dipper
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monarch-initiative
Data Ingestion Pipeline for Monarch
The current README is a dead-end as far understanding anything about the modeling used in dipper, how to download the results, etc. At the same time the docs are too...
The ZFIN UI shows links from FISH phenotypes to published figures showing supporting data. Data download only show links from FISH to figures (see file [here](https://zfin.org/downloads/genofig_fish.txt)) - so it is...
Now that we're getting close to having the ClinVar XML in dipper, we should determine if the tab delimited file is still needed.
some of the genes in omia are fake identifiers created by OMIA themselves, but we're converting to NCBIGene. these need to be fixed. i _think_ they are all prefixed with...
The DIPper pipeline creates oban:Associations for each G2P link it ingests from each data source, dumping these into output ttl files that get loaded into SciGraph. These Associations represent an...
Making a ticket here for tracking purposes, here is the time line of events: RGD implemented - https://github.com/monarch-initiative/dipper/pull/516 RGD broken - Jan 2018 @putmantime proposed fix - https://github.com/monarch-initiative/dipper/pull/563 (closed without...
species.ab.gz https://github.com/monarch-initiative/dipper/blob/7c4cbb834f295d9929574d1a3c8f1d1ad698208e/dipper/sources/FlyBase.py#L95 does not exist. fbal_to_fbgn_fb.tsv.gz https://github.com/monarch-initiative/dipper/blob/7c4cbb834f295d9929574d1a3c8f1d1ad698208e/dipper/sources/FlyBase.py#L109 does not exist.
First pass ingest of ClinVar-XML (#276)) only pulled minimal evidence and provenance information. As SEPIO matures, we will soon be at a point where we can revisit this source to...
188 variants in the latest ingest are rdf:type'd as a zygosity, such as GENO:0000402 (compound heterozygous) For example: ``` . ``` We should be using GENO:0000608 (has_zygosity) instead of rdf:type
For example the row: ``` 2020-06-25 25555482 Gelernter J 2014-09-16 Biol Psychiatry www.ncbi.nlm.nih.gov/pubmed/25555482 Genome-wide association study of nicotine dependence in American populations: identification of novel risk loci in both African-Americans...