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| .. _doc_datasources: | ||
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| =========== | ||
| Datasources | ||
| =========== | ||
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| This section documents the datasources used as input for the static data available in VarFish. | ||
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| The download and precomputation is done by the Snakemake workflow in ``varfish-db-downloader``. | ||
| This git repository uses continous integration with a reduced dataset (and some small data that is used from the repository directly, such as a list of curated microdeletion/-duplication regions from the literature) for automated testing. | ||
| The reduced dataset is downloaded automatically from URLs in a ``download_urls.yml`` file. | ||
| Thus, there is full transparency and traceability of the data sources used. | ||
| Further, a nightly CI job is run to check whether the URLs are still available (but not if the data has changed). | ||
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| .. _doc_datasources_repo: | ||
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| ------------------ | ||
| Data in Repository | ||
| ------------------ | ||
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| The following datasources are used directly from the repository. | ||
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| .. list-table:: | ||
| :header-rows: 1 | ||
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| * - Name | ||
| - License | ||
| - Synopsis | ||
| - Source | ||
| * - ACMG SF List v3.1 | ||
| - public domain | ||
| - Supplementary Findings Gene List of ACMG | ||
| - `PMID:35802134 <https://europepmc.org/article/med/35802134>`__ | ||
| * - DOMINO | ||
| - N/A | ||
| - Score for assessing the probability for a gene to harbour dominant changes | ||
| - Institute of Molecular and Clinical Ophthalmology Basel; `PMID:28985496 <https://europepmc.org/article/med/28985496>`__ | ||
| * - Enrichment Regions | ||
| - N/A | ||
| - Target regions of NGS enrichment kits | ||
| - `UCSC Table Browser <https://genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=map&hgta_track=exomeProbesets&hgta_table=MGI_Exome_Capture_V5&hgta_doSchema=describe+table+schema>`__ | ||
| * - Patho MMS | ||
| - N/A | ||
| - Curated regions for microdeletion and microduplication scores | ||
| - `PMID:36435749 <https://europepmc.org/article/med/36435749>`__ | ||
| * - sHet | ||
| - N/A | ||
| - Gene haploinsuffiency score | ||
| - `PMID:31004148 <https://europepmc.org/article/med/31004148>`__ | ||
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| .. _doc_datasources_downloaded_data: | ||
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| --------------- | ||
| Downloaded Data | ||
| --------------- | ||
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| The following datasources are downloaded from public internet resources. | ||
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| .. list-table:: | ||
| :header-rows: 1 | ||
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| * - Name | ||
| - License | ||
| - Synopsis | ||
| - Source | ||
| * - AlphaMissense | ||
| - `CC BY-NC-SA 4.0 <https://github.com/google-deepmind/alphamissense?tab=readme-ov-file#alphamissense-predictions-license>`__ | ||
| - AlphaMissense score | ||
| - `AlphaMissense <https://github.com/google-deepmind/alphamissense>`__ | ||
| * - CADD Score | ||
| - `free for non-commercial <https://cadd.gs.washington.edu/>`__ | ||
| - sequence variant pathogenicity scores | ||
| - `CADD <https://cadd.gs.washington.edu/>`__ | ||
| * - ClinGen | ||
| - `CC0 <https://clinicalgenome.org/docs/terms-of-use/>`__ | ||
| - clinical gene and genome annotation | ||
| - `ClinGen <https://clinicalgenome.org/>`__ | ||
| * - Comparative Toxicogenomics Database | ||
| - `free for non-commercial <https://www.catalystresearch.io/products/ctd>`__ | ||
| - database of biological named entities | ||
| - `CTD <https://ctdbase.org/>`__ | ||
| * - dbNSFP academic | ||
| - suitable for academic use | ||
| - nonsynonymous variant pathogenicity scores | ||
| - `dbNSFP <https://sites.google.com/site/jpopgen/dbNSFP>`__ | ||
| * - dbNSFP commercial | ||
| - suitable for commercial use | ||
| - nonsynonymous variant pathogenicity scores | ||
| - `dbNSFP <https://sites.google.com/site/jpopgen/dbNSFP>`__ | ||
| * - dbSNP | ||
| - `no restrictions <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ | ||
| - Structural variants from dbSNP | ||
| - `NCBI dbVar <https://www.ncbi.nlm.nih.gov/snp>`__ | ||
| * - dbVar | ||
| - `no restrictions <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ | ||
| - Structural variants from dbVar | ||
| - `NCBI dbVar <https://www.ncbi.nlm.nih.gov/dbvar>`__ | ||
| * - Database of Genomic Variants (DGV) | ||
| - no restrictions | ||
| - Structural variants from DGV | ||
| - `The Centre for Applied Genomics <http://dgv.tcag.ca/dgv/app/home>`__ | ||
| * - DECIPHER HI | ||
| - N/A | ||
| - DECIPHER haploinsufficiency score | ||
| - `PMID:20976243 <https://europepmc.org/article/MED/20976243>`__ | ||
| * - ENSEMBL | ||
| - `no restriction <http://www.ensembl.org/info/about/legal/disclaimer.html>`__ | ||
| - ENSEMBL gene/genome annotation and transcripts | ||
| - `ENSEMBL <http://www.ensembl.org/index.html>`__ | ||
| * - ExAC CNVs | ||
| - `no restrictions <https://gnomad.broadinstitute.org/policies>`__ | ||
| - Copy number variants from ExAC | ||
| - `gnomAD <https://gnomad.broadinstitute.org/>`__ | ||
| * - GenomicsEngland PanelApp | ||
| - `non-commercial <https://prod-media-panelapp.genomicsengland.co.uk/media/files/GEL_-_PanelApp_Terms_of_Use_December_2019.pdf>`__ | ||
| - Gene panels with disease associations from Genomics England | ||
| - `GenomicsEngland <https://panelapp.genomicsengland.co.uk/>`__ | ||
| * - gnomAD exomes and genomes | ||
| - `no restrictions <https://gnomad.broadinstitute.org/policies>`__ | ||
| - sequence and structural variants, gene constraint scores | ||
| - `gnomAD <https://gnomad.broadinstitute.org/>`__ | ||
| * - GTeX | ||
| - `free <https://www.gtexportal.org/home/license>`__ | ||
| - tissue-specific gene expression | ||
| - `GTEx <https://www.gtexportal.org/home/>`__ | ||
| * - HelixMtDb | ||
| - N/A | ||
| - mitochondrial genome frequencies | ||
| - `HelixMtDb <https://www.helix.com/mitochondrial-variant-database>`__ | ||
| * - HGNC | ||
| - `CC0 <https://www.genenames.org/about/license/>`__ | ||
| - gene information | ||
| - `HGNC <https://www.genenames.org/>`__ | ||
| * - HPO | ||
| - `free <https://hpo.jax.org/app/license>`__ | ||
| - Human Phenotype Ontology | ||
| - `HPO <https://hpo.jax.org/app>`__ | ||
| * - Human Disease Ontology (DO) | ||
| - `CC0 <https://obofoundry.org/ontology/doid.html>`__ | ||
| - ontology of human diseases | ||
| - `Disease Ontology <https://disease-ontology.org/>`__ | ||
| * - MONDO | ||
| - `CC BY 4.0 <http://obofoundry.org/ontology/mondo.html>`__ | ||
| - Mondo Disease Ontology | ||
| - `OBO Foundry <http://obofoundry.org/ontology/mondo.html>`__ | ||
| * - NCBI ClinVar | ||
| - `no restrictions <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ | ||
| - clinical variant interpretation | ||
| - `NCBI ClinVar <https://www.ncbi.nlm.nih.gov/clinvar>`__ | ||
| * - NCBI Gene | ||
| - `no restrictions <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ | ||
| - gene information | ||
| - `NCBI Gene <https://www.ncbi.nlm.nih.gov/gene>`__ | ||
| * - NCBI mim2gene | ||
| - `no restrictions <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ | ||
| - gene-disease associations | ||
| - `NCBI MedGen <https://ftp.ncbi.nih.gov/gene/DATA>`__ | ||
| * - NCBI RefSeq | ||
| - `no restrictions <https://www.ncbi.nlm.nih.gov/home/about/policies/>`__ | ||
| - gene/genome annotation and transcripts | ||
| - `NCBI RefSeq <https://www.ncbi.nlm.nih.gov/refseq>`__ | ||
| * - OMIM titles | ||
| - restricted | ||
| - some OMIM disease names are contained in other databases such as HPO | ||
| - misc. other datasources | ||
| * - ORDO | ||
| - `CC BY 4.0 <https://www.ebi.ac.uk/ols4/ontologies/ordo>`__ | ||
| - Orphanet Rare Disease Ontology | ||
| - `BioOntology.org <http://www.bioontology.org>`__ | ||
| * - Orphadata | ||
| - `CC BY 4.0 <https://www.orphadata.com/legal-notice/>`__ | ||
| - Orphanet disease-gene associations | ||
| - `Orphadata <https://www.orphadata.org/>`__ | ||
| * - rCNV Score | ||
| - N/A | ||
| - dosage sensitivity score | ||
| - `PMID:35917817 <https://europepmc.org/article/med/35917817>`__ | ||
| * - TAD annotation | ||
| - N/A | ||
| - Topologically Associated Domains annotation | ||
| - `YUE Lab <http://3dgenome.fsm.northwestern.edu>`__ | ||
| * - 1000G SV map | ||
| - `Fort Lauderdale Agreement <https://www.internationalgenome.org/faq/do-i-need-permission-to-use-igsr-data-in-my-own-scientific-research/>`__ | ||
| - structural variants from thousand genomes phase 3 | ||
| - `IGSR <https://www.internationalgenome.org/data-portal/data-collection/structural-variation>`__ | ||
| * - UCSC assembly-related tracks | ||
| - `no restrictions <https://genome.ucsc.edu/license/>`__ | ||
| - assembly-related tracks, genomicSuperDups, rmsk, altSeqLiftOverPsl, fixSeqLiftOverPsl, multiz100way | ||
| - `UCSC Table Browser <https://genome.ucsc.edu/cgi-bin/hgTables>`__ |
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| Original file line number | Diff line number | Diff line change |
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@@ -11,3 +11,4 @@ VarFish Development Docs | |
| doc_dataflows | ||
| doc_futureplans | ||
| doc_repooverview | ||
| doc_datasources | ||