Add genereview links from MedGen FTP to release output has ROBOT template

[matentzn]

For context, read https://github.com/monarch-initiative/mondo/issues/7425

What we need:

A simple three column ROBOT template

mondo_id	linkout	source
ID	A rdfs:seeAlso	>A oboInOwl:hasDbXref
MONDO:123	http://.....	MONDO:MEDGEN

linkout is a URL pointing to a genereviews page.

@twhetzel Prioritise this as you see fit! I think this is a quick one issue, and I think this should take no more than 3 hours to implement.

Note:

The question of how to find the genereviews page in the MedGen data needs to be answered first.

[joeflack4]

Yeah, haven't heard of this myself, and I don't see anything about it in the FTP files that I currently have downloaded.

FTP dir search / analysis

``` pwd /Users/joeflack4/projects/medgen/ftp.ncbi.nlm.nih.gov grep -r review ./pub/medgen/MedGenIDMappings.txt:C0421312|Repeat prescription reviewed by hospital|601008|MedGen| ./pub/medgen/MedGenIDMappings.txt:C0421312|Repeat prescription reviewed by hospital|170930003|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C1278447|Medication review due|701503|MedGen| ./pub/medgen/MedGenIDMappings.txt:C1278447|Medication review due|314529007|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C1278448|Medication review done|314530002|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C1278448|Medication review done|701504|MedGen| ./pub/medgen/MedGenIDMappings.txt:C1303152|Repeat prescription reviewed by pharmacist|401176004|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C1303152|Repeat prescription reviewed by pharmacist|724640|MedGen| ./pub/medgen/MedGenIDMappings.txt:C1319528|Smoking review not indicated|728281|MedGen| ./pub/medgen/MedGenIDMappings.txt:C1319515|Diabetic retinopathy 12 month review|408384004|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C1319515|Diabetic retinopathy 12 month review|728271|MedGen| ./pub/medgen/MedGenIDMappings.txt:C1319516|Diabetic retinopathy 6 month review|408385003|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C1319528|Smoking review not indicated|408398007|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C1319516|Diabetic retinopathy 6 month review|728272|MedGen| ./pub/medgen/MedGenIDMappings.txt:C1445897|Medication review declined|412725004|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C1445897|Medication review declined|732909|MedGen| ./pub/medgen/MedGenIDMappings.txt:C1531679|Did not attend community psychiatric nurse review|413986001|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C1531679|Did not attend community psychiatric nurse review|734486|MedGen| ./pub/medgen/MedGenIDMappings.txt:C3698076|Did not attend asthma review|785340|MedGen| ./pub/medgen/MedGenIDMappings.txt:C3698076|Did not attend asthma review|699191007|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C4304287|Prostate cancer care review done|720008007|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C4304287|Prostate cancer care review done|929956|MedGen| ./pub/medgen/MedGenIDMappings.txt:C4304797|Medication review done by community pharmacist|719327002|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C4304797|Medication review done by community pharmacist|930466|MedGen| ./pub/medgen/MedGenIDMappings.txt:C4304798|Medication review done by pharmacy technician|719326006|SNOMEDCT_US| ./pub/medgen/MedGenIDMappings.txt:C4304798|Medication review done by pharmacy technician|930467|MedGen| ./pub/medgen/MedGenIDMappings.txt:C4316636|Imaging finding reviewed|940349|MedGen| ./pub/medgen/MedGenIDMappings.txt:C4316636|Imaging finding reviewed|452321000124100|SNOMEDCT_US| tree . └── pub └── medgen ├── HPO_CUI_history.txt ├── MERGED.RRF.gz ├── MGCONSO.RRF.gz ├── MGDEF.RRF.gz ├── MGG_BioconceptsUpdate.log ├── MGREL.RRF.gz ├── MGSAT.RRF.gz ├── MGSTY.RRF.gz ├── MONDO_CUI_history.txt ├── MedGenIDMappings.txt ├── MedGenIDMappings.txt.gz ├── MedGen_CUI_history.txt ├── MedGen_HPO_Mapping.txt.gz ├── MedGen_HPO_OMIM_Mapping.txt.gz ├── MedGen_Sources.txt ├── MedGen_UID_CUI_history.txt ├── NAMES.RRF.gz ├── ORDO_CUI_history.txt ├── README.txt ├── csv │   ├── MERGED.csv.gz │   ├── MGCONSO.csv.gz │   ├── MGDEF.csv.gz │   ├── MGREL.csv.gz │   ├── MGSAT.csv.gz │   ├── MGSTY.csv.gz │   └── NAMES.csv.gz ├── medgen_pubmed_lnk.txt.gz └── presentations └── Conditions_Phenotypes.pptx 5 directories, 28 files tree | grep review # nothing ```

[matentzn]

@kanems do you have gene review links on your FTP site?

[kanems]

@matentzn MedGen does not currently have an FTP report with the GeneReviews links. But GeneReviews provides info on their book and FTP site that could be useful to get the link format and mapping based on OMIM #. https://www.ncbi.nlm.nih.gov/books/NBK138605/ (If Mondo has a need/desire to get the GeneReviews links based on CUI mappings, we can discuss that in more detail, but it is not readily available at this time.)

[matentzn]

Thank you @kanems, very helpful!