Added before migrating to Test.

svn path=/; revision=133

diff --git a/preecej/semantic_wiki/templates/Annotation.wiki b/preecej/semantic_wiki/templates/Annotation.wiki
index bfef2bbf1415fb5d20d24b8a544625141e1fadd4..4e9f9bd469f5366a7a44c4c811c5ebf5eba61a88 100644 (file)
--- a/preecej/semantic_wiki/templates/Annotation.wiki
+++ b/preecej/semantic_wiki/templates/Annotation.wiki
@@ -7,6 +7,7 @@ It should be called in the following format:
 |Species ID=
 |Gene Symbol=
 |Gene Name=
+|Gene Locus=
 |Gene Type=
 |EC Number(s)=
 |Chromosome=
@@ -15,10 +16,15 @@ It should be called in the following format:
 }}
 </pre>
 Edit the page to see the template text.
-</noinclude><includeonly>
+</noinclude><includeonly>__NOTOC__
+<font size=6 color="#67536c">'''[[Has Gene Symbol::{{{Gene Symbol|}}}]] (''[[Has Species Name::{{{Species Name|}}}]]'')'''</font>
 
-__NOTOC__
-<font size=6>'''[[Has Gene Symbol::{{{Gene Symbol|}}}]] (''[[Has Species Name::{{{Species Name|}}}]]'')'''</font>
+{{#get_web_data:
+  |url=http://eutils.ncbi.nlm.nih.gov/entrez/eutils//esearch.fcgi?db=taxonomy&term={{{Species Name|}}}
+  |format=XML
+  |data=species_id=id
+}}
+{{#set:Has Species ID={{#external_value:species_id}} }}
 
 = Annotation =
 
@@ -27,7 +33,7 @@ __NOTOC__
 | [[Has Species Name::{{{Species Name|}}}]]
 |-
 ! Species ID
-| [[Has Species ID::{{{Species ID|}}}]]
+| NCBI:[[Has Species ID::{{#external_value:species_id}}]]
 |-
 ! Gene Symbol
 | [[Has Gene Symbol::{{{Gene Symbol|}}}]]
@@ -37,7 +43,7 @@ __NOTOC__
 |-
 ! Gene Synonyms
 | {{#if: {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}} ]] }}
-    | {{#ask:[[Is Gene Synonym Pair::~{{PAGENAME}}/Gene_Synonyms]]
+    | {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}}]]
         | ?is_Gene_Synonym
         | headers=hide
         | mainlabel=-
@@ -46,6 +52,9 @@ __NOTOC__
     | None available
 }}
 |-
+! Gene Locus
+| [[Has Gene Locus::{{{Gene Locus|}}}]]
+|-
 ! Gene Type
 | [[Has Gene Type::{{{Gene Type|}}}]]
 |-

diff --git a/preecej/semantic_wiki/templates/External_Reference_Repeater.wiki b/preecej/semantic_wiki/templates/External_Reference_Repeater.wiki
new file mode 100644 (file)
index 0000000..1772131
--- /dev/null
+++ b/preecej/semantic_wiki/templates/External_Reference_Repeater.wiki
@@ -0,0 +1,24 @@
+<noinclude>
+This is the "External Reference Repeater" template.
+It should be called in the following format:
+<pre>
+{{External Reference Repeater
+|External Source=
+|External Accession ID=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>{{#set_internal:is_External_Reference
+|from_External_Source={{{External Source|}}}
+|has_External_Accession_ID={{{External Accession ID|}}}
+}}
+
+{| class="wikitable"
+! Source
+| [[From External Source::{{{External Source|}}}]]
+|-
+! Accession ID
+| [[Has External Accession ID::{{{External Accession ID|}}}]]
+|}
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/External_References.wiki b/preecej/semantic_wiki/templates/External_References.wiki
new file mode 100644 (file)
index 0000000..a965393
--- /dev/null
+++ b/preecej/semantic_wiki/templates/External_References.wiki
@@ -0,0 +1,18 @@
+<noinclude>
+This is the "External References" template.
+It should be called in the following format:
+<pre>
+{{External References
+|Annotation Page=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>
+{| class="wikitable"
+! Annotation Page
+| [[Is Associated With Annotation::{{{Annotation Page|}}}]]
+|}
+
+[[Category:External References]]
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Gene_Synonym_Repeater.wiki b/preecej/semantic_wiki/templates/Gene_Synonym_Repeater.wiki
new file mode 100644 (file)
index 0000000..20681d1
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Gene_Synonym_Repeater.wiki
@@ -0,0 +1,14 @@
+<noinclude>
+This is the "Gene Synonym Repeater" template.
+It should be called in the following format:
+<pre>
+{{Gene Synonym Repeater
+|Gene Synonym=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>{| class="wikitable"
+! Gene Synonym
+| [[Is Gene Synonym::{{{Gene Synonym|}}}]]
+|}<nowiki/></includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Gene_Synonyms.wiki b/preecej/semantic_wiki/templates/Gene_Synonyms.wiki
new file mode 100644 (file)
index 0000000..8ed271d
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Gene_Synonyms.wiki
@@ -0,0 +1,21 @@
+<noinclude>
+This is the "Gene Synonyms" template.
+It should be called in the following format:
+<pre>
+{{Gene Synonyms
+|Annotation Page=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>
+{| class="wikitable"
+! Annotation Page
+| [[Is Associated With Annotation::{{{Annotation Page|}}}]]
+|-
+! Gene Name
+| {{#show: {{{Annotation Page|}}}|?has_Gene_Name}}
+|}
+
+[[Category:Gene Synonyms]]
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Ontological_Reference_Repeater.wiki b/preecej/semantic_wiki/templates/Ontological_Reference_Repeater.wiki
new file mode 100644 (file)
index 0000000..49a080e
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Ontological_Reference_Repeater.wiki
@@ -0,0 +1,38 @@
+<noinclude>
+This is the "Ontological Reference Repeater" template.
+It should be called in the following format:
+<pre>
+{{Ontological Reference Repeater
+|Ontology=
+|Term ID=
+|Term Name=
+|Aspect=
+|Evidence Code=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>
+{{#set_internal:is_Ontological_Reference
+|from_Ontology={{{Ontology|}}}
+|has_Term_ID={{{Term ID|}}}
+|has_Term_Name={{{Term Name|}}}
+|has_Aspect={{{Aspect|}}}
+}}
+{| class="wikitable"
+! Ontology
+| [[From Ontology::{{{Ontology|}}}]]
+|-
+! Term Name
+| [[Has Term Name::{{{Term Name|}}}]]
+|-
+! Term ID
+| [[Has Term ID::{{{Term ID|}}}]]
+|-
+! Branch
+| [[Has Aspect::{{{Aspect|}}}]]
+|-
+! Evidence Code
+| [[Has Evidence Code::{{{Evidence Code|}}}]]
+|}
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Ontological_References.wiki b/preecej/semantic_wiki/templates/Ontological_References.wiki
new file mode 100644 (file)
index 0000000..4e88f08
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Ontological_References.wiki
@@ -0,0 +1,18 @@
+<noinclude>
+This is the "Ontological References" template.
+It should be called in the following format:
+<pre>
+{{Ontological References
+|Annotation Page=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>
+{| class="wikitable"
+! Annotation Page
+| [[Is Associated With Annotation::{{{Annotation Page|}}}]]
+|}
+
+[[Category:Ontological References]]
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Plant_Ontology_Reference_Repeater.wiki b/preecej/semantic_wiki/templates/Plant_Ontology_Reference_Repeater.wiki
new file mode 100644 (file)
index 0000000..78f439a
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Plant_Ontology_Reference_Repeater.wiki
@@ -0,0 +1,40 @@
+<noinclude>
+This is the "Plant Ontology Reference Repeater" template.
+It should be called in the following format:
+<pre>
+{{Plant Ontology Reference Repeater
+|Term ID=
+|Term Name=
+|Aspect=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>{{#get_web_data:
+  |url=http://dev.planteome.org/w/prototyping/TermSearch_JSON.php?user=paw&field=name&type=term_detail&qval={{{Term Name|}}}&format=json
+  |format=JSON
+  |data=term_id=id,term_aspect=aspect,term_definition=definition,term_comment=comment
+}}
+{{#set_internal:is_Ontological_Reference
+|from_Ontology=Plant Ontology
+|has_Term_ID={{#external_value:term_id}}
+|has_Term_Name={{{Term Name|}}}
+|has_Aspect={{#external_value:term_aspect}}
+}}
+{| class="wikitable"
+! Ontology
+| Plant Ontology
+|-
+! Term Name
+| [[Has Term Name::{{{Term Name|}}}]]
+|-
+! Term ID
+| [[Has Term ID::{{#external_value:term_id}}]]
+|-
+! Branch
+| {{#external_value:term_aspect}}
+|-
+! Definition
+| {{#external_value:term_definition}}
+|}
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Provenance.wiki b/preecej/semantic_wiki/templates/Provenance.wiki
new file mode 100644 (file)
index 0000000..2e1764f
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Provenance.wiki
@@ -0,0 +1,18 @@
+<noinclude>
+This is the "Provenance" template.
+It should be called in the following format:
+<pre>
+{{Provenance
+|Annotation Page=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>
+{| class="wikitable"
+! Annotation
+| [[Is Associated With Annotation::{{{Annotation Page|}}}]]
+|}
+
+[[Category:Provenance]]
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Provenance_Repeater.wiki b/preecej/semantic_wiki/templates/Provenance_Repeater.wiki
new file mode 100644 (file)
index 0000000..0f76db8
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Provenance_Repeater.wiki
@@ -0,0 +1,29 @@
+<noinclude>
+This is the "Provenance Repeater" template.
+It should be called in the following format:
+<pre>
+{{Provenance Repeater
+|Source=
+|Source Accession ID=
+|Source Template=
+|Source Field=
+}}
+</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|}}} }}
+
+{| class="wikitable"
+! Source
+| [[Has Source::{{{Source|}}}]]
+|-
+! Accession ID
+| [[Has Source Accession ID::{{{Source Accession ID|}}}]]
+|-
+! Field
+| [[Is Associated With Field::{{{Source Field|}}}]]  (''Template'': {{{Source Template|}}})
+|}<nowiki/></includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Publication.wiki b/preecej/semantic_wiki/templates/Publication.wiki
new file mode 100644 (file)
index 0000000..e447cd8
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Publication.wiki
@@ -0,0 +1,54 @@
+<noinclude>
+This is the "Publication" template.
+It should be called in the following format:
+<pre>
+{{Publication
+|Publication=
+|Publication ID=
+|Publication Title=
+|First Author=
+|Journal Name=
+|Volume=
+|Year=
+|Pages=
+|Annotation References=
+|New Annotation Reference=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>
+{| class="wikitable"
+! Publication
+| [[Has Publication Type::{{{Publication|}}}]]
+|-
+! Publication Identifier
+| [[Has Publication ID::{{{Publication ID|}}}]]
+|-
+! Publication Title
+| [[Has Publication Title::{{{Publication Title|}}}]]
+|-
+! First Author
+| [[Has First Author::{{{First Author|}}}]]
+|-
+! Journal Name
+| [[Has Journal Name::{{{Journal Name|}}}]]
+|-
+! Volume
+| [[Has Publication Volume::{{{Volume|}}}]]
+|-
+! Year
+| [[Has Publication Year::{{{Year|}}}]]
+|-
+! Pages
+| [[Has Publication Pages::{{{Pages|}}}]]
+|-
+! 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:Publications]]
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Reference_Publication.wiki b/preecej/semantic_wiki/templates/Reference_Publication.wiki
new file mode 100644 (file)
index 0000000..d7a1751
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Reference_Publication.wiki
@@ -0,0 +1,61 @@
+<noinclude>
+This is the "Reference Publication" template.
+It should be called in the following format:
+<pre>
+{{Reference Publication
+|Publication=
+|Publication ID=
+|Publication Title=
+|First Author=
+|Journal Name=
+|Volume=
+|Year=
+|Pages=
+|Annotation References=
+|New Annotation Reference=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>
+
+{{#get_web_data:
+url=http://dev.planteome.org/w/prototyping/NCBI_eDocSummary.php?pub_id={{{Publication ID|}}}
+|format=XML
+|data=pub_id=Id,year=PubDate,first_author=LastAuthor,journal_name=FullJournalName,title=Title,volume=Volume,pages=Pages
+}}
+
+{| class="wikitable"
+! Publication
+| [[Has Publication Type::{{{Publication|}}}]]
+|-
+! Publication Identifier
+| [[Has Publication ID::{{{Publication ID|}}}]]
+|-
+! Publication Title
+| [[Has Publication Title::{{#for_external_table:{{{title}}} }}]]
+|-
+! First Author
+| [[Has First Author::{{#for_external_table:{{{first_author}}} }}]]
+|-
+! Journal Name
+| [[Has Journal Name::{{#for_external_table:{{{journal_name}}} }}]]
+|-
+! Volume
+| [[Has Publication Volume::{{#for_external_table:{{{volume}}} }}]]
+|-
+! Year
+| [[Has Publication Year::{{#for_external_table:{{{year}}} }}]]
+|-
+! Pages
+| [[Has Publication Pages::{{#for_external_table:{{{pages}}} }}]]
+|-
+! 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]]
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Sequence_Repeater.wiki b/preecej/semantic_wiki/templates/Sequence_Repeater.wiki
new file mode 100644 (file)
index 0000000..e9c84b6
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Sequence_Repeater.wiki
@@ -0,0 +1,28 @@
+<noinclude>
+This is the "Sequence Repeater" template.
+It should be called in the following format:
+<pre>
+{{Sequence Repeater
+|Sequence Type=
+|Sequence Source=
+|External Accession ID=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>{{#set_internal:is_Sequence_Reference
+|has_Sequence_Type={{{Sequence Type}}}
+|has_Sequence_Source={{{Sequence Source|}}}
+|has_External_Accession_ID={{{External Accession ID|}}}
+}}
+{| class="wikitable"
+! Sequence Type
+| [[Has Sequence Type::{{{Sequence Type|}}}]]
+|-
+! Sequence Source
+| [[Has Sequence Source::{{{Sequence Source|}}}]]
+|-
+! Accession ID
+| [[Has External Accession ID::{{{External Accession ID|}}}]]
+|}
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Sequences.wiki b/preecej/semantic_wiki/templates/Sequences.wiki
new file mode 100644 (file)
index 0000000..2a98b35
--- /dev/null
+++ b/preecej/semantic_wiki/templates/Sequences.wiki
@@ -0,0 +1,18 @@
+<noinclude>
+This is the "Sequences" template.
+It should be called in the following format:
+<pre>
+{{Sequences
+|Annotation Page=
+}}
+</pre>
+Edit the page to see the template text.
+</noinclude><includeonly>
+{| class="wikitable"
+! Annotation Page
+| [[Is Associated With Annotation::{{{Annotation Page|}}}]]
+|}
+
+[[Category:Sequences]]
+</includeonly>
+

diff --git a/preecej/semantic_wiki/templates/Source.wiki b/preecej/semantic_wiki/templates/Source.wiki
index 9aa3ea2fcbcbd8d0cf7d6592e03197b886258a71..3cb52f77d7fd908753785f796257691bdfb4aeb5 100644 (file)
--- a/preecej/semantic_wiki/templates/Source.wiki
+++ b/preecej/semantic_wiki/templates/Source.wiki
@@ -3,7 +3,6 @@ This is the "Source" template.
 It should be called in the following format:
 <pre>
 {{Source
-|Accession ID=
 |Source Date Stamp=
 |Source Database=
 |Source Version=
@@ -14,9 +13,6 @@ It should be called in the following format:
 Edit the page to see the template text.
 </noinclude><includeonly>
 {| class="wikitable"
-! Accession ID
-| [[Has Accession ID::{{{Accession ID|}}}]]
-|-
 ! Release Date
 | [[Has Date Stamp::{{{Source Date Stamp|}}}]]
 |-