string: large-scale data and text mining

95

STRING Large-scale data and text mining Lars Juhl Jensen

Upload: lars-juhl-jensen

Post on 27-Jun-2015

225 views

Category:

Science

4 download

Report

Download

Tags:

Embed Size (px):

DESCRIPTION

STRING: Large-scale data and text mining

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

a real example

Page 17: STRING: Large-scale data and text mining

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

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

Page 20: STRING: Large-scale data and text mining

Cell

Cellulosomes

Cellulose

Page 21: STRING: Large-scale data and text mining

experimental data

Page 22: STRING: Large-scale data and text mining

gene coexpression

Page 23: STRING: Large-scale data and text mining

Page 24: STRING: Large-scale data and text mining

protein interactions

Page 25: STRING: Large-scale data and text mining

Jensen & Bork, Science, 2008

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 your own datastring-db.org

stitch-db.org

compartments.jensenlab.org

tissues.jensenlab.org

diseases.jensenlab.org

CSE 634 – Data Mining: Text Mining

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

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 and data mining

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

Text Mining for Clementine Improve Insights with Text Mining

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

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,

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

Text Mining with Oracle - Text Mining Summit

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

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

STRING - Protein networks from data and 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

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 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 Classification using String Kernels

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 3/5: String Processing

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

Text mining & Web mining

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

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

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

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

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

មេរៀនទី 08-String and Text

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

STRING Large-scale data and text mining

CS583 – Data Mining and Text Mining

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