Difference between revisions of "Talk:Natural Collections Description"

Latest revision as of 14:20, 7 January 2013

Preferred Namespaces and URIs

Defined namespaces in NCD

TODO decide for namespace prefixes of Collection, CollectionType, Person, TaxonOccurrenceInteraction, TermWithSource --Andreas Plank 09:58, 20 November 2012 (CET)

Namespace "base" should be "tbase" --Andreas Plank 12:00, 23 November 2012 (CET)

Namespace "tct" of OccurrenceStatusTerm in OccurrenceStatusTerm.rdf is probably wrong --Andreas Plank 13:27, 23 November 2012 (CET)

According to declaration of namespaces we could change all defined namespaces by prefixing them with "ncd.". I made a proposal in column "ncd. prefixes" in the table below. For that I removed some "t…" prefixes and kept "t…" prefixes only where I thought it would be necessary --Andreas Plank 13:27, 23 November 2012 (CET)

Overview of namespace definitions and their source files of scheme Natural Collections Description from TDWG
Defined XML namespace	ncd. prefixes (by Andreas Plank)	namespace URI	Defined in file
xmlns:base	ncd.base	http://rs.tdwg.org/ontology/Base#	CollectionType.rdf
xmlns:base	ncd.base	http://rs.tdwg.org/ontology/Base#	CyclicityTerm.rdf
xmlns:base	ncd.base	http://rs.tdwg.org/ontology/Base#	GeographicRegion.rdf
xmlns:base	ncd.base	http://rs.tdwg.org/ontology/Base#	InstitutionType.rdf
xmlns:base	ncd.base	http://rs.tdwg.org/ontology/Base#	OccurrenceStatusTerm.rdf
xmlns:base	ncd.base	http://rs.tdwg.org/ontology/Base#	SPMInfoItems.rdf
xmlns:base	ncd.base	http://rs.tdwg.org/ontology/Base#	TaxonRank.rdf
xmlns:base	ncd.base	http://rs.tdwg.org/ontology/Base#	TermWithSource.rdf
xmlns:gr	ncd.gr	http://rs.tdwg.org/ontology/voc/GeographicRegion#	GeographicRegion.rdf
xmlns:spm	ncd.spm	http://rs.tdwg.org/ontology/voc/SpeciesProfileModel#	SpeciesProfileModel.rdf
xmlns:spmi	ncd.spmi	http://rs.tdwg.org/ontology/voc/SPMInfoItems#	SPMInfoItems.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	Collection.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	ContactDetails.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	DigitalImage.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	Institution.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	OccurrenceRecord.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	Person.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	Procedure.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	PublicationCitation.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	SpeciesProfileModel.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	Specimen.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	TaxonConcept.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	TaxonName.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	TaxonOccurrence.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	TaxonOccurrenceInteraction.rdf
xmlns:tbase	ncd.base	http://rs.tdwg.org/ontology/Base#	Team.rdf
xmlns:tc	ncd.tc	http://rs.tdwg.org/ontology/voc/TaxonConcept#	TaxonConcept.rdf
xmlns:tcd	ncd.cd	http://rs.tdwg.org/ontology/voc/ContactDetails#	ContactDetails.rdf
xmlns:tcom	ncd.com	http://rs.tdwg.org/ontology/voc/Common	TaxonConcept.rdf
xmlns:tcom	ncd.com	http://rs.tdwg.org/ontology/voc/Common	TaxonOccurrenceInteraction.rdf
xmlns:tcom	ncd.com	http://rs.tdwg.org/ontology/voc/Common#	Collection.rdf
xmlns:tcom	ncd.com	http://rs.tdwg.org/ontology/voc/Common#	Institution.rdf
xmlns:tcom	ncd.com	http://rs.tdwg.org/ontology/voc/Common#	OccurrenceRecord.rdf
xmlns:tcom	ncd.com	http://rs.tdwg.org/ontology/voc/Common#	SpeciesProfileModel.rdf
xmlns:tcom	ncd.com	http://rs.tdwg.org/ontology/voc/Common#	Specimen.rdf
xmlns:tcom	ncd.com	http://rs.tdwg.org/ontology/voc/Common#	TaxonName.rdf
xmlns:tcom	ncd.com	http://rs.tdwg.org/ontology/voc/Common#	TaxonOccurrence.rdf
xmlns:tcore	ncd.core	http://rs.tdwg.org/ontology/Core#	Collection.rdf
xmlns:tcore	ncd.core	http://rs.tdwg.org/ontology/Core#	ContactDetails.rdf
xmlns:tcore	ncd.core	http://rs.tdwg.org/ontology/Core#	DigitalImage.rdf
xmlns:tcore	ncd.core	http://rs.tdwg.org/ontology/Core#	Institution.rdf
xmlns:tcore	ncd.core	http://rs.tdwg.org/ontology/Core#	OccurrenceRecord.rdf
xmlns:tcore	ncd.core	http://rs.tdwg.org/ontology/Core#	Procedure.rdf
xmlns:tcore	ncd.core	http://rs.tdwg.org/ontology/Core#	PublicationCitation.rdf
xmlns:tcore	ncd.core	http://rs.tdwg.org/ontology/Core#	SpeciesProfileModel.rdf
xmlns:tcore	ncd.core	http://rs.tdwg.org/ontology/Core#	Specimen.rdf
xmlns:tcore	ncd.core	http://rs.tdwg.org/ontology/Core#	TaxonOccurrence.rdf
xmlns:tct	ncd.ct	http://rs.tdwg.org/ontology/voc/CyclicityTerm#	CyclicityTerm.rdf
xmlns:tct	ncd.ost	http://rs.tdwg.org/ontology/voc/OccurrenceStatusTerm#	OccurrenceStatusTerm.rdf
xmlns:tdi	ncd.di	http://rs.tdwg.org/ontology/voc/DigitalImage#	DigitalImage.rdf
xmlns:tinst	ncd.inst	http://rs.tdwg.org/ontology/voc/Institution#	Institution.rdf
xmlns:titype	ncd.itype	http://rs.tdwg.org/ontology/voc/InstitutionType#	Institution.rdf
xmlns:tn	ncd.tn	http://rs.tdwg.org/ontology/voc/TaxonName#	TaxonName.rdf
xmlns:tor	ncd.or	http://rs.tdwg.org/ontology/voc/OccurrenceRecord#	OccurrenceRecord.rdf
xmlns:tp	ncd.p	http://rs.tdwg.org/ontology/Person#	Team.rdf
xmlns:tp	ncd.p	http://rs.tdwg.org/ontology/voc/Person#	Person.rdf
xmlns:tproc	ncd.proc	http://rs.tdwg.org/ontology/voc/Procedure#	Procedure.rdf
xmlns:tpub	ncd.pub	http://rs.tdwg.org/ontology/voc/PublicationCitation#	PublicationCitation.rdf
xmlns:trank	ncd.trank	http://rs.tdwg.org/ontology/voc/TaxonRank#	TaxonRank.rdf
xmlns:tsp	ncd.sp	http://rs.tdwg.org/ontology/voc/Specimen#	Specimen.rdf
xmlns:tt	ncd.t	http://rs.tdwg.org/ontology/voc/Team#	Team.rdf
xmlns:tto	ncd.to	http://rs.tdwg.org/ontology/voc/TaxonOccurrence#	TaxonOccurrence.rdf
-	ncd.coll	http://rs.tdwg.org/ontology/voc/Collection#	namespace not yet defined in Collection.rdf
-	ncd.colltype	http://rs.tdwg.org/ontology/voc/CollectionType#	namespace not yet defined in CollectionType.rdf

Form links for creation of NCD concepts

Formlinks are for testing. If data go to the right form field when clicking on a link, then they can be used.

Generation script (Linux)

bash script generateFormlinks4NCD.sh placed in the folder with all RDF files…

#!/bin/bash
ncdPrefixes=("ncd.base" "ncd.cd" "ncd.coll" "ncd.colltype" "ncd.com" 
             "ncd.core" "ncd.ct" "ncd.di" "ncd.gr" "ncd.inst" 
             "ncd.itype" "ncd.or" "ncd.ost" "ncd.p" "ncd.proc" 
             "ncd.pub" "ncd.sp" "ncd.spm" "ncd.spmi" "ncd.t" 
             "ncd.tc" "ncd.tn" "ncd.to" "ncd.trank" )
         # TODO unused: "TaxonOccurrenceInteraction.rdf" "TermWithSource.rdf"
ncdFiles=("Base.rdf" "ContactDetails.rdf" "Collection.rdf" "CollectionType.rdf" "Common.rdf" 
          "Core.rdf" "CyclicityTerm.rdf" "DigitalImage.rdf" "GeographicRegion.rdf" "Institution.rdf" 
          "InstitutionType.rdf" "OccurrenceRecord.rdf" "OccurrenceStatusTerm.rdf" "Person.rdf" "Procedure.rdf" 
          "PublicationCitation.rdf" "Specimen.rdf" "SpeciesProfileModel.rdf" "SPMInfoItems.rdf" "Team.rdf" 
          "TaxonConcept.rdf" "TaxonName.rdf" "TaxonOccurrence.rdf" "TaxonRank.rdf")
for (( i=0; i<${#ncdPrefixes[@]}; i++ ));do
  fileName=${ncdFiles[$i]}
  nsPrefix=${ncdPrefixes[$i]}
  printf "%2d: %15s %s …" $((i + 1)) $nsPrefix $fileName
  if [ -e  $fileName ];then
    if ! [ -d  "./export" ];then
      mkdir "./export"
    fi
    gawk --assign glob_coll_namespacePrefix="$nsPrefix" -f parseNCD.awk "${fileName%.*}.rdf" > "./export/${fileName%.*}.mwt"
    printf " (OK)\n"
  else
    printf " (not existing)\n"
  fi
done

awk script parseNCD.awk for generating wikitext formlinks…

#!/bin/awk
# BEGIN {} # block executed before processing
# END {} # block executed after processing
# FS input field separator (default: " ")
# RS record separator (default: newline)

# TODO 
# 2012-12-05 18:13:45: glob_instanceOfClass als value mit rdfs:range innheralb des Klassennamens? 
# 2012-11-27 11:04:50 check instances of Classes if they are assigned to the right concept type or/and instance-relation (skos:Collection or skos:inScheme or vann:termGroup etc)

##########################################
# This file converts NCD Collection.rdf
# into SMW {{#formlink}}. See also in the 
# BEGIN {…} section. An adapted version of
# this file may also be applicable to the 
# other RDF files in NCD scheme
#---- Usage: save this file as NCD-Collection.awk and execute:
# fileName="ContactDetails"; gawk --assign glob_coll_namespacePrefix="ncd.cd" -f parseNCD.awk "NCD-$fileName.rdf" > "NCD-$fileName.mwt"
##########################################


#### programm developer checks ###########
# Check for all elements within range of 
# e.g. owl:DatatypeProperty to owl:DatatypeProperty
#
# sed --quiet "/owl:DatatypeProperty/,/owl:DatatypeProperty/{ s@\t*@@g; s@[ >].*@@g; p;}"  "NCDTest-Collection.rdf" | sort --unique
# sed --quiet "/owl:ObjectProperty/,/owl:ObjectProperty/{ s@\t*@@g; s@[ >].*@@g; p;}"  "NCDTest-Collection.rdf" | sort --unique
# sed --quiet "/owl:Class/,/owl:Class/{ s@\t*@@g; s@[ >].*@@g; p;}"  "NCDTest-Collection.rdf" | sort --unique
# awk '$0~/<[A-Za-z]+ /{ print $0}' "NCDTest-Collection.rdf" | sed --quiet "s@.*\(<[A-Za-z]\+\).*@\1@g;p" | sort --unique
#--- check elements for instances of classes: get all instances in $filename and list all elements in it (just a programm developer check)
#--- just display execution command:
# filename="NCDTest-Collection.rdf";awk '$0~/<[A-Za-z]+ /{ print $0}' "$filename" | sed --quiet "s@.*<\([A-Za-z]\+\).*@\1@g;p" | sort --unique | sed "s@\(.*\)@sed --quiet \"/<\1/,/<\\\/\1/{ s\@\\\t*\@\@g; s\@[ >].*\@\@g; p;}\" \"$filename\" | sort --unique@"
## execute command:
# filename="NCDTest-Collection.rdf";awk '$0~/<[A-Za-z]+ /{ print $0}' "$filename" | sed --quiet "s@.*<\([A-Za-z]\+\).*@\1@g;p" | sort --unique | sed "s@\(.*\)@sed --quiet \"/<\1/,/<\\\/\1/{ s\@\\\t*\@\@g; s\@[ >].*\@\@g; p;}\" \"$filename\" | sort --unique@" | sh | sort --unique

# perl -pne 'BEGIN {undef $/} s/&nbsp;&nbsp;│<!--\n\n-->\n\n<!--\n-->&nbsp;&nbsp; +/\n* /gm'  NCDTest-Collection.mwt > NCDTest-Collection-export.mwt
##########################################
# GLOBAL VARIABLES start with glob_…
##########################################


BEGIN {
  FS ="\"" # field separator to quotation mark " (default is " ")
  if(glob_coll_namespacePrefix=="") {glob_coll_namespacePrefix="ncd.missing"}
}# BEGIN

####### functions start ##################
  function ltrim(s) { sub(/^[ \t]+/, "", s); return s }
  function rtrim(s) { sub(/[ \t]+$/, "", s); return s }
  function trim(s)  { return rtrim(ltrim(s)); }
  
  function get_rdfsLabel() {
    #<rdfs:label>Collection Identifier</rdfs:label> 
    return trim(gensub(/.*<(rdfs:label)>(.+)<\/rdfs:label>.*/, "\\2", "g", $0))
  }# get_rdfsLabel
  
  function get_attributeValueUrlEncoded() {
    # must be FS="\"" !!
    #<rdfs:domain rdf:resource="#Collection"/>
    firstAttributeValue=$2
    if (firstAttributeValue~/^#/) {
      firstAttributeValue=gensub(/^#/, glob_coll_namespaceUriEncoded, "g",  firstAttributeValue)
    } else {
      firstAttributeValue=gensub(/#/, "%23", "g", firstAttributeValue)
    }
    return firstAttributeValue
  }# get_attributeValueUrlEncoded
  
  function get_xmlDataElement (xpathQuery) {
    # use xml_grep and sed to get trimmed single line values
    # "xml_grep xml_grep --text_only --cond \"" xpathQuery "\" " FILENAME " | sed 's@^ *@@;:a;N;$!ba;s/\\n\\t\\+//g;'" | getline output
    # has less features, e.g. get only the attribute
    "xpath " FILENAME " \"" xpathQuery "\"  2>/dev/null | tr --delete '\\n' | sed 's@[ \\t]\\+@ @g;' " | getline output
    #  2>/dev/null removes the xpath's script insertions like "-- NODE --"
    output = gensub(/<a *href *= *['\"]([^'\">]+)['\"][^>]*>([^<]+)<\/a>/,"<nowiki>\\1</nowiki>", "g", output)#"
    output = trim(output)
    output = gensub(/<\/p> *<p>/,"</p>%0A%0A<p>", "g", output)
    output = gensub(/[ \t]*<\/?p>[ \t]*/,"", "g", output)
    output = gensub(/\[\.\.\.\]/,"[…]", "g", output)
    return output
  }

  function get_conceptType(typeUrl){
    
    switch (tolower(gensub(/.*#/,"", "g", typeUrl))) {
     case "datatypeproperty":
         type="data type"
     case "class":
         type="class"
     case "value":
         type="value"
     default:
         type="property"
     }
     return type
  }
  function emptyGlobalVariables() {
    glob_conceptDefinition = "";
    glob_conceptDomain = "";
    glob_conceptID = "";
    glob_conceptNotes = "";
    glob_conceptRange = "";
    glob_conceptType = "";
    glob_rdfs_isDefinedBy = "";
    glob_rdfs_Label = "";
    glob_rdfs_subClassOf = "";
    glob_rdfs_subPropertyOf = "";
    glob_instanceOfClass = "";
  }# emptyGlobalVariables
  
  function create_formLink_Concept_collection() {
    print "* {{#formlink: form=Concept collection\n" \
      " |link text=" glob_coll_title "&nbsp;[[File:Pencil.png|link=]]\n" \
      " |target=" glob_coll_title "\n" \
      " |query string =<!--"
      print "-->Concept collection[concept scheme]=Natural Collections Description<!--"
      if (glob_coll_creators) {print "-->&Concept collection[creators]=" gensub(/ *\/ */, ", ", "g", glob_coll_creators) "<!--" }
      if (glob_coll_description) {print "-->&Concept collection[description]=" glob_coll_description "<!--"}
      if (glob_coll_notes) {print "-->&Concept collection[notes]=" glob_coll_notes "<!--"}
      if (glob_coll_issued) {print "-->&Concept collection[issued]=" glob_coll_issued "<!--"}
      if (glob_coll_modified) {print "-->&Concept collection[modified]=" glob_coll_modified "<!--"}
      if (glob_coll_namespaceUriEncoded) {print "-->&Concept collection[preferred namespace uri]=<nowiki>" glob_coll_namespaceUriEncoded "</nowiki>" "<!--"}
      if (glob_coll_namespacePrefix) {print "-->&Concept collection[preferred namespace prefix]=" glob_coll_namespacePrefix "<!--"}
    print "-->}}\n----\n<!--"
    }
  function create_formLink(conceptID, kindOfConceptComment, startNewOutputSection) {
    # use global variables to generate the form link
    
    #### start ####
    print ((startNewOutputSection == 0) ? "-->&nbsp;&nbsp;" : "-->\n*" ) \
      " {{#formlink: form=Concept\n | link text =" \
      glob_coll_namespacePrefix ":" conceptID "&nbsp;[[File:Pencil.png|link=]]\n | target =" glob_coll_namespacePrefix ":" conceptID "\n | query string =<!--" kindOfConceptComment
    if (glob_rdfs_Label) print "-->Concept[label]=" glob_rdfs_Label "<!--"
    # append all other fields
    if (glob_conceptDefinition) print "-->&Concept[definition]=" trim(glob_conceptDefinition) "<!--"
    if (glob_conceptNotes) print "-->&Concept[notes]=" trim(glob_conceptNotes) "<!--"
    if (glob_conceptType) print "-->&Concept[concept type]=" trim(glob_conceptType) "<!--"
    if (glob_rdfs_isDefinedBy) 
      print "-->&Concept[is defined by]=<nowiki>" trim(glob_rdfs_isDefinedBy) "</nowiki><!--"
    else
      print "-->&Concept[is defined by]=<nowiki>" glob_coll_namespace_isDefinedBy "</nowiki><!--"
    
    #if (glob_conceptDomain || glob_conceptRange) 
    print "-->&Concept scheme relation[1][scheme]=Natural Collections Description<!--"
    # if instance of class then restrict it to rdfs:domain
    i_cr=1 # index concept relation
    if (glob_instanceOfClass) glob_conceptDomain = glob_coll_namespaceUriEncoded glob_instanceOfClass
    if (glob_conceptDomain) print "-->&Concept scheme relation[1][property domain]=<nowiki>" trim(glob_conceptDomain) "</nowiki><!--"
    if (glob_conceptRange)  print "-->&Concept scheme relation[1][property range]=<nowiki>" trim(glob_conceptRange) "</nowiki><!--"
    if (glob_rdfs_subPropertyOf) {print "-->&Concept relation[" i_cr "][relation]=rdfs: subproperty of<!--"}
    if (glob_rdfs_subPropertyOf) {print "-->&Concept relation[" i_cr "][uri]=<nowiki>" trim(glob_rdfs_subPropertyOf) "</nowiki><!--"
      i_cr=i_cr +1
    }
    
    if (glob_rdfs_subClassOf)    {print "-->&Concept relation[" i_cr "][relation]=rdfs: subclass of<!--"}
    if (glob_rdfs_subClassOf)    {print "-->&Concept relation[" i_cr "][uri]=<nowiki>" trim(glob_rdfs_subClassOf) "</nowiki><!--"
      i_cr=i_cr +1
    }
    
    if (glob_coll_title)         {print "-->&Concept relation[" i_cr "][relation]=skos: collection<!--"}
    if (glob_coll_title)         {print "-->&Concept relation[" i_cr "][internal page]=" glob_coll_title "<!--"
      i_cr=i_cr +1
    }
    #### end ####
    print  "-->}}&nbsp;&nbsp;&#x2502;<!--"
    emptyGlobalVariables()
  }# create_formLink
####### functions end ####################

########## Ontology (Collection) ################
/.*<owl:Ontology/,/.*<\/owl:Ontology>/ {
  if ($0~/<owl:Ontology/) {
    glob_coll_namespace_isDefinedBy=$2
    glob_coll_namespaceUriEncoded=$2 "%23"
    glob_coll_namespaceUri=$2 "#"
  }
  if ($0~/<dcterms:issued/) { glob_coll_issued=gensub(/.*([0-9]{4})-([0-9]{2})-([0-9]{2}).*/, "\\1%2F\\2%2F\\3", "g", get_xmlDataElement("*/owl:Ontology/dcterms:issued/text()")) }
  if ($0~/<dcterms:modified/) { glob_coll_modified=gensub(/.*([0-9]{4})-([0-9]{2})-([0-9]{2}).*/, "\\1%2F\\2%2F\\3", "g", get_xmlDataElement("*/owl:Ontology/dcterms:modified/text()")) }
  glob_coll_title = "NCD" gensub(/([A-Z])/, " \\1", "g", gensub(/(NCD-|\.rdf)/,"", "g", FILENAME))
  if ($0~/<dc:publisher/) {}
  if ($0~/<dc:creator/) {glob_coll_creators=get_xmlDataElement("*/owl:Ontology/dc:creator/text()")}
  if ($0~/<dc:description/) {glob_coll_description=get_xmlDataElement("*/owl:Ontology/dc:description/node()")}
  if ($0~/<rdfs:comment/) {glob_coll_notes=get_xmlDataElement("*/owl:Ontology/rdfs:comment/node()")}
  if ($0~/<\/owl:Ontology>/) {
    create_formLink_Concept_collection()
  }
}

########## ObjectProperty ################
# in the range of <owl:ObjectProperty … </owl:ObjectProperty> do:
/.*<owl:ObjectProperty/,/.*<\/owl:ObjectProperty>/ {
  glob_conceptType = "property"
  # <rdfs:comment <rdfs:domain <rdfs:isDefinedBy <rdfs:label <rdfs:range <rdfs:subPropertyOf
  # get glob_conceptID in <owl:ObjectProperty rdf:ID="collectionId">
  if ($0~/.*<owl:ObjectProperty/) { # print $2 # check data
    glob_conceptID=$2
    glob_conceptDefinition = get_xmlDataElement("*/owl:ObjectProperty[@rdf:ID='" glob_conceptID "']/rdfs:comment/node()")
  }
  else {
    if ($0~/<rdfs:label/) { glob_rdfs_Label = get_rdfsLabel() }
    if ($0~/.*<rdfs:domain/) { glob_conceptDomain = get_attributeValueUrlEncoded() }
      # print "domain: " glob_conceptDomain
    if ($0~/.*<rdfs:range/) { glob_conceptRange = get_attributeValueUrlEncoded() }
      # print "range: " glob_conceptRange
    if ($0~/.*<rdfs:isDefinedBy/) { glob_rdfs_isDefinedBy = get_attributeValueUrlEncoded() }
      # print "rdfs:isDefinedBy: " glob_rdfs_isDefinedBy
    if ($0~/.*<rdfs:subPropertyOf/) { glob_rdfs_subPropertyOf = get_attributeValueUrlEncoded() }
      # print "rdfs:subPropertyOf: " glob_rdfs_subPropertyOf
  }# definitions within <owl:ObjectProperty>…</owl:ObjectProperty>

  if ($0~/.*<\/owl:ObjectProperty>/) {
    print create_formLink(glob_conceptID, "ObjectProperty")
  }
}# values in ObjectProperty

########## DatatypeProperty ##############
# in the range of <owl:DatatypeProperty … </owl:DatatypeProperty> do:
/<owl:DatatypeProperty/,/<\/owl:DatatypeProperty>/ {
  glob_conceptType="data type"
  # <rdfs:comment <rdfs:domain <rdfs:isDefinedBy <rdfs:label <rdfs:range <rdfs:subPropertyOf
  # get glob_conceptID in <owl:DatatypeProperty rdf:ID="collectionId">
  if ($0~/.*<owl:DatatypeProperty/) { # print $2 # check data
    glob_conceptID=$2
    glob_conceptDefinition = get_xmlDataElement("*/owl:DatatypeProperty[@rdf:ID='" glob_conceptID "']/rdfs:comment/node()")
      # print "rdfs:comment (definition): " glob_conceptDefinition
  }
  else {
    if ($0~/.*<rdfs:label/) { glob_rdfs_Label = get_rdfsLabel()  }
      # print "rdfs:label: " glob_rdfs_Label
    if ($0~/.*<rdfs:domain/) { glob_conceptDomain = get_attributeValueUrlEncoded() }
      # print "domain: " glob_conceptDomain
    if ($0~/.*<rdfs:range/) { glob_conceptRange = get_attributeValueUrlEncoded() }
    if ($0~/.*<rdf:type/) { glob_conceptType = get_conceptType(get_attributeValueUrlEncoded()) }
      # print "range: " glob_conceptRange
    if ($0~/.*<rdfs:isDefinedBy/) { glob_rdfs_isDefinedBy = get_attributeValueUrlEncoded() }
      # print "rdfs:isDefinedBy: " glob_rdfs_isDefinedBy
    if ($0~/.*<rdfs:subPropertyOf/) { glob_rdfs_subPropertyOf = get_attributeValueUrlEncoded() }
      # print "rdfs:subPropertyOf: " glob_rdfs_subPropertyOf
  }# definitions within <owl:DatatypeProperty>…</owl:DatatypeProperty>

  if ($0~/.*<\/owl:DatatypeProperty>/) {
    #### Create the form link ####
    print create_formLink(glob_conceptID, "DatatypeProperty")
  }
}# values in DatatypeProperty


########## owl:Class and its instances ####
# Classes and instances of a particular class
$0~/<owl:Class/ {# Class definition starts
  classNameID=$2
  readingOwlClass=classNameID
  glob_conceptDefinition = get_xmlDataElement("*/owl:Class[@rdf:ID='" classNameID "']/rdfs:comment/node()")
}# owl:Class

readingOwlClass != "" {
  glob_conceptType = "class"
  if ($0~/<rdfs:label>/) { glob_rdfs_Label = get_rdfsLabel() }
  if ($0~/.*<rdfs:subClassOf/) { glob_rdfs_subClassOf = get_attributeValueUrlEncoded() }
    # print "rdfs:subClassOf: " glob_rdfs_subClassOf
  if ($0~/.*<rdfs:isDefinedBy/) { glob_rdfs_isDefinedBy = get_attributeValueUrlEncoded() }
    # print "rdfs:isDefinedBy: " glob_rdfs_isDefinedBy
  if ($0~/.*<rdf:type/) { glob_conceptType = get_conceptType(get_attributeValueUrlEncoded()) }
}
$0~/.*<\/owl:Class>/ {# Class definition closes
  readingOwlClass=""
  print create_formLink(classNameID, "Class", 1); # separate for output
}

# reading instances of this class
classNameID != "" {
  if(index ($0, "<" classNameID ) > 0) {# an instance of the class was found, e.g. <PrimaryGroupingPrincipleTypeTerm …> of <owl:Class rdf:ID="PrimaryGroupingPrincipleTypeTerm">
    glob_conceptType="value"
    glob_conceptID=$2
    readingInstanceOfClass=classNameID
  }# a class property found
  if(readingInstanceOfClass) {
    if ($0~/.*<rdfs:label/) glob_rdfs_Label = get_rdfsLabel() # get_xmlDataElement("*/" classNameID "[@rdf:ID='" glob_conceptID "']/rdfs:label/node()")
    if ($0~/.*<rdfs:comment/) glob_conceptNotes = get_xmlDataElement("*/" classNameID "[@rdf:ID='" glob_conceptID "']/rdfs:comment/node()")
    if ($0~/.*<dc:title/) { } # don't know yet what to do with it
    if ($0~/.*<base:definition/) glob_conceptDefinition = get_xmlDataElement("*/" classNameID "[@rdf:ID='" glob_conceptID "']/base:definition/node()")
    if ($0~/.*<tbase:definition/) glob_conceptDefinition = get_xmlDataElement("*/" classNameID "[@rdf:ID='" glob_conceptID "']/tbase:definition/node()")
    if ($0~/.*<rdfs:subClassOf/) { glob_rdfs_subClassOf = get_attributeValueUrlEncoded() }
    if ($0~/.*<rdf:type/) { glob_conceptType = get_conceptType(get_attributeValueUrlEncoded()) }
    # no glob_rdfs_subPropertyOf but a glob_instanceOfClass
    glob_instanceOfClass = classNameID
  }
  if(index ($0, "</" classNameID ">") > 0) {# the 
    readingInstanceOfClass=""
    print create_formLink(glob_conceptID, "instance of class " classNameID);
  }
}

# xml_grep --text_only "owl:Ontology/rdfs:comment" NCDTest-Collection.rdf | sed ':a;N;$!ba;s/\n\t\+//g; s@ *\t*\(.\+\) *\t*@\1@g'
# TODO properties in a class

ContactDetails

The NCD RDF sourcfile file is flawed:

URL is not defined by http://www.w3.org/2001/vcard-rdf/3.0#URL check ContactDetails.rdf of NCD
TYPE is not defined by http://www.w3.org/2001/vcard-rdf/3.0#TYPE check ContactDetails.rdf of NCD

NCD Contact Details

ncd.cd:ContactDetails │ ncd.cd:TEL │ ncd.cd:EMAIL │ ncd.cd:ADR │ ncd.cd:GEO │ ncd.cd:URL │ ncd.cd:LOGO │ ncd.cd:NOTE │
ncd.cd:Address │ ncd.cd:TYPE │ ncd.cd:Pobox │ ncd.cd:Extadd │ ncd.cd:Street │ ncd.cd:Locality │ ncd.cd:Region │ ncd.cd:Pcode │ ncd.cd:Country │
ncd.cd:ContactTypeTerm │

CyclicityTerm

NCD Cyclicity Term

ncd.ct:CyclicityTerm │ ncd.ct:Circadian │ ncd.ct:SemiLunar │ ncd.ct:Lunar │ ncd.ct:Seasonal │ ncd.ct:Annual │

DigitalImage

DigitalImage.rdf seems wrong: <owl:Ontology rdf:about="http://rs.tdwg.org/ontology/voc/ContactDetails"> cannot be true, possibly <owl:Ontology rdf:about="http://rs.tdwg.org/ontology/voc/DigitalImage"> is correct

NCD Digital Image

ncd.di:DigitalImage │

[1] so: ContactDetails.rdf, DigitalImage.rdf, Institution.rdf, OccurrenceRecord.rdf, Person.rdf, Procedure.rdf, PublicationCitation.rdf, SpeciesProfileModel.rdf, Specimen.rdf, TaxonConcept.rdf, TaxonName.rdf, TaxonOccurrence.rdf, TaxonOccurrenceInteraction.rdf, Team.rdf

[2] so CyclicityTerm.rdf, GeographicRegion.rdf, InstitutionType.rdf, OccurrenceStatusTerm.rdf, SPMInfoItems.rdf, TaxonRank.rdf, TermWithSource.rdf

[1]

[2]

Difference between revisions of "Talk:Natural Collections Description"

Latest revision as of 14:20, 7 January 2013

Contents

Preferred Namespaces and URIs

Defined namespaces in NCD

Form links for creation of NCD concepts

Generation script (Linux)

Base

Core

Collection

CollectionType

Common

ContactDetails

CyclicityTerm

DigitalImage

Navigation menu

Personal tools

Namespaces

Variants

Views

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Collection	Preferred namespace	Preferred namespace URI	Is in svn Ontology.owl	Comments
Base	tbase ~~base~~	http://rs.tdwg.org/ontology/Base#	yes	Collection.rdf^[1] defines the namespace "tbase" xmlns:tbase="http://rs.tdwg.org/ontology/Base#"; note: it is also defined as ns "base" in CollectionType.rdf^[2] → probably mistakenly. ↑ also: ContactDetails.rdf, DigitalImage.rdf, Institution.rdf, OccurrenceRecord.rdf, Person.rdf, Procedure.rdf, PublicationCitation.rdf, SpeciesProfileModel.rdf, Specimen.rdf, TaxonConcept.rdf, TaxonName.rdf, TaxonOccurrence.rdf, TaxonOccurrenceInteraction.rdf, Team.rdf ↑ also CyclicityTerm.rdf, GeographicRegion.rdf, InstitutionType.rdf, OccurrenceStatusTerm.rdf, SPMInfoItems.rdf, TaxonRank.rdf, TermWithSource.rdf
Core	tcore	http://rs.tdwg.org/ontology/Core#	yes	Procedure.rdf defines the namespace "tcore" xmlns:tcore="http://rs.tdwg.org/ontology/Core#"
Collection	tc ?tco ?tcoll ?ncd-collection	http://rs.tdwg.org/ontology/voc/Collection#	yes	namespace “ncd-collection” was decided by Gregor Hagedorn, Andreas Plank; following the "t…" naming scheme the briefest namespace is "tco"; tc is already defined by TaxonConcept
CollectionType	~~tct~~ ?tcot ?tcollt ?tcolltype ?ncd-collectiontype	http://rs.tdwg.org/ontology/voc/CollectionType#	yes	suggested namespace by Andreas Plank; following the "t…" naming scheme "tcot" namespace is the briefest; tct is already defined by OccurrenceStatusTerm
Common	tcom	http://rs.tdwg.org/ontology/voc/Common#	yes	TaxonConcept.rdf or Institution.rdf (among many others) define namespace "tcom" xmlns:tcom="http://rs.tdwg.org/ontology/voc/Common#"; common to all concepts
ContactDetails	tcd	http://rs.tdwg.org/ontology/voc/ContactDetails#	yes	namespace "tcd" because ContactDetails.rdf defines xmlns:tcd="http://rs.tdwg.org/ontology/voc/ContactDetails#"
CyclicityTerm	tct	http://rs.tdwg.org/ontology/voc/CyclicityTerm#	no	seems in development, namespace "tct" because CyclicityTerm.rdf defines xmlns:tdi="http://rs.tdwg.org/ontology/voc/CyclicityTerm#"; conflicts with OccurrenceStatusTerm that probably defines its "tct" namespace mistakenly
DigitalImage	tdi	http://rs.tdwg.org/ontology/voc/DigitalImage#	yes	namespace "tdi" because DigitalImage.rdf defines xmlns:tdi="http://rs.tdwg.org/ontology/voc/DigitalImage#"
GeographicRegion	gr	http://rs.tdwg.org/ontology/voc/GeographicRegion#	no	namespace "gr" because GeographicRegion.rdf defines xmlns:gr="http://rs.tdwg.org/ontology/voc/GeographicRegion#"
Institution	tinst	http://rs.tdwg.org/ontology/voc/Institution#	yes	namespace "tinst" because Institution.rdf defines xmlns:tinst="http://rs.tdwg.org/ontology/voc/Institution#"
InstitutionType	titype	http://rs.tdwg.org/ontology/voc/InstitutionType#	yes	namespace "titype" because Institution.rdf defines xmlns:titype="http://rs.tdwg.org/ontology/voc/InstitutionType#"
OccurrenceRecord	tor	http://rs.tdwg.org/ontology/voc/OccurrenceRecord#	no	namespace "tor" because OccurrenceRecord.rdf defines xmlns:tor="http://rs.tdwg.org/ontology/voc/OccurrenceRecord#"
OccurrenceStatusTerm	tct	http://rs.tdwg.org/ontology/voc/OccurrenceStatusTerm#	yes	namespace "tct" because OccurrenceStatusTerm.rdf defines xmlns:tct="http://rs.tdwg.org/ontology/voc/OccurrenceStatusTerm#", conflicts with CyclicityTerm
Person	tp	http://rs.tdwg.org/ontology/voc/Person#	yes	namespace "tp" because Person.rdf xmlns:tp="http://rs.tdwg.org/ontology/voc/Person#"; conflicts with taxpub's preferred namespace "tp"
Procedure	tproc	http://rs.tdwg.org/ontology/voc/Procedure#	yes	Procedure.rdf defines the namespace xmlns:tproc="http://rs.tdwg.org/ontology/voc/Procedure#"
PublicationCitation	tpub	http://rs.tdwg.org/ontology/voc/PublicationCitation#	yes	PublicationCitation.rdf defines the namespace xmlns:tpub="http://rs.tdwg.org/ontology/voc/PublicationCitation#"
SpeciesProfileModel	spm	http://rs.tdwg.org/ontology/voc/SpeciesProfileModel#	yes	SpeciesProfileModel.rdf defines the namespace xmlns:spm="http://rs.tdwg.org/ontology/voc/SpeciesProfileModel#"
SPMInfoItems	spmi	http://rs.tdwg.org/ontology/voc/SPMInfoItems#	no	SPMInfoItems.rdf defines the namespace xmlns:spmi="http://rs.tdwg.org/ontology/voc/SPMInfoItems#"; it's not in the subversion Ontology.owl but listed on TDWG website http://rs.tdwg.org/ontology/voc/
Specimen	tsp	http://rs.tdwg.org/ontology/voc/Specimen#	yes	Specimen.rdf defines the namespace xmlns:tsp="http://rs.tdwg.org/ontology/voc/Specimen#"
TaxonConcept	tc	http://rs.tdwg.org/ontology/voc/TaxonConcept#	yes	TaxonConcept.rdf defines the namespace xmlns:tc="http://rs.tdwg.org/ontology/voc/TaxonConcept#"
TaxonName	tn	http://rs.tdwg.org/ontology/voc/TaxonName#	yes	TaxonName.rdf defines the namespace xmlns:tn="http://rs.tdwg.org/ontology/voc/TaxonName#"
TaxonOccurrence	tto	http://rs.tdwg.org/ontology/voc/TaxonOccurrence#	yes	TaxonOccurrence.rdf defines the namespace xmlns:tto="http://rs.tdwg.org/ontology/voc/TaxonOccurrence#
TaxonOccurrenceInteraction	??	http://rs.tdwg.org/ontology/voc/TaxonOccurrenceInteraction#	no	TaxonOccurrenceInteraction.rdf defines no namespace; it is not in the subversion Ontology.owl but listed on TDWG website http://rs.tdwg.org/ontology/voc/
TaxonRank	trank	http://rs.tdwg.org/ontology/voc/TaxonRank#	yes	TaxonRank.rdf defines the namespace xmlns:trank="http://rs.tdwg.org/ontology/voc/TaxonRank#"
Team	tt	http://rs.tdwg.org/ontology/voc/Team#	yes	Team.rdf defines the namespace xmlns:tt="http://rs.tdwg.org/ontology/voc/Team#"
TermWithSource	??	http://rs.tdwg.org/ontology/voc/TermWithSource#	no	TermWithSource.rdf defines the namespace; seems in development (is not listed either on TDWG website http://rs.tdwg.org/ontology/voc/)