EML Overview

1
EML Overview

• Second KNB Data Management Workshop
• 2-4 February 2005
• Mark Servilla
• LTER Network Office
• University of New Mexico, Albuquerque

2
Agenda

• EML Defined
• Goals of EML
• Related Metadata Standards
• XML Overview
• Practical Usage
• Module Organization
• Development, Documentation and Communication

3
What is EML?

• Ecological Metadata Language is
• an ecological metadata standard
• very extensible it can be used to describe many
  different types of data
• comprehensive and supports a rich set of
  constructs to fully describe data
• XML and is defined by an XML Schema
• exploitable by different computer applications

4
Goals of EML

• Address lack of dataset documentation
• Provide structure to traditionally unstructured
  information
• Aid transition toward synthetic research
• Enable both human-readable and machine-readable
  metadata
• Enable long-term archives
• Simple transfer format ascii text document
• Conform to accepted Internet-based standards for
  the implementation of EML (XML, XML Schema)
• Community-driven development process
• Intended to be both ancillary and integral to
  processing data

5
Related metadata standards

• Dublin Core Element Set
• Corresponds roughly to eml-resource
• Content Standard for Digital Geospatial Metadata
  (CSDGM)
• Federal Geographic Data Committee (FGDC)
• Corresponds to eml-spatialRaster,
  eml-spatialVector,eml-spatialReference
• Overlaps in other modules (eml-resource)
• Biological Data Profile (BDP) of the CSDGM
• Biological Data Working Group of the FGDC
• Shares structure for taxonomicCoverage,
  geologicAge, and ascii table structures
• ISO 19115 Geographic information Metadata
• Incorporated in the eml-spatial modules
• Eml-party derived from ISO 19115
• Darwin Core
• Partially overlaps with eml-coverage
• Geography Markup Language (GML)

6
Abridged History of EML
Second EML workshop
KNB Tools Workshop
Michener et al. paper
First EML workshop
FGDC CSDGM 2.0
FGDC CSDGM RS
EML ASU meeting
XML 1.0 released
FGDC CSDGM
NCEAS formed
BDP approved
FGDC created
NBII created
FLED report
ISO 19115
GML 3.0
EML 1.0.0
EML 1.4.x
EML 2.0.0
EML 2.0.1
EML 1.3.0
Early ecological metadata work in LTER and
elsewhere
EML 2.0.0rc1-3
EML 2.0.0 beta1-9
7
Conversion among standards

• EML represents a superset of
• BDP
• CSDGM
• ISO 19115 (I think)
• Dublin Core
• Theoretically can convert from EML to those
• Extensive overlap among all of these standards
• Practically, have conversion script for
• EML ? BDP
• Uses XSLT so can be used in a variety of software
  
• Need to incorporate this into tools like Morpho
  and Metacat
• Need other conversion scripts!

8
Review
XML eXtensible Markup Language

• Development influenced by SGML and HTML Version
  1.0 in early 1998
• A semantic language that lets you more
  meaningfully annotate text (where HTML lets you
  define how text can be displayed, XML provides it
  with meaning).
• Important for presentation, exchange, and
  management of information
• Tools include DTD, Schema, XSL, and more

9
XML Document Structure
lt?xml version1.0 standaloneyesgt lt!-- This
is an example bibliography. --gt ltBIBgt ltBOOK
nicknameDragon bookgt ltAUTHOR idahogt
Aho, A. V. lt/AUTHORgt ltAUTHOR idsethigt
Sethi, R. lt/AUTHORgt ltAUTHOR idullmangt
Ullman, J. D. lt/AUTHORgt ltTITLEgt
Compilers Principles, Techniques, and Tools
lt/TITLEgt ltPUBLISHERgt Addison-Wesley
lt/PUBLISHERgt ltYEARgt 1985 lt/YEARgt
lt/BOOKgt lt/BIBgt
10
XML Document Structure
lt?xml version1.0 standaloneyesgt lt!-- This
is an example bibliography. --gt ltBIBgt ltBOOK
nicknameDragon bookgt ltAUTHOR idahogt
Aho, A. V. lt/AUTHORgt ltAUTHOR idsethigt
Sethi, R. lt/AUTHORgt ltAUTHOR idullmangt
Ullman, J. D. lt/AUTHORgt ltTITLEgt
Compilers Principles, Techniques, and Tools
lt/TITLEgt ltPUBLISHERgt Addison-Wesley
lt/PUBLISHERgt ltYEARgt 1985 lt/YEARgt
lt/BOOKgt lt/BIBgt
Prolog
11
XML Document Structure
lt?xml version1.0 standaloneyesgt lt!-- This
is an example bibliography. --gt ltBIBgt ltBOOK
nicknameDragon bookgt ltAUTHOR idahogt
Aho, A. V. lt/AUTHORgt ltAUTHOR idsethigt
Sethi, R. lt/AUTHORgt ltAUTHOR idullmangt
Ullman, J. D. lt/AUTHORgt ltTITLEgt
Compilers Principles, Techniques, and Tools
lt/TITLEgt ltPUBLISHERgt Addison-Wesley
lt/PUBLISHERgt ltYEARgt 1985 lt/YEARgt
lt/BOOKgt lt/BIBgt
Comment
12
XML Document Structure
lt?xml version1.0 standaloneyesgt lt!-- This
is an example bibliography. --gt ltBIBgt ltBOOK
nicknameDragon bookgt ltAUTHOR idahogt
Aho, A. V. lt/AUTHORgt ltAUTHOR idsethigt
Sethi, R. lt/AUTHORgt ltAUTHOR idullmangt
Ullman, J. D. lt/AUTHORgt ltTITLEgt
Compilers Principles, Techniques, and Tools
lt/TITLEgt ltPUBLISHERgt Addison-Wesley
lt/PUBLISHERgt ltYEARgt 1985 lt/YEARgt
lt/BOOKgt lt/BIBgt
Opening Tag
(Root Element)
Closing Tag
13
XML Document Structure
lt?xml version1.0 standaloneyesgt lt!-- This
is an example bibliography. --gt ltBIBgt ltBOOK
nicknameDragon bookgt ltAUTHOR idahogt
Aho, A. V. lt/AUTHORgt ltAUTHOR idsethigt
Sethi, R. lt/AUTHORgt ltAUTHOR idullmangt
Ullman, J. D. lt/AUTHORgt ltTITLEgt
Compilers Principles, Techniques, and Tools
lt/TITLEgt ltPUBLISHERgt Addison-Wesley
lt/PUBLISHERgt ltYEARgt 1985 lt/YEARgt
lt/BOOKgt lt/BIBgt
Element Content
14
XML Document Structure
lt?xml version1.0 standaloneyesgt lt!-- This
is an example bibliography. --gt ltBIBgt ltBOOK
nicknameDragon bookgt ltAUTHOR idahogt
Aho, A. V. lt/AUTHORgt ltAUTHOR idsethigt
Sethi, R. lt/AUTHORgt ltAUTHOR idullmangt
Ullman, J. D. lt/AUTHORgt ltTITLEgt
Compilers Principles, Techniques, and Tools
lt/TITLEgt ltPUBLISHERgt Addison-Wesley
lt/PUBLISHERgt ltYEARgt 1985 lt/YEARgt
lt/BOOKgt lt/BIBgt
Element Attribute
15
XML is Hierarchical by Design
ltBIBgt
ltBOOKgt
ltBOOKgt
ltBOOKgt
16
A simple EML example
17
Can be created in a text editor
18
or in custom applications
19
or in special XML editors
20
EML Module Organization

• Organized as discreet, logical units
• Modular design for reuse of sections
• Self describing field documentation is embedded
  in the EML files themselves

Pete Taylor photo
21
EML Module Organization cont.

• EML is the top-level container
• Four thematic modules
• Single resource module that is available to other
  modules

22
Resource Module

• Provides for reuse of common information
• title
• creator

23
Dataset Module

• Specific to the description of experimental data

24
Citation Module

• Specific to the description of a citation

25
Software Module

• Specific to the description of software

26
Protocol Module

• Specific to the description of scientific protocol

27
EML Development Communication

• Open Source project, welcomes contributions
• Developed by members of the community
• eml-dev_at_ecoinformatics.org

Pete Taylor photo

• irc.ecoinformatics.org, eml channel for
  discussion
• Source code managed in cvs.ecoinformatics.org
  repository
• Documented specification found on the KNB website
• An EML validating service is available at
• http//knb.ecoinformatics.org/emlparser

28
EML Distribution

• Currently at Release 2.0.1
• Releases of EML are downloadable
• http//knb.ecoinformatics.org/software/eml
• Development version available at
• http//cvs.ecoinformatics.org/cvs/cvsweb.cgi/eml

29
Acknowledgements
This material is based upon work supported
by The National Science Foundation under Grant
Numbers 9980154, 9904777, 0131178, 9905838,
0129792, and 0225676. The National Center for
Ecological Analysis and Synthesis, a Center
funded by NSF (Grant Number 0072909), the
University of California, and the UC Santa
Barbara campus. The Andrew W. Mellon
Foundation. PBI Collaborators NCEAS, University
of New Mexico (Long Term Ecological Research
Network Office), San Diego Supercomputer Center,
University of Kansas (Center for Biodiversity
Research) Kepler contributors SEEK, Ptolemy II,
SDM/SciDAC, GEON