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Session V: Life Science Identifiers - Use Cases, Future Directions.

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Presentation on theme: "Session V: Life Science Identifiers - Use Cases, Future Directions."— Presentation transcript:

1 Session V: Life Science Identifiers - Use Cases, Future Directions

2 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

3 Today OMG Spec google “+LSID +bioinformatics” –686 results (10/27/04, 2:40pm) –700 results (10/27/04, 7:20am)

4 Broad Use Cases

5 How GenePattern is using LSIDs 1.Identify analysis tasks and pipelines via LSIDs 2.Create sharable pipelines referencing tasks via LSIDs 3.Provide a repository and retrieval for analysis tasks by LSID

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

7 Example: ALL/AML Analysis all_aml_train 27 ALL, 11 AML expression samples all_aml_test 20 ALL, 14 AML expression samples Preprocess urn:lsid:broad.mit.edu :cancer.software.genepattern.mod ule.analysis:00020:0 Training DataTest Data Class Neighbors urn:lsid:broad.mit.edu:cancer.software.genepattern.module. analysis:00001:0 Weighted Voting Cross-Validation urn:lsid:broad.mit.edu:cancer.softw are.genepattern.module.analysis:00 028:0 Weighted Voting Train-test urn:lsid:broad.mit.edu:cancer.s oftware.genepattern.module.an alysis:00027:0 Preprocess urn:lsid:broad.mit.edu :cancer.software.genepattern.mo dule.analysis:00020:0 Golub and Slonim et al., 1999 SOM Clustering urn:lsid:broad.mit. edu:cancer.softwar e.genepattern.mod ule.analysis:00029: 0 urn:lsid:broad.mit.edu:cancer.software.genepattern.module.pipeline:00001:0

8 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…

9 Future… urn:lsid:broad.mit.edu: cancer.microarray: abcde:1.0 urn:lsid:broad.mit.edu: cancer.microarray: zyxwv:1.0 Preprocess urn:lsid:broad.mit.edu :cancer.software.genepattern.mod ule.analysis:00020:0 Training DataTest Data Class Neighbors urn:lsid:broad.mit.edu:cancer.software.genepattern.module. analysis:00001:0 Weighted Voting Cross-Validation urn:lsid:broad.mit.edu:cancer.softw are.genepattern.module.analysis:00 028:0 Weighted Voting Train-test urn:lsid:broad.mit.edu:cancer.s oftware.genepattern.module.an alysis:00027:0 Preprocess urn:lsid:broad.mit.edu :cancer.software.genepattern.mo dule.analysis:00020:0 Golub and Slonim et al., 1999 SOM Clustering urn:lsid:broad.mit. edu:cancer.softwar e.genepattern.mod ule.analysis:00029: 0 urn:lsid:broad.mit.edu:cancer.software.genepattern.module.pipeline:00001:0

10 Other LSID use at the Broad 1.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

11 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

12 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?

13 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 @end of yesterday in MyGrid talk

14 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

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