Upload File

string large-scale data and text mining

95
STRING Large-scale data and text mining Lars Juhl Jensen

Upload: brandon-luby

Post on 04-Jan-2016

24 views

Category:

Documents


0 download

Report

Tags:

DESCRIPTION

STRING Large-scale data and text mining. Lars Juhl Jensen. association networks. guilt by association. biological systems. protein networks. STRING. 1100+ genomes. computational predictions. gene fusion. Korbel et al., Nature Biotechnology , 2004. gene neighborhood. - PowerPoint PPT Presentation

TRANSCRIPT

Page 1: STRING Large-scale data and text mining

STRINGLarge-scale data and text

mining

Lars Juhl Jensen

Page 2: STRING Large-scale data and text mining

association networks

Page 3: STRING Large-scale data and text mining

guilt by association

Page 4: STRING Large-scale data and text mining
Page 5: STRING Large-scale data and text mining

biological systems

Page 6: STRING Large-scale data and text mining

protein networks

Page 7: STRING Large-scale data and text mining

STRING

Page 8: STRING Large-scale data and text mining

1100+ genomes

Page 9: STRING Large-scale data and text mining

computational predictions

Page 10: STRING Large-scale data and text mining

gene fusion

Page 11: STRING Large-scale data and text mining

Korbel et al., Nature Biotechnology, 2004

Page 12: STRING Large-scale data and text mining

gene neighborhood

Page 13: STRING Large-scale data and text mining

Korbel et al., Nature Biotechnology, 2004

Page 14: STRING Large-scale data and text mining

phylogenetic profiles

Page 15: STRING Large-scale data and text mining

Korbel et al., Nature Biotechnology, 2004

Page 16: STRING Large-scale data and text mining

experimental data

Page 17: STRING Large-scale data and text mining

gene coexpression

Page 18: STRING Large-scale data and text mining
Page 19: STRING Large-scale data and text mining

protein interactions

Page 20: STRING Large-scale data and text mining

Jensen & Bork, Science, 2008

Page 21: STRING Large-scale data and text mining

a real example

Page 22: STRING Large-scale data and text mining
Page 23: STRING Large-scale data and text mining
Page 24: STRING Large-scale data and text mining
Page 25: STRING Large-scale data and text mining

Cell

Cellulosomes

Cellulose

Page 26: STRING Large-scale data and text mining

curated knowledge

Page 27: STRING Large-scale data and text mining

complexes

Page 28: STRING Large-scale data and text mining

pathways

Page 29: STRING Large-scale data and text mining

Letunic & Bork, Trends in Biochemical Sciences, 2008

Page 30: STRING Large-scale data and text mining

many databases

Page 31: STRING Large-scale data and text mining

different formats

Page 32: STRING Large-scale data and text mining

different identifiers

Page 33: STRING Large-scale data and text mining

variable quality

Page 34: STRING Large-scale data and text mining

not comparable

Page 35: STRING Large-scale data and text mining

not same species

Page 36: STRING Large-scale data and text mining

hard work

Page 37: STRING Large-scale data and text mining

(Ph.D. students)

Page 38: STRING Large-scale data and text mining

common identifiers

Page 39: STRING Large-scale data and text mining

quality scores

Page 40: STRING Large-scale data and text mining

von Mering et al., Nucleic Acids Research, 2005

Page 41: STRING Large-scale data and text mining

score calibration

Page 42: STRING Large-scale data and text mining

von Mering et al., Nucleic Acids Research, 2005

Page 43: STRING Large-scale data and text mining

homology-based transfer

Page 44: STRING Large-scale data and text mining

Franceschini et al., Nucleic Acids Research, 2013

Page 45: STRING Large-scale data and text mining

missing most of the data

Page 46: STRING Large-scale data and text mining

text mining

Page 47: STRING Large-scale data and text mining

>10 km

Page 48: STRING Large-scale data and text mining

too much to read

Page 49: STRING Large-scale data and text mining

computer

Page 50: STRING Large-scale data and text mining

comprehensive lexicon

Page 51: STRING Large-scale data and text mining

CDC2

Page 52: STRING Large-scale data and text mining

cyclin dependent kinase 1

Page 53: STRING Large-scale data and text mining

expansion rules

Page 54: STRING Large-scale data and text mining

hCdc2

Page 55: STRING Large-scale data and text mining

CDC2

Page 56: STRING Large-scale data and text mining

flexible matching

Page 57: STRING Large-scale data and text mining

cyclin-dependent kinase 1

Page 58: STRING Large-scale data and text mining

cyclin dependent kinase 1

Page 59: STRING Large-scale data and text mining

“black list”

Page 60: STRING Large-scale data and text mining

SDS

Page 61: STRING Large-scale data and text mining

co-mentioning

Page 62: STRING Large-scale data and text mining

counting

Page 63: STRING Large-scale data and text mining

within documents

Page 64: STRING Large-scale data and text mining

within paragraphs

Page 65: STRING Large-scale data and text mining

within sentences

Page 66: STRING Large-scale data and text mining

natural language processing

Page 67: STRING Large-scale data and text mining

Gene and protein namesCue words for entity recognitionVerbs for relation extraction

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

Page 68: STRING Large-scale data and text mining

text corpus

Page 69: STRING Large-scale data and text mining

~2 million full-text articles

Page 70: STRING Large-scale data and text mining

~22 million abstracts

Page 71: STRING Large-scale data and text mining

Exercise 1Go to http://string-db.org

Query for Mt H37Rv adhD

(Rv3086)

Change between different

views

Check evidence for adhD–lipR

link

Extent network to 50

interactors

Page 72: STRING Large-scale data and text mining
Page 73: STRING Large-scale data and text mining
Page 74: STRING Large-scale data and text mining

Exercise 2Go to the paper PMC2995261

Extract the protein names in

table 1

Create STRING network of

them

Change to “advanced” mode

Analyze for clusters and

enrichment

Page 75: STRING Large-scale data and text mining

multi-page tables

Page 76: STRING Large-scale data and text mining

related resources

Page 77: STRING Large-scale data and text mining

general approach

Page 78: STRING Large-scale data and text mining

curated knowledge

Page 79: STRING Large-scale data and text mining

experimental data

Page 80: STRING Large-scale data and text mining

text mining

Page 81: STRING Large-scale data and text mining

computational predictions

Page 82: STRING Large-scale data and text mining

common identifiers

Page 83: STRING Large-scale data and text mining

quality scores

Page 84: STRING Large-scale data and text mining

score calibration

Page 85: STRING Large-scale data and text mining

visualization

Page 86: STRING Large-scale data and text mining

protein networks

Page 87: STRING Large-scale data and text mining

string-db.org

Page 88: STRING Large-scale data and text mining

chemical networks

Page 89: STRING Large-scale data and text mining

stitch-db.org

Page 90: STRING Large-scale data and text mining

subcellular localization

Page 91: STRING Large-scale data and text mining

compartments.jensenlab.org

Page 92: STRING Large-scale data and text mining

tissue expression

Page 93: STRING Large-scale data and text mining

tissues.jensenlab.org

Page 94: STRING Large-scale data and text mining

disease associations

Page 95: STRING Large-scale data and text mining

Work on own datastring-db.org

stitch-db.org

compartments.jensenlab.org

tissues.jensenlab.org

diseases.jensenlab.org


Introduction to Text Mining - uni-paderborn.de...Introduction to Text Mining Part VII: Text Mining using Clustering Henning Wachsmuth Text Mining VII Text Mining using Clustering ©Wachsmuth

Text Mining Webinar - KNIME€¦ · Text Mining Webinar The Textprocessing Extension Rosaria Silipo and Kilian Thiel. KNIME Text Mining Webinar 2 Agenda ... Text Mining Workflow Create

Introduction to Text Mining · Introduction to Text Mining Part V: Text Mining using Grammars Henning Wachsmuth Text Mining V Text Mining using Grammars ©Wachsmuth 2018 1

Text Classification using String Kernelspapers.nips.cc/paper/1869-text-classification-using-string-kernels.pdf · Text Classification using String Kernels HUlna Lodhi John Shawe-Taylor

Introduction to Text Mining - en.cs.uni-paderborn.de · Introduction to Text Mining Part VIII: Text Mining using Classification and Regression Henning Wachsmuth Text Mining VIII

Your Database Can Do Complex String Manipulation Too!Your Database Can Do Complex String Manipulation Too! ... Big Data text mining looking for valuable nuggets ! not so easy requires

Text mining & Web mining

Text Mining 3/5: String Processing

Text Mining for Clementine Improve Insights with Text Mining

Text Mining with Oracle - Text Mining Summit

Chapter 5: Text and Web Mining. Learning Objectives Describe text mining and understand the need for text mining Differentiate between text mining, Web

Introduction to Text Mining and SAS Text Minersupport.sas.com/publishing/pubcat/chaps/59410.pdf · Introduction to Text Mining and SAS Text Miner Tips for Text Mining 3 The Text Mining

Historical Text Mining Historical Text Mining, and Historical Text Mining…ucrel.lancs.ac.uk/events/htm06/RobSandersonHTM06.pdf ·  · 2006-08-30Historical Text Mining Historical

Text Mining Text Classification Text ClusteringText Mining Text Classification Text Clustering 2004. 11

Text Classification using String Kernels

CSE 634 – Data Mining: Text Mining · Text Mining vs. • Data Mining – In Text Mining, patterns are extracted from natural language text rather than databases. • Web Mining

STRING: Large-scale data and text mining

មេរៀនទី 08-String and Text

A Brief Survey of Text Mining · Text Mining = Text Data Mining. Text mining can be also defined — similar to data mining — as the application of algorithms and methods from

Text mining and data mining

Information Retrieval & Text Mining - Intranet DEIBhome.deib.polimi.it/.../DMTM/DMTM1112_TextMining.pdf · 2012-06-13 · Information Retrieval & Text Mining Data Mining and Text

Text Mining Medline - Oracle€¦ · Data MiningData mining Text Mining Spectrum Data Mining Chemical/sequence Data Model. Title: Text Mining Medline Author: user Created Date: 7/27/2004

CSE 634 – Data Mining: Text Mining

Mining Unstructured Data (Text Data Mining) - Chapters Site IIA Nov5...Mining Unstructured Data (Text Data Mining) ... Text Mining tools and tips for beginning to use text ... free

Introduction to Text Mining - uni-paderborn.de · Introduction to Text Mining Part VII: Text Mining using Similarities and Clustering Henning Wachsmuth Text Mining VII Text Mining

Data Mining in Bioinformatics Day 9: String & Text Mining in … · Karsten Borgwardt: Data Mining in Bioinformatics, Page 9 General idea Combine HMMs and SVMs for sequence classification

STRING KERNEL TESTING ACCELERATION USING MICRON S … · Motivation 3 • String Kernel (SK) is a widely used kernel in machine learning and text mining • Fast processing is required,

CS583 – Data Mining and Text Mining

Text mining

Introduction to Text Mining - EDBT 2006 · Text Mining Text Mining (Def. Wikipedia) Text mining, also known as intelligent text analysis, text data mining or knowledge-discovery in

Mining Text Using Keyword Distributions - Hebrew …pluto.huji.ac.il/~rfeldman/papers/feldmanHirsh.pdfKeywords: data mining, text mining, text categorization, distribution comparison,

Web Mining & Text Mining

Text Mining Infrastructure in R - University of Idahostevel/517/Text Mining Infrastructure in R.pdf4 Text Mining Infrastructure in R an established text mining framework with architecture

Text Mining

STRING - Protein networks from data and text mining