From 2dcacbb60c89eea64bceb58631e7fd3fb8d4cc14 Mon Sep 17 00:00:00 2001 From: preecej Date: Fri, 1 Jul 2011 00:11:57 +0000 Subject: [PATCH] Began storage of wiki forms and templates. svn path=/; revision=107 --- .../semantic_wiki/PS_TransformForImport.pl | 2 +- preecej/semantic_wiki/forms/Annotation.wiki | 145 ++++++++++++++++++ .../semantic_wiki/templates/Annotation.wiki | 115 ++++++++++++++ 3 files changed, 261 insertions(+), 1 deletion(-) create mode 100644 preecej/semantic_wiki/forms/Annotation.wiki create mode 100644 preecej/semantic_wiki/templates/Annotation.wiki diff --git a/preecej/semantic_wiki/PS_TransformForImport.pl b/preecej/semantic_wiki/PS_TransformForImport.pl index 1a219b0..ac74a48 100644 --- a/preecej/semantic_wiki/PS_TransformForImport.pl +++ b/preecej/semantic_wiki/PS_TransformForImport.pl @@ -306,7 +306,7 @@ sub write_xml } } if (!(defined $curr_accession_id)) { - die "Error: No Accession ID available\n"; + die "Error: No Accession ID available. Ending program.\n"; } # iterate through the annotation data and assign to elements diff --git a/preecej/semantic_wiki/forms/Annotation.wiki b/preecej/semantic_wiki/forms/Annotation.wiki new file mode 100644 index 0000000..464eb3a --- /dev/null +++ b/preecej/semantic_wiki/forms/Annotation.wiki @@ -0,0 +1,145 @@ + +This is the "Annotation" form. +To create a page with this form, enter the page name below; +if a page with that name already exists, you will be sent to a form to edit that page. +{{#forminput:form=Annotation}} + + +{{{info|page name=Annotation:}}} +__NOTOC__ +{{#ifexist: {{PAGENAME}} + |'''{{#show:{{PAGENAME}}|?has_Gene_Symbol}} (''{{#show:{{PAGENAME}}|?has_Species_Name}}'')''' + | +}} + += Annotation = + +{{{for template|Annotation}}} + +{| class="formtable" +! Accession ID: +| {{{field|Accession ID}}} +|- +! Species Name: +| {{{field|Species Name}}} +|- +! Species ID: +| {{{field|Species ID}}} +|- +! Gene Symbol: +| {{#if: + {{#ask:[[Category:Provenance]][[Is Associated With Annotation::~{{PAGENAME}}/Provenance]] + [[Is Associated With Field::Gene Symbol]] + [[Is Associated With Template::Annotation]] + |?is_Provenance + }} + |{{{field|Gene Symbol|restricted}}} + |{{{field|Gene Symbol}}} + }} +|- +! Gene Name: +| {{{field|Gene Name}}} +|- +! Gene Synonyms: +| synonym code here... +|- +! Gene Type: +| {{{field|Gene Type}}} +|- +! EC Number(s): +| {{{field|EC Numbers|list|delimiter=,}}} +|- +! Chromosome: +| {{#if: + {{#ask:[[Category:Provenance]][[Is Associated With Annotation::~{{PAGENAME}}/Provenance]] + [[Is Associated With Field::Chromosome]] + [[Is Associated With Template::Annotation]] + |?is_Provenance + }} + |{{{field|Chromosome|restricted}}} + |{{{field|Chromosome}}} + }} +|- +! Has Phenotype: +| {{{field|Has Phenotype}}} +|- +! Description: +| {{{field|Annotation Description}}} +|} + +{{{end template}}} + += External References = + +{{#ifexist: {{PAGENAME}} + | {{#if: {{#ask:[[Category:External_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | Add, edit, or remove external reference data {{#formlink:form=External_References|link text=here|target={{PAGENAME}}/External_References }}. + {{#ask:[[Is External Reference::~{{PAGENAME}}/External_References* ]] + | mainlabel=- + |? from_External_Source + |? has_External_Accession_ID + }} + | Add external references for this annotation.
{{#formlink:form=External_References|link text=Add|link type=button|query string=External_References[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} + }} + | To add external references, first save your basic annotation information on the "Annotation" tab. +}} + += Ontologies = + +{{#ifexist: {{PAGENAME}} + | {{#if: {{#ask:[[Category:Ontological_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | Add, edit, or remove ontology references {{#formlink:form=Ontological_References|link text=here|target={{PAGENAME}}/Ontologies }}. + {{#ask:[[Is Ontological Reference::~{{PAGENAME}}/Ontologies*]] + | mainlabel=- + |? has_Term_ID + |? has_Term_Name + |? has_Aspect + }} + | Add ontological associations for this annotation.
{{#formlink:form=Ontological_References|link text=Add|link type=button|query string=Ontological_References[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} + }} + | To add ontological references, first save your basic annotation information on the "Annotation" tab. +}} + += Sequences = + +{{#ifexist: {{PAGENAME}} + | {{#if: {{#ask:[[Category:Sequences]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | Add, edit, or remove sequence references {{#formlink:form=Sequences|link text=here|target={{PAGENAME}}/Sequences }}. + {{#ask:[[Is Sequence Reference::~{{PAGENAME}}/Sequences*]] + | mainlabel=- + |? has_Sequence_Type + |? has_Sequence_Source + |? has_External_Accession_ID + }} + | Add sequence references for this annotation.
{{#formlink:form=Sequences|link text=Add|link type=button|query string=Sequences[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }} + }} + | To add sequence references, first save your basic annotation information on the "Annotation" tab. +}} + += Literature = + +{{#ifexist: {{PAGENAME}} + | Add a reference to a publication listed with PubMed or the DOI registry {{#formlink:form=Reference_Publication|link text=here|link type=|query string=Reference_Publication[New Annotation Reference]={{PAGENAME}} }}.
+ +Need to add a reference to a publication without a PubMed ID or DOI (Digital Object Identifier)?
+{{#formlink:form=Publication|link text=Add a new publication reference|link type=|query string=Publication[New Annotation Reference]={{PAGENAME}} }} + + {{#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 ID + }} + | + }} + | To add publication references, first save your basic annotation information on the "Annotation" tab. +}} + + +{{{standard input|summary}}} + +{{{standard input|watch}}} + +{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}} + + + diff --git a/preecej/semantic_wiki/templates/Annotation.wiki b/preecej/semantic_wiki/templates/Annotation.wiki new file mode 100644 index 0000000..4e4e8b5 --- /dev/null +++ b/preecej/semantic_wiki/templates/Annotation.wiki @@ -0,0 +1,115 @@ + +This is the "Annotation" template. +It should be called in the following format: +
+{{Annotation
+|Accession ID=
+|Species Name=
+|Species ID=
+|Gene Symbol=
+|Gene Name=
+|Gene Type=
+|EC Number(s)=
+|Chromosome=
+|Has Phenotype=
+|Annotation Description=
+}}
+
+Edit the page to see the template text. + + +__NOTOC__ +'''[[Has Gene Symbol::{{{Gene Symbol|}}}]] (''[[Has Species Name::{{{Species Name|}}}]]'')''' + += Annotation = + +{| class="wikitable" +! Accession ID +| [[Has Accession ID::{{{Accession ID|}}}]] +|- +! Species Name +| [[Has Species Name::{{{Species Name|}}}]] +|- +! Species ID +| [[Has Species ID::{{{Species ID|}}}]] +|- +! Gene Symbol +| [[Has Gene Symbol::{{{Gene Symbol|}}}]] +|- +! Gene Name +| [[Has Gene Name::{{{Gene Name|}}}]] +|- +! Gene Synonyms +| coming soon... +|- +! Gene Type +| [[Has Gene Type::{{{Gene Type|}}}]] +|- +! EC number(s) +| {{#arraymap:{{{EC Numbers|}}}|,|x|[[Has EC Numbers::x]]}} +|- +! Chromosome +| [[Exists On Chromosome Number::{{{Chromosome|}}}]] +|- +! Has Phenotype? +| [[Has Phenotype::{{{Has Phenotype|}}}]] +|} + +{| class="wikitable" +! Description +| [[Has Annotation Description::{{{Annotation Description|}}}]] +|} + +{{#ifexist: {{PAGENAME}}/Provenance + | To review the provenance of this data, click [[{{PAGENAME}}/Provenance|here]]. + | +}} + += External References = + +{{#if: {{#ask:[[Category:External_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | {{#ask:[[Is External Reference::~{{PAGENAME}}/External_References]] + | mainlabel=- + |? from_External_Source + |? has_External_Accession_ID + }} + | There are no external references available for this annotation. +}} + += Ontologies = + +{{#if: {{#ask:[[Category:Ontological_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | {{#ask:[[Is Ontological Reference::~{{PAGENAME}}/Ontologies]] + | mainlabel=- + |? has_Term_ID + |? has_Term_Name + |? has_Aspect + }} + | There are no ontological associations available for this gene annotation. +}} + += Sequences = + +{{#if: {{#ask:[[Category:Sequences]][[Is Associated With Annotation::{{PAGENAME}} ]] }} + | {{#ask:[[Is Sequence Reference::~{{PAGENAME}}/Sequences]] + | mainlabel=- + |? has_Sequence_Type + |? has_Sequence_Source + |? has_External_Accession_ID + }} + | There is no sequence data available for this gene annotation. +}} + += Literature = + +{{#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 ID + }} + | There are no publications associated with this annotation. +}} + +[[Category:Annotations]] + + -- 2.34.1