diff --git a/metadata/datasets/cgd.yaml b/metadata/datasets/cgd.yaml index 626ca85c..e80818ef 100644 --- a/metadata/datasets/cgd.yaml +++ b/metadata/datasets/cgd.yaml @@ -16,10 +16,10 @@ datasets: dataset: cgd submitter: cgd compression: gzip - source: http://www.candidagenome.org/download/go/gene_association.cgd.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active - species_code: + species_code: taxa: - NCBITaxon:5476 - NCBITaxon:5478 diff --git a/metadata/datasets/dictybase.yaml b/metadata/datasets/dictybase.yaml index 749d07e4..f72f5709 100644 --- a/metadata/datasets/dictybase.yaml +++ b/metadata/datasets/dictybase.yaml @@ -52,8 +52,7 @@ datasets: dataset: dictybase submitter: dictyBase compression: gzip - #source: https://release.geneontology.org/2024-03-28/products/upstream_and_raw_data/dictybase-src.gaf.gz - source: https://ftp.ebi.ac.uk/pub/contrib/goa/dictyBase.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Ddis diff --git a/metadata/datasets/ecocyc.yaml b/metadata/datasets/ecocyc.yaml index 4522435c..b27144c6 100644 --- a/metadata/datasets/ecocyc.yaml +++ b/metadata/datasets/ecocyc.yaml @@ -14,7 +14,7 @@ datasets: type: gaf dataset: ecocyc submitter: ecocyc - source: https://ftp.ebi.ac.uk/pub/databases/GO/goa/proteomes/18.E_coli_MG1655.goa + source: http://skyhook.berkeleybop.org/empty.gaf entity_type: status: active species_code: Ecol diff --git a/metadata/datasets/fb.yaml b/metadata/datasets/fb.yaml index 984696bf..54206060 100644 --- a/metadata/datasets/fb.yaml +++ b/metadata/datasets/fb.yaml @@ -16,7 +16,7 @@ datasets: dataset: fb submitter: fb compression: gzip - source: ftp://ftp.flybase.net/releases/current/precomputed_files/go/gene_association.fb.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Dmel diff --git a/metadata/datasets/genedb.yaml b/metadata/datasets/genedb.yaml index 8cd28621..6ff2d6e0 100644 --- a/metadata/datasets/genedb.yaml +++ b/metadata/datasets/genedb.yaml @@ -16,7 +16,7 @@ datasets: dataset: genedb_lmajor submitter: genedb compression: gzip - source: ftp://ftp.sanger.ac.uk/pub/project/pathogens/as44/Lmajor.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Lmaj @@ -31,12 +31,12 @@ datasets: dataset: genedb_tbrucei submitter: genedb compression: gzip - source: ftp://ftp.sanger.ac.uk/pub/project/pathogens/as44/Tbruceibrucei927.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz status: active species_code: Tbru taxa: - NCBITaxon:185431 - - + - id: genedb_pfalciparum.gaf label: "genedb_pfalciparum gaf file" description: "gaf file for genedb_pfalciparum from GeneDB" @@ -45,7 +45,7 @@ datasets: dataset: genedb_pfalciparum submitter: genedb compression: gzip - source: ftp://ftp.sanger.ac.uk/pub/project/pathogens/as44/Pfalciparum.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Pfal diff --git a/metadata/datasets/goa.yaml b/metadata/datasets/goa.yaml index b798145a..eb1c106e 100644 --- a/metadata/datasets/goa.yaml +++ b/metadata/datasets/goa.yaml @@ -744,8 +744,7 @@ datasets: dataset: goa_chicken submitter: goa compression: gzip - source: https://mirror.geneontology.io/goa_chicken_plus.gaf.gz - mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/CHICKEN/goa_chicken_plus.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: protein status: active species_code: Ggal @@ -765,8 +764,7 @@ datasets: dataset: goa_cow submitter: goa compression: gzip - source: https://mirror.geneontology.io/goa_cow_plus.gaf.gz - mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/COW/goa_cow_plus.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: protein status: active species_code: Btau @@ -784,8 +782,7 @@ datasets: dataset: goa_dog submitter: goa compression: gzip - source: https://mirror.geneontology.io/goa_dog_plus.gaf.gz - mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/DOG/goa_dog_plus.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: protein status: active species_code: Cfam @@ -801,8 +798,7 @@ datasets: dataset: goa_human submitter: goa compression: gzip - source: https://mirror.geneontology.io/goa_human_plus.gaf.gz - mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/HUMAN/goa_human_plus.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: protein status: active species_code: Hsap @@ -818,8 +814,7 @@ datasets: dataset: goa_pdb submitter: goa compression: gzip - source: https://mirror.geneontology.io/goa_pdb.gaf.gz - mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/PDB/goa_pdb.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: protein status: active species_code: @@ -835,8 +830,7 @@ datasets: dataset: goa_pig submitter: goa compression: gzip - source: https://mirror.geneontology.io/goa_pig_plus.gaf.gz - mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/PIG/goa_pig_plus.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: protein status: active species_code: Sscr @@ -852,8 +846,7 @@ datasets: dataset: goa_uniprot_all submitter: goa compression: gzip - mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_all.gaf.gz - source: https://mirror.geneontology.io/goa_uniprot_all.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: all status: active aggregates: goa @@ -903,8 +896,7 @@ datasets: dataset: goa_uniprot_gcrp submitter: goa compression: gzip - mirror_of: https://ftp.ebi.ac.uk/pub/databases/GO/goa/UNIPROT/goa_uniprot_gcrp.gaf.gz - source: https://mirror.geneontology.io/goa_uniprot_gcrp.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: all status: active aggregates: goa diff --git a/metadata/datasets/japonicusdb.yaml b/metadata/datasets/japonicusdb.yaml index 2d3a13de..5ec0c1b3 100644 --- a/metadata/datasets/japonicusdb.yaml +++ b/metadata/datasets/japonicusdb.yaml @@ -16,7 +16,7 @@ datasets: dataset: japonicusdb submitter: japonicusdb compression: gzip - source: https://www.japonicusdb.org/data/annotations/Gene_ontology/gene_association.japonicusdb.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Sjap diff --git a/metadata/datasets/pombase.yaml b/metadata/datasets/pombase.yaml index d49ddf83..e02e7ac4 100644 --- a/metadata/datasets/pombase.yaml +++ b/metadata/datasets/pombase.yaml @@ -16,8 +16,7 @@ datasets: dataset: pombase submitter: pombase compression: gzip - #source: https://release.geneontology.org/2024-03-28/products/upstream_and_raw_data/pombase-src.gaf.gz - source: https://www.pombase.org/data/annotations/Gene_ontology/gene_association.pombase.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Spom diff --git a/metadata/datasets/pseudocap.yaml b/metadata/datasets/pseudocap.yaml index 6873590e..624f12c0 100644 --- a/metadata/datasets/pseudocap.yaml +++ b/metadata/datasets/pseudocap.yaml @@ -16,7 +16,7 @@ datasets: dataset: pseudocap submitter: pseudocap compression: gzip - source: https://github.com/brinkmanlab/pseudomonas-genome-database/raw/master/pseudocap-annotation-files/gene_association.pseudocap.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Pseudomonas diff --git a/metadata/datasets/reactome.yaml b/metadata/datasets/reactome.yaml index 971d288e..1f10ed90 100644 --- a/metadata/datasets/reactome.yaml +++ b/metadata/datasets/reactome.yaml @@ -16,7 +16,7 @@ datasets: dataset: reactome submitter: reactome compression: gzip - source: https://www.reactome.org/download/current/gene_association.reactome.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: inactive species_code: diff --git a/metadata/datasets/rgd.yaml b/metadata/datasets/rgd.yaml index 3a8bbceb..e4ee7e94 100644 --- a/metadata/datasets/rgd.yaml +++ b/metadata/datasets/rgd.yaml @@ -16,7 +16,7 @@ datasets: dataset: rgd submitter: rgd compression: gzip - source: https://github.com/rat-genome-database/rgd-annotation-files/raw/master/gene_association.rgd.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Rnor diff --git a/metadata/datasets/sgd.yaml b/metadata/datasets/sgd.yaml index e57cfc86..788dafd9 100644 --- a/metadata/datasets/sgd.yaml +++ b/metadata/datasets/sgd.yaml @@ -16,7 +16,7 @@ datasets: dataset: sgd submitter: sgd compression: gzip - source: https://sgd-prod-upload.s3.amazonaws.com/latest/gene_association.sgd.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Scer diff --git a/metadata/datasets/sgn.yaml b/metadata/datasets/sgn.yaml index ef1b74f1..340b4b3e 100644 --- a/metadata/datasets/sgn.yaml +++ b/metadata/datasets/sgn.yaml @@ -16,7 +16,7 @@ datasets: dataset: sgn submitter: sgn compression: gzip - source: https://solgenomics.net/ftp/ontology/GO/gene_association.sgn.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: gene status: active species_code: Solanaceae diff --git a/metadata/datasets/tair.yaml b/metadata/datasets/tair.yaml index 45d9a896..253c1e1a 100644 --- a/metadata/datasets/tair.yaml +++ b/metadata/datasets/tair.yaml @@ -16,7 +16,7 @@ datasets: dataset: tair submitter: tair compression: gzip - source: https://www.arabidopsis.org/api/download-files/download?filePath=GO_and_PO_Annotations/Gene_Ontology_Annotations/gene_association.tair.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Atal diff --git a/metadata/datasets/wb.yaml b/metadata/datasets/wb.yaml index 6806e718..0ff99d45 100644 --- a/metadata/datasets/wb.yaml +++ b/metadata/datasets/wb.yaml @@ -23,9 +23,7 @@ datasets: dataset: wb submitter: wb compression: gzip - source: https://downloads.wormbase.org/species/c_elegans/PRJNA13758/annotation/gene_association/c_elegans.canonical_bioproject.current.gene_association.wb.gz - #source: http://release.geneontology.org/2024-03-28/products/upstream_and_raw_data/wb-src.gaf.gz - #source: ftp://ftp.wormbase.org/pub/wormbase/species/c_elegans/PRJNA13758/annotation/gene_association/c_elegans.PRJNA13758.current.gene_association.wb.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Cele diff --git a/metadata/datasets/xenbase.yaml b/metadata/datasets/xenbase.yaml index 6434214c..b7cbc1f5 100644 --- a/metadata/datasets/xenbase.yaml +++ b/metadata/datasets/xenbase.yaml @@ -31,7 +31,7 @@ datasets: dataset: xenbase submitter: xenbase compression: gzip - source: https://ftp.xenbase.org/pub/DataExchange/GO/xenbase.EBI.only.2.2.gaf.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Xenopus diff --git a/metadata/datasets/zfin.yaml b/metadata/datasets/zfin.yaml index d09fea3a..f8b62706 100644 --- a/metadata/datasets/zfin.yaml +++ b/metadata/datasets/zfin.yaml @@ -16,7 +16,7 @@ datasets: dataset: zfin submitter: zfin compression: gzip - source: https://zfin.org/downloads/gene_association2.2_automated_only.zfin.gz + source: http://skyhook.berkeleybop.org/empty.gaf.gz entity_type: status: active species_code: Drer