UniChem - An EBI compound structure cross-referencing resource

We have faced for some time some issues with compound integration with ChEMBL - specifically the loading of compound sets into ChEMBL for cross referencing, between for example, ChEBI, PDBe compounds, etc. The ChEMBL update cycle is relatively slow with respect to some other resources, and there is inevitable thrash with compounds not being present, especially for exciting new data. Without doing something different for compound integration, we were starting to face a scenario where we had a compound table with many millions of compounds without any bioactivity data, and following this the inevitable slowdown in searching, etc.

We also had some issues facing us about curation of other people's primary data, changing compound structures, or their rendering, etc.

So, we decided to set up an external system to resolve cross-references between various databases. This is a very simple Standard InChI lookup, containing compounds from resources such as ChEMBL, ChEBI, PDBe, DrugBank, KEGG, BindingDB, PubChem, and so forth. UniChem can also handle versioning of the contained resources. We will be migrating various components of the current ChEMBL interface across to use web services on UniChem, this way, the cross links will always be fresh and correct, and we can focus on curation and optimisation of ChEMBL content. There are some other resources, like ZINC, STITCH, and ChemSpider, for example, that would be great to integrate, if we can get hold of the required data.

The easiest way for us to handle deposition into UniChem is for us to take an ftp: feed of a simple table of resource_id, standard_InChI, and standard_InChI_key.

At the moment, UniChem sits behind our firewall, but if people want to have a play, let us know.

We will write something more specific and detailed, but would welcome thoughts of whether this resolver should be externally facing, and what other resources would be good to integrate?

The image above may or may not be the UniChem logo.

Comments

Michael Kuhn said…

So the idea is that you give UniChem an InChIKey, and get back the identifiers of the source databases? To some extent, this already works in PubChem:
http://www.ncbi.nlm.nih.gov/pcsubstance?term=KEGG%5Bsource%5D%20%20BSYNRYMUTXBXSQ-UHFFFAOYSA-N" Although you don't control the versions, of course.

Regarding STITCH, we're downstream of PubChem and also don't create new interactions that you could integrate into ChEMBL. Therefore, it's probably easiest to leave STITCH out of UniChem and rather link to STITCH via InChIKey:
http://stitch.embl.de/interactions/BSYNRYMUTXBXSQ-UHFFFAOYSA-N

~Michael

25 November 2011 at 12:26

jpo said…

Thanks for the comment. I guess the linking out to STITCH via InChI key is one-way only (or at least practically is one-way).

We should have simple cross reference to STITCH in a future version of the ChEMBL interface.

Longer term we have a plan with UniChem to provide some additional services off this, such as a trivial name/synonym service, etc. Keeping on top of names is a real pain for us, and others do it really well.

27 November 2011 at 10:03

fredrik said…

I think it would be really great with the addition of some vendor databases like emolecules.com. To have the ability to filter ChEMBL based on commercial availability would give great benefits.

/Fredrik

28 November 2011 at 10:43

Unknown said…

You can already get a purchasable subset of ChEMBL via ZINC. Both ChEMBL15 http://zinc.docking.org/pbcs/chembl15 and ChEMBL DrugStore http://zinc.docking.org/pbcs/drugstore. The molecules are in ready-to-dock formats, free to download. We also offer purchasable subsets of many other subsets like IUPHAR, FDA, DrugBank, bindingdb, and also supersets, like all purchasable natural products, metabolites, drugs, in man compounds, etc, etc.

25 February 2013 at 06:26

Here's a nice Christmas gift - ChEMBL 35 is out!

Use your well-deserved Christmas holidays to spend time with your loved ones and explore the new release of ChEMBL 35! This fresh release comes with a wealth of new data sets and some new data sources as well. Examples include a total of 14 datasets deposited by by the ASAP ( AI-driven Structure-enabled Antiviral Platform) project, a new NTD data se t by Aberystwyth University on anti-schistosome activity, nine new chemical probe data sets, and seven new data sets for the Chemogenomic library of the EUbOPEN project. We also inlcuded a few new fields that do impr ove the provenance and FAIRness of the data we host in ChEMBL: 1) A CONTACT field has been added to the DOCs table which should contain a contact profile of someone willing to be contacted about details of the dataset (ideally an ORCID ID; up to 3 contacts can be provided). 2) In an effort to provide more detailed information about the source of a deposited dat...

Improvements in SureChEMBL's chemistry search and adoption of RDKit

Dear SureChEMBL users, If you frequently rely on our "chemistry search" feature, today brings great news! We’ve recently implemented a major update that makes your search experience faster than ever. What's New? Last week, we upgraded our structure search engine by aligning it with the core code base used in ChEMBL . This update allows SureChEMBL to leverage our FPSim2 Python package , returning results in approximately one second. The similarity search relies on 256-bit RDKit -calculated ECFP4 fingerprints, and a single instance requires approximately 1 GB of RAM to run. SureChEMBL’s FPSim2 file is not currently available for download, but we are considering generating it periodicaly and have created it once for you to try in Google Colab ! For substructure searches, we now also use an RDKit -based solution via SubstructLibrary , which returns results several times faster than our previous implementation. Additionally, structure search results are now sorted by...

ChEMBL 34 is out!

We are delighted to announce the release of ChEMBL 34, which includes a full update to drug and clinical candidate drug data. This version of the database, prepared on 28/03/2024 contains: 2,431,025 compounds (of which 2,409,270 have mol files) 3,106,257 compound records (non-unique compounds) 20,772,701 activities 1,644,390 assays 15,598 targets 89,892 documents Data can be downloaded from the ChEMBL FTP site: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/ Please see ChEMBL_34 release notes for full details of all changes in this release: https://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_34/chembl_34_release_notes.txt New Data Sources European Medicines Agency (src_id = 66): European Medicines Agency's data correspond to EMA drugs prior to 20 January 2023 (excluding ...

Improved querying for SureChEMBL

Dear SureChEMBL users, Earlier this year we ran a survey to identify what you, the users, would like to see next in SureChEMBL. Thank you for offering your feedback! This gave us the opportunity to have some interesting discussions both internally and externally. While we can't publicly reveal precisely our plans for the coming months (everything will be delivered at the right time), we can at least say that improving the compound structure extraction quality is a priority. Unfortunately, the change won't happen overnight as reprocessing 167 millions patents takes a while. However, the good news is that the new generation of optical chemical structure recognition shows good performance, even for patent images! We hope we can share our results with you soon. So in the meantime, what are we doing? You may have noticed a few changes on the SureChEMBL main page. No more "Beta" flag since we consider the system to be stable enough (it does not mean that you will never ...

ChEMBL brings drug bioactivity data to the Protein Data Bank in Europe

In the quest to develop new drugs, understanding the 3D structure of molecules is crucial. Resources like the Protein Data Bank in Europe (PDBe) and the Cambridge Structural Database (CSD) provide these 3D blueprints for many biological molecules. However, researchers also need to know how these molecules interact with their biological target – their bioactivity. ChEMBL is a treasure trove of bioactivity data for countless drug-like molecules. It tells us how strongly a molecule binds to a target, how it affects a biological process, and even how it might be metabolized. But here's the catch: while ChEMBL provides extensive information on a molecule's activity and cross references to other data sources, it doesn't always tell us if a 3D structure is available for a specific drug-target complex. This can be a roadblock for researchers who need that structural information to design effective drugs. Therefore, connecting ChEMBL data with resources like PDBe and CSD is essen...

The ChEMBL-og

Search This Blog