EcoGrid in SEEK A Data Grid System for Ecology Bertram Ludaescher University of California, Davis Arcot Rajasekar San Diego Supercomputer Center, University of California, San Diego

What is SEEK? Science Environment for Ecological Knowledge (SEEK) Multidisciplinary research project to create: Distributed data network (EcoGrid) Environmental, ecological, and systematics data Scalable systems for scientific analysis (workflow systems) Systems for semi-automated data and model integration Collaborators NCEAS, UNM, SDSC, U Kansas Vermont, Napier, ASU, UNC

Science Environment for Ecological Knowledge Research Objectives Access to ecological, environmental, and biodiversity data Enable data sharing & re-use Enhance data discovery at global scales Scalable analysis and synthesis Taxonomic, Spatial, Temporal, Conceptual integration of data Address data heterogeneity issues Enable communication and collaboration for analysis Enable re-use of analytical components Collaborators NCEAS, UNM, SDSC, U Kansas Vermont, Napier, ASU, UNC

SEEK Overview

SEEK Components Science Environment for Ecological Knowledge Kepler Modeling scientific workflows EcoGrid Making diverse environmental data systems interoperate Semantic Mediation System “Smart” data discovery and integration Knowledge Representation WG Taxon WG BEAM WG Education, Outreach, Training

SEEK EcoGrid Goal: allow diverse environmental data systems to interoperate Hides complexity of underlying systems using lightweight interfaces Integrate diverse data networks from ecology, biodiversity, and environmental sciences Data systems Any system can implement these interfaces Prototyping using: Metacat, SRB, DiGIR, Xanthoria, etc. Supports multiple metadata standards EML, Darwin Core as foci

EcoGrid client interactions Modes of interaction Client-server Fully distributed Peer-to-peer EcoGrid Registry Node discovery Service discovery Aggregation services Centralized access Reliability Data preservation

Ecogrid Focus Data and Metadata Distributed Data XML-based Metadata Service to Semantic Mediation Layer Access to Ontologies and Taxon Services Helping with Semantic Data Integration Service to Analysis and Modelling Layer Interaction with Kepler - Workflows Interaction with Grid Computing Facilities Access to Legacy Apps LifeMapper Spatial Data Workbench

EcoGrid Node

Layers in EcoGrid

Ecological Metadata Language Metadata: a means to manage ecological data There is no universal data model for ecology Accommodate heterogeneity and dispersion EML Common language for archiving and transporting data Discovery information Creator, Title, Abstract, Keyword, etc. Content Context Physical, logical structure SEEK will add semantic structure

An Example EML Document Alegria Temperatures PISCO: Intertidal Temperature Data: Alegria, California: Carol Blanchette PISCO UCSB Marine Science Institute Santa Barbara CA These temperature data were collected at Alegria Beach, California, and were... OceanographicSensorData Thermistor PISCOCategories Please contact the authors for permission to use these data. Please also acknowledge the authors in any publications. C.Blanchette Transform

Metadata driven data ingestion Key information needed to read and machine process a data file is in the metadata File descriptors (CSV, Excel, RDBMS, etc.) Entity (table) and Attribute (column) descriptions Name Type (integer, float, string, etc.) Codes (missing values, nulls, etc.) Integrity constraints In the future, this will include semantic typing

Heterogeneous Data integration Requires advanced metadata and processing Attributes must be semantically typed Collection protocols must be known Units and measurement scale must be known Measurement relationships must be known e.g., that ArealDensity=Count/Area

Ecological ontologies What was measured (e.g., biomass) Type of measurement (e.g., Energy) Context of measurement (e.g., Psychotria limonensis) How it was measured (e.g., dry weight) SEEK intends to enable community-created ecological ontologies using OWL Represents a controlled vocabulary for ecological metadata More about this in Bertram’s talk

EcoGrid Resources ANDLUQHBRNTL Metacat node Legacy system LTER Network (24) Natural History Collections (>> 100) Organization of Biological Field Stations (180) UC Natural Reserve System (36) Partnership for Interdisciplinary Studies of Coastal Oceans (4) Multi-agency Rocky Intertidal Network (60) SRB node DiGIR node VCR VegBank node Xanthoria node

EcoGrid Resources EcoGrid Registry SRB MetaCat Xanthoria Diggir VegBank

EcoGrid Node

EcoGrid Query Service Ecogrid Query adopts a query schema, Query Document Schema, as a common query language within Ecogrid. <egq:query queryId="test.1.1" system=" xmlns:egq="ecogrid://ecoinformatics.org/ecogrid-query-1.0.0beta1" xmlns:xsi=" xsi:schemaLocation="ecogrid://ecoinformatics.org/ecogrid-query-1.0.0beta1../../src/xsd/query.xsd"> eml://ecoinformatics.org/eml size owner min. value max. value value units --> metadata query for Eco Models /home/whywhere.seek %World Geodetic System% /home/whywhere.seek %World Geodetic System% 39.11

Ecogrid Services implementation for GET/PUT  The ‘get’ call from ecogrid client enables retrieval of the content of a dataset/file such as SRB, MetaCat.  The ‘get’ function also be enables SQL querying of relational databases (Oracle, DB2, etc), which are pre- registered as a data source in SRB.  Put for data: Ecogrid put service allows users to create (upload) files into EcoGrid resources such as MetCat, SRB.  Put for metadata: Ecogrid put service also allows ingestion of metadata such as EML in MetaCat or User- defined metadata in SRB.

EcoGrid Queries in Kepler

EML Metadata Display in Kepler

EcoGrid Sources in Kepler

Query Builder

Status Read, Query & Register Completed Simple Registry Operational EcoGrid Wrappers completed for: MetaCat SRB DiGGiR Xanthoria Available Interfaces WSDL Simple Web Interactivity Kepler

Acknowledgements This material is based upon work supported by: The National Science Foundation under Grant Numbers , , , , , and The National Center for Ecological Analysis and Synthesis, a Center funded by NSF (Grant Number ), 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