Presentation is loading. Please wait.

Presentation is loading. Please wait.

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

Published bySandra Barker Modified over 8 years ago

Similar presentations

Presentation on theme: "Session II: Scientific Publishing and Semantic Web W3C Semantic Web for Life Sciences Workshop October 27, 2004 Moderator: Alan R. Aronson."— Presentation transcript:

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 NLM Alan R. Aronson (National Library of Medicine) Urchin RSS / The Urchin/Kowari Project Ben Lund, David Wood (Nature Publishing Group, Tucana Technologies) Semantic Web and Elsevier Marc Krellenstein (Elsevier) Semantic Web for Data Interpretation & Integration: Lessons Learned from Scientific Publishing and 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 Language and Meaning Language Meaning Semantic Interpretation Semantic Relation(Concept,Concept) World Model Relations Entities Words Syntactic Structure Predicates Arguments

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

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

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

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

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

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

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

Similar presentations

CILC2011 A framework for structured knowledge extraction and representation from natural language via deep sentence analysis Stefania Costantini Niva Florio.

CILC2011 A framework for structured knowledge extraction and representation from natural language via deep sentence analysis Stefania Costantini Niva Florio.
 Christel Kemke 2007/08 COMP 4060 Natural Language Processing Feature Structures and Unification.

 Christel Kemke 2007/08 COMP 4060 Natural Language Processing Feature Structures and Unification.
QA-LaSIE Components The question document and each candidate answer document pass through all nine components of the QA-LaSIE system in the order shown.

QA-LaSIE Components The question document and each candidate answer document pass through all nine components of the QA-LaSIE system in the order shown.
Proceedings of the Conference on Intelligent Text Processing and Computational Linguistics (CICLing-2007) Learning for Semantic Parsing Advisor: Hsin-His.

Proceedings of the Conference on Intelligent Text Processing and Computational Linguistics (CICLing-2007) Learning for Semantic Parsing Advisor: Hsin-His.
Automatic Concept Indexing and Classification for Improved Retrieval in the Hazardous Substances Data Bank Doszkocs, Tamas; Chang, Hua Florence; Aronson,

Automatic Concept Indexing and Classification for Improved Retrieval in the Hazardous Substances Data Bank Doszkocs, Tamas; Chang, Hua Florence; Aronson,
The NLM Indexing Initiative Alan R. Aronson, PhD Lister Hill Center, National Library of Medicine American Society of Indexers Annual Meeting May 15, 2004.

The NLM Indexing Initiative Alan R. Aronson, PhD Lister Hill Center, National Library of Medicine American Society of Indexers Annual Meeting May 15, 2004.
Semantic indexing in PubMed CERN Workshop on Innovations in Scholarly Communication (OAI8) CERN Workshop on Innovations in Scholarly Communication (OAI8)

Semantic indexing in PubMed CERN Workshop on Innovations in Scholarly Communication (OAI8) CERN Workshop on Innovations in Scholarly Communication (OAI8)
Indexing the Biomedical Literature in a Time of Increased Demand and Limited Resources BioASQ Workshop September 27, 2013 Alan R. Aronson Lister Hill Center,

Indexing the Biomedical Literature in a Time of Increased Demand and Limited Resources BioASQ Workshop September 27, 2013 Alan R. Aronson Lister Hill Center,
U. S. National Library of Medicine NLM Indexing Initiative Tools for NLP: MetaMap and the Medical Text Indexer Natural Language Processing: State of the.

U. S. National Library of Medicine NLM Indexing Initiative Tools for NLP: MetaMap and the Medical Text Indexer Natural Language Processing: State of the.
Codifying Semantic Information in Medical Questions Using Lexical Sources Paul E. Pancoast Arthur B. Smith Chi-Ren Shyu.

Codifying Semantic Information in Medical Questions Using Lexical Sources Paul E. Pancoast Arthur B. Smith Chi-Ren Shyu.
The Role of the UMLS in Vocabulary Control CENDI Conference “Controlled Vocabulary and the Internet” Stuart J. Nelson, MD.

The Role of the UMLS in Vocabulary Control CENDI Conference “Controlled Vocabulary and the Internet” Stuart J. Nelson, MD.
NATIONAL LIBRARY OF MEDICINE The PubMed ID and Entrez, PubMed and PubMed Central Edwin Sequeira National Center for Biotechnology Information June 21,

NATIONAL LIBRARY OF MEDICINE The PubMed ID and Entrez, PubMed and PubMed Central Edwin Sequeira National Center for Biotechnology Information June 21,
1 Question Answering in Biomedicine Student: Andreea Tutos Id: 41064739 Supervisor: Diego Molla.

1 Question Answering in Biomedicine Student: Andreea Tutos Id: Supervisor: Diego Molla.
74.793 NLP and Speech Course Review. Morphological Analyzer Lexicon Part-of-Speech (POS) Tagging Grammar Rules Parser thethe – determiner Det NP → Det.

NLP and Speech Course Review. Morphological Analyzer Lexicon Part-of-Speech (POS) Tagging Grammar Rules Parser thethe – determiner Det NP → Det.
U. S. National Library of Medicine Welcome to the first MMTx User’s Group Meeting AMIA 2003 November 11, 2003.

U. S. National Library of Medicine Welcome to the first MMTx User’s Group Meeting AMIA 2003 November 11, 2003.
Semantic Web and Web Mining: Networking with Industry and Academia İsmail Hakkı Toroslu IST EVENT 2006.

Semantic Web and Web Mining: Networking with Industry and Academia İsmail Hakkı Toroslu IST EVENT 2006.
A Flexible Workbench for Document Analysis and Text Mining NLDB’2004, Salford, June 23-25 2004 1 Gulla, Brasethvik and Kaada A Flexible Workbench for Document.

A Flexible Workbench for Document Analysis and Text Mining NLDB’2004, Salford, June Gulla, Brasethvik and Kaada A Flexible Workbench for Document.
Brian A. Carlsen Apelon, Inc. Tools For Classification Integration Networked Knowledge Organization Systems/Services Workshop June 28, 2001.

Brian A. Carlsen Apelon, Inc. Tools For Classification Integration Networked Knowledge Organization Systems/Services Workshop June 28, 2001.
Automating Keyphrase Extraction with Multi-Objective Genetic Algorithms (MOGA) Jia-Long Wu Alice M. Agogino Berkeley Expert System Laboratory U.C. Berkeley.

Automating Keyphrase Extraction with Multi-Objective Genetic Algorithms (MOGA) Jia-Long Wu Alice M. Agogino Berkeley Expert System Laboratory U.C. Berkeley.
Development of a Pediatric Text-Corpus for Part-of-Speech Tagging John Pestian 1, Lukasz Itert 1,2, and Włodzisław Duch 2,3 1 BioMedical Informatics, 3333.

Development of a Pediatric Text-Corpus for Part-of-Speech Tagging John Pestian 1, Lukasz Itert 1,2, and Włodzisław Duch 2,3 1 BioMedical Informatics, 3333.

Similar presentations

Ads by Google