30:[] 2e:{"title":"GTEx","cells":[{"id":0,"value":"md`# GTEx\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":11,"value":"html`\n

\nHi Mila, I had a look at GTEx as promised and these are my notes on the ability to engage it directly as a Cloud resource. I found two APIs, one native to the GTEx project, the other as part of a eQTL partnership with Emsembl. Both APIs in good order, ready to use in exploratory projects. Let me know if you have something in mind you'd like to try as a pilot test.\n

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":156,"value":"md`\n## Cloud4Bio\nCollecting feedback and synergies between [Cloud4Bio](cloud4bio.github.io) participants working with GTEx.\n### List of observable notebooks:\n* **https://observablehq.com/@episphere/gtex** - this page, where I'll be testing support libraries below for your work. Source code for the libraries at https://github.com/episphere/gtex. You can get them with a commend like this gt=require('https://episphere.github.io/gtex/gtex.js').\n* ...\n* ...\n\n

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":38,"value":"html`\n

1. APIs

1.1 GTEx

\nChecking if GTEx can be caled directly:\n

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":15,"value":"dt = (await fetch('https://gtexportal.org/rest/v1/association/egene?tissueSiteDetailId=All&draw=1&columns=&order=&start=1&length=10&search=&sortDirection=asc&page=0&pageSize=1000&_=1554000206491&v=clversion&geneSymbol=HNF1A')).json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":85,"value":"html`\n

GTEx API documentation: gtexportal.org/home/api-docs.

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":41,"value":"html`\n

1.2. Ensembl

\nNext I had a look at what other API's may be available to traverse this dataset. It turns out Ensembl has a partnership with GTEx and makes its data available through its own API.\n

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":49,"value":"tissues = (await fetch('https://rest.ensembl.org/eqtl/tissue/homo_sapiens?content-type=application/json')).json() ","pinned":false,"hidden":false,"mode":"ojs"},{"id":67,"value":"html`\n

Daina Eiser asks

Q: How can I access pancreatic tissue and HNF1A (ENSG00000135100.13) gene expression?

A: The API documentation for gene expression is at gtexportal.org/home/api-docs/#!/expression/geneExpression. Let's compose the call for pancreas, where we find ${HNF1Apancreas.geneExpression[0].data.length} values:

\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":81,"value":"HNF1Apancreas= (await fetch('https://gtexportal.org/rest/v1/expression/geneExpression?datasetId=gtex_v7&gencodeId=ENSG00000135100.13&tissueSiteDetailId=Pancreas&format=json')).json()","pinned":true,"hidden":false,"mode":"ojs"},{"id":135,"value":"expressionData = HNF1Apancreas.geneExpression[0].data","pinned":true,"hidden":false,"mode":"ojs"},{"id":139,"value":"plotIt([{\n y:HNF1Apancreas.geneExpression[0].data,\n}],{\n yaxis: {\n title:'HNF1A gene expression'\n }\n})","pinned":true,"hidden":false,"mode":"ojs"},{"id":95,"value":"html`\n

So we have the expression data, what analysis do you want to perform?. A close inspections of the API shows that we can group these values by age and by gender. We could also gave a look at Ensembl to see if we get more detail there.

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":109,"value":"html`\n

gtex.js

Now that we know where the data is, we're ready for a gtex client object that mediates the interopeartion. The gtex module is being developed at github.com/episphere/gtex, see #gt below.

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":173,"value":"md`\n## Aggregate per specimen of subject\nDaina and Oscar want to aggregate results per speciment and/or per subject. Checking the [API Swager](https://gtexportal.org/home/api-docs) looks like this aggregation can be done via the [histology resource](https://gtexportal.org/home/api-docs/#!/histology/image), for all ${images.image.length} of them :-O!\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":179,"value":"images = (await fetch('https://gtexportal.org/rest/v1/histology/image?format=json')).json()","pinned":false,"hidden":false,"mode":"ojs"},{"id":186,"value":"md`\nLet's now see if we can use, say, for patient #62, subjectId or tissueSampleId to aggregate expression, demographic and phenotypic data. for example,

\n{\n  ageBracket: \"60-69\"\n  hardyScale: \"xxxx removed xxxx\"\n  histologyImageId: \"GTEX-111FC-0826\"\n  pathologyNotes: \"2 pieces, small attachment of fat, vessel, and nerve\"\n  pathologyNotesCategories: Object {}\n  sex: \"male\"\n  subjectId: \"GTEX-111FC\"\n  tissueSampleId: \"GTEX-111FC-0826\"\n  tissueSiteDetail: \"Heart - Left Ventricle\"\n}\n

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":207,"value":"md`\nindeed we can, some resources take it as a query parameter. For example, with https://gtexportal.org/rest/v1/biobank/sample?format=json&subjectId=GTEX-111FC we can retrieve the list of ${testSample.sample.length} samples associated with this patient.\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":209,"value":"testSample = (await fetch('https://gtexportal.org/rest/v1/biobank/sample?format=json&subjectId=GTEX-111FC')).json()","pinned":true,"hidden":false,"mode":"ojs"},{"id":225,"value":"md`\n... actually get a long list of samples, say 10,000, doesn't appear to be a problem. \n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":191,"value":"samples = (await fetch('https://gtexportal.org/rest/v1/biobank/sample?format=json&pageSize=10000&sortBy=sampleId&sortDirection=asc')).json() ","pinned":false,"hidden":false,"mode":"ojs"},{"id":230,"value":"md`\n### Aggregation library\ngtex library was extented to do the aggregating. Note this might normally be a job for something like [graphql](graphql.org) (discuss). Accordingly, a method was developed to query for samples, .getSample, for example, three samples were found with the tissueSampleId \"GTEX-111FC-0826\" above. Any number of such queries can now be provides as an object, for example, gtex.getSample({tissueSampleId:'GTEX-111FC-0826'}):\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":243,"value":"gt.getSample({tissueSampleId:'GTEX-111FC-0826'})","pinned":true,"hidden":false,"mode":"ojs"},{"id":118,"value":"html`\n

Methods

\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":265,"value":"md`### load gtex library as gt`","pinned":true,"hidden":false,"mode":"ojs"},{"id":70,"value":"//gt = require('http://localhost:8000/gtex/gtex.js') \ngt = require('https://episphere.github.io/gtex/gtex.js') ","pinned":true,"hidden":false,"mode":"ojs"},{"id":267,"value":"md`### load graphics library`","pinned":true,"hidden":false,"mode":"ojs"},{"id":124,"value":"import {plotIt} from '@episphere/paper'","pinned":false,"hidden":false,"mode":"ojs"},{"id":271,"value":"md`### Miscelaneous`","pinned":true,"hidden":false,"mode":"ojs"},{"id":149,"value":"blb = (await fetch('https://dcc.icgc.org/api/v1/download?fn=/release_16/Projects/COAD-US/simple_somatic_mutation.open.COAD-US.tsv.gz')).blob()","pinned":true,"hidden":false,"mode":"ojs"},{"id":154,"value":"segunUrl='https://gtexportal.org/rest/v1/association/dyneqtl?gencodeId=ENSG00000179750.11&variantId=rs1014971&tissueSiteDetailId=Liver&datasetId=gtex_v7'","pinned":true,"hidden":false,"mode":"ojs"},{"id":275,"value":"testGenotype = (await fetch(segunUrl)).json()","pinned":true,"hidden":false,"mode":"ojs"},{"id":273,"value":"nicole = (await fetch('https://episphere.github.io/sas-connect/Reduced_BEI.json')).json()","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W30","stdlib":"1","titling":"auto"}