Session V: Life Science Identifiers Use Cases, Future Directions

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Session V Life Science Identifiers - Use Cases,
Future Directions
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Recent History

• LSIDs 3 years old
• I3C evaluating AGAVE, BSML
• encoded IDs as tuples/triples
• If we could not agree on a data standard, could
  we at least agree on how we write the identifiers

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Today

• OMG Spec
• google LSID bioinformatics
• 686 results (10/27/04, 240pm)
• 700 results (10/27/04, 720am)

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Broad Use Cases
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How GenePattern is using LSIDs

• Identify analysis tasks and pipelines via LSIDs
• Create sharable pipelines referencing tasks via
  LSIDs
• Provide a repository and retrieval for analysis
  tasks by LSID

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Example ALL/AML Analysis
Training Data
Test Data
all_aml_train 27 ALL, 11 AML expression samples
all_aml_test 20 ALL, 14 AML expression samples

Preprocess Filter uninformative genes
Preprocess Filter uninformative genes
SOM Clustering Cluster samples to separate tumor
types
Weighted Voting Train-test Build a classifier
and compute its accuracy on a test set
Class Neighbors Find genes that most closely
match a profile
Weighted Voting Cross-Validation Build a
classifier and compute its accuracy using
cross-validation
Golub and Slonim et al., 1999
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Example ALL/AML Analysis
urnlsidbroad.mit.educancer.software.genepattern
.module.pipeline000010
Training Data
Test Data
all_aml_train 27 ALL, 11 AML expression samples
all_aml_test 20 ALL, 14 AML expression samples

Preprocess urnlsidbroad.mit.edu cancer.software
.genepattern.module.analysis000200
Preprocess urnlsidbroad.mit.edu cancer.softwar
e.genepattern.module.analysis000200
SOM Clustering urnlsidbroad.mit.educancer.soft
ware.genepattern.module.analysis000290
Weighted Voting Train-test urnlsidbroad.mit.edu
cancer.software.genepattern.module.analysis00027
0
Class Neighbors urnlsidbroad.mit.educancer.sof
tware.genepattern.module.analysis000010
Weighted Voting Cross-Validation urnlsidbroad.m
it.educancer.software.genepattern.module.analysis
000280
Golub and Slonim et al., 1999
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• LSIDs enable
• Reproducible research
• exactly repeating an in silico experiment
• modernizing pipelines to latest
• Tracking module provenance
• Someday
• Data will be available via LSID too

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Future
urnlsidbroad.mit.educancer.software.genepattern
.module.pipeline000010
Training Data
Test Data
urnlsidbroad.mit.edu cancer.microarray abcde1
.0
urnlsidbroad.mit.edu cancer.microarray zyxwv1
.0

Preprocess urnlsidbroad.mit.edu cancer.software
.genepattern.module.analysis000200
Preprocess urnlsidbroad.mit.edu cancer.softwar
e.genepattern.module.analysis000200
SOM Clustering urnlsidbroad.mit.educancer.soft
ware.genepattern.module.analysis000290
Weighted Voting Train-test urnlsidbroad.mit.edu
cancer.software.genepattern.module.analysis00027
0
Class Neighbors urnlsidbroad.mit.educancer.sof
tware.genepattern.module.analysis000010
Weighted Voting Cross-Validation urnlsidbroad.m
it.educancer.software.genepattern.module.analysis
000280
Golub and Slonim et al., 1999
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Other LSID use at the Broad

• Sample management
• Sharing samples (tissues, clones, etc) between
  program groups
• LSIDs identify samples
• Permits scientists to find all experiments done
  with a sample in any Broad program

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Other LSID use at the Broad

• 2. GeneCruiser web service
• annotation web service for microarray probes
• maps probe set identifiers to GO, GenBank,
  SwissProt etc
• Interface returns LSIDs to these other sources
  for their identifiers

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Use Cases and Future Directions

• What does it actually mean to identify a
  biological object such as "a gene"?
• How does LSID address structural elements of
  biological and chemical objects?
• What are the lessons learned from early
  implementations of LSID?

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Use Cases and Future Directions

• What granularity of object do we identify?
• Should LSID be a URI not a URN?
• Should virtual persistent identifiers for
  derived/calculated properties be used?
• What are the barriers to widespread use?
• Data/Metadata split is this a problem?
• Phil Lord mentioned _at_end of yesterday in MyGrid
  talk

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Best LSID quote

• LSIDs are in a sense just a sociological con
  trick, since they are nothing more than cheap and
  cheerful URNs David Shotten