From: preecej Date: Wed, 6 Jul 2011 22:15:00 +0000 (+0000) Subject: Changed name of import file from PS_* to paw_* X-Git-Url: http://gitweb.planteome.org/?a=commitdiff_plain;h=1632bc3efad51638f7cc65a2ac5a8589e65b1204;p=old-jaiswallab-svn%2F.git Changed name of import file from PS_* to paw_* svn path=/; revision=110 --- diff --git a/preecej/semantic_wiki/PS_TransformForImport.pl b/preecej/semantic_wiki/PS_TransformForImport.pl deleted file mode 100644 index 6d5fc5c..0000000 --- a/preecej/semantic_wiki/PS_TransformForImport.pl +++ /dev/null @@ -1,370 +0,0 @@ -#!/usr/bin/perl -w - -=head1 NAME - -Plant Semantics Import Transformation Script - -=head1 VERSION - -0.2 - -=head1 DESCRIPTION - -Transform external gene annotation data into an XML document readable -by the MediaWiki extension DataTransfer (Special:ImportXML) feature. -Also generates appropriate provenance of data based on header of -import file. - -=head1 USAGE - -PS_TransformForImport.pl -i INPUT_FILE -t TYPE -o OUTPUT_FILE - -=head1 OPTIONS - - -i Name of input CSV or tab-del file. - -t Specifies input type of file ('csv' or 'tab') - -o Name of output file. - -v View verbose information - -d View debugging information - -=head1 DEPENDENCIES - -Requires that the input files contain two headers: the first will hold -the provenance information associated with the imported data, and the -second will specify the template and field names for the annotation -data. - -=head2 Provenance Header Format Example - - [Provenance] - Source Date Time Stamp=Apr 2 2008 - Source Database=Oryzabase - Source Version=rel. 10 - Source URI=http://www.shigen.nig.ac.jp/rice/oryzabase/ - Source File=http://www.shigen.nig.ac.jp/rice/oryzabase/genes/... - -=head2 Data Header Format Example (field separator may also be a tab) - - [Format] - Template=Gene - Fields=Species Name,Gene Symbol,Gene Name,Chromosome,Gene Type,Accession ID - [Data] - val1,val2,val3,... - " - " - " - - NOTE: One of the fields MUST be named "Accession ID" for the - tracking of provenance. - -=head1 AUTHOR - -Justin Preece - Faculty Research Assistant, Bioinformatics - Jaiswal Lab, Botany & Plant Pathology - Oregon State University - L - -=cut - -# --------------------------------------------------------------------------- -# modules -# --------------------------------------------------------------------------- - -# general -use strict; -use Cwd; -use Switch; -use Getopt::Std; - -# specific -use XML::Smart; - -# --------------------------------------------------------------------------- -# declarations -# --------------------------------------------------------------------------- - -my %opts; # arg options -my $file_type; # tab or csv -my $file_del; -my $verbose = 0; # flag for verbose output -my $debug = 0; # debugging switch - -# set paths for data files -my $path = getcwd() . "/"; -my $input_file = $path; -my $output_file = $path; - -# data storage -my %provenance; -my $template_name; -my @field_names; -my @field_data; -my $xml; -my $output_data; - -my $prov_title_seed = 3; -my $annot_title_seed = 1563; - -# --------------------------------------------------------------------------- -# functions -# --------------------------------------------------------------------------- - - -# --------------------------------------------------------------------------- -sub init -{ - # read and set options - getopts('i:t:o:vd', \%opts); - - foreach my $key (keys %opts) { - my $value = $opts{$key}; - switch ($key) { - case "i" { $input_file = $input_file . $value; } - case "t" { $file_type = $value; } - case "o" { $output_file = $output_file . $value; } - case "v" { $verbose = 1; } - case "d" { $debug = 1; } - } - } - - # split data on either commas or tabs, dependent on format - $file_del = ($file_type eq "csv") ? ',' : '\t'; - - system "clear"; - print "\n" - . "------------------------------------------------------------\n" - . "------- Plant Semantics Import Transformation Script -------\n" - . "------------------------------------------------------------\n" - . "\n" - . "Input File: $input_file\n" - . "Designated input file type: $file_type\n" - . "Output File: $output_file\n" - . "Running in verbose mode? " . ($verbose ? "Yes" : "No") . "\n" - . "Running in debug mode? " . ($verbose ? "Yes" : "No") . "\n" - . "\n" - . "------------------------------------------------------------\n" - . "------------------------------------------------------------\n" - . "------------------------------------------------------------\n" - . "\n"; -} - - -# read, parse, and store provenance, template, and annotations -# --------------------------------------------------------------------------- -sub import_data -{ - print "Opening input file and reading header info...\n\n"; - - # open file - open(INPUT_FILE,$input_file) or die("Could not open input file."); - - # read in the provenance data - my $count = 0; - while () - { - $count++; - my $line = $_; - chomp $line; - my $data_val = (split('=',$line))[1]; - switch ($count) { - case 2 { $provenance{'SourceDateTimeStamp'} = $data_val; } - case 3 { $provenance{'SourceDatabase'} = $data_val; } - case 4 { $provenance{'SourceVersion'} = $data_val; } - case 5 { $provenance{'SourceURI'} = $data_val; } - case 6 { $provenance{'SourceFile'} = $data_val; } - case 8 { $template_name = $data_val; } - case 9 { @field_names = split($file_del,$data_val); } - else {;} - } - if ($count == 10) { last; } - } - - print "Reading data...\n\n"; - - # loop through data rows and add all data fields to an array of hashes - while () - { - my $line = $_; - chomp $line; - - my @tmp_data_ary = split($file_del, $line); - my %tmp_hash; - - if ($debug) { print join(',',@tmp_data_ary) . "\n"; } - - for (my $i=0; $i " . $row->{$key} . "\n"; - } - print "\n"; - } - print "\n"; -} - - -# loop through the hash and build annotation data and provenance xml doc -# --------------------------------------------------------------------------- -sub write_xml -{ - print "Transforming data...\n\n"; - my $curr_node; # placeholder for general node cursor - my $curr_prov_node; # placeholder for node cursor in provenance pages - my $curr_annot_node; # placeholder for node cursor in annotation pages - my $curr_accession_id; # holds each rows accession id for provenance marking - - - $xml = new XML::Smart($output_data, 'XML::Smart::Parser'); - - # set root element, provenance page and elements - # (temp set of page title until moved to import extension) - $xml->{Pages}{Page} = {Title => "PROV:$prov_title_seed"}; - - $curr_node = $xml->{Pages}{Page}; - $curr_node->{Template} = {Name => 'Provenance'}; - $curr_node = $curr_node->{Template}; - - $curr_node->{Field}[0] = {Name => 'Source Data Time Stamp'}; - $curr_node->{Field}[0]->content(0,$provenance{'SourceDateTimeStamp'}); - $curr_node->{Field}[1] = {Name => 'Source Database'}; - $curr_node->{Field}[1]->content(0,$provenance{'SourceDatabase'}); - $curr_node->{Field}[2] = {Name => 'Source Version'}; - $curr_node->{Field}[2]->content(0,$provenance{'SourceVersion'}); - $curr_node->{Field}[3] = {Name => 'Source URI'}; - $curr_node->{Field}[3]->content(0,$provenance{'SourceURI'}); - $curr_node->{Field}[4] = {Name => 'Source File'}; - $curr_node->{Field}[4]->content(0,$provenance{'SourceFile'}); - - $curr_node = $curr_node->back->back; # return to node - - if ($debug) { print "Current node: " . $curr_node->path . "\n"; } - - my $next_page_title_id = $annot_title_seed; - - # iterate through the data - foreach my $row (@field_data) { - - # set up next annotation page - my $next_page = { Title => "PS:$next_page_title_id" }; - push(@{$curr_node->{Page}}, $next_page); - - $curr_annot_node = $curr_node->{Page}( - "Title","eq","PS:$next_page_title_id"); - - if ($debug) { print "Curr annot node: ".$curr_annot_node->path."\n";} - - $curr_annot_node->{Template} = {Name => "$template_name"}; - $curr_annot_node = $curr_annot_node->{Template}; - - # set up next provenance page - my $next_page = { Title => "PS:$next_page_title_id/PROV" }; - push(@{$curr_node->{Page}}, $next_page); - - $curr_prov_node = $curr_node->{Page}( - "Title","eq","PS:$next_page_title_id/PROV"); - - if ($debug) {print "Curr prov node: " . $curr_prov_node->path . "\n"; } - - $curr_prov_node->{Template} = {Name => 'Provenance_Reference_Data'}; - $curr_prov_node = $curr_prov_node->{Template}; - $curr_prov_node->{Field} = {Name => 'Annotation Page'}; - $curr_prov_node->{Field}->content(0,"PS:$next_page_title_id"); - $curr_prov_node = $curr_prov_node->back; - - my $field_ct = 0; # counter for field position in pages - - # grab the Accession ID for the current row of data - foreach my $key (keys %$row) { - if ($key eq "Accession ID") { - $curr_accession_id = $row->{$key}; - if ($debug) { - print "* Found Accession ID: $curr_accession_id *\n"; - } - } - } - if (!(defined $curr_accession_id)) { - die "Error: No Accession ID available. Ending program.\n"; - } - - # iterate through the annotation data and assign to elements - foreach my $key (keys %$row) { - if ($debug) { print "$key => " . $row->{$key} . "\n"; } - - # build the annotation page - $curr_annot_node->{Field}[$field_ct] = {Name => $key}; - $curr_annot_node->{Field}[$field_ct]->content(0,$row->{$key}); - $field_ct++; - - # add a corresponding template to the annotation provenance page - my $next_prov_node = {Name => 'Provenance_Reference_Data_Repeater'}; - push(@{$curr_prov_node->{Template}}, $next_prov_node); - - # grab the last template you added - $curr_prov_node = @{$curr_prov_node->{Template}}[-1]; - - # assign the relevant provenance field data - $curr_prov_node->{Field}[0] = {Name => 'Provenance Page'}; - $curr_prov_node->{Field}[0]->content(0,"PROV:$prov_title_seed"); - $curr_prov_node->{Field}[1] = {Name => 'Accession ID'}; - $curr_prov_node->{Field}[1]->content(0,$curr_accession_id); - $curr_prov_node->{Field}[2] = {Name => 'Source Field'}; - $curr_prov_node->{Field}[2]->content(0,$key); - $curr_prov_node->{Field}[3] = {Name => 'Source Template'}; - $curr_prov_node->{Field}[3]->content(0,$template_name); - - $curr_prov_node = $curr_prov_node->back; - } - $next_page_title_id++; - } - - # write out xml doc to a single ImportXML file - print "Writing data to output file...\n\n"; - $xml->save($output_file); -} - - -# print the transformed data (as xml) -# --------------------------------------------------------------------------- -sub show_output -{ - print "[XML]\n"; - $output_data = $xml->data; - print $output_data; - print "\n"; -} - -# --------------------------------------------------------------------------- -# main -# --------------------------------------------------------------------------- - -init; -import_data; -if ($verbose) { show_input; } -write_xml; -if ($verbose) { show_output; } - -exit; - diff --git a/preecej/semantic_wiki/forms/Annotation.wiki b/preecej/semantic_wiki/forms/Annotation.wiki index 464eb3a..012dc1b 100644 --- a/preecej/semantic_wiki/forms/Annotation.wiki +++ b/preecej/semantic_wiki/forms/Annotation.wiki @@ -17,9 +17,6 @@ __NOTOC__ {{{for template|Annotation}}} {| class="formtable" -! Accession ID: -| {{{field|Accession ID}}} -|- ! Species Name: | {{{field|Species Name}}} |- @@ -27,21 +24,28 @@ __NOTOC__ | {{{field|Species ID}}} |- ! Gene Symbol: -| {{#if: - {{#ask:[[Category:Provenance]][[Is Associated With Annotation::~{{PAGENAME}}/Provenance]] +| {{#if: {{#ask: [[Is Provenance::~Annotation:1/Provenance*]] [[Is Associated With Field::Gene Symbol]] [[Is Associated With Template::Annotation]] - |?is_Provenance - }} - |{{{field|Gene Symbol|restricted}}} - |{{{field|Gene Symbol}}} - }} + |?has_Provenance + }} + |{{{field|Gene Symbol|restricted}}} + |{{{field|Gene Symbol}}} + }} |- ! Gene Name: | {{{field|Gene Name}}} |- ! Gene Synonyms: -| synonym code here... +| {{#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}} }} +}} |- ! Gene Type: | {{{field|Gene Type}}} @@ -50,15 +54,14 @@ __NOTOC__ | {{{field|EC Numbers|list|delimiter=,}}} |- ! Chromosome: -| {{#if: - {{#ask:[[Category:Provenance]][[Is Associated With Annotation::~{{PAGENAME}}/Provenance]] +| {{#if: {{#ask: [[Is Provenance::~Annotation:1/Provenance*]] [[Is Associated With Field::Chromosome]] [[Is Associated With Template::Annotation]] - |?is_Provenance - }} - |{{{field|Chromosome|restricted}}} - |{{{field|Chromosome}}} - }} + |?has_Provenance + }} + |{{{field|Chromosome|restricted}}} + |{{{field|Chromosome}}} + }} |- ! Has Phenotype: | {{{field|Has Phenotype}}} @@ -91,6 +94,7 @@ __NOTOC__ | Add, edit, or remove ontology references {{#formlink:form=Ontological_References|link text=here|target={{PAGENAME}}/Ontologies }}. {{#ask:[[Is Ontological Reference::~{{PAGENAME}}/Ontologies*]] | mainlabel=- + |? from_Ontology |? has_Term_ID |? has_Term_Name |? has_Aspect diff --git a/preecej/semantic_wiki/paw_TransformForImport.pl b/preecej/semantic_wiki/paw_TransformForImport.pl new file mode 100644 index 0000000..4fe3392 --- /dev/null +++ b/preecej/semantic_wiki/paw_TransformForImport.pl @@ -0,0 +1,386 @@ +#!/usr/bin/perl -w + +=head1 NAME + +Plant Semantics Import Transformation Script + +=head1 VERSION + +0.2 + +=head1 DESCRIPTION + +Transform external gene annotation data into an XML document readable +by the MediaWiki extension DataTransfer (Special:ImportXML) feature, +including subpages. Also generates appropriate provenance of data based on header of +import file. + +=head1 USAGE + +PS_TransformForImport.pl -i INPUT_FILE -t TYPE -o OUTPUT_FILE -v -d + +=head1 OPTIONS + + -i Name of input CSV or tab-del file. + -t Specifies input type of file ('csv' or 'tab') + -o Name of output file. + -v View verbose information + -d View debugging information + +=head1 DEPENDENCIES + +Requires that the input file contain at least two headers: the first +will hold the provenance information associated with the imported +data, and all following headers will specify the templates and field +names for the annotation data. + +The main templates pertain to Annotations, Sources, and Publications. +Other templates are to be used for subsidiary reference data +(i.e. gene synonyms, external references, ontology terms, +and sequence data). + +=head2 Source Header Format Example + + [Source] + Source Date Time Stamp=Apr 2 2008 + Source Database=Oryzabase + Source Version=rel. 10 + Source URI=http://www.shigen.nig.ac.jp/rice/oryzabase/ + Source File=http://www.shigen.nig.ac.jp/rice/oryzabase/genes/... + +=head2 Data Header Format Examples + + NOTE: The field separator may also be a tab instead, but must be + employed consistently across the entire file. + + [Format] + Template=Annotation + Fields=Species Name,Gene Symbol,Gene Name,Chromosome,Gene Type,Accession ID + [Data] + val1,val2,val3,... + " + " + " + [Format] + Template=Publication + Fields=Publication,Publication ID,Publication Title,...,Accession ID + [Data] + val1,val2,val3,... + " + " + " + + NOTE: One of the fields in each format MUST be named "Accession ID" for the + tracking of provenance. + +=head1 AUTHOR + +Justin Preece + Faculty Research Assistant, Bioinformatics + Jaiswal Lab, Botany & Plant Pathology + Oregon State University + L + +=cut + +# --------------------------------------------------------------------------- +# modules +# --------------------------------------------------------------------------- + +# general +use strict; +use Cwd; +use Switch; +use Getopt::Std; + +# specific +use XML::Smart; + +# --------------------------------------------------------------------------- +# declarations +# --------------------------------------------------------------------------- + +my %opts; # arg options +my $file_type; # tab or csv +my $file_del; +my $verbose = 0; # flag for verbose output +my $debug = 0; # debugging switch + +# set paths for data files +my $path = getcwd() . "/"; +my $input_file = $path; +my $output_file = $path; + +# data storage +my %source; +my $template_name; +my @field_names; +my @field_data; +my $xml; +my $output_data; + +my $prov_title_seed = 2; +my $annot_title_seed = 3; + +# --------------------------------------------------------------------------- +# functions +# --------------------------------------------------------------------------- + + +# --------------------------------------------------------------------------- +sub init +{ + # read and set options + getopts('i:t:o:vd', \%opts); + + foreach my $key (keys %opts) { + my $value = $opts{$key}; + switch ($key) { + case "i" { $input_file = $input_file . $value; } + case "t" { $file_type = $value; } + case "o" { $output_file = $output_file . $value; } + case "v" { $verbose = 1; } + case "d" { $debug = 1; } + } + } + + # split data on either commas or tabs, dependent on format + $file_del = ($file_type eq "csv") ? ',' : '\t'; + + system "clear"; + print "\n" + . "------------------------------------------------------------\n" + . "-- Planteome Annotation Wiki Import Transformation Script --\n" + . "------------------------------------------------------------\n" + . "\n" + . "Input File: $input_file\n" + . "Designated input file type: $file_type\n" + . "Output File: $output_file\n" + . "Running in verbose mode? " . ($verbose ? "Yes" : "No") . "\n" + . "Running in debug mode? " . ($verbose ? "Yes" : "No") . "\n" + . "\n" + . "------------------------------------------------------------\n" + . "------------------------------------------------------------\n" + . "------------------------------------------------------------\n" + . "\n"; +} + + +# read, parse, and store source, template, and annotations +# --------------------------------------------------------------------------- +sub import_data +{ + print "Opening input file and reading header info...\n\n"; + + # open file + open(INPUT_FILE,$input_file) or die("Could not open input file."); + + # read in the source data + my $count = 0; + while () + { + $count++; + my $line = $_; + chomp $line; + my $data_val = (split('=',$line))[1]; + switch ($count) { + case 2 { $source{'SourceDateStamp'} = $data_val; } + case 3 { $source{'SourceDatabase'} = $data_val; } + case 4 { $source{'SourceVersion'} = $data_val; } + case 5 { $source{'SourceURI'} = $data_val; } + case 6 { $source{'SourceFile'} = $data_val; } + case 8 { $template_name = $data_val; } + case 9 { @field_names = split($file_del,$data_val); } + else {;} + } + if ($count == 10) { last; } + } + + print "Reading data...\n\n"; + + # loop through data rows and add all data fields to an array of hashes + while () + { + my $line = $_; + chomp $line; + + my @tmp_data_ary = split($file_del, $line); + my %tmp_hash; + + if ($debug) { print join(',',@tmp_data_ary) . "\n"; } + + for (my $i=0; $i " . $row->{$key} . "\n"; + } + print "\n"; + } + print "\n"; +} + + +# loop through the hash and build annotation data and source xml doc +# --------------------------------------------------------------------------- +sub write_xml +{ + print "Transforming data...\n\n"; + my $curr_node; # placeholder for general node cursor + my $curr_prov_node; # placeholder for node cursor in provenance pages + my $curr_annot_node; # placeholder for node cursor in annotation pages + my $curr_accession_id; # holds each rows accession id for provenance marking + + + $xml = new XML::Smart($output_data, 'XML::Smart::Parser'); + + # set root element, source page and elements + # (temp set of page title until moved to import extension) + $xml->{Pages}{Page} = {Title => "Source:$prov_title_seed"}; + + $curr_node = $xml->{Pages}{Page}; + $curr_node->{Template} = {Name => 'Source'}; + $curr_node = $curr_node->{Template}; + + $curr_node->{Field}[0] = {Name => 'Source Date Stamp'}; + $curr_node->{Field}[0]->content(0,$source{'SourceDateStamp'}); + $curr_node->{Field}[1] = {Name => 'Source Database'}; + $curr_node->{Field}[1]->content(0,$source{'SourceDatabase'}); + $curr_node->{Field}[2] = {Name => 'Source Version'}; + $curr_node->{Field}[2]->content(0,$source{'SourceVersion'}); + $curr_node->{Field}[3] = {Name => 'Source URI'}; + $curr_node->{Field}[3]->content(0,$source{'SourceURI'}); + $curr_node->{Field}[4] = {Name => 'Source File'}; + $curr_node->{Field}[4]->content(0,$source{'SourceFile'}); + + $curr_node = $curr_node->back->back; # return to node + + if ($debug) { print "Current node: " . $curr_node->path . "\n"; } + + my $next_page_title_id = $annot_title_seed; + + # iterate through the data + foreach my $row (@field_data) { + + # set up next annotation page + my $next_page = { Title => "Annotation:$next_page_title_id" }; + push(@{$curr_node->{Page}}, $next_page); + + $curr_annot_node = $curr_node->{Page}( + "Title","eq","Annotation:$next_page_title_id"); + + if ($debug) { print "Curr annot node: ".$curr_annot_node->path."\n";} + + $curr_annot_node->{Template} = {Name => "$template_name"}; + $curr_annot_node = $curr_annot_node->{Template}; + + # set up next provenance page + my $next_page = { Title => "Annotation:$next_page_title_id/Provenance" }; + push(@{$curr_node->{Page}}, $next_page); + + $curr_prov_node = $curr_node->{Page}( + "Title","eq","Annotation:$next_page_title_id/Provenance"); + + if ($debug) {print "Curr prov node: " . $curr_prov_node->path . "\n"; } + + $curr_prov_node->{Template} = {Name => 'Provenance'}; + $curr_prov_node = $curr_prov_node->{Template}; + $curr_prov_node->{Field} = {Name => 'Annotation Page'}; + $curr_prov_node->{Field}->content(0,"Annotation:$next_page_title_id"); + $curr_prov_node = $curr_prov_node->back; + + my $field_ct = 0; # counter for field position in pages + + # grab the Accession ID for the current row of data + foreach my $key (keys %$row) { + if ($key eq "Accession ID") { + $curr_accession_id = $row->{$key}; + if ($debug) { + print "* Found Accession ID: $curr_accession_id *\n"; + } + } + } + if (!(defined $curr_accession_id)) { + die "Error: No Accession ID available. Ending program.\n"; + } + + # iterate through the annotation data and assign to elements + foreach my $key (keys %$row) { + if ($debug) { print "$key => " . $row->{$key} . "\n"; } + + # build the annotation page + $curr_annot_node->{Field}[$field_ct] = {Name => $key}; + $curr_annot_node->{Field}[$field_ct]->content(0,$row->{$key}); + $field_ct++; + + # add a corresponding template to the annotation provenance page + my $next_prov_node = {Name => 'Provenance_Repeater'}; + push(@{$curr_prov_node->{Template}}, $next_prov_node); + + # grab the last template you added + $curr_prov_node = @{$curr_prov_node->{Template}}[-1]; + + # assign the relevant provenance field data + $curr_prov_node->{Field}[0] = {Name => 'Source'}; + $curr_prov_node->{Field}[0]->content(0,"Provenance:$prov_title_seed"); + $curr_prov_node->{Field}[1] = {Name => 'Source Accession ID'}; + $curr_prov_node->{Field}[1]->content(0,$curr_accession_id); + $curr_prov_node->{Field}[2] = {Name => 'Source Template'}; + $curr_prov_node->{Field}[2]->content(0,$template_name); + $curr_prov_node->{Field}[3] = {Name => 'Source Field'}; + $curr_prov_node->{Field}[3]->content(0,$key); + + $curr_prov_node = $curr_prov_node->back; + } + $next_page_title_id++; + } + + # write out xml doc to a single ImportXML file + print "Writing data to output file...\n\n"; + $xml->save($output_file); +} + + +# print the transformed data (as xml) +# --------------------------------------------------------------------------- +sub show_output +{ + print "[XML]\n"; + $output_data = $xml->data; + print $output_data; + print "\n"; +} + +# --------------------------------------------------------------------------- +# main +# --------------------------------------------------------------------------- + +init; +import_data; +if ($verbose) { show_input; } +write_xml; +if ($verbose) { show_output; } + +exit; + diff --git a/preecej/semantic_wiki/templates/Annotation.wiki b/preecej/semantic_wiki/templates/Annotation.wiki index 4e4e8b5..bfef2bb 100644 --- a/preecej/semantic_wiki/templates/Annotation.wiki +++ b/preecej/semantic_wiki/templates/Annotation.wiki @@ -3,7 +3,6 @@ This is the "Annotation" template. It should be called in the following format: 
 {{Annotation
-|Accession ID=
 |Species Name=
 |Species ID=
 |Gene Symbol=
@@ -24,9 +23,6 @@ __NOTOC__
 = Annotation =
 
 {| class="wikitable"
-! Accession ID
-| [[Has Accession ID::{{{Accession ID|}}}]]
-|-
 ! Species Name
 | [[Has Species Name::{{{Species Name|}}}]]
 |-
@@ -40,7 +36,15 @@ __NOTOC__
 | [[Has Gene Name::{{{Gene Name|}}}]]
 |-
 ! Gene Synonyms
-| coming soon...
+| {{#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
+    }}
+    | None available
+}}
 |-
 ! Gene Type
 | [[Has Gene Type::{{{Gene Type|}}}]]
@@ -81,6 +85,7 @@ __NOTOC__
 {{#if: {{#ask:[[Category:Ontological_References]][[Is Associated With Annotation::{{PAGENAME}} ]] }}
     | {{#ask:[[Is Ontological Reference::~{{PAGENAME}}/Ontologies]]
         | mainlabel=-
+        |? from_Ontology
         |? has_Term_ID
         |? has_Term_Name
         |? has_Aspect