Add allele->genotype, allele->gene, gene->genotype associations from Alliance

[kevinschaper]

This may be an update to https://github.com/monarch-initiative/alliance-genotype-ingest/ rather than a whole new modular ingest. (in fact, there's commented out code for genotype to variant associations). Which may mean also needing to bring in allele to gene associations from an additional file.

It should probably pull from https://www.alliancegenome.org/downloads#variants-alleles for allele to gene (AlleleId, AlleleAssociatedGeneId), while the allele to genotype is found in the AGM files used in the allance-genotype-ingest already

I think the allele nodes will likely also be able to come from the variants-alleles file, using AlleleId, AlleleSymbol, AlleleSynonyms, VariantsTypeId.

I'm initially examining this by looking at the zebrafish file, and I'm seeing some odd looking concatenated pub IDs in the VariantInformationReference

ZFIN:ZDB-PUB-231023-61PMID:37868296,ZFIN:ZDB-PUB-200102-5,ZFIN:ZDB-PUB-211221-18PMID:34921227,ZFIN:ZDB-PUB-190209-15PMID:30733854

The concatenation is weird, but I think it would work fine to extract PMID:[\d]+ and just ignore the ZDB-PUB IDs, since they appear to be pointing to the same publications. (https://zfin.org/ZFIN:ZDB-PUB-231023-61 links to http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=search&db=PubMed&dopt=Abstract&term=37868296 for example)