: Extraction of Structure-Property-Relationship data (SPR) Compound bio-profiles and bio-similarity Automated toxicology reports News and Alerts 24
25 Automated Tox Reports 25
26 Agenda Available ontologies & software Services OCMiner processing pipeline technology Project examples: Extraction of Structure-Property-Relationship data (SPR) Compound bio-profiles and bio-similarity Automated toxicology reports News and Alerts 26
27 Example: Vitamin News & Alert System Filtering out negative and positive news for vitamins: 27
28 Example: Fish Oil Alert System 28
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