Created
July 30, 2014 16:55
-
-
Save ngopal/c3c303a611ba900b9141 to your computer and use it in GitHub Desktop.
Visualizing Alzheimer's Disease Using Reactome Data in D3
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| { | |
| "sbml": { | |
| "-xmlns": "http://www.sbml.org/sbml/level2/version4", | |
| "-level": "2", | |
| "-version": "4", | |
| "model": { | |
| "-id": "pathway_977225", | |
| "-name": "Amyloids", | |
| "-metaid": "metaid_0", | |
| "notes": { | |
| "p": [ | |
| { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Amyloid is a term used to describe typically extracellular deposits of aggregated proteins, sometimes known as plaques. Abnormal accumulation of amyloid is amyloidosis, a term associated with diseased organs and tissues, particularly neurodegenerative diseases such as Alzheimer's, Parkinson's and Huntingdon's. Amyloid deposits consist predominantly of amyloid fibrils, rigid, nonbranching structures that form ordered assemblies, characteristically with a cross betasheet structure where the sheets run parallel to the direction of the fibril (Sawaya et al. 2007). Often the fibril has a lefthanded twist (Nelson Eisenberg 2006). At least 27 human proteins form amyloid fibrils (Sipe et al. 2010). Many of these proteins have nonpathological functions; the trigger that leads to abnormal aggregations differs between proteins and is not well understood but in many cases the peptides are abnormal fragments or mutant forms arising from polymorphisms, suggesting that the initial event may be aggregation of misfolded or unfolded peptides. Early studies of AmyloidBeta assembly led to a widely accepted model that assembly was a nucleationdependent polymerization reaction (Teplow 1998) but it is now understood to be more complex, with multiple 'offpathway' events leading to a variety of oligomeric structures in addition to fibrils (Roychaudhuri et al. 2008). An increasing body of evidence suggests that these oligomeric forms are primarily responsible for the neurotoxic effects of Amyloidbeta (Roychaudhuri et al. 2008), alphasynuclein (Winner et al. 2011) and tau (Dance Strobel 2009, MerazRios et al. 2010). Amyloid oligomers are believed to have a common structural motif that is independent of the protein involved and not present in fibrils (Kayed et al. 2003). Conformation dependent, aggregation specific antibodies suggest that there are 3 general classes of amyloid oligomer structures (Glabe 2009) including annular structures which may be responsible for the widely reported membrane permeabilization effect of amyloid oligomers. Toxicity of amyloid oligomers preceeds the appearance of plaques in mouse models (Ferretti et al. 2011). " | |
| }, | |
| { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Fibrils are often associated with other molecules, notably heparan sulfate proteoglycans and Serum Amyloid Pcomponent, which are universally associated and seem to stabilize fibrils, possibly by protecting them from degradation." | |
| } | |
| ] | |
| }, | |
| "annotation": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "SBML engine: Jsbml" | |
| }, | |
| "sbgn": { | |
| "-xmlns": "http://sbgn.org/libsbgn/0.2", | |
| "map": { | |
| "-language": "process description", | |
| "glyph": [ | |
| { | |
| "-class": "macromolecule", | |
| "-id": "entityVertex_7193679", | |
| "label": { "-text": "APCS_20_223" }, | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "168.0", | |
| "-x": "273.0", | |
| "-y": "267.0" | |
| }, | |
| "glyph": { | |
| "-class": "unit of information", | |
| "-id": "entityVertex_7193679_mt", | |
| "label": { "-text": "mt:prot" }, | |
| "bbox": { | |
| "-h": "24.0", | |
| "-w": "56.0", | |
| "-x": "289.0", | |
| "-y": "255.0" | |
| } | |
| } | |
| }, | |
| { | |
| "-class": "simple chemical", | |
| "-id": "entityVertex_7193680", | |
| "label": { "-text": "Ca2" }, | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "90.0", | |
| "-x": "282.0", | |
| "-y": "675.0" | |
| } | |
| }, | |
| { | |
| "-class": "complex", | |
| "-id": "entityVertex_7193681", | |
| "label": { "-text": "Serum" }, | |
| "bbox": { | |
| "-h": "45.0", | |
| "-w": "168.0", | |
| "-x": "930.0", | |
| "-y": "468.0" | |
| }, | |
| "glyph": { | |
| "-class": "annotation", | |
| "-id": "entityVertex_7193681_annotation", | |
| "label": { "-text": "APCS(20-223), Ca2+" }, | |
| "callout": { | |
| "-target": "entityVertex_7193681", | |
| "point": { | |
| "-x": "1098.0", | |
| "-y": "513.0" | |
| } | |
| }, | |
| "bbox": { | |
| "-h": "24.0", | |
| "-w": "144.0", | |
| "-x": "1114.0", | |
| "-y": "537.0" | |
| } | |
| } | |
| }, | |
| { | |
| "-class": "unspecified entity", | |
| "-id": "entityVertex_7193682", | |
| "label": { "-text": "Amyloid_fibril" }, | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "133.5", | |
| "-x": "354.0", | |
| "-y": "1281.0" | |
| } | |
| }, | |
| { | |
| "-class": "unspecified entity", | |
| "-id": "entityVertex_7193683", | |
| "label": { "-text": "Amyloid_fibril_main" }, | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "181.5", | |
| "-x": "1251.0", | |
| "-y": "1281.0" | |
| } | |
| }, | |
| { | |
| "-class": "simple chemical", | |
| "-id": "entityVertex_7193684", | |
| "label": { "-text": "GAG" }, | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "187.5", | |
| "-x": "1770.0", | |
| "-y": "651.0" | |
| } | |
| }, | |
| { | |
| "-class": "complex", | |
| "-id": "entityVertex_7193685", | |
| "label": { "-text": "Amyloid_fibrils" }, | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "136.5", | |
| "-x": "2298.0", | |
| "-y": "933.0" | |
| }, | |
| "glyph": { | |
| "-class": "annotation", | |
| "-id": "entityVertex_7193685_annotation", | |
| "label": { "-text": "Amyloid fibril main peptide chains, Serum amyloid P-component homopentamer, HSPG2(22-4391), GAG" }, | |
| "callout": { | |
| "-target": "entityVertex_7193685", | |
| "point": { | |
| "-x": "2434.5", | |
| "-y": "969.0" | |
| } | |
| }, | |
| "bbox": { | |
| "-h": "24.0", | |
| "-w": "760.0", | |
| "-x": "2450.5", | |
| "-y": "993.0" | |
| } | |
| } | |
| }, | |
| { | |
| "-class": "macromolecule", | |
| "-id": "entityVertex_7193686", | |
| "label": { "-text": "HSPG2_22_4391" }, | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "166.5", | |
| "-x": "1791.0", | |
| "-y": "1302.0" | |
| }, | |
| "glyph": { | |
| "-class": "unit of information", | |
| "-id": "entityVertex_7193686_mt", | |
| "label": { "-text": "mt:prot" }, | |
| "bbox": { | |
| "-h": "24.0", | |
| "-w": "56.0", | |
| "-x": "1807.0", | |
| "-y": "1290.0" | |
| } | |
| } | |
| }, | |
| { | |
| "-class": "complex multimer", | |
| "-id": "entityVertex_7193687", | |
| "label": { "-text": "Serum" }, | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "163.5", | |
| "-x": "936.0", | |
| "-y": "930.0" | |
| }, | |
| "glyph": { | |
| "-class": "annotation", | |
| "-id": "entityVertex_7193687_annotation", | |
| "label": { "-text": "Serum amyloid P-component homopentamer" }, | |
| "callout": { | |
| "-target": "entityVertex_7193687", | |
| "point": { | |
| "-x": "1099.5", | |
| "-y": "966.0" | |
| } | |
| }, | |
| "bbox": { | |
| "-h": "24.0", | |
| "-w": "304.0", | |
| "-x": "1115.5", | |
| "-y": "990.0" | |
| } | |
| } | |
| }, | |
| { | |
| "-class": "unspecified entity", | |
| "-id": "entityVertex_7193688", | |
| "label": { "-text": "Double_stranded" }, | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "183.0", | |
| "-x": "915.0", | |
| "-y": "42.0" | |
| } | |
| }, | |
| { | |
| "-class": "complex", | |
| "-id": "entityVertex_7193689", | |
| "label": { "-text": "Serum" }, | |
| "bbox": { | |
| "-h": "57.6", | |
| "-w": "175.5", | |
| "-x": "1671.0", | |
| "-y": "219.0" | |
| }, | |
| "glyph": { | |
| "-class": "annotation", | |
| "-id": "entityVertex_7193689_annotation", | |
| "label": { "-text": "Serum amyloid P-component homopentamer, Double-stranded DNA and chromatin" }, | |
| "callout": { | |
| "-target": "entityVertex_7193689", | |
| "point": { | |
| "-x": "1846.5", | |
| "-y": "276.6" | |
| } | |
| }, | |
| "bbox": { | |
| "-h": "24.0", | |
| "-w": "584.0", | |
| "-x": "1862.5", | |
| "-y": "300.6" | |
| } | |
| } | |
| }, | |
| { | |
| "-class": "process", | |
| "-id": "reactionVertex_7193690", | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "36.0", | |
| "-x": "744.0", | |
| "-y": "540.0" | |
| }, | |
| "port": { | |
| "-id": "reactionVertex_7193690.1", | |
| "-x": "780.0", | |
| "-y": "558.0" | |
| } | |
| }, | |
| { | |
| "-class": "process", | |
| "-id": "reactionVertex_7193694", | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "36.0", | |
| "-x": "846.0", | |
| "-y": "1335.0" | |
| }, | |
| "port": { | |
| "-id": "reactionVertex_7193694.1", | |
| "-x": "882.0", | |
| "-y": "1353.0" | |
| } | |
| }, | |
| { | |
| "-class": "process", | |
| "-id": "reactionVertex_7193697", | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "36.0", | |
| "-x": "2091.0", | |
| "-y": "969.0" | |
| }, | |
| "port": { | |
| "-id": "reactionVertex_7193697.1", | |
| "-x": "2127.0", | |
| "-y": "987.0" | |
| } | |
| }, | |
| { | |
| "-class": "process", | |
| "-id": "reactionVertex_7193703", | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "36.0", | |
| "-x": "1098.0", | |
| "-y": "801.0" | |
| }, | |
| "port": { | |
| "-id": "reactionVertex_7193703.1", | |
| "-x": "1116.0", | |
| "-y": "837.0" | |
| } | |
| }, | |
| { | |
| "-class": "process", | |
| "-id": "reactionVertex_7193706", | |
| "bbox": { | |
| "-h": "36.0", | |
| "-w": "36.0", | |
| "-x": "1476.0", | |
| "-y": "315.0" | |
| }, | |
| "port": { | |
| "-id": "reactionVertex_7193706.1", | |
| "-x": "1512.0", | |
| "-y": "333.0" | |
| } | |
| } | |
| ], | |
| "arc": [ | |
| { | |
| "-class": "consumption", | |
| "-id": "edge_7193691", | |
| "-source": "entityVertex_7193679", | |
| "-target": "reactionVertex_7193690", | |
| "start": { | |
| "-x": "441.0", | |
| "-y": "285.0" | |
| }, | |
| "end": { | |
| "-x": "744.0", | |
| "-y": "558.0" | |
| } | |
| }, | |
| { | |
| "-class": "consumption", | |
| "-id": "edge_7193692", | |
| "-source": "entityVertex_7193680", | |
| "-target": "reactionVertex_7193690", | |
| "start": { | |
| "-x": "372.0", | |
| "-y": "693.0" | |
| }, | |
| "end": { | |
| "-x": "744.0", | |
| "-y": "558.0" | |
| } | |
| }, | |
| { | |
| "-class": "production", | |
| "-id": "edge_7193693", | |
| "-source": "reactionVertex_7193690.1", | |
| "-target": "entityVertex_7193681", | |
| "start": { | |
| "-x": "780.0", | |
| "-y": "558.0" | |
| }, | |
| "end": { | |
| "-x": "930.0", | |
| "-y": "490.5" | |
| } | |
| }, | |
| { | |
| "-class": "consumption", | |
| "-id": "edge_7193695", | |
| "-source": "entityVertex_7193682", | |
| "-target": "reactionVertex_7193694", | |
| "start": { | |
| "-x": "487.5", | |
| "-y": "1299.0" | |
| }, | |
| "end": { | |
| "-x": "846.0", | |
| "-y": "1353.0" | |
| } | |
| }, | |
| { | |
| "-class": "production", | |
| "-id": "edge_7193696", | |
| "-source": "reactionVertex_7193694.1", | |
| "-target": "entityVertex_7193683", | |
| "start": { | |
| "-x": "882.0", | |
| "-y": "1353.0" | |
| }, | |
| "end": { | |
| "-x": "1251.0", | |
| "-y": "1299.0" | |
| } | |
| }, | |
| { | |
| "-class": "consumption", | |
| "-id": "edge_7193698", | |
| "-source": "entityVertex_7193681", | |
| "-target": "reactionVertex_7193697", | |
| "start": { | |
| "-x": "1098.0", | |
| "-y": "490.5" | |
| }, | |
| "end": { | |
| "-x": "2091.0", | |
| "-y": "987.0" | |
| } | |
| }, | |
| { | |
| "-class": "consumption", | |
| "-id": "edge_7193699", | |
| "-source": "entityVertex_7193683", | |
| "-target": "reactionVertex_7193697", | |
| "start": { | |
| "-x": "1432.5", | |
| "-y": "1299.0" | |
| }, | |
| "end": { | |
| "-x": "2091.0", | |
| "-y": "987.0" | |
| } | |
| }, | |
| { | |
| "-class": "consumption", | |
| "-id": "edge_7193700", | |
| "-source": "entityVertex_7193686", | |
| "-target": "reactionVertex_7193697", | |
| "start": { | |
| "-x": "1957.5", | |
| "-y": "1320.0" | |
| }, | |
| "end": { | |
| "-x": "2109.0", | |
| "-y": "1005.0" | |
| } | |
| }, | |
| { | |
| "-class": "consumption", | |
| "-id": "edge_7193701", | |
| "-source": "entityVertex_7193684", | |
| "-target": "reactionVertex_7193697", | |
| "start": { | |
| "-x": "1957.5", | |
| "-y": "669.0" | |
| }, | |
| "end": { | |
| "-x": "2109.0", | |
| "-y": "969.0" | |
| } | |
| }, | |
| { | |
| "-class": "production", | |
| "-id": "edge_7193702", | |
| "-source": "reactionVertex_7193697.1", | |
| "-target": "entityVertex_7193685", | |
| "start": { | |
| "-x": "2127.0", | |
| "-y": "987.0" | |
| }, | |
| "end": { | |
| "-x": "2298.0", | |
| "-y": "951.0" | |
| } | |
| }, | |
| { | |
| "-class": "consumption", | |
| "-id": "edge_7193704", | |
| "-source": "entityVertex_7193681", | |
| "-target": "reactionVertex_7193703", | |
| "start": { | |
| "-x": "1014.0", | |
| "-y": "513.0" | |
| }, | |
| "end": { | |
| "-x": "1116.0", | |
| "-y": "801.0" | |
| } | |
| }, | |
| { | |
| "-class": "production", | |
| "-id": "edge_7193705", | |
| "-source": "reactionVertex_7193703.1", | |
| "-target": "entityVertex_7193687", | |
| "start": { | |
| "-x": "1116.0", | |
| "-y": "837.0" | |
| }, | |
| "end": { | |
| "-x": "1099.5", | |
| "-y": "948.0" | |
| } | |
| }, | |
| { | |
| "-class": "consumption", | |
| "-id": "edge_7193707", | |
| "-source": "entityVertex_7193681", | |
| "-target": "reactionVertex_7193706", | |
| "start": { | |
| "-x": "1098.0", | |
| "-y": "490.5" | |
| }, | |
| "end": { | |
| "-x": "1476.0", | |
| "-y": "333.0" | |
| } | |
| }, | |
| { | |
| "-class": "consumption", | |
| "-id": "edge_7193708", | |
| "-source": "entityVertex_7193688", | |
| "-target": "reactionVertex_7193706", | |
| "start": { | |
| "-x": "1098.0", | |
| "-y": "60.0" | |
| }, | |
| "end": { | |
| "-x": "1476.0", | |
| "-y": "333.0" | |
| } | |
| }, | |
| { | |
| "-class": "production", | |
| "-id": "edge_7193709", | |
| "-source": "reactionVertex_7193706.1", | |
| "-target": "entityVertex_7193689", | |
| "start": { | |
| "-x": "1512.0", | |
| "-y": "333.0" | |
| }, | |
| "end": { | |
| "-x": "1671.0", | |
| "-y": "247.8" | |
| } | |
| } | |
| ] | |
| } | |
| }, | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:dc": "http://purl.org/dc/elements/1.1/", | |
| "-xmlns:vCard": "http://www.w3.org/2001/vcard-rdf/3.0#", | |
| "-xmlns:dcterms": "http://purl.org/dc/terms/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_0", | |
| "dc:creator": { | |
| "rdf:Bag": { | |
| "rdf:li": { | |
| "-rdf:parseType": "Resource", | |
| "vCard:N": { | |
| "-rdf:parseType": "Resource", | |
| "vCard:Family": "Jupe", | |
| "vCard:Given": "Steve" | |
| }, | |
| "vCard:EMAIL": "sjupe@ebi.ac.uk", | |
| "vCard:ORG": { "-rdf:parseType": "Resource" } | |
| } | |
| } | |
| }, | |
| "dcterms:created": { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2010-11-15T18:26:30Z" | |
| }, | |
| "dcterms:modified": [ | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2011-05-05T20:47:53Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2011-05-08T17:01:38Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2011-05-08T17:06:15Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2011-05-08T17:10:51Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2013-06-08T16:28:02Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-04T17:16:57Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-04T18:10:38Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-04T20:50:17Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-05T03:38:45Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-05T09:43:28Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-05T17:03:27Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-06T00:55:04Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-06T07:48:24Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-06T12:04:37Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-06T15:36:28Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-06T21:35:21Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-07T12:24:17Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-07T18:41:29Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-07T20:23:45Z" | |
| }, | |
| { | |
| "-rdf:parseType": "Resource", | |
| "dcterms:W3CDTF": "2014-07-29T19:10:24Z" | |
| } | |
| ], | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_75925" } | |
| } | |
| }, | |
| "bqbiol:isDescribedBy": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:pubmed:16302959" } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| "listOfCompartments": { | |
| "compartment": { | |
| "-id": "compartment_984", | |
| "-name": "extracellular region", | |
| "-metaid": "metaid_2", | |
| "-sboTerm": "SBO:0000290", | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_2", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:obo.go:GO%3A0005576" } | |
| } | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| "listOfSpecies": { | |
| "species": [ | |
| { | |
| "-id": "species_976776", | |
| "-name": "Serum amyloid P-component homopentamer [extracellular region]", | |
| "-metaid": "metaid_3", | |
| "-sboTerm": "SBO:0000253", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome Complex. Here is Reactomes nested structure for this complex: (P02743,P02743,P02743,P02743,P02743,29108,29108,29108,29108,29108,29108,29108,29108,29108,29108)" | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_3", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_76328" } | |
| } | |
| }, | |
| "bqbiol:hasPart": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:kegg.compound:C00076" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02743" }, | |
| { "-rdf:resource": "urn:miriam:obo.chebi:CHEBI%3A29108" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "species_976787", | |
| "-name": "Serum amyloid P decamer [extracellular region]", | |
| "-metaid": "metaid_5", | |
| "-sboTerm": "SBO:0000253", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome Complex. Here is Reactomes nested structure for this complex: ((P02743,P02743,P02743,P02743,P02743,29108,29108,29108,29108,29108,29108,29108,29108,29108,29108),(P02743,P02743,P02743,P02743,P02743,29108,29108,29108,29108,29108,29108,29108,29108,29108,29108))" | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_5", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_76463" } | |
| } | |
| }, | |
| "bqbiol:hasPart": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:kegg.compound:C00076" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02743" }, | |
| { "-rdf:resource": "urn:miriam:obo.chebi:CHEBI%3A29108" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "species_977144", | |
| "-name": "Amyloid fibril main peptide chains [extracellular region]", | |
| "-metaid": "metaid_8", | |
| "-sboTerm": "SBO:0000240", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome DefinedSet. This is a list of alternative entities, any of which can perform the given function." | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_8", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_76011" } | |
| } | |
| }, | |
| "bqbiol:hasPart": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:uniprot:Q9Y287" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P06727" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01308" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01258" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:Q15582" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P0DJI8" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P61626" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P05067" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P06396" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P37840" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01034" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02766" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P10997" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01236" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P61769" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:Q08431" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02671" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02788" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P04279" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01160" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:A1E959" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02647" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "species_977180", | |
| "-name": "GAG [extracellular region]", | |
| "-metaid": "metaid_10", | |
| "-sboTerm": "SBO:0000247", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome SimpleEntity. This is a small compound." | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_10", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:obo.chebi:CHEBI%3A18085" }, | |
| { "-rdf:resource": "urn:miriam:reactome:REACT_76455" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "species_1011570", | |
| "-name": "HSPG2(22-4391) [extracellular region]", | |
| "-metaid": "metaid_13", | |
| "-sboTerm": "SBO:0000297", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome EntityWithAccessionedSequence. This is a protein." | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_13", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:uniprot:P98160" }, | |
| { "-rdf:resource": "urn:miriam:reactome:REACT_76697" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "species_977084", | |
| "-name": "Amyloid fibrils [extracellular region, plasma membrane]", | |
| "-metaid": "metaid_15", | |
| "-sboTerm": "SBO:0000253", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome Complex. Reactome uses a nested structure for complexes, which cannot be fully represented in SBML." | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_15", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_76626" } | |
| } | |
| }, | |
| "bqbiol:hasPart": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:uniprot:P01034" }, | |
| { "-rdf:resource": "urn:miriam:kegg.compound:C00076" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02766" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01236" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P10997" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02743" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:Q08431" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P61769" }, | |
| { "-rdf:resource": "urn:miriam:obo.chebi:CHEBI%3A29108" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02788" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:A1E959" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01160" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02647" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:Q9Y287" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01308" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P06727" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P0DJI8" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:Q15582" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01258" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P05067" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P61626" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P06396" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P37840" }, | |
| { "-rdf:resource": "urn:miriam:obo.chebi:CHEBI%3A18085" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P98160" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02671" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P04279" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "species_976737", | |
| "-name": "APCS(20-223) [extracellular region]", | |
| "-metaid": "metaid_18", | |
| "-sboTerm": "SBO:0000297", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome EntityWithAccessionedSequence. This is a protein." | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_18", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:uniprot:P02743" }, | |
| { "-rdf:resource": "urn:miriam:reactome:REACT_76593" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "species_74112", | |
| "-name": "Ca2+ [extracellular region]", | |
| "-metaid": "metaid_20", | |
| "-sboTerm": "SBO:0000247", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome SimpleEntity. This is a small compound." | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_20", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:kegg.compound:C00076" }, | |
| { "-rdf:resource": "urn:miriam:reactome:REACT_5668" }, | |
| { "-rdf:resource": "urn:miriam:obo.chebi:CHEBI%3A29108" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "species_977589", | |
| "-name": "Double-stranded DNA and chromatin [extracellular region]", | |
| "-metaid": "metaid_25", | |
| "-sboTerm": "SBO:0000240", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome DefinedSet. This is a list of alternative entities, any of which can perform the given function." | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_25", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_76370" } | |
| } | |
| }, | |
| "bqbiol:hasPart": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:uniprot:P84243" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P68431" }, | |
| { "-rdf:resource": "urn:miriam:obo.chebi:CHEBI%3A16991" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:Q71DI3" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P62805" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "species_977223", | |
| "-name": "Serum amyloid P-component pentamer:Double-stranded DNA [extracellular region]", | |
| "-metaid": "metaid_27", | |
| "-sboTerm": "SBO:0000253", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome Complex. Reactome uses a nested structure for complexes, which cannot be fully represented in SBML." | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_27", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_76462" } | |
| } | |
| }, | |
| "bqbiol:hasPart": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:uniprot:P84243" }, | |
| { "-rdf:resource": "urn:miriam:kegg.compound:C00076" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P68431" }, | |
| { "-rdf:resource": "urn:miriam:obo.chebi:CHEBI%3A16991" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02743" }, | |
| { "-rdf:resource": "urn:miriam:obo.chebi:CHEBI%3A29108" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:Q71DI3" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P62805" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "species_977175", | |
| "-name": "Amyloid fibril monomers [extracellular region]", | |
| "-metaid": "metaid_30", | |
| "-sboTerm": "SBO:0000240", | |
| "-compartment": "compartment_984", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Derived from a Reactome DefinedSet. This is a list of alternative entities, any of which can perform the given function." | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_30", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_76278" } | |
| } | |
| }, | |
| "bqbiol:hasPart": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:uniprot:Q9Y287" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01308" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P06727" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P0DJI8" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01258" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:Q15582" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P61626" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P05067" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P06396" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P37840" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01034" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02766" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P10997" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01236" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P61769" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:Q08431" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02671" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02788" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P04279" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P01160" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:A1E959" }, | |
| { "-rdf:resource": "urn:miriam:uniprot:P02647" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| } | |
| } | |
| ] | |
| }, | |
| "listOfReactions": { | |
| "reaction": [ | |
| { | |
| "-id": "reaction_976817", | |
| "-name": "Formation of serum amyloid P decamer", | |
| "-metaid": "metaid_1", | |
| "-reversible": "false", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "At physiological pH serum amyloid P component is a decamer of two pentameric rings lying face to face. This noncovalent interaction is readily dissociated by reducing the pH." | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_1", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_75878" } | |
| } | |
| }, | |
| "bqbiol:isDescribedBy": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:pubmed:8114934" } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| "listOfReactants": { | |
| "speciesReference": { | |
| "-id": "speciesreference_976817_input_976776", | |
| "-species": "species_976776", | |
| "-metaid": "metaid_4", | |
| "-sboTerm": "SBO:0000010", | |
| "-stoichiometry": "2" | |
| } | |
| }, | |
| "listOfProducts": { | |
| "speciesReference": { | |
| "-id": "speciesreference_976817_output_976787", | |
| "-species": "species_976787", | |
| "-metaid": "metaid_6", | |
| "-sboTerm": "SBO:0000011" | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "reaction_976734", | |
| "-name": "Amyloid fibrils have additional components", | |
| "-metaid": "metaid_7", | |
| "-reversible": "false", | |
| "notes": { | |
| "p": [ | |
| { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "In addition to the main fibril peptide, mature amyloid fibrils have additional components. Serum amyloid P component (SAP) binds to all types of amyloid fibrils and is a universal constituent of amyloid deposits. SAP binding protects amyloid fibrils from proteolytic degradation (Tennent et al. 1995, Westermark 2005). SAP may function as a chaperone for amyloid formation (Coker et al. 2000)." | |
| }, | |
| { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Glycosaminoglycans (GAGs) and proteoglycans are found associated with all types of amyloid deposits (Alexandrescu 2005). Of the different types of GAG heparan sulfate and dermatan sulfate are the most prominent in amyloid deposits (Hirschfield Hawkins, 2003). GAGs have been implicated in the nucleation of fibrils, they can also stabilize mature fibrils against dissociation (Yamaguchi et al. 2003) and proteolytic degradation (GuptaBansal et al. 1995)." | |
| }, | |
| { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Perlecan coimmunolocalizes with all types of amyloids (Snow Wright 1989), accelerating fibril formation (Castillo et al. 1998), stabilizing them once formed (Castillo et al. 1997), and protecting them from proteolytic degradation (GuptaBansal et al. 1995)." | |
| }, | |
| { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "ApoE tightly binds to soluble ABeta peptide forming complexes that resist dissociation; it also binds to ABeta in its fibril form (Bales et al. 2002). " | |
| } | |
| ] | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_7", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_75905" } | |
| } | |
| }, | |
| "bqbiol:isDescribedBy": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:pubmed:118839" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:2409350" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:20807650" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:null" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:10583407" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| "listOfReactants": { | |
| "speciesReference": [ | |
| { | |
| "-id": "speciesreference_976734_input_977144", | |
| "-species": "species_977144", | |
| "-metaid": "metaid_9", | |
| "-sboTerm": "SBO:0000010" | |
| }, | |
| { | |
| "-id": "speciesreference_976734_input_977180", | |
| "-species": "species_977180", | |
| "-metaid": "metaid_11", | |
| "-sboTerm": "SBO:0000010" | |
| }, | |
| { | |
| "-id": "speciesreference_976734_input_976776", | |
| "-species": "species_976776", | |
| "-metaid": "metaid_12", | |
| "-sboTerm": "SBO:0000010" | |
| }, | |
| { | |
| "-id": "speciesreference_976734_input_1011570", | |
| "-species": "species_1011570", | |
| "-metaid": "metaid_14", | |
| "-sboTerm": "SBO:0000010" | |
| } | |
| ] | |
| }, | |
| "listOfProducts": { | |
| "speciesReference": { | |
| "-id": "speciesreference_976734_output_977084", | |
| "-species": "species_977084", | |
| "-metaid": "metaid_16", | |
| "-sboTerm": "SBO:0000011" | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "reaction_976723", | |
| "-name": "Serum amyloid P-component forms homopentamers", | |
| "-metaid": "metaid_17", | |
| "-reversible": "false", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Serum amyloid P component (SAP) is a member of the pentraxin family, characterized by the formation of pentameric ring structures. Each member of the ring has two associated calcium ions. SAP is an acute phase reactant, highly induced by IL6. It has 50% homology with the related Creactive peptide. " | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_17", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_75902" } | |
| } | |
| }, | |
| "bqbiol:isDescribedBy": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:pubmed:8114934" } | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| "listOfReactants": { | |
| "speciesReference": [ | |
| { | |
| "-id": "speciesreference_976723_input_976737", | |
| "-species": "species_976737", | |
| "-metaid": "metaid_19", | |
| "-sboTerm": "SBO:0000010", | |
| "-stoichiometry": "5" | |
| }, | |
| { | |
| "-id": "speciesreference_976723_input_74112", | |
| "-species": "species_74112", | |
| "-metaid": "metaid_21", | |
| "-sboTerm": "SBO:0000010", | |
| "-stoichiometry": "10" | |
| } | |
| ] | |
| }, | |
| "listOfProducts": { | |
| "speciesReference": { | |
| "-id": "speciesreference_976723_output_976776", | |
| "-species": "species_976776", | |
| "-metaid": "metaid_22", | |
| "-sboTerm": "SBO:0000011" | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "reaction_977224", | |
| "-name": "Serum amyloid P binds DNA and chromatin", | |
| "-metaid": "metaid_23", | |
| "-reversible": "false", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Serum amyloid P component (SAP) binds DNA and chromatin in a calcium dependent manner in physiological conditions (Pepys et al. 1987). This binding displaces H1type histones (Butler et al. 1990), solubilizing chromatin which is otherwise insoluble in extracellular fluids. SAP may therefore participate in the in vivo handling of chromatin exposed by cell death. SAP knockout mice spontaneously develop antinuclear autoimmunity and severe glomerulonephritis, a phenotype resembling human systemic lupus erythematosus, a serious autoimmune disease, suggesting that SAP binding may play a role in reducing the immunogenicity of chromatin and preventing autoimmunity (Bickerstaff et al. 1999). " | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_23", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_75858" } | |
| } | |
| }, | |
| "bqbiol:isDescribedBy": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:pubmed:3675579" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:8033412" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| "listOfReactants": { | |
| "speciesReference": [ | |
| { | |
| "-id": "speciesreference_977224_input_976776", | |
| "-species": "species_976776", | |
| "-metaid": "metaid_24", | |
| "-sboTerm": "SBO:0000010" | |
| }, | |
| { | |
| "-id": "speciesreference_977224_input_977589", | |
| "-species": "species_977589", | |
| "-metaid": "metaid_26", | |
| "-sboTerm": "SBO:0000010" | |
| } | |
| ] | |
| }, | |
| "listOfProducts": { | |
| "speciesReference": { | |
| "-id": "speciesreference_977224_output_977223", | |
| "-species": "species_977223", | |
| "-metaid": "metaid_28", | |
| "-sboTerm": "SBO:0000011" | |
| } | |
| } | |
| }, | |
| { | |
| "-id": "reaction_977136", | |
| "-name": "Amyloid precursor proteins form ordered fibrils", | |
| "-metaid": "metaid_29", | |
| "-reversible": "false", | |
| "notes": { | |
| "p": { | |
| "-xmlns": "http://www.w3.org/1999/xhtml", | |
| "#text": "Amyloid fibril formation is associated with a wide range of diseases (Chiti Dobson 2006), thoughthe accumulation and deposition of fibrillar material does not correlate well with disease pathogenesis and it is now widely believed that oligomeric amyloid forms are largely responsible for the cytotoxic effects of amyloid (Glabe 2009). Fibrils have been described as more like crystalline polymer structures than the protein monomers they are derived from (Wetzel et al. 2007). Fibril formation is usually preceded by the association of monomers into oligomeric structures (Kodali Wetzel 2007). For Betaamyloid, these are spherical structures with around 12 units (Bernstein et al. 2005). Larger structures called protofibrils are also observed, nonspherical filamentous structures lacking a periodic substructure (Goldsbury 2005). " | |
| } | |
| }, | |
| "annotation": { | |
| "rdf:RDF": { | |
| "-xmlns:rdf": "http://www.w3.org/1999/02/22-rdf-syntax-ns#", | |
| "-xmlns:bqbiol": "http://biomodels.net/biology-qualifiers/", | |
| "-xmlns:bqmodel": "http://biomodels.net/model-qualifiers/", | |
| "rdf:Description": { | |
| "-rdf:about": "#metaid_29", | |
| "bqbiol:is": { | |
| "rdf:Bag": { | |
| "rdf:li": { "-rdf:resource": "urn:miriam:reactome:REACT_75876" } | |
| } | |
| }, | |
| "bqbiol:isDescribedBy": { | |
| "rdf:Bag": { | |
| "rdf:li": [ | |
| { "-rdf:resource": "urn:miriam:pubmed:279930" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:1849145" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:2900981" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:1270801" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:3053705" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:15962837" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:18449172" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:8464497" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:9054935" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:11401442" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:8490014" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:3080684" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:8097946" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:3035556" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:3094007" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:1837051" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:11467836" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:2118650" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:2195544" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:8870004" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:8159701" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:18484335" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:3142462" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:10391242" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:10411933" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:9006323" }, | |
| { "-rdf:resource": "urn:miriam:pubmed:9862427" } | |
| ] | |
| } | |
| } | |
| } | |
| } | |
| }, | |
| "listOfReactants": { | |
| "speciesReference": { | |
| "-id": "speciesreference_977136_input_977175", | |
| "-species": "species_977175", | |
| "-metaid": "metaid_31", | |
| "-sboTerm": "SBO:0000010" | |
| } | |
| }, | |
| "listOfProducts": { | |
| "speciesReference": { | |
| "-id": "speciesreference_977136_output_977144", | |
| "-species": "species_977144", | |
| "-metaid": "metaid_32", | |
| "-sboTerm": "SBO:0000011" | |
| } | |
| } | |
| } | |
| ] | |
| } | |
| } | |
| } | |
| } |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| App = Ember.Application.create(); | |
| App.Router.map(function() { | |
| this.resource('app'); | |
| }); | |
| App.IndexRoute = Ember.Route.extend({ | |
| model: function() { | |
| return ['red', 'yellow', 'blue', 'brown']; | |
| } | |
| }); | |
| function reflect(thang) { | |
| return thang; | |
| } | |
| function SBMLtoJSON(SBMLurl) { | |
| $.ajax({ | |
| type: "GET", | |
| url: SBMLurl, | |
| dataType: "xml", | |
| success: function (result) { | |
| return parseXML(result); | |
| } | |
| }); | |
| } | |
| Ember.Handlebars.registerBoundHelper('greeter', function(value) { | |
| if (value === undefined) { | |
| return ' ' | |
| } | |
| else if (value == '') { | |
| return ' ' | |
| } | |
| else { | |
| //return reflect(value); | |
| return reflect(value); | |
| } | |
| }) | |
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <!DOCTYPE html> | |
| <html> | |
| <head> | |
| <meta charset="utf-8"> | |
| <style> | |
| .node { | |
| stroke: #fff; | |
| stroke-width: 1.5px; | |
| } | |
| .link { | |
| stroke: #999; | |
| stroke-opacity: .6; | |
| } | |
| </style> | |
| <title>Visualization of Reactome SBML Files</title> | |
| <link href="http://netdna.bootstrapcdn.com/bootstrap/3.0.0/css/bootstrap.min.css" rel="stylesheet" /> | |
| </head> | |
| <body> | |
| <script src="js/libs/jquery-1.10.2.js"></script> | |
| <script src="js/libs/handlebars-1.1.2.js"></script> | |
| <script src="js/libs/ember-1.5.1.js"></script> | |
| <script src="http://d3js.org/d3.v3.min.js"></script> | |
| <script> | |
| var width = 960, | |
| height = 500; | |
| var color = d3.scale.category20(); | |
| var force = d3.layout.force() | |
| .charge(-120) | |
| .linkDistance(30) | |
| .size([width, height]); | |
| var svg = d3.select("body").append("svg") | |
| .attr("width", width) | |
| .attr("height", height); | |
| var reactants = []; | |
| var products = []; | |
| var reactions = []; | |
| var nodes = []; | |
| var links = []; | |
| var Rgraph = {}; | |
| // on drop down pathway name change, load new file | |
| d3.json("js/alzheimerR.json", function(error, result) { | |
| // Create the nodes and edges connections for reactions and species | |
| var edges = []; | |
| for (i = 0; i < result.sbml.model.listOfReactions.reaction.length; i++) { | |
| // Reactions to Products | |
| edges.push('{"source":'+'"'+result.sbml.model.listOfReactions.reaction[i]['-id']+'","target":'+'"'+result.sbml.model.listOfReactions.reaction[i].listOfProducts.speciesReference['-species']+'"}'); | |
| reactions.push(result.sbml.model.listOfReactions.reaction[i]['-id']); | |
| products.push(result.sbml.model.listOfReactions.reaction[i].listOfProducts.speciesReference['-species']); | |
| for (k = 0; k < result.sbml.model.listOfReactions.reaction[i].listOfReactants.speciesReference.length; k++) { | |
| // Reactants to Reactions | |
| edges.push('{"source":'+'"'+result.sbml.model.listOfReactions.reaction[i].listOfReactants.speciesReference[k]['-species']+'","target":'+'"'+result.sbml.model.listOfReactions.reaction[i]['-id']+'"}'); | |
| reactants.push(result.sbml.model.listOfReactions.reaction[i].listOfReactants.speciesReference[k]['-species']); | |
| } | |
| } | |
| for (i = 0; i < result.sbml.model.listOfSpecies.species.length; i++) { | |
| //console.log(result.sbml.model.listOfSpecies.species[i]); | |
| if (typeof(result.sbml.model.listOfSpecies.species[i].annotation['rdf:RDF']['rdf:Description']['bqbiol:is']['rdf:Bag']['rdf:li']) === "object") { | |
| for (k = 0; k < result.sbml.model.listOfSpecies.species[i].annotation['rdf:RDF']['rdf:Description']['bqbiol:is']['rdf:Bag']['rdf:li'].length; k++) { | |
| console.log(result.sbml.model.listOfSpecies.species[i].annotation['rdf:RDF']['rdf:Description']['bqbiol:is']['rdf:Bag']['rdf:li'][k]['-rdf:resource']); | |
| } | |
| } | |
| else { | |
| console.log(result.sbml.model.listOfSpecies.species[i].annotation['rdf:RDF']['rdf:Description']['bqbiol:is']['rdf:Bag']['rdf:li']['-rdf:resource']); | |
| } | |
| } | |
| // setup nodes | |
| var combined = products.concat(reactants).concat(reactions); | |
| for (n = 0; n < combined.length; n++) { | |
| nodes.push('{"name":"'+combined[n]+'"}'); | |
| // if ((/^species/).test(combined[n])) { | |
| // nodes.push('{"name":"'+combined[n]+'","group":1}'); | |
| // } | |
| // else { | |
| // nodes.push('{"name":"'+combined[n]+'","group":"2"}'); | |
| // } | |
| } | |
| // change source and target edges names to reflect node order | |
| for (x = 0; x < edges.length; x++) { | |
| links.push('{"source":'+nodes.indexOf('{"name":"'+JSON.parse(edges[x]).source+'"}')+', "target":'+nodes.indexOf('{"name":"'+JSON.parse(edges[x]).target+'"}')+'}'); | |
| } | |
| // add groups to nodes for colors | |
| var nodesWithGroup = []; | |
| nodes.forEach(function(n) { | |
| if ((/^species/).test(JSON.parse(n).name)) { | |
| nodesWithGroup.push(n.substring(0, n.length - 1)+',"group":1}'); | |
| } | |
| else { | |
| nodesWithGroup.push(n.substring(0, n.length - 1)+',"group":2}'); | |
| } | |
| }) | |
| Rgraph.nodes = nodesWithGroup; | |
| Rgraph.links = links; | |
| console.log(Rgraph); | |
| var graph = {}; | |
| graph.nodes = JSON.parse('['+String(Rgraph.nodes)+']'); | |
| graph.links = JSON.parse('['+String(Rgraph.links)+']'); | |
| force | |
| .nodes(graph.nodes) | |
| .links(graph.links) | |
| .start(); | |
| var link = svg.selectAll(".link") | |
| .data(graph.links) | |
| .enter().append("line") | |
| .attr("class", "link"); | |
| var node = svg.selectAll(".node") | |
| .data(graph.nodes) | |
| .enter().append("circle") | |
| .attr("class", "node") | |
| .attr("r", 5) | |
| .style("fill", function(d) { return color(d.group); }) | |
| .call(force.drag); | |
| node.append("title") | |
| .text(function(d) { return d.name; }); | |
| force.on("tick", function() { | |
| link.attr("x1", function(d) { return d.source.x; }) | |
| .attr("y1", function(d) { return d.source.y; }) | |
| .attr("x2", function(d) { return d.target.x; }) | |
| .attr("y2", function(d) { return d.target.y; }); | |
| node.attr("cx", function(d) { return d.x; }) | |
| .attr("cy", function(d) { return d.y; }); | |
| }); | |
| }); | |
| </script> | |
| <script src="js/app.js"></script> | |
| <script src="js/xml2json.js"></script> | |
| <script type="text/x-handlebars"> | |
| {{input type="text" value=greet placeholder="say hi"}} | |
| {{greeter greet}} | |
| </script> | |
| </body> | |
| </html> |
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment