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oceanproteinportal / api

A Python API module for the Ocean Protein Portal
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Main Search Needs Spectral Counts and Stations #15

Closed kaimikacolin closed 1 year ago

kaimikacolin commented 2 years ago

https://github.com/oceanproteinportal/knowledge-graph/issues/1

I found this issue in the previous repo, and was hoping we could get around it in the same way that the "Peptides Found" view does, but now I see that the station map highlights relies on it as well.

Is it possible to get these into the search results? I don't believe we need coordinates, only Station, Count, and Depth for now.

jaclynsaunders commented 2 years ago

@kaimikacolin - How's this?

PREFIX view: <http://schema.oceanproteinportal.org/v2/views/>
PREFIX opp: <http://schema.oceanproteinportal.org/v2/>
PREFIX sosa: <http://www.w3.org/ns/sosa/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX onto: <http://www.ontotext.com/>
PREFIX schema: <http://schema.org/>
PREFIX v2: <http://schema.oceanproteinportal.org/v2/>
SELECT DISTINCT ?dataset ?dataset_name ?expedition ?protein_name ?product_name ?ids ?protein_sequence ?station_name ?depth ?spectral_counts ?peptideCount
WHERE {
    {
        SELECT ?protein_view ?protein_id ?spectral_counts ?sample_feature ?depth ?station_name
        WHERE {
            VALUES ?p { view:productName view:identifiers view:proteinID }
            ?protein_view a view:ProteinFound .     
            ?protein_view ?p ?o .
            FILTER REGEX(STR(?o), "FE", "i")

            ?protein_view view:viewOf ?protein_id .
            ?protein_view a view:ProteinFound .     
            ?protein_id opp:sampleProteinProperty ?obs .
            ?obs opp:observationInSample ?sample .
            ?obs a opp:ProteinTotalSpectralCount .

            ?obs schema:value ?spectral_counts .
            FILTER (?spectral_counts > "0"^^xsd:float)

            ?sample sosa:isSampleOf ?sample_feature . 
            ?sample_feature opp:depth ?depth .
            FILTER (?depth >= "50"^^xsd:float && ?depth <= "200"^^xsd:float) .
            ?sample_feature v2:inVicinityOfStation ?station .
            ?station v2:stationName ?station_name . 
            ?sample sosa:isResultOf ?sample_event .
            ?sample_event sosa:resultTime ?date_time .
            FILTER (?date_time >= "2015-01-01T10:00:00"^^xsd:dateTime && ?date_time <= "2022-01-01T10:00:00"^^xsd:dateTime) .
        }
    }

    ?protein_view view:sequence ?protein_sequence . 
    ?protein_view view:productName ?product_name .
    ?protein_view view:proteinID ?protein_name .
    ?protein_view view:dataset ?dataset .
    ?protein_view view:datasetName ?dataset_name .
    ?protein_view view:expedition ?expedition .
    OPTIONAL { ?protein_view view:peptideCountForBestProteinIdentification ?peptideCount . }
    OPTIONAL {?protein_view view:identifiers ?ids . }
}

GraphDB viewer link%0A%20%20%20%20%20%20%20%20%20%20%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fprotein_view%20view%3AviewOf%20%3Fprotein_id%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fprotein_view%20a%20view%3AProteinFound%20.%20%20%20%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fprotein_id%20opp%3AsampleProteinProperty%20%3Fobs%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fobs%20opp%3AobservationInSample%20%3Fsample%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fobs%20a%20opp%3AProteinTotalSpectralCount%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fobs%20schema%3Avalue%20%3Fspectral_counts%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20FILTER%20(%3Fspectral_counts%20%3E%20%220%22%5E%5Exsd%3Afloat)%0A%20%20%20%20%20%20%20%20%20%20%20%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fsample%20sosa%3AisSampleOf%20%3Fsample_feature%20.%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fsample_feature%20opp%3Adepth%20%3Fdepth%20.%0A%20%09%09%20%20%20%20FILTER%20(%3Fdepth%20%3E%3D%20%2250%22%5E%5Exsd%3Afloat%20%26%26%20%3Fdepth%20%3C%3D%20%22200%22%5E%5Exsd%3Afloat)%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fsample_feature%20v2%3AinVicinityOfStation%20%3Fstation%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fstation%20v2%3AstationName%20%3Fstation_name%20.%20%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fsample%20sosa%3AisResultOf%20%3Fsample_event%20.%0A%20%20%20%20%20%20%20%20%20%20%20%20%3Fsample_event%20sosa%3AresultTime%20%3Fdate_time%20.%0A%20%09%09%20%20%20%20FILTER%20(%3Fdate_time%20%3E%3D%20%222015-01-01T10%3A00%3A00%22%5E%5Exsd%3AdateTime%20%26%26%20%3Fdate_time%20%3C%3D%20%222022-01-01T10%3A00%3A00%22%5E%5Exsd%3AdateTime)%20.%0A%20%20%20%20%20%20%20%20%7D%0A%20%20%20%20%7D%0A%0A%20%20%20%20%3Fprotein_view%20view%3Asequence%20%3Fprotein_sequence%20.%20%0A%20%20%20%20%3Fprotein_view%20view%3AproductName%20%3Fproduct_name%20.%0A%20%20%20%20%3Fprotein_view%20view%3AproteinID%20%3Fprotein_name%20.%0A%20%20%20%20%3Fprotein_view%20view%3Adataset%20%3Fdataset%20.%0A%20%20%20%20%3Fprotein_view%20view%3AdatasetName%20%3Fdataset_name%20.%0A%20%20%20%20%3Fprotein_view%20view%3Aexpedition%20%3Fexpedition%20.%0A%20%20%20%20OPTIONAL%20%7B%20%3Fprotein_view%20view%3ApeptideCountForBestProteinIdentification%20%3FpeptideCount%20.%20%7D%0A%20%20%20%20OPTIONAL%20%7B%3Fprotein_view%20view%3Aidentifiers%20%3Fids%20.%20%7D%0A%7D)

kaimikacolin commented 2 years ago

I spoke too soon on this, in ES each entry had an array of spectral counts, stations, depths, and cruises. To power the pivot view of protein data, we'll need to recreate this data: Screen Shot 2022-07-24 at 18 03 40

This is the data returned in ES for 1 protein:

{ "_index": "combined-part-two", "_type": "protein", "_id": "50df9f58-e0b6-3bd3-afdb-0733cb9babca", "_score": 0.0, "_source": { "_dataset": "20c1ddaa-1af4-3904-82a8-c8c650461f81", "guid": "50df9f58-e0b6-3bd3-afdb-0733cb9babca", "proteinId": "NODE_1109786_length_336_cov_1.01423_1_336_+", "spectralCount": [ { "count": 0, "cruise": { "value": "FK160115", "uri": "http: //lod.bco-dmo.org/id/deployment/708387" }, "station": "4", "depth": 20, "dateTime": "2016-01-20T06:00:00", "coordinate": { "lat": 10, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "4", "depth": 60, "dateTime": "2016-01-20T06:00:00", "coordinate": { "lat": 10, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "4", "depth": 125, "dateTime": "2016-01-20T06:00:00", "coordinate": { "lat": 10, "lon": -156 } }, { "count": 1, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "4", "depth": 200, "dateTime": "2016-01-20T06:00:00", "coordinate": { "lat": 10, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "4", "depth": 300, "dateTime": "2016-01-20T06:00:00", "coordinate": { "lat": 10, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "4", "depth": 400, "dateTime": "2016-01-20T06:00:00", "coordinate": { "lat": 10, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "4", "depth": 600, "dateTime": "2016-01-20T06:00:00", "coordinate": { "lat": 10, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "5", "depth": 20, "dateTime": "2016-01-21T04:00:00", "coordinate": { "lat": 8, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "5", "depth": 60, "dateTime": "2016-01-21T04:00:00", "coordinate": { "lat": 8, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "5", "depth": 120, "dateTime": "2016-01-21T04:00:00", "coordinate": { "lat": 8, "lon": -156 } }, { "count": 3, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "5", "depth": 200, "dateTime": "2016-01-21T04:00:00", "coordinate": { "lat": 8, "lon": -156 } }, { "count": 1, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "5", "depth": 300, "dateTime": "2016-01-21T04:00:00", "coordinate": { "lat": 8, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "5", "depth": 400, "dateTime": "2016-01-21T04:00:00", "coordinate": { "lat": 8, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "5", "depth": 500, "dateTime": "2016-01-21T04:00:00", "coordinate": { "lat": 8, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "5", "depth": 600, "dateTime": "2016-01-21T04:00:00", "coordinate": { "lat": 8, "lon": -156 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 20, "dateTime": "2016-01-22T22:00:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 60, "dateTime": "2016-01-22T22:00:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 80, "dateTime": "2016-01-22T22:00:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 110, "dateTime": "2016-01-22T22:00:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 125, "dateTime": "2016-01-22T22:00:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 140, "dateTime": "2016-01-22T22:00:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 180, "dateTime": "2016-01-22T22:00:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 2, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 250, "dateTime": "2016-01-22T22:00:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 300, "dateTime": "2016-01-23T09:59:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 350, "dateTime": "2016-01-23T09:59:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 400, "dateTime": "2016-01-23T09:59:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 500, "dateTime": "2016-01-23T09:59:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 600, "dateTime": "2016-01-23T09:59:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 800, "dateTime": "2016-01-23T09:59:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 1000, "dateTime": "2016-01-23T09:59:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "6", "depth": 1250, "dateTime": "2016-01-23T09:59:00", "coordinate": { "lat": 10, "lon": -150 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "7", "depth": 20, "dateTime": "2016-01-25T06:00:00", "coordinate": { "lat": 10, "lon": -145 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "7", "depth": 60, "dateTime": "2016-01-25T06:00:00", "coordinate": { "lat": 10, "lon": -145 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "7", "depth": 125, "dateTime": "2016-01-25T06:00:00", "coordinate": { "lat": 10, "lon": -145 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "7", "depth": 155, "dateTime": "2016-01-25T06:00:00", "coordinate": { "lat": 10, "lon": -145 } }, { "count": 1, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "7", "depth": 200, "dateTime": "2016-01-25T06:00:00", "coordinate": { "lat": 10, "lon": -145 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "7", "depth": 300, "dateTime": "2016-01-25T06:00:00", "coordinate": { "lat": 10, "lon": -145 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "7", "depth": 400, "dateTime": "2016-01-25T06:00:00", "coordinate": { "lat": 10, "lon": -145 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "7", "depth": 600, "dateTime": "2016-01-25T06:00:00", "coordinate": { "lat": 10, "lon": -145 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 20, "dateTime": "2016-01-27T06:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 39, "dateTime": "2016-01-26T20:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 60, "dateTime": "2016-01-27T06:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 62, "dateTime": "2016-01-26T20:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 77, "dateTime": "2016-01-26T20:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 120, "dateTime": "2016-01-26T20:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 121, "dateTime": "2016-01-27T06:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 129, "dateTime": "2016-01-26T20:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 2, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 166, "dateTime": "2016-01-26T20:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 1, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 237, "dateTime": "2016-01-26T20:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 350, "dateTime": "2016-01-27T06:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 500, "dateTime": "2016-01-27T06:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 800, "dateTime": "2016-01-27T06:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "8", "depth": 1000, "dateTime": "2016-01-27T06:30:00", "coordinate": { "lat": 10, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "9", "depth": 20, "dateTime": "2016-01-28T06:15:00", "coordinate": { "lat": 9, "lon": -140 } }, { "count": 0, "cruise": { "value": "FK160115", "uri": "http://lod.bco-dmo.org/id/deployment/708387" }, "station": "9", "depth": 120, "dateTime": 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jaclynsaunders commented 1 year ago

@kaimikacolin -- I believe this has been solved, so closing. Let me know if this is still an issue