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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
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)
May, 2015 COMBINE (archive) meta data | Martin Scharm 2
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
May, 2015 COMBINE (archive) meta data | Martin Scharm 3
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
May, 2015 COMBINE (archive) meta data | Martin Scharm 4
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."
May, 2015 COMBINE (archive) meta data | Martin Scharm 5
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?
May, 2015 COMBINE (archive) meta data | Martin Scharm 6
Meta Datais based on SBML meta
May, 2015 COMBINE (archive) meta data | Martin Scharm 7
Meta Datais based on SBML meta
May, 2015 COMBINE (archive) meta data | Martin Scharm 7
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
May, 2015 COMBINE (archive) meta data | Martin Scharm 8
Making use of other ontologiesextending the current standard
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
May, 2015 COMBINE (archive) meta data | Martin Scharm 8
Making use of other ontologiesextending the current standard
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
May, 2015 COMBINE (archive) meta data | Martin Scharm 8
Making use of other ontologiesextending the current standard
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]
/model/BIOMD0000000144.xml
pav:curatedBy
http://identifiers.org/biomodels.db/MODEL1509031628
prov:wasDerivedFrom
type prov:Entity
May, 2015 COMBINE (archive) meta data | Martin Scharm 8
Making use of other ontologiesextending the current standard
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
May, 2015 COMBINE (archive) meta data | Martin Scharm 8
Making use of other ontologiesextending the current standard
PROV
PAV
ORE
NEPOMUK/experiment/Calzone2007-simulation-figure-1B.xml
/model/BIOMD0000000144.xml
nie:depends
type prov:Entity
type prov:Entitytype nie:DataObject
May, 2015 COMBINE (archive) meta data | Martin Scharm 8
Help us!
• interested?
• want to contribute and/or discuss?
• sign up for groups.google.com/forum/#!forum/combine-meta
May, 2015 COMBINE (archive) meta data | Martin Scharm 9