From 28921b0d3d5daa249328c78013a34d6392b32c72 Mon Sep 17 00:00:00 2001 From: Kevin Schaper Date: Wed, 27 Nov 2024 20:22:25 -0800 Subject: [PATCH] hodgepodge commit, updates for phenio changes, latest kghub-downloader, xenbase url fixes, pull in modular biogrid, update qc expect --- poetry.lock | 319 +++++++++--------- pyproject.toml | 2 +- scripts/after_download.sh | 2 +- scripts/load_solr.sh | 4 +- src/monarch_ingest/download.yaml | 16 +- src/monarch_ingest/ingests.yaml | 20 +- .../ingests/pombase/gene_to_phenotype.yaml | 2 +- src/monarch_ingest/qc_expect.yaml | 8 +- 8 files changed, 179 insertions(+), 194 deletions(-) diff --git a/poetry.lock b/poetry.lock index f43dd608..c757871d 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1040,20 +1040,6 @@ files = [ docs = ["Sphinx", "furo"] test = ["objgraph", "psutil"] -[[package]] -name = "griffe" -version = "0.45.0" -description = "Signatures for entire Python programs. 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b/pyproject.toml @@ -20,7 +20,7 @@ biolink-model = "^4.2.0" bmt = "^1.0.15" cat-merge = "0.2.1" closurizer = "0.7.0" -kghub-downloader = "^0.3.10" +kghub-downloader = "^0.4.1" kgx = "^2.4.2" koza = "^0.6.1" linkml = "^1.7.8" diff --git a/scripts/after_download.sh b/scripts/after_download.sh index 0a66a9f8..0f5515e6 100755 --- a/scripts/after_download.sh +++ b/scripts/after_download.sh @@ -26,7 +26,7 @@ ${ZCAT} data/alliance/BGI_HUMAN.json.gz | jq -r '.data[] | "\(.basicGeneticEnti sqlite3 -cmd ".mode tabs" -cmd ".headers on" data/dictybase/ddpheno.db "select subject as id, value as name from rdfs_label_statement where predicate = 'rdfs:label' and subject like 'DDPHENO:%'" > data/dictybase/ddpheno.tsv # Unpack the phenio relation graph file -tar -xzf data/monarch/phenio-relation-graph.tar.gz -C data/monarch/ +gunzip data/monarch/phenio-relation-graph.tsv.gz awk '{ if ($2 == "rdfs:subClassOf" || $2 == "BFO:0000050" || $2 == "UPHENO:0000001") { print } }' data/monarch/phenio-relation-graph.tsv > data/monarch/phenio-relation-filtered.tsv diff --git a/scripts/load_solr.sh b/scripts/load_solr.sh index 93f24ea6..df731d9a 100755 --- a/scripts/load_solr.sh +++ b/scripts/load_solr.sh @@ -19,8 +19,8 @@ echo "Download the schema from monarch-py" # retrieve the schema from the main branch on monarch-app -curl -O https://raw.githubusercontent.com/monarch-initiative/monarch-app/add-species-context-qualifier/backend/src/monarch_py/datamodels/model.yaml -curl -O https://raw.githubusercontent.com/monarch-initiative/monarch-app/add-species-context-qualifier/backend/src/monarch_py/datamodels/similarity.yaml +curl -O https://raw.githubusercontent.com/monarch-initiative/monarch-app/main/backend/src/monarch_py/datamodels/model.yaml +curl -O https://raw.githubusercontent.com/monarch-initiative/monarch-app/main/backend/src/monarch_py/datamodels/similarity.yaml echo "Starting the server" poetry run lsolr start-server diff --git a/src/monarch_ingest/download.yaml b/src/monarch_ingest/download.yaml index e2372afa..8f9bfee4 100644 --- a/src/monarch_ingest/download.yaml +++ b/src/monarch_ingest/download.yaml @@ -246,8 +246,8 @@ local_name: data/monarch/kg-phenio.tar.gz tag: phenio - - url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio-relation-graph.tar.gz - local_name: data/monarch/phenio-relation-graph.tar.gz + url: https://github.com/monarch-initiative/phenio/releases/latest/download/phenio-relation-graph.tsv.gz + local_name: data/monarch/phenio-relation-graph.tsv.gz tag: phenio - url: https://s3.amazonaws.com/bbop-sqlite/phenio.db.gz @@ -446,11 +446,11 @@ ### Xenbase - - url: http://ftp.xenbase.org/pub/GenePageReports/XenbaseGenepageToGeneIdMapping.txt + url: https://download.xenbase.org/xenbase/GenePageReports/XenbaseGenepageToGeneIdMapping.txt local_name: data/xenbase/XenbaseGenepageToGeneIdMapping.txt tag: xenbase_publication_to_gene - - url: http://ftp.xenbase.org/pub/GenePageReports/LiteratureMatchedGenesByPaper.txt + url: https://download.xenbase.org/xenbase/GenePageReports/LiteratureMatchedGenesByPaper.txt local_name: data/xenbase/LiteratureMatchedGenesByPaper.txt tag: xenbase_publication_to_gene - @@ -461,17 +461,17 @@ #### Xenopus orthologs - # Homo sapiens (human) - url: http://ftp.xenbase.org/pub/GenePageReports/XenbaseGeneHumanOrthologMapping.txt + url: https://download.xenbase.org/xenbase/GenePageReports/XenbaseGeneHumanOrthologMapping.txt local_name: data/xenbase/XenbaseGeneHumanOrthologMapping.txt tag: xenbase_orthologs - # Mus musculus (house mouse) - url: http://ftp.xenbase.org/pub/GenePageReports/XenbaseGeneMouseOrthologMapping.txt + url: https://download.xenbase.org/xenbase/GenePageReports/XenbaseGeneMouseOrthologMapping.txt local_name: data/xenbase/XenbaseGeneMouseOrthologMapping.txt tag: xenbase_orthologs - # Danio rerio (Zebrafish) - url: http://ftp.xenbase.org/pub/GenePageReports/XenbaseGeneZebrafishOrthologMapping.txt + url: https://download.xenbase.org/xenbase/GenePageReports/XenbaseGeneZebrafishOrthologMapping.txt local_name: data/xenbase/XenbaseGeneZebrafishOrthologMapping.txt tag: xenbase_orthologs @@ -479,7 +479,7 @@ # TODO: parse this oddball non-Entrez ortholog file separately? # - # Non-Entrez OMIM, MGI, and ZFIN genes - url: http://ftp.xenbase.org/pub/GenePageReports/XenbaseGeneNonEntrezOrthologMapping.txt + url: https://download.xenbase.org/xenbase/GenePageReports/XenbaseGeneNonEntrezOrthologMapping.txt local_name: data/xenbase/XenbaseGeneNonEntrezOrthologMapping.txt tag: xenbase_non_entrez_orthologs diff --git a/src/monarch_ingest/ingests.yaml b/src/monarch_ingest/ingests.yaml index ab9236a0..131464c4 100644 --- a/src/monarch_ingest/ingests.yaml +++ b/src/monarch_ingest/ingests.yaml @@ -8,6 +8,9 @@ alliance_phenotype: alliance_disease_association: url: - 'https://github.com/monarch-initiative/alliance-disease-association-ingest/releases/latest/download/alliance_disease_edges.tsv' +biogrid: + url: + - 'https://github.com/monarch-initiative/biogrid-ingest/releases/latest/download/biogrid_gene_to_gene_edges.tsv' clingen_variant: url: - 'https://github.com/monarch-initiative/clingen-ingest/releases/latest/download/clingen_variant_nodes.tsv' @@ -23,14 +26,15 @@ hpoa: - 'https://github.com/monarch-initiative/monarch-phenotype-profile-ingest/releases/latest/download/hpoa_gene_to_disease_edges.tsv' - 'https://github.com/monarch-initiative/monarch-phenotype-profile-ingest/releases/latest/download/hpoa_gene_to_phenotype_edges.tsv' maxo_annotation: - url: 'https://github.com/monarch-initiative/maxo-annotation-ingest/releases/latest/download/maxo_annotation_edges.tsv' + url: + - 'https://github.com/monarch-initiative/maxo-annotation-ingest/releases/latest/download/maxo_annotation_edges.tsv' ncbi_gene: url: - - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9615_nodes.tsv' - - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9913_nodes.tsv' - - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9823_nodes.tsv' - - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9031_nodes.tsv' - - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_227321_nodes.tsv' + - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9615_nodes.tsv' + - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9913_nodes.tsv' + - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9823_nodes.tsv' + - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_9031_nodes.tsv' + - 'https://github.com/monarch-initiative/ncbi-gene/releases/latest/download/ncbi_gene_227321_nodes.tsv' zfin_genotype_to_phenotype: url: - 'https://github.com/monarch-initiative/zfin-genotype-to-phenotype-ingest/releases/latest/download/zfin_genotype_to_phenotype_edges.tsv' @@ -46,12 +50,8 @@ alliance_gene: config: 'ingests/alliance/gene.yaml' alliance_gene_to_expression: config: 'ingests/alliance/gene_to_expression.yaml' -# alliance_publication: -# config: 'ingests/alliance/publication.yaml' bgee_gene_to_expression: config: 'ingests/bgee/gene_to_expression.yaml' -biogrid: - config: 'ingests/biogrid/biogrid.yaml' ctd_chemical_to_disease: config: 'ingests/ctd/chemical_to_disease.yaml' dictybase_gene: diff --git a/src/monarch_ingest/ingests/pombase/gene_to_phenotype.yaml b/src/monarch_ingest/ingests/pombase/gene_to_phenotype.yaml index 7ce749c0..b25a0974 100644 --- a/src/monarch_ingest/ingests/pombase/gene_to_phenotype.yaml +++ b/src/monarch_ingest/ingests/pombase/gene_to_phenotype.yaml @@ -21,7 +21,7 @@ columns: - 'Parental strain' - 'Strain name (background)' - 'Genotype description' - - 'Gene name' + - 'Gene symbol' - 'Allele name' - 'Allele synonym' - 'Allele type' diff --git a/src/monarch_ingest/qc_expect.yaml b/src/monarch_ingest/qc_expect.yaml index 38abfd44..209e58df 100644 --- a/src/monarch_ingest/qc_expect.yaml +++ b/src/monarch_ingest/qc_expect.yaml @@ -35,8 +35,8 @@ edges: min: 1870000 bgee_gene_to_expression_edges: min: 430000 - biogrid_edges: - min: 1400000 + biogrid_gene_to_gene_edges: + min: 1340000 ctd_chemical_to_disease_edges: min: 5000 dictybase_gene_to_phenotype_edges: @@ -62,13 +62,13 @@ edges: reactome_gene_to_pathway_edges: min: 200000 string_protein_links_edges: - min: 1470000 + min: 1420000 xenbase_gene_to_phenotype_edges: min: 2000 alliance_phenotype_edges: min: 650000 alliance_disease_edges: - min: 10000 + min: 9900 zfin_genotype_to_phenotype_edges: min: 125000 clinvar_variant_edges: