Hi! I cleaned up your code for you!

examples/arxiv-provenance/di.txt

@@ -78,7 +78,7 @@ n3 for the entire document; thats to be autogenerated'
     a adsbase:WrittenProduct;
 	adsbase:title				"Unparticle Physics";
 	adsbase:languageIn				"en";
-	cito:peerReviewed "true"^^xsd:boolean ; # peer review status  
+	cito:peerReviewed "true"^^xsd:boolean ; # peer review status
 	#What should below be? should be have a abstract in ads?
 	adsbib:workIdentifier "2007PhRvL..98v1601G";
 	adsbib:hasAggregation [
@@ -92,19 +92,19 @@ n3 for the entire document; thats to be autogenerated'
 	            adsbib:hasExpression <http://prl.aps.org/abstract/PRL/v98/i22/e221601>;
 	            adsbib:aggregationIdentifier "eprint=hep-ph/0703260";
 	        ];
-	        
+
 	];
 	adsbib:hasAbstract 		[
 	                        a cito:Abstract;
 	                        adsbib:abstractText
 	"""
 					    I discuss some simple aspects of the low-energy physics of a nontrivial scale invariant sector of an effective field theory—physics that cannot be described in terms of particles. I argue that it is important to take seriously the possibility that the unparticle stuff described by such a theory might actually exist in our world. I suggest a scenario in which some details of the production of unparticle stuff can be calculated. I find that in the appropriate low-energy limit, unparticle stuff with scale dimension dU looks like a nonintegral number dU of invisible particles. Thus dramatic evidence for a nontrivial scale invariant sector could show up experimentally in missing energy distributions.
-                            """^^rdfs:XMLLiteral;#should we use rdfs:xmlliteral or just string? 
+                            """^^rdfs:XMLLiteral;#should we use rdfs:xmlliteral or just string?
     ];
-                            
+
 	#why do we not use a bnode here? is it for affiliation reasons? DO AFFILIATION
 	pav:authoredBy :howardgeorgi;
-	
+
 	#need biblio description (also known as citeas or below), preferred quoting, tags
 	#should this, since at level of work, be aggregator specific? or thats for spires to do
 	#what do we cite? we cite expressions, and through those relate to work
@@ -126,12 +126,12 @@ n3 for the entire document; thats to be autogenerated'
         }
     """;
     #or should it be: Georgi, H.\ 2007, Physical Review Letters, 98, 221601		
-	## Tags: SKOS	
-	
+	## Tags: SKOS
+
 	adsbase:keywordConcept pacs:Other_nonperturbative_techniques;
     adsbase:keywordConcept pacs:Other_particles;
     adsbase:keywordText "Other nonperturbative techniques, Other particles";
-	## Eprint Stuff for Arxiv: we have v1, v2, v3 down, but how do we get the general notion of eprint, not just as an expression?	
+	## Eprint Stuff for Arxiv: we have v1, v2, v3 down, but how do we get the general notion of eprint, not just as an expression?
 	adsbib:defaultRealizedThrough <http://prl.aps.org/abstract/PRL/v98/i22/e221601>;						
 .
 
@@ -140,7 +140,7 @@ n3 for the entire document; thats to be autogenerated'
 #How do we, and do we, track the directional history of provenance
 
 #DO LOCATORS
-<http://prl.aps.org/abstract/PRL/v98/i22/e221601> 
+<http://prl.aps.org/abstract/PRL/v98/i22/e221601>
     a cito:JournalArticle;#expression
     adsbib:publishedIn adsconfig:PRL;
     adsbib:doi "10.1103/PhysRevLett.98.221601";
@@ -152,7 +152,7 @@ n3 for the entire document; thats to be autogenerated'
     adsbib:pages "{221601-+}";
     pav:submittedOn "24 March 2007"^^xsd:dateTime;
     pav:publishedOn "29 May 2007"^^xsd:dateTime;
-    #we have a revised on but not an accepted on date but 
+    #we have a revised on but not an accepted on date but
     #should we use revisedOn as acceptedOn?
     cito:isRealizationOf <http://adsabs.harvard.edu/abs/2007PhRvL..98v1601G>;
     adsbib:alsoHasEprint <http://arxiv.org/abs/hep-ph/0703260>;
@@ -173,17 +173,17 @@ n3 for the entire document; thats to be autogenerated'
     """;
 .
 
-#Should the next two really be two different expressions?    
-<http://arxiv.org/abs/hep-ph/0703260> 
+#Should the next two really be two different expressions?
+<http://arxiv.org/abs/hep-ph/0703260>
     a adsbib:Eprint;#expression
     adsbib:publishedIn adsconfig:ARXIV;
     adsbib:channel "hep-ph";
     adsbib:eprintid "arXiv:hep-ph/0703260v3";
     cito:isRealizationOf <http://adsabs.harvard.edu/abs/2007PhRvL..98v1601G>;
     adsbib:alsoPublishedIn <http://prl.aps.org/abstract/PRL/v98/i22/e221601>;
 .
-    
-<http://arxiv.org/abs/hep-ph/0703260v3> 
+
+<http://arxiv.org/abs/hep-ph/0703260v3>
     a adsbib:Eprint;#expression
     a adsbib:ExpressionVersion;
     adsbib:publishedIn adsconfig:ARXIV;
@@ -197,8 +197,8 @@ n3 for the entire document; thats to be autogenerated'
     pav:previousVersion <http://arxiv.org/abs/hep-ph/0703260v2>;
     adsbib:citeMeAs "arXiv:hep-ph/0703260v3";
 .
-    
-<http://arxiv.org/abs/hep-ph/0703260v2> 
+
+<http://arxiv.org/abs/hep-ph/0703260v2>
     a adsbib:Eprint;#expression
     a adsbib:ExpressionVersion;
     adsbib:publishedIn adsconfig:ARXIV;
@@ -210,8 +210,8 @@ n3 for the entire document; thats to be autogenerated'
     pav:previousVersion <http://arxiv.org/abs/hep-ph/0703260v1>;
     adsbib:citeMeAs "arXiv:hep-ph/0703260v2";
 .
-    
-<http://arxiv.org/abs/hep-ph/0703260v1> 
+
+<http://arxiv.org/abs/hep-ph/0703260v1>
     a cito:Eprint;#expression
     a adsbib:ExpressionVersion;
     adsbib:publishedIn adsconfig:ARXIV;
@@ -223,4 +223,4 @@ n3 for the entire document; thats to be autogenerated'
     adsbib:citeMeAs "arXiv:hep-ph/0703260v1";
 .
 
-# /end 
+# /end

examples/arxiv-provenance/fixtures1.txt

@@ -28,7 +28,7 @@
 :APS a adsbase:Publisher;
     foaf:name "American Physical Society";
 .
-    
+
 :PRL a cito:Journal;
     adsbib:publishedBy :APS;
 .
@@ -40,7 +40,7 @@
 :adsrdf001 a agent:Software;
     agent:softwareVersion "0.01";
 .
-    
+
 :HARVARD a foaf:Organization;
     foaf:name "Harvard University";
 .

examples/arxiv-provenance/ref.sprires.out.txt

@@ -3,7 +3,7 @@
 @prefix rdf: 	<http://www.w3.org/1999/02/22-rdf-syntax-ns#>.
 @prefix rdfs:	<http://www.w3.org/2000/01/rdf-schema#>.
 @prefix dc:  	<http://purl.org/dc/elements/1.1/>.
-@prefix foaf:	<http://xmlns.com/foaf/0.1/>. 	
+@prefix foaf:	<http://xmlns.com/foaf/0.1/>.
 @prefix dcterms: <http://purl.org/dc/terms/>.
 @prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
 @prefix adsbase: <http://github.com/rahuldave/ontoads/owl/adsbase.owl#>.
@@ -20,7 +20,7 @@
 <>  a cito:CitationMetadata ; # work
     a cito:EntityMetadata ; # work
     #add something here for expression versioning
-	cito:cites <http://adsabs.harvard.edu/abs/2007PhRvL..98v1601G> ;  
+	cito:cites <http://adsabs.harvard.edu/abs/2007PhRvL..98v1601G> ;
 	cito:citesAsSourceDocument <http://adsabs.harvard.edu/abs/2007PhRvL..98v1601G> ;
 	pav:importedFromSource  adsconfig:ADS;
 	pav:importedBy adsconfig:adsrdf002; #if we had manual data entry how would we model?

examples/arxiv-provenance/refs.spires.bbl

@@ -1,4 +1,4 @@
-#extracted from spires: 2010-05-20 14:36:12 
+#extracted from spires: 2010-05-20 14:36:12
 @Article{Banks:1981nn,
      author    = "Banks, Tom and Zaks, A.",
      title     = "{On the Phase Structure of Vector-Like Gauge Theories with

owl/AVM.rdf

@@ -5,21 +5,21 @@
   <!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
   <!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#">
   <!ENTITY xsd "http://www.w3.org/2001/XMLSchema#">
-  <!ENTITY dc   "http://purl.org/dc/elements/1.1/" > 
-  <!ENTITY dct   "http://purl.org/dc/terms/" > 
+  <!ENTITY dc   "http://purl.org/dc/elements/1.1/" >
+  <!ENTITY dct   "http://purl.org/dc/terms/" >
 
   <!ENTITY skos "http://www.w3.org/2008/05/skos#">
-  <!ENTITY foaf "http://xmlns.com/foaf/0.1/"> 
-      <!-- Main namespace --> 
+  <!ENTITY foaf "http://xmlns.com/foaf/0.1/">
+      <!-- Main namespace -->
   <!ENTITY avm "http://www.ivoa.net/rdf/Vocabularies/AVM">
-  
-  <!ENTITY local "file:///home/rdave/Projects/adsonto/packages/pellet-1.3/AVM.rdf"> 
-  	<!ENTITY path "http://semantics.ads.org/ontologies/0.1/AVM.owl"> 
-  	<!ENTITY file "local;"> 
-  <!ENTITY foaf-local "file:///home/rdave/Projects/adsonto/packages/pellet-1.3/foaf-essential.owl">	
+
+  <!ENTITY local "file:///home/rdave/Projects/adsonto/packages/pellet-1.3/AVM.rdf">
+  	<!ENTITY path "http://semantics.ads.org/ontologies/0.1/AVM.owl">
+  	<!ENTITY file "local;">
+  <!ENTITY foaf-local "file:///home/rdave/Projects/adsonto/packages/pellet-1.3/foaf-essential.owl">
   <!ENTITY foaf-path "http://swan.mindinformatics.org/ontologies/1.2/foaf-essential.owl">
   <!ENTITY foaf-file "&foaf-local;">
-  <!ENTITY skos-local "file:///home/rdave/Projects/adsonto/packages/pellet-1.3/skos-essential.owl">	
+  <!ENTITY skos-local "file:///home/rdave/Projects/adsonto/packages/pellet-1.3/skos-essential.owl">
   <!ENTITY skos-path "http://swan.mindinformatics.org/ontologies/1.2/skos-essential.owl">
   <!ENTITY skos-file "&skos-path;">
 ]>
@@ -31,31 +31,31 @@
    xmlns:rdf="&rdf;"
    xmlns:rdfs="&rdfs;"
    xmlns:owl="&owl;"
-   xmlns:skos="&skos;" 
+   xmlns:skos="&skos;"
    xml:base="&avm;">
 
-    <owl:Ontology rdf:about="&file;"> 
-		<rdf:type rdf:resource="&owl;Ontology"/> 
-		<rdfs:label rdf:datatype="&xsd;string">AVM: ADS OWL_DL version</rdfs:label> 
- 
-    	<owl:imports rdf:resource="&foaf-file;"/> 
+    <owl:Ontology rdf:about="&file;">
+		<rdf:type rdf:resource="&owl;Ontology"/>
+		<rdfs:label rdf:datatype="&xsd;string">AVM: ADS OWL_DL version</rdfs:label>
+
+    	<owl:imports rdf:resource="&foaf-file;"/>
     	<owl:imports rdf:resource="&skos-file;"/>
-    	<dc:language>en</dc:language> 
-    	<dc:title xml:lang="en">AVM ontology</dc:title> 
-    	<dc:creator rdf:resource="http://www.ads.org/people/rahul-dave/" /> 
-    	<dc:contributor rdf:datatype="&xsd;string">Rahul Dave</dc:contributor> 
-    	<dc:publisher rdf:resource="http://semantics.ads.org" /> 
-        <dc:date rdf:datatype="&xsd;string">Thursday 04 March 2010</dc:date> 
-        <dc:format rdf:datatype="&xsd;string">rdf/xml</dc:format>    
-    </owl:Ontology>   
-   <!-- 
+    	<dc:language>en</dc:language>
+    	<dc:title xml:lang="en">AVM ontology</dc:title>
+    	<dc:creator rdf:resource="http://www.ads.org/people/rahul-dave/" />
+    	<dc:contributor rdf:datatype="&xsd;string">Rahul Dave</dc:contributor>
+    	<dc:publisher rdf:resource="http://semantics.ads.org" />
+        <dc:date rdf:datatype="&xsd;string">Thursday 04 March 2010</dc:date>
+        <dc:format rdf:datatype="&xsd;string">rdf/xml</dc:format>
+    </owl:Ontology>
+   <!--
     ///////////////////////////////////////////////////////////////////////////////////////
     //
     // Annotation Properties
     //
     ///////////////////////////////////////////////////////////////////////////////////////
      -->
-     
+
   	<rdf:Description rdf:about="&dc;title">
   	  	<rdf:type rdf:resource="&owl;AnnotationProperty"/>
   	</rdf:Description>
@@ -77,7 +77,7 @@
   	<rdf:Description rdf:about="&dc;contributor">
     	<rdf:type rdf:resource="&owl;AnnotationProperty"/>
   	</rdf:Description>
- 
+
  <rdf:Description rdf:about="&dct;title">
   	  	<rdf:type rdf:resource="&owl;AnnotationProperty"/>
   	</rdf:Description>
@@ -94,8 +94,8 @@
     	<rdf:type rdf:resource="&owl;AnnotationProperty"/>
   	</rdf:Description>
   	 <owl:AnnotationProperty rdf:about="&skos;notation"/>
-  	 
-  	 
+
+
   <skos:ConceptScheme rdf:about="">
     <dct:created>2009-10-07</dct:created>
     <!--Improper use of dct below screated anonymous bnode for dct-creator i think and broke owl-dl compatability-->
@@ -127,12 +127,12 @@ reference document http://www.virtualastronomy.org/AVM_Version1.1May312008.pdf
     <skos:hasTopConcept rdf:resource="#avm-8"/>
     <skos:hasTopConcept rdf:resource="#avm-9"/>
   </skos:ConceptScheme>
-  
+
   <!--rdf:Description rdf:about="#_notation">
     <rdf:type rdf:resource="&rdf;datatype"/>
     <dct:description>The notation here is described in the document http://www.virtualastronomy.org/AVM_Version1.1May312008.pdf</dct:description>
   </rdf:Description-->
-  
+
   <skos:Concept rdf:about="#avm-1">
     <skos:altLabel xml:lang="en">Planet</skos:altLabel>
     <skos:inScheme rdf:resource=""/>

owl/adsbasedesign.markdown

@@ -4,18 +4,18 @@ What of this can be got from sweet?
 
 From our discussion:
 
-	ads:FundingAgency 
+	ads:FundingAgency
 	ads:ObservationAgency
 	ads:Proposal
 		ads:ObservingProposal
 	ads:FundingInitiative
 	ads:FundingProgram
 	ads:Grant (has a grant identifier)
-	
+
 	ads:Collaboration
-	
+
 And from ads:
-	
+
     ads:Observatory
         ads:SpaceCraft
         ads:GroundBasedObservatory
@@ -25,12 +25,12 @@ And from ads:
     --ads:DataArchive
     ads:Dataset
     ads:DataProduct
-    
+
 Should we be dealing with co-ordinates at all? Dosent seem sweet provides us
 much useful stuff; and we can always connect to sweet later. Why would we want this?
 Its for Alyssa's heat maps, object positions, field layers etc. But how do we
 define without going into a complete nutness about co-ordinate systems? Or perhaps
-just deal with objects and concepts, not the floats associated with it. 
+just deal with objects and concepts, not the floats associated with it.
 
 The kind of object should be in the object ontology, as well as position and such.
 At this level we only need to know something about the sky.