pcm32
commented
3 years ago Thanks @sfexova , this listing and criteria will prove very useful! @alfonsomunozpomer maybe the easiest fix for doing it in less than a week could be to add a file <Accession>.skip-anatomogram in the directory of the experiment and then when the web application sees that this file exists it could avoid showing the anatomogram for that accession (possibly keeping that decision cached I guess)? Otherwise we would need to go through the database and I reckon it would be more work. Cleaner in the long run though.
At the moment anatomograms are displayed whenever the [organism] is human and the [organism part] is one for which an anatomogram exists even if there is no data that can actually be displayed in the relevant anatomogram: e.g https://wwwdev.ebi.ac.uk/gxa/sc/experiments/E-GEOD-130473/downloads - is fetal liver (have anatomograms for adult tissues only) https://wwwdev.ebi.ac.uk/gxa/sc/experiments/E-HCAD-8/results/anatomogram - T-cells not part of the diagrams https://wwwdev.ebi.ac.uk/gxa/sc/experiments/E-MTAB-6653/results/anatomogram - don't have inferred cell types https://wwwdev.ebi.ac.uk/gxa/sc/experiments/E-GEOD-86618/results/anatomogram - don't have inferred cell types https://wwwdev.ebi.ac.uk/gxa/sc/experiments/E-CURD-11/results/anatomogram - don't have inferred cell types https://wwwdev.ebi.ac.uk/gxa/sc/experiments/E-MTAB-6308/results/anatomogram - don't have inferred cell type https://wwwdev.ebi.ac.uk/gxa/sc/experiments/E-HCAD-10/results/anatomogram - only have fetal data (not adult) https://wwwdev.ebi.ac.uk/gxa/sc/experiments/E-CURD-10/results/anatomogram - don't have inferred cell types
The best thing would be removing the anatomograms from these experiments before the public release if at all possible as displaying the anatomograms for these is not correct but a lasting change to the implementation logic may be too complicated to do in that time-frame - if yes, can we 'manually' remove them for now, before a permanent solution is found?
For future development I thing the logic for display should be [organism] - human, [developmental stage] - adult, [organism part] - anatomogram available, [inferred cell type - ontology labels] - available AND some terms therein or their parent terms are used in the relevant anatomogram stack But not sure how difficult this would be to implement (especially the last bit as that assumes ontology expansion for each ontology term used in an anatomogram is somehow available to check against) Also for placenta the [dev stage] is tricky as it's a part fetal/ part mother (adult) organ but that should be the only exception where the [dev stage] check would not be applicable