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api.js
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api.js
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/*
* monarch/api.js
*
* Status: BETA
*
* This API contains both *high level* calls to be used within the Monarch UI layer, as well as *lower level* calls for directly accessing
* NIF Services - currently just OntoQuest and Federation services
*
* This high level calls should abstract away from details of where information about a disease, phenotype, gene etc is stored.
*
* The idea is that this application layer can live on either the server (i.e. within Rhino) or on the client.
* Currently the status is that you MUST use Rhino whilst we are in testing phase. Some minor rewrites will be required to ise jQuery in place.
*
*
*/
// ========================================
// SETUP
// ========================================
if (typeof bbop == 'undefined') { var bbop = {};}
if (typeof bbop.monarch == 'undefined') { bbop.monarch = {};}
// ========================================
// ENGINE
// ========================================
/*
* Namespace: monarch.api
*
* Constructor: bbop.monarch.Engine
*
* constructor for Engine object
*
* Example: engine = new bbop.monarch.Engine();
*
* Arguments: opts : associative array. Keys: ontology_services_url,
* federation_services_url
*/
bbop.monarch.Engine = function(opts) {
if (bbop.monarch.defaultConfig != null) {
console.log("Using pre-set configuration: ");
this.config = bbop.monarch.defaultConfig;
}
else {
console.log("Using default configuration");
this.config = {};
}
// set defaults
if (this.config.ontology_services_url == null) {
this.config.ontology_services_url = 'http://nif-services-stage.neuinfo.org/ontoquest-lamhdi/'; // monarch
// ontology
// in
// ontoloquest
}
if (this.config.federation_services_url == null) {
this.config.federation_services_url = "http://beta.neuinfo.org/services/v1/federation/";
}
if (this.config.annotate_services_url == null) {
this.config.annotate_services_url = "http://neuinfo.org/services/v1/annotate/";
}
if (this.config.owlsim_services_url == null) {
this.config.owlsim_services_url = "http://owlsim.crbs.ucsd.edu/";
}
// TODO - deprecate this
this.config.closure_resources = [
"nif-0000-03216-7",
"nif-0000-00053-4",
"nif-0000-00096-6",
"nif-0000-00558-2",
"nif-0000-03216-9",
"nif-0000-21427-10",
"nlx_151835-1",
"nlx_152525-2",
// "nlx_152525-3" // requires further testing
];
if (this.config.autocomplete_url == null) {
this.config.autocomplete_url="http://nif-services.neuinfo.org/servicesv1/v1/vocabulary.json";
}
this.config.summary_categories = this.getConfig('summary_categories');
console.log("config: "+JSON.stringify(this.config));
// @Deprecated
if (typeof console != null) {
// RingoJS
this.fetchUrlImplementation = function(url) {
var httpclient = require('ringo/httpclient');
console.log("URL: "+url);
var exchangeObj = httpclient.get(url);
console.log("RESULT: "+exchangeObj);
console.log("STATUS: "+exchangeObj.status);
return exchangeObj.content;
};
}
var subprocess = require('ringo/subprocess');
this.debugInfo =
{
dateServerStarted : new Date(Date.now()),
serverInfo : subprocess.command("uname -a"),
apiVersionInfo : this.apiVersionInfo(),
};
// allow caller to override defaults
if (opts != null) {
for (var k in opts) {
this.config[k] = opts[k];
}
}
}
bbop.monarch.Engine.prototype.setConfiguration = function(c) {
for (var k in c) {
console.log("Setting config "+k+" = "+c[k]);
this.config[k] = c[k];
}
}
bbop.monarch.Engine.prototype.apiVersionInfo = function() {
// TODO: fill this in automatically with external config file value?
return "monarch-api-2014-04-04";
}
bbop.monarch.Engine.prototype.introspect = function() {
var meta =
{
debugInfo : this.debugInfo,
config : this.config,
cacheSize : (this.cache != null ? this.cache.contents().length : 0)
};
return meta;
}
// //////////////////////////////////////////////////////////////////
//
// APPLICATION LOGIC
//
// Anything related to genes, phenotypes, diseases and their
// connections - this is where you want to be.
/*
* Function: fetchDiseaseInfo
*
* Retrieves JSON block providing info about a disease
*
* The returned object will be the same as that for fetchClassInfo, enhanced
* with disease-specific information
*
* Known issues: If a DOID is used, similarity scores will not be returned. This
* should be resolved when the Federation API makes use of equivalence axioms.
*
* Example: var diseaseInfo = engine.fetchDiseaseInfo("DOID_1430");
*
* Status: status: PARTIALLY IMPLEMENTED
*
* Arguments: id : An identifier. One of: IRI string, OBO-style ID or NIF-style
* ID
*
* Returns: JSON blob with info about the disease
*/
bbop.monarch.Engine.prototype.fetchDiseaseInfo = function(id, opts) {
var engine = this;
if (this.cache != null) {
console.log("Checking cache for "+id);
var cached = this.cache.fetch('disease', id);
if (cached != null) {
if (cached.apiVersionInfo == null || cached.apiVersionInfo != this.apiVersionInfo()) {
console.log("cached version is out of date - will not use");
}
else {
return cached;
}
}
}
else {
console.log("No cache for this engine");
}
// every disease is represented as a class in the ontology
var obj = this.fetchClassInfo(id, {level:1});
obj.apiVersionInfo = this.apiVersionInfo();
// TEMP; workaround needed for orphanet
if (id.match(/ORPHANET/)) {
var resource = {id : 'nif-0000-21306-1', label : 'ORPHANET'};
console.log("workaround for orphanet -- looking up label in "+resource.id);
// look it up in the orphanet resource to get the label
var instlabel = engine.fetchInstanceLabelByType(id,resource.id,'disease');
console.log('FOUND:'+JSON.stringify(instlabel));
if ((instlabel != null) && (instlabel.results != null) && (instlabel.results.length > 0)) {
obj = { id : id, label : instlabel.results[0].label };
};
}
// TEMPORARY - we are waiting for OQ to index the disease ontology
if (obj == null) {
obj = {
id: id,
label : id
};
}
// enhance this basic ontology class with cross-ontology axioms
// for example, disease to locus (anatomy) or GO.
// TODO - load this into monarch ontology
// enhance this basic ontology class with data. In particular:
// * PHENOTYPES
// * GENOMIC
// TODO - enhance this object with calls to Federation services
var resource_id;
var phenotype_associations = [];
var gene_associations = [];
var pathway_associations = [];
var models = [];
var alleles = [];
var sim = [];
var similar_diseases = [];
var similar_mice = [];
var pathways = [];
// we want to fetch phenotypes from HPO annotations by keying using
// OMIM, ORPHANET, DECIPHER IDs. Due to the way the merged DO works,
// these *should* be the primary IDs.
// we also might want the closure - e.g. for a generic disease,
// get phenotypes for specific forms of this disease
// for now, just use the entry point ID
var disease_ids = [id];
var engine = this;
for (var i=0; i<disease_ids.length; i++) {
var disease_id = disease_ids[i];
var resultObj;
// PHENOTYPES
resultObj = this.fetchOmimDiseasePhenotypeAsAssocations(id);
phenotype_associations = phenotype_associations.concat(resultObj.results);
// MODELS (currently assorted) // TODO
resultObj = this.fetchMonarchIntegratedDiseaseModels(id);
models = models.concat(resultObj.results);
// GENES - DGA
resultObj = engine.fetchDiseaseGeneAssociations(id);
gene_associations = gene_associations.concat(resultObj);
resultObj = this.fetchSequenceAlterationPhenotypeAsAssociations(id,'9606');
alleles = alleles.concat(resultObj.results);
sim = sim.concat(this.fetchMonarchDiseaseByDiseasePrecompute(id).results);
// fetch the top 25 similar diseases
similar_diseases = similar_diseases.concat(this.searchByDisease(id,'9606',25));
similar_mice = similar_mice.concat(this.searchByDisease(id,'10090',25));
// old
// resultObj = this.fetchPathwaysForDisease(id);
// pathways = pathways.concat(resultObj.results);
resultObj = engine.fetchAssertedDiseasePathwayAssociations(id,obj.label);
pathway_associations = pathway_associations.concat(resultObj);
resultObj = engine.fetchInferredDiseasePathwayAssociations(id,obj.label,gene_associations);
pathway_associations = pathway_associations.concat(resultObj);
}
// add annotation sufficiency score to the associations
/*
* var pheno_features = phenotype_associations.map(function(p) { return { id :
* p.phenotype.id, "isPresent" : (p.modifier == "normal" ? "false" : "true") }
* }); var annotation_profile = { id : obj.id, label : obj.label, features :
* pheno_features };
*
* //could be configurable set of categories in the future var categories =
* getConfig('summary_categories'); var info_profile =
* engine.getInformationProfile(annotation_profile,categories);
*
* phenotype_associations.annotation_sufficiency = info_profile.scaled_score
*/
obj.annotation_sufficiency = engine.getAnnotationSufficiencyScoreFromAssociations(phenotype_associations);
obj.gene_associations = gene_associations;
obj.phenotype_associations = phenotype_associations;
obj.models = models;
obj.similar_models = {'10090' : similar_mice};
obj.alleles = alleles;
obj.sim = sim
obj.similar_diseases = similar_diseases;
// obj.pathways = pathways;
obj.pathway_associations = pathway_associations;
this.addJsonLdContext(obj);
if (this.cache != null) {
this.cache.store('disease', id, obj);
}
console.log('pathway_assoc'+JSON.stringify(obj.pathway_associations,null,' '));
return obj;
}
bbop.monarch.Engine.prototype.getAnnotationSufficiencyScoreFromAssociations = function(assocs) {
var engine = this;
console.log('assoc:'+JSON.stringify(assocs,null,' '));
// assoc style not uniform. sometimes it is p.phenotype.id; other times it
// is in has_phenotype
// TODO standardize association formats
var features = assocs.map(
function(p) {
var phenotype_id = null;
var modifier = null;
if (p.phenotype != null) {
phenotype_id = p.phenotype.id;
modifier = p.modifier;
} else if (p.has_phenotype != null && p.has_phenotype.type != null) {
phenotype_id = p.has_phenotype.type.id;
modifier = p.has_phenotype.modifier;
}
return { id : phenotype_id,"isPresent" : (modifier == "normal" ? "false" : "true") } }
);
var annotation_profile = { features : features };
// could be configurable set of categories in the future
var categories = engine.config.summary_categories;
// var categories = getConfig('summary_categories');
var info_profile = engine.getInformationProfile(annotation_profile,categories);
console.log("ANNOTATION_SUFFICIENCY: "+info_profile.scaled_score);
return info_profile.scaled_score
}
/*
* Function: fetchPhenotypeInfo
*
* Retrieves JSON block providing info about a phenotype
*
* Status: STUB - just diseases. No transitive closure.
*
* Retrieves JSON block providing info about a phenotype
*
* The returned object will be the same as that for fetchClassInfo, enhanced
* with phenotype-specific information
*
* Arguments: id : An identifier. One of: IRI string, OBO-style ID or NIF-style
* ID opts : An associative array (EXTENSIBLE, OPTIONAL)
*
* Returns: JSON blob with info about the phenotype
*/
bbop.monarch.Engine.prototype.fetchPhenotypeInfo = function(id, opts) {
console.log("Phenotype: "+id);
if (this.cache != null) {
var cached = this.cache.fetch('phenotype', id);
if (cached != null) {
if (cached.apiVersionInfo == null || cached.apiVersionInfo != this.apiVersionInfo()) {
console.log("cached version is out of date - will not use");
}
else {
return cached;
}
}
}
// every phenotype is represented as a class in the ontology
var obj = this.fetchClassInfo(id, {level:1});
obj.apiVersionInfo = this.apiVersionInfo();
// enhance this basic ontology class with cross-ontology axioms
// for example, phenotype to GO or anatomy
// TODO - load this into monarch ontology
// enhance this basic ontology class with data. In particular:
// * DISEASE/DISORDER
// - OMIM diseeases by phenotype - DONE
// * GENOMIC
// - OMIM genes by phenotype
// - model organism genes or genotypes with this phenotype (requires
// uberpheno plus reasoning)
var disease_associations = [];
// ** OMIM **
var resultObj = this.fetchOmimDiseasePhenotypeAsAssocations(id);
var numResults = resultObj.resultCount; // we don't do anything with this
// yet
// later on we may have disease associations from other views, not just OMIM
obj.disease_associations = resultObj.results;
// disease-pairs matched using this phenotype (EXPERIMENTAL)
obj.sim =this.fetchMonarchDiseaseByDiseasePrecompute(id).results;
// TODO: this should probably be smarter to figure out what species the
// phenotype is in and then only query the relevant species
// TODO: is taxon id attached to the phenotype term?
obj.genotype_associations = this.fetchGenoPhenoAsAssociationsBySpecies(id,'10090').results; // Mouse
obj.genotype_associations = obj.genotype_associations.concat(this.fetchGenoPhenoAsAssociationsBySpecies(id,'7955').results); // Fish
obj.genotype_associations = obj.genotype_associations.concat(this.fetchGenoPhenoAsAssociationsBySpecies(id,'6239').results); // Worm
obj.genotype_associations = obj.genotype_associations.concat(this.fetchGenoPhenoAsAssociationsBySpecies(id,'9606').results); // Human
// obj.genotype_associations =
// obj.genotype_associations.concat(this.fetchWormGenoPhenoAsAssocations(id).results);
// ** GENES **
// TODO: based on the genotype_associations fetched, we shold be able to get
// the implicated genes
// TODO
if (this.cache != null) {
this.cache.store('phenotype', id, obj);
}
return obj;
}
/*
* Function: fetchGenotypeInfo
*
* Retrieves JSON block providing info about a genotype
*
* The structure follows geno, e.g.
* > { id: ZDB-GENO-...?, label:, a<tm1>/a<+>;foo<x>/foo<x>(AB), type:
* effective_genotype > has_part : [ > > { id: , label:, a<tm1>/a<+>;foo<x>/foo<x>(AB),
* type: intrinsic_genotype ## aka SO:genotype > has_reference_part : { > id:..,
* label:AB, type: genomic_background > } > has_variant_part : { > id:..,
* label:, a<tm1>/a<+>;foo<x>/foo<x>, type: genomic_variation_complement, >
* has_variant_part : [ > { > id:.., label:, a<tm1>/a<+>, type:
* variation_single_locus_complement, > has_variant_part : [ > { > id: ZDB-ALT-,
* label: a<tm1>, type: variant_locus, > is_locus_instance_of : { > id:
* ZDB-GENE-..., label: a, type: gene_locus, > has_variant_part : { > id:,
* label: tm1, type: point_mutation > } > }}]}]}}]}
*
* Arguments: id : An identifier. One of: IRI string, OBO-style ID or NIF-style
* ID opts : An associative array (EXTENSIBLE, OPTIONAL)
*
* Returns: JSON blob with info about the genotype
*/
bbop.monarch.Engine.prototype.fetchGenotypeInfo = function(id, opts) {
if (this.cache != null) {
var cached = this.cache.fetch('genotype', id);
if (cached != null) {
if (cached.apiVersionInfo == null || cached.apiVersionInfo != this.apiVersionInfo()) {
console.log("cached version is out of date - will not use");
}
else {
console.log("Using Cached version of "+id);
return cached;
}
}
}
// TODO: identifier resolver needed
var obj = this.fetchGenotype(id,'10090'); // Mouse
// console.log("mouseGENO:"+JSON.stringify(obj));
if (obj == null) {
var obj = this.fetchGenotype(id,'7955'); // Fish
} else {
console.log("mouse genotype found");
}
if (obj == null) {
var obj = this.fetchGenotype(id,'6239'); // Worm
} else {
console.log("worm genotype found");
}
if (obj == null) {
var obj = this.fetchGenotype(id,'9606'); // Human
} else {
console.log("human genotype found");
}
// console.log("GENO:"+JSON.stringify(obj));
// TODO - make this more elegant
// TODO: should get this directly from the genotype... not sure why it's not
// there
// obj.phenotype_associations =
// this.fetchGenoPhenoAsAssociationsBySpecies(id,obj.taxon.id).results;
if (obj == null) {
obj = {};
obj.id = id;
}
obj.phenotype_associations = this.fetchGenoPhenoAsAssociationsBySpecies(id,'10090').results; // Mouse
obj.phenotype_associations = obj.phenotype_associations.concat(this.fetchGenoPhenoAsAssociationsBySpecies(id,'7955').results); // Fish
obj.phenotype_associations = obj.phenotype_associations.concat(this.fetchGenoPhenoAsAssociationsBySpecies(id,'6239').results); // Worm
obj.phenotype_associations = obj.phenotype_associations.concat(this.fetchGenoPhenoAsAssociationsBySpecies(id,'9606').results); // Human
obj.annotation_sufficiency = engine.getAnnotationSufficiencyScoreFromAssociations(obj.phenotype_associations);
obj.apiVersionInfo = this.apiVersionInfo();
if (this.cache != null) {
this.cache.store('genotype', id, obj);
}
return obj;
}
bbop.monarch.Engine.prototype.fetchAnatomyInfo = function(id, opts) {
if (this.cache != null) {
var cached = this.cache.fetch('anatomy', id);
if (cached != null) {
return cached;
}
}
// every anatomy is represented as a class in the ontology
var obj = this.fetchClassInfo(id, {level:1});
var pheno_ids = this.getPhenotypesByEntityClass(id);
pheno_ids = pheno_ids.map(function(id) { return id.replace("http://purl.obolibrary.org/obo/","").replace("_",":") });
obj.phenotype_ids = pheno_ids;
var cx = this;
obj.phenotypes = pheno_ids.map(function(id){ return cx.fetchClassInfo(id, {level:0})});
// for (var k in pheno_ids) {
// var pid = pheno_ids[k];
// var p = this.fetchPhenotypeInfo(pid);
//
// }
var useExperimentalUnion = false;
if (useExperimentalUnion) {
var mega_id = pheno_ids.join(" OR ");
// var ph = this.fetchPhenotypeInfo({unionOf : pheno_ids});
// copy-and-pasted from fetchPhenotypeInfo - TODO DRY
obj.disease_associations = this.fetchOmimDiseasePhenotypeAsAssocations(mega_id);
// TODO: this should probably be smarter to figure out what species the
// phenotype is in and then only query the relevant species
// TODO: is taxon id attached to the phenotype term?
obj.genotype_associations = this.fetchGenoPhenoAsAssociationsBySpecies(mega_id,'10090').results; // Mouse
obj.genotype_associations = obj.genotype_associations.concat(this.fetchGenoPhenoAsAssociationsBySpecies(mega_id,'7955').results); // Fish
obj.genotype_associations = obj.genotype_associations.concat(this.fetchGenoPhenoAsAssociationsBySpecies(mega_id,'6239').results); // Worm
obj.genotype_associations = obj.genotype_associations.concat(this.fetchGenoPhenoAsAssociationsBySpecies(mega_id,'9606').results); // Human
}
// obj.disease_associations = ph.disease_associations;
// obj.genotype_associations = ph.genotype_associations;
// obj.disease_associations = this.fetchOmimDiseaseAnatomyAsAssocations(id);
// // TODO - smarter query
// obj.phenotype_associations =
// this.fetchOmimGenePhenotypeAsAssocations(id); // TODO - smarter query
// obj.phenotype_associations =
// this.fetchGenoPhenoAsAssociationsBySpecies(id,'9606').results;
// obj.gene_associations = this.fetchGeneExpressionAsAssocations(id);
if (this.cache != null) {
this.cache.store('anatomy', id, obj);
}
return obj;
}
/*
* Function: fetchGeneInfo
*
* Status: PARTIALLY IMPLEMENTED
*
* TODO - decide whether core gene info should come from ontology or federation
*
* Retrieves JSON block providing info about a gene, currently from MyGene
*
* The returned object will be the same as that for fetchClassInfo, enhanced
* with gene-specific information
*
*
* Arguments: id : An identifier. One of: IRI string, OBO-style ID or NIF-style
* ID
*
* Returns: JSON blob with info about the gene
*/
bbop.monarch.Engine.prototype.fetchGeneInfo = function(id, opts) {
if (this.cache != null) {
var cached = this.cache.fetch('gene', id);
if (cached != null) {
if (cached.apiVersionInfo == null || cached.apiVersionInfo != this.apiVersionInfo()) {
console.log("cached version is out of date - will not use");
}
else {
return cached;
}
}
}
var gene;
var resource_id;
var phenotype_associations = [];
var orthologs = [];
var interactions = [];
var gene_associations = [];
var disease_associations = [];
var models = [];
var alleles = [];
var sim = [];
var similar_diseases = [];
var similar_mice = [];
var pathways = [];
var genotype_associations = [];
var xrefs = {};
var xref_table = [];
var analyze_phenotypes;
// This will call MyGene services to get the basic gene information
// can be augmented a lot.
// See http://mygene.info/v2/api//Remove NCBI prefix
id = id.replace(/NCBI[Gg]ene_/,"NCBIGene:");
var myGeneID = id.replace(/NCBI_?[Gg]ene:/,"");
var obj = this.fetchGeneInfoFromMyGene(myGeneID);
if (obj.source == "NOT FOUND") {
// couldn't find the gene from MyGene, so look it up in our
// mapping table
var mappings = this.mapGeneToNCBIgene(id);
console.log(JSON.stringify(mappings));
// let's just take the first one for now, if there's >1
var ncbigene_ids = Object.keys(mappings);
var ncbigene = {};
if (ncbigene_ids.length > 0) {
ncbigene = mappings[ncbigene_ids[0]];
if (ncbigene.id){
ncbi_id = ncbigene.id;
ncbi_id = ncbi_id.replace(/NCBI_?[Gg]ene:/,'');
ncbigene.ncbi_id = ncbi_id;
}
// TODO get all xrefs
}
gene = ncbigene;
gene.references = [];
} else {
gene = {
// we found it, now make the object in our style
id : 'NCBIGene:'+obj.entrezgene,
ncbi_id : obj.entrezgene,
label : obj.symbol,
description : obj.name,
summary : obj.summary,
taxon : { id : obj.taxid },
tax_xref : {
id: "NCBITaxon:" + obj.taxid,
label: obj.taxid
},
references : [
{
id:'NCBIGene:'+obj.entrezgene,
source : 'NCBIGene'
}
],
source : "MyGene"
};
if (obj.map_location){
gene.location = obj.map_location;
}
if (obj.ensembl){
if (obj.ensembl.gene){
gene.references.push({
id:'Ensembl:'+obj.ensembl.gene,
source : 'Ensembl'
});
}
}
}
console.log("GENE: "+JSON.stringify(gene));
// Get organism
if (gene.ncbi_id){
var filters = ["geneid:"+this.quote(gene.ncbi_id.toString())];
var resource_id = 'nif-0000-02801-1';
var fetchOrg =
this.fetchDataFromResource(null,
resource_id,null,null,filters
) ;
// TODO how to handle multiple results (should only have 1)
if (fetchOrg.results[0]){
if (gene.taxon.id.toString() === fetchOrg.results[0].tax_id.toString()){
gene.species = fetchOrg.results[0].species;
}
}
}
// obj.kegg_stuff = this.mapNCBIGeneToKO(id);
// TODO: how should i handle multiple mappings to ncbi?
var genePathways = this.fetchPathwaysForGene(gene.id);
if (genePathways == null || genePathways.pathways == null) {
console.warn("No pathway info");
}
else {
// gene.pathways = pathwayInfo.pathways;
var pathway_associations = [];
// console.log('GENEPATHWAYS:'+JSON.stringify(genePathways));
if (genePathways.pathways){
for (var j=0; j<genePathways.pathways.length; j++) {
var pathway = genePathways.pathways[j];
// pathway.id = pathway.id;
var assoc = {
id : "monarch:disco/" + gene.v_uuid,
// TODO these are actually inferred via orthology, say this?
type : "Association",
gene : {id : gene.id, label : gene.label},
pathway : pathway,
source : pathway.source,
resource : pathway.source,
references : pathway.references
};
pathway_associations.push(assoc);
}
}
gene.pathway_associations = pathway_associations;
}
// TODO: include SO type id?
gene.type = "gene";
// Generate cross references
var geneMap = this.mapNCBIGeneToSource(gene.id);
var unique = {};
for (var k=0; k < gene.references.length; k++){
unique[gene.references[k].id] = 1;
}
if (geneMap.results){
for (var i=0;i < geneMap.results.length; i++){
if ((geneMap.results[i].source === 'EMBL-Bank')||
(geneMap.results[i].source === 'NCBI_Genome')||
(geneMap.results[i].source === 'NIA')||
(geneMap.results[i].source === 'NCBI_nuccore')||
(geneMap.results[i].source === 'NCBI_locus_tag')||
(geneMap.results[i].source === 'DoTS')||
(geneMap.results[i].source === 'HomoloGene')||
(!geneMap.results[i].source)||
(geneMap.results[i].source === 'CCDS')||
(geneMap.results[i].source === 'BIOGRID')||
// These generate link outs
(geneMap.results[i].source === 'NCBI_gi')||
(geneMap.results[i].source === 'NCBIGene')||
(geneMap.results[i].source === 'NCBI_GP')||
// (geneMap.results[i].source === 'RefSeq')||
(geneMap.results[i].source === 'EC')||
(geneMap.results[i].source === 'RefSeq_NA')||
(geneMap.results[i].source === 'RefSeq_Prot')||
(geneMap.results[i].source === 'VEGA')||
// (geneMap.results[i].source === 'Vega')||
// (geneMap.results[i].source === 'UniGene')||
(geneMap.results[i].source === 'Unigene')||
// OMIM is returning results for the wrong organism
// (geneMap.results[i].source === 'OMIM')||
(geneMap.results[i].id.match(/MGD\-MRK\-/))||
// Attempt to remove Ensembl protein and transcript linkouts
(geneMap.results[i].id.match(/ENS.*[PT]/))
)
{
continue;
}
if (geneMap.results[i].id in unique){
continue;
}
gene.references.push(geneMap.results[i]);
unique[geneMap.results[i].id] = 1;
}
}
// Map NCBI gene to disease data
if (gene.id){
disease_associations = this.fetchDiseaseGeneAssociations(gene.id);
} else {
disease_associations = this.fetchDiseaseGeneAssociations(id);
}
// Map NCBI gene to phenotype data
// PHENOTYPES
var resultObj = this.fetchGenePhenotypeAsAssociation(gene.id);
if (resultObj.results.length > 0){
phenotype_associations = phenotype_associations.concat(resultObj.results);
gene.annotation_sufficiency = engine.getAnnotationSufficiencyScoreFromAssociations(phenotype_associations);
}
// This code is generate associations for tables using ids other than NCBI
// gene
// typically for model organisms.
if (gene.references[0]){
// Check to make sure gene is the same for each result
for (var i=0;i < gene.references.length; i++){
var modelObj = this.fetchModelOrgGenePhenotypeAsAssociation(gene.references[i].id,
gene.references[i].source,
gene);
var genoTypeObj = this.fetchGeneGenoTypeAsAssociation(gene.references[i].id,
gene.references[i].source,
gene);
var orthoObj = this.fetchGeneOrthologAsAssociation(gene.references[i].id,gene.label,gene);
var alleleObj = this.fetchGeneAlleleAsAssociation(gene.references[i].id,
gene.references[i].source,
gene);
if (orthoObj){
orthologs = orthologs.concat(orthoObj.results)
}
if (alleleObj){
alleles = alleles.concat(alleleObj.results);
}
if (modelObj){
phenotype_associations = phenotype_associations.concat(modelObj.results);
}
if (genoTypeObj){
genotype_associations = genotype_associations.concat(genoTypeObj.results);
}
//Generate cross references table
if (xrefs[gene.references[i].source]){
xrefs[gene.references[i].source] =
xrefs[gene.references[i].source].concat({id: gene.references[i].id});
} else {
xrefs[gene.references[i].source] = [];
xrefs[gene.references[i].source] =
xrefs[gene.references[i].source].concat({id: gene.references[i].id});
}
}
}
// Generate human-genotype and human-allele relationships
// HACK - This is a hardcode based on NCBI taxon id, this should be changed
// eventually to a non-hardcoded approach
if ((gene.taxon) && (gene.taxon.id)) {
if (gene.taxon.id.toString() === '9606'){
var genoTypeObj = this.fetchGeneGenoTypeAsAssociation(gene.id,
'human',
gene);
var alleleObj = this.fetchGeneAlleleAsAssociation(gene.id,
'human',
gene);
if (genoTypeObj){
genotype_associations = genotype_associations.concat(genoTypeObj.results);
}
if (alleleObj){
alleles = alleles.concat(alleleObj.results);
}
}
}
// HACK to generate content for MGI IDs
// that are not found in mygene or our lookup table
if (id.match(/MGI/)&&(!gene.id)) {
formID = id.replace(/MGI_/,'MGI:');
gene.id = formID;
gene.label = formID;
var modelObj = this.fetchModelOrgGenePhenotypeAsAssociation(formID,
'MGI',
gene);
var genoTypeObj = this.fetchGeneGenoTypeAsAssociation(formID,
'MGI',
gene);
var orthoObj = this.fetchGeneOrthologAsAssociation(formID,'MGI',gene);
var alleleObj = this.fetchGeneAlleleAsAssociation(formID,'MGI',gene);
if (orthoObj){
orthologs = orthologs.concat(orthoObj.results)
}
if (alleleObj){
alleles = alleles.concat(alleleObj.results);
}
if (modelObj){
phenotype_associations = phenotype_associations.concat(modelObj.results);
}
if (genoTypeObj){
genotype_associations = genotype_associations.concat(genoTypeObj.results);
}
}
// Find gene interactions
var interactionObj = this.fetchGeneInteractions(id);
if (interactionObj){
interactions = interactions.concat(interactionObj.results);
}
// Add results to gene object
gene.phenotype_associations = phenotype_associations;
gene.genotype_associations = genotype_associations;
gene.alleles = alleles;
gene.orthologs = orthologs;
gene.interactions = interactions;
gene.disease_associations = disease_associations;
//Build xref table from xrefs object
var xrefs_keys = Object.keys(xrefs);
for (var i=0; i < xrefs_keys.length; i++){
var xref_row = {
id : xrefs[xrefs_keys[i]],
source : xrefs_keys[i]
}
xref_table = xref_table.concat(xref_row);
}
//Update gene.references instead of creating a redudant table
gene.references = xref_table;
// Generate inferred diseases from orthologs
if ((!gene.disease_associations[0])&&(gene.orthologs)&&(gene.taxon)&&(gene.taxon.id != 9606)){
for (var i=0;i < gene.orthologs.length; i++){
if (gene.orthologs[i].organism == 'Homo sapiens'){
var disObj = this.fetchDiseaseGeneAssociations(gene.orthologs[i].ortholog.id);
if (disObj){
disease_associations = disease_associations.concat(disObj);
}
}
}
if (disease_associations[0]){
for (var i=0;i < disease_associations.length; i++){
disease_associations[i].association_type = 'putative - via ortholog';
disease_associations[i].model_gene = {};
disease_associations[i].model_gene.id = disease_associations[i].gene.id;
disease_associations[i].model_gene.label = disease_associations[i].gene.label;
disease_associations[i].gene.id = id;
disease_associations[i].model_species = 'Homo sapiens';
if (gene.label){
disease_associations[i].gene.label = gene.label;
} else {
disease_associations[i].gene.label = '';
}
}
}
gene.disease_associations = disease_associations;
}
// Sort references and orthologs
gene.references.sort(function (reference, query) { return (reference.source > query.source) ? 1 : -1 });
gene.orthologs.sort(function (reference, query) { return (reference.organism > query.organism) ? 1 : -1 });
// Create analyze phenotype link
if (gene.phenotype_associations){
analyze_phenotypes = '/analyze/phenotypes/?input_items=';
for (var i=0;i < gene.phenotype_associations.length; i++){
var next = i + 1;
if (gene.phenotype_associations[next]){
analyze_phenotypes = analyze_phenotypes + gene.phenotype_associations[i].phenotype.id + "+";
} else {
analyze_phenotypes = analyze_phenotypes + gene.phenotype_associations[i].phenotype.id;
}
}
analyze_phenotypes = analyze_phenotypes + "&limit=100";
if (gene.taxon){
if (gene.taxon.id){
analyze_phenotypes = analyze_phenotypes + "&target_species=" + gene.taxon.id.toString();
}
}
}
gene.analyze_phenotypes = analyze_phenotypes;
// Capitalize first letter of gene description
// HACK - Perhaps this should be done on the client side
if (gene.description){
var capLabel = gene.description.charAt(0).toUpperCase()
+ gene.description.substring(1);
gene.description = capLabel;
}
if (this.cache != null) {
this.cache.store('gene', id, obj);
}
return gene;
}