Quality Control - ISH
Aim:
To check the quality of the annotated high-resolution renal ISH data in GUDMAP against data in peer-reviewed, published literature.
Method:
- For each gene 'xxx' in the annotated, high resolution, ISH entries in GUDMAP, search PUBMED for xxxx kidney.
- Manually select abstracts that look as if they have ISH data in them.
- Filter these for coincidence (or near-coincidence) with the stage(s) in GUDMAP.
- View the ISH in the papers and read the text and score for agreement or disagreement with GUDMAP. Note when published text is wrong with respect to published figures (this sometimes happens when a paper is really about other organs and mentions kidney in passing: it is common for any tube-like things to be called a 'glomerulus').
Results:
There were 78 genes that appeared in both high-resolution GUDMAP ISH and Pubmed ISH: of these, 14 had entries in both GUDMAP and publications that covered the same developmental stage. 71% agreed completely, 14% showed partial agreement with no actual disagreement (this means that the paper and GUDMAP studied sets of renal structures that overlap only partially; for example the ureter was visible in only one data set and annotation). 14% showed disagreement in text but not in the images: in each case the GUDMAP annotation was correct and the other obviously wrong.
