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SCAMIT and Morphbank

SCAMIT and Morphbank. Nov 18 2008 - City of San Diego Environmental Monitoring Lab Nov 19 2008 - LACSD Marine Biology Lab Nov 20 2008 - OCSD Environmental and Ocean Monitoring Section. Deborah Paul, Greg Riccardi, Austin Mast, Katja Seltmann, Chantelle Dorsey. Topics. Morphbank Update

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SCAMIT and Morphbank

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  1. SCAMIT and Morphbank Nov 18 2008 - City of San Diego Environmental Monitoring Lab Nov 19 2008 - LACSD Marine Biology Lab Nov 20 2008 - OCSD Environmental and Ocean Monitoring Section Deborah Paul, Greg Riccardi, Austin Mast, Katja Seltmann, Chantelle Dorsey

  2. Topics • Morphbank Update • morphbank.net • New Features • New Data Provider Workbook

  3. Morphbank Update • Morphbank at TDWG • CToL • Usability Workshop • Interoperability • Services • FSU Department of Scientific Computing Support

  4. morphbank.net • Getting a Morphbank account • Log in • Account settings • My Manager • Tools > Submit • Where to Edit

  5. morphbank.net • Tools > Login > Request user account

  6. morphbank.net • Login > Tools > Account Settings

  7. morphbank.net • My Manager > Morphbank Objects Tellina

  8. morphbank.net • My Manager > Collections

  9. morphbank.net • Click to access metadata for all Morphbank objects

  10. morphbank.net • Contributor, Submitter, Group • Morphbank Names and Morphbank Ids

  11. morphbank.net • Tools > Submit • Choose Group, • then Tools > Submit: Locality, Specimen, View, Image, Publication, Taxon Name • Click opens Popup • Choose exisiting • or Add New • Specimen Id & View Id autofill

  12. morphbank.net • Click to edit objects

  13. New Features • Services • http://services.morphbank.net/mb2/ • RSS feeds, GoogleMaps, GoogleReader • User-defined fields • Provider Uids

  14. http://services.morphbank.net/mb2/ • Use services to • find geolocated Morphbank objects with GoogleMaps • retrieve ids for Morphbank objects • get data in XML format • create custom RSS feeds, Google Reader

  15. services.morphbank.net/mb2/ • Creates a database query • see the API • Returns output in format selected • Keep up with the latest changes • Allows dynamic searching

  16. services.morphbank.net • Query for geolocated objects http://services.morphbank.net/mb2/request?method=search&objecttype=Image&objecttype=Specimen&keywords=SERNEC&geolocated=true&limit=10&firstResult=0&user=&group=&change=&lastDateChanged=&numChangeDays=1&id=&taxonName=&format=thumb

  17. services.morphbank.net http://services.morphbank.net/mb2/request?method=search&objecttype=Image&keywords=wendy+storms&limit=15&firstResult=0&user=&group=&change=&lastDateChanged=&numChangeDays=&id=&taxonName=&format=idRetrieve Image ids • Query for Image ids

  18. services.morphbank.net/mb2/ Query returns XML http://services.morphbank.net/mb2/request?method=search&objecttype=Specimen&keywords=CToL&limit=1&firstResult=0&user=&group=&change=&lastDateChanged=&numChangeDays=&id=&taxonName=&format=svc • Schema • Request Type • Number Affected • Object Type • specimen • Morphbank Id • Provider UID • User Property

  19. Intermission - time for change

  20. Time for change • New Morphbank Custom Workbook • Some features • DarwinCore Schema fields • Few required fields • User Properties • Provider UIDs • Potential Dual Use

  21. New Morphbank Workbook General Points • SCAMIT image and data processing protocol • Standardize the image uids, image naming • Avoid spaces & special characters in file names • Be in the SCAMIT group when uploading • Submitters need Morphbank account • Start uploading minimal sets • facilitates tweaking the overall process • speeds up the learning curve • Basic Excel Workbook • Minimal fields required from 5 Morphbank Objects: Image, Specimen, View, Locality, External Links • Provider UIDs encouraged • User Properties supported • Workbook for Morphbank and SCAMIT Databases

  22. New Morphbank Workbook • Useful URLs • Download the new workbook • http://www.morphbank.net/docs/customWorkbook.xls • Help with the workbook fields • http://www.morphbank.net/About/Manual/customWorkbook.php • Current Morphbank services xml schema • http://www.morphbank.net/schema/services.xsd • Darwin Core Fields (DarwinCore2 aka v1.2) • http://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreVersions

  23. New Morphbank Workbook • Workbook has 3 worksheets • Sheet 1: for data • Sheet 2: for user Properties • Sheet 3: for Contributor, Submitter, Group, & Date-to-Publish information • Sheet 1 – Field Descriptions in Morphbank Online User Manual • http://www.morphbank.net/About/Manual/customWorkbook.php • instructions for this workbook • links to Field descriptions • Sheet 1 • color-coded by Morphbank object types: image, specimen, view, locality • minimal required fields (image file name) • could submit with only image file name + description • fields not needed can be deleted • extra <userProperty> and External Links can be added by the provider • Decide which fields to use & how to use them, consistency matters • Rename the workbook & Save a copy • Send it and images to Morphbank • SCAMIT can use this workbook to populate the SCAMIT database • And the fields are...

  24. SCAMIT Workbook Fields

  25. To the Workbook ...

  26. SCAMIT Workbook Sheet 3 • Enter Names as they appear in Morphbank • Or, use Contributor, Submitter and Group Ids • Date to Publish in yyyy-mm-dd format

  27. SCAMIT Workbook Sheet 2 • <userProperty> + Morphbank Object • works with Sheet 1

  28. SCAMIT Workbook Sheet 1 • Morphbank objects color-coded: image, specimen, view, locality • Provider uids stored for image, specimen, view • prefix + id • Add more <userProperty> columns • External Links have 3 related columns • Relationships • One Image – One Specimen • Many Images – One Specimen > Requires Provider UIDs • Help with fields • http://www.morphbank.net/About/Manual/customWorkbook.php • Help via email • mbadmin@scs.fsu.edu

  29. Thanks! from Morphbank

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