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pd2af
Commit dced0a43 authored by Denis Shirshov's avatar Denis Shirshov
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atom_settings/language-sbgn-lisp/grammars/sbgn-lisp.cson
View file @ dced0a43
......@@ -87,7 +87,7 @@ repository:
# PD:
{
name: "entity.name.function.racket"
match: "unspecified-entity|perturbing-agent|source-and-sink|
match: "unspecified-entity|perturbing-agent|source-and-sink|source|sink|
(simple-chemical|macromolecule|complex|nucleic-acid-feature)(-multimer)?"
}
# AF:
......
code/template-functions.rkt
View file @ dced0a43
......@@ -123,12 +123,6 @@
(format "(af ~a)" af-str)
(format "(af (default:compartment ~a ~a))" af-coors af-str))))
(af-xml (eval (preprocess-lisp-sbgn af-full-str) ns))
; (translated-af-context (try
; (translate-pd pd-full-str)
; (catch empty)))
; (canonical-af-context (get-af-context af-full-str))
; (translatable? (contexts-equal? translated-af-context canonical-af-context))
)
(write-file-to-dir #:dir folder-path #:file "pd.sbgn" pd-xml)
(write-file-to-dir #:dir folder-path #:file "af.sbgn" af-xml)
......@@ -143,4 +137,4 @@
(~a 0)))
(define-catch (go-through-tests test-file)
(read-data-from-file test-file ns))
(load-data-from-file test-file ns))
code/test-xml.rkt
View file @ dced0a43
......@@ -21,4 +21,4 @@
(write-file "../html/generated/result.sbgn" af-xml)
))
(test-xml "../knowledge/sbgn_examples/metabolismregulation.org/MR100-aspirin-v3A.sbgn")
(test-xml "../knowledge/sbgn_examples/metabolismregulation.org/MR007-inos.sbgn")
html/generated/result.sbgn
View file @ dced0a43
This diff is collapsed.
html/specification.html
View file @ dced0a43
......@@ -1675,24 +1675,24 @@
</div>
<div class="expandable_body" ng-show="show[9]">
<h3>9.1 Currency metabolites 1</h3>
<h3>9.1 MR001-glycolysis</h3>
<div><div class="test_button passed" ng-init="increment_passed(9)"></div>
</div>
<table class="rules-table">
<tr>
<td>
<div><img src="specification/currency_metabolites_1/pd.png" width="232" /></div>
<div><img src="specification/MR001-glycolysis/pd.png" width="0" /></div>
</td>
<td>
<img src="specification/currency_metabolites_1/af.png" width="70" />
<img src="specification/MR001-glycolysis/af.png" width="0" />
</td>
</tr>
<tr style="font-size:90%;" class="links">
<td>
<a href="specification/currency_metabolites_1/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/currency_metabolites_1/pd.sbgn" target="_blank">Newt</a>
<a href="specification/MR001-glycolysis/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/MR001-glycolysis/pd.sbgn" target="_blank">Newt</a>
</td>
<td>
<a href="specification/currency_metabolites_1/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/currency_metabolites_1/af.sbgn" target="_blank">Newt</a>
<a href="specification/MR001-glycolysis/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/MR001-glycolysis/af.sbgn" target="_blank">Newt</a>
</td>
</tr>
<tr style="line-height: 3em;">
......@@ -1703,24 +1703,24 @@
</tr>
</table>
<h3>9.2 Noncurrency metabolites 1</h3>
<h3>9.2 MR002-glycolysis-alt</h3>
<div><div class="test_button passed" ng-init="increment_passed(9)"></div>
</div>
<table class="rules-table">
<tr>
<td>
<div><img src="specification/noncurrency_metabolites_1/pd.png" width="232" /></div>
<div><img src="specification/MR002-glycolysis-alt/pd.png" width="0" /></div>
</td>
<td>
<img src="specification/noncurrency_metabolites_1/af.png" width="290" />
<img src="specification/MR002-glycolysis-alt/af.png" width="0" />
</td>
</tr>
<tr style="font-size:90%;" class="links">
<td>
<a href="specification/noncurrency_metabolites_1/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/noncurrency_metabolites_1/pd.sbgn" target="_blank">Newt</a>
<a href="specification/MR002-glycolysis-alt/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/MR002-glycolysis-alt/pd.sbgn" target="_blank">Newt</a>
</td>
<td>
<a href="specification/noncurrency_metabolites_1/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/noncurrency_metabolites_1/af.sbgn" target="_blank">Newt</a>
<a href="specification/MR002-glycolysis-alt/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/MR002-glycolysis-alt/af.sbgn" target="_blank">Newt</a>
</td>
</tr>
<tr style="line-height: 3em;">
......@@ -1731,24 +1731,24 @@
</tr>
</table>
<h3>9.3 Regulation combining 1</h3>
<h3>9.3 MR003-eicosanoids</h3>
<div><div class="test_button passed" ng-init="increment_passed(9)"></div>
</div>
<table class="rules-table">
<tr>
<td>
<div><img src="specification/regulation_combining_1/pd.png" width="232" /></div>
<div><img src="specification/MR003-eicosanoids/pd.png" width="0" /></div>
</td>
<td>
<img src="specification/regulation_combining_1/af.png" width="230" />
<img src="specification/MR003-eicosanoids/af.png" width="0" />
</td>
</tr>
<tr style="font-size:90%;" class="links">
<td>
<a href="specification/regulation_combining_1/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/regulation_combining_1/pd.sbgn" target="_blank">Newt</a>
<a href="specification/MR003-eicosanoids/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/MR003-eicosanoids/pd.sbgn" target="_blank">Newt</a>
</td>
<td>
<a href="specification/regulation_combining_1/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/regulation_combining_1/af.sbgn" target="_blank">Newt</a>
<a href="specification/MR003-eicosanoids/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/MR003-eicosanoids/af.sbgn" target="_blank">Newt</a>
</td>
</tr>
<tr style="line-height: 3em;">
......@@ -1759,6 +1759,74 @@
</tr>
</table>
<h3>9.4 MR004-mevalonate</h3>
<div><div class="test_button passed" ng-init="increment_passed(9)"></div>
</div>
<table class="rules-table">
<tr>
<td>
<div><img src="specification/MR004-mevalonate/pd.png" width="0" /></div>
</td>
<td>
<img src="specification/MR004-mevalonate/af.png" width="0" />
</td>
</tr>
<tr style="font-size:90%;" class="links">
<td>
<a href="specification/MR004-mevalonate/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/MR004-mevalonate/pd.sbgn" target="_blank">Newt</a>
</td>
<td>
<a href="specification/MR004-mevalonate/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/MR004-mevalonate/af.sbgn" target="_blank">Newt</a>
</td>
</tr>
<tr style="line-height: 3em;">
<td colspan="2" style="text-align:left;"></td>
</tr>
<tr style="line-height: 3em;">
<td colspan="2" style="text-align:left;"></td>
</tr>
</table>
<h3>9.5 MR007-inos</h3>
<div><div class="test_button passed" ng-init="increment_passed(9)"></div>
</div>
<table class="rules-table">
<tr>
<td>
<div><img src="specification/MR007-inos/pd.png" width="0" /></div>
</td>
<td>
<img src="specification/MR007-inos/af.png" width="0" />
</td>
</tr>
<tr style="font-size:90%;" class="links">
<td>
<a href="specification/MR007-inos/pd.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/MR007-inos/pd.sbgn" target="_blank">Newt</a>
</td>
<td>
<a href="specification/MR007-inos/af.sbgn">SBGN-ML</a>&ensp;<a href="http://web.newteditor.org/?URL=http://188.166.159.222/specification/MR007-inos/af.sbgn" target="_blank">Newt</a>
</td>
</tr>
<tr style="line-height: 3em;">
<td colspan="2" style="text-align:left;"></td>
</tr>
<tr style="line-height: 3em;">
<td colspan="2" style="text-align:left;"></td>
</tr>
</table>
</div>
</div>
<div class="expandable_block">
<div class="expandable_header skipped" ng-class="{set_failed: bugs[10], set_passed: !bugs[10] && passed[10] > 0}">
<div class="window_button maximize" ng-hide="show[10]" ng-click="toggle_show(10)"></div>
<div class="window_button minimize" ng-show="show[10]" ng-click="toggle_show(10)"></div>
<!--(define tabtree (parse-tab-tree "../tests/test-results.tree"))-->
<h2>Metabolism Regulation Maps <span>#(failed[10])#/#(passed[10])#</span></h2>
</div>
<div class="expandable_body" ng-show="show[10]">
</div>
</div>
......@@ -1766,7 +1834,7 @@
<div class="placeholder" ng-hide="show1 || show2"></div>
<footer>
<div>Page generated <b>15.05.2019</b></div>
<div>Page generated <b>20.05.2019</b></div>
</footer>
<!-- Yandex.Metrika counter -->
......
html/specification/MR001-glycolysis-alt/af.sbgn 0 → 100644
View file @ dced0a43
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="activity flow">
<glyph id="ADCY" class="biological activity">
<label text="ADCY" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="ATP" class="biological activity">
<label text="ATP" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="ATP-uoi-202" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="PPi" class="biological activity">
<label text="PPi" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="PPi-uoi-203" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="cAMP" class="biological activity">
<label text="cAMP" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="cAMP-uoi-204" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="C1" class="biological activity">
<label text="PKA cat-dimer-PKA reg-dimer" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="C1-uoi-205" class="unit of information">
<label text="" />
<entity name="complex" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="C2" class="biological activity">
<label text="PKA cat-dimer-PKA reg-dimer-cAMP" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="C2-uoi-206" class="unit of information">
<label text="" />
<entity name="complex" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="PKA_reg-dimer-cAMP" class="biological activity">
<label text="PKA reg-dimer-cAMP" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="PKA_cat" class="biological activity">
<label text="PKA cat" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="PFKFB2" class="biological activity">
<label text="PFKFB2" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="PFKFB2-P" class="biological activity">
<label text="PFKFB2-P" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="β-D-fructose-6P" class="biological activity">
<label text="β-D-fructose-6P" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="β-D-fructose-6P-uoi-207" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="β-D-fructose-1-6P2" class="biological activity">
<label text="β-D-fructose-1-6P2" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="β-D-fructose-1-6P2-uoi-208" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="β-D-fructose-2-6P2" class="biological activity">
<label text="β-D-fructose-2-6P2" />
<bbox x="0" y="0" w="80" h="40" />
<glyph id="β-D-fructose-2-6P2-uoi-209" class="unit of information">
<label text="" />
<entity name="simple chemical" />
<bbox x="20.0" y="-5.0" w="40" h="10" />
</glyph>
</glyph>
<glyph id="GPI" class="biological activity">
<label text="GPI" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="F1-6BP" class="biological activity">
<label text="F1-6BP" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="PFK1" class="biological activity">
<label text="PFK1" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="and-171" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-171-in" x="39.5" y="37.0" />
<port id="and-171-out" x="39.5" y="2.0" />
</glyph>
<glyph id="and-176" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-176-in" x="39.5" y="37.0" />
<port id="and-176-out" x="39.5" y="2.0" />
</glyph>
<glyph id="hyperarc-79" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="hyperarc-79-in" x="39.5" y="37.0" />
<port id="hyperarc-79-out" x="39.5" y="2.0" />
</glyph>
<glyph id="and-185" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-185-in" x="39.5" y="37.0" />
<port id="and-185-out" x="39.5" y="2.0" />
</glyph>
<glyph id="and-189" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-189-in" x="39.5" y="37.0" />
<port id="and-189-out" x="39.5" y="2.0" />
</glyph>
<glyph id="and-194" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-194-in" x="39.5" y="37.0" />
<port id="and-194-out" x="39.5" y="2.0" />
</glyph>
<glyph id="and-198" class="and">
<bbox x="27.0" y="7.0" w="25" h="25" />
<port id="and-198-in" x="39.5" y="37.0" />
<port id="and-198-out" x="39.5" y="2.0" />
</glyph>
<arc class="positive influence" id="positive-influence-174" source="and-171-out" target="cAMP">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="positive influence" id="positive-influence-175" source="and-171-out" target="PPi">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-172" source="ADCY" target="and-171-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-173" source="ATP" target="and-171-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="positive influence" id="positive-influence-179" source="and-176-out" target="C2">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-177" source="cAMP" target="and-176-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-178" source="C1" target="and-176-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="positive influence" id="positive-influence-181" source="hyperarc-79-out" target="PKA_cat">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="positive influence" id="positive-influence-182" source="hyperarc-79-out" target="PKA_reg-dimer-cAMP">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-180" source="C2" target="hyperarc-79-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="negative influence" id="negative-influence-183" source="PKA_cat" target="PFKFB2">
<start x="80.0" y="20.0" />
<end x="0" y="20.0" />
</arc>
<arc class="positive influence" id="positive-influence-184" source="PKA_cat" target="PFKFB2-P">
<start x="80.0" y="20.0" />
<end x="0" y="20.0" />
</arc>
<arc class="positive influence" id="positive-influence-188" source="and-185-out" target="β-D-fructose-2-6P2">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-186" source="β-D-fructose-6P" target="and-185-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-187" source="PFKFB2" target="and-185-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="positive influence" id="positive-influence-192" source="and-189-out" target="β-D-fructose-6P">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-190" source="β-D-fructose-2-6P2" target="and-189-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-191" source="PFKFB2-P" target="and-189-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="positive influence" id="positive-influence-193" source="GPI" target="β-D-fructose-6P">
<start x="80.0" y="20.0" />
<end x="0" y="20.0" />
</arc>
<arc class="positive influence" id="positive-influence-197" source="and-194-out" target="β-D-fructose-6P">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-195" source="F1-6BP" target="and-194-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-196" source="β-D-fructose-1-6P2" target="and-194-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="positive influence" id="positive-influence-201" source="and-198-out" target="β-D-fructose-1-6P2">
<start x="27.0" y="19.5" />
<end x="80.0" y="20.0" />
</arc>
<arc class="logic arc" id="logic-arc-199" source="β-D-fructose-6P" target="and-198-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
<arc class="logic arc" id="logic-arc-200" source="PFK1" target="and-198-in">
<start x="0" y="20.0" />
<end x="39.5" y="37.0" />
</arc>
</map>
</sbgn>
\ No newline at end of file
html/specification/MR001-glycolysis-alt/pd.sbgn 0 → 100644
View file @ dced0a43
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<sbgn xmlns="http://sbgn.org/libsbgn/0.2">
<map language="process description">
<glyph id="ADCY" class="macromolecule">
<label text="ADCY" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="ATP" class="simple chemical">
<label text="ATP" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="PPi" class="simple chemical">
<label text="PPi" />
<bbox x="0" y="0" w="80" h="40" />
</glyph>
<glyph id="cAMP" class="simple chemical">
<label text="cAMP" />
<bbox x="0" y="0" w="80" h="40" />
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<glyph class="complex" id="C1">
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