dipper

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Please note: `https://raw.githubusercontent.com/biolink/biolink-model/master/biolink-model.yaml` will no longer be available at this path in biolink 4.0.0. Instead it will be here: https://raw.githubusercontent.com/biolink/biolink-model/master/project/owl/biolink-model.owl.ttl or via w3id here (this is still the same link...

sierra-moxon

# Patching CVE-2007-4559 Hi, we are security researchers from the Advanced Research Center at [Trellix](https://www.trellix.com). We have began a campaign to patch a widespread bug named CVE-2007-4559. CVE-2007-4559 is a...

TrellixVulnTeam

Temporal ordering of phenotypes in both the curated data and algorithms

14

Include temporal ordering of phenotypes in both the curated data and algorithms, allowing search for models that recapitulate patterns of phenotype progression As per R24 [here](https://docs.google.com/document/d/1s5waFXyzyYz8oZe6MYZ4WwTb1BzdTgki-PiQ7JTmRfE/edit) cc: @pnrobinson

jmcmurry

STRING download hostname is different from main STRING hostname

RichardBruskiewich

Fix 'is biomarker for' relationship by either renaming it or removing it when not appropriate

4

The current is_biomarker relationship is almost always picking out items that are not biomarkers for the disease. Can we consider renaming the relation type to something that is less committal....

pnrobinson

Refine content and use of the curie-map.yml for identifiers site-wide

4

See for example: http://monarchinitiative.org/disease/DOID:14330 Fix inconsistencies: - [ ] see `MSH` and `MESH` both used above in the UI vs `MESH` in the curie map - [ ] Eg. `SNOMEDCT_US_2015_03_01`...

jmcmurry

Use obo foundry unique label in ingests of species-specific resources

1

E.g. `hgnc:1 :iao:obo-foundry-unique-label "Shh (human)"`

cmungall

Pharos https://pharos.nih.gov/idg/index TCRD http://juniper.health.unm.edu/tcrd/ DrugCentral http://drugcentral.org/ kindly add them as Sources in Monarch

TudorOprea

Pull in drug response phenotypes and protective variants from ClinVar

1

For example: https://www.ncbi.nlm.nih.gov/clinvar/variation/722/ - NAT2 variant and OMIM:243400 (Slow Acetylation) We could pull these in if there is an associated OMIM or medgen identifier. Protective variant: https://www.ncbi.nlm.nih.gov/clinvar/variation/4467/

kshefchek

odd identifier to protein showing up for NCBI gene

7

For example: human NCBI:5435. Searching for the encoding gene via the ENCODES relation returns several ENSEMBL proteins, UniProtKB:P61218, itself, and (oddly) "**:.well-known/genid/NCBIGene5435product**" Clearly not a legit ID

selewis