1. Database Population and Curation Michael J. Donoghue, Yale University William H. Piel, University at Buffalo

2. Data Entry/Populating Manual Entry -- students and staff Data Migration -- from TreeBASE to ITR Value Added Data -- federating data Submission System -- burden on user Sustainability -- beyond ITR

3. Manual Entry Advantages –Selective coverage –Full control of quality and depth –Good source for student training/outreach Disadvantages –Work intensive, seemingly endless –Not all data can be digitized –Analyses not as accurate as user-entered

5. Manual Entry PIs build Endnote database of desired studies: –Author names –Citation –Abstract Students prepare datasets –Scan and OCR characters and character descriptions from the paper or PDF or download sequence data from Genbank; Google for data; seek data from authors – Use regular expressions in BBEdit (or equivalent) so that data is ready for MacClade –Recreate trees with PAUP and MacClade as needed –Verify Parameters (e.g. tree lengths) –Examine paper for basic outline of analyses –Enter data into TreeBASE; later into ITR product

6. Data Migration Currently: –1,526 authors –847 studies –2,273 trees –32,490 taxa. Modest but, with about 80% connectivity Connectivity will increase after solving the nomenclature Pandora's box

8. Data Migration Design an export format –XML? –NEXUS with proprietary block? –Diacritical translation/ASCII Character Sets –Preserve Matrix IDs and Study IDs? –Resolve nomenclature in TreeBASE or ITR?

9. Data Migration TreeBASE's "Shadow Database" –For submissions "in progress" (~ 500) –Uses slightly different data schema –Uses slightly different IDs (positive integers) –Treatment depends on ITR data model

10. Value Added Data Automated vs. Manually Curated VA –Do we upgrade existing and new datasets? –Identify taxa using SOAP with ITIS/Genbank? –Identify genes based on automated BLASTs? –Rank trees per study: identify "the" tree? –Automate some tree parameters? –Others? GIS for phylogeography Culture numbers and other IDs

11. Other Changes to the Data Model Expand data types (distance, genomic, etc) Adapt to "Electronic Notebook"model –Much more complex analysis description Separate "real data" from benchmark/simulated Separate "published data" from data under active research

12. Submission System TreeBASE Submission will continue –Demands constant editorial effort New Submission System GUI: –Must maximize burden on the user –But cannot be excessively arduous –Must incorporate quality control flags –Best to use solid, client-side helper applications

13. Sustainability Consider strategies for sustainability –Lobby societies and journals Require Author Submission Pass on modest Submission Charges? –Establish a Tree-of-Life electronic journal Designed to publish massive trees –Mission-Oriented Funding Sources NIH Foundations