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

Deborah Paul, Greg Riccardi, Austin Mast, Katja Seltmann, Chantelle DorseyDeborah Paul, Greg Riccardi, Austin Mast, Katja Seltmann, Chantelle Dorsey

TopicsTopics

• Morphbank UpdateMorphbank Update

• morphbank.netmorphbank.net

• New FeaturesNew Features

• New Data Provider WorkbookNew Data Provider Workbook

• Morphbank at TDWGMorphbank at TDWG

• CToLCToL

• Usability WorkshopUsability Workshop

• InteroperabilityInteroperability

• ServicesServices

• FSU Department of FSU Department of Scientific Computing Scientific Computing SupportSupport

Morphbank UpdateMorphbank Update

morphbank.netmorphbank.net

• Getting a Morphbank accountGetting a Morphbank account

• Log inLog in

• Account settingsAccount settings

• My ManagerMy Manager

• Tools > SubmitTools > Submit

• Where to EditWhere to Edit

morphbank.netmorphbank.net• Tools > Login > Request user accountTools > Login > Request user account

morphbank.netmorphbank.net• Login > Tools > Account SettingsLogin > Tools > Account Settings

• My Manager > Morphbank ObjectsMy Manager > Morphbank Objects

morphbank.net

TellinaTellina

• My Manager > CollectionsMy Manager > Collections

morphbank.netmorphbank.net

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

morphbank.netmorphbank.net• Contributor, Submitter, GroupContributor, Submitter, Group

– Morphbank Names and Morphbank IdsMorphbank Names and Morphbank Ids

morphbank.net• Tools > SubmitTools > Submit

– Choose Group, Choose Group, – then Tools > Submit: Locality, Specimen, View, Image, Publication, Taxon Namethen Tools > Submit: Locality, Specimen, View, Image, Publication, Taxon Name

• Click opens PopupClick opens Popup– Choose exisitingChoose exisiting– or Add Newor Add New

• Specimen Id & Specimen Id & View Id autofillView Id autofill

morphbank.netmorphbank.net• Click to edit objectsClick to edit objects

New FeaturesNew Features

• ServicesServices– http://services.morphbank.net/mb2/

• RSS feeds, GoogleMaps, GoogleReaderRSS feeds, GoogleMaps, GoogleReader

• User-defined fieldsUser-defined fields

• Provider UidsProvider Uids

http://services.morphbank.net/mb2/

• 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

• Allows dynamic searchingAllows dynamic searching

services.morphbank.net/mb2/

services.morphbank.netservices.morphbank.net• Query for geolocated objectsQuery for geolocated objectshttp://services.morphbank.net/mb2/request?http://services.morphbank.net/mb2/request?

method=search&objecttype=Image&objecttype=Specimen&keywords=SERNEC&geolocated=true&limit=10&method=search&objecttype=Image&objecttype=Specimen&keywords=SERNEC&geolocated=true&limit=10&firstResult=0&user=&group=&change=&lastDateChanged=&numChangeDays=1&id=&taxonName=&format=firstResult=0&user=&group=&change=&lastDateChanged=&numChangeDays=1&id=&taxonName=&format=thumbthumb

services.morphbank.netservices.morphbank.net• Query for Image idsQuery for Image idshttp://services.morphbank.net/mb2/request?http://services.morphbank.net/mb2/request?

method=search&objecttype=Image&keywords=wendy+storms&limit=15&firstResultmethod=search&objecttype=Image&keywords=wendy+storms&limit=15&firstResult=0&user=&group=&change=&lastDateChanged=&numChangeDays=&id=&taxonNa=0&user=&group=&change=&lastDateChanged=&numChangeDays=&id=&taxonName=&format=idRetrieve Image idsme=&format=idRetrieve Image ids

services.morphbank.net/services.morphbank.net/mb2/mb2/Query returns XMLQuery returns XMLhttp://services.morphbank.net/mb2/request?http://services.morphbank.net/mb2/request?

method=search&objecttype=Specimen&keywords=CToL&limit=1&firstResult=0&user=&grmethod=search&objecttype=Specimen&keywords=CToL&limit=1&firstResult=0&user=&group=&change=&lastDateChanged=&numChangeDays=&id=&taxonName=&format=svcoup=&change=&lastDateChanged=&numChangeDays=&id=&taxonName=&format=svc

• SchemaSchema

• Request TypeRequest Type

• Number AffectedNumber Affected

• Object TypeObject Type– specimenspecimen– Morphbank IdMorphbank Id– Provider UIDProvider UID

• User PropertyUser Property

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:

Image, Specimen, View, Locality, External LinksImage, Specimen, View, Locality, External Links• Provider UIDs encouragedProvider UIDs encouraged• User Properties supportedUser Properties supported

– Workbook for Morphbank and SCAMIT DatabasesWorkbook for Morphbank and SCAMIT Databases

• General PointsGeneral Points

New Morphbank WorkbookNew Morphbank Workbook

• Useful URLsUseful URLs– Download the new workbookDownload the new workbook

• http://www.morphbank.net/docs/customWorkbook.xls– Help with the workbook fieldsHelp with the workbook fields

• http://www.morphbank.net/About/Manual/customWorkbook.phphttp://www.morphbank.net/About/Manual/customWorkbook.php

– Current Morphbank services xml schemaCurrent Morphbank services xml schema• http://www.morphbank.net/schema/services.xsdhttp://www.morphbank.net/schema/services.xsd

– Darwin Core Fields (DarwinCore2 aka v1.2)Darwin Core Fields (DarwinCore2 aka v1.2)• http://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreVersionshttp://wiki.tdwg.org/twiki/bin/view/DarwinCore/DarwinCoreVersions

New Morphbank WorkbookNew Morphbank Workbook

• 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

• Sheet 1Sheet 1– color-coded by Morphbank object types: image, specimen, view, localitycolor-coded by Morphbank object types: image, specimen, view, locality– minimal required fields (image file name)minimal required fields (image file name)

• 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

SCAMIT Workbook Sheet 2SCAMIT Workbook Sheet 2

• Morphbank objects color-coded: image, specimen, view, localityMorphbank objects color-coded: image, specimen, view, locality• Provider uids stored for image, specimen, view Provider uids stored for image, specimen, view

– 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

• Help via emailHelp via email– mbadmin@scs.fsu.edumbadmin@scs.fsu.edu

SCAMIT Workbook Sheet 1SCAMIT Workbook Sheet 1

Thanks! from MorphbankThanks! from Morphbank