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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