Skip to content

Instantly share code, notes, and snippets.

@abargnesi

abargnesi/evidence-collection.json

Last active September 28, 2015 13:46
Show Gist options

  • Select an option

    Learn more about clone URLs
  • Save abargnesi/63fd5ee5a0ae76b7a33e to your computer and use it in GitHub Desktop.

Select an option

Learn more about clone URLs
Save abargnesi/63fd5ee5a0ae76b7a33e to your computer and use it in GitHub Desktop.
Download ZIP
Example of evidence-collection response.
Raw
evidence-collection.json
{
"evidence-collection": [
{
"evidence": {
"bel_statement": "kin(p(HGNC:AKT1)) directlyIncreases p(HGNC:FOXO3,pmod(P,T,32))",
"citation": {
"type": "PubMed",
"name": "Biochem J 2001 Mar 15 354(Pt 3) 605-12",
"id": "11237865",
"date": "",
"authors": [
],
"comment": ""
},
"summary_text": "FKHR, FKHRL1 and AFX are each phosphorylated by PKB at three residues in vitro, and, in co-transfection experiments with FKHR, these were shown to be Thr-24, Ser-256 and Ser-319 [9-14]. The half time for phosphorylation of each site was 2-5 min. In contrast, the mutation S256A completely prevented phosphorylation at Thr-24 and Ser-319 ... but the mutation T24A did not prevent phosphorylation at Ser-256 or Ser-319 ..., and the mutation S319A did not prevent the phosphorylation of Thr-24 and Ser-256...",
"experiment_context": [
{
"name": "Cellstructure",
"value": "Cell Nucleus"
},
{
"name": "Species",
"value": "9606"
}
],
"references": {
"namespaces": {
"CHEBI": "http://resource.belframework.org/belframework/20150611/namespace/chebi.belns",
"EGID": "http://resource.belframework.org/belframework/20150611/namespace/entrez-gene-ids.belns",
"GOBP": "http://resource.belframework.org/belframework/20150611/namespace/go-biological-process.belns",
"GOCCID": "http://resource.belframework.org/belframework/20150611/namespace/go-cellular-component-ids.belns",
"HGNC": "http://resource.belframework.org/belframework/20150611/namespace/hgnc-human-genes.belns",
"MESHCS": "http://resource.belframework.org/belframework/20150611/namespace/mesh-cellular-structures.belns",
"MESHD": "http://resource.belframework.org/belframework/20150611/namespace/mesh-diseases.belns",
"MESHPP": "http://resource.belframework.org/belframework/20150611/namespace/mesh-processes.belns",
"MGI": "http://resource.belframework.org/belframework/20150611/namespace/mgi-mouse-genes.belns",
"RGD": "http://resource.belframework.org/belframework/20150611/namespace/rgd-rat-genes.belns",
"SCHEM": "http://resource.belframework.org/belframework/20150611/namespace/selventa-legacy-chemicals.belns",
"SCOMP": "http://resource.belframework.org/belframework/20150611/namespace/selventa-named-complexes.belns",
"SDIS": "http://resource.belframework.org/belframework/20150611/namespace/selventa-legacy-diseases.belns",
"SFAM": "http://resource.belframework.org/belframework/20150611/namespace/selventa-protein-families.belns"
},
"annotations": {
"Anatomy": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/anatomy.belanno"
},
"Cell": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/cell.belanno"
},
"CellLine": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/cell-line.belanno"
},
"CellStructure": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/cell-structure.belanno"
},
"Disease": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/disease.belanno"
},
"MeSHAnatomy": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/mesh-anatomy.belanno"
},
"MeSHDisease": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/mesh-diseases.belanno"
},
"Species": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/species-taxonomy-id.belanno"
}
}
},
"metadata": [
{
"name": "document_header",
"value": {
"Name": "BEL Framework Large Corpus Document",
"Description": "Approximately 61,000 statements.",
"Version": "20150611",
"Copyright": "Copyright (c) 2011-2015, Selventa. All rights reserved.",
"Authors": "Selventa",
"Licenses": "Creative Commons Attribution-Non-Commercial-ShareAlike 3.0 Unported License",
"ContactInfo": "[email protected]"
}
}
]
},
"_links": {
"self": {
"type": "evidence",
"href": "http://localhost:9000/api/evidence/560154bf8a4cca1317001fba"
},
"collection": {
"type": "evidence-collection",
"href": "http://localhost:9000/api/evidence"
}
}
},
{
"evidence": {
"bel_statement": "kin(p(HGNC:AKT1)) directlyIncreases p(HGNC:FOXO4,pmod(P,T,32))",
"citation": {
"type": "PubMed",
"name": "J Cell Biol 2002 Mar 4 156(5) 817-28",
"id": "11864996",
"date": "",
"authors": [
],
"comment": ""
},
"summary_text": "To investigate the normal intracellular distribution of 14-3-3 proteins and their ligands, U2OS cells were immunostained with a polyclonal antibody that recognizes all 14-3-3 isotypes (pan-14-3-3) or with a monoclonal antibody generated against the 14-3-3sigma isotype (Fig. 1 A). Upon growth factor stimulation, Akt is activated, directly phosphorylating FKHRL1 at T32 and S253, and to a lesser extent at S315, and resulting in FKHRL1 relocalization from the nucleus to the cytoplasm .... Similar AKT-dependent changes in subcellular localization have also been observed for the additional FKHRL1 human homologs AFX and FKHR.... Phosphorylation at T32 and S253 causes FKHRL1 to bind to 14-3-3, suggesting that the interaction between FKHRL1 and 14-3-3 may play an important role in regulating the subcellular localization of the complex.",
"experiment_context": [
{
"name": "Species",
"value": "9606"
},
{
"name": "Cellstructure",
"value": "Cell Nucleus"
}
],
"references": {
"namespaces": {
"CHEBI": "http://resource.belframework.org/belframework/20150611/namespace/chebi.belns",
"EGID": "http://resource.belframework.org/belframework/20150611/namespace/entrez-gene-ids.belns",
"GOBP": "http://resource.belframework.org/belframework/20150611/namespace/go-biological-process.belns",
"GOCCID": "http://resource.belframework.org/belframework/20150611/namespace/go-cellular-component-ids.belns",
"HGNC": "http://resource.belframework.org/belframework/20150611/namespace/hgnc-human-genes.belns",
"MESHCS": "http://resource.belframework.org/belframework/20150611/namespace/mesh-cellular-structures.belns",
"MESHD": "http://resource.belframework.org/belframework/20150611/namespace/mesh-diseases.belns",
"MESHPP": "http://resource.belframework.org/belframework/20150611/namespace/mesh-processes.belns",
"MGI": "http://resource.belframework.org/belframework/20150611/namespace/mgi-mouse-genes.belns",
"RGD": "http://resource.belframework.org/belframework/20150611/namespace/rgd-rat-genes.belns",
"SCHEM": "http://resource.belframework.org/belframework/20150611/namespace/selventa-legacy-chemicals.belns",
"SCOMP": "http://resource.belframework.org/belframework/20150611/namespace/selventa-named-complexes.belns",
"SDIS": "http://resource.belframework.org/belframework/20150611/namespace/selventa-legacy-diseases.belns",
"SFAM": "http://resource.belframework.org/belframework/20150611/namespace/selventa-protein-families.belns"
},
"annotations": {
"Anatomy": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/anatomy.belanno"
},
"Cell": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/cell.belanno"
},
"CellLine": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/cell-line.belanno"
},
"CellStructure": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/cell-structure.belanno"
},
"Disease": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/disease.belanno"
},
"MeSHAnatomy": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/mesh-anatomy.belanno"
},
"MeSHDisease": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/mesh-diseases.belanno"
},
"Species": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/species-taxonomy-id.belanno"
}
}
},
"metadata": [
{
"name": "document_header",
"value": {
"Name": "BEL Framework Large Corpus Document",
"Description": "Approximately 61,000 statements.",
"Version": "20150611",
"Copyright": "Copyright (c) 2011-2015, Selventa. All rights reserved.",
"Authors": "Selventa",
"Licenses": "Creative Commons Attribution-Non-Commercial-ShareAlike 3.0 Unported License",
"ContactInfo": "[email protected]"
}
}
]
},
"_links": {
"self": {
"type": "evidence",
"href": "http://localhost:9000/api/evidence/560157018a4cca131700355e"
},
"collection": {
"type": "evidence-collection",
"href": "http://localhost:9000/api/evidence"
}
}
}
],
"facets": [
{
"category": "metadata",
"name": "document_header",
"values": [
{
"value": [
"Licenses",
"Creative Commons Attribution-Non-Commercial-ShareAlike 3.0 Unported License"
],
"filter": "{\"category\":\"metadata\",\"name\":\"document_header\",\"value\":[\"Licenses\",\"Creative Commons Attribution-Non-Commercial-ShareAlike 3.0 Unported License\"]}",
"count": 52399
},
{
"value": [
"ContactInfo",
"[email protected]"
],
"filter": "{\"category\":\"metadata\",\"name\":\"document_header\",\"value\":[\"ContactInfo\",\"[email protected]\"]}",
"count": 52399
}
]
},
{
"category": "experiment_context",
"name": "Species",
"values": [
{
"value": "9606",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Species\",\"value\":\"9606\"}",
"count": 33236
},
{
"value": "10090",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Species\",\"value\":\"10090\"}",
"count": 13817
}
]
},
{
"category": "experiment_context",
"name": "Anatomy",
"values": [
{
"value": "liver",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Anatomy\",\"value\":\"liver\"}",
"count": 1608
},
{
"value": "skeletal muscle tissue",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Anatomy\",\"value\":\"skeletal muscle tissue\"}",
"count": 1134
}
]
},
{
"category": "experiment_context",
"name": "Cell",
"values": [
{
"value": "endothelial cell",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Cell\",\"value\":\"endothelial cell\"}",
"count": 1048
},
{
"value": "macrophage",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Cell\",\"value\":\"macrophage\"}",
"count": 979
}
]
},
{
"category": "experiment_context",
"name": "Textlocation",
"values": [
{
"value": "Review",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Textlocation\",\"value\":\"Review\"}",
"count": 885
},
{
"value": "Results",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Textlocation\",\"value\":\"Results\"}",
"count": 711
}
]
},
{
"category": "experiment_context",
"name": "Cellline",
"values": [
{
"value": "HUVEC cell line",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Cellline\",\"value\":\"HUVEC cell line\"}",
"count": 703
},
{
"value": "MCF7 cell",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Cellline\",\"value\":\"MCF7 cell\"}",
"count": 600
}
]
},
{
"category": "citation",
"name": "id",
"values": [
{
"value": "15212693",
"filter": "{\"category\":\"citation\",\"name\":\"id\",\"value\":\"15212693\"}",
"count": 549
},
{
"value": "15706034",
"filter": "{\"category\":\"citation\",\"name\":\"id\",\"value\":\"15706034\"}",
"count": 330
}
]
},
{
"category": "experiment_context",
"name": "Cellstructure",
"values": [
{
"value": "Cytoplasm",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Cellstructure\",\"value\":\"Cytoplasm\"}",
"count": 539
},
{
"value": "Cell Membrane",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Cellstructure\",\"value\":\"Cell Membrane\"}",
"count": 383
}
]
},
{
"category": "experiment_context",
"name": "Disease",
"values": [
{
"value": "atherosclerosis",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Disease\",\"value\":\"atherosclerosis\"}",
"count": 416
},
{
"value": "leukemia",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Disease\",\"value\":\"leukemia\"}",
"count": 320
}
]
},
{
"category": "experiment_context",
"name": "Meshanatomy",
"values": [
{
"value": "bronchoalveolar lavage fluid",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Meshanatomy\",\"value\":\"bronchoalveolar lavage fluid\"}",
"count": 111
},
{
"value": "tumor",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Meshanatomy\",\"value\":\"tumor\"}",
"count": 86
}
]
},
{
"category": "experiment_context",
"name": "Meshdisease",
"values": [
{
"value": "Hypercholesterolemia",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Meshdisease\",\"value\":\"Hypercholesterolemia\"}",
"count": 22
},
{
"value": "Head and Neck Neoplasms",
"filter": "{\"category\":\"experiment_context\",\"name\":\"Meshdisease\",\"value\":\"Head and Neck Neoplasms\"}",
"count": 18
}
]
}
],
"metadata": {
"collection_paging": {
"total": 52401,
"total_filtered": 52401,
"total_pages": 26201,
"current_page": 12511,
"current_page_size": 2
}
},
"_links": {
"self": {
"type": "evidence-collection",
"href": "http://localhost:9000/api/evidence?start=25020&size=2&"
},
"start": {
"type": "evidence-collection",
"href": "http://localhost:9000/api/evidence?start=0&size=2&"
},
"previous": {
"type": "evidence-collection",
"href": "http://localhost:9000/api/evidence?start=25018&size=2&"
},
"next": {
"type": "evidence-collection",
"href": "http://localhost:9000/api/evidence?start=25022&size=2&"
}
}
}
Raw
evidence-resource.json
{
"evidence": {
"bel_statement": "kin(p(HGNC:AKT1)) directlyIncreases p(HGNC:FOXO3,pmod(P,T,32))",
"citation": {
"type": "PubMed",
"name": "Biochem J 2001 Mar 15 354(Pt 3) 605-12",
"id": "11237865",
"date": "",
"authors": [
],
"comment": ""
},
"summary_text": "FKHR, FKHRL1 and AFX are each phosphorylated by PKB at three residues in vitro, and, in co-transfection experiments with FKHR, these were shown to be Thr-24, Ser-256 and Ser-319 [9-14]. The half time for phosphorylation of each site was 2-5 min. In contrast, the mutation S256A completely prevented phosphorylation at Thr-24 and Ser-319 ... but the mutation T24A did not prevent phosphorylation at Ser-256 or Ser-319 ..., and the mutation S319A did not prevent the phosphorylation of Thr-24 and Ser-256...",
"experiment_context": [
{
"name": "Cellstructure",
"value": "Cell Nucleus"
},
{
"name": "Species",
"value": "9606"
}
],
"references": {
"namespaces": {
"CHEBI": "http://resource.belframework.org/belframework/20150611/namespace/chebi.belns",
"EGID": "http://resource.belframework.org/belframework/20150611/namespace/entrez-gene-ids.belns",
"GOBP": "http://resource.belframework.org/belframework/20150611/namespace/go-biological-process.belns",
"GOCCID": "http://resource.belframework.org/belframework/20150611/namespace/go-cellular-component-ids.belns",
"HGNC": "http://resource.belframework.org/belframework/20150611/namespace/hgnc-human-genes.belns",
"MESHCS": "http://resource.belframework.org/belframework/20150611/namespace/mesh-cellular-structures.belns",
"MESHD": "http://resource.belframework.org/belframework/20150611/namespace/mesh-diseases.belns",
"MESHPP": "http://resource.belframework.org/belframework/20150611/namespace/mesh-processes.belns",
"MGI": "http://resource.belframework.org/belframework/20150611/namespace/mgi-mouse-genes.belns",
"RGD": "http://resource.belframework.org/belframework/20150611/namespace/rgd-rat-genes.belns",
"SCHEM": "http://resource.belframework.org/belframework/20150611/namespace/selventa-legacy-chemicals.belns",
"SCOMP": "http://resource.belframework.org/belframework/20150611/namespace/selventa-named-complexes.belns",
"SDIS": "http://resource.belframework.org/belframework/20150611/namespace/selventa-legacy-diseases.belns",
"SFAM": "http://resource.belframework.org/belframework/20150611/namespace/selventa-protein-families.belns"
},
"annotations": {
"Anatomy": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/anatomy.belanno"
},
"Cell": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/cell.belanno"
},
"CellLine": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/cell-line.belanno"
},
"CellStructure": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/cell-structure.belanno"
},
"Disease": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/disease.belanno"
},
"MeSHAnatomy": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/mesh-anatomy.belanno"
},
"MeSHDisease": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/mesh-diseases.belanno"
},
"Species": {
"type": "url",
"domain": "http://resource.belframework.org/belframework/20150611/annotation/species-taxonomy-id.belanno"
}
}
},
"metadata": [
{
"name": "document_header",
"value": {
"Name": "BEL Framework Large Corpus Document",
"Description": "Approximately 61,000 statements.",
"Version": "20150611",
"Copyright": "Copyright (c) 2011-2015, Selventa. All rights reserved.",
"Authors": "Selventa",
"Licenses": "Creative Commons Attribution-Non-Commercial-ShareAlike 3.0 Unported License",
"ContactInfo": "[email protected]"
}
}
]
},
"_links": {
"self": {
"type": "evidence",
"href": "http://localhost:9000/api/evidence/560154bf8a4cca1317001fba"
},
"collection": {
"type": "evidence-collection",
"href": "http://localhost:9000/api/evidence"
}
}
}
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment