Comments (7)
Hi!
Thanks for the chembl_webresource_client
- we are using it at @volkamerlab a lot!
My question is related to @czodrowskilab's question here (I think), so I'll add it here.
Is there a field for the date when
- a compound or
- a bioactivity
was added to ChEMBL?
I know of the document_year
field, which I can fetch for bioactivities:
bioactivities = bioactivities_api.filter(
target_chembl_id='CHEMBL941').only(
'activity_id',
'document_year'
)
)
Given the ChEMBL database scheme, I guess it works as follows:
From doc_id
(field) in activities
(table) go to doc_id
(field) in docs
(table) and extract year
(field).
This probably also works similarly for compounds.
However, the document's year
- does not necessarily did to equal the bioactivity or compound deposition date in ChEMBL and
- does not need to be the same for compounds and bioactivities, right?
Thus, back to my question: What is the best way to filter compound or bioactivity entries in ChEMBL by their deposition date?
Thank you for your time.
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Hi, sorry for not having replied this before.
As Dominique says, this is currently not possible but we are working towards supporting it on future ChEMBL versions.
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I am realizing:
The deposition date probably equal the ChEMBL version in which the compound/bioactivity was added.
Is there a way to access the version?
In the ChEMBL scheme, the version table seems not to be connected with any other table:
https://www.ebi.ac.uk/chembl/db_schema
from chembl_webresource_client.
Update on this matter:
The ChEMBL support team (https://www.ebi.ac.uk/support/) let me know that it is currently not possible to extract data from the web services (or the
interface) for a previous ChEMBL release.
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Dear ChEMBL team,
Thank you for chembl_webresource_client
. Is there any update on whether the version could be directly/indirectly linked to an activity record?
Like @czodrowskilab, I am also interested in splitting the activity data for a target by chembl version in which it first appeared (to mimic time-split).
Thanks,
Vishal
from chembl_webresource_client.
We are working on implementing time stamps for deposited data sets. We are exploring how to deal with updates of documents now. Tentatively, we'll release this with CHEMBL 34.
from chembl_webresource_client.
However, time stamps for data sets are already available ( and have always been) via the VERSION
table which includes CREATION_DATE
for every ChEMBL release. By querying for which release a document has been added, you'll get your time stamps. After we've solved the question about updated documents, we plan to make that information more easily accessible, likely via a new table.
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Related Issues (20)
- .filter for different names in "document_journal" column HOT 1
- Query hangs after reaching specific entry HOT 1
- Error for url https://www.ebi.ac.uk/chembl/api/data/activity.json, server response: <!doctype html> HOT 6
- Mechanism results do not match what is on the website HOT 3
- Isomeric SMILES string
- Problem with unichem.structure HOT 4
- Http Application error HOT 5
- Querying by inchi
- new_client is failing to import from chembl_webresource_client HOT 1
- Assay offsets and limit HOT 2
- How do I retrieve the Unichem Cross references as a dictionary/list for a CHEMBL compound?
- Fail to import new_client due to API problem HOT 5
- Fixed
- Space between words of the query
- HttpApplicationError HOT 8
- confidence score
- Error for url
- ChEMBL webresourse client issue
- status 500 with chembl_webresource_client.new_client
- Problem of parallelized big data mining via batch chunks
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