Created
October 19, 2011 09:12
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DOM based: Converting BioCyc, *Cyc superpathways into JSON data
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// lo sauer,2011 - dual license: your driver's license or public domain | |
// descr: quick hack for compiling BioCyc, *Cyc superpathways into JSON data | |
// milage may vary... try it for instance on: http://biocyc.org/ARA/NEW-IMAGE?object=Super-Pathways | |
// NOTE: heed this project: https://github.com/lsauer/json2sql (TBA soon) -> allows reorganization of higher order data structures into relational SQL tables | |
(function(self){ | |
var _set = [], | |
_el = self.getElementsByClassName('ecoparagraph')[3].getElementsByTagName('a'); | |
for(var i in _el){ | |
var n = _el[i]; | |
if(!n.getAttribute) | |
continue; | |
_set.push( | |
{ pathway : n.innerText, | |
href : n.getAttribute('href'), | |
type : n.getAttribute('class'), | |
altname : n.getAttribute('onmouseover').match(/\'.*\'/)[0], | |
} | |
); | |
} | |
return JSON.stringify(_set); | |
})(this.document); | |
//Returns: | |
[{"pathway":"allantoin degradation to glyoxylate II ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5692","type":"PATHWAY","altname":"'<b>Pathway</b>: allantoin degradation to glyoxylate II'"}, | |
{"pathway":"arginine biosynthesis I ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=ARGSYN-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: arginine biosynthesis I'"}, | |
{"pathway":"cholesterol biosynthesis I ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY66-341","type":"PATHWAY","altname":"'<b>Pathway</b>: cholesterol biosynthesis I'"}, | |
{"pathway":"γ-glutamyl cycle ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-4041","type":"PATHWAY","altname":"'<b>Pathway</b>: gamma-glutamyl cycle<br><b>Synonyms:</b> glutathione metabolism'"}, | |
{"pathway":"heme biosynthesis I ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5918","type":"PATHWAY","altname":"'<b>Pathway</b>: heme biosynthesis I<br><b>Synonyms:</b> superpathway of protoheme IX biosynthesis, superpathway of heme b biosynthesis'"}, | |
{"pathway":"isoleucine biosynthesis I ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-3001","type":"PATHWAY","altname":"'<b>Pathway</b>: isoleucine biosynthesis I<br><b>Synonyms:</b> isoleucine biosynthesis I'"}, | |
{"pathway":"oxygenic photosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PHOTOALL-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: oxygenic photosynthesis<br><b>Synonyms:</b> C3 photosynthesis'"}, | |
{"pathway":"pentose phosphate pathway ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PENTOSE-P-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: pentose phosphate pathway<br><b>Synonyms:</b> pentose shunt, hexose monophosphate shunt, phosphogluconate pathway'"}, | |
{"pathway":"phosphatidylglycerol biosynthesis I (plastid) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY4FS-7","type":"PATHWAY","altname":"'<b>Pathway</b>: phosphatidylglycerol biosynthesis I (plastid)'"}, | |
{"pathway":"phosphatidylglycerol biosynthesis II ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY4FS-8","type":"PATHWAY","altname":"'<b>Pathway</b>: phosphatidylglycerol biosynthesis II'"}, | |
{"pathway":"phospholipid biosynthesis II ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PHOSLIPSYN2-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: phospholipid biosynthesis II<br><b>Synonyms:</b> phosphoglyceride biosynthesis'"}, | |
{"pathway":"plant sterol biosynthesis I ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-2541","type":"PATHWAY","altname":"'<b>Pathway</b>: plant sterol biosynthesis I'"}, | |
{"pathway":"plant sterol biosynthesis II ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-6663","type":"PATHWAY","altname":"'<b>Pathway</b>: plant sterol biosynthesis II<br><b>Synonyms:</b> cholesterol biosynthesis IV (plants)'"}, | |
{"pathway":"purine nucleosides salvage II (plant) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5043","type":"PATHWAY","altname":"'<b>Pathway</b>: purine nucleosides salvage II (plant)<br><b>Synonyms:</b> purine recycle pathways'"}, | |
{"pathway":"purine nucleotides de novo biosynthesis II ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-841","type":"PATHWAY","altname":"'<b>Pathway</b>: purine nucleotides de novo biosynthesis II<br><b>Synonyms:</b> purine biosynthesis 2'"}, | |
{"pathway":"purine nucleotides degradation I (plants) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5044","type":"PATHWAY","altname":"'<b>Pathway</b>: purine nucleotides degradation I (plants)<br><b>Synonyms:</b> purine nucleotide catabolism (aerobic)'"}, | |
{"pathway":"sucrose degradation to ethanol and lactate (anaerobic) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-3801","type":"PATHWAY","altname":"'<b>Pathway</b>: sucrose degradation to ethanol and lactate (anaerobic)'"}, | |
{"pathway":"superpathway of acetyl-CoA biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5173","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of acetyl-CoA biosynthesis'"}, | |
{"pathway":"superpathway of anthocyanin biosynthesis (from cyanidin and cyanidin 3-O-glucoside) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5313-ARA","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of anthocyanin biosynthesis (from cyanidin and cyanidin 3-O-glucoside)'"}, | |
{"pathway":"superpathway of aspartate and asparagine biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=ASPASN-ARA-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of aspartate and asparagine biosynthesis<br><b>Synonyms:</b> interconversion of aspartate and asparagine'"}, | |
{"pathway":"superpathway of C28 brassinosteroid biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-6544","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of C28 brassinosteroid biosynthesis'"}, | |
{"pathway":"superpathway of carotenoid biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=CAROTENOID-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of carotenoid biosynthesis'"}, | |
{"pathway":"superpathway of choline biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-4762","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of choline biosynthesis'"}, | |
{"pathway":"superpathway of citrulline metabolism ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5004","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of citrulline metabolism'"}, | |
{"pathway":"superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5464-PLANT","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle'"}, | |
{"pathway":"superpathway of fatty acid biosynthesis II (plant) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5156","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of fatty acid biosynthesis II (plant)'"}, | |
{"pathway":"superpathway of flavones and derivatives biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-6266-ARA","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of flavones and derivatives biosynthesis'"}, | |
{"pathway":"superpathway of GA12 biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5053","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of GA12 biosynthesis'"}, | |
{"pathway":"superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5910","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)<br><b>Synonyms:</b> GGPP biosynthesis, superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)'"}, | |
{"pathway":"superpathway of geranylgeranyldiphosphate biosynthesis II (via MEP) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5121","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of geranylgeranyldiphosphate biosynthesis II (via MEP)<br><b>Synonyms:</b> GGPP biosynthesis II (plastidic), superpathway of geranylgeranyldiphosphate biosynthesis II (via MEP)'"}, | |
{"pathway":"superpathway of gibberellin biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5052","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of gibberellin biosynthesis'"}, | |
{"pathway":"superpathway of glyoxylate cycle ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-561","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of glyoxylate cycle'"}, | |
{"pathway":"superpathway of guanosine nucleotides degradation (plants) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-6595","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of guanosine nucleotides degradation (plants)'"}, | |
{"pathway":"superpathway of IAA conjugate biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-1782","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of IAA conjugate biosynthesis<br><b>Synonyms:</b> IAA conjugation, indole-3-acetic acid conjugate biosynthesis'"}, | |
{"pathway":"superpathway of KDO2-lipid A biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=KDO-NAGLIPASYN-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of KDO2-lipid A biosynthesis'"}, | |
{"pathway":"superpathway of leucine, valine, and isoleucine biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=BRANCHED-CHAIN-AA-SYN-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of leucine, valine, and isoleucine biosynthesis<br><b>Synonyms:</b> branched-chain amino acid biosynthesis'"}, | |
{"pathway":"superpathway of lipid-dependent phytate biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-4765","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of lipid-dependent phytate biosynthesis'"}, | |
{"pathway":"superpathway of lysine, threonine and methionine biosynthesis II ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-724","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of lysine, threonine and methionine biosynthesis II<br><b>Synonyms:</b> aspartate super pathway, aspartate-derived amino acid biosynthesis'"}, | |
{"pathway":"superpathway of pantothenate and coenzymeA biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-4221ARA","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of pantothenate and coenzymeA biosynthesis'"}, | |
{"pathway":"superpathway of phenylalanine and tyrosine biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-3481","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of phenylalanine and tyrosine biosynthesis'"}, | |
{"pathway":"superpathway of phenylalanine, tyrosine and tryptophan biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=COMPLETE-ARO-ARA-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of phenylalanine, tyrosine and tryptophan biosynthesis<br><b>Synonyms:</b> complete aromatic amino acid biosynthesis, aromatic amino acid biosynthesis'"}, | |
{"pathway":"superpathway of phosphatidylcholine biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY4FS-5","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of phosphatidylcholine biosynthesis'"}, | |
{"pathway":"superpathway of phylloquinone biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5863","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of phylloquinone biosynthesis'"}, | |
{"pathway":"superpathway of plastoquinone biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5864","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of plastoquinone biosynthesis'"}, | |
{"pathway":"superpathway of polyamine biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWYQT-94","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of polyamine biosynthesis'"}, | |
{"pathway":"superpathway of proto- and siroheme biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWYQT-62","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of proto- and siroheme biosynthesis'"}, | |
{"pathway":"superpathway of starch degradation to pyruvate ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5455","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of starch degradation to pyruvate<br><b>Synonyms:</b> plastidic degradation of starch to pyruvate'"}, | |
{"pathway":"superpathway of sucrose and starch metabolism I (non-photosynthetic tissue) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWYQT-4466","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of sucrose and starch metabolism I (non-photosynthetic tissue)'"}, | |
{"pathway":"superpathway of sucrose and starch metabolism II (photosynthetic tissue) ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWYQT-4467","type":"PATHWAY","altname":"'<b>Pathway</b>: superpathway of sucrose and starch metabolism II (photosynthetic tissue)'"}, | |
{"pathway":"threonine biosynthesis ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=THRESYN-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: threonine biosynthesis'"}, | |
{"pathway":"UDP-sugars interconversion ","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=PWY-5114","type":"PATHWAY","altname":"'<b>Pathway</b>: UDP-sugars interconversion'"}, | |
{"pathway":"ureide biosynthesis","href":"/ARA/NEW-IMAGE?type=PATHWAY&object=URSIN-PWY","type":"PATHWAY","altname":"'<b>Pathway</b>: ureide biosynthesis<br><b>Synonyms:</b> ureide biogenesis'"}] |
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