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Session II: Scientific Publishing and Semantic Web

Session II: Scientific Publishing and Semantic Web. W3C Semantic Web for Life Sciences Workshop October 27, 2004. Moderator: Alan R. Aronson.

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Session II: Scientific Publishing and Semantic Web

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  1. Session II: Scientific Publishing and Semantic Web W3C Semantic Web for Life Sciences Workshop October 27, 2004 Moderator: Alan R. Aronson

  2. Foundations of Semantic Text Processing at NLMAlan R. Aronson(National Library of Medicine)Urchin RSS /The Urchin/Kowari ProjectBen Lund, David Wood(Nature Publishing Group, Tucana Technologies)Semantic Web and ElsevierMarc Krellenstein (Elsevier) Semantic Web for Data Interpretation & Integration:Lessons Learned from Scientific Publishingand the Distributed Annotation System Steve Chervitz(Affymetrix)

  3. Foundations of Semantic Text Processing at NLM Alan R. Aronson, PhD National Library of Medicine W3C Semantic Web for Life Sciences Workshop October 27, 2004

  4. Outline • Unified Medical Language System (UMLS) Knowledge Sources • The MetaMap Program • The NLM Indexing Initiative • SemRep (Semantic Representation)

  5. The Unified Medical Language System • UMLS Knowledge Sources • Metathesaurus • Semantic Network • SPECIALIST Lexicon • MetamorphoSys (Metathesaurus subset extraction) • Lexical/spelling tools (lvg, norm, Gspell) • Knowledge Source Server

  6. MetaMap • Maps text to the Metathesaurus • Parse text into phrases • Generate word variants • Retrieve Metathesaurus candidates • Evaluate candidates against text phrases • Form final mapping • Linguistically rigorous • Partial matching • Web interface and Java-based application

  7. NLM Indexing Initiative (II) • Investigate automated and semi-automated indexing methodologies • Develop methods that result in acceptable retrieval performance • Concept-based algorithms • Extensive use of UMLS resources • Medical Text Indexer (MTI), a tool for • semi-automated assistance in MEDLINE indexing • automatic indexing of some abstracts collections

  8. SemRep • Family of programs to extract semantic relationships from biomedical text • SemRep (the progenitor) • Arbiter (binding relationships) • EDGAR (drug-gene relationships) • SemSpec (hypernymic propositions) • SemGen (etiology of genetic diseases)

  9. Words Syntactic Structure Predicates Arguments World Model Relations Entities Semantic Interpretation Semantic Relation(Concept,Concept) Language and Meaning Language Meaning

  10. Lexical Look-up and Tagger of hypercalcemic renal failure aggressive combination chemotherapy in the management adj noun prep det noun prep adj noun noun noun

  11. NP NP NP Parser prep det head prep mod mod head mod mod head of hypercalcemic renal failure aggressive combination chemotherapy in the management adj noun noun prep det noun prep adj noun noun

  12. Drug Therapy, Combination Kidney Failure topp dsyn NP NP NP MetaMap prep det head prep mod mod head mod mod head of hypercalcemic renal failure aggressive combination chemotherapy in the management adj noun noun prep det noun prep adj noun noun Therapeutic or Preventive Procedure Disease or Syndrome

  13. Drug Therapy, Combination Kidney Failure NP NP NP SemRep prep det head prep mod mod head mod mod head of hypercalcemic renal failure aggressive combination chemotherapy in the management adj noun noun prep det noun prep adj noun noun topp dsyn Dependency grammar applies syntactic constraints for nominalization

  14. Drug Therapy, Combination Kidney Failure NP NP NP SemRep prep det head prep mod mod head mod mod head of hypercalcemic renal failure aggressive combination chemotherapy in the management adj noun noun prep det noun prep adj noun noun TREATS topp dsyn phsu-TREATS-dsyn medd-TREATS-dsyn topp-TREATS-dsyn Match semantic types between arguments and Semantic Network topp-TREATS-inpo topp-TREATS-sosy topp-TREATS-anab

  15. NLM Web Pointers • UMLS Knowledge Source Server: http://umlsks.nlm.nih.gov/ • Semantic Knowledge Representation Project: http://skr.nlm.nih.gov/ • NLM Indexing Initiative: http://ii.nlm.nih.gov/

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