COMBINE (archive) meta data

SYSTEMS BIOLOGY

BIOINFORMATICS

ROSTOCKS E Ssimulation experiment management system

COMBINE (archive) meta data

MARTIN SCHARM1

1Department of Systems Biology & Bioinformatics, University of Rostock2Department of Information Management, University of Manchester

http://sems.uni-rostock.de

COMBINE 2015,Salt Lake City, Utah, US

May, 2015 COMBINE (archive) meta data | Martin Scharm 1

http://www.sbi.uni-rostock.de/team/single/martin-scharm/

http://sems.uni-rostock.de


The COMBINE archivesharing reproducible research results

TM

COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project.Bergmann et. al., BMC Systems Biology (2014)



The COMBINE archiveis already being used

internet

internet

SEARCHubiquitin

internet

RESULTSEXPORT

EXPORT

EXPORT

EXPORT

Query databasefor annotations, persons,simulation descriptions

Retrieve informationabout models, simulations,figures, documentation

Export simulation studyas COMBINE archive

Download archiveand open the studywith your favouritesimulation tool

Open archive in CATto modify its contents andto share it with others

internet

API Commincationsenrich your studieswith simulation results

Simulate a Studywith just a single click

Extracting reproducible simulation studies from model repositories using the CombineArchive Toolkit.Scharm et. al., DM4LS @ BTW 2015, Hamburg, GER



The COMBINE archiveall singing, all dancing

The CombineArchiveWeb Application - A Web-based Tool to Handle Files Associated with Modelling Results.Scharm et. al., SWAT4LS 2014, Berlin, GER

Find the archive on GitHub:github.com/SemsProject/CombineArchiveShowCase


https://github.com/SemsProject/CombineArchiveShowCase


Meta DataC

OM

BIN

E a

rchi

ve

BIOMD0000000144.xmldc:creator=[[email protected],[email protected],[email protected]]dcterms:created=[6/8/2007, 12:29:58 AM]dcterms:modified=[3/27/2008, 5:00:00 PM] [8/20/2008, 4:00:00 PM] [12/2/2008, 4:00:00 PM] [3/24/2009, 5:00:00 PM] [9/1/2009, 4:00:00 PM] [1/25/2010, 4:00:00 PM] [9/29/2010, 4:00:00 PM] [4/14/2011, 4:00:00 PM] [2/7/2012, 4:00:00 PM] [5/19/2012, 4:00:00 PM] [7/5/2012, 8:48:32 AM] [8/10/2012, 4:00:00 PM] [12/11/2012, 4:00:00 PM] dcterms:description="Model encoded in SBML as described in /documentation/Calzone2007.pdf . This model was downloaded from the BioModels Database Jun 11th, 2015. Modification times were taken from the model code and enriched by comparing all releases of the BioModels Database."

Calzone2007-simulation-figure-1B.xmldc:creator=[[email protected]]dcterms:created=[6/11/2015, 4:58:55 AM]dcterms:modified=[6/11/2015, 4:58:55 AM] [6/11/2015, 5:16:25 AM]dcterms:description="Simulation description adapted from /experiment/Calzone2007-simulation-all-figures.xml . This SED-ML script reproduces Figure 1B of the article /documentation/Calzone2007.pdf ."

Fig1B-bottom-webtools.pngdc:creator=[[email protected]]dcterms:created=[6/11/2015, 5:10:05 AM]dcterms:modified=[6/11/2015, 5:10:05 AM]dcterms:description="Simulation result obtained by executing the SED-ML script /experiment/Calzone2007-simulation-figure-1B.xml using the SED-ML Web Tools."



Meta Datais actually very limited

CO

MB

INE

arc

hive

BIOMD0000000144.xmldc:creator=[[email protected],[email protected],[email protected]]dcterms:created=[6/8/2007, 12:29:58 AM]dcterms:modified=[3/27/2008, 5:00:00 PM] [8/20/2008, 4:00:00 PM] [12/2/2008, 4:00:00 PM] [3/24/2009, 5:00:00 PM] [9/1/2009, 4:00:00 PM] [1/25/2010, 4:00:00 PM] [9/29/2010, 4:00:00 PM] [4/14/2011, 4:00:00 PM] [2/7/2012, 4:00:00 PM] [5/19/2012, 4:00:00 PM] [7/5/2012, 8:48:32 AM] [8/10/2012, 4:00:00 PM] [12/11/2012, 4:00:00 PM] dcterms:description="Model encoded in SBML as described in /documentation/Calzone2007.pdf . This model was downloaded from the BioModels Database Jun 11th, 2015. Modification times were taken from the model code and enriched by comparing all releases of the BioModels Database."

Calzone2007-simulation-figure-1B.xmldc:creator=[[email protected]]dcterms:created=[6/11/2015, 4:58:55 AM]dcterms:modified=[6/11/2015, 4:58:55 AM] [6/11/2015, 5:16:25 AM]dcterms:description="Simulation description adapted from /experiment/Calzone2007-simulation-all-figures.xml . This SED-ML script reproduces Figure 1B of the article /documentation/Calzone2007.pdf ."

Fig1B-bottom-webtools.pngdc:creator=[[email protected]]dcterms:created=[6/11/2015, 5:10:05 AM]dcterms:modified=[6/11/2015, 5:10:05 AM]dcterms:description="Simulation result obtained by executing the SED-ML script /experiment/Calzone2007-simulation-figure-1B.xml using the SED-ML Web Tools."

What happend?

Where does it come from??

Did they all really create the model?



Meta Datais based on SBML meta



Making use of other ontologiesextending the current standard

PROV

used

endedAtTime

wasAssociatedWith

actedOnBehalfOf

wasGeneratedBy

wasAttributedTo

wasDerivedFrom

wasInformedBy

Activity

Entity

Agent

xsd:dateTime

startedAtTime

xsd:dateTime




PROV

simulateModelWithSwt

/model/BIOMD0000000144.xml

prov:used prov:qualifiedAssociation

martin

prov:associatedWith

type prov:Activity

/experiment/Calzone2007-simulation-figure-1B.xml

prov:hadPlan

WebTools

prov:agent

http://orcid.org/0000-0003-4519-7030

prov:wasRevisionOf

http://binfalse.de

foaf:homepage

type prov:Persontype prov:Agenttype foaf:Persontype dc:Agentfoaf:gender malefoaf:name Martin Scharmfoaf:jabberID [email protected]:familyName Scharmfoaf:lastName Scharmfoaf:givenName Martinfoaf:mbox mailto:[email protected]

/result/Fig1B-bottom-webtools.svg

prov:wasGeneratedBy

type prov:Entity

type prov:Entitytype prov:Plandc:description simulation description to reproduce fig 1B

type prov:Entity

/result/Fig1B-top-webtools.svg

prov:wasGeneratedBy

type prov:Entity

type prov:SoftwareAgentfoaf:name SED-ML WebTool




PROV

PAV hanne

type dc:Agenttype foaf:Persontype prov:Persontype prov:Agentfoaf:gender femalerdfs:label Hanne Nielsenfoaf:familyName Nielsenfoaf:givenName Hannefoaf:mbox mailto:[email protected]

/model/calzone_thieffry_tyson_novak_2007.cellml

http://models.cellml.org/[..]/calzone_thieffry_tyson_novak_2007.cellml

pav:retrievedFrom

type prov:Entitypav:createdOn 2009-02-18 11:19:58Zpav:retrievedOn 2015-04-07 13:18:50

/model/calzone_2007.svg

pav:createdBy foaf:depicts

http://models.cellml.org/[..]/calzone_2007.svg

pav:retrievedFrom

type prov:Entitypav:createdOn 2009-10-27 00:37:35pav:retrievedOn 2015-04-07 13:18:50

/model/calzone_2007-in-red.svg

pav:previousVersion

type prov:Entity




PROV

PAV

ebi

http://ebi.ac.uk/

foaf:homepage

type prov:Organizationtype prov:Agentfoaf:name EMBL EBI

lenover

prov:actedOnBehalfOf

type dc:Agenttype foaf:Persontype prov:Persontype prov:Agentfoaf:lastName Le Novèrefoaf:givenName nicolasfoaf:mbox mailto:[email protected]


pav:curatedBy

http://identifiers.org/biomodels.db/MODEL1509031628

prov:wasDerivedFrom

type prov:Entity




PROV

PAV

ORE

/documentation/Calzone2007-supplementary-material.pdf

http://europepmc.org/[..]/msb4100171-s1.pdf

pav:retrievedFrom

type prov:Entitypav:retrievedOn 2015-06-11 00:00:00

/documentation/Calzone2007.pdf

http://europepmc.org/[..]/ptpmcrender.fcgi

pav:retrievedFrom

type prov:Entitypav:retrievedOn 2015-06-11 00:00:00

http://identifiers.org/pubmed/17667953

ore:aggregatesore:aggregates

calzone

dcterms:creator

type ore:Aggregationdc:title Dynamical modeling of syncytial mitotic cycles in Drosophila embryosdcterms:created 2007-01-08 00:00:00

type prov:Agent




PROV

PAV

ORE

NEPOMUK/experiment/Calzone2007-simulation-figure-1B.xml


nie:depends

type prov:Entity

type prov:Entitytype nie:DataObject



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COMBINE (archive) meta data

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