Transcript Morpho

How to Create EML
Packages Using Morpho
and Store them in an
ILTER Metacat
Kristin 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:
EML:
• 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
EML
EML
Israel
LTER
Metacat
EML
SAEON
Metacat
EML
Brazil
Metacat
All ILTER
Metacats will be
linked, so all
metadata can be
accessed from a
single web page
JaLTER
Metacat
TERN
Metacat
US
LTER
Metacat
EML
Search Page for US LTER Metacat
This Web
Page
searches
the US
LTER
Metacat
A Similar
Web Page
will be built
to search
all ILTER
metadata
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/morphopo
rtal.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
Searching for data
packages
• 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
Searching for data
packages
• Search on local disks or network
• Search multiple terms using “More”
• You can combine a subject search with
taxonomic and spatial constraints
Searching for data
packages
• Select taxonomic rank and enter name
• Can search multiple taxa using “More”
Searching for data
packages
• 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
Searching for data
packages
• Select area of interest by moving box or enter
coordinates by hand
• Zoom in to allow greater precision using the
graphical box
Searching for data
packages
• 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
Searching for data
packages
• 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
Searching for data
packages
• 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
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
Editing Data Packages:
Data Set Owner
• Enter in the
information for the
owner, then hit “OK”
• You have to enter
one of the redlabeled 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”
Editing Data Packages:
Contact Person
• 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
Editing Data Packages:
Contact Person
• 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
Editing Data Packages:
Contact Person
• To select an
entry from
another data
package:
– select the
package on
the left
– then the
contact on
the right
Editing Data Packages:
Contact Person
• 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”
Editing Data Packages:
Spatial Coverage
• Enter a
description for
the area
• There are many
ways to select
the area
– Enter
coordinates
manually
– Select from list
– Box Tool
– Point Tool
Editing Data Packages:
Spatial Coverage
• Enter a
description for
the area
• Many ways to
select the area
– Enter coordinates
manually
– Select from list
– Box Tool
– Point Tool
Editing Data Packages:
Spatial Coverage
• Enter a
description for
the area
• Many ways to
select the area
– Enter
coordinates
manually
– Select from list
– Box Tool
– Point Tool
Editing Data Packages:
Spatial Coverage
• Enter a
description for
the area
• Many ways to
select the area
– Enter
coordinates
manually
– Select from list
– Box Tool
– Point Tool
Editing Data Packages:
Spatial Coverage
• Enter a
description for
the area
• 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”
Editing Data Packages:
Temporal Coverage
• Enter in the date
and hit “OK” if
your data were
collected on a
single day
• Alternatively, you
can enter a
range of
coverage
Editing Data Packages:
Temporal 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”
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”
Editing Data Packages:
Methods
• 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
Editing Data Packages:
Access Rights
• Select whether to
give read access
to the public
• To add an
additional
access privilege
or restriction, hit
“Add”
Editing Data Packages:
Access Rights
• Select whether to
give read access
to the public
• To add an
additional
access privilege
or restriction, hit
“Add”
Editing Data Packages:
Access Rights
• Click “Refresh
the user list…”
• Select the user
or group to give
special access
rules
• Select “Allow” or
“Deny”
• Select the type
of access
Editing Data Packages:
Access Rights
• Click “Refresh
the user list…”
• Select the user
or group to give
special access
rules
• Select “Allow” or
“Deny”
• Select the type
of access
Editing Data Packages:
Access Rights
• Click “Refresh
the user list…”
• Select the user
or group to give
special access
rules
• Select “Allow” or
“Deny”
• Select the type
of access
Editing Data Packages:
Access Rights
• 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 [email protected]. 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 [email protected]
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
[email protected].
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
[email protected] for
instructions.