I3C Registry Group

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I3C Registry Group

• SEM-GRD RG GGF7
• Mar 6, 2003
• Mike Niemi
• niemi_at_us.ibm.com

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I3C I3C promotes and guides the development of
interoperable software frameworks and solutions
in the life sciences, based on open, public
specifications. Our objective is to enable the
widest availability of open interoperable
software to solve critical problems in drug
development and life sciences research. For
more info http//www.i3c.org
I3C Registry
Group Mission Statement The overall goal is to
discover and bind to services at either
design-time or run-time using a registry. This
is for the purpose of data and application
integration in the Life Sciences. We will
define best practices based on BioMOBY, myGrid,
and business registries such as UDDI.
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Work in Progress

• Track BioMOBY, myGrid,
• - Goals Education, community
• Whitepapers
• Requirements
• Technology options trends
• I3C Sandbox
• Resides at the Whitehead Institute (MIT)
• Run UDDI, BioMOBY, LSID Resolver,
• Eventually host the I3C Registry
• I3C Hackathon
• To be held in Boston in May
• Possible project LSID-ify BioMOBY

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Background
BioMOBY (Model Organism Bring Your-own Database)
BioMOBY is an international research project
involving biological data hosts, biological data
service providors, and coders whose aim is to
explore various methodologies for biological
data representation, distribution, and
discovery. 
http//biomoby.org
researchers usually will have a piece of data
in-hand that they wish to investigate more deeply

What known genes are similar to the gene I just
cloned? Of those, which are annotated as cyclins?
Show me an alignment of those genes.
BioMOBY .. is an information discovery system
that identifies and retrieves related data.
Mark Wilkinson and Matthew Links http//biomoby.or
g/wilkinson_links_2002.pdf
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Background, cont.
LSID (Life Science Identifier) LSID is an
I3C initiative LSID is a naming convention
for naming biologically significant resources.
e.g. URNLSIDebi.ac.ukSWISS-PROT.acc
essionP343553 URNLSIDrcsb.orgPDB1D4X
22 URNLSIDncbi.nlm.nih.govGenBank.acce
ssionNT_0010632 LSID Resolver A method
for the retrieval of the object and associated
metadata that was named by the LSID URN.
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Requirements Gathering Approach
 

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Approach

The WGs help identify
The actual Registry use-cases
Use-cases / requirements
Simple static workflow builder
Smart agents
Biological Use-cases
Registry
Components, Data Sources, Attributes
BioMOBY LSID and myGrid

Function-rich description mechanisms (key/value,
taxonomies, ontologies) Fault tolerance,
performance, security, cost-model Tools, UI/API,
replication/backup

A range of applications being developed By
BioMOBY, myGrid, Semantic Web, etc.
Common requirements
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Approach 1. Sample
biological use-case Storyboard
2.
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Approach 3. Sample registry
use-cases
2 organizations have developed internal web
services and now user at org a wants to
seamlessly use services at org b. A user
would like to seamlessly integrate functions from
multiple application packages on their desktop.
The user works in a research environment where
new tools are being constantly developed. The
user would like to be able to find new functions
as they become available and have some assurance
that the function is stable (will perform as
expected, will be available over the term of
their research, etc)
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Approach

• Identify common system requirements such as
  security,
• performance, reliability, etc.
• Map requirements to technology options.

Result Whitepapers on www.i3c.org website
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I3C Registry GroupOther work in progress
I3C Registry WG Test Client A testbed for
exploring and defining best practices to meet the
WG goals. Basic features (TBD) will be
- Discover and bind to web services using a
UDDI registry, LSID(?), BioMOBY,
Semantic Grid, Semantic Web, - Save
workflows using std. workflow format(s).
- Pass results using std. XML formats.
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I3C Registry WG Test Client A testbed for
exploring best practices in the WG.
Mouse over object to see attributes (from
registry)
Drag objects from palette
Services and data sources discovered in the
registry
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Other means of discovering services BioMOBY,
Semantic Web, etc.
Customized I3C Admin. Panel with a simplified
interface for I3C needs.
Import/export BPEL
Create simple workflows
Mousing over input or output will display its
attributes (from the registry). Also, all like
inputs/ outputs light up in green.