September 2006 - tdwg-tag - lists.tdwg.org

[Tdwg-guid] IODP paleontology meeting and LSID
by Robert Huber 19 Sep '06

19 Sep '06

Dear all, I was invited to attend the IODP Paleontology meeting on taxonomic dictionaries and control lists end of september in Houston, USA. The IODP (Integrated Ocean Drilling Program)is one of the most important international earth science projects. http://iodp.org. IODP is currently evaluating new technologies for its data and information management. And one hot topic for its paleontology and biostratigraphy work is ..having control on taxonomic names.. I think LSIDs could be very interseting for IODP if they could use some kind of a 'reverse lookup', resolving LSIDs for names. I was asked to give a short presentation on GUIDS/LSID and I thought maybe one of you already has some interesting material to show? Any help is welcome! Btw. are there are any exciting news since summer? I am especially interested in: -how is the RDF/TCS thing evolving -> standardised metadata? -how have the nomenclators been proceeding? I heard e.g. about the ZooBank prototype any LSID plans for that yet? -DarwinCore and GBIF.. is there a way to resolve LSID from names? best regards, Robert Dr. Robert Huber WDC-MARE / PANGAEA - www.pangaea.de, www.wdc-mare.org Stratigraphy.net - www.stratigraphy.net _____________________________________________ MARUM - Institute for Marine Environmental Sciences (location) University Bremen Leobener Strasse POP 330 440 28359 Bremen Phone ++49 421 218-65593, Fax ++49 421 218-65505 e-mail rhuber(a)wdc-mare.org, robert.huber(a)stratigraphy.net

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[tdwg-tapir] Schema modification: r555 - trunk/protocol
by tdwg-tapir＠lists.tdwg.org 11 Sep '06

11 Sep '06

Author: markus Date: 2006-09-11 11:20:56 +0200 (Mon, 11 Sep 2006) New Revision: 555 Modified: trunk/protocol/tapir.xsd Log: numerous minor updates that arose during the first implementation and documentation phase. Summarized at http://ww3.bgbm.org/protocolwiki/ImplementationAndDocumentationChanges Modified: trunk/protocol/tapir.xsd =================================================================== --- trunk/protocol/tapir.xsd 2006-08-03 10:29:39 UTC (rev 554) +++ trunk/protocol/tapir.xsd 2006-09-11 09:20:56 UTC (rev 555) @@ -48,13 +48,22 @@ </xsd:annotation> <xsd:restriction base="xsd:string"/> </xsd:simpleType> - <xsd:simpleType name="qualifiedConceptIdType"> + <xsd:simpleType + name="qualifiedConceptIdType"> <xsd:annotation> - <xsd:documentation>A simpleType to represent qualified concept identifiers. This can - either be the full format NAMESPACE#LOCAL_CONCEPT or an alias which can be any - string e.g. unitID(a)abcd1.20.</xsd:documentation> + <xsd:documentation>Concept identifiers are just strings for TAPIR, so the protocol does + not enforce any pattern. However it is recommended to use globally, resolvable and + permanent unique identifiers for them. It is also recommended to avoid using + characters that are reserved in the "query" part of URLs, since concepts can be + referenced there by many TAPIR parameters and would need to be escaped. When + defining concepts based on xml schemas we recommend to simply concatenate the + namespace of the schema with the local xpath to the instance element. For example + /DataSets/DataSet/Units/Unit/InstitutionID in ABCD becomes + http://www.tdwg.org/schemas/abcd/2.06/DataSets/DataSet/Units/Unit/Instituti… + </xsd:documentation> </xsd:annotation> - <xsd:restriction base="xsd:string"/> + <xsd:restriction + base="xsd:string"/> </xsd:simpleType>   @@ -224,10 +233,10 @@ <xsd:element name="outputModel" type="outputModelType"></xsd:element> <xsd:complexType name="outputModelType"> <xsd:annotation> - <xsd:documentation>Response structures are part of a View definition which + <xsd:documentation>Response structures are part of a model definition which includes three sections: a record schema (structure), a mapping section for linking to the datasource model and an indexing section that is used as a reference for record counting and paging responses. - The outputModel template is a separate, external XML document, called by a search operation or View, + The outputModel template is a separate, external XML document, called by a search operation, that uses 'outputModel' as the root element. </xsd:documentation> </xsd:annotation> <xsd:sequence> @@ -299,7 +308,10 @@ <xsd:element name="searchTemplate" substitutionGroup="queryTemplate" type="searchTemplateType"/> <xsd:group name="searchTemplateGroup"> <xsd:sequence> - <xsd:element name="outputModel" type="externalResourceType"/> + <xsd:choice> + <xsd:element name="externalOutputModel" type="externalResourceType"></xsd:element> + <xsd:element name="outputModel" type="outputModelType"></xsd:element> + </xsd:choice> <xsd:element name="partial" minOccurs="0"> <xsd:annotation> <xsd:documentation>Select only a subset of the @@ -327,7 +339,7 @@ <xsd:element ref="filter" minOccurs="0"/> <xsd:element name="orderBy" minOccurs="0"> <xsd:annotation> - <xsd:documentation>A list of qualified concepts to be used for ordering the view + <xsd:documentation>A list of qualified concepts to be used for ordering the model results.</xsd:documentation> </xsd:annotation> <xsd:complexType> @@ -335,7 +347,7 @@ <xsd:element name="concept" maxOccurs="unbounded"> <xsd:annotation> <xsd:documentation>Repeatable element. One or more concepts to be used for ordering the - view. If the attribute "descend" is set to true, a descending + model. If the attribute "descend" is set to true, a descending ordering will be used instead of the default ascending one.</xsd:documentation> </xsd:annotation> <xsd:complexType> @@ -378,7 +390,7 @@ </xsd:annotation> <xsd:complexType> <xsd:sequence> - <xsd:element name="concept" type="qualifiedConceptReferenceType" minOccurs="0" maxOccurs="unbounded"> + <xsd:element name="concept" type="qualifiedConceptReferenceType" minOccurs="1" maxOccurs="unbounded"> <xsd:annotation> <xsd:documentation>A single qualified concept</xsd:documentation> </xsd:annotation> @@ -408,7 +420,7 @@ <xsd:element name="filter"> <xsd:annotation> <xsd:documentation>An abstract filter encoding that could be translated to other local - query languages. Can be used by search, inventory and view operations to specify + query languages. Can be used by search and inventory operations to specify searching conditions.</xsd:documentation> </xsd:annotation> <xsd:complexType> @@ -714,17 +726,17 @@ <xsd:choice> <xsd:element name="ping"> <xsd:complexType> - <xsd:attributeGroup ref="operationRequestGroup"/> + <xsd:attributeGroup ref="globalParametersGroup"/> </xsd:complexType> </xsd:element> <xsd:element name="capabilities"> <xsd:complexType> - <xsd:attributeGroup ref="operationRequestGroup"/> + <xsd:attributeGroup ref="globalParametersGroup"/> </xsd:complexType> </xsd:element> <xsd:element name="metadata"> <xsd:complexType> - <xsd:attributeGroup ref="operationRequestGroup"/> + <xsd:attributeGroup ref="globalParametersGroup"/> </xsd:complexType> </xsd:element> <xsd:element name="inventory"> @@ -733,20 +745,20 @@ <xsd:element name="template" type="externalResourceType"/> <xsd:group ref="inventoryTemplateGroup"/> </xsd:choice> - <xsd:attributeGroup ref="operationRequestGroup"/> + <xsd:attributeGroup ref="globalParametersGroup"/> <xsd:attributeGroup ref="pagingParametersGroup"/> </xsd:complexType> </xsd:element> <xsd:element name="search"> <xsd:annotation> - <xsd:documentation>A search with the view definition used for the search as an attribute. If left out defaults to the one specified by the provider and exposed in the capabilities.</xsd:documentation> + <xsd:documentation>A search with TBD... </xsd:documentation> </xsd:annotation> <xsd:complexType> <xsd:choice> <xsd:element name="template" type="externalResourceType"/> <xsd:group ref="searchTemplateGroup"/> </xsd:choice> - <xsd:attributeGroup ref="operationRequestGroup"/> + <xsd:attributeGroup ref="globalParametersGroup"/> <xsd:attributeGroup ref="pagingParametersGroup"/> <xsd:attribute name="envelope" type="xsd:boolean" use="optional" default="true"/> </xsd:complexType> @@ -755,7 +767,7 @@ <xsd:element name="diagnostics" type="diagnosticsListType" minOccurs="0"/> </xsd:sequence> </xsd:complexType> - <xsd:attributeGroup name="operationRequestGroup"> + <xsd:attributeGroup name="globalParametersGroup"> <xsd:attribute name="xslt" type="xsd:anyURI" use="optional"/> <xsd:attribute name="xslt-apply" type="xsd:boolean" use="optional" default="false"/> <xsd:attribute name="log-only" type="xsd:boolean" use="optional" default="false"/> @@ -783,11 +795,12 @@ <xsd:element name="header" type="headerType"/> <xsd:choice> <xsd:element ref="pong"/> - <xsd:element ref="metadata"/><xsd:element ref="capabilities"/> - - <xsd:element name="inventory" type="inventoryResultType"/> - <xsd:element name="search" type="searchResultType"/> - <xsd:element name="error" type="diagnosticMessageType"/> + <xsd:element ref="metadata"/> + <xsd:element ref="capabilities"/> + <xsd:element ref="inventory" /> + <xsd:element ref="search" /> + <xsd:element ref="error" /> + <xsd:element ref="logged" /> </xsd:choice> <xsd:element name="diagnostics" type="diagnosticsListType" minOccurs="0"> <xsd:annotation> @@ -838,42 +851,39 @@ <xsd:element name="capabilities"> <xsd:complexType/> </xsd:element> - <xsd:element name="view" minOccurs="0"> + <xsd:element name="inventory" minOccurs="0"> <xsd:complexType> <xsd:sequence> - <xsd:element name="queryTemplates"> - <xsd:complexType> - <xsd:sequence> - <xsd:element name="queryTemplate" type="externalResourceType" maxOccurs="unbounded"/> - </xsd:sequence> - </xsd:complexType> - </xsd:element> + <xsd:element name="templates" type="templatesCapabilitiesType" minOccurs="0"/> + <xsd:element name="anyConcepts" minOccurs="0"><xsd:complexType/></xsd:element> </xsd:sequence> </xsd:complexType> </xsd:element> - <xsd:element name="inventory" minOccurs="0"> - <xsd:complexType/> - </xsd:element> <xsd:element name="search" minOccurs="0"> <xsd:complexType> <xsd:sequence> - <xsd:element name="staticOutputModels" minOccurs="0"> + <xsd:element name="templates" type="templatesCapabilitiesType" minOccurs="0" /> + <xsd:element name="outputModels" minOccurs="0"> <xsd:complexType> <xsd:sequence> - <xsd:element name="outputModel" type="externalResourceType" maxOccurs="unbounded"/> - </xsd:sequence> - </xsd:complexType> - </xsd:element> - <xsd:element name="dynamicOutputModels" minOccurs="0"> - <xsd:complexType> - <xsd:sequence> - <xsd:element name="structure" type="responseStructureCapabilitiesType"> - <xsd:annotation> - <xsd:documentation>The supported subset of - the XML Schema - language.</xsd:documentation> - </xsd:annotation> + <xsd:element name="knownOutputModels" minOccurs="0" > + <xsd:complexType> + <xsd:sequence> + <xsd:element name="outputModel" type="externalResourceType" maxOccurs="unbounded"/> + </xsd:sequence> + </xsd:complexType> </xsd:element> + <xsd:element name="anyOutputModels" minOccurs="0"> + <xsd:complexType> + <xsd:sequence> + <xsd:element name="responseStructure" type="responseStructureCapabilitiesType"> + <xsd:annotation> + <xsd:documentation>The supported subset of the XML Schema language.</xsd:documentation> + </xsd:annotation> + </xsd:element> + </xsd:sequence> + </xsd:complexType> + </xsd:element> </xsd:sequence> </xsd:complexType> </xsd:element> @@ -881,22 +891,43 @@ </xsd:complexType> </xsd:element> </xsd:sequence> - <xsd:attribute name="logRequests" use="required" > - <xsd:simpleType> - <xsd:restriction base="xsd:string"> - <xsd:enumeration value="required"/> - <xsd:enumeration value="accepted"/> - <xsd:enumeration value="denied"/> - </xsd:restriction> - </xsd:simpleType> - </xsd:attribute> </xsd:complexType> </xsd:element> - <xsd:element name="filter" type="filterCapabilitiesType"> - <xsd:annotation> - <xsd:documentation>Information about the supported filter operators of this - service.</xsd:documentation> - </xsd:annotation> + <xsd:element name="requests"> + <xsd:complexType> + <xsd:sequence> + <xsd:element name="encoding"> + <xsd:complexType> + <xsd:sequence> + <xsd:element name="kvp"><xsd:complexType/></xsd:element> + <xsd:element name="xml" minOccurs="0"><xsd:complexType/></xsd:element> + </xsd:sequence> + </xsd:complexType> + </xsd:element> + <xsd:element name="globalParameters"> + <xsd:complexType> + <xsd:sequence> + <xsd:element name="logOnly"> + <xsd:simpleType> + <xsd:restriction base="xsd:string"> + <xsd:enumeration value="required"/> + <xsd:enumeration value="accepted"/> + <xsd:enumeration value="denied"/> + </xsd:restriction> + </xsd:simpleType> + </xsd:element> + <xsd:element name="xlst" minOccurs="0"><xsd:complexType/></xsd:element> + </xsd:sequence> + </xsd:complexType> + </xsd:element> + <xsd:element name="filter" type="filterCapabilitiesType"> + <xsd:annotation> + <xsd:documentation>Information about the supported filter operators of this + service.</xsd:documentation> + </xsd:annotation> + </xsd:element> + </xsd:sequence> + </xsd:complexType> </xsd:element> <xsd:element name="concepts"> <xsd:annotation> @@ -1018,6 +1049,22 @@ <xsd:element ref="custom" minOccurs="0"/> </xsd:sequence> </xsd:complexType> + + <xsd:complexType name="templatesCapabilitiesType"> + <xsd:sequence> + <xsd:element name="template" maxOccurs="unbounded"> + <xsd:complexType> + <xsd:complexContent> + <xsd:extension base="externalResourceType"> + <xsd:attribute name="wsdl" type="xsd:anyURI"> + <xsd:annotation><xsd:documentation>URL pointing to a WSDL file describing this template interface</xsd:documentation></xsd:annotation> + </xsd:attribute> + </xsd:extension> + </xsd:complexContent> + </xsd:complexType> + </xsd:element> + </xsd:sequence> + </xsd:complexType> <xsd:complexType name="responseStructureCapabilitiesType"> <xsd:annotation> <xsd:documentation>A complete indication about what subset of the response structure @@ -1508,11 +1555,16 @@ resource or an indication of its security status.</xsd:documentation> </xsd:annotation> </xsd:element> - <xsd:element ref="dct:modified"> + <xsd:element ref="dct:modified" minOccurs="0"> <xsd:annotation> <xsd:documentation></xsd:documentation> </xsd:annotation> </xsd:element> + <xsd:element ref="dct:created" minOccurs="0"> + <xsd:annotation> + <xsd:documentation></xsd:documentation> + </xsd:annotation> + </xsd:element> <xsd:element name="indexingPreferences" minOccurs="0"> <xsd:complexType> <xsd:attribute name="startTime" type="xsd:time"/> @@ -1627,6 +1679,7 @@ <xsd:attribute ref="lang"/> </xsd:complexType>  + <xsd:element name="inventory" type="inventoryResultType" /> <xsd:complexType name="inventoryResultType"> <xsd:annotation> <xsd:documentation>Format of inventory operation result.</xsd:documentation> @@ -1673,6 +1726,7 @@ </xsd:sequence> </xsd:complexType>  + <xsd:element name="search" type="searchResultType" /> <xsd:complexType name="searchResultType"> <xsd:annotation> <xsd:documentation>Format of search operation result.</xsd:documentation> @@ -1687,4 +1741,13 @@ </xsd:element> </xsd:sequence> </xsd:complexType> +  + <xsd:element name="error" type="diagnosticMessageType"/> +  + <xsd:element name="logged" type="loggedResultType"/> + <xsd:complexType name="loggedResultType"> + <xsd:annotation> + <xsd:documentation>Format of logged operation result indicated by setting a true logOnly attribute in the request.</xsd:documentation> + </xsd:annotation> + </xsd:complexType> </xsd:schema>

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[tdwg-tapir] Last minute changes
by Renato De Giovanni 06 Sep '06

06 Sep '06

Dear all, I've been in contact with Markus, Javier (both updating the PyWrapper TAPIR provider software) and Charles (responsible for the TAPIR specification) and we would still like to propose a set of changes to the protocol before releasing its 1.0 version. I would say that this is mainly an effort to make the protocol clearer and more symmetric across operations. We also tried to better define the three different levels of provider implementation. So, if you're interested and if you have some time to look at the following page, please let us know if there's anything you think should be better discussed there, and also let us know if you have any comments or different ideas: http://ww3.bgbm.org/protocolwiki/ImplementationAndDocumentationChanges Best Regards, -- Renato

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Potential rigorous frameworks for TAG
by Bob Morris 04 Sep '06

04 Sep '06

Preparing the syllabus for my graduate software engineering course, I stumbled on http://www.eclipse.org/modeling/ which leads eventually to the recently adopted OMG Ontology Definition Metamodel (ODM) http://www.omg.org/docs/ad/06-05-01.pdf In Model Directed Architecture, a Metamodel constrains how you can model your problems. Metamodels are always implicitly or explicitly behind any modeling tools. Explicit is better, because then the tools can analyze your conformance to the model. The eclipse modeling framework (EMF) supports this, so that tools like the IBM Rational Software Modeling and Rational Software Architect eclipse packages can implement it. Probably so do other modeling tools. In the detailed TOC of the above PDF, one will find every single topic around which the TAG discussions have swirled, and more. I'm sure that everyone on this list shares my excitement in finding that there is potentially a rigorous framework for the tag ontology efforts and will drop everything else to absorb this 338 page specification before coming to St. Louis, at which the program should be revised to comprise nothing else but its discussion for the entire week. Hah, hah, just serious. --Bob -- Robert A. Morris Professor of Computer Science UMASS-Boston http://www.cs.umb.edu/~ram phone (+1)617 287 6466

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