30:T4ab,html`

For example, at the time of this survey, MIT & Harvard Broad Institute's firebrowse(ref) TCGA data resource does not support SSL (secure socket layer). To overcome that obstacle to data being called from a HTTPS application, such as an observable nodetbook, a cloud hosted proxy was developed and is made publicly available, both the code, at github.com/episphere/blca and the service, at blca.herokuapp.com. If, instead, the obstacle is one of confusion knowing what operators to use in engage the resource's API, then a support libray, blca.js, is maintained and served from that same gitub repository. In each case, the use of each reasource will proceed until an interactive graphic representation can be produced in this notebook through programatic operation of the data resource. To established the interoperability, the reader of this report will have to have the option of which gene expression is plotted. The type of plot will of course reflect the purpose of the data resource and the way the data modelwas acordingly identified.

`31:[] 2e:{"title":"Bladder Cancer","cells":[{"id":0,"value":"html`\n

Bladder Cancer

Hi Mila, we had a great session today, where Oscar walked us (thank you!) through additional data sources far beyond the original focus on GTEx. In addition to GTEx we touched on GDC, ICGC, cBio, firebrowse and Ensembl. The challenge is that the APIs of each resource are in differnt stages of maturation and falling back to the conventional use of the data portals doesn't scale well to the analysis you need. In this live report we'll try to assemble an analytical toolset that makes the best use we can of those reference BigData resources to first study gene expression in bladder cancer. If all goes well, we'll then expand to other data types. \n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":4,"value":"html`\n

Abstract

The molecular characterization of Bladder cancer is distributed by a variety of reference BigData resources with Application Programming Interfaces (APIs) at different stages of maturation. In this live report we'll approach this heterogeneus data landscape to assemble a user-facing analytical toolset that has no dependencies or require downloading or installing additional software and can run in any device with a web browser - including mobile devices. The use of Observable Notebooks was selected for this purpose because it meets these requiments and because it lends itself to collaborative extensability alond the same lines as jupyter notebooks.

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":45,"value":"html`\n

Results

Aggregating gene expression data from bladder cancer (BLCA) studies is the method of choice in this survey. In each case the assessment will be performed by the level of programatic interoperability that can be achieved from a web-based Observable Notebook. When an obstacle is found, such as lack of SSL, of authorization for cross-domain calling, or semantic opacity regarting the construction of the API operators, we'll make every effort to bridge over the obstacles.

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":110,"value":"$30","pinned":false,"hidden":false,"mode":"ojs"},{"id":99,"value":"html`\n

firebrowse

Data Portal: firebrowse.org.

API documentation: firebrowse.org/api-docs.

Reference: ncbi.nlm.nih.gov/pubmed/28062517.

Interoperability issues: lack of SSL.

\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":115,"value":"plotIt([{\n y:xx.mRNASeq.map(ex=>ex['expression_log2']),\n x:xx.mRNASeq.map(ex=>ex['z-score']),\n ids:xx.mRNASeq.map(ex=>ex['tcga_participant_barcode']),\n mode: 'markers',\n type: 'scatter',\n}],{\n title:'BLCA, FireBrowse mRNASeq expression data on PSCA',\n yaxis:{\n title:'gene expression, log2',\n },\n xaxis:{\n title:'z-score',\n }\n})","pinned":false,"hidden":false,"mode":"ojs"},{"id":8,"value":"html`\n

Methods

\n\n`","pinned":false,"hidden":false,"mode":"ojs"},{"id":56,"value":"blca = require('https://episphere.github.io/blca/blca.js')","pinned":true,"hidden":false,"mode":"ojs"},{"id":68,"value":"url = 'http://firebrowse.org/api/v1/Samples/mRNASeq?format=json&gene=PSCA&cohort=BLCA&protocol=RSEM&page=1&page_size=1000&sort_by=cohort'","pinned":false,"hidden":false,"mode":"ojs"},{"id":58,"value":"//xx = (await fetch('http://localhost:3000/?'+encodeURIComponent(url))).json()\nxx = (await fetch('https://blca.herokuapp.com/?'+encodeURIComponent(url))).json() ","pinned":false,"hidden":false,"mode":"ojs"},{"id":80,"value":"import {plotIt} from '@episphere/paper'","pinned":true,"hidden":false,"mode":"ojs"},{"id":124,"value":"xx.mRNASeq.map(ex=>ex['tcga_participant_barcode'])","pinned":true,"hidden":false,"mode":"ojs"}],"files":"$W31","stdlib":"1","titling":"auto"}