Commit 4fcfa18f authored by Daniel Teixeira's avatar Daniel Teixeira
Browse files

adding documentation

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<div ng-controller="BeaconController" ng-cloak class="container">
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<h1>Beacon ArrayMap</h1>
<p>Implementation of Beacon v0.2 for ArrayMap</p>
<p>First Prototype of a <a target="_blank" href="https://genomicsandhealth.org/work-products-demonstration-projects/beacon-project-0">Beacon</a>
<a target="_blank" href="https://docs.google.com/document/d/154GBOixuZxpoPykGKcPOyrYUcgEXVe2NvKx61P4Ybn4/edit"> v0.2</a> implementation for <a target="_blank" href="http://arraymap.org/">ArrayMap</a>.</p>
<p>See <a href="documentation">documentation and open questions</a>.</p>
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//
Updated by dteixeir on 15/02/16
Created by sduvaud on 10/02/16.
extends layout
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h1 Documentation
p Implementation of Beacon v0.2 for ArrayMap
p Specifications and open questions.
p Back to #[a(href="/") Home Page. #[span]]
h4 Current implementation: To be validated!
p To understand better the implementation, #[a(target="_blank" href="/samples?limit=1") check an arraymap sample in JSON], that would correspond to #[a(target="_blank" href="http://arraymap.org/samples/?project=arraymap&uid_m=GSM255289") a sample in arraymap website (UID:GSM255289) #[span]]
p
ul
li #[b chomosome] - Checks that the #[b chromosome] is found on the arraymap segments (example: SEGMENTS_HG18[i].CHRO=9)
li #[b position] - If the #[b position] asked is between SEGSTART and SEGEND #[b it returns exists=overlap otherwise it always returns false.]
li #[b reference] - Beacon #[b reference parameter] GRCh37 and GRCh38 correspond to SEGMENTS_HG18 and SEGMENTS_HG19 respectively, #[b is this correct?]
li(class="text-danger") Alleles parameter is required on the request of Beacon v0.2 specification, however in Arraymap it doesn't make sense. Could it be optional=true?
li dataset_id - For the dataset_id, we mapped the 400 datasets found in here: #[a(href="http://arraymap.org/subsets/?subsettype=ICDM&qcveto=1&project=arraymap&db=arraymap&genome=hg18") ICD Morphologies. #[span]]
li(class="text-danger") variantClass - a new parameter was added. If this value is not specified it returns error "Precise variants are not supported by ArrayMap". ArrayMap does not have precise variants in the datasets, so it's not correct to reply to this without beeing more specific about the question. #[b Will the Beacon community accept the VariantClass parameter? ]
| Jordi said if it wouldn't be too much complicated for v0.3 that could be taken in consideration.
p Here is an example: #[a(target="_blank" href="/v0.2/query?chromosome=9&position=57649422&dataset=8010/3&variantClass=DEL") /v0.2/query?chromosome=9&position=57649422&dataset=8010/3&variantClass=DEL] that queries chromosome 9 at position 57649422 for the dataset 8010/3 and havinf a deletion (variantClass=DEL)
h4 QueryResource
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td yes
td yes
td no control for now (dropdown list?)
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td position
td yes
td yes
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td yes
td no
td Genome ID. Should be added
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td allele
td yes
td no
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td yes
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h4 Forthcoming implementation: Open questions
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