Should CAS numbers be in ChEMBL and/or UniChem?

A very quick survey to add excitement to either your holiday or work-day! None of these sucker links, where there appears a 0.24% complete progress bar on the second page, it's just a simple yes/no question on whether it's a good idea to add CAS registry numbers to ChEMBL and/or UniChem. No promises that we could deliver this, but depending on what you vote for, we will consider our options.

Update: Given the multiple channels out there, there are also comments on this on LinkedIn (in the ChUG - "ChEMBL User Group" group - why not join, if you're not already) and a couple on Google+.

Update 2: I'll let the poll run till the end of the week (Friday 8th 2014) - and then write something up on the results.

Comments

Egon Willighagen said…

I would argue against this. The CAS registry number is proprietary and not easy to use. Particularly, you are not allowed to collect them, though they have an informal limit at 10k registry numbers. This causes serious licensing issues with ChEMBL: you will have to make it a separate database and release it separate files. CC-BY-SA does not allow further restrictions such as those imposed for the CAS registry number.

1 August 2014 at 12:15

jpo said…

I would disagree with the statement that I'm not allowed to collect them. How can anyone stop me from public sources of course. For example, is there a license carve out on the wikipedia CAS numbers? wikipedia content is CC-BY-SA, so perfect alignment with the current ChEMBL license. There are lots of other sources of large sets of CAS RNs - NCI resolver, ChemSpider, PubChem, UNII). There are also many on public, non-copyrighted documents, patents, INN/USAN documents, etc. To say that i'm not allowed to do anything with them, is just bonkers.

There is a formal limit of 10K, if you sign (or your organisation, with relevant scope of the license).

I'm of mixed view myself as to whether it is worth doing something with ChEMBL - hence to poll - see what the community thinks. For some of the stuff I'm currently working on (clinical candidate disclosures) they are required, and I have never seen a statement to say I can't reuse them in any document I've come across). The whole idea is that they (CAS RNs) are useful to cross reference chemical (and biological) objects with systems that choose to use them.

Sorry for briefish reply, holiday, and just back from the beach with wet trunks!

1 August 2014 at 13:08

jpo said…

1 August 2014 at 13:08

SureChEMBL Available Now

Followers of the ChEMBL group's activities and this blog will be aware of our involvement in the migration of the previously commercially available SureChem chemistry patent system, to a new, free-for-all system, known as SureChEMBL. Today we are very pleased to announce that the migration process is complete and the SureChEMBL website is now online. SureChEMBL provides the research community with the ability to search the patent literature using Lucene-based keyword queries and, much more importantly, chemistry-based queries. If you are not familiar with SureChEMBL, we recommend you review the content of these earlier blogposts here and here . SureChEMBL is a live system, which is continuously extracting chemical entities from the patent literature. The time it takes for a new chemical in the patent literature to become searchable in the SureChEMBL system is 1-2 days (WO patents can sometimes take a bit longer due to an additional reprocessing step). At time of writi

New SureChEMBL announcement

(Generated with DALL-E 3 ∙ 30 October 2023 at 1:48 pm) We have some very exciting news to report: the new SureChEMBL is now available! Hooray! What is SureChEMBL, you may ask. Good question! In our portfolio of chemical biology services, alongside our established database of bioactivity data for drug-like molecules ChEMBL , our dictionary of annotated small molecule entities ChEBI , and our compound cross-referencing system UniChem , we also deliver a database of annotated patents! Almost 10 years ago , EMBL-EBI acquired the SureChem system of chemically annotated patents and made this freely accessible in the public domain as SureChEMBL. Since then, our team has continued to maintain and deliver SureChEMBL. However, this has become increasingly challenging due to the complexities of the underlying codebase. We were awarded a Wellcome Trust grant in 2021 to completely overhaul SureChEMBL, with a new UI, backend infrastructure, and new f

ChEMBL & SureChEMBL anniversary symposium

In 2024 we celebrate the 15th anniversary of the first public release of the ChEMBL database as well as the 10th anniversary of SureChEMBL. To recognise this important landmark we are organising a two-day symposium to celebrate the work achieved by ChEMBL and SureChEMBL, and look forward to its future. Save the date for the ChEMBL 15 Year Symposium October 1-2, 2024 Day one will consist of four workshops, a basic ChEMBL drug design workshop; an advanced ChEMBL workshop (EUbOPEN community workshop); a ChEMBL data deposition workshop; and a SureChEMBL workshop. Day two will consist of a series of talks from invited speakers, a few poster flash talks, a local nature walk, as well as celebratory cake. During the breaks, the poster session will be a great opportunity to catch up with other users and collaborators of the ChEMBL resources and chat to colleagues, co-workers and others to find out more about how the database is being used. Lunch and refreshments will be pro

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 vaccines). 71 out of the 882 newly added EMA drugs are only authorised by EMA, rather than from other regulatory bodies e.g.

RDKit, C++ and Jupyter Notebook

Fancy playing with RDKit C++ API without needing to set up a C++ project and compile it? But wait... isn't C++ a compiled programming language? How this can be even possible? Thanks to Cling (CERN's C++ interpreter) and xeus-cling jupyter kernel is possible to use C++ as an intepreted language inside a jupyter notebook! We prepared a simple notebook showing few examples of RDKit functionalities and a docker image in case you want to run it. With the single requirement of docker being installed in your computer you'll be able to easily run the examples following the three steps below: docker pull eloyfelix/rdkit_jupyter_cling docker run -d -p 9999:9999 eloyfelix/rdkit_jupyter_cling open http://localhost:9999/notebooks/rdkit_cling.ipynb in a browser

The ChEMBL-og

Search This Blog