COMBINE (archive) meta data
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This document discusses metadata for the COMBINE archive format. It begins by explaining that the COMBINE archive allows sharing of all information needed to reproduce a modeling project in a single file. It then provides examples of metadata for models, simulations, and results within a COMBINE archive. Finally, it proposes extending the metadata by integrating additional ontologies such as PROV and PAV to capture more detailed information about models, simulations, people, and relationships between these elements.
![Meta Data
COMBINEarchive
BIOMD0000000144.xml
dc:creator=[enuo@caltech.edu,lenov@ebi.ac.uk,laurence.calzone@curie.fr]
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.xml
dc:creator=[martin.scharm@uni-rostock.de]
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.png
dc:creator=[martin.scharm@uni-rostock.de]
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](https://image.slidesharecdn.com/combine2015-scharm-151015190818-lva1-app6891/85/COMBINE-archive-meta-data-5-320.jpg)
![Meta Data
is actually very limited
COMBINEarchive
BIOMD0000000144.xml
dc:creator=[enuo@caltech.edu,lenov@ebi.ac.uk,laurence.calzone@curie.fr]
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.xml
dc:creator=[martin.scharm@uni-rostock.de]
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.png
dc:creator=[martin.scharm@uni-rostock.de]
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](https://image.slidesharecdn.com/combine2015-scharm-151015190818-lva1-app6891/85/COMBINE-archive-meta-data-6-320.jpg)
![Making use of other ontologies
extending the current standard
PROV
PAV
hanne
type dc:Agent
type foaf:Person
type prov:Person
type prov:Agent
foaf:gender female
rdfs:label Hanne Nielsen
foaf:familyName Nielsen
foaf:givenName Hanne
foaf:mbox mailto:hnie010@aucklanduni.ac.nz
/model/calzone_thieffry_tyson_novak_2007.cellml
http://models.cellml.org/[..]/calzone_thieffry_tyson_novak_2007.cellml
pav:retrievedFrom
type prov:Entity
pav:createdOn 2009-02-18 11:19:58Z
pav: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:Entity
pav:createdOn 2009-10-27 00:37:35
pav: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](https://image.slidesharecdn.com/combine2015-scharm-151015190818-lva1-app6891/85/COMBINE-archive-meta-data-11-320.jpg)
![Making use of other ontologies
extending the current standard
PROV
PAV
ORE
/documentation/Calzone2007-supplementary-material.pdf
http://europepmc.org/[..]/msb4100171-s1.pdf
pav:retrievedFrom
type prov:Entity
pav:retrievedOn 2015-06-11 00:00:00
/documentation/Calzone2007.pdf
http://europepmc.org/[..]/ptpmcrender.fcgi
pav:retrievedFrom
type prov:Entity
pav:retrievedOn 2015-06-11 00:00:00
http://identifiers.org/pubmed/17667953
ore:aggregates
ore:aggregates
calzone
dcterms:creator
type ore:Aggregation
dc:title Dynamical modeling of syncytial mitotic cycles in Drosophila embryos
dcterms:created 2007-01-08 00:00:00
type prov:Agent
May, 2015 COMBINE (archive) meta data | Martin Scharm 8](https://image.slidesharecdn.com/combine2015-scharm-151015190818-lva1-app6891/85/COMBINE-archive-meta-data-13-320.jpg)
COMBINE (archive) meta data
- 1. SYSTEMS BIOLOGY BIOINFORMATICS ROSTOCK S E Ssimulation experiment management system COMBINE (archive) meta data MARTIN SCHARM1 1 Department of Systems Biology & Bioinformatics, University of Rostock 2 Department 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
- 2. The COMBINE archive sharing 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
- 3. The COMBINE archive is already being used internet internet SEARCHubiquitin internet RESULTS EXPORT EXPORT EXPORT EXPORT Query database for annotations, persons, simulation descriptions Retrieve information about models, simulations, figures, documentation Export simulation study as COMBINE archive Download archive and open the study with your favourite simulation tool Open archive in CAT to modify its contents and to share it with others internet API Commincations enrich your studies with simulation results Simulate a Study with 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
- 4. The COMBINE archive all 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
- 5. Meta Data COMBINEarchive BIOMD0000000144.xml dc: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.xml dc: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.png dc: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
- 6. Meta Data is actually very limited COMBINEarchive BIOMD0000000144.xml dc: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.xml dc: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.png dc: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
- 7. Meta Data is based on SBML meta May, 2015 COMBINE (archive) meta data | Martin Scharm 7
- 8. Meta Data is based on SBML meta May, 2015 COMBINE (archive) meta data | Martin Scharm 7
- 9. Making use of other ontologies extending 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
- 10. Making use of other ontologies extending 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:Person type prov:Agent type foaf:Person type dc:Agent foaf:gender male foaf:name Martin Scharm foaf:jabberID [email protected] foaf:familyName Scharm foaf:lastName Scharm foaf:givenName Martin foaf:mbox mailto:[email protected] /result/Fig1B-bottom-webtools.svg prov:wasGeneratedBy type prov:Entity type prov:Entity type prov:Plan dc:description simulation description to reproduce fig 1B type prov:Entity /result/Fig1B-top-webtools.svg prov:wasGeneratedBy type prov:Entity type prov:SoftwareAgent foaf:name SED-ML WebTool May, 2015 COMBINE (archive) meta data | Martin Scharm 8
- 11. Making use of other ontologies extending the current standard PROV PAV hanne type dc:Agent type foaf:Person type prov:Person type prov:Agent foaf:gender female rdfs:label Hanne Nielsen foaf:familyName Nielsen foaf:givenName Hanne foaf: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:Entity pav:createdOn 2009-02-18 11:19:58Z pav: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:Entity pav:createdOn 2009-10-27 00:37:35 pav: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
- 12. Making use of other ontologies extending the current standard PROV PAV ebi http://ebi.ac.uk/ foaf:homepage type prov:Organization type prov:Agent foaf:name EMBL EBI lenover prov:actedOnBehalfOf type dc:Agent type foaf:Person type prov:Person type prov:Agent foaf:lastName Le Novère foaf:givenName nicolas foaf: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
- 13. Making use of other ontologies extending the current standard PROV PAV ORE /documentation/Calzone2007-supplementary-material.pdf http://europepmc.org/[..]/msb4100171-s1.pdf pav:retrievedFrom type prov:Entity pav:retrievedOn 2015-06-11 00:00:00 /documentation/Calzone2007.pdf http://europepmc.org/[..]/ptpmcrender.fcgi pav:retrievedFrom type prov:Entity pav:retrievedOn 2015-06-11 00:00:00 http://identifiers.org/pubmed/17667953 ore:aggregates ore:aggregates calzone dcterms:creator type ore:Aggregation dc:title Dynamical modeling of syncytial mitotic cycles in Drosophila embryos dcterms:created 2007-01-08 00:00:00 type prov:Agent May, 2015 COMBINE (archive) meta data | Martin Scharm 8
- 14. Making use of other ontologies extending the current standard PROV PAV ORE NEPOMUK /experiment/Calzone2007-simulation-figure-1B.xml /model/BIOMD0000000144.xml nie:depends type prov:Entity type prov:Entity type nie:DataObject May, 2015 COMBINE (archive) meta data | Martin Scharm 8
- 15. 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