External resources used by the Scout server

External resources fetched by scout download

The scout download commands fetch the following external resources. scout download everything runs all of them (OMIM only if --api-key is given). Access is needed, from where the CLI runs, during database update and initial setup.

Command	Resource	URL	Defined in
omim	mim2gene	https://omim.org/static/omim/data/mim2gene.txt	scout/utils/scout_requests.py
omim	mimTitles, morbidmap, genemap2 (API key required)	https://data.omim.org/downloads/<api_key>/{mimTitles,morbidmap,genemap2}.txt	scout/utils/scout_requests.py
hpo	genes_to_phenotype, phenotype_to_genes, phenotype.hpoa	http://purl.obolibrary.org/obo/hp/hpoa/{genes_to_phenotype.txt,phenotype_to_genes.txt,phenotype.hpoa}	scout/constants/phenotype.py
hpo	HPO terms (hp.obo)	https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.obo	scout/constants/phenotype.py
orpha	Orpha to HPO	https://www.orphadata.com/data/xml/en_product4.xml	scout/constants/phenotype.py
orpha	Orpha to genes	https://www.orphadata.com/data/xml/en_product6.xml	scout/constants/phenotype.py
orpha	Orpha inheritance	https://www.orphadata.com/data/xml/en_product9_ages.xml	scout/constants/phenotype.py
clingen	Gene validity	https://search.clinicalgenome.org/kb/gene-validity/download	scout/constants/phenotype.py
clingen	Gene dosage	https://search.clinicalgenome.org/kb/gene-dosage/downloadall	scout/constants/phenotype.py
hgnc	HGNC complete set	https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt	scout/utils/scout_requests.py
exac	gnomAD v4.1.1 constraint metrics (tried in order, mirrors)	https://storage.googleapis.com/gcp-public-data--gnomad/release/4.1.1/constraint/gnomad.v4.1.1.constraint_metrics.tsv.bgz https://gnomad-public-us-east-1.s3.amazonaws.com/release/4.1.1/constraint/gnomad.v4.1.1.constraint_metrics.tsv.bgz https://datasetgnomad.blob.core.windows.net/dataset/release/4.1.1/constraint/gnomad.v4.1.1.constraint_metrics.tsv.bgz	scout/utils/scout_requests.py
ensembl	Genes, transcripts, exons (Ensembl BioMart via Schug)	https://schug.scilifelab.se/genes/ensembl_genes/?build=<GRCh37\|GRCh38> https://schug.scilifelab.se/transcripts/ensembl_transcripts/?build=<GRCh37\|GRCh38> https://schug.scilifelab.se/exons/ensembl_exons/?build=<GRCh37\|GRCh38>	scout/utils/ensembl_biomart_clients.py
panelapp	PanelApp panels (API)	https://panelapp.genomicsengland.co.uk/api/v1/panels/	scout/server/extensions/panelapp_extension.py

Schug is a SciLifeLab Clinical Genomics Solna service that provides a proxy to Ensembl BioMart. You are welcome to use it, or deploy a copy of that service on a machine of your own. The proxy is used to fetch gene, transcript and exon data for the different genome builds.

External resources contacted by the server at runtime

These are requested by the running Scout server (not by scout download), so the server needs outbound access to them.

Purpose	URL	Defined in
Genome build liftover (Broad Institute), used for alignment viewer coordinates and MARRVEL links	https://liftover-xwkwwwxdwq-uc.a.run.app/liftover/	scout/utils/broad_liftover_client.py
Refseq version lookup (NCBI Entrez), used in ClinVar submissions	https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=nuccore&term=<refseq>&idtype=acc	scout/utils/scout_requests.py
ClinVar submissions (default)	https://submit.ncbi.nlm.nih.gov/api/v1/submissions/ (test: https://submit.ncbi.nlm.nih.gov/apitest/v1/submissions/, override with CLINVAR_API_URL)	scout/constants/clinvar.py
HGVS validation (VariantValidator)	https://rest.variantvalidator.org/VariantValidator/variantvalidator/<build>/<descriptor>/select	scout/utils/hgvs.py
LitVar2 publication lookup	https://www.ncbi.nlm.nih.gov/research/litvar2-api/sensor/<rsid> https://www.ncbi.nlm.nih.gov/research/litvar2-api/variant/autocomplete/	scout/server/blueprints/variant/views.py
Rank model files (SNV and SV), old cases - likely other solution for KS	https://raw.githubusercontent.com/Clinical-Genomics/reference-files/master/rare-disease/rank_model/{rank_model,svrank_model}_-v<version>-.ini (configurable via RANK_MODEL_LINK_PREFIX / SV_RANK_MODEL_LINK_PREFIX)	scout/server/config.py, scout/adapter/mongo/rank_model.py
PanelApp panels (panel updates from the UI)	https://panelapp.genomicsengland.co.uk/api/v1/panels/	scout/server/extensions/panelapp_extension.py

Optional services configured by the admin (no fixed URL): Gens (GENS_HOST), Chanjo (SQLALCHEMY_DATABASE_URI), Chanjo2 (CHANJO2_URL), Scout Reviewer (SCOUT_REVIEWER_URL), tip2toe (PHENOPACKET_API_URL), Matchmaker Exchange (MME_URL), Beacon (BEACON_URL), Keycloak (KEYCLOAK), BioNano Access (BIONANO_ACCESS), and rerunner (RERUNNER_API_ENTRYPOINT).

Remote files used by the IGV browser (reference genomes, cytobands, public tracks) are fetched by the user's browser, not the server. They are defined in scout/constants/igv_tracks.py.