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EML—Applications for PEEIR

EML—Applications for PEEIR. KNB Overview. “Knowledge Network for Biocomplexity” Started in 1999 Auspices/people from NCEAS and LTER http://knb.ecoinformatics.org Lots of stuff to help ecologists integrate data

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EML—Applications for PEEIR

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  1. EML—Applications for PEEIR

  2. KNB Overview • “Knowledge Network for Biocomplexity” • Started in 1999 • Auspices/people from NCEAS and LTER • http://knb.ecoinformatics.org • Lots of stuff to help ecologists integrate data • Open source code and process, available at http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/eml/

  3. EML/XML • XML format for ecological data and metadata • XML a “markup” language • XML “schemas” describe a set of other “base” XML document containing “real” information • EML is set of schemas that describe that format • Data Markup • Metadata Markup

  4. Other KNB products • Morpho • Gui application for setting up an EML data structure and for entering data into it. • Written in Java, network enabled • Metacat • Backend to store data/metadata in EML. • Security/Authentication • Transform between EML/SQL/HTML • Validate EML

  5. XML/EML Example <?xml version="1.0"?> <eml:eml packageId="eml.1.1" system="http://knb.ecoinformatics.org" \ xmlns:eml="eml://ecoinformatics.org/eml-2.0.0"> <dataset> <title>Biodiversity surveys for Lesser Tree Frogs… </title> <creator id="23445" scope="document"> <individualName> <givenName>Jane</givenName> <surName>Smith</surName> </individualName> <electronicMailAddress>jane@data.org</electronicMailAddress> </creator> <contact> <references>23445</references> </contact> </dataset> </eml:eml>

  6. XML SchemaExample <?xml version="1.0" encoding="utf-8"?> <xs:schema xmlns:xs="http://www.w3.org/2001/XMLSchema"> <xs:element name="book"> <xs:complexType> <xs:sequence> <xs:element name="title" type="xs:string"/> <xs:element name="author" type="xs:string"/> <xs:element name="character" minOccurs="0" maxOccurs="unbounded"> <xs:complexType> <xs:sequence> <xs:element name="name" type="xs:string"/> <xs:element name="friend-of-type="xs:string“ minOccurs="0" maxOccurs="unbounded"/>

  7. Schema Cont’d <xs:element name="since" type="xs:date"/> <xs:element name="qualification" type="xs:string"/> </xs:sequence> </xs:complexType> </xs:element> </xs:sequence> <xs:attribute name="isbn" type="xs:string"/> </xs:complexType> </xs:element> </xs:schema>

  8. EML Advantages • Automatic transformation using XSLT or stylesheets • XML to HTML • XML to text or other format • XML to different XML • Automatic validation • Correct Hierarchical Structure • Correct Range and Type for data • Structure can help discovery

  9. EML Disadvantages • Complex • Verbose • Hierarchical data hard to interface with relational data • Hard to read without stylesheet

  10. Other Similar Systems • FGDC • Similarities: • Fine grained • Somewhat extendible • Uses some XML things • Differences • Unique format • Different internal development process

  11. PEEIR Data Needs • Need format for data transfer and archiving • Need data store that is easily queried and optimized for ad hoc analysis • Need data store that can integrate with visualization software

  12. Suitability of EML • Good for archive/transfer. • OK for query friendly store, but not as good as relational DB • Probably not so good for integrating with visualization software

  13. Summary • Probably advocate for a limited use of EML for metadata only • Keep data per se in combination of SQL, text, and binary files

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