Open PHACTS KNIME and Pipeline Pilot Components

Open PHACTS has released a collection of Pipeline Pilot and KNIME workflow components which integrate with the Open PHACTS API. Integration with these well-established graphical workflow tools allows the pharmacological and physicochemical data within the Open PHACTS Discovery Platform to be easily accessed and consumed.

Open PHACTS (Open PHArmacological Concepts Triple Store) is a project of the Innovative Medicines Initiative (IMI) and has seen SMEs, academia and the pharmaceutical industry work together to create a freely-available online platform to multiple, integrated sources of publicly available pharmacological data. The project ends in 2014 and the project’s not-for-profit successor organisation, the Open PHACTS Foundation, will continue to support and develop the infrastructure created.

The Open PHACTS Discovery Platform has been designed to answer various critical pharmacology questions, many of which can be addressed using the newly released Pipeline Pilot and KNIME nodes. The portal to the workflow integration collection can be found at dev.openphacts.org/workflow.

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PKIS data in ChEMBL

The Protein Kinase Inhibitor Set (PKIS) made available by GSK was recently mentioned on In the Pipeline . In collaboration with GSK, we are making the data being generated on these compounds available via the ChEMBL database. We are also creating a portal for the compound set, where the structures can be browsed and downloaded, direct links to the data are provided and useful information can be posted. A preliminary version is available here : feedback would be appreciated. The data generated on the PKIS set and deposited in ChEMBL may be downloaded in CSV format here (note that the Luciferase dataset described in the recent PLoS paper will be in the next release of ChEMBL). Alternatively, to view the data in the ChEMBL web interface, follow these steps: On the home page, enter 'GSK_PKIS' in the search box and click on the 'Assays' button... On the 'Please select...' menu on the right, choose 'Display Bioactivities'...

A python client for accessing ChEMBL web services

Motivation The CheMBL Web Services provide simple reliable programmatic access to the data stored in ChEMBL database. RESTful API approaches are quite easy to master in most languages but still require writing a few lines of code. Additionally, it can be a challenging task to write a nontrivial application using REST without any examples. These factors were the motivation for us to write a small client library for accessing web services from Python. Why Python? We choose this language because Python has become extremely popular (and still growing in use) in scientific applications; there are several Open Source chemical toolkits available in this language, and so the wealth of ChEMBL resources and functionality of those toolkits can be easily combined. Moreover, Python is a very web-friendly language and we wanted to show how easy complex resource acquisition can be expressed in Python. Reinventing the wheel? There are already some libraries providing access to ChEMBL d

Release of ChEMBL 33

We are pleased to announce the release of ChEMBL 33! This fresh release comes with a few new data soures and also some new features: we added bioactivity data for understudied SLC targets from the RESOLUTE project and included a flag for Natural Products and for Chemical Probes. An annotation for the ACTION_TYPE of a measurement was included for approx. 270 K bioactivities. We also time-stamped every document in ChEMBL with their CREATION_DATE! Have fun playing around with ChEMBL 33 over the summer and please send feedback via chembl-help@ebi.ac.uk . ChEMBL database version ChEMBL 33 release notes ___________________________________________ # This version of the database, prepared on 31/05/2023 contains: 2,399,743 compounds (of which 2,372,674 have mol files) 3,051,613 compound records (non-unique compounds) 20,334,684 activities 1,610,596 assays 15,398 targets 88,630 documents BioAssay Data Sources: Number Assays: Number

Data Deposition made easy

Bioactivity data in ChEMBL originates from two main sources: biomedical literature and data entering ChEMBL via data deposition. Over the years, we have seen an increase in deposited data sets (as shown in the Figure above). To make data deposition easier, we recently did some major updates to our deposition guide and supplemented it with a deposition video , and a brief checklist for depositors. Compound structural data must be supplied to the ChEMBL team in CTAB format / as MOL file. If a whole set of structures is supplied, then an SDF file is required. There are several ways to convert a list of SMILES to SDF. One way is to use our public ChEMBL Beaker API. Its functionalities are explained in more detail here and they can be tested interactively here . Just a few lines of code are needed to convert a list of SMILES strings into SD format. from chembl_webresource_client.utils import utils smiles = [ "CCO" , "CC(=O)C1=CC=CC=C1C(=O)O" , "CCN(CC)C(

Chemistry and Nature

As the Great Big Green Week (UK) draws to a close, so does EMBL-EBI’s own Sustainability week. The Wellcome Genome Campus held events in the areas of recycling, energy use, and biodiversity. The ChEMBL team was keen to get involved and we developed our own Nature Trail event highlighting some of the bioactive compounds from the flora and fauna found on-site, and elsewhere. Our favourite examples include the sensation of mint and chilli and the glorious smell of rain! The full Nature Trail can be made available for external Public Engagement events upon request . Databases, such as ChEMBL , are large stores of structured data, including genetic, biological, and chemistry data for life sciences research. Data on the natural world is often held by wildlife organisations; this can be used to research biodiversity and species decline. Various Citizen Science initiatives mean that everyone can get involved in submitting nature records. So why not join in with the Butterfly Conservation’s B

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