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Add new data table for additional target safety information #609

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andrewhercules opened this issue May 22, 2019 · 10 comments

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@andrewhercules
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commented May 22, 2019

New data table will be added to Target Safety block with known risks.

A full design spec will be completed once data has been processed by @EPetsalaki.

@EPetsalaki

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commented May 22, 2019

Here is a first version of the new json file for 19_06: known safety data. It needs minor editing in the text, but the json schema should remain the same.

New fields:

  • known safety split into 2 sections: adverse effects and safety liability. Targets CDK2 and AKT1 have both safety liability and adverse effect information.
  • safety liability has reference info, organs affected and a string field with the safety information (NOT EFO-mapped list of side effects)
  • reference format is changed into a list (was string). 3 fields for reference info (all list format): reference (author names), pmid & ref_link. The reference links are provided if no pmid is available. If there is both a reference link and a pmid, use the pmid.
  • additional field "unspecified interaction effects" within adverse effects section (if we don't know if it's activation or inhibition effects). No data currently in this field, but we are expecting to have some there soon, so this is included as well so that we can decide on how to show these.
@andrewhercules

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commented May 24, 2019

@EPetsalaki, can we please update the references to return a list of objects with ref_label, ref_link, and pmid attributes?

"references": [
    {
        "ref_label": "Bowes et al. (2012)",
        "ref_link": "",
        "pmid": "23197038",
    },
],

or

"references": [
    {
        "ref_label": "Urban et al. (2012)",
        "ref_link": "https://doi.org/10.1002/9781118098141.ch2",
        "pmid": "",
    },
    {
        "ref_label": "HeCaToS_2.2",
        "ref_link": "https://www.hecatos.eu/home",
        "pmid": "",
    }
],
@EPetsalaki

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commented May 24, 2019

Done! Please find the new file (24th May) here.

@andrewhercules

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commented May 24, 2019

Thanks @EPetsalaki - looks great! 👍

@andrewhercules

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commented May 24, 2019

Building on the work done for #460, there are some changes that we will make for the upcoming 19.06 release as there is new safety_risk_info data to display.

Updated designs

Existing data table (e.g. ACHE)

target_safety_ache

New data table for safety_risk_info data (e.g. MTOR or PIK3CA

target_safety_mtor

Layout change if both adverse_events and safety_risk_info data is available (e.g. AKT1 or CDK2)

target_safety_akt1

Updated interaction notes

To accommodate the new data, can we please:

  1. Update the tab description text box to read Known safety effects and safety risk information for HGNC-GENE-SYMBOL

  2. Add a heading to each table - Known safety effects and Safety risk information

  3. Create a new data table for the safety_risk_info with the following columns - Main organs and systems affected, Safety liability information, and Publications

  4. If both data tables are displayed, reuse the same layout used for tabs that have multiple tables (e.g. Genetic evidence tab for ESR1 and genetic disorder) similar

Also, there is a change in how the data used for the Publications column in both data tables is returned by the API. Previously, they were individual values, but to accommodate multiple values for a single row, it will now be an array of objects found in the references attribute.

For example

"references": [
    {
        "pmid": "",
        "ref_link": "https://doi.org/10.1002/9781118098141.ch2",
        "ref_label": "Urban et al. (2012)"
    },
    {
        "pmid": "",
        "ref_link": "https://www.hecatos.eu/home",
        "ref_label": "HeCaToS_2.2"
    }
],

or

"references": [
    {
        "pmid": "21283106",
        "ref_link": "",
        "ref_label": "Force et al. (2011)"
    },
    {
        "pmid": "",
        "ref_link": "https://www.hecatos.eu/home",
        "ref_label": "HeCaToS_5"
    }
],

Can we please display the ref_label and construct a link to EuropePMC using the pmid value. However, if the pmid is not available, please construct to the ref_link value instead.

@EPetsalaki

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commented Jun 4, 2019

Hello, can we use a tooltip on the 'HeCaToS' reference? The content that should appear in the tootip is 'HeCaToS Deliverable D01.5 (2015) funded by "EU 7th Framework Programme (HEALTH-F4-2013-602156)."'

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 11, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 11, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 11, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 11, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 11, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 11, 2019

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 11, 2019

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commented Jun 11, 2019

@EPetsalaki ideally that tooltip would come with the API response, otherwise we have to start matching strings in front end... what do you think @andrewhercules ?

@d0choa

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commented Jun 11, 2019

Correct me if I’m wrong @EPetsalaki or @andrewhercules but I think we discussed to do it in the front-end.

It’s a very particular thing. It won’t change for HeCaTos and it’s unlikely we have others in the near future.

@andrewhercules

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commented Jun 11, 2019

@d0choa, yes we decided to do it on the front-end because it is a very specific issue and the entire safety section will go through further iterations as more safety data is added.

@LucaFumis, can you please include the tooltip? I know it's not ideal but it's short-term until more safety data (e.g. buckets) are ready. :-)

LucaFumis added a commit to opentargets/webapp that referenced this issue Jun 12, 2019

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commented Jun 12, 2019

As per discussion with @andrewhercule, added standard title attribute for HeCaTos link which shows on rollover after a second or so.

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