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Knb.ecoinformatics.org LTER EML Best Practices Data Discovery in the Biological Sciences 7-9 February 2005 Mark Servilla LTER Network Office University.

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Presentation on theme: "Knb.ecoinformatics.org LTER EML Best Practices Data Discovery in the Biological Sciences 7-9 February 2005 Mark Servilla LTER Network Office University."— Presentation transcript:

1 knb.ecoinformatics.org LTER EML Best Practices Data Discovery in the Biological Sciences 7-9 February 2005 Mark Servilla LTER Network Office University of New Mexico, Albuquerque

2 knb.ecoinformatics.org Agenda Goals & Motivation LTER Metadata Tiers Recommended EML elements Additional Recommendations

3 knb.ecoinformatics.org Goals & Motivation Guidelines to achieve the following goals –Maximize interoperability of LTER EML documents to facilitate data synthesis –Minimize heterogeneity of LTER EML documents to simplify development and re-use of software tools and style sheets –Identify useful subsets of the EML to support specific functionality tiers targeted by the LTER NIS Advisory Committee (NISAC) –Provide guidance to sites in their initial implementation of EML, and a roadmap for improving their implementation to achieve higher functionality Why do we need an “EML Best Practices” document?

4 knb.ecoinformatics.org LTER Tiered Trajectory for Metadata

5 knb.ecoinformatics.org Increasing Levels of Completeness Identification Discovery Evaluation Access Integration Semantic Use

6 knb.ecoinformatics.org Level 1 - Identification Description – Minimum content for adequate data set discovery Major Elements Added : –Title –Creator –Contact –Publisher –Publication Date –Keywords –Abstract –Dataset/distribution (i.e. URL for dataset information)

7 knb.ecoinformatics.org Level 1 Code Example <eml:eml xmlns:eml="eml://ecoinformatics.org/eml-2.0.1" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="eml://ecoinformatics.org/eml-2.0.1 http://someserver.fls.edu/eml-2.0.1/eml.xsd" packageId="knb-lter-fls.1.1" system="FLS” scope="system"> FLS-1 Arthropods Long-term Ground Arthropod Monitoring Dataset at Silver City, NM USA from 1998 to 2004...

8 knb.ecoinformatics.org John Ecologist FLS LTER Department of Ecology University of New Mexico PO Box 1234 Albuquerque NM 87131-1234 (505) 999-9999 jeco@unm.edu http://www.unm.edu/~jeco Level 1 Code Example cont.

9 knb.ecoinformatics.org Description – Level 1 content, plus coverage information to support targeted searches Major Elements Added : –Geographic Coverage –Taxonomic Coverage –Temporal Coverage Level 2 - Discovery

10 knb.ecoinformatics.org Silver City, NM USA -112.373634 -111.612936 +33.708829 +33.298975 304 627 meter... Level 2 Code Example

11 knb.ecoinformatics.org... 1998-11-12 2003-12-31 Orthopteran insects (grasshoppers) were id using the 2004 BigKey to Orthoptera Kingdom Animalia Phylum Arthropoda Level 2 Code Example cont.

12 knb.ecoinformatics.org Description – Level 2 content, plus data set details to enable end-user evaluation of the methodology and data entities Major Elements Added : –Intellectual Rights –Project –Methods –Data Table/Entity Group –Data Table/Attributes (constrained by current version of EML ) Level 3 - Evaluation

13 knb.ecoinformatics.org Level 3 Code Example The dataset is released to the public and may be used for academic or commercial purposes subject to the following restrictions: LTER will make every effort possible to control and document the quality of the data it publishes. Data are made available "as is"......

14 knb.ecoinformatics.org Level 3 Code Example cont.... Fictitious LTER Site (FLS) permanent monitoring program Dr. Eva Scientist addr-1 principalInvestigator The FLS basic monitoring program consists of monitoring of arthropod populations, plant net primary productivity, and bird populations. Monitoring takes place at 3 sites, 4 times a year. Climate parameters are continuously measured at all stations.

15 knb.ecoinformatics.org Level 3 Code Example cont. FSL Protocol for Surveying Ground Arthropods has been... FLS Protocol for Surveying Ground Arthropods pers-1 2000-02-23 This protocol is being used by FLS arthropod... Ecology... http://fls.univ.edu/protocols/arthro.html...

16 knb.ecoinformatics.org Level 3 Code Example cont. SBE MicroCAT 37-SM (S/N 1790); manufacturer: Sea-Bird Electronics (model: 37-SM MicroCAT); parameter: Conductivity (accuracy: 0.0003 S/m, readability: 0.00001 S/m, range: 0 to 7 S/m); last calibration: Feb 28, 2001 SBE MicroCAT 37-SM (S/N 1790); manufacturer: Sea-Bird Electronics (model: 37-SM MicroCAT); parameter: Pressure (water) (accuracy: 0.2m, readability: 0.0004m, range: 0 to 20m); last calibration: Feb 28, 2001 SBE MicroCAT 37-SM (S/N 1790); manufacturer: Sea-Bird Electronics (model: 37-SM MicroCAT); parameter: Temperature (water)(accuracy: 0.002C, readability: 0.0001C, range: -5 to 35C); last calibration: Feb 28, 2001...

17 knb.ecoinformatics.org Level 3 Code Example cont.... arthro_hab Habitat description for the sampling locations temp Water Temperature float celsius 0.001 real NaN value not recorded or invalid...

18 knb.ecoinformatics.org Level 3 Code Example cont. cond Conductivity measured with SeaBird Electronics CTD-911 float siemensPerMeter 0.0001 real 0 40...

19 knb.ecoinformatics.org Level 3 Code Example cont.... <unit id="siemensPerMeter" name="siemensPerMeter" unitType="conductance" parentSI="siemen" multiplerToSI="1"> electrical conductance of a solution (conductivity)...

20 knb.ecoinformatics.org Level 4 - Access Description – Level 3 content plus data access details to support automated data retrieval Major Elements Added : –Access –Physical

21 knb.ecoinformatics.org PUBLIC read uid=fls,o=LTER,dc=ecoinformatics,dc=org all Level 4 Code Example

22 knb.ecoinformatics.org... flslter.299.1 59847 1 column, http://fls.unm.edu/flslter.296.1... Level 4 Code Example

23 knb.ecoinformatics.org Level 5 - Integration Description – Level 4 content plus complete attribute and quality control details to support computer-assisted data integration and re- sampling; Integration-level metadata should support computer-mediated access and processing of data, and therefore requires that all aspects of the data package be fully described. Major Elements Added : –Attribute List (full descriptions) –Measurement Scale –Units –Constraint –Quality Control

24 knb.ecoinformatics.org Level 5 Code Example... pkarthro_taxa dbo.arthro_taxa.taxon arthro_taxa.taxonNotNull dbo.arthro_taxa.taxon...

25 knb.ecoinformatics.org Level 5 Code Example Passage of clouds during a profile reduces the incident radiation, and leads to erroneous estimates of Kd. Variation of incident irradiance was described in two ways (before binning): 1) the coefficient of variation (cv) over the 10m depth interval, and 2) difference......

26 knb.ecoinformatics.org Level 6 - Semantic Description – Level 5 content plus semantic information (currently under development by SEEK, and may require extension to the EML schema)

27 knb.ecoinformatics.org packageID and Metacat document naming convention LDAP access control in Metacat Organizational citation Additional Recommendations Metacat and by extension the Metacat harvester rely on numerical data set ids and revision numbers for document management and synchronization - packageId attributes for EML contributed to the KNB Metacat should be formed as follows: knb-lter-[site].[dataset number].[revision], e.g. knb-lter-sev.187.4 Scope UniqueID Revision# Metacat access control format conforms to the LDAP Distinguished Name concept: uid=FLS,o=lter,dc=ecoinformatics,dc=org The “Organization” field on the Metacat query results page is populated using the first eml:eml/dataset/creator/organizationName element in the document, so it is recommended that for LTER-contributed data sets the LTER site be included as the first creator: Sevilleta LTER

28 knb.ecoinformatics.org Access to EML Best Practices 1.0 http://cvs.lternet.edu/cgi-bin/viewcvs.cgi/emlbestpractices/emlbestpractices-1.0/emlbestpractices_oct2004.doc http://cvs.lternet.edu

29 knb.ecoinformatics.org Credits James Brunt (LNO) Corinna Gries (CAP) Jeanine McGann (LNO) Margaret O’Brien (SBC) Ken Ramsey (JRN) Wade Sheldon (GCE)

30 knb.ecoinformatics.org 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

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