SCAMIT and SCAMIT and Morphbank Morphbank Nov 18 2008 - City of San Diego Environmental Nov 18 2008 - City of San Diego Environmental Monitoring Lab Monitoring Lab Nov 19 2008 - LACSD Marine Biology Lab Nov 19 2008 - LACSD Marine Biology Lab Nov 20 2008 - OCSD Environmental and Ocean Nov 20 2008 - OCSD Environmental and Ocean Monitoring Section Monitoring Section orah Paul, Greg Riccardi, Austin Mast, Katja Seltmann, Chantelle Dor orah Paul, Greg Riccardi, Austin Mast, Katja Seltmann, Chantelle Dor
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SCAMIT and Morphbank Nov 18 2008 - City of San Diego Environmental Monitoring Lab Nov 18 2008 - City of San Diego Environmental Monitoring Lab Nov 19 2008.
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SCAMIT and SCAMIT and MorphbankMorphbank
Nov 18 2008 - City of San Diego Environmental Nov 18 2008 - City of San Diego Environmental Monitoring LabMonitoring Lab Nov 19 2008 - LACSD Marine Biology LabNov 19 2008 - LACSD Marine Biology Lab Nov 20 2008 - OCSD Environmental and Ocean Nov 20 2008 - OCSD Environmental and Ocean Monitoring SectionMonitoring Section
• Use services toUse services to– find geolocated Morphbank objects with find geolocated Morphbank objects with
GoogleMapsGoogleMaps– retrieve ids for Morphbank objectsretrieve ids for Morphbank objects– get data in XML formatget data in XML format– create custom RSS feeds, Google Readercreate custom RSS feeds, Google Reader
• Creates a database queryCreates a database query– see the APIsee the API
• Returns output in format Returns output in format selectedselected
• Keep up with the latest Keep up with the latest changeschanges
services.morphbank.netservices.morphbank.net• Query for geolocated objectsQuery for geolocated objectshttp://services.morphbank.net/mb2/request?http://services.morphbank.net/mb2/request?
services.morphbank.netservices.morphbank.net• Query for Image idsQuery for Image idshttp://services.morphbank.net/mb2/request?http://services.morphbank.net/mb2/request?
Intermission - time for Intermission - time for changechange
Time for changeTime for change
• New Morphbank New Morphbank Custom WorkbookCustom Workbook– Some featuresSome features
• DarwinCore Schema fieldsDarwinCore Schema fields• Few required fieldsFew required fields• User PropertiesUser Properties• Provider UIDsProvider UIDs• Potential Dual UsePotential Dual Use
New Morphbank WorkbookNew Morphbank Workbook
– SCAMIT image and data processing protocolSCAMIT image and data processing protocol• Standardize the image uids, image namingStandardize the image uids, image naming• Avoid spaces & special characters in file namesAvoid spaces & special characters in file names• Be in the SCAMIT group when uploadingBe in the SCAMIT group when uploading• Submitters need Morphbank accountSubmitters need Morphbank account• Start uploading minimal setsStart uploading minimal sets
– facilitates tweaking the overall processfacilitates tweaking the overall process– speeds up the learning curvespeeds up the learning curve
– Basic Excel WorkbookBasic Excel Workbook• Minimal fields required from 5 Morphbank Objects: Minimal fields required from 5 Morphbank Objects:
– Current Morphbank services xml schemaCurrent Morphbank services xml schema• http://www.morphbank.net/schema/services.xsdhttp://www.morphbank.net/schema/services.xsd
• Workbook has 3 worksheetsWorkbook has 3 worksheets– Sheet 1: for dataSheet 1: for data– Sheet 2: for user PropertiesSheet 2: for user Properties– Sheet 3: for Contributor, Submitter, Group, & Date-to-Publish informationSheet 3: for Contributor, Submitter, Group, & Date-to-Publish information
• Sheet 1 – Field Descriptions in Morphbank Online User ManualSheet 1 – Field Descriptions in Morphbank Online User Manual– http://www.morphbank.net/About/Manual/customWorkbook.phphttp://www.morphbank.net/About/Manual/customWorkbook.php
• instructions for this workbookinstructions for this workbook• links to Field descriptionslinks to Field descriptions
• could submit with only image file name + descriptioncould submit with only image file name + description– fields not needed can be deletedfields not needed can be deleted– extra <userProperty> and External Links can be added by the providerextra <userProperty> and External Links can be added by the provider
• Decide which fields to use & how to use them, consistency mattersDecide which fields to use & how to use them, consistency matters• Rename the workbook & Save a copyRename the workbook & Save a copy• Send it and images to MorphbankSend it and images to Morphbank• SCAMIT can use this workbook to populate the SCAMIT databaseSCAMIT can use this workbook to populate the SCAMIT database• And the fields are...And the fields are...
SCAMIT Workbook FieldsSCAMIT Workbook Fields
To the Workbook ...To the Workbook ...
• Enter Names as they appear in MorphbankEnter Names as they appear in Morphbank• Or, use Contributor, Submitter and Group IdsOr, use Contributor, Submitter and Group Ids• Date to Publish in yyyy-mm-dd formatDate to Publish in yyyy-mm-dd format
SCAMIT Workbook Sheet 3SCAMIT Workbook Sheet 3
• <userProperty> + Morphbank Object<userProperty> + Morphbank Object– works with Sheet 1 works with Sheet 1
– prefix + idprefix + id• Add more <userProperty> columnsAdd more <userProperty> columns• External Links have 3 related columnsExternal Links have 3 related columns• RelationshipsRelationships
– One Image – One SpecimenOne Image – One Specimen– Many Images – One Specimen > Requires Provider UIDsMany Images – One Specimen > Requires Provider UIDs
• Help with fieldsHelp with fields– http://www.morphbank.net/About/Manual/customWorkbook.phphttp://www.morphbank.net/About/Manual/customWorkbook.php