UML Modeling/CDE Creation

sounderslipInternet and Web Development

Oct 22, 2013 (3 years and 10 months ago)

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UML Modeling/CDE Creation
BioPAX experience

Gary Bader

Sander Group

Memorial Sloan
-
Kettering Cancer Center

(BioPAX Developed by the BioPAX Workgroup, BioPAX.org)

Creating BioPAX


BioPAX is modeled in OWL


OWL = Web Ontology Language


XML
-
based W3C standard for ‘ontology’ description


Like an object
-
oriented version of XML Schema


can
define a class hierarchy


Very similar to UML (different jargon)


Semantic web, but BioPAX is not using or dependent on
semantic web infrastructure


We care about sharing pathway information (biology), not
building the semantic web (computer science), though we try to
support the “AI reasoning” use case

Protégé


Ontology editor (open
-
source, Java)


Support OWL via plug
-
in


http://protege.stanford.edu/


Download v3.0 full


Can use to edit BioPAX ontology, view
BioPAX pathway files (download from
biopax.org or supporting DBs)

XMI, UML


UML can be stored in a .xmi file


XMI is a wrapper for XML
-
formatted UML


http://www.omg.org/technology/documents/mode
ling_spec_catalog.htm


UML:
http://www.omg.org/docs/formal/03
-
03
-
01.pdf


Version 1.4 (Current 1.5)


See section 5.2 (p.615)


XMI:
http://www.omg.org/docs/formal/03
-
05
-
02.pdf


Version 1.2 (Current 2.0)


UML Reference card:


http://www.holub.com/goodies/uml/

XMI Wrapper

UML

OWL


UML


Protege OWL


UML
recipe


Install Protege 2.1.2, install UML backend plugin


Load OWL file


Save project (Project
-
>Save)


Convert to UML (Project
-
>Convert Project to Format
-
>UML) (Protege
will fail to load the ontology back in)


Load back into Protege (Project
-
>Build new project
-
>UML)


Remove OWL, RDF meta
-
information within Protege


Delete extraneous OWL and RDF classes, move entity up to subclass of
:THING


Make sure to also delete :THING
-
>SYSTEM
-
CLASS
-
>META
-
CLASS
-
>CLASS
-
>STANDARD
-
CLASS
-
>all OWL, rdfs classes


Remove extraneous OWL, RDF meta
-
properties


Project
-
>Save as... (to resave the modified xmi file)


Load into Poseidon and rename the package to e.g. BioPAX
-
Level1

Issues


All cardinality constraints on associations are lost


Must manually re
-
create in EA


These are saved by caDSR import, but not viewable over
web interface


"Comment“ used for all comments, instead of
"Documentation" for classes and "Description" for
attributes.


Enumeration (controlled vocabularies) must be
manually input


None of the UML packages view file well


Enumeration difficult to view


Bad layout + class diagram view features


Any ideas?


Tried: Poseidon, MetaMill, MagicDraw, EA

Next steps


Wait for BioPAX Level 2 finalization (few
weeks)


Convert to XMI/UML + massage


Send to George Komatsoulis to run semantic
connector (Thanks George and friends!)


Manually validate semantic connector results
and load into caDSR


BioPAX Level 2 has 42 classes, 70
properties


expect lots of CDE creation

Open Questions


Updating: BioPAX is evolving


New classes/attributes easy to deal with


Changing comments, cardinality restrictions, etc.
not yet dealt with by SDK


Updating likely to involve a lot of manual effort


Others?