#### Teleconference Information

Thursday June1 , 4-5 PM ET\
Moderator: Brian Davis

**Meeting Materials:**

See Gforge: <http://gforge.nci.nih.gov/projects/extern-standard/>

Files tab

Action items from Last meeting (May 25^th^)

+----------------+--------------------------------------+-------------+
| ##             | #### Description                     | ##          |
| ## Assigned To |                                      | ## Due Date |
+----------------+--------------------------------------+-------------+
| #              | #### Continue "silver level          | #### June 1 |
| ### Xin Zheng  |  review" of MAGE OM/caArray with EA  |             |
|                | model provided by George Komatsoulis |             |
+----------------+--------------------------------------+-------------+
| ###            | #### Continue with BioPAX contact    | #### June 1 |
| # Tahsin Kurc  | Claire Wolfe on "Techincal Issues in |             |
|                |  Loading BIOPAX UML model into caDSR |             |
+----------------+--------------------------------------+-------------+
| #### Pat       | #### Start "si                       | #### June 1 |
| rick McConnell | lver level review" mzXML/rProteomics |             |
+----------------+--------------------------------------+-------------+
| ##             | #### Ask George Komatsoulis          | #### May 25 |
| ## Brian Davis |  to include Xin in process for loadi |             |
|                | ng new MAGE OM into the caDSR, inclu |             |
|                | ding access to a MAGE UML (EA model) |             |
+----------------+--------------------------------------+-------------+
| ##             | ####                                 | #### June 1 |
| ## Tahsin Kurc |  Ask his Architecture Colleagues wha |             |
|                | t the options are for single CDEs ma |             |
|                | pping ot multiple Schemas in the GME |             |
+----------------+--------------------------------------+-------------+
| ##             | #### Notes and Action items          | #### May 25 |
| ## Brian Davis |                                      |             |
+----------------+--------------------------------------+-------------+
| #### Tahsin    | #### Get in touc                     | #### June 1 |
|                | h with David Cluney (DICOM) to see i |             |
|                | f it fits the "Model Only" example o |             |
|                | f an external standard to consider.  |             |
+----------------+--------------------------------------+-------------+
| ##             | #### Re-wri                          | #### May 26 |
| ## Brian Davis | te Group Charter with a section: que |             |
|                | stions raised but not yet considered |             |
+----------------+--------------------------------------+-------------+

**Key Decisions and/or Outcomes**

#### Action Items

+----------------+--------------------------------------+-------------+
| ##             | #### Description                     | ##          |
| ## Assigned To |                                      | ## Due Date |
+----------------+--------------------------------------+-------------+
| #### Pat       | #### Provide slid                    | #### June2  |
| rick McConnell | e shows o group, post to GForge site |             |
+----------------+--------------------------------------+-------------+
| #### Pat       | #### Re-write "Issues Slide" to W    | #### June 8 |
| rick McConnell | ord Document and post to GFroge site |             |
+----------------+--------------------------------------+-------------+
| #### Brian     | #                                    | #### June 8 |
|  Davis and all | ### Think about draft for white pape |             |
|                | r based on what we have done so far. |             |
+----------------+--------------------------------------+-------------+
| ##             | ####                                 | #### June 8 |
| ## Tahsin Kurc |  Ask his Architecture Colleagues wha |             |
|                | t the options are for single CDEs ma |             |
|                | pping ot multiple Schemas in the GME |             |
+----------------+--------------------------------------+-------------+
| ##             | #### Notes and Actio                 | #### June 2 |
| ## Brian Davis | n items to group by email and GForge |             |
+----------------+--------------------------------------+-------------+
| #### Tahsin    | #### Get in touc                     | #### June 8 |
|                | h with David Cluney (DICOM) to see i |             |
|                | f it fits the "Model Only" example o |             |
|                | f an external standard to consider.  |             |
+----------------+--------------------------------------+-------------+
| ####           | #### Provide point                   | #### June 8 |
| Harold Solbrig | ers/liks to documents : XML schema m |             |
|                | apping to UML and OWL mapping to UML |             |
+----------------+--------------------------------------+-------------+

#### 

#### Attendees

  ----------------------------------- -----------------------------------
  Xin Zheng                           Albert Einstein

  Patrick McConnell                   Duke University

  Tahsin Kurc                         OSU

  Tommie Curtis                       SAIC

  Brian Davis                         3^rd^ Millennium

  Harold Solbrig (sort of)            Mayo Clinic
  ----------------------------------- -----------------------------------

#### Meeting Notes

Brian went over action items from last meeting.

Brian suggested we are now in a position to create an outline for one of
our deliverables: a white paper.

Tahsin agreed and broached the possibility of it being published in
journal or in a conference proceedings.

Patrick presented his work (and issues) in making RProteomics silver
level compliant" and adjusting the external standard mzXML according to
caBIG guidelines)

[See his slides of problems/issues (he will post on Gforge
site):]{.mark} <http://gforge.nci.nih.gov/projects/extern-standard/> )

1\) Patrick and his group created their own Tool "xmi generator" that
takes XML schema to XMI file that can be loaded into EA (to make a UML
model)

Had tried Hypermodel but found it was too "literal", too much "direct
translation"

2\) Tommie asked: could you load enumerations? No

Tahsin, enumerations were an issue for BioPax, too.

But caBIG tooling is now catching up (may be able to put enumerations in
EA to be loaded into caDSR)

3\) Major hang up: Xml is very hierarchical and usually generates "empty
classes". caBIG does not like empty classes (there are no CDEs made from
an empty class.

4\) Names within xml schema may be very poor semantically, sometimes
when convert XML schema to UML, class and attributes have the same name
(not allowed in caBIG)

5\) Namespace is not a problem anymore

6\) Extensions of simple types (still be a problem, even after we figure
out the 'suite or menu of primitive datatypes to be used within caBIg
within the group : Default datatypes in caDSR (see:
<http://gforge.nci.nih.gov/projects/cadsr-datatypes/> )

Harold says there is a way to get it in, but if it's a mixed datatype,
then your really talking about opaque text (eg, a single HTML document)
that is not really meant to be broken up. Might be "string" in caBIG UML
.

Hibernate is the reason for "id" being attached to each class (O-R
mapping and exposure in API made by codegenerator in caCORE SDK). This
may be a place holder for LSID also. Need clarification of ID
requirement , LSID plan.

Harold: this may cause problems with Constrained strings, if you put new
things on them you should not

BUT MAYBE ITS OK FOR NOW

7\) Some XML schema construct not supported by UML

Eg, CHOICE: (OR ) stereotypes

(How would we figure it out?) do we need a laundry list of what doesn't
work and have

XML to UML has been done (OMG)

We can look and see what is mapped[. (Harold will send us links to this
mapping)]{.mark}

Translation between XML schema and UML

MOF2 under EFG or something

(MOF2 facility is key)

At some point we would want the caDSR to handle all the core EMF Sets
and what everyone else uses

Patrick is concerned is that the construction is not so good: too
literal

Can certainly express all of XML schema in UML schema in UML 2

Can we bring in well thought out data models in to caBIG,

"Make the UML models as appetizing as possible"

For output, we have at least two options:

1\) One that was broached at the F2F meeting in February 1 an 2 2006, is
that we would have two XML output streams:

a\) A caBIG-ified XML stream (probably based on a caBIG UML model of the
external Standard)

b\) the external standard XML stream

2\) Secondly, We could have an intermediate mapping between the xml
schema and the UML model such that there is one output (the "external
standard" XML stream) but there is a translation that will transform the
caBIG UML model to the "standard" XML schema.

8\) Also caGrid 1.0 should have a global datatypes

9\) Many simple types don't exist in caDSR (workingon this)

Collection of primitives.

Xin (MAGE OM) will look at Mage site and look at best practices

And work with Patricks list of issues

Tahsin (BioPax)

Two thirds of process

Harmonizing Biopax have a UML model and XMI file and did concept
mappings

But someone with domain knowledge has to do the mapping

Lots of associations with no dorection

Enumerated types and value domains are a problem

Tahsin has the xmi and UML models

One problem is that we can't umake API because has dashes in them, so
can't create object models with dashes in them

Harold : non-directional associations in UML models from OWL: this may
be a problem with every single model we try to convert.

ODM (ontology Definition Metamodel uses MOF, can find overlaps and
differences OWL, UML RDF, to come up with a semantic map

Owl can have a nested interclass

(intersection of a class) that is unnamed.