Publication adjustments

svn path=/; revision=176

diff --git a/preecej/semantic_wiki/forms/Annotation.wiki b/preecej/semantic_wiki/forms/Annotation.wiki
index 32913a31efc076ff583b426f25aa343232c4b772..b9c677db094568828a42ac4c078288fd0b45359d 100644 (file)
--- a/preecej/semantic_wiki/forms/Annotation.wiki
+++ b/preecej/semantic_wiki/forms/Annotation.wiki
@@ -20,8 +20,8 @@ __NOTOC__
 {| class="formtable"
 ! Species Name:
 | {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
-            [[Is Associated With Field::Species Name]]
-            [[Is Associated With Template::Annotation]]
+            [[Is Associated With Field Or Object::Species Name]]
+            [[Is Associated With Category::Annotations]]
             |?is_Provenance
          }}
     | {{{field|Species Name|autocomplete on property=Has Reference Taxon|restricted}}}
@@ -30,8 +30,8 @@ __NOTOC__
 |-
 ! Gene Symbol:
 | {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
-            [[Is Associated With Field::Gene Symbol]]
-            [[Is Associated With Template::Annotation]]
+            [[Is Associated With Field Or Object::Gene Symbol]]
+            [[Is Associated With Category::Annotations]]
             |?is_Provenance
          }}
     |{{{field|Gene Symbol|restricted}}}
@@ -40,8 +40,8 @@ __NOTOC__
 |-
 ! Gene Name:
 | {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
-            [[Is Associated With Field::Gene Name]]
-            [[Is Associated With Template::Annotation]]
+            [[Is Associated With Field Or Object::Gene Name]]
+            [[Is Associated With Category::Annotations]]
             |?is_Provenance
          }}
     | {{{field|Gene Name|restricted}}}
@@ -64,8 +64,8 @@ __NOTOC__
 |-
 ! Gene Locus:
 | {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
-            [[Is Associated With Field::Gene Locus]]
-            [[Is Associated With Template::Annotation]]
+            [[Is Associated With Field Or Object::Gene Locus]]
+            [[Is Associated With Category::Annotations]]
             |?is_Provenance
          }}
     | {{{field|Gene Locus|restricted}}}
@@ -74,8 +74,8 @@ __NOTOC__
 |-
 ! Gene Type:
 | {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
-            [[Is Associated With Field::Gene Type]]
-            [[Is Associated With Template::Annotation]]
+            [[Is Associated With Field Or Object::Gene Type]]
+            [[Is Associated With Category::Annotations]]
             |?is_Provenance
          }}
     | {{{field|Gene Type|restricted}}}
@@ -84,8 +84,8 @@ __NOTOC__
 |-
 ! EC Number(s):
 | {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
-            [[Is Associated With Field::EC Numbers]]
-            [[Is Associated With Template::Annotation]]
+            [[Is Associated With Field Or Object::EC Numbers]]
+            [[Is Associated With Category::Annotations]]
             |?is_Provenance
          }}
     | {{{field|EC Numbers|restricted|list|delimiter=,}}}
@@ -94,8 +94,8 @@ __NOTOC__
 |-
 ! Chromosome:
 | {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
-            [[Is Associated With Field::Chromosome]]
-            [[Is Associated With Template::Annotation]]
+            [[Is Associated With Field Or Object::Chromosome]]
+            [[Is Associated With Category::Annotations]]
             |?is_Provenance
          }}
     |{{{field|Chromosome|restricted}}}
@@ -104,8 +104,8 @@ __NOTOC__
 |-
 ! Has Phenotype:
 | {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
-            [[Is Associated With Field::Has Phenotype]]
-            [[Is Associated With Template::Annotation]]
+            [[Is Associated With Field Or Object::Has Phenotype]]
+            [[Is Associated With Category::Annotations]]
             |?is_Provenance
          }}
     | {{{field|Has Phenotype|restricted}}}
@@ -114,8 +114,8 @@ __NOTOC__
 |-
 ! Description:
 | {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
-            [[Is Associated With Field::Annotation Description]]
-            [[Is Associated With Template::Annotation]]
+            [[Is Associated With Field Or Object::Annotation Description]]
+            [[Is Associated With Category::Annotations]]
             |?is_Provenance
          }}
     | {{{field|Annotation Description|restricted}}}
@@ -186,6 +186,8 @@ Need to add a reference to a publication without a PubMed ID or DOI (Digital Obj
     {{#if: {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] }}
       | {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]]
           |? has First Author
+          |? has Publication Title
+          |? has Journal Name
           |? has Publication ID
         }}
       |

diff --git a/preecej/semantic_wiki/forms/Ontological_References.wiki b/preecej/semantic_wiki/forms/Ontological_References.wiki
index 9b6a248fd26e66c1613b98d9ebc0eed9d51ea05e..eef09a014c3b2d3b84c3ab0de823964ae95777ec 100644 (file)
--- a/preecej/semantic_wiki/forms/Ontological_References.wiki
+++ b/preecej/semantic_wiki/forms/Ontological_References.wiki
@@ -9,6 +9,7 @@ if a page with that name already exists, you will be sent to a form to edit that
 </noinclude><includeonly>
 <div id="wikiPreview" style="display: none; padding-bottom: 25px; margin-bottom: 25px; border-bottom: 1px solid #AAAAAA;"></div>
 {{{info|page name=Ontologies}}}
+__NOTOC__
 
 {{{for template|Ontological References}}}
 {| class="formtable"

diff --git a/preecej/semantic_wiki/forms/Provenance.wiki b/preecej/semantic_wiki/forms/Provenance.wiki
index e2a16c84c8c25c9070b2d1f13e41c6e631810e59..6baec4b1b64102fc77626bc5f797e806d8e1ec05 100644 (file)
--- a/preecej/semantic_wiki/forms/Provenance.wiki
+++ b/preecej/semantic_wiki/forms/Provenance.wiki
@@ -17,8 +17,8 @@ if a page with that name already exists, you will be sent to a form to edit that
 {{{end template}}}
 
 {{{for template|Provenance Repeater|multiple}}}
-'''Field:''' {{{field|Source Field}}}
-'''Template:''' {{{field|Source Template}}}
+'''Field or Object:''' {{{field|Source Field or Object}}}
+'''Category:''' {{{field|Source Category}}}
 '''Accession ID:''' {{{field|Source Accession ID}}}
 '''Source:''' {{{field|Source}}}
 {{{end template}}}

diff --git a/preecej/semantic_wiki/paw_TransformForImport.pl b/preecej/semantic_wiki/paw_TransformForImport.pl
index c20c010ca4a09e9ced61acaf9503cfcb69465501..ef70b33ca90838c5a941bd7ef4cf07c631435368 100644 (file)
--- a/preecej/semantic_wiki/paw_TransformForImport.pl
+++ b/preecej/semantic_wiki/paw_TransformForImport.pl
@@ -138,9 +138,9 @@ my %annotations; # keyed on Gene Symbol
 
 # page id seeds, until I can figure out how to auto-increment w/in the import 
 # script
-my $SOURCE_TITLE_SEED = 2;
-my $ANNOT_TITLE_SEED = 21;
-my $PUB_TITLE_SEED = 7;
+my $SOURCE_TITLE_SEED = 1;
+my $ANNOT_TITLE_SEED = 1;
+my $PUB_TITLE_SEED = 1;
 
 $Data::Dumper::Pad = "... "; 
 
@@ -933,6 +933,7 @@ sub transform_gaf
         {
             $writer->startTag("Page",Title=>"Publication:$pub_title_count");
                 $writer->startTag("Template",Name=>"Reference_Publication");
+                    $writer->dataElement("Field", "PubMed", Name=>"Publication"); # TODO: replace hard-coded pub type w/ something dynamic
                     $writer->dataElement("Field", $ref_pub, Name=>"Publication ID");
                     my @annot_refs; # holds com-del string of annotation page references
                     foreach my $annot_ref (keys %{$ref_pubs{$ref_pub}})

diff --git a/preecej/semantic_wiki/templates/Annotation.wiki b/preecej/semantic_wiki/templates/Annotation.wiki
index 259a61cab6bf57e9eb0f741b80e72bd1e1790c39..f6d4f548c067311724d10c8d9d68f927fb8a0e6b 100644 (file)
--- a/preecej/semantic_wiki/templates/Annotation.wiki
+++ b/preecej/semantic_wiki/templates/Annotation.wiki
@@ -121,6 +121,8 @@ Edit the page to see the template text.
 {{#if: {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] }}
     | {{#ask:[[Category:Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]] OR [[Category:Reference Publications]][[Is Associated With Annotations::~*{{PAGENAME}}* ]]
         |? has First Author
+        |? has Publication Title
+        |? has Journal Name
         |? has Publication ID
       }}
     | There are no publications associated with this annotation.

diff --git a/preecej/semantic_wiki/templates/Provenance_Repeater.wiki b/preecej/semantic_wiki/templates/Provenance_Repeater.wiki
index 0f76db8810e4b53a0c86197f303730fab0eee6f4..f46fa2f8654a639ac176f7121a70fcafa57290c7 100644 (file)
--- a/preecej/semantic_wiki/templates/Provenance_Repeater.wiki
+++ b/preecej/semantic_wiki/templates/Provenance_Repeater.wiki
@@ -5,16 +5,16 @@ It should be called in the following format:
 {{Provenance Repeater
 |Source=
 |Source Accession ID=
-|Source Template=
-|Source Field=
+|Source Category=
+|Source Field or Object=
 }}
 </pre>
 Edit the page to see the template text.
 </noinclude><includeonly>{{#set_internal:is_Provenance
 |has_Source={{{Source|}}}
 |has_Source_Accession_ID={{{Source Accession ID|}}}
-|is_Associated_With_Field={{{Source Field|}}}
-|is_Associated_With_Template={{{Source Template|}}} }}
+|is_Associated_With_Field_Or_Object={{{Source Field or Object|}}}
+|is_Associated_With_Category={{{Source Category|}}} }}
 
 {| class="wikitable"
 ! Source
@@ -24,6 +24,6 @@ Edit the page to see the template text.
 | [[Has Source Accession ID::{{{Source Accession ID|}}}]]
 |-
 ! Field
-| [[Is Associated With Field::{{{Source Field|}}}]]  (''Template'': {{{Source Template|}}})
+| [[Is Associated With Field Or Object::{{{Source Field or Object|}}}]]  (''Category'': {{{Source Category|}}})
 |}<nowiki/></includeonly>
 

diff --git a/preecej/semantic_wiki/templates/Reference_Publication.wiki b/preecej/semantic_wiki/templates/Reference_Publication.wiki
index 942bce8610a319607c8f28fd154a4bd894cf4d75..1d22e3a6d6f6d7270f3d21537d4d695c63725d27 100644 (file)
--- a/preecej/semantic_wiki/templates/Reference_Publication.wiki
+++ b/preecej/semantic_wiki/templates/Reference_Publication.wiki
@@ -25,7 +25,7 @@ url=http://dev.planteome.org/w/services/NCBI_eDocSummary.php?pub_id={{{Publicati
 }}
 
 {| class="wikitable"
-! Publication
+! Publication Catalogue
 | [[Has Publication Type::{{{Publication|}}}]]
 |-
 ! Publication Identifier
@@ -51,11 +51,10 @@ url=http://dev.planteome.org/w/services/NCBI_eDocSummary.php?pub_id={{{Publicati
 |-
 ! Annotation References
 | {{#arraymap:{{{Annotation References|}}}|,|x|[[Is Associated With Annotations::x]]}}
-|-
-! New Annotation Reference (to be hidden)
-| [[Has New Annotation Association::{{{New Annotation Reference|}}}]]
 |}
 
+<!--[[Has New Annotation Association::{{{New Annotation Reference|}}}]]-->
+
 [[Category:Reference Publications]]
 </includeonly>