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Things to amend - March 2023 #1313
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There is a new version of the drug indications browser on the staging environment: The references are now more clearly separated by the chembl id where they come from: |
Hi @nclopezo e.g. When I look at the drug indications for e.g. SORAFENIB CHEMBL1336, then the first row of the compound report card indications shows CHEMBL1336 as the alternative form (but it is the parent!). See screenshot: The efo_id and efo_term are missing from the table in the compound report card? |
CHEMBL1699 (memantine hydrochloride) doesn't show any indications from the salt page (https://wwwdev.ebi.ac.uk/chembl/compound_report_card/CHEMBL1699/) but it does show indications from the parent page (https://wwwdev.ebi.ac.uk/chembl/compound_report_card/CHEMBL807/) |
Those problems should be fixed now. |
@nclopezo
|
There's also an issue with the link to Clinical Trials - but I believe the issue is either at the Clinical Trials end, or results from how we format the ClinicalTrial URL? e.g. this returns ALL results. https://clinicaltrials.gov/search?id=%22NCT02870569%22OR%22NCT03602495%22 But this returns the correct results: Do you have any comments about this? Paula and I think that Clinical Trials is in the process of updating their API, and this may be the issue? For their URL, do you think that we are incorrectly formatting the URL currently? ie something has changed in the formatting of the URL that we are not aware of? If you think that we need to change the method to format the URL, then please do say? Thanks for your advice! |
|
The default sorting has now been applied. |
@FionaEBI. Regarding the incoherence in the references, the data comes with those references. I guess this is not expected? @juanfmx2 The references for CHEMBL1336, with mesh id D013964, have the following data: {
"drug_indication" : {
"indication_refs_by_molecule" : {
"CHEMBL1200485" : [
{
"ref_id" : "NCT00095693",
"ref_url" : "https://clinicaltrials.gov/search?id=%22NCT00095693%22",
"ref_type" : "ClinicalTrials"
}
],
"CHEMBL1336" : [
{
"ref_id" : "NCT00887107,NCT01025453,NCT01141309,NCT01263951,NCT02084732,NCT02143726,NCT03565536",
"ref_url" : "https://clinicaltrials.gov/search?id=%22NCT00887107%22OR%22NCT01025453%22OR%22NCT01141309%22OR%22NCT01263951%22OR%22NCT02084732%22OR%22NCT02143726%22OR%22NCT03565536%22",
"ref_type" : "ClinicalTrials"
}
],
"CHEMBL4297490" : [
{
"ref_id" : "NCT02870569,NCT03602495",
"ref_url" : "https://clinicaltrials.gov/search?id=%22NCT02870569%22OR%22NCT03602495%22",
"ref_type" : "ClinicalTrials"
}
]
}
}
} And this is what is shown in the table. Is this incorrect? You can get the data with this query: GET chembl_drug_indication_by_parent/_search
{
"_source": "drug_indication.indication_refs_by_molecule",
"query": {
"bool": {
"must": [
{
"terms": {
"drug_indication.parent_molecule_chembl_id": [
"CHEMBL1336"
]
}
},
{
"terms": {
"drug_indication.mesh_id": [
"D013964"
]
}
}
]
}
}
} |
@nclopezo
select md.chembl_id, md.pref_name, ind., iref. And I've put a screenshot of the sql results: Please can we discuss this further? I'd like to know how the Elastic Search query is created - where exactly does it take the data from? Please can you point me to the code? Thanks. 2 re url links: |
The query to get the data is created like this:
From the indications obtained in the query, it looks at the |
There is a new page for Drug Mechanisms available on wwwdev: https://wwwdev.ebi.ac.uk/chembl/ @juanfmx2, for drug indications, the way it decides if the section is shown is
But I didn't find an easy way to do it for drug mechanisms on the In the old version it just waits until the data is loaded, and if no mechanisms are received it hides the section. I would prefer to do it from a property on the |
Amend the drug_indications and drug_mechanism section of the compound report card so that parent and alternative drug forms are clearly specified (use the existing example that we have for drug_warnings on the compound report card)
Drop the section of the compound report card called “Clinical Data” because the link to clinical trials is not curated data, and the link to the Cochrane Data is nothing to do with ChEMBL as far as we are aware (this was part of the old interface)
Amend the drug_mechanisms section of the compound report card so that any salt data is aggregated onto the parent drug. But salt data is not assigned (sideways) to the other salts within a compound family. This would make the mechanism data consistent with drug_indications and drug_warning data.
Create a “source” bubble on the front page that has a table that can link each source to the various ChEMBL entities (compounds, targets, assays, documents etc).
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