wikipathways: how open source and open data can make omics technology more useful

WikiPathways: how open source code and open data

can make omics technology more useful

@Chris_EveloDepartment of Bioinformatics - BiGCaT

Maastricht University

Gerhard Michal 1974

Recon2 a Google map of human metabolism

Collaborating Systems Biology and Metabolomics groups: 2013

http://www.wikipathways.org/index.php/Pathway:WP430

http://www.wikipathways.org/index.php/Pathway:WP1601

http://www.wikipathways.org

• XML format (BioPAX)• RESTful web services• HTML embed code• RDF and SPARQL endpoint

http://www.cytoscape.org

ideassynthes

is

data

• First unknown user (Jan ’08)• First unknown user (Jan ’08)

• Online (Mar ‘07)

Set Early Milestones Success!


400

160

80

20122011

20102007

2005

6,200

3,200

20092008

2006

Number of human pathways

Number of unique human genes

320

240

4,700


2,800

1,400

0

20122011

20102009

2008

Over 1 million pageviews by 280,000 unique visitors

~22%

• First unknown user (Jan ’08)• Models

• Communities

• Tools and pipelines

• Publishing models

Don’t Try to Change the World

Work with (not against) established:

• First unknown user (Jan ’08)

• Tweak established models

• Grow communities

• Change perspectives• everyone is a curator• knowledge should be

open

Go Ahead, Change the World



• Change perspectives


• New attribution systems

• redefine “publication”• redefine “productive”



• Change perspectives

• New attribution systems


• New analysis pipelines• connect with other

community-curated resources

• Subversion source repository

• License!

• Development web site

• Bug tracker

• Mailing lists

• Development and Release plans

• Modular (plugins, OSGi)

Professional Open Source

Key Academic Innovation Partners

04/10/2023

23

Johns Hopkins

Yale

CU Boulder

UNICAMP, Brazil

U of Illinois

Charles U, Czech Republic

U of Kent, UK

U of São Paulo, Brazil

UCSF

Arizona State

U of Michigan

Stanford

UC Berkeley

U of Oviedo, Spain

Tohoku U, Japan

Tsinghua U, China

Southeast U, China

UC Davis

Harvard

U of Maryland UC San Diego

U of Texas

U of Calgary

Baylor U

MIT

Princeton

Hamner Inst.

Maastricht U, NL

Karolinska Inst., Sweden

NIBRT, Ireland

Karlsruhe U, Germany

U of Twente, NL

Technion, Israel

U of Washington

Technical U of Denmark

Monash ULife Sciences

Chemical Analysis

Electronics U of W. Australia

U of Tasmania

Curtin U.

U of Alicante, Spain

U of Pretoria, S. Africa

U of Queensland Macquarie U

U of Sydney

U of Manchester, UK

U Teknologi MARA, Malaysia

Chungnam Nat’l U, Korea

Seoul Nat’l U, Korea

NTU, Singapore

NUS, Singapore

U of Houston

U Tech, Sydney

RMIT U

About 100 active university collaborations annually

Agilent Thought Leader Program

04/10/2023

24

Thought Leader Awards

Promote fundamental advances in life science through contribution to research of thought leaders

• Align societal trends, academic research and rapidly advancing Agilent measurement platforms:

Synthetic Biology, Structural Biology, OMICS & Integrated Biology, in vitro Toxicology, and Environemntal & Food Safety

• Candidates selected based on scientific leadership, productivity, project significance (invitational program)

• High-level executive sponsorship and active support throughout Agilent enable breakthrough research

Early Career Professor Award Establish strong collaborativerelationships with highly promising early career professors

2013 focus: Contributions to cancer diagnostics

TL Networkhttp://www.agilent.com/univ_relation/TLP/index.shtml

LC/MSGC/MS

Microarrays BiologicalPathways

MassHunter Qual/QuantChemStation AMDIS

Feature Extraction GeneSpring Platform

Agilent Integrated Biology Workflows

Alignment to Reference Genome

NGS

GeneSpring

Agilent’s Platform for Multi-Omics Data Analysis

GeneSpring modules

MPP (Mass Profiler Pro) Proteomics Metabolomics

NGS (Next-Gen Sequencing) SureSelect Target Enrichment Whole Genome Sequencing

PA (Pathway Analysis)

GX (Gene Expression) mRNA, miRNA, Exon arrays GWAS, CNV via SNP arrays

GeneSpring modules

GX mRNAmicroRNAQPCRAlternative SplicingGWAS & CNV via SNP arrays




GX (Gene Expression)

GeneSpring modules

NGS SureSelect Target Enrichment Whole Genome Sequencing DNA-Seq RNA-SeqMethyl-SeqChIP-Seqsmall RNA-Seq





NGS Analysis Workflow: 1. Align data 2. Load BAM/SAM into GS NGS3. Measure Gene Expression, Find variants, methyl calls4. Biological Contextualization (Integrated Genomics, GO, Pathways)

GeneSpring modules

MPP • Import, store, and visualize Agilent

Metabolomics & Proteomics data (LC/MS, GC/MS)

• Generic file import• Statistical analysis• ID Browser for compound identification





GeneSpring modules

PA Multi-Omic AnalysisCanonical PathwaysNetwork Discovery





Pathway Architect • Map and visualize data from one or two types of –omic data on pathways

• Search, browse and filter pathways

Supports pathways from:

•WikiPathways

•BioCyc

•Supported pathway formats

•BioPAX 3 – Pathway Commons, Reactome,

NCI Nature Pathway

•GPML – PathVisio –custom drawing

Export compound list from pathways

Metabolite Data Overlay

List of all pathway entities, dynamically linked to pathway selection

Genomics and Metabolomics data overlay on Tryptophan Metabolism WikiPathway

metabolites proteins

Genomics and Proteomics data overlay on Proteasome Degradation WikiPathway

Genomics Proteomics and Genomics Proteomics

Analysis with WikiPathways in Pathway Architect

Import of WikiPathways

Select WikiPathways for analysis

View overlaid data on

WikiPathways

Examine Data And Export for Next Experiment

Export Pathway Entities

Examine Experimental

Data

Pathway-Directed Experiment Creation

Propose new experiments based on pathway analysis

• Re-examine acquired untargeted metabolomics data based on pathway analysis

• Design new experiments (metabolite, protein or genes) based on pathway results interpretation

PCDL

eArray

Spectrum Mill

Build custom metabolite database

Targeted MS/MS

Custom microarray or NGS design

Typical workflow used for identification of a relevant pathway using GeneSpring

Identification of differential expression

Statistical analysis and filtering

Curated pathway analysis using Wikipathways

Network analysis using NLP to identify

interaction of pathways

Identification of Candidate Genes

Step 1) Identification of differentially expressed genes via hierarchical cluster analysis

Step 2) Volcano plot of showing significantly differentially expressed between two conditions

From Differential Expression to Pathways

Step 3) Significantly changed pathways in Müller cells identified

using pathway analysis in GeneSpring

Step 4) The Protein-Protein Interactions analysis was further performed to identify the direct interaction of these genes products in GeneSpring

Pathway analysis showed significant changes in MAPK signaling at both conditions. Network analysis shows interaction of MAPK with other gene products.Compare network analysis/extension in Cytoscape.

Combine further with

Open Knowledgee.g. IMI semantic web project Open PHACTSPathway content and extension

Open Datae.g. ISAtab based study capturingin phenotype database (dbNP)pathway analysis and profiling

RDF 3

Nanopub

Data 1

RDF 1

Descriptor

Data 2

RDF 2

Descriptor

Data 3

Descriptor

RDF 4

Nanopub

Data 4

Descriptor

RDF Data Cache

Semantic Data Workflow Engine

SparqlWeb Service API WebServices

OPS GUIOPS FrameworkArchitecture. Dec 2011

App Framework

Identity & Vocabulary

Management

Note: Things may change!

Public Vocabularies

Chemistry Normalisation &

Registration

OPS Data Model

Feed in WikiPathwaysrelationships, use BioPAXto create the RDF

Faculty of Health, Medicine and Life Sciences

Data capturing

Using ISA to connect to the rest of world

customprogramscustom

programscustom

dbscustom

dbs

GSCF

TemplatesTemplatesTemplatesTemplatesTemplatesTemplates

GroupsGroups

Protocols

Protocols

SubjectsSubjects

SamplesSamples

EventsEvents

AssaysAssays

NCBOOntologies

Data im

portxls, cvs, text

Molgenis EBIrepository

customdbs

Output xls ISAtab

API

customprograms

web interface

Generic Study Capture FrameworkData input / output

Faculty of Health, Medicine and Life Sciences

GSCF

TemplatesTemplatesTemplatesTemplatesTemplatesTemplates

GroupsGroups

Protocols

Protocols

Subjects

Subjects

Samples

Samples

EventsEvents

dbNP Architecture

AssaysAssays

Web user interface

Query module

Structured querying

Structured querying

Full-text queryingFull-text querying

Profile-based analysis

Profile-based analysis

Study comparison

Study comparison

Pa

thw

ays, G

O, m

eta

bo

lite p

rofile

s

Simple Assay moduleBody weight, BMI, etc.

Epigenetics module

Transcriptomics module

Raw data Nimblegen Illumina

Resulting Genome Feature data

Clean CPG island

data

Raw data cell files

Result datap-valuesz-values

Clean datagene

expression

Use PathVisioRPC to use WikiPathways content

Carlos BellCarroll Gipson

Jill MartinKevin BelangerDaniel Campos

Sarah MorningstarHelen Hayes

Franco B. MuellerAlfred Mohamed

ChrisCharles

Ewan Daviswiki_user:38adeliacurryy

Egon WillighagenDeanne Taylor

Bjoern OestRon Arnold

William HicksBill Roberts

James CarlsonFelix Jensen

Homer PhillipsBetty Grosso

Ezer Serrato Qui√±onesErnestina Phillips

Angelbridgette loerte

jasonCarlos Borroto

Jackson GirdlestoneJulia E. Torres

Libby RemlingerElizebeth Espinosa

Emma HalfeyNell Yu

LessMomeyThambaru Wijesekara

Barbar HuieJeremy Slivnick

SailendraBaris

Federica EduatiStephen Houchens

Kerri MoronYuette BealeEmilio GordyJayson BrazilVeola Celaya

Dilshan SumeshkaJude WheelerTyrone Rey

Jacquiline FlorezLarry Parnell

Teresa RzezniczakMagali JaillardPierre NordeenKurt MccrossenHeidi Sheneman

Hester Stekelenburgjun ding

vivivan1988Madhan

Paul Davisvivian1988

Sherlynholiday gclub

Ken YanoBahar Taneri

Alexis Lefebvrefrances

ericwexlerBBQ

James BjorkOG

Babiker Malik OsmanJohn Schmidt

David Winsemiusxiao xiao

Claudio Villanueva Ph.D.Scott Tyler

xuningJuan Diego Rojas

Harm Nijveenanirab naraemily jolly

Iyana Brownemily jollyKathy IveyMary Johnemily jollychristi lea

Danielle Cristina de AlmeidaKenny Wu

Adrien Defayjerome compain

Jenifer Laragideon wackers

GraceWei Xu

muhtadiDror Hilman

LogeayMaya Fox

sdfsaHuashi Ding

pradeep kumar sreenivasaiahYesim Aydin Son

emily jollyMamajasia928RafaelHinkel

chris gillRachel

Jyoti SharmaKaylee

Dr. Renu GoelAlexander

MateuszKasperek112Freya CrawfordJames WilliamsByron CabreraArthur Cromer

Christopher NeelyDanae Harrell

Tawana EcksteinFrank HyltonDavid KempJoel Smith

Amber RichardsJesus CarlsonMike Carter

MmaarrccpPopeeFrancesco Chemello

Frank Frey

jiang liulove

Zephyr L√≥pez CervillaSudarsanareddy Lokireddy

ÊùéÈöÜJan Krumeich

Maartje LevelsKira FischerDavid Chen

wyq012zy123211897Lucia Ribeiro

Ahmed G. A. AliVictoria

Johann RipfelAshish

Abhishekmezhoud

karim mezhoudErica L. McDermott

luckyzanoSharona Elgavish

Justin PreeceDave Sause

KHALID RASHIDFuat Kurbanov

Madhu NandakumarFerry Jagers

JT. SaitoMark Scott

TzvetanGregory Tombline

Elke DorenbosCarine Oliveira

Glenda Nicioli da Silvavf

Nikhil BhatlaSabine Daemen

Clemens WittwehrIssam El Naqa

Cory BatenchukDe-Cheng Chao

Sara Ibrahimabhishek

TicamufiquJon

LiamFelix R√ºckert

Maria Pires PachecoRay Andrews II

ramesh airah mae

Lucas SmithNels Nelson

EricZsombor Sz≈ëke-Kov√°cs

Anna WieseYasodha

R. NiemansFrederic Schaper

Rianne FijtenMisha Vrolijk

Ferbercamiel hoogendoorn

bart smeetsValin

Carlos J Pirola

Giovanni Dall'OlioStan Gaj

Dexter DuncanLaura van Zon

Lorraine Brennanzhongyuliu

Paolo RomanoRuke Achoja

Neil SwainstonBadrul Yahaya

Doug HoweWilfred J. Poppinga

Fouad Janatjinggao

Bj√∂rn JohanssonSumihiro

mauro palaSD Englert

sdsadfkatal

Anita BandrowskiRobinbvcx

Andrew Stubbsfdssad

Damariz RiveroSudeshna Das

Jason Rosenzweigfsdfsadfghgfgdewr

Rudolf BlackDaniel Wuttke

Arunweb uggshoeKeith Wagner

chun chentesty

Lou ShaokeHisham EldaiPiet MolenaarNicolas DAVID

MatthewCaroline Miller

AMC Human GeneticsDavid Chen

KarinLieneke SteeghsPatrick KuijpersLoes Jeurissen

pSabrinatommy

Thomas TheelenJohanna

Anne DirkseMichael Rutjens

Samuel SklarLuis

Mettu S Reddywangpeng

Essam SharafDinesh Barupalwangya nqiuChancy Lim

Madeline KoshoPavel Krecek

Jim KaputBrian Caliando

Benjamin SchillerEmily Fox

Theresa BerensSimon D√ºningTrygve BakkenMarc Gillespie

RobIliana Campillo SachMalcolm Campbell

Georg W. OttoJoerg Bernhardt

Kellie SimsstephenPaul Katz

SLEric StephanCalvin Chan

Yannick Le PriolJanet HigginsClaude Aflalo

PolinaAxel Schwekendiek

Judith M. BoerchendijunRithyaga

vlad ionescuShamith Samarajiwa

JordanChristopher Szeto

An LebacqKatrin SameithVincent Sluijter

Martijn van der BruggenFred Opperdoeshollandorange

Van Anh Huynh-ThuAntony Le Bechec

Hans RoubosKanda Nivesanond

Bertrand De MeulderCaroline Mrejen

Justin Elserpriya ranjan

EamonnKristina

Neerincx APankaj Jaiswal

Philip ZimmermannKevin HermansJonas HummelRalph StrausDavid Theres

NatalieJelena

Charly Johnpalitha dharmawrdhana

Eric H.HarleyJohn W. NewmanLuigi MaioranaLope A. Florez

Robin HawJason Park

Sergey Dmitrievliaoyaojun

Nattha Wannissorn

Thomas KelderMartijn van IerselKristina HanspersMartina Kutmon

Andra WaagmeesterChris Evelo

Bruce Conklin

Susan CoortNathan

SalomonisNick

SantistevanMaintenance

botMichiel

AdriaensKamesh JEd HsiaoNathan J Bowenanne

michielsenmark van grinsven

RishiMiranda Stobbe

Dilyara Yanbaeva

Sander OuburgFrank

DennissenTos TJM

BerendschotAntje Weseler

willemNoortje van der

VorstmitkoMartin

HaagmansAxel Weber

PrabahtGabby KrensPatrick AhlesLars Eijssen

IvarsBen van OmmenSuzan

WopereisHubert Hug

Luna De FerrariRobert

MuetzelfeldtMichael Gribskov

Carsten J√§ckelJildau

BouwmanDan Bolser

Alipi NaydenovBrent Derry

Michal Galdzicki

Julian PlanaDan Fornika

Yang AnTest User Account

Satya MishraAndrew Gibson

Derek N Robertson

Frank Kolakowski

Mark van der GiezenCannin

Markus HoferSuheeta Roy

Hunter Richards

Jesse PaquetteThaddeus Allen

Hee Jung Chung

Samantha Cooper

Matthias Wabljalyyu

Eva SamalWard

CunninghamPieter

GoossensGR Oliver

Adrian Contreras

wikipathways.org

Acknowledgements

nrnb.org

wikipathways: how open source and open data can make omics technology more useful

Technology

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