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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

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