morpho metadata management software seek training january 2004

Morpho – metadata management software

SEEK TrainingJanuary 2004

Morpho

Is a data management software tool for ecologists.

http://knb.ecoinformatics.org/software/morpho/

Morpho• provides a way for ecologists to

share data by defining a common structure to document their data (i.e. create metadata) so that other ecologists and/or software programs can correctly interpret the data.

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

So basically, Morpho is an xml editor

• But what is xml?

xml• Like html, xml uses a system of coded tags

<xxx>…..</xxx>

• Whereas html defines the look and feel of text, xml defines the content.

XML vs. EmlAs xml can define any content and Morpho is designed for ecologists this xml format has been structured for ecological data and is called EML.

EMLEcological Metadata Language is a content standard for documenting ecological data that is implemented using XML schema to define the structure.

EMLThe basic structure of EML emerged from the work of Michener et al. (1997), in which a set of metadata (information about the data which is pertinent to use the data) descriptors specific to the ecological sciences were developed.

Morpho allows you to create & edit metadata

without writing EML codes or remembering the structure of EML and the five classes of Metadata descriptors

Additionally Morpho allows you to

• Search & query metadata collections

• View data & data collections

• Verify/edit data • Provide access

control

Through the Metacat server

Metacat• is a generic

XML database that allows storage, query, and retrieval of arbitrary XML documents

So as you now have a basic understanding of …Morpho

• What it is• What it does • How it works

You will now have an opportunity to explore Morpho

In this exercise you will…

• Determine what constitutes useable data.

• Apply Ecological Metadata Descriptors to data

• Use Morpho to up load and edit a data package

Allison and Cicchetti example• Taxonomic issues (gaps in our knowledge and

understanding of discovering, describing and naming individual species and working out their relationships to provide a classification) are seen by many as an impediment to sound management and conservation of biodiversity -- Global Taxonomy Initiative.

• While primary research on systemics is crucial so is the creation and maintenance of easily accessible databases with reliable information on species names and their hierarchical classification. As an early career scientist in biology, much of the research you will conduct can provide valuable and pertinent taxonomic information and metadata.

• In this exercise we will provide you an opportunity to use Morpho to add and edit metadata to a pre-existing data set. Using data from the 1976 classic article Sleep in Mammals: Ecological and Constitutional Correlates, by Allison Cicchetti, you learn the importance of adequate metadata and the difficulty in using archived data.

Step 1: Locate Allison and Cicchetti data using the web

Using either your favorite web browser or ecological database locate the data from the 1976 article Sleep in Mammals: Ecological and Constitutional Correlates, by Allison Cicchetti.

While conducting your web search please respond to the following questions.

1. What resources are available for locating ecological data?

2. Is the data saved in a useable format?3. What information is there?4. What information is missing?5. Is this information integral?6. Is there enough adequate metadata to

use this data?

Once you havelocated useable dataplease download andsave the data file to afolder called Allison_Cicchetti_lastname on the local drive (Cdrive) in the folder

workspace.

Step 2: Use Morpho to edit Data

Open Morpho

Locate the morpho software on your computer

Open Morpho • This is the

screen that will open on your computer

• As a new user you will need to create a new profile

Creating a new profile in Morpho

Follow theinstructions in thewizard pop upwindow that opensby creating aprofile name andadding your firstand last name inthe open dialogueboxes and clicknext.

At this point you will notice that you have to register for a new metacat account at the KNB site so you must stop with Morpho and go to the KNB website.

Registering with KNB

http://knb.ecoinformatics.org/

in the lower left-hand part of your screen you will notice a login & registration box

Click on link “create new account” to open the window where you can create your metacat account

• This window will open

• Please fill in the registration information

• Register as unaffiliated

Creating your Metacat Account

• Write down this information as you will need your username and password to create your profile in Morpho!

• You can use this account to search for data on the KNB website and to access data on Morpho

Creating your Metacat Account

• Once you have registered at the KNB site and have established your metacat account you can finish creating your profile in Morpho….

Creating a Profile in Morpho

• enter your metacat account information from the KNB website

Creating a Profile in Morpho

Creating a Profile in Morpho

• Add an identifier Prefix

• This identifier will become the prefix of your stored metadata file names.

• This identifier prefix can be anything

Creating a Profile in Morpho• Enter the

Metacat username and the organization name which you registered on the knb.ecoinformatics.org site.

Creating a Profile in Morpho• Enter a

prefix that will be added to all the data set you enter under this profile.

Creating a Profile in Morpho

• The last step is to login into the metacat server.

• enter your Metacat password.

• This is the password you created on the KNB website

Using Morpho on Archived Data

Allison and Cicchetti example using Morpho *

• We will begin to use Morpho by uploading your saved allison and cicchetti to Morpho or the data

• The software has a wizard package that walks you through step by step to upload data.

• During this process, you will notice that much of the metadata can be added with this wizard

Adding a new data package to Morpho with the Package Wizard

Adding a new data package to Morpho with the Package Wizard

• To upload saved data to Morpho locate data on hard drive by clicking browse

• This window will open

• Go to the C drive

• Open workspace and locate your saved allison and cicchetti data

• if data is saved as an asci file the wizard can automatically save the metadata associated with the data

Adding a new data package to Morpho

• Enter the contact information for the data set you are adding

• Fields in red are required

View and check data tableIf the asci file was saved with delimiters Morpho will format data table according to delimiters

If your datawas notsaved as adelimited ascifile…pleaseuse canneddata set(commadelimitated)located inworkspace itis calledallison andcicchetti dataForexercise.txt

View and check data tableIf the asci file was saved with delimiters Morpho will format data table according to delimiters

Add a Table Name and description of data

Add/edit metadata to each column of data

• Move cursor to find information about fields

• Fields in red are required

Save data package to Morpho• You have the

option in Morpho to save locally or to network. In this instance you will want to save locally – on your hard drive.

• By saving to the network others will have access to your data – remember you can change this (local or network) using Morpho later

Using morpho to edit metadata• Once data

is up loaded to Morpho you can edit data or metadata

• This is the window that opens after you press finish in the morpho wizard.

Either click on Data in the data package window

Or click on edit at the appropriate level of metadata

The Morpho editor will open

• Information with red dots is required

• Multiple editor windows can be opened at each metadata level

• At this point we would like you to review the five levels of metadata descriptors (Data set, Research origin, Data set status & accessibility, Data structural and Supplemental) and note what information was available through the archived data and what valuable metadata was missing.

• If valuable metadata is missing locate additional resources (perhaps the article) from your prior web search or a new web search to fill in metadata

Remember these metadata descriptors were designed to

answer the questions• What relevant data exist?• Why were those data collected and

are they suitable for a particular use?• How can these data be obtained?• How are the data organized and

structured?• What additional information is

available that would facilitate data use and interpretation?

Adding metadata for each of the five classes of Ecological Metadata Descriptors using

morphoI. Data set descriptorsII. Research origin descriptorsIII. Data set status and accessibility IV. Data structural descriptorsV. Supplemental descriptors

Data set descriptors

• Identity

• Identification code

Data set descriptors

• Originator

Data set descriptors

• Abstract

Data set descriptors

• Keywords

Research origin descriptors

• Project description

• Research methods

Research origin descriptors

• Experimental or sampling design

Data set status & accessibility

• Where data is located

• Who is the contact person

Data set status & accessibility

•How to access and use the data

Data set status & accessibility

• Dates of when the data were accessed & modified

Data structural descriptors

Data structural descriptors

Data structural descriptors

• Variable information

Data structural descriptors

• Units of measurement

Data structural descriptors• Data

type• Data

format• Data

anomalies

Supplemental Descriptors

• Data acquisition

• Quality assurance

• Supplemental materials

Supplemental Descriptors• Computer

programs

• Archival info

• Publications/results

• History of data set usage

• Once you have completed going through and adding all the metadata you can you can close the editor and save the data locally.

Now it’s your turn….

• Using one of your own data sets• Determine metadata • Add your own data package to

morpho• Edit metadata