EPGRIS template

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(No Transcript)
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EPGRIS technical issue
XML and EURISCO
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XML and EURISCO

• XML
• what it is
• advantages
• XML and EURISCO
• XML schema

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XML and EURISCO

• basic EURISCO upload format
• rectangular file
• n columns, m rows, and lots of missing values
• first row headers
• other rows accession data
• columns tab separated

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XML and EURISCO

• what is XML?
• Extended Markup Language
• actual data embedded in series of tags
• ltopening taggtthe datalt/closing taggt
• e.g. ltACCENUMBgtDAU16lt/ACCENUMBgt
• the tags define the data
• each type of data has its own tag
• you can make up as many tags as desired
• tag definitions stored in meta-file (called
  schema)
• many datafiles can use the same set of
  definitions
• one meta-file for entire dataset

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XML and EURISCO

• XML version of first record
• ltaccessiongt
• ltNICODEgtNLDlt/NICODEgt
• ltINSTCODEgtNLD037lt/INSTCODEgt
• ltACCENUMBgtCGN0001lt/ACCENUMBgt
• lt/accessiongt

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XML and EURISCO

• XML version of entire matrix
• ltnational_inventorygt
• ltaccessiongt ltNICODEgtNLDlt/NICODEgt
• ltINSTCODEgtNLD037lt/INSTCODEgt
• ltACCENUMBgtCGN0001lt/ACCENUMBgt lt/accessiongt
• ltaccessiongt ltNICODEgtNLDlt/NICODEgt
• ltINSTCODEgtNLD037lt/INSTCODEgt
• ltACCENUMBgtCGN0002lt/ACCENUMBgt lt/accessiongt
• ltaccessiongt ltNICODEgtNLDlt/NICODEgt
• ltINSTCODEgtNLD037lt/INSTCODEgt
• ltACCENUMBgtCGN0003lt/ACCENUMBgt
• ltCOLLNUMBgtPG53lt/COLLNUMBgt lt/accessiongt
• ltaccessiongt ltNICODEgtNLDlt/NICODEgt
• ltINSTCODEgtNLD037lt/INSTCODEgt
• ltACCENUMBgtCGN0004lt/ACCENUMBgt lt/accessiongt
• lt/national_inventory gt

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XML and EURISCO

• XML alternative version of entire matrix
• ltnational_inventorygt
• ltNICODEgtNLDlt/NICODEgt
• ltINSTCODEgtNLD037lt/INSTCODEgt
• ltaccessiongt ltACCENUMBgtCGN0001lt/ACCENUMBgt lt/acces
  siongt
• ltaccessiongt ltACCENUMBgtCGN0002lt/ACCENUMBgt lt/acces
  siongt
• ltaccessiongt ltACCENUMBgtCGN0003lt/ACCENUMBgt
• ltCOLLNUMBgtPG53lt/COLLNUMBgt lt/accessiongt
• ltaccessiongt ltACCENUMBgtCGN0004lt/ACCENUMBgt lt/acces
  siongt
• lt/national_inventorygt

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XML and EURISCO

• XML allows hierarchical structuring of data
• within a National Inventory there are one or more
  collections
• within a collection there is a curator, an url,
  date of the file, etc
• within a curator there is a name, telephone, etc.
• within a collections there are one or more
  accessions
• within an accession there are descriptors

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XML and EURISCO

• extended matrix file (EURISCO compatible)
• ltnational_inventory gt
• ltNICODEgtNLDlt/NICODEgt
• ltcollectiongt
• ltINSTCODEgtNLD037lt/INSTCODEgt
• ltcuratorgt
• ltnamegtIetje Boukemalt/namegt
• ltphonegt31 317 477077lt/phonegt
• lt/curatorgt
• ltaccessiongt EURISCO descriptors with data
  lt/accessiongt
• ltaccessiongt EURISCO descriptors with data
  lt/accessiongt
• ltaccessiongt EURISCO descriptors with data
  lt/accessiongt
• ltaccessiongt EURISCO descriptors with data
  lt/accessiongt
• lt/collectiongt
• lt/national_inventory gt

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XML and EURISCO

• advantages of XML over rectangular files
• easily extendable
• if additional tags are defined, these can be used
• meta-information can be given at the beginning of
  file
• character set (clear advantage)
• data can easily be processed (parsed)
• Internet Explorer can display XML (advantage only
  for IE users)
• XML is widely used for platform and software
  independent data exchange (clear advantage)
• promotion of standardisation (EPGRIS-schema)

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XML and EURISCO

• extended matrix file in IE5

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XML and EURISCO

• XML and EURISCO
• XML will be an alternative upload file format
• allowed tags
• EURISCO descriptor list
• additional tags based on existing standards
• an EURISCO schema will be defined
• XML Schema allows definition of structure,
  descriptors, allowed ranges, data types, etc.
• contents and structure of XML-data can be
  validated with the XML Schema
• EURISCO schema - a standard available and
  published for the user community

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XML and EURISCO

• EURISCO schema
• to be developed by EPGRIS
• will include all EURISCO descriptors
• will include other descriptors from other
  standard schemas
• Global Biodiversity Information Facility
  (GBIF-Schema)
• Geographical Markup Language (GML)

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XML and EURISCO

• very first draft EURISCO schema
• contains elements to give descriptive information
  about
• supplier
• ltxselement ref"Supplier"/gt
• data source
• ltxselement ref"DataSource"/gt
• collection data itself
• ltxselement ref"ComponentDataSet"/gt

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XML and EURISCO

• in the Schema this looks like
• ltxselement name"DataSet"gt
• ltxscomplexTypegt
• ltxssequencegt
• ltxselement ref"Supplier"/gt
• ltxselement ref"DataSource"/gt
• ltxselement ref"ComponentDataSet"/gt
• lt/xssequencegt
• lt/xscomplexTypegt
• lt/xselementgt
• read as the Element DataSet has three other
  elements, called Supplier, DataSource and
  ComponentDataSet

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XML and EURISCO

• element ComponentDataSet contains inter alia an
  element Accession
• can occur as often as needed
• ltxselement name"ComponentDataSet"gt
• ltxscomplexTypegt
• ltxssequencegt
• ltxselement ref"CollectionName"/gt
• ltxselement ref"Institution"/gt
• ltxselement ref"Custodian"/gt
• ltxselement ref"DateExtracted"/gt
• ltxselement ref"Accession"
  maxOccurs"unbounded"/gt
• lt/xssequencegt
• lt/xscomplexTypegt
• lt/xselementgt

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XML and EURISCO

• element Accession contains
• some elements from the MCPDL
• other elements such as Taxonomy
• ltxselement name"Accession"gt
• ltxscomplexTypegt
• ltxssequencegt
• ltxselement ref"Taxonomy minOccurs"1/gt
• ltxselement name"ACCENAME type"xsstring/gt
• ltxselement name"ACCENUMB type"xsstring
• minOccurs"1/gt
• ltxselement name"ACQDATE type"xsstring/gt
• ltxselement name"ANCEST type"xsstring/gt
• ltxselement name"BREDCODE type"xsstring/gt
• lt/xssequencegt
• lt/xscomplexTypegt
• lt/xselementgt

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XML and EURISCO

• element Taxonomy groups together taxonomic MCPD
• elements GENUS, SPECIES, SPAUTHOR, SUBTAXA,
  SUBTAUTHOR, CROPNAME
• ltxselement name"Taxonomy"gt
• ltxscomplexTypegt
• ltxssequencegt
• ltxselement ref"GENUS" minOccurs"1"
  maxOccurs"1"/gt
• ltxselement ref"SPECIES"/gt
• ltxselement ref"SPAUTHOR"/gt
• ltxselement ref"SUBTAXA"/gt
• ltxselement ref"SUBTAUTHOR"/gt
• ltxselement ref"CROPNAME"/gt
• lt/xssequencegt
• lt/xscomplexTypegt
• lt/xselementgt

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XML and EURISCO

• the Schema defines for example
• element Genus is mandatory (minOccurs1).
• ltxselement ref"Genus" minOccurs"1"
  maxOccurs"1"/gt
• the parser (programme reading the XML-data)
  checks the data and tells whether they are valid
  regarding the definition in the Schema
• error-checking becomes very easy

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XML and EURISCO

• an example of XML-Data
• ltAccessiongt
• ltTaxonomygt
• ltGENUSgtDaucuslt/GENUSgt
• ltSPECIESgtcarotalt/SPECIESgt
• ltSPAUTHORgtL.lt/SPAUTHORgt
• lt/Taxonomygt
• ltACCENUMBgtDAU16lt/ACCENUMBgt
• ltACCENAMEgtD-AUWlt/ACCENAMEgt
• ltCOLLNUMBgt876lt/COLLNUMBgt
• ltCOLLCODEgtROM006lt/COLLCODEgt
• ltOTHERNUMBgt56789lt/OTHERNUMBgt
• lt/Accessiongt

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XML and EURISCO

• in the XML-file a reference to an XSL-file can be
  given
• xsl style sheet, instruction how to display the
  data
• lt?xml-stylesheet type"text/xsl"
  href"euriscoschema.xsl"?gt
• example (one line from euriscoschema.xsl)
• lttrgtlttdgtltxslvalue-of select"ACCENUMB"/gtlt/tdgtlt/tr
  gt
• if the XML-file is opened with Internet Explorer
  the data is displayed as follows

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XML and EURISCO
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XML and EURISCO

• concluding remarks
• XML is developing into a standard for data
  exchange
• XML is relatively easy to learn, read, understand
• many XML tutorials on the Internet (e.g.
  www.w3schools.com)
• EURISCO should be able to handle XML-files
• a EURISCO schema, defining the structure, should
  be developed based on existing schemas