I think you may have misunderstood the OMIM note:
I think they are requesting donations, in order to remain freely available, though either of the current interfaces:
https://www.ncbi.nlm.nih.gov/omim
Also, if there was some issue with OMIM, I think ClinVar may be better for rare diseases than the GWAS Catalog (and sometimes you can find specialized databases for your disease of interest). However, it doesn't hurt if you can get both sets of annotations :)
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This depends on what kind of information you are interested in.
genes(mutations) and phenotype.