{{{info|page name=Annotation:<unique number;start=1>}}}
__NOTOC__
{{#ifexist: {{PAGENAME}}
- |<font size=6>'''{{#show:{{PAGENAME}}|?has_Gene_Symbol}} (''{{#show:{{PAGENAME}}|?has_Species_Name}}'')'''</font>
+ |<font size=6 color="#67536c">'''{{#show:{{PAGENAME}}|?has_Gene_Symbol}} (''{{#show:{{PAGENAME}}|?has_Species_Name}}'')'''</font>
|
}}
+
= Annotation =
{{{for template|Annotation}}}
{| class="formtable"
! Species Name:
-| {{{field|Species Name}}}
-|-
-! Species ID:
-| {{{field|Species ID}}}
+| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
+ [[Is Associated With Field::Species Name]]
+ [[Is Associated With Template::Annotation]]
+ |?is_Provenance
+ }}
+ | {{{field|Species Name|restricted}}}
+ | {{{field|Species Name|autocomplete on property=Has Reference Taxon}}}
+ }}
|-
! Gene Symbol:
-| {{#if: {{#ask: [[Is Provenance::~Annotation:1/Provenance*]]
+| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
[[Is Associated With Field::Gene Symbol]]
[[Is Associated With Template::Annotation]]
- |?has_Provenance
+ |?is_Provenance
}}
|{{{field|Gene Symbol|restricted}}}
|{{{field|Gene Symbol}}}
}}
|-
! Gene Name:
-| {{{field|Gene Name}}}
+| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
+ [[Is Associated With Field::Gene Name]]
+ [[Is Associated With Template::Annotation]]
+ |?is_Provenance
+ }}
+ | {{{field|Gene Name|restricted}}}
+ | {{{field|Gene Name}}}
+ }}
|-
! Gene Synonyms:
-| {{#if: {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}} ]] }}
- | {{#ask:[[Is Gene Synonym Pair::~{{PAGENAME}}/Gene_Synonyms]]
- | ?is_Gene_Synonym
- | headers=hide
- | mainlabel=-
- | format=list
- }} {{#formlink:form=Gene_Synonyms|link text=Edit|link type=button|target={{PAGENAME}}/Gene_Synonyms }}
- | {{#formlink:form=Gene_Synonyms|link text=Add Synonyms|link type=button|query string=Gene_Synonyms[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }}
+| {{#ifexist: {{PAGENAME}}
+ | {{#if: {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}} ]] }}
+ | {{#ask:[[Category:Gene_Synonyms]][[Is Associated With Annotation::{{PAGENAME}} ]]
+ | ?is_Gene_Synonym
+ | headers=hide
+ | mainlabel=-
+ | format=list
+ }} {{#formlink:form=Gene_Synonyms|link text=Edit|link type=button|target={{PAGENAME}}/Gene_Synonyms }}
+ | {{#formlink:form=Gene_Synonyms|link text=Add Synonyms|link type=button|query string=Gene_Synonyms[Annotation Page]={{PAGENAME}}&super_page={{PAGENAME}} }}
+ }}
+ | To add gene synonyms, first save your basic annotation information on this "Annotation" tab.
}}
|-
+! Gene Locus:
+| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
+ [[Is Associated With Field::Gene Locus]]
+ [[Is Associated With Template::Annotation]]
+ |?is_Provenance
+ }}
+ | {{{field|Gene Locus|restricted}}}
+ | {{{field|Gene Locus}}}
+ }}
+|-
! Gene Type:
-| {{{field|Gene Type}}}
+| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
+ [[Is Associated With Field::Gene Type]]
+ [[Is Associated With Template::Annotation]]
+ |?is_Provenance
+ }}
+ | {{{field|Gene Type|restricted}}}
+ | {{{field|Gene Type}}}
+ }}
|-
! EC Number(s):
-| {{{field|EC Numbers|list|delimiter=,}}}
+| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
+ [[Is Associated With Field::EC Numbers]]
+ [[Is Associated With Template::Annotation]]
+ |?is_Provenance
+ }}
+ | {{{field|EC Numbers|restricted|list|delimiter=,}}}
+ | {{{field|EC Numbers|list|delimiter=,}}}
+ }}
|-
! Chromosome:
-| {{#if: {{#ask: [[Is Provenance::~Annotation:1/Provenance*]]
+| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
[[Is Associated With Field::Chromosome]]
[[Is Associated With Template::Annotation]]
- |?has_Provenance
+ |?is_Provenance
}}
|{{{field|Chromosome|restricted}}}
|{{{field|Chromosome}}}
}}
|-
! Has Phenotype:
-| {{{field|Has Phenotype}}}
+| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
+ [[Is Associated With Field::Has Phenotype]]
+ [[Is Associated With Template::Annotation]]
+ |?is_Provenance
+ }}
+ | {{{field|Has Phenotype|restricted}}}
+ | {{{field|Has Phenotype}}}
+ }}
|-
! Description:
-| {{{field|Annotation Description}}}
+| {{#if: {{#ask: [[Is Provenance::~{{PAGENAME}}/Provenance*]]
+ [[Is Associated With Field::Annotation Description]]
+ [[Is Associated With Template::Annotation]]
+ |?is_Provenance
+ }}
+ | {{{field|Annotation Description|restricted}}}
+ | {{{field|Annotation Description}}}
+ }}
|}
{{{end template}}}
--- /dev/null
+<noinclude>
+This is the "External References" 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=External References}}
+
+</noinclude><includeonly>
+<div id="wikiPreview" style="display: none; padding-bottom: 25px; margin-bottom: 25px; border-bottom: 1px solid #AAAAAA;"></div>
+{{{info|page name=External_References}}}
+
+{{{for template|External References}}}
+{| class="formtable"
+! Annotation Page:
+| {{{field|Annotation Page}}}
+|}
+{{{end template}}}
+
+{{{for template|External Reference Repeater|multiple}}}
+'''Source:''' {{{field|External Source}}}
+'''Accession ID:''' {{{field|External Accession ID}}}
+{{{end template}}}
+
+{{{standard input|summary}}}
+
+{{{standard input|watch}}}
+
+{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}}
+</includeonly>
+
--- /dev/null
+<noinclude>
+This is the "Gene Synonyms" 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=Gene Synonyms}}
+
+</noinclude><includeonly>
+<div id="wikiPreview" style="display: none; padding-bottom: 25px; margin-bottom: 25px; border-bottom: 1px solid #AAAAAA;"></div>
+{{{info|page name=Gene_Synonyms}}}
+
+{{{for template|Gene Synonyms}}}
+{| class="formtable"
+! Annotation Page:
+| {{{field|Annotation Page}}}
+|}
+{{{end template}}}
+
+{{{for template|Gene Synonym Repeater|multiple}}}
+
+<!----------------------------
+
+=== Gene Synonyms Test ===
+
+Annotation Page: {{#show:{{PAGENAME}}|?Is Associated With Annotation}}
+
+Provenance Page Test: {{#ask: [[Is Provenance::~Annotation:1/Provenance* ]] }}
+
+Specific Gene-Synonym Pair test:
+{{#ask: [[Is Gene Synonym Pair::{{PAGENAME}}]]
+ [[Is Gene Synonym::Gene Synonym 1]]
+ [[Is Associated With Gene Name::Gene Name 1]]
+ |link=none
+}}
+
+Provenance for Specific Synonym (Test): {{#ask: [[Is Provenance::~{{#show:{{PAGENAME}}|?Is Associated With Annotation|link=none}}/Provenance*]][[Is Associated With Field::Annotation:1/Gene Synonyms#1 ]] }}
+
+Gene Synonym Page Request: {{#ask: [[Is Gene Synonym Pair::{{PAGENAME}} ]] }}
+
+Gene Synonym Pair:
+{{#ask: [[Is Gene Synonym Pair::{{PAGENAME}}]]
+ [[Is Gene Synonym::Gene Synonym 1]]
+ [[Is Associated With Gene Name::Gene Name 1]]|link=none
+}}
+
+Provenance for Specific Synonym (subquery):
+{{#ask:
+ [[Is Provenance::~{{#show:{{PAGENAME}}|?Is Associated With Annotation|link=none}}/Provenance*]]
+ [[Is Associated With Field::{{#ask:
+ [[Is Gene Synonym Pair::{{PAGENAME}}]]
+ [[Is Gene Synonym::Gene Synonym 2]]
+ [[Is Associated With Gene Name::Gene Name 1]]
+ |link=none
+ }}
+ ]]
+}}
+
+Synonym: {{#show: {{PAGENAME}}#2 | ?Is Gene Synonym Pair}}
+
+Specific Gene-Synonym Pair test:
+{{#ask: [[Is Gene Synonym Pair::{{PAGENAME}}]]
+ [[Is Gene Synonym::Gene Synonym 2]]
+ [[Is Associated With Gene Name::Gene Name 1]]
+ |link=none
+}}
+
+-----------------------------
+
+{{#if:
+ {{#ask:
+ [[Is Provenance::~{{#show:{{PAGENAME}}|?Is Associated With Annotation|link=none}}/Provenance*]]
+ [[Is Associated With Field::{{#ask:
+ [[Is Gene Synonym Pair::{{PAGENAME}}]]
+ [[Is Gene Synonym::Gene Synonym 1]]
+ [[Is Associated With Gene Name::Gene Name 1]]
+ |link=none
+ }}
+ ]]
+ }}
+ |'''Gene Name:''' {{{field|Gene Name|autocomplete on property=has_Gene_Name|restricted}}}
+'''Gene Synonym:''' {{{field|Gene Synonym|restricted}}}
+ |'''Gene Name:''' {{{field|Gene Name|autocomplete on property=has_Gene_Name}}}
+'''Gene Synonym:''' {{{field|Gene Synonym}}}
+}}
+
+----------------------------->
+
+'''Gene Synonym:''' {{{field|Gene Synonym}}}
+
+<!----------------------------->
+
+{{{end template}}}
+
+{{{standard input|summary}}}
+
+{{{standard input|watch}}}
+
+{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}}
+</includeonly>
+
--- /dev/null
+<noinclude>
+This is the "Ontological References" 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=Ontological References}}
+
+</noinclude><includeonly>
+<div id="wikiPreview" style="display: none; padding-bottom: 25px; margin-bottom: 25px; border-bottom: 1px solid #AAAAAA;"></div>
+{{{info|page name=Ontologies}}}
+
+{{{for template|Ontological References}}}
+{| class="formtable"
+! Annotation Page:
+| {{{field|Annotation Page}}}
+|}
+{{{end template}}}
+
+=== Plant Ontology ===
+{{{for template|Plant Ontology Reference Repeater|multiple}}}
+'''Term Name:''' {{{field|Term Name|autocomplete from url=remote_PO_terms}}}
+{{{end template}}}
+
+=== Other Ontologies ===
+{{{for template|Ontological Reference Repeater|multiple}}}
+'''Ontology:''' {{{field|Ontology|}}}
+'''Term Name:''' {{{field|Term Name|}}}
+'''Term ID:''' {{{field|Term ID|}}}
+'''Branch:''' {{{field|Aspect|}}}
+<br>'''Evidence Code:''' {{{field|Evidence Code|}}}
+{{{end template}}}
+
+{{{standard input|summary}}}
+
+{{{standard input|watch}}}
+
+{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}}
+</includeonly>
+
--- /dev/null
+<noinclude>
+This is the "Provenance" 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=Provenance}}
+
+</noinclude><includeonly>
+<div id="wikiPreview" style="display: none; padding-bottom: 25px; margin-bottom: 25px; border-bottom: 1px solid #AAAAAA;"></div>
+{{{info|page name=Provenance}}}
+
+{{{for template|Provenance}}}
+{| class="formtable"
+! Annotation Page:
+| {{{field|Annotation Page}}}
+|}
+{{{end template}}}
+
+{{{for template|Provenance Repeater|multiple}}}
+'''Field:''' {{{field|Source Field}}}
+'''Template:''' {{{field|Source Template}}}
+'''Accession ID:''' {{{field|Source Accession ID}}}
+'''Source:''' {{{field|Source}}}
+{{{end template}}}
+
+{{{standard input|summary}}}
+
+{{{standard input|watch}}}
+
+{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}}
+</includeonly>
+
--- /dev/null
+<noinclude>
+This is the "Publication" 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=Publication}}
+
+</noinclude><includeonly>
+<div id="wikiPreview" style="display: none; padding-bottom: 25px; margin-bottom: 25px; border-bottom: 1px solid #AAAAAA;"></div>
+{{{info|page name=Publication:<unique number;start=1>}}}
+{{{for template|Publication}}}
+
+{{#set:Annotation References={{{Annotation References|}}}, {{{New Annotation Reference|}}} }}
+
+{| class="formtable"
+! Publication:
+| {{{field|Publication}}}
+|-
+! Publication ID:
+| {{{field|Publication ID}}}
+|-
+! Publication Title:
+| {{{field|Publication Title}}}
+|-
+! First Author:
+| {{{field|First Author}}}
+|-
+! Journal Name:
+| {{{field|Journal Name}}}
+|-
+! Volume:
+| {{{field|Volume}}}
+|-
+! Year:
+| {{{field|Year}}}
+|-
+! Pages:
+| {{{field|Pages}}}
+|-
+! Annotation References:
+| {{{field|Annotation References}}}
+|-
+! New Annotation Reference (to be hidden):
+| {{{field|New Annotation Reference}}}
+|}
+{{{end template}}}
+
+{{{standard input|summary}}}
+
+{{{standard input|watch}}}
+
+{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}}
+</includeonly>
+
--- /dev/null
+<noinclude>
+This is the "Reference Publication" 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=Reference Publication}}
+
+</noinclude><includeonly>
+<div id="wikiPreview" style="display: none; padding-bottom: 25px; margin-bottom: 25px; border-bottom: 1px solid #AAAAAA;"></div>
+{{{info|page name=Publication:<unique number;start=1>}}}
+{{{for template|Reference Publication}}}
+{| class="formtable"
+! Publication:
+| {{{field|Publication}}}
+|-
+! Publication ID:
+| {{{field|Publication ID}}}
+|-
+! Publication Title:
+| {{{field|Publication Title|hidden}}}
+|-
+! First Author:
+| {{{field|First Author|hidden}}}
+|-
+! Journal Name:
+| {{{field|Journal Name|hidden}}}
+|-
+! Volume:
+| {{{field|Volume|hidden}}}
+|-
+! Year:
+| {{{field|Year|hidden}}}
+|-
+! Pages:
+| {{{field|Pages|hidden}}}
+|-
+! Annotation References:
+| {{{field|Annotation References}}}
+|-
+! New Annotation Reference (to be hidden):
+| {{{field|New Annotation Reference}}}
+|}
+{{{end template}}}
+
+{{{standard input|summary}}}
+
+{{{standard input|watch}}}
+
+{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}}
+</includeonly>
+
--- /dev/null
+<noinclude>
+This is the "Sequences" 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=Sequences}}
+
+</noinclude><includeonly>
+<div id="wikiPreview" style="display: none; padding-bottom: 25px; margin-bottom: 25px; border-bottom: 1px solid #AAAAAA;"></div>
+{{{info|page name=Sequences}}}
+
+{{{for template|Sequences}}}
+{| class="formtable"
+! Annotation Page:
+| {{{field|Annotation Page}}}
+|}
+{{{end template}}}
+
+{{{for template|Sequence Repeater|multiple}}}
+'''Sequence Type:''' {{{field|Sequence Type}}}
+'''Sequence Source:''' {{{field|Sequence Source}}}
+'''Accession ID:''' {{{field|External Accession ID}}}
+{{{end template}}}
+
+{{{standard input|summary}}}
+
+{{{standard input|watch}}}
+
+{{{standard input|save}}} {{{standard input|changes}}} {{{standard input|cancel}}}
+</includeonly>
+
{{{for template|Source}}}
{| class="formtable"
-! Accession ID:
-| {{{field|Accession ID}}}
-|-
! Source Date Stamp:
| {{{field|Source Date Stamp}}}
|-
projects / old-jaiswallab-svn / .git / commitdiff