Ontologies for bioinformatics:
Gespeichert in:
| Hauptverfasser: | , |
|---|---|
| Format: | Buch |
| Sprache: | English |
| Veröffentlicht: |
Cambridge, Mass.
MIT Press
2006
|
| Schriftenreihe: | Computational molecular biology
|
| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | Includes bibliographical references and index |
| Beschreibung: | XIV, 424 S. |
| ISBN: | 0262025914 |
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Datensatz im Suchindex
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| adam_text | ONTOLOGIES FOR BIOINFORMATICS KENNETH BACLAWSKI TIANHUA NIU THE MIT
PRESS CAMBRIDGE, MASSACHUSETTS LONDON, ENGLAND CONTENTS PREFACE XI I
INTRODUCTION TO ONTOLOGIES 1 1 HIERARCHIES AND RELATIONSHIPS 3 1.1
TRADITIONAL RECORD STRUCTURES 3 1.2 THE EXTENSIBLE MARKUP LANGUAGE 5 1.3
HIERARCHICAL ORGANIZATION 7 1.4 CREATING AND UPDATING XML 10 1.5 THE
MEANING OF A HIERARCHY 17 1.6 RELATIONSHIPS 25 1.7 NAMESPACES 28 1.8
EXERCISES 32 2 XML SEMANTICS 35 2.1 THE MEANING OF MEANING 35 2.2
INFOSETS 38 2.3 XML SCHEMA 42 2.4 XML DATA 46 2.5 EXERCISES 49 3 RULES
AND INFERENCE 51 3.1 INTRODUCTION TO RULE-BASED SYSTEMS 51 3.2 FORWARD-
AND BACKWARD-CHAINING RULE ENGINES 54 3.3 THEOREM PROVERS AND OTHER
REASONERS 56 3.4 PERFORMANCE OF AUTOMATED REASONERS 59 CONTENTS 4 THE
SEMANTIC WEB AND BIOINFORMATICS APPLICATIONS 61 4.1 THE SEMANTIC WEB IN
BIOINFORMATICS 61 4.2 THE RESOURCE DESCRIPTION FRAMEWORK 63 4.3 XML
TOPIC MAPS 77 4.4 THE WEB ONTOLOGY LANGUAGE 79 4.5 EXERCISES 87 5 SURVEY
OF ONTOLOGIES IN BIOINFORMATICS 89 5.1 BIO-ONTOLOGIES 89 5.1.1 UNIFIED
MEDICAL LANGUAGE SYSTEM 90 5.1.2 THE GENE ONTOLOGY 92 5.1.3 ONTOLOGIES
OF BIOINFORMATICS ONTOLOGIES 98 5.2 ONTOLOGY LANGUAGES IN BIOINFORMATICS
99 5.3 MACROMOLECULAR SEQUENCE DATABASES 106 5.3.1 NUCLEOTIDE SEQUENCE
DATABASES 107 5.3.2 PROTEIN SEQUENCE DATABASES 108 5.4 STRUCTURAL
DATABASES 108 5.4.1 NUCLEOTIDE STRUCTURE DATABASES 108 5.4.2 PROTEIN
STRUCTURE DATABASES 109 5.5 TRANSCRIPTION FACTOR DATABASES 115 5.6
SPECIES-SPECIFIC DATABASES 116 5.7 SPECIALIZED PROTEIN DATABASES 118 5.8
GENE EXPRESSION DATABASES 119 5.8.1 TRANSCRIPTOMICS DATABASES 119 5.8.2
PROTEOMICS DATABASES 120 5.9 PATHWAY DATABASES 121 5.10 SINGLE
NUCLEOTIDE POLYMORPHISMS 123 II BUILDING AND USING ONTOLOGIES 127 6
INFORMATION RETRIEVAL 129 6.1 THE SEARCH PROCESS 129 6.2 VECTOR SPACE
RETRIEVAL 131 6.3 USING ONTOLOGIES FOR FORMULATING QUERIES 140 6 4
ORGANIZING BY CITATION 142 6.5 VECTOR SPACE RETRIEVAL OF KNOWLEDGE
REPRESENTATIONS 146 CONTENTS VU 7 SEQUENCE SIMILARITY SEARCHING TOOLS 15
5 7.1 BASIC CONCEPTS 155 7.2 DYNAMIC PROGRAMMING ALGORITHM 158 7.3 FASTA
159 7.4 BLAST 161 7.4.1 THE BLAST ALGORITHM 161 7.4.2 BLAST SEARCH TYPES
164 7.4.3 SCORES AND VALUES 166 7.4.4 BLAST VARIANTS 168 7.5 EXERCISES
174 8 QUERY LANGUAGES 175 8.1 XML NAVIGATION USING XPATH 176 8.2
QUERYING XML USING XQUERY 180 8.3 SEMANTIC WEB QUERIES 183 8.4 EXERCISES
184 9 THE TRANSFORMATION PROCESS 187 9.1 EXPERIMENTAL AND STATISTICAL
METHODS AS TRANSFORMATIONS 187 9.2 PRESENTATION OF INFORMATION 190 9.3
CHANGING THE POINT OF VIEW 195 9.4 TRANSFORMATION TECHNIQUES 197 9.5
AUTOMATING TRANSFORMATIONS 200 10 TRANSFORMING WITH TRADITIONAL
PROGRAMMING LANGUAGES 203 10.1 TEXT TRANSFORMATIONS 204 10.1.1
LINE-ORIENTED TRANSFORMATION 205 10.1.2 MULTIDIMENSIONAL ARRAYS 217
10.1.3 PERL PROCEDURES 222 10.1.4 PATTERN MATCHING 225 10.1.5 PERL DATA
STRUCTURES 230 10.2 TRANSFORMING XML 234 10.2.1 USING PERL MODULES AND
OBJECTS 234 10.2.2 PROCESSING XML ELEMENTS 236 10.2.3 THE DOCUMENT
OBJECT MODEL 244 10.2.4 PRODUCING XML 245 10.2.5 TRANSFORMING XML TO XML
253 10.3 EXERCISES 259 11 THE XML TRANSFORMATION LANGUAGE 261 11.1
TRANSFORMATION AS DIGESTION 261 11.2 PROGRAMMING IN XSLT 265 11.3
NAVIGATION AND COMPUTATION 267 11.4 CONDITIONALS 269 11.5 PRECISE
FORMATTING 271 11.6 MULTIPLE SOURCE DOCUMENTS 273 11.7 PROCEDURAL
PROGRAMMING 275 11.8 EXERCISES 280 12 BUILDING BIOINFORMATICS ONTOLOGIES
281 12.1 PURPOSE OF ONTOLOGY DEVELOPMENT 282 12.2 SELECTING AN ONTOLOGY
LANGUAGE 285 12.3 ONTOLOGY DEVELOPMENT TOOLS 288 12.4 ACQUIRING DOMAIN
KNOWLEDGE 291 12.5 REUSING EXISTING ONTOLOGIES 293 12.6 DESIGNING THE
CONCEPT HIERARCHY 296 12.6.1 UNIFORM HIERARCHY 300 12.6.2 CLASSES VS.
INSTANCES 301 12.6.3 ONTOLOGICAL COMMITMENT 301 12.6.4 STRICT TAXONOMIES
302 12.7 DESIGNING THE PROPERTIES 303 12.7.1 CLASSES VS. PROPERTY VALUES
305 12.7.2 DOMAIN AND RANGE CONSTRAINTS 307 12.7.3 CARDINALITY
CONSTRAINTS 310 12.8 VALIDATING AND MODIFYING THE ONTOLOGY 12.9
EXERCISES 318 313 III REASONING WITH UNCERTAINTY 319 13 INDUCTIVE VS.
DEDUCTIVE REASONING 321 13.1 SOURCES AND SEMANTICS OF UNCERTAINTY 322
13.2 EXTENSIONAL APPROACHES TO UNCERTAINTY 324 13.3 INTENSIONAL
APPROACHES TO UNCERTAINTY 14 BAYESIAN NETWORKS 33 1 14.1 THE BAYESIAN
NETWORK FORMALISM 332 14.2 STOCHASTIC INFERENCE 335 325 CONTENTS 14.3
CONSTRUCTING BAYESIAN NETWORKS 341 14.3.1 BN REQUIREMENTS 342 14.3.2
MACHINE LEARNING 343 14.3.3 BUILDING BNS FROM COMPONENTS 346 14.3.4
ONTOLOGIES AS BNS 347 14.3.5 BN DESIGN PATTERNS 348 14.3.6 VALIDATING
AND REVISING BNS 351 14.4 EXERCISES 354 15 COMBINING INFORMATION 355
15.1 COMBINING DISCRETE INFORMATION 356 15.2 COMBINING CONTINUOUS
INFORMATION 359 15.3 INFORMATION COMBINATION AS A BN DESIGN PATTERN 15.4
MEASURING PROBABILITY 363 15.5 DEMPSTER-SHAFER THEORY 365 16 THE
BAYESIAN WEB 369 16.1 INTRODUCTION 369 16.2 REQUIREMENTS FOR BAYESIAN
NETWORK INTEROPERABILITY 16.3 EXTENDING THE SEMANTIC WEB 371 16.4
ONTOLOGIES FOR BAYESIAN NETWORKS 372 17 ANSWERS TO SELECTED EXERCISES
379 REFERENCES 393 INDEX 413
|
| adam_txt |
ONTOLOGIES FOR BIOINFORMATICS KENNETH BACLAWSKI TIANHUA NIU THE MIT
PRESS CAMBRIDGE, MASSACHUSETTS LONDON, ENGLAND CONTENTS PREFACE XI I
INTRODUCTION TO ONTOLOGIES 1 1 HIERARCHIES AND RELATIONSHIPS 3 1.1
TRADITIONAL RECORD STRUCTURES 3 1.2 THE EXTENSIBLE MARKUP LANGUAGE 5 1.3
HIERARCHICAL ORGANIZATION 7 1.4 CREATING AND UPDATING XML 10 1.5 THE
MEANING OF A HIERARCHY 17 1.6 RELATIONSHIPS 25 1.7 NAMESPACES 28 1.8
EXERCISES 32 2 XML SEMANTICS 35 2.1 THE MEANING OF MEANING 35 2.2
INFOSETS 38 2.3 XML SCHEMA 42 2.4 XML DATA 46 2.5 EXERCISES 49 3 RULES
AND INFERENCE 51 3.1 INTRODUCTION TO RULE-BASED SYSTEMS 51 3.2 FORWARD-
AND BACKWARD-CHAINING RULE ENGINES 54 3.3 THEOREM PROVERS AND OTHER
REASONERS 56 3.4 PERFORMANCE OF AUTOMATED REASONERS 59 CONTENTS 4 THE
SEMANTIC WEB AND BIOINFORMATICS APPLICATIONS 61 4.1 THE SEMANTIC WEB IN
BIOINFORMATICS 61 4.2 THE RESOURCE DESCRIPTION FRAMEWORK 63 4.3 XML
TOPIC MAPS 77 4.4 THE WEB ONTOLOGY LANGUAGE 79 4.5 EXERCISES 87 5 SURVEY
OF ONTOLOGIES IN BIOINFORMATICS 89 5.1 BIO-ONTOLOGIES 89 5.1.1 UNIFIED
MEDICAL LANGUAGE SYSTEM 90 5.1.2 THE GENE ONTOLOGY 92 5.1.3 ONTOLOGIES
OF BIOINFORMATICS ONTOLOGIES 98 5.2 ONTOLOGY LANGUAGES IN BIOINFORMATICS
99 5.3 MACROMOLECULAR SEQUENCE DATABASES 106 5.3.1 NUCLEOTIDE SEQUENCE
DATABASES 107 5.3.2 PROTEIN SEQUENCE DATABASES 108 5.4 STRUCTURAL
DATABASES 108 5.4.1 NUCLEOTIDE STRUCTURE DATABASES 108 5.4.2 PROTEIN
STRUCTURE DATABASES 109 5.5 TRANSCRIPTION FACTOR DATABASES 115 5.6
SPECIES-SPECIFIC DATABASES 116 5.7 SPECIALIZED PROTEIN DATABASES 118 5.8
GENE EXPRESSION DATABASES 119 5.8.1 TRANSCRIPTOMICS DATABASES 119 5.8.2
PROTEOMICS DATABASES 120 5.9 PATHWAY DATABASES 121 5.10 SINGLE
NUCLEOTIDE POLYMORPHISMS 123 II BUILDING AND USING ONTOLOGIES 127 6
INFORMATION RETRIEVAL 129 6.1 THE SEARCH PROCESS 129 6.2 VECTOR SPACE
RETRIEVAL 131 6.3 USING ONTOLOGIES FOR FORMULATING QUERIES 140 6 4
ORGANIZING BY CITATION 142 6.5 VECTOR SPACE RETRIEVAL OF KNOWLEDGE
REPRESENTATIONS 146 CONTENTS VU 7 SEQUENCE SIMILARITY SEARCHING TOOLS 15
5 7.1 BASIC CONCEPTS 155 7.2 DYNAMIC PROGRAMMING ALGORITHM 158 7.3 FASTA
159 7.4 BLAST 161 7.4.1 THE BLAST ALGORITHM 161 7.4.2 BLAST SEARCH TYPES
164 7.4.3 SCORES AND VALUES 166 7.4.4 BLAST VARIANTS 168 7.5 EXERCISES
174 8 QUERY LANGUAGES 175 8.1 XML NAVIGATION USING XPATH 176 8.2
QUERYING XML USING XQUERY 180 8.3 SEMANTIC WEB QUERIES 183 8.4 EXERCISES
184 9 THE TRANSFORMATION PROCESS 187 9.1 EXPERIMENTAL AND STATISTICAL
METHODS AS TRANSFORMATIONS 187 9.2 PRESENTATION OF INFORMATION 190 9.3
CHANGING THE POINT OF VIEW 195 9.4 TRANSFORMATION TECHNIQUES 197 9.5
AUTOMATING TRANSFORMATIONS 200 10 TRANSFORMING WITH TRADITIONAL
PROGRAMMING LANGUAGES 203 10.1 TEXT TRANSFORMATIONS 204 10.1.1
LINE-ORIENTED TRANSFORMATION 205 10.1.2 MULTIDIMENSIONAL ARRAYS 217
10.1.3 PERL PROCEDURES 222 10.1.4 PATTERN MATCHING 225 10.1.5 PERL DATA
STRUCTURES 230 10.2 TRANSFORMING XML 234 10.2.1 USING PERL MODULES AND
OBJECTS 234 10.2.2 PROCESSING XML ELEMENTS 236 10.2.3 THE DOCUMENT
OBJECT MODEL 244 10.2.4 PRODUCING XML 245 10.2.5 TRANSFORMING XML TO XML
253 10.3 EXERCISES 259 11 THE XML TRANSFORMATION LANGUAGE 261 11.1
TRANSFORMATION AS DIGESTION 261 11.2 PROGRAMMING IN XSLT 265 11.3
NAVIGATION AND COMPUTATION 267 11.4 CONDITIONALS 269 11.5 PRECISE
FORMATTING 271 11.6 MULTIPLE SOURCE DOCUMENTS 273 11.7 PROCEDURAL
PROGRAMMING 275 11.8 EXERCISES 280 12 BUILDING BIOINFORMATICS ONTOLOGIES
281 12.1 PURPOSE OF ONTOLOGY DEVELOPMENT 282 12.2 SELECTING AN ONTOLOGY
LANGUAGE 285 12.3 ONTOLOGY DEVELOPMENT TOOLS 288 12.4 ACQUIRING DOMAIN
KNOWLEDGE 291 12.5 REUSING EXISTING ONTOLOGIES 293 12.6 DESIGNING THE
CONCEPT HIERARCHY 296 12.6.1 UNIFORM HIERARCHY 300 12.6.2 CLASSES VS.
INSTANCES 301 12.6.3 ONTOLOGICAL COMMITMENT 301 12.6.4 STRICT TAXONOMIES
302 12.7 DESIGNING THE PROPERTIES 303 12.7.1 CLASSES VS. PROPERTY VALUES
305 12.7.2 DOMAIN AND RANGE CONSTRAINTS 307 12.7.3 CARDINALITY
CONSTRAINTS 310 12.8 VALIDATING AND MODIFYING THE ONTOLOGY 12.9
EXERCISES 318 313 III REASONING WITH UNCERTAINTY 319 13 INDUCTIVE VS.
DEDUCTIVE REASONING 321 13.1 SOURCES AND SEMANTICS OF UNCERTAINTY 322
13.2 EXTENSIONAL APPROACHES TO UNCERTAINTY 324 13.3 INTENSIONAL
APPROACHES TO UNCERTAINTY 14 BAYESIAN NETWORKS 33 1 14.1 THE BAYESIAN
NETWORK FORMALISM 332 14.2 STOCHASTIC INFERENCE 335 325 CONTENTS 14.3
CONSTRUCTING BAYESIAN NETWORKS 341 14.3.1 BN REQUIREMENTS 342 14.3.2
MACHINE LEARNING 343 14.3.3 BUILDING BNS FROM COMPONENTS 346 14.3.4
ONTOLOGIES AS BNS 347 14.3.5 BN DESIGN PATTERNS 348 14.3.6 VALIDATING
AND REVISING BNS 351 14.4 EXERCISES 354 15 COMBINING INFORMATION 355
15.1 COMBINING DISCRETE INFORMATION 356 15.2 COMBINING CONTINUOUS
INFORMATION 359 15.3 INFORMATION COMBINATION AS A BN DESIGN PATTERN 15.4
MEASURING PROBABILITY 363 15.5 DEMPSTER-SHAFER THEORY 365 16 THE
BAYESIAN WEB 369 16.1 INTRODUCTION 369 16.2 REQUIREMENTS FOR BAYESIAN
NETWORK INTEROPERABILITY 16.3 EXTENDING THE SEMANTIC WEB 371 16.4
ONTOLOGIES FOR BAYESIAN NETWORKS 372 17 ANSWERS TO SELECTED EXERCISES
379 REFERENCES 393 INDEX 413 |
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| dewey-full | 572.8/0285 |
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| dewey-search | 572.8/0285 |
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| discipline_str_mv | Biologie Informatik |
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| id | DE-604.BV021493352 |
| illustrated | Not Illustrated |
| index_date | 2024-07-02T14:13:25Z |
| indexdate | 2024-07-09T20:37:03Z |
| institution | BVB |
| isbn | 0262025914 |
| language | English |
| lccn | 2005042803 |
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| publisher | MIT Press |
| record_format | marc |
| series2 | Computational molecular biology |
| spelling | Baclawski, Kenneth Verfasser aut Ontologies for bioinformatics Kenneth Baclawski ; Tianhua Niu Cambridge, Mass. MIT Press 2006 XIV, 424 S. txt rdacontent n rdamedia nc rdacarrier Computational molecular biology Includes bibliographical references and index Bio-informatica gtt Bio-informatique - Méthodologie Ontologieën (informatiewetenschap) gtt Bioinformatics Methodology Bioinformatik (DE-588)4611085-9 gnd rswk-swf Ontologie Wissensverarbeitung (DE-588)4827894-4 gnd rswk-swf Methodologie (DE-588)4139716-2 gnd rswk-swf Bioinformatik (DE-588)4611085-9 s Ontologie Wissensverarbeitung (DE-588)4827894-4 s DE-604 Methodologie (DE-588)4139716-2 s Niu, Tianhua Verfasser aut GBV Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014710151&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Baclawski, Kenneth Niu, Tianhua Ontologies for bioinformatics Bio-informatica gtt Bio-informatique - Méthodologie Ontologieën (informatiewetenschap) gtt Bioinformatics Methodology Bioinformatik (DE-588)4611085-9 gnd Ontologie Wissensverarbeitung (DE-588)4827894-4 gnd Methodologie (DE-588)4139716-2 gnd |
| subject_GND | (DE-588)4611085-9 (DE-588)4827894-4 (DE-588)4139716-2 |
| title | Ontologies for bioinformatics |
| title_auth | Ontologies for bioinformatics |
| title_exact_search | Ontologies for bioinformatics |
| title_exact_search_txtP | Ontologies for bioinformatics |
| title_full | Ontologies for bioinformatics Kenneth Baclawski ; Tianhua Niu |
| title_fullStr | Ontologies for bioinformatics Kenneth Baclawski ; Tianhua Niu |
| title_full_unstemmed | Ontologies for bioinformatics Kenneth Baclawski ; Tianhua Niu |
| title_short | Ontologies for bioinformatics |
| title_sort | ontologies for bioinformatics |
| topic | Bio-informatica gtt Bio-informatique - Méthodologie Ontologieën (informatiewetenschap) gtt Bioinformatics Methodology Bioinformatik (DE-588)4611085-9 gnd Ontologie Wissensverarbeitung (DE-588)4827894-4 gnd Methodologie (DE-588)4139716-2 gnd |
| topic_facet | Bio-informatica Bio-informatique - Méthodologie Ontologieën (informatiewetenschap) Bioinformatics Methodology Bioinformatik Ontologie Wissensverarbeitung Methodologie |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=014710151&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT baclawskikenneth ontologiesforbioinformatics AT niutianhua ontologiesforbioinformatics |