building semantic web tools for bioinformatics
play

Building Semantic Web tools for Bioinformatics Andrea Splendiani - PowerPoint PPT Presentation

Apr 09, 2023 •616 likes •1.55k views

Building Semantic Web tools for Bioinformatics Andrea Splendiani (andrea.splendiani@bbsrc.ac.uk) 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009 Outline HowTo: export your data in semantic web formats,

  1. Building Semantic Web tools for Bioinformatics Andrea Splendiani (andrea.splendiani@bbsrc.ac.uk) 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  2. Outline HowTo: export your data in semantic web formats, The building build a knowledge Semantic Web blocks of the application bases and query it. Semantic Web development Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  3. Outline HowTo: export your data in semantic web formats, The building build a knowledge Semantic Web blocks of the application bases and query it. Semantic Web development Extra time: Application examples Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  4. Outline HowTo: export your data in semantic web formats, The building build a knowledge Semantic Web blocks of the application bases and query it. Semantic Web development Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  5. Outline The building blocks of the Semantic Web HowTo: export your data in semantic web formats, build a knowledge Semantic Web application bases and query it. development Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  6. The building blocks of the Semantic Web • The Semantic web is a set of technologies • Different technologies address different needs, and not all of them need to be used • Different technologies have different level of maturity Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  7. The building blocks of the Semantic Web • The Semantic web is a set of technologies • Different technologies address different needs, and not all of them need to be used • Different technologies have different level of maturity Mature technology Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  8. The building blocks of the Semantic Web • The Semantic web is a set of technologies • Different technologies address different needs, and not all of them need to be used • Different technologies have different level of maturity Mature technology Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  9. The building blocks of the Semantic Web • The Semantic web is a set of technologies • Different technologies address different needs, and not all of them need to be used • Different technologies have different level of maturity Mature technology Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  10. The building blocks of the Semantic Web • The Semantic web is a set of technologies • Different technologies address different needs, and not all of them need to be used • Different technologies have different level of maturity Mature technology Refinements in progress, usable. Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  11. The building blocks of the Semantic Web • The Semantic web is a set of technologies • Different technologies address different needs, and not all of them need to be used • Different technologies have different level of maturity Mature technology Refinements in progress, usable. Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  12. The building blocks of the Semantic Web • The Semantic web is a set of technologies • Different technologies address different needs, and not all of them need to be used • Different technologies have different level of maturity Mature technology Refinements in progress, usable. Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  13. The building blocks of the Semantic Web • The Semantic web is a set of technologies • Different technologies address different needs, and not all of them need to be used • Different technologies have different level of maturity Mature technology Refinements in progress, usable. Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  14. The building blocks of the Semantic Web • The Semantic web is a set of technologies • Different technologies address different needs, and not all of them need to be used • Different technologies have different level of maturity Mature technology Refinements in progress, usable. Not so standard yet, but usable. Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  15. The building blocks of the Semantic Web • The Semantic web is a set of technologies • Different technologies address different needs, and not all of them need to be used • Different technologies have different level of maturity Mature technology Refinements in progress, usable. Not so standard yet, but usable. Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  16. The building blocks of the Semantic Web Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  17. The building blocks of the Semantic Web URIs are global names for information resources. Examples: Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  18. The building blocks of the Semantic Web URIs are global names for information resources. Examples: • http://www.ncbi.nlm.nih.gov/nuccore/1836110 Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  19. The building blocks of the Semantic Web URIs are global names for information resources. Examples: • http://www.ncbi.nlm.nih.gov/nuccore/1836110 • http://purl.org/obo/owl/NCBITaxon#NCBITaxon_6 Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  20. The building blocks of the Semantic Web URIs are global names for information resources. Examples: • http://www.ncbi.nlm.nih.gov/nuccore/1836110 • http://purl.org/obo/owl/NCBITaxon#NCBITaxon_6 • http://bio2rdf.org/html/go:0032283 Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  21. The building blocks of the Semantic Web URIs are global names for information resources. Examples: • http://www.ncbi.nlm.nih.gov/nuccore/1836110 • http://purl.org/obo/owl/NCBITaxon#NCBITaxon_6 • http://bio2rdf.org/html/go:0032283 (http://www.ebi.ac.uk/ego/GTerm?id=GO:0032283) Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  22. The building blocks of the Semantic Web URIs are global names for information resources. Examples: • http://www.ncbi.nlm.nih.gov/nuccore/1836110 • http://purl.org/obo/owl/NCBITaxon#NCBITaxon_6 • http://bio2rdf.org/html/go:0032283 (http://www.ebi.ac.uk/ego/GTerm?id=GO:0032283) • info:pmid/18460179 Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  23. The building blocks of the Semantic Web URIs are global names for information resources. Examples: • http://www.ncbi.nlm.nih.gov/nuccore/1836110 • http://purl.org/obo/owl/NCBITaxon#NCBITaxon_6 • http://bio2rdf.org/html/go:0032283 (http://www.ebi.ac.uk/ego/GTerm?id=GO:0032283) • info:pmid/18460179 • http://biocyc.org/biopax/biopax#smallMolecule84998 Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

  24. The building blocks of the Semantic Web URIs are global names for information resources. Examples: • http://www.ncbi.nlm.nih.gov/nuccore/1836110 • http://purl.org/obo/owl/NCBITaxon#NCBITaxon_6 • http://bio2rdf.org/html/go:0032283 (http://www.ebi.ac.uk/ego/GTerm?id=GO:0032283) • info:pmid/18460179 • http://biocyc.org/biopax/biopax#smallMolecule84998 • http://www.reactome.org/biopax#H2O__ChEBI_15377_ Building Semantic Web tools for Bioinformatics 6th annual meeting of the Bioinformatics ITalian Sociaety, Genova, 18-20 Apr. 2009

Recommend

Perspectives of the application of semantic technologies in Bioinformatics Paolo Romano

Perspectives of the application of semantic technologies in Bioinformatics Paolo Romano

Perspectives of the application of semantic technologies in Bioinformatics Paolo Romano (paolo.romano@istge.it, skype:p.romano) Bioinformatics, National Cancer Research Institute, Genoa March 20, 2009 1 Tutorial on "Semantic Web

557 views • 51 slides
Bioinformatics Bioinformatics is the combination of biology and information technology. The

Bioinformatics Bioinformatics is the combination of biology and information technology. The

Bioinformatics Bioinformatics is the combination of biology and information technology. The discipline encompasses any computational tools and methods used to manage, analyze and manipulate large sets of biological data. Essentially,

594 views • 14 slides
SEMANTIC WEB TECHNOLOGIES: FUNDAMENTALS TOOLS FUNDAMENTALS, TOOLS, CASES AND BEST PRACTICES

SEMANTIC WEB TECHNOLOGIES: FUNDAMENTALS TOOLS FUNDAMENTALS, TOOLS, CASES AND BEST PRACTICES

SEMANTIC WEB TECHNOLOGIES: FUNDAMENTALS TOOLS FUNDAMENTALS, TOOLS, CASES AND BEST PRACTICES Luka Pavli University of Maribor Faculty of Electrical Engineering and Computer Science Johannes Kepler Universitt Linz , October 2010 Luka

1.3k views • 126 slides
FungalWeb A Semantic Web for Exploring Knowledge-Based Bioinformatics Greg Butler Volker

FungalWeb A Semantic Web for Exploring Knowledge-Based Bioinformatics Greg Butler Volker

FungalWeb A Semantic Web for Exploring Knowledge-Based Bioinformatics Greg Butler Volker Haarslev, Chris Baker, Sabine Bergler Leila Kosseim, Doina Precup, Justin Powlowski Nematollah Shiri, Adrian Tsang Centre for Structural and Functional

227 views • 20 slides
: on the Semantic Web : on the Semantic Web Building a Semantic Prototype for Danish Building a

: on the Semantic Web : on the Semantic Web Building a Semantic Prototype for Danish Building a

Family History Research Family History Research : on the Semantic Web : on the Semantic Web Building a Semantic Prototype for Danish Building a Semantic Prototype for Danish Genealogical Research Genealogical Research By By Charla Woodbury

744 views • 27 slides
Acquisition of semantic relations between terms: how far can we get with standard NLP tools? Ina

Acquisition of semantic relations between terms: how far can we get with standard NLP tools? Ina

Acquisition of semantic relations between terms Acquisition of semantic relations between terms: how far can we get with standard NLP tools? Ina Rsiger, Julia Bettinger, Johannes Schfer, Michael Dorna and Ulrich Heid 12 December 2016 5th

651 views • 38 slides
BauDataWeb The European Building and Construction Materials Database for the Semantic Web

BauDataWeb The European Building and Construction Materials Database for the Semantic Web

BauDataWeb The European Building and Construction Materials Database for the Semantic Web http://semantic.eurobau.com/ A joint project by inndata Datentechnik GmbH and the E-Business & Web Science Research Group, Universitt der Bundeswehr

429 views • 19 slides
Semantic Computing Research Group Building a national Semantic Web infrastructure with

Semantic Computing Research Group Building a national Semantic Web infrastructure with

Semantic Computing Research Group Building a national Semantic Web infrastructure with applications Eero Hyvnen Aalto University, Department of Computer Science http://www.seco.tkk.fi/ eero.hyvonen@aalto.fi 1 SeCo Mission and Focus

656 views • 64 slides
Building and Documenting Bioinformatics Workflows with Python-based Snakemake Johannes K

Building and Documenting Bioinformatics Workflows with Python-based Snakemake Johannes K

Genome Informatics Building and Documenting Bioinformatics Workflows with Python-based Snakemake Johannes K oster, Sven Rahmann German Conference on Bioinformatics September 2012 1 / 13 Genome Structure Informatics 1 Motivation 2

1.13k views • 35 slides
Adapting NLP Tools and Frame-Semantic Resources for the Semantic Analysis of Ritual Descriptions

Adapting NLP Tools and Frame-Semantic Resources for the Semantic Analysis of Ritual Descriptions

Adapting NLP Tools and Frame-Semantic Resources for the Semantic Analysis of Ritual Descriptions Nikolina Koleva UdS 22. February 2012 Nikolina Koleva (UdS) 22. February 2012 1 / 22 Outline Introduction 1 NLP Tools and Resources for

1.04k views • 74 slides
MHC-Peptide Interaction Studies using Bioinformatics tools Presented by Kunde Ramamoorthy

MHC-Peptide Interaction Studies using Bioinformatics tools Presented by Kunde Ramamoorthy

MHC-Peptide Interaction Studies using Bioinformatics tools Presented by Kunde Ramamoorthy Govindarajan Overview Introduction to Major histocompatibility complex What is MHC MHC gene organization MHC classification Structure,

395 views • 38 slides
Bioinformatics Bioinformatics Tools for RNA Tools for RNA Data Analysis Data Analysis Joseph

Bioinformatics Bioinformatics Tools for RNA Tools for RNA Data Analysis Data Analysis Joseph

Bioinformatics Bioinformatics Tools for RNA Tools for RNA Data Analysis Data Analysis Joseph Santos Joseph Santos Bloomfield Tech High School Bloomfield Tech High School Bloomfield, New Jersey Bloomfield, New Jersey 1 1 Contents

281 views • 23 slides
Recent and Planned Enhancements to Pathway Tools and BioCyc Peter Karp Bioinformatics Research

Recent and Planned Enhancements to Pathway Tools and BioCyc Peter Karp Bioinformatics Research

Recent and Planned Enhancements to Pathway Tools and BioCyc Peter Karp Bioinformatics Research Group SRI International pkarp@ai.sri.com SRI International Bioinformatics 1 Pathway/Genome Databases on the Web

458 views • 20 slides
Novel components at the periphery of long read genome assembly tools A bioinformatics thesis

Novel components at the periphery of long read genome assembly tools A bioinformatics thesis

Novel components at the periphery of long read genome assembly tools A bioinformatics thesis Pierre Marijon Directeurs: Jean-Stphane Varr, Rayan Chikhi 2 december 2019 quipe BONSAI, Inria, University of Lille Introduction Go back to

1.16k views • 105 slides
Bioinformatics Outline What is bioinformatics? Who are bioinformaticians? Hardware

Bioinformatics Outline What is bioinformatics? Who are bioinformaticians? Hardware

Bioinformatics Outline What is bioinformatics? Who are bioinformaticians? Hardware Software What is bioinformatics? What is bioinformatics? Someone to analyze my data The boring stuff I do Someone to help me between experiments

204 views • 16 slides
2 nd Joint NIAID-ISTC Workshop on Bioinformatics Tools and Innovation Through Collaboration

2 nd Joint NIAID-ISTC Workshop on Bioinformatics Tools and Innovation Through Collaboration

2 nd Joint NIAID-ISTC Workshop on Bioinformatics Tools and Innovation Through Collaboration Alexander V. Sintsov Institute for Systems Biology SPb Moscow, Russia August 31, 2011 National Institute of Allergy and Infectious Diseases (NIAID)

169 views • 13 slides
Semantic Web Rules - Tools and Languages - Tutorial at Rule ML 2006, Athens, GA Holger Knublauch

Semantic Web Rules - Tools and Languages - Tutorial at Rule ML 2006, Athens, GA Holger Knublauch

Semantic Web Rules - Tools and Languages - Tutorial at Rule ML 2006, Athens, GA Holger Knublauch Semantic Web Languages RDF Schema OWL SWRL Jena Rules Language SPARQL RDF Triples are the common foundation RDF

319 views • 29 slides
ICS 101: Tools for the Information World Web development - The Semantic web Nov. 29, 2016

ICS 101: Tools for the Information World Web development - The Semantic web Nov. 29, 2016

1 ICS 101: Tools for the Information World Web development - The Semantic web Nov. 29, 2016 Instructor: Luz M. Quiroga University of Hawaii. Affiliated to: ICS LIS - CIS 2 Agenda: n Part 1:The WWW some concepts, history n Part 2: The

273 views • 25 slides
Experiments Design and Analysis Fotis E. Psomopoulos CODATA-RDA Advanced Bioinformatics

Experiments Design and Analysis Fotis E. Psomopoulos CODATA-RDA Advanced Bioinformatics

Experiments Design and Analysis Fotis E. Psomopoulos CODATA-RDA Advanced Bioinformatics Workshop, 19-23 August 2019, Trieste, Italy A short intro to me 2 Bioinformatics and Data Mining tools and pipelines to address

884 views • 43 slides
Introduction to Bioinformatics Dortmund, 16.-20.07.2007 Lectures: Sven Rahmann Exercises: Udo

Introduction to Bioinformatics Dortmund, 16.-20.07.2007 Lectures: Sven Rahmann Exercises: Udo

Introduction to Bioinformatics Dortmund, 16.-20.07.2007 Lectures: Sven Rahmann Exercises: Udo Feldkamp, Michael Wurst 1 Goals of this course Learn about Software tools Databases Methods (Algorithms) in bioinformatics Know

458 views • 21 slides
Bioinformatics: Network Analysis Kinetics of Regulatory Networks: Basic Building Blocks COMP 572

Bioinformatics: Network Analysis Kinetics of Regulatory Networks: Basic Building Blocks COMP 572

Bioinformatics: Network Analysis Kinetics of Regulatory Networks: Basic Building Blocks COMP 572 (BIOS 572 / BIOE 564) - Fall 2013 Luay Nakhleh, Rice University 1 Basic Building Blocks Here we show how simple signaling pathways can be

371 views • 20 slides
Semantic Web 2008 Se a t c eb 008 Semantic Web ca. 2008 S ti W b 2008 Semantic Web

Semantic Web 2008 Se a t c eb 008 Semantic Web ca. 2008 S ti W b 2008 Semantic Web

Semantic Web 2008 Se a t c eb 008 Semantic Web ca. 2008 S ti W b 2008 Semantic Web companies starting & growing Siderean, SandPiper, SiberLogic, Ontology Works, Intellidimension, Intellisophic, TopQuadrant, Data Grid, Mondeca,

481 views • 23 slides
Bioinformatics Tools for Analyzing Enzyme Families Greg Butler Department of Computer Science

Bioinformatics Tools for Analyzing Enzyme Families Greg Butler Department of Computer Science

Bioinformatics Tools for Analyzing Enzyme Families Greg Butler Department of Computer Science and Software Engineering Centre for Structural and Functional Genomics Concordia University, Montreal www.cs.concordia.ca/~gregb

398 views • 37 slides
Evaluation of Ontology Evaluation of Ontology Merging Tools in Merging Tools in Bioinformatics

Evaluation of Ontology Evaluation of Ontology Merging Tools in Merging Tools in Bioinformatics

Evaluation of Ontology Evaluation of Ontology Merging Tools in Merging Tools in Bioinformatics Bioinformatics P Lambrix Lambrix, A Edberg , A Edberg P Proceedings of the Pacific Symposium on Proceedings of the Pacific Symposium on

859 views • 16 slides

More recommend