The Barcoding Pipeline Amy Driskell Laboratories of Analytical Biology (LAB) National Museum of Natural History Smithsonia...
Module II Module III
A Simplified Version Specimen Acquisition Extraction & Data Generation Data Mgmt Barcode Sequence Deposition
A Simplified Version Data Mgmt Specimen Acquisition Extraction & Data Generation Barcode Sequence Deposition Locality Perm...
All data downstream from specimen collection/harvesting event must maintain their connection to the specimen!!
Not an easy task <ul><li>A barcode compliant record comprises (among other things): </li></ul><ul><li>Location data (from ...
Current Best Practices <ul><li>Codified spreadsheets  (collect exactly the metadata needed) </li></ul><ul><li>Immediate me...
Pipeline Use User A: handles all steps from start to finish Specimen Acquisition Extraction & Data Generation Data Mgmt Ba...
Pipeline Use User B: hands off specimens for data generation Specimen Acquisition Extraction & Data Generation Data Mgmt B...
Pipeline Use User C: hands off specimens, uses barcode data Specimen Acquisition Extraction & Data Generation Data Mgmt Ba...
Whatever your role in the barcoding pipeline: Start out right    thoroughly and correctly collect and store all metadata ...
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Amy Driskell - The Barcoding pipeline

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an explanation of the barcoding pipeline, what data objects need to be tracked through the pipeline, and the possible entry and exit points to the pipeline

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Amy Driskell - The Barcoding pipeline

  1. 1. The Barcoding Pipeline Amy Driskell Laboratories of Analytical Biology (LAB) National Museum of Natural History Smithsonian Institution
  2. 2. Module II Module III
  3. 3. A Simplified Version Specimen Acquisition Extraction & Data Generation Data Mgmt Barcode Sequence Deposition
  4. 4. A Simplified Version Data Mgmt Specimen Acquisition Extraction & Data Generation Barcode Sequence Deposition Locality Permit Info Age, sex, Collector Name Photos Identifier Taxonomy Museum ID Lab processes Taxon specific info Extraction Method Primers PCR protocols extract location Cleaned barcode sequence Trace Files Assembly parameters Raw data processing
  5. 5. All data downstream from specimen collection/harvesting event must maintain their connection to the specimen!!
  6. 6. Not an easy task <ul><li>A barcode compliant record comprises (among other things): </li></ul><ul><li>Location data (from Step 1) </li></ul><ul><li>Taxonomic data (from Step 1) </li></ul><ul><li>Voucher institution and ID (from Step 1) </li></ul><ul><li>Primer data* (from Step 2) </li></ul><ul><li>Sequence data, including raw data* (from Step 3) </li></ul>Other data: specimen photographs, specific lab procedures, additional specimen info
  7. 7. Current Best Practices <ul><li>Codified spreadsheets (collect exactly the metadata needed) </li></ul><ul><li>Immediate metadata validation (lat/long, taxonomy, locality data) </li></ul><ul><li>Linked specimen and laboratory databases** (nail raw data to completed sequence) </li></ul><ul><li>Automated (or semi-) deposition from databases to BOLD/Genbank </li></ul>
  8. 8. Pipeline Use User A: handles all steps from start to finish Specimen Acquisition Extraction & Data Generation Data Mgmt Barcode Sequence Deposition Data User
  9. 9. Pipeline Use User B: hands off specimens for data generation Specimen Acquisition Extraction & Data Generation Data Mgmt Barcode Sequence Deposition Data User
  10. 10. Pipeline Use User C: hands off specimens, uses barcode data Specimen Acquisition Extraction & Data Generation Data Mgmt Barcode Sequence Deposition
  11. 11. Whatever your role in the barcoding pipeline: Start out right  thoroughly and correctly collect and store all metadata at the time of specimen collection and TREAT IT AS WELL AS YOU DO THE SPECIMEN All other aspects of barcoding flow downstream from here.

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