ChEMBL Resources

Resources:
ChEMBL
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SureChEMBL
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ChEMBL-NTD
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ChEMBL-Malaria
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The SARfaris: GPCR, Kinase, ADME
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UniChem
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DrugEBIlity
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ECBD

Wednesday, 28 March 2018

Have you heard of CORBEL?






Briefly, CORBEL is an initiative of thirteen biological and medical research infrastructures, which together create a platform for harmonised user access to biological and medical technologies, biological samples and data services required by cutting-edge biomedical research.

Do you know that ChEMBL, through ELIXIR, participates to the project and provides its expertise in, among other things, identification of existing bioactivities for compounds of interest, profiling of chemotypes, target identification, data storage and distribution? But of course, CORBEL gives you access to different services working in many different biomedical areas. You want to screen the compounds you have identified and then use Electron Microscopy to observe their effect on a cell type of your interest, there are services for you! This is just an example of how CORBEL can contribute to boost your research projects(s), don’t forget we are  37 partners!  

As part of the WP4, Community Driven Cross-Infrastructure joint research – Bioscience, we were recently in Berlin to attend a Service Operator meeting and to meet the CORBEL users that requested our contribution to their project. That was a great opportunity to talk with them about their work and how ChEMBL could help them to achieve great things!

To keep it short, let’s just add that CORBEL has just launched a 2nd Open Call. To get an idea of what that might look like please have a look at the 1st Open Call selected projects. That might be the opportunity for you to submit your project and, if you request our help, for us to assist you in your work!



https://europa.eu/european-union/sites/europaeu/files/docs/body/flag_yellow_high.jpg
This project has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 654248

Tuesday, 6 March 2018

ChEMBL tissues: Increasing depth, breadth and accuracy of annotations



Our current tissue annotation efforts have been on increasing the breadth and depth of the tissue effort first started in ChEMBL 22. The figure above represents the increased depth and coverage from that initial point till now. 

We continue to use a suite of tissue ontologies namely: Uberon, Experimental Factor Ontology (http://www.ebi.ac.uk/ols/ontologies/efo), CALOHA (ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/caloha.obo) and Brenda Tissue Ontology ((http://www.ebi.ac.uk/ols/ontologies/bto)  to identify assays where the tissue is the assay system. We have increased the detail of information we capture to reflect the more granular tissues mentioned in the assays such as 'Popliteal lymph node' and 'Substantia nigra' pars compacta where previously the higher level term ‘lymph node’ and ‘Substantia nigra’ might have been captured.

Plasma based assays

We have recently focused annotation efforts on plasma based assays  in response to end user interest in this assays as well as acknowledging the general prevalence of plasma as an assay system for many functional/ADME assays.

Assays with multiple tissue types
We have also increased tissue curation of bioassays whose measurements are recorded across multiple tissues in a single assay e.g ‘Kidney/Liver’, ‘Heart/Liver’. In these cases, bespoke entries are created in the Tissue Dictionary, representing the tissue combination.
 
Ongoing improvements to tissue curation

·      These newly created tissue targets and assays annotated with these will be available in the next ChEMBL release (ChEMBL 24).
·      Our future web interface tissue search functionality will also make use of hierarchies inherent in the tissue ontologies to retrieve the more granular tissue terms on searching with a higher level term. An example would be that a tissue search for a high level term would include child terms of the higher level term e.g  A search for assays annotated with the tissue ‘compound eye’ UBERON:0000018 should also ideally retrieve assays annotated with direct children of this higher level term e.g ommatidium (UBERON:0000971).
·      The nature of ontological terms is such that species differences may not always be abundantly clear where single tissue term is used across different taxonomic groups to describe tissues that perform the same function in the different species but have clear anatomical differences. An example being the term eye which refers to the ‘compound eye’ UBERON:0000018 found in insects vs ‘camera type eye’ UBERON:0000019 as found in humans. We plan to use taxonomic constraint information to disambiguate cases like these and improve the correctness of mappings.
 
For queries and questions on tissue annotation-related matters please contact our help desk chembl-help@ebi.ac.uk