From 41c634ca76b1f79cc332caa2ef733a28bbd63169 Mon Sep 17 00:00:00 2001 From: preecej Date: Wed, 7 Sep 2011 18:07:41 +0000 Subject: [PATCH] Publication adjustments svn path=/; revision=176 --- preecej/semantic_wiki/forms/Annotation.wiki | 38 ++++++++++--------- .../forms/Ontological_References.wiki | 1 + preecej/semantic_wiki/forms/Provenance.wiki | 4 +- .../semantic_wiki/paw_TransformForImport.pl | 7 ++-- .../semantic_wiki/templates/Annotation.wiki | 2 + .../templates/Provenance_Repeater.wiki | 10 ++--- .../templates/Reference_Publication.wiki | 7 ++-- 7 files changed, 37 insertions(+), 32 deletions(-) diff --git a/preecej/semantic_wiki/forms/Annotation.wiki b/preecej/semantic_wiki/forms/Annotation.wiki index 32913a3..b9c677d 100644 --- 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 9b6a248..eef09a0 100644 --- 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 {{{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 e2a16c8..6baec4b 100644 --- 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 c20c010..ef70b33 100644 --- 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 259a61c..f6d4f54 100644 --- 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 0f76db8..f46fa2f 100644 --- 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= }} Edit the page to see the template text. {{#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|}}}) |} diff --git a/preecej/semantic_wiki/templates/Reference_Publication.wiki b/preecej/semantic_wiki/templates/Reference_Publication.wiki index 942bce8..1d22e3a 100644 --- 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|}}}]] |} + + [[Category:Reference Publications]] -- 2.34.1