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SCAMIT and Morphbank

This document outlines the latest updates and features of Morphbank, a platform designed for the management and sharing of biological data. Key highlights include enhancements to usability, new workbook functionalities for data providers, interoperability services, and guidelines for collaborating institutions such as the City of San Diego Environmental Monitoring Lab and the LACSD Marine Biology Lab. Users can access metadata, utilize dynamic searching services, and manage their accounts efficiently through Morphbank. Explore how these upgrades facilitate data submission and improve service accessibility.

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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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