Ontology problem ? or something else?

Dear all,

I came across a problem which may be related to the ontology. Maybe it’s nothing or maybe there is a ‘bug’.
Sometime, the target information we see in a particular cancer will not show up in the ultimate superior ontology like ‘Cancer’. Example: If you ask for information on target ‘STX10’, you will see a score (weak) of 0.02 in the TextMining score for the disease neuroblastoma. However, if you search per disease and type ‘cancer’, then filter on STX10 the score coming back is…none. (it should be note that it does not seems to be the case for some other targets I tried). Looking at the ontology of Neuroblastoma (see the picture below) indeed I don’t see the ontology neublastoma link to ‘Cancer’ (?). Is that the problem here?


Hi Nicolas,

Indeed the cancer branch of EFO had some important issues on the classification of certain tumours. Last month, EFO released v 3.33 which contains a major overhaul of the neoplasm branch:

EFO 3.33.0 release includes a major re-structuring of the neoplasm branch, utilising the hierarchy curated by Mondo in order to fix a few cases of incorrect parentage and to clean up term annotations. This is a large change in the ontology and therefore if there are any issues, please do not hesitate to get in touch. Additionally, 3.33.0 includes further alignments between EFO and MONDO as well as terms required for Open Targets projects, HCA, Array Express/Expression Atlas and the GWAS Catalog. Work is also continuing on improving our measurements branch.

EFO v3.33 will go live in the Open Targets Platform in the upcoming 21.09 release. You can explore the improved neuroblastoma classification from EBI OLS.

I hope this resolves your question

many thanks for your quick answer.
It does not “resolve” my problem, as it is one :slight_smile: but it does answer indeed my question and pinpoint that we better be careful around this issue! :slight_smile:
(PS. any date so far for the release :wink: ?)

We always aim for the last 7 working days of the month. Things are on track, so we might be on the earlier side of this window

Nice! thanks for the excellent job!