How to Create EML Packages Using Morpho and Store them in an ILTER Metacat Kristin Vanderbilt Based...

How to Create EML Packages Using

Morpho and Store them in an ILTER

MetacatKristin Vanderbilt

Based on material developed by Samantha Romanello and

Will Tyburczy

What is EML?

• It’s a metadata standard developed by ecologists

• EML is a structured format for metadata written in XML

EML (Ecological Metadata Language) looks like this:

• Is not meant for humans to read!• Captures metadata in a structurerd

XML format that computers can easily read.

• EML from many sites can be put into a single database (a Metacat) so that cross-site searches for data can be done

Israel LTER Metacat

TERN Metacat

JaLTERMetacat

US LTER

Metacat

SAEON Metacat

Brazil Metacat

All ILTER Metacats will be

linked, so all metadata can be accessed from a single web page

All ILTER Metacats will be

linked, so all metadata can be accessed from a single web page

Search Page for US LTER Metacat

A Similar Web Page will be built to search all ILTER metadata

This Web Page searches the US LTER Metacat

ILTER Metadata Recommendations

• At the 2008 ILTER meeting in Slovakia, the ILTER voted to adopt EML as the ILTER Metadata Standard

• It was agreed that ILTER members would create ‘Discovery Level EML’ and submit the EML to network metadata caches (known as Metacats)

ILTER Metadata

• ILTER EML packages must have the following elements (in English):– Title– Owner– Abstract– Keywords– Package-ID (A unique identifier for the EML

package)• There are many other elements, but

only these five are required by the ILTER

These Slides Show:

• How to create an EML data package using the Morpho Metadata Editor

• How to insert that EML data package into an ILTER Metacat

NOTE: A “data package” is a file that contains metadata as EML and may also contain data

What is Morpho?

• It provides a way for ecologists to share data by defining a common structure to document their data

• It uses an XML format to create the common structure.

• So, basically, Morpho is an XML editor

What can Morpho do?

• Create EML data packages• Import data in to a data package• Save data packages – both locally and

over the network• Search for data packages – both locally

and over the network• Open and edit data packages• Export data packages

Let’s get started making a Discovery Level EML Document

First, Register with KNB (Knowledge Network for Biocomplexity)

• KNB developed Morpho• By registering with KNB, you can

search data in the KNB Metacat and also save your metadata to a Metacat

• Registration is necessary in order to use Morpho

Register with KNB • To begin, register as a

user at the KNB site http://knb.ecoinformatics.org/index.jsp

• Scroll down the page until you find the login & registration box in lower left of the page

• Click on the link ‘create a new account’

• Write down your username, organization and password as you will use this in Morpho. Use ‘LTER’ as your organization.

Downloading & Installing Morpho

• Next go to http://knb.ecoinformatics.org/morphoportal.jsp to download the most recent version of Morpho (1.8.0).

• There is an installer that will walk you through the installation.

Opening Morpho

• Once you have installed Morpho. Locate Morpho in your program file and start the application.

Opening Morpho

• When you open Morpho for the first time, you will see a New Profile window.

Creating a profile

• Enter a name for the profile– Suggested: first

initial and last name (kvanderbilt)

• Enter your name• Hit “Next”

Creating a profile

• Enter the username and affiliation of your KNB account

• This is the same username and organization you created on the KNB site

• Hit “Next”

Creating a profile

• Select an identifier prefix

• Usually the same as your account username

• Used as the first part of the name of your data packages

• Hit “Finished”

Network Login

• A screen will open asking you for your password.

• This is the same password that you created on the KNB site

• By logging in, you can search for data in a Metacat through Morpho and you can contribute your metadata to a Metacat

• If you don’t login (Skip Login), your metadata is stored locally

The main window

• All controls are accessible via the menu bar

• Butterfly icon indicates that program is processing

The main window

• All controls accessible via the menu bar

• Butterfly icon indicates that program is processing

Logging in

• You can see your network status in two places

• The main window

• The login status icon on the lower right

Logging in

• You can see your network status in two places

• The main window

• The login status icon on the lower right

Try a search for data packages:

Searching for data packages

• You can search on your local computer or on the network (which defaults to the KNB Metacat)

• You can search multiple terms using “More”• You can combine subject search with taxonomic

and spatial constraints

• You can search on local computer or network (which defaults to the KNB Metacat)

• You can search multiple terms using “More”• You can combine subject search with taxonomic

and spatial constraints

• Search on local disks or network• Search multiple terms using “More”• You can combine a subject search with

taxonomic and spatial constraints

• Select taxonomic rank and enter name• Can search multiple taxa using “More”

• Select taxonomic rank and enter name• You can search multiple taxa using

“More”

Searching for data packages: by location

• Select area of interest by moving box or enter coordinates by hand

• Zoom in to allow greater precision using the graphical box

• Select area of interest by moving box or enter coordinates by hand

• Zoom in to allow greater precision using the graphical box

• Data packages matching criteria are listed by last modification date

• Red icon indicates the package includes data table level EML

• Double click a package to open it

Start the Wizard to Create EML

Creating a data package:The Data Package Wizard• Step-by-step

interface for creating valid EML documents

• Required elements are listed in RED

• After creating documents, the interface for the various sections is reachable via the “Documentation” menu

Creating a data package:The Data Package Wizard• Step-by-step

interface for creating valid EML documents

• Required elements are listed in RED

• After creating documents, the interface for the various sections is reachable via the “Documentation” menu

Editing Data Packages:Title and Abstract

• Enter a descriptive title

• Briefly describe the content and purpose of the data in the abstract

Editing Data Packages:Title and Abstract

• Enter a descriptive title

• Briefly describe the content and purpose of the data in the abstract (note: abstract is not required)

Editing Data Packages:Keywords

• Hit “Add” to enter keywords (required)

Use the first radio button when adding keywords

• Hit ‘Add’ and enter a keyword in the space provided.

• To edit or delete existing keywords, select them and hit the ‘Delete’ button

Editing Data Packages:Data Set Owner

• To add an owner, hit “Add” (required)

• To edit or delete an owner, select the listing, then hit the appropriate button

• To add an owner, hit “Add” (required)

• To edit or delete an owner, select the listing, then hit the appropriate button

• Enter in the information for the owner, then hit “OK”

• You have to enter one of the red-labeled entities: either enter Last Name, Organization (e.g., Sevilleta LTER) or Position Name (e.g., Sevilleta IM)

Editing Data Packages:Contact Person

• Works similarly to data set owners

• To add a contact, hit “Add”

• You can select a previous entry in the data package to specify the same person

• You can also specify a person from another data package

• You can select a previous entry in the data package to specify the same person

• You can also specify a person from another data package

• To select an entry from another data package: – select the

package on the left

– then the contact on the right

• To select an entry from another data package: – select the

package on the left

– then the contact on the right

You have completed a basic EML document

• At this point, you have entered enough information to generate a discovery-level EML document.

• You can either click “next” on all the rest of the windows in the Wizard, or you can continue to add more detail to your metadata.

• If you are done entering metadata, then go to slide 83

Editing Data Packages:Associated Parties

• Works similarly to entering owners and contacts

Editing Data Packages:Associated Parties

• Works similarly to entering owners and contacts

• Can enter “Role” by hand or select from the drop down list

Editing Data Packages:Research Project

• Check the box if the dataset is part of a larger research project

• This is a subjective call, so use it when you feel it is appropriate (For instance, the Sevilleta Warming Study is part of the larger Sevilleta LTER program)

Editing Data Packages:Research Project

• Enter the information about the research project

Editing Data Packages:Usage Rights

• Describe usage restrictions for the dataset, if any

Editing Data Packages:Spatial Coverage

• To add an area of spatial coverage to the data, hit “Add”

• Enter a description for the area

• There are many ways to select the area– Enter

coordinates manually

– Select from list– Box Tool– Point Tool

• Many ways to select the area– Enter

• Many ways to select the area– Enter coordinates

manually– Select from list– Box Tool– Point Tool

Editing Data Packages:Temporal Coverage

• To add a new temporal coverage, hit “Add”

• Enter in the date and hit “OK” if your data were collected on a single day

• Alternatively, you can enter a range of coverage

• Enter in the date and hit “OK”

• Alternatively, you can enter a range of coverage

Editing Data Packages:Taxonomic Coverage• To enter

additional taxonomic information, hit “Add” beside the top frame

• To enter information above genus level, select the appropriate entry and hit “Edit”

Editing Data Packages:Taxonomic Coverage• To enter

additional taxonomic information, hit “Add” beside the top frame

• To enter information above genus level, select the appropriate entry and hit “Edit”

Editing Data Packages:Taxonomic Coverage• Enter in the

names and common names for each rank

• Ranks can be added, deleted, or modified as appropriate

Editing Data Packages:Taxonomic Coverage• Enter in the names

and common names for each rank

• Ranks can be added, deleted, or modified as appropriate

Editing Data Packages:Taxonomic Coverage• To enter a

classification reference (e.g. Lights Manual), hit “Add” under “Classification System”

Editing Data Packages:Taxonomic Coverage• Fill in the

information for the reference

Editing Data Packages:Methods

• Enter a description for the method of sampling and the extent of the study

• To enter a new step in the methods, hit “Add”

• Enter a description for the method of sampling and the extent of the study

• To enter a new step in the methods, hit “Add”

• Fill in the description of the method

Editing Data Packages:Access Rights

• Control who is allowed to view, edit, delete, and change access rights to your data package

• Only applies to copies saved on the network– anyone can view

and edit data packages saved on the local machine

• Select whether to give read access to the public

• To add an additional access privilege or restriction, hit “Add”

• Select whether to give read access to the public

• To add an additional access privilege or restriction, hit “Add”

• Click “Refresh the user list…”

• Select the user or group to give special access rules

• Select “Allow” or “Deny”

• Select the type of access

Click ‘Finish’ to finish entering metadata

After you click ‘finish’, you will see your metadata:

Save your metadata

Saving Data: Local

• Select “Save…” from the “File” Menu

• Select “Save Locally” from the pop-up window, then deselect “Save to Network” if necessary

Saving Data: Local

• You should see “local” and a computer icon in the upper right hand corner below the butterfly

Saving Data: Network

• Now you will save your EML documents to your regional networks.

• Procedures for doing this differ between regions, as shown in next slides.

Save EML document to your ILTER Regional Metacat: Asia

• In the EAP-ILTER, the regional metacat is hosted by TERN. Please contact Sheng-Shan Lu at sslu@tfri.gov.tw. The URL for the Asia metacat is:– http://lter-tern.org/tern

Save EML document to your ILTER Regional Metacat: Africa

• In Africa, the ELTOSA regional Metacat is hosted by SAEON. Please contact Victoria Goodall at victoria@saeon.ac.za and she will arrange a username and password for you. You will then be able to upload your EML to http://saeonocean.co.az/knb/

Save EML document to your ILTER Regional Metacat: Europe

• The LTER Europe metacat is hosted by LTER Israel. To submit documents, please contact David Blankman at dblankman1@gmail.com.

Save EML document to your ILTER Regional Metacat: Americas

• If you are part of the Americas regional LTER, you can submit your email to the LTER Metacat. Please contact Kristin Vanderbilt at vanderbi@sevilleta.unm.edu for instructions.

How to Create EML Packages Using Morpho and Store them in an ILTER Metacat Kristin Vanderbilt Based...

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