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r1 - 06 May 2003 - 08:58:00 - ChrisWroeYou are here: myGrid wiki >  Mygrid Web  > GDScenarioReqs > GDScenarioReqsWithWP6Annotation > ClassificationWizardNotes > TypeMatchScenario
-- ChrisWroe - 06 May 2003

Four layers of type match:

Semantic

Source provides Target expects Comment
DNA sequence sequence exact semantic match
sequence DNA sequence semantic type mismatch - the target is expecting something more specific and so it is not appropriate to send the data to this service
DNA sequence sequence DNA sequence is a kind of sequence as represented in the ontology, and so it is appropriate to send to this service
EMBL record nucleotide sequence An EMBL record contains a nucleotide sequence as represented in the ontology. Need a pointer to a service that can parse an EMBL record and return a sequence
EMBL accession number EMBL record An EMBL record identifies a EMBL record. Need a pointer to a service that can retrieve an EMBL record from an EMBL accession number

Cardinality

Source provides Target expects Comment
Single value Single value Exact match
Single value >=1 as a collection Single value must be wrapped using CollectionFormat?
Collection Single value Collection must be iterated through and each item sent to the service. Results must be mapped to input values
Collection format one record per line Collection format one record per XML element Requires a catalogue of CollectionFormat? (s) and a pointer to a service that can do the transformation whether a local java object or a remote web service

Format (or complex data type)

There are two different scenarios.

  1. The two formats covney similiar semantics but in a different syntactic form.
  2. One format is more general than the other. The more general format explicitly conveys additional semantic information as an extra field.

Source provides Target expects Comment
EMBL nucleotide sequence fasta sequence It should be possible to map the information in one format to the other. Requires a service to do so
EMBL ID as simple text 'AF061303' EMBOSS universal sequence address 'EMBL:AF061303' EMBOSS would fail with the plain ID. To transfer between formats you need to transfer some of the semantics from the semantic type description (i.e. that it is an ID from EMBL) to the actual data itself (i.e add an EMBL qualifier). Would be simplest to get a service to do this

Carrier datatype

This is the simple datatype used to convey the data over the wire, and is what the WSDL, and workflow primarily deal in. I'm not sure what the issues are here.

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