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MODENA EC50/25 measurement groups #97

Closed ghost closed 7 years ago

ghost commented 7 years ago

I am trying to find out if there are sufficient examples for modelling one of the EC50/25 endpoints in the MODENA dataset. The JSON_LD representations returns entries like

`{"@id"=>"ep:ID16863", "@type"=>"bao:BAO_0000179", "standardisedUnit"=>"opsUnit:MicrogramPerMilliliter", "IAO_0000136"=>"substance:XLSX-adf890e9-3623-3a0e-b601-11f8e5e2f3cb", "has-unit"=>"ug/ml", "sio:has-value"=>2076.8564466795024, "label"=>"EC50"}`

From this entry it is unclear if the EC50 value was obtained by the Cell viability, LDH release, ATP or MTT assay.

The ep:ID16863 "@id" seems to belong to the following measurement group:

`{"@id"=>"mgroup:XLSX-f5ba28f1-d236-415d-af07-6ffe7b15585e", "@type"=>"bao:BAO_0000040", "OBI_0000299"=>["ep:ID16864", "ep:ID16863", "ep:ID16862"]}`

But curl -H 'Accept:application/ld+json' https://data.enanomapper.net/measuregroup:XLSX-41595fe0-3c7b-4725-b209-f0267aa83da7 returns (sorry I cannot figure out how to escape html strings here):

<html>
<head>
   <title>Status page</title>
</head>
<body style="font-family: sans-serif;">
<h3>The method specified in the request is not allowed for the resource identified by the request URI</h3><p>You can get technical details <a href="http://www.w3.org/Protocols/rfc2616/rfc2616-sec10.html#sec10.4.6">here</a>.<br>
Please continue your visit at our <a href="/">home page</a>.
</p>
</body>
</html>

How can I find the assay corresponding to this data entry? BTW: I have the same problem with JSON studies.

vedina commented 7 years ago

there is no /measuregroup resource, hence the returned error is correct

vedina commented 7 years ago

The plain json clearly specifies the study parameters

see the html https://data.enanomapper.net/substance/XLSX-adf890e9-3623-3a0e-b601-11f8e5e2f3cb/study

The JSON structure is shown below (the same entry as for the RDF in next post)

image

vedina commented 7 years ago

The RDF data model should be able to represent all info about the study, without additional queries.

Example below with N3 - it does link LDH with the EC50 entry. NPO_1709 is the term for the LDH assay. The assay XLSX-41595fe0-3c7b-4725-b209-f0267aa83da7 is of type NPO_1709 and has the measure group mgroup:XLSX-41595fe0-3c7b-4725-b209-f0267aa83da7.

The same links should exist with all RDF serializations

https://data.enanomapper.net/substance/XLSX-adf890e9-3623-3a0e-b601-11f8e5e2f3cb?media=text/n3

ref:E086C4B4  dc:publisher  owner:MODENA ;
        dc:title      "015" .

ap:076C0843  a    obo:OBI_0000272 ;
        dc:title  "LDH" 

as:XLSX-41595fe0-3c7b-4725-b209-f0267aa83da7
        a                npo:NPO_1709 , bao:BAO_0000015 ;
        dc:title         "015" ;
        dcterms:source   ref:E086C4B4 ;
        bao:BAO_0000209  mgroup:XLSX-41595fe0-3c7b-4725-b209-f0267aa83da7 ;
        bao:BAO_0002846  ap:076C0843 .

mgroup:XLSX-41595fe0-3c7b-4725-b209-f0267aa83da7
        a                bao:BAO_0000040 ;
        obo:OBI_0000299  ep:ID16867 , ep:ID16866 , ep:ID16865 .

ep:ID16866  a                 bao:BAO_0000179 ;
        rdfs:label            "EC50" ;
        ops:standardisedUnit  opsUnit:MicrogramPerMilliliter ;
        obo:IAO_0000136       substance:XLSX-adf890e9-3623-3a0e-b601-11f8e5e2f3cb ;
        sio:has-unit          "ug/ml" ;
        sio:has-value         "113.05101991460714"^^xsd:double .

@egonw may explain more about the RDF representation

ghost commented 7 years ago

Thanks, I can find LDH, ATP and MTT assays (I think I did not check before filing the issue)! But I was primarily interested in Cell viablility, does it have a different name?

ghost commented 7 years ago

Just for my understanding: Whats the purpose of measurement groups (mgroup)?

vedina commented 7 years ago

yes, there is an ontology term for cell viability, but cell viability is an endpoint, measured by any of these three assays

vedina commented 7 years ago

The measure group is one of the concepts of the BAO data model, which is used by the RDF serialisaiton for substances and studies here. This paper describes the BAO data model . There is nice illustration , including measure group https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4108877/figure/F5/

(very roughly speaking it's a way to represent one assay may measure more than one value) You may notice the picture shows hierarchical organisation of measure groups, we are not supporting this yet, but will in very near future.

ghost commented 7 years ago

Thanks for clarification!