Information integration

•Download as PPT, PDF•

2 likes•432 views

Lars Juhl Jensen

Information integration

Lars Juhl Jensen

Part 1
the eukaryotic cell cycle

essential process

grow and divide

one cell

two cells

four phases

G1 phase

growth

S phase

DNA replication

G2 phase

growth

M phase

cell division

regulation

gene expression

phosphorylation

targeted degradation

protein interactions

Example 1
my protein and friends

http://string-db.org

Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011

Part 2
association networks

guild by association

STRING

>1100 genomes

genomic context

gene fusion

Korbel et al., Nature Biotechnology, 2004

conserved neighborhood

Korbel et al., Nature Biotechnology, 2004

phylogenetic profiles

Korbel et al., Nature Biotechnology, 2004

protein interactions

Jensen & Bork, Science, 2008

genetic interactions

Beyer et al., Nature Reviews Genetics, 2007

gene coexpression

curated knowledge

Letunic & Bork, Trends in Biochemical Sciences, 2008

>10 km

text mining

co-mentioning

NLP
Natural Language Processing

Gene and protein names
Cue words for entity recognition
Verbs for relation extraction

[nxgene The GAL4 gene]

[nxexpr The expression of
[nxgene the cytochrome genes
[nxpg CYC1 and CYC7]]]
is controlled by
[nxpg HAP1]

different sources

different formats

different names

not comparable

variable quality

many parsers

comprehensive lexicon

quality scores

look at the data

von Mering et al., Nucleic Acids Research, 2005

scoring scheme

benchmark

von Mering et al., Nucleic Acids Research, 2005

probabilistic scores

combine scores

Example 2
evidence filters and viewers

highest confidence only

experiments only

evidence viewers

Part 3
analysis of cell-cycle data

gene expression

cell cultures

synchronization

microarrays

time courses

look at the data

Gauthier et al., Nucleic Acids Research, 2007

scoring scheme

benchmark

time of peak expression

protein interactions

temporal network

de Lichtenberg, Jensen et al., Science, 2005

Example 3
a network for my proteins

http://string-db.org

high confidence only

experiments only

network expansion

Part 4
external data

save network

open in Cytoscape

layout

clustering

project data onto network

de Lichtenberg, Jensen et al., Science, 2005

very flexible

lose the STRING interface

payload mechanism

show external data

nodes

edges

hosted on your server

Example 4
my data in STRING

http://cyclebase-string.jensenlab.org

Conclusions

know your question

collect data

look at the data

benchmark

Thank you!

larsjuhljensen

Information integration

Recommended

Biomarker bioinformatics: Network-based candidate prioritization

Biomarker bioinformatics: Network-based candidate prioritization

Biomarker bioinformatics: Network-based candidate prioritizationLars Juhl Jensen

STRING/STITCH tutorial

STRING/STITCH tutorial

STRING/STITCH tutorialbiocs

Large-scale integration of data and text

Large-scale integration of data and text

Large-scale integration of data and textLars Juhl Jensen

STRING: Large-scale data and text mining

STRING: Large-scale data and text mining

STRING: Large-scale data and text miningLars Juhl Jensen

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and textLars Juhl Jensen

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and textLars Juhl Jensen

Protein association networks: Large-scale integration of data and text

Protein association networks: Large-scale integration of data and text

Protein association networks: Large-scale integration of data and textLars Juhl Jensen

STRING - Protein networks from data and text mining

STRING - Protein networks from data and text mining

STRING - Protein networks from data and text miningLars Juhl Jensen

Recommended

Biomarker bioinformatics: Network-based candidate prioritization

Biomarker bioinformatics: Network-based candidate prioritization

Biomarker bioinformatics: Network-based candidate prioritizationLars Juhl Jensen

STRING/STITCH tutorial

STRING/STITCH tutorial

STRING/STITCH tutorialbiocs

Large-scale integration of data and text

Large-scale integration of data and text

Large-scale integration of data and textLars Juhl Jensen

STRING: Large-scale data and text mining

STRING: Large-scale data and text mining

STRING: Large-scale data and text miningLars Juhl Jensen

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and textLars Juhl Jensen

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and textLars Juhl Jensen

Protein association networks: Large-scale integration of data and text

Protein association networks: Large-scale integration of data and text

Protein association networks: Large-scale integration of data and textLars Juhl Jensen

STRING - Protein networks from data and text mining

STRING - Protein networks from data and text mining

STRING - Protein networks from data and text miningLars Juhl Jensen

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and textLars Juhl Jensen

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and textLars Juhl Jensen

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and textLars Juhl Jensen

STRING & related databases: Large-scale integration of heterogeneous data

STRING & related databases: Large-scale integration of heterogeneous data

STRING & related databases: Large-scale integration of heterogeneous dataLars Juhl Jensen

Network biology: Large-scale data and text mining

Network biology: Large-scale data and text mining

Network biology: Large-scale data and text miningLars Juhl Jensen

Network biology - Large-scale integration of data and text

Network biology - Large-scale integration of data and text

Network biology - Large-scale integration of data and textLars Juhl Jensen

Network Biology: A crash course on STRING and Cytoscape

Network Biology: A crash course on STRING and Cytoscape

Network Biology: A crash course on STRING and CytoscapeLars Juhl Jensen

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and textLars Juhl Jensen

Network Biology: Large-scale integration of data and text

Network Biology: Large-scale integration of data and text

Network Biology: Large-scale integration of data and textLars Juhl Jensen

Introduction to STRING

Introduction to STRING

Introduction to STRINGLars Juhl Jensen

Gene Association Networks: Large-scale integration of data and text

Gene Association Networks: Large-scale integration of data and text

Gene Association Networks: Large-scale integration of data and textLars Juhl Jensen

The STRING database and related tools

The STRING database and related tools

The STRING database and related toolsLars Juhl Jensen

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and textLars Juhl Jensen

Making gene networks through data integration

Making gene networks through data integration

Making gene networks through data integrationLars Juhl Jensen

Systems biology: Bioinformatics on complete biological system

Systems biology: Bioinformatics on complete biological system

Systems biology: Bioinformatics on complete biological systemLars Juhl Jensen

STRING - Large-scale integration of data and text

STRING - Large-scale integration of data and text

STRING - Large-scale integration of data and textLars Juhl Jensen

STRING: Protein networks from data and text mining

STRING: Protein networks from data and text mining

STRING: Protein networks from data and text miningLars Juhl Jensen

Large-scale integration of data and text

Large-scale integration of data and text

Large-scale integration of data and textLars Juhl Jensen

Protein association networks with STRING

Protein association networks with STRING

Protein association networks with STRINGLars Juhl Jensen

Text and data integration

Text and data integration

Text and data integrationLars Juhl Jensen

Text miningLars Juhl Jensen

Disease systems biology

Disease systems biology

Disease systems biologyLars Juhl Jensen

More Related Content

What's hot

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and textLars Juhl Jensen

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and textLars Juhl Jensen

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and textLars Juhl Jensen

STRING & related databases: Large-scale integration of heterogeneous data

STRING & related databases: Large-scale integration of heterogeneous data

STRING & related databases: Large-scale integration of heterogeneous dataLars Juhl Jensen

Network biology: Large-scale data and text mining

Network biology: Large-scale data and text mining

Network biology: Large-scale data and text miningLars Juhl Jensen

Network biology - Large-scale integration of data and text

Network biology - Large-scale integration of data and text

Network biology - Large-scale integration of data and textLars Juhl Jensen

Network Biology: A crash course on STRING and Cytoscape

Network Biology: A crash course on STRING and Cytoscape

Network Biology: A crash course on STRING and CytoscapeLars Juhl Jensen

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and textLars Juhl Jensen

Network Biology: Large-scale integration of data and text

Network Biology: Large-scale integration of data and text

Network Biology: Large-scale integration of data and textLars Juhl Jensen

Introduction to STRING

Introduction to STRING

Introduction to STRINGLars Juhl Jensen

Gene Association Networks: Large-scale integration of data and text

Gene Association Networks: Large-scale integration of data and text

Gene Association Networks: Large-scale integration of data and textLars Juhl Jensen

The STRING database and related tools

The STRING database and related tools

The STRING database and related toolsLars Juhl Jensen

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and textLars Juhl Jensen

Making gene networks through data integration

Making gene networks through data integration

Making gene networks through data integrationLars Juhl Jensen

Systems biology: Bioinformatics on complete biological system

Systems biology: Bioinformatics on complete biological system

Systems biology: Bioinformatics on complete biological systemLars Juhl Jensen

STRING - Large-scale integration of data and text

STRING - Large-scale integration of data and text

STRING - Large-scale integration of data and textLars Juhl Jensen

STRING: Protein networks from data and text mining

STRING: Protein networks from data and text mining

STRING: Protein networks from data and text miningLars Juhl Jensen

Large-scale integration of data and text

Large-scale integration of data and text

Large-scale integration of data and textLars Juhl Jensen

Protein association networks with STRING

Protein association networks with STRING

Protein association networks with STRINGLars Juhl Jensen

Text and data integration

Text and data integration

Text and data integrationLars Juhl Jensen

What's hot (20)

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and text

Gene association networks: Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

STRING & related databases: Large-scale integration of heterogeneous data

STRING & related databases: Large-scale integration of heterogeneous data

STRING & related databases: Large-scale integration of heterogeneous data

Network biology: Large-scale data and text mining

Network biology: Large-scale data and text mining

Network biology: Large-scale data and text mining

Network biology - Large-scale integration of data and text

Network biology - Large-scale integration of data and text

Network biology - Large-scale integration of data and text

Network Biology: A crash course on STRING and Cytoscape

Network Biology: A crash course on STRING and Cytoscape

Network Biology: A crash course on STRING and Cytoscape

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Network Biology: Large-scale integration of data and text

Network Biology: Large-scale integration of data and text

Network Biology: Large-scale integration of data and text

Introduction to STRING

Introduction to STRING

Introduction to STRING

Gene Association Networks: Large-scale integration of data and text

Gene Association Networks: Large-scale integration of data and text

Gene Association Networks: Large-scale integration of data and text

The STRING database and related tools

The STRING database and related tools

The STRING database and related tools

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Gene association networks - Large-scale integration of data and text

Making gene networks through data integration

Making gene networks through data integration

Making gene networks through data integration

Systems biology: Bioinformatics on complete biological system

Systems biology: Bioinformatics on complete biological system

Systems biology: Bioinformatics on complete biological system

STRING - Large-scale integration of data and text

STRING - Large-scale integration of data and text

STRING - Large-scale integration of data and text

STRING: Protein networks from data and text mining

STRING: Protein networks from data and text mining

STRING: Protein networks from data and text mining

Large-scale integration of data and text

Large-scale integration of data and text

Large-scale integration of data and text

Protein association networks with STRING

Protein association networks with STRING

Protein association networks with STRING

Text and data integration

Text and data integration

Text and data integration

Viewers also liked

Text miningLars Juhl Jensen

Disease systems biology

Disease systems biology

Disease systems biologyLars Juhl Jensen

Reflect and friends - Tools and resources for mining biomedical text

Reflect and friends - Tools and resources for mining biomedical text

Reflect and friends - Tools and resources for mining biomedical textLars Juhl Jensen

Networks of proteins and diseases

Networks of proteins and diseases

Networks of proteins and diseasesLars Juhl Jensen

Systems biology: Large-scale biomedical data mining

Systems biology: Large-scale biomedical data mining

Systems biology: Large-scale biomedical data miningLars Juhl Jensen

Network biology: Large-scale data integration and text mining

Network biology: Large-scale data integration and text mining

Network biology: Large-scale data integration and text miningLars Juhl Jensen

Text mining and data integration

Text mining and data integration

Text mining and data integrationLars Juhl Jensen

Identification of drug targets from side-effect similarity

Identification of drug targets from side-effect similarity

Identification of drug targets from side-effect similarityLars Juhl Jensen

Viewers also liked (8)

Text mining

Disease systems biology

Disease systems biology

Disease systems biology

Reflect and friends - Tools and resources for mining biomedical text

Reflect and friends - Tools and resources for mining biomedical text

Reflect and friends - Tools and resources for mining biomedical text

Networks of proteins and diseases

Networks of proteins and diseases

Networks of proteins and diseases

Systems biology: Large-scale biomedical data mining

Systems biology: Large-scale biomedical data mining

Systems biology: Large-scale biomedical data mining

Network biology: Large-scale data integration and text mining

Network biology: Large-scale data integration and text mining

Network biology: Large-scale data integration and text mining

Text mining and data integration

Text mining and data integration

Text mining and data integration

Identification of drug targets from side-effect similarity

Identification of drug targets from side-effect similarity

Identification of drug targets from side-effect similarity

Similar to Information integration

Protein interaction networks

Protein interaction networks

Protein interaction networksLars Juhl Jensen

Using networks to derive function

Using networks to derive function

Using networks to derive functionLars Juhl Jensen

Systems biology - Understanding biology at the systems level

Systems biology - Understanding biology at the systems level

Systems biology - Understanding biology at the systems levelLars Juhl Jensen

Data integration - Integration of functional associations using STRING

Data integration - Integration of functional associations using STRING

Data integration - Integration of functional associations using STRINGLars Juhl Jensen

Integration of heterogeneous data

Integration of heterogeneous data

Integration of heterogeneous dataLars Juhl Jensen

Cross-species data integration

Cross-species data integration

Cross-species data integrationLars Juhl Jensen

Data integration and functional association networks

Data integration and functional association networks

Data integration and functional association networksLars Juhl Jensen

Advanced bioinformaticsof proteomics datasets

Advanced bioinformaticsof proteomics datasets

Advanced bioinformaticsof proteomics datasetsLars Juhl Jensen

Network biology: Large-scale integration of data and text

Network biology: Large-scale integration of data and text

Network biology: Large-scale integration of data and textLars Juhl Jensen

The STRING database

The STRING database

The STRING databaseLars Juhl Jensen

STRING: Protein association networks

STRING: Protein association networks

STRING: Protein association networksLars Juhl Jensen

STRING: protein association networks

STRING: protein association networks

STRING: protein association networksLars Juhl Jensen

Network biology: Large-scale integration of data and text

Network biology: Large-scale integration of data and text

Network biology: Large-scale integration of data and textLars Juhl Jensen

Network biology: Large-scale data and text mining

Network biology: Large-scale data and text mining

Network biology: Large-scale data and text miningLars Juhl Jensen

Networks of proteins and diseases

Networks of proteins and diseases

Networks of proteins and diseasesLars Juhl Jensen

Systems biology: Bioinformatics on complete biological systems

Systems biology: Bioinformatics on complete biological systems

Systems biology: Bioinformatics on complete biological systemsLars Juhl Jensen

Integration of heterogeneous data

Integration of heterogeneous data

Integration of heterogeneous dataLars Juhl Jensen

STRING - Modeling of biological systems through cross-species data integ...

STRING - Modeling of biological systems through cross-species data integ...

STRING - Modeling of biological systems through cross-species data integ...Lars Juhl Jensen

Similar to Information integration (18)

Protein interaction networks

Protein interaction networks

Protein interaction networks

Using networks to derive function

Using networks to derive function

Using networks to derive function

Systems biology - Understanding biology at the systems level

Systems biology - Understanding biology at the systems level

Systems biology - Understanding biology at the systems level

Data integration - Integration of functional associations using STRING

Data integration - Integration of functional associations using STRING

Data integration - Integration of functional associations using STRING

Integration of heterogeneous data

Integration of heterogeneous data

Integration of heterogeneous data

Cross-species data integration

Cross-species data integration

Cross-species data integration

Data integration and functional association networks

Data integration and functional association networks

Data integration and functional association networks

Advanced bioinformaticsof proteomics datasets

Advanced bioinformaticsof proteomics datasets

Advanced bioinformaticsof proteomics datasets

Network biology: Large-scale integration of data and text

Network biology: Large-scale integration of data and text

Network biology: Large-scale integration of data and text

The STRING database

The STRING database

The STRING database

STRING: Protein association networks

STRING: Protein association networks

STRING: Protein association networks

STRING: protein association networks

STRING: protein association networks

STRING: protein association networks

Network biology: Large-scale integration of data and text

Network biology: Large-scale integration of data and text

Network biology: Large-scale integration of data and text

Network biology: Large-scale data and text mining

Network biology: Large-scale data and text mining

Network biology: Large-scale data and text mining

Networks of proteins and diseases

Networks of proteins and diseases

Networks of proteins and diseases

Systems biology: Bioinformatics on complete biological systems

Systems biology: Bioinformatics on complete biological systems

Systems biology: Bioinformatics on complete biological systems

Integration of heterogeneous data

Integration of heterogeneous data

Integration of heterogeneous data

STRING - Modeling of biological systems through cross-species data integ...

STRING - Modeling of biological systems through cross-species data integ...

STRING - Modeling of biological systems through cross-species data integ...

More from Lars Juhl Jensen

One tagger, many uses: Illustrating the power of dictionary-based named entit...

One tagger, many uses: Illustrating the power of dictionary-based named entit...

One tagger, many uses: Illustrating the power of dictionary-based named entit...Lars Juhl Jensen

One tagger, many uses: Simple text-mining strategies for biomedicine

One tagger, many uses: Simple text-mining strategies for biomedicine

One tagger, many uses: Simple text-mining strategies for biomedicineLars Juhl Jensen

Extract 2.0: Text-mining-assisted interactive annotation

Extract 2.0: Text-mining-assisted interactive annotation

Extract 2.0: Text-mining-assisted interactive annotationLars Juhl Jensen

Network visualization: A crash course on using Cytoscape

Network visualization: A crash course on using Cytoscape

Network visualization: A crash course on using CytoscapeLars Juhl Jensen

STRING & STITCH: Network integration of heterogeneous data

STRING & STITCH: Network integration of heterogeneous data

STRING & STITCH: Network integration of heterogeneous dataLars Juhl Jensen

Biomedical text mining: Automatic processing of unstructured text

Biomedical text mining: Automatic processing of unstructured text

Biomedical text mining: Automatic processing of unstructured textLars Juhl Jensen

Medical network analysis: Linking diseases and genes through data and text mi...

Medical network analysis: Linking diseases and genes through data and text mi...

Medical network analysis: Linking diseases and genes through data and text mi...Lars Juhl Jensen

Cellular networks

Cellular networks

Cellular networksLars Juhl Jensen

Cellular Network Biology: Large-scale integration of data and text

Cellular Network Biology: Large-scale integration of data and text

Cellular Network Biology: Large-scale integration of data and textLars Juhl Jensen

Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...

Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...

Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...Lars Juhl Jensen

Tagger: Rapid dictionary-based named entity recognition

Tagger: Rapid dictionary-based named entity recognition

Tagger: Rapid dictionary-based named entity recognitionLars Juhl Jensen

Medical text mining: Linking diseases, drugs, and adverse reactions

Medical text mining: Linking diseases, drugs, and adverse reactions

Medical text mining: Linking diseases, drugs, and adverse reactionsLars Juhl Jensen

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactionsLars Juhl Jensen

Cellular Network Biology

Cellular Network Biology

Cellular Network BiologyLars Juhl Jensen

The Art of Counting: Scoring and ranking co-occurrences in literature

The Art of Counting: Scoring and ranking co-occurrences in literature

The Art of Counting: Scoring and ranking co-occurrences in literatureLars Juhl Jensen

Text-mining-based retrieval of protein networks

Text-mining-based retrieval of protein networks

Text-mining-based retrieval of protein networksLars Juhl Jensen

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactionsLars Juhl Jensen

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactionsLars Juhl Jensen

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactionsLars Juhl Jensen

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactionsLars Juhl Jensen

More from Lars Juhl Jensen (20)

One tagger, many uses: Illustrating the power of dictionary-based named entit...

One tagger, many uses: Illustrating the power of dictionary-based named entit...

One tagger, many uses: Illustrating the power of dictionary-based named entit...

One tagger, many uses: Simple text-mining strategies for biomedicine

One tagger, many uses: Simple text-mining strategies for biomedicine

One tagger, many uses: Simple text-mining strategies for biomedicine

Extract 2.0: Text-mining-assisted interactive annotation

Extract 2.0: Text-mining-assisted interactive annotation

Extract 2.0: Text-mining-assisted interactive annotation

Network visualization: A crash course on using Cytoscape

Network visualization: A crash course on using Cytoscape

Network visualization: A crash course on using Cytoscape

STRING & STITCH: Network integration of heterogeneous data

STRING & STITCH: Network integration of heterogeneous data

STRING & STITCH: Network integration of heterogeneous data

Biomedical text mining: Automatic processing of unstructured text

Biomedical text mining: Automatic processing of unstructured text

Biomedical text mining: Automatic processing of unstructured text

Medical network analysis: Linking diseases and genes through data and text mi...

Medical network analysis: Linking diseases and genes through data and text mi...

Medical network analysis: Linking diseases and genes through data and text mi...

Cellular networks

Cellular networks

Cellular networks

Cellular Network Biology: Large-scale integration of data and text

Cellular Network Biology: Large-scale integration of data and text

Cellular Network Biology: Large-scale integration of data and text

Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...

Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...

Statistics on big biomedical data: Methods and pitfalls when analyzing high-t...

Tagger: Rapid dictionary-based named entity recognition

Tagger: Rapid dictionary-based named entity recognition

Tagger: Rapid dictionary-based named entity recognition

Medical text mining: Linking diseases, drugs, and adverse reactions

Medical text mining: Linking diseases, drugs, and adverse reactions

Medical text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Cellular Network Biology

Cellular Network Biology

Cellular Network Biology

The Art of Counting: Scoring and ranking co-occurrences in literature

The Art of Counting: Scoring and ranking co-occurrences in literature

The Art of Counting: Scoring and ranking co-occurrences in literature

Text-mining-based retrieval of protein networks

Text-mining-based retrieval of protein networks

Text-mining-based retrieval of protein networks

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Medical data and text mining: Linking diseases, drugs, and adverse reactions

Recently uploaded

E-Vehicle_Hacking_by_Parul Sharma_null_owasp.pptx

E-Vehicle_Hacking_by_Parul Sharma_null_owasp.pptx

E-Vehicle_Hacking_by_Parul Sharma_null_owasp.pptxnull - The Open Security Community

Science&tech:THE INFORMATION AGE STS.pdf

Science&tech:THE INFORMATION AGE STS.pdf

Science&tech:THE INFORMATION AGE STS.pdfjimielynbastida

My Hashitalk Indonesia April 2024 Presentation

My Hashitalk Indonesia April 2024 Presentation

My Hashitalk Indonesia April 2024 PresentationRidwan Fadjar

Bun (KitWorks Team Study 노별마루 발표 2024.4.22)

Bun (KitWorks Team Study 노별마루 발표 2024.4.22)

Bun (KitWorks Team Study 노별마루 발표 2024.4.22)Wonjun Hwang

Key Features Of Token Development (1).pptx

Key Features Of Token Development (1).pptx

Key Features Of Token Development (1).pptxLBM Solutions

Human Factors of XR: Using Human Factors to Design XR Systems

Human Factors of XR: Using Human Factors to Design XR Systems

Human Factors of XR: Using Human Factors to Design XR SystemsMark Billinghurst

Automating Business Process via MuleSoft Composer | Bangalore MuleSoft Meetup...

Automating Business Process via MuleSoft Composer | Bangalore MuleSoft Meetup...

Automating Business Process via MuleSoft Composer | Bangalore MuleSoft Meetup...shyamraj55

My INSURER PTE LTD - Insurtech Innovation Award 2024

My INSURER PTE LTD - Insurtech Innovation Award 2024

My INSURER PTE LTD - Insurtech Innovation Award 2024The Digital Insurer

"LLMs for Python Engineers: Advanced Data Analysis and Semantic Kernel",Oleks...

"LLMs for Python Engineers: Advanced Data Analysis and Semantic Kernel",Oleks...

"LLMs for Python Engineers: Advanced Data Analysis and Semantic Kernel",Oleks...Fwdays

Dev Dives: Streamline document processing with UiPath Studio Web

Dev Dives: Streamline document processing with UiPath Studio Web

Dev Dives: Streamline document processing with UiPath Studio WebUiPathCommunity

Transcript: New from BookNet Canada for 2024: BNC BiblioShare - Tech Forum 2024

Transcript: New from BookNet Canada for 2024: BNC BiblioShare - Tech Forum 2024

Transcript: New from BookNet Canada for 2024: BNC BiblioShare - Tech Forum 2024BookNet Canada

Hot Sexy call girls in Panjabi Bagh 🔝 9953056974 🔝 Delhi escort Service

Hot Sexy call girls in Panjabi Bagh 🔝 9953056974 🔝 Delhi escort Service

Hot Sexy call girls in Panjabi Bagh 🔝 9953056974 🔝 Delhi escort Service9953056974 Low Rate Call Girls In Saket, Delhi NCR

Install Stable Diffusion in windows machine

Install Stable Diffusion in windows machine

Install Stable Diffusion in windows machinePadma Pradeep

Unleash Your Potential - Namagunga Girls Coding Club

Unleash Your Potential - Namagunga Girls Coding Club

Unleash Your Potential - Namagunga Girls Coding ClubKalema Edgar

AI as an Interface for Commercial Buildings

AI as an Interface for Commercial Buildings

AI as an Interface for Commercial BuildingsMemoori

Tampa BSides - Chef's Tour of Microsoft Security Adoption Framework (SAF)

Tampa BSides - Chef's Tour of Microsoft Security Adoption Framework (SAF)

Tampa BSides - Chef's Tour of Microsoft Security Adoption Framework (SAF)Mark Simos

Connect Wave/ connectwave Pitch Deck Presentation

Connect Wave/ connectwave Pitch Deck Presentation

Connect Wave/ connectwave Pitch Deck PresentationSlibray Presentation

Vertex AI Gemini Prompt Engineering Tips

Vertex AI Gemini Prompt Engineering Tips

Vertex AI Gemini Prompt Engineering TipsMiki Katsuragi

Unraveling Multimodality with Large Language Models.pdf

Unraveling Multimodality with Large Language Models.pdf

Unraveling Multimodality with Large Language Models.pdfAlex Barbosa Coqueiro

costume and set research powerpoint presentation

costume and set research powerpoint presentation

costume and set research powerpoint presentationphoebematthew05

Recently uploaded (20)

E-Vehicle_Hacking_by_Parul Sharma_null_owasp.pptx

E-Vehicle_Hacking_by_Parul Sharma_null_owasp.pptx

E-Vehicle_Hacking_by_Parul Sharma_null_owasp.pptx

Science&tech:THE INFORMATION AGE STS.pdf

Science&tech:THE INFORMATION AGE STS.pdf

Science&tech:THE INFORMATION AGE STS.pdf

My Hashitalk Indonesia April 2024 Presentation

My Hashitalk Indonesia April 2024 Presentation

My Hashitalk Indonesia April 2024 Presentation

Bun (KitWorks Team Study 노별마루 발표 2024.4.22)

Bun (KitWorks Team Study 노별마루 발표 2024.4.22)

Bun (KitWorks Team Study 노별마루 발표 2024.4.22)

Key Features Of Token Development (1).pptx

Key Features Of Token Development (1).pptx

Key Features Of Token Development (1).pptx

Human Factors of XR: Using Human Factors to Design XR Systems

Human Factors of XR: Using Human Factors to Design XR Systems

Human Factors of XR: Using Human Factors to Design XR Systems

Automating Business Process via MuleSoft Composer | Bangalore MuleSoft Meetup...

Automating Business Process via MuleSoft Composer | Bangalore MuleSoft Meetup...

Automating Business Process via MuleSoft Composer | Bangalore MuleSoft Meetup...

My INSURER PTE LTD - Insurtech Innovation Award 2024

My INSURER PTE LTD - Insurtech Innovation Award 2024

My INSURER PTE LTD - Insurtech Innovation Award 2024

"LLMs for Python Engineers: Advanced Data Analysis and Semantic Kernel",Oleks...

"LLMs for Python Engineers: Advanced Data Analysis and Semantic Kernel",Oleks...

"LLMs for Python Engineers: Advanced Data Analysis and Semantic Kernel",Oleks...

Dev Dives: Streamline document processing with UiPath Studio Web

Dev Dives: Streamline document processing with UiPath Studio Web

Dev Dives: Streamline document processing with UiPath Studio Web

Transcript: New from BookNet Canada for 2024: BNC BiblioShare - Tech Forum 2024

Transcript: New from BookNet Canada for 2024: BNC BiblioShare - Tech Forum 2024

Transcript: New from BookNet Canada for 2024: BNC BiblioShare - Tech Forum 2024

Hot Sexy call girls in Panjabi Bagh 🔝 9953056974 🔝 Delhi escort Service

Hot Sexy call girls in Panjabi Bagh 🔝 9953056974 🔝 Delhi escort Service

Hot Sexy call girls in Panjabi Bagh 🔝 9953056974 🔝 Delhi escort Service

Install Stable Diffusion in windows machine

Install Stable Diffusion in windows machine

Install Stable Diffusion in windows machine

Unleash Your Potential - Namagunga Girls Coding Club

Unleash Your Potential - Namagunga Girls Coding Club

Unleash Your Potential - Namagunga Girls Coding Club

AI as an Interface for Commercial Buildings

AI as an Interface for Commercial Buildings

AI as an Interface for Commercial Buildings

Tampa BSides - Chef's Tour of Microsoft Security Adoption Framework (SAF)

Tampa BSides - Chef's Tour of Microsoft Security Adoption Framework (SAF)

Tampa BSides - Chef's Tour of Microsoft Security Adoption Framework (SAF)

Connect Wave/ connectwave Pitch Deck Presentation

Connect Wave/ connectwave Pitch Deck Presentation

Connect Wave/ connectwave Pitch Deck Presentation

Vertex AI Gemini Prompt Engineering Tips

Vertex AI Gemini Prompt Engineering Tips

Vertex AI Gemini Prompt Engineering Tips

Unraveling Multimodality with Large Language Models.pdf

Unraveling Multimodality with Large Language Models.pdf

Unraveling Multimodality with Large Language Models.pdf

costume and set research powerpoint presentation

costume and set research powerpoint presentation

costume and set research powerpoint presentation

Information integration

1. Information integration Lars Juhl Jensen

2.

3.

4.

5.

6. Part 1 the eukaryotic cell cycle

7. essential process

8. grow and divide

11. four phases

15. DNA replication

19. cell division

20.

22. gene expression

23. phosphorylation

24. targeted degradation

25. protein interactions

26. Example 1 my protein and friends

27. http://string-db.org

28. Szklarczyk, Franceschini et al., Nucleic Acids Research, 2011

29.

30.

31. Part 2 association networks

32. guild by association

33.

35. >1100 genomes

36. genomic context

37. gene fusion

38. Korbel et al., Nature Biotechnology, 2004

39. conserved neighborhood

40. Korbel et al., Nature Biotechnology, 2004

41. phylogenetic profiles

42. Korbel et al., Nature Biotechnology, 2004

43. protein interactions

44. Jensen & Bork, Science, 2008

45. genetic interactions

46. Beyer et al., Nature Reviews Genetics, 2007

47. gene coexpression

48.

49. curated knowledge

50. Letunic & Bork, Trends in Biochemical Sciences, 2008

52. text mining

53. co-mentioning

54. NLP Natural Language Processing

55. Gene and protein names Cue words for entity recognition Verbs for relation extraction [nxgene The GAL4 gene] [nxexpr The expression of [nxgene the cytochrome genes [nxpg CYC1 and CYC7]]] is controlled by [nxpg HAP1]

56. different sources

57. different formats

58. different names

59. not comparable

60. variable quality

61. many parsers

62. comprehensive lexicon

63. quality scores

64. look at the data

65. von Mering et al., Nucleic Acids Research, 2005

66. scoring scheme

68. von Mering et al., Nucleic Acids Research, 2005

69. probabilistic scores

70. combine scores

71. Example 2 evidence filters and viewers

72.

73.

74. highest confidence only

75.

76. experiments only

77.

78. evidence viewers

79.

80.

81. Part 3 analysis of cell-cycle data

82. gene expression

83. cell cultures

84. synchronization

85. microarrays

86. time courses

87. look at the data

88. Gauthier et al., Nucleic Acids Research, 2007

89. scoring scheme

91. time of peak expression

92.

93. protein interactions

94. temporal network

95. de Lichtenberg, Jensen et al., Science, 2005

96. Example 3 a network for my proteins

97. http://string-db.org

98.

99.

100. high confidence only

101. experiments only

102.

103. network expansion

104.

105.

106. Part 4 external data

107. save network

108.

109. open in Cytoscape

111. clustering

112. project data onto network

113. de Lichtenberg, Jensen et al., Science, 2005

114. very flexible

115. lose the STRING interface

116. payload mechanism

117. show external data

120. hosted on your server

121. Example 4 my data in STRING

122. http://cyclebase-string.jensenlab.org

123.

124.

125.

126. Conclusions

127. know your question

128. collect data

129. look at the data

131.

132. Thank you!

133. larsjuhljensen