From b9c191c21a2bd472cce32ce1914ebe12160c7f62 Mon Sep 17 00:00:00 2001 From: goat Date: Mon, 22 Jul 2024 08:25:01 +0000 Subject: [PATCH] Add changes from workflow running release 2024.07.22 --- .../ncbi_datasets_eukaryota_sample.types.yaml | 2 +- sources/assembly-data-sample/ncbi_datasets_sample.types.yaml | 2 +- sources/assembly-data-taxon/cngb_taxon.types.yaml | 2 +- .../ncbi_datasets_eukaryota_taxon.types.yaml | 2 +- sources/assembly-data/cngb.types.yaml | 2 +- sources/assembly-data/ncbi_datasets_eukaryota.types.yaml | 2 +- sources/assembly-data/refseq_organelles.types.yaml | 2 +- sources/assembly-data/ucsc_ids.types.yaml | 2 +- sources/btk/btk.types.yaml | 2 +- .../FILE_DTOL_Plant_Genome_Size_Estimates.types.yaml | 2 +- .../FILE_DTOL_assembly_informatics_status_kmer_draft.types.yaml | 2 +- sources/sra/sra.types.yaml | 2 +- sources/status-lists/FILE_ATLASEA.types.yaml | 2 +- sources/status-lists/FILE_BEENOME100.types.yaml | 2 +- sources/status-lists/FILE_CBP_expanded.types.yaml | 2 +- sources/status-lists/FILE_DTOL_nhm.types.yaml | 2 +- sources/status-lists/FILE_DTOL_sts.types.yaml | 2 +- sources/status-lists/FILE_DToL_chordata_collected.types.yaml | 2 +- sources/status-lists/FILE_EBP_Nor_long_list.types.yaml | 2 +- sources/status-lists/FILE_ERGA-BGE_Community.types.yaml | 2 +- sources/status-lists/FILE_ERGA-BGE_Greece-Hsp.types.yaml | 2 +- sources/status-lists/FILE_ERGA-BGE_Slovenia-Hsp.types.yaml | 2 +- sources/status-lists/FILE_ERGA-BGE_Spain-Hsp.types.yaml | 2 +- sources/status-lists/FILE_ERGA-CH.types.yaml | 2 +- sources/status-lists/FILE_LOEWE-TBG.types.yaml | 2 +- sources/status-lists/FILE_OTHER_status.types.yaml | 2 +- sources/status-lists/FILE_eurofish.types.yaml | 2 +- sources/status-lists/FILE_jgi1kfg_status.types.yaml | 2 +- sources/status-lists/FILE_vgp_table_tracker.types.yaml | 2 +- sources/status-lists/FILE_yggdrasil.types.yaml | 2 +- sources/tolids/name | 2 +- sources/tolids/tolids.names.yaml | 2 +- 32 files changed, 32 insertions(+), 32 deletions(-) diff --git a/sources/assembly-data-sample/ncbi_datasets_eukaryota_sample.types.yaml b/sources/assembly-data-sample/ncbi_datasets_eukaryota_sample.types.yaml index b0559f02d..0fa7e69f4 100644 --- a/sources/assembly-data-sample/ncbi_datasets_eukaryota_sample.types.yaml +++ b/sources/assembly-data-sample/ncbi_datasets_eukaryota_sample.types.yaml @@ -95,7 +95,7 @@ file: organelle: nucleus source: INSDC source_url_stub: https://www.ncbi.nlm.nih.gov/assembly/ - source_date: "2024-07-20" + source_date: "2024-07-22" identifiers: assembly_id: header: genbankAssmAccession diff --git a/sources/assembly-data-sample/ncbi_datasets_sample.types.yaml b/sources/assembly-data-sample/ncbi_datasets_sample.types.yaml index beb3706a2..47d6a75e3 100644 --- a/sources/assembly-data-sample/ncbi_datasets_sample.types.yaml +++ b/sources/assembly-data-sample/ncbi_datasets_sample.types.yaml @@ -60,7 +60,7 @@ file: - TAXON_assembly.types.yaml source: INSDC source_url_stub: https://www.ncbi.nlm.nih.gov/assembly/ - source_date: "2024-07-20" + source_date: "2024-07-22" identifiers: sample_id: header: biosampleAccession diff --git a/sources/assembly-data-taxon/cngb_taxon.types.yaml b/sources/assembly-data-taxon/cngb_taxon.types.yaml index 8d2022c06..663a3c599 100644 --- a/sources/assembly-data-taxon/cngb_taxon.types.yaml +++ b/sources/assembly-data-taxon/cngb_taxon.types.yaml @@ -18,7 +18,7 @@ file: header: true name: cngb.tsv organelle: nucleus - source_date: "2024-07-20" + source_date: "2024-07-22" identifiers: assembly_id: constraint: diff --git a/sources/assembly-data-taxon/ncbi_datasets_eukaryota_taxon.types.yaml b/sources/assembly-data-taxon/ncbi_datasets_eukaryota_taxon.types.yaml index 0ab28c9fb..951856a77 100644 --- a/sources/assembly-data-taxon/ncbi_datasets_eukaryota_taxon.types.yaml +++ b/sources/assembly-data-taxon/ncbi_datasets_eukaryota_taxon.types.yaml @@ -203,7 +203,7 @@ file: organelle: nucleus source: INSDC source_url_stub: https://www.ncbi.nlm.nih.gov/assembly/ - source_date: "2024-07-20" + source_date: "2024-07-22" identifiers: assembly_id: constraint: diff --git a/sources/assembly-data/cngb.types.yaml b/sources/assembly-data/cngb.types.yaml index 4863139bc..8cf5560bb 100644 --- a/sources/assembly-data/cngb.types.yaml +++ b/sources/assembly-data/cngb.types.yaml @@ -17,7 +17,7 @@ file: organelle: nucleus source: CNGB source_url_stub: https://db.cngb.org/search/assembly/ - source_date: "2024-07-20" + source_date: "2024-07-22" taxonomy: taxon: header: organismName diff --git a/sources/assembly-data/ncbi_datasets_eukaryota.types.yaml b/sources/assembly-data/ncbi_datasets_eukaryota.types.yaml index 12a3cef84..270c1804e 100644 --- a/sources/assembly-data/ncbi_datasets_eukaryota.types.yaml +++ b/sources/assembly-data/ncbi_datasets_eukaryota.types.yaml @@ -153,7 +153,7 @@ file: - TAXON_assembly.types.yaml source: INSDC source_url_stub: https://www.ncbi.nlm.nih.gov/assembly/ - source_date: "2024-07-20" + source_date: "2024-07-22" identifiers: assembly_id: header: genbankAccession diff --git a/sources/assembly-data/refseq_organelles.types.yaml b/sources/assembly-data/refseq_organelles.types.yaml index 8ee7999fd..4b3fe9266 100644 --- a/sources/assembly-data/refseq_organelles.types.yaml +++ b/sources/assembly-data/refseq_organelles.types.yaml @@ -39,7 +39,7 @@ file: - ATTR_assembly.types.yaml source: NCBI source_url_stub: https://www.ncbi.nlm.nih.gov/nuccore/ - source_date: "2024-07-20" + source_date: "2024-07-22" identifiers: assembly_id: header: refseqAccession diff --git a/sources/assembly-data/ucsc_ids.types.yaml b/sources/assembly-data/ucsc_ids.types.yaml index c4c78d6e2..3526a799e 100644 --- a/sources/assembly-data/ucsc_ids.types.yaml +++ b/sources/assembly-data/ucsc_ids.types.yaml @@ -3,7 +3,7 @@ file: format: tsv header: false name: UCSC_GI.assemblyHubList.tsv.gz - source_date: "2024-07-20" + source_date: "2024-07-22" identifiers: assembly_id: index: 0 diff --git a/sources/btk/btk.types.yaml b/sources/btk/btk.types.yaml index 0dd94310d..fc5b19d0a 100644 --- a/sources/btk/btk.types.yaml +++ b/sources/btk/btk.types.yaml @@ -21,7 +21,7 @@ file: - ATTR_assembly.types.yaml - ATTR_btk.types.yaml - TAXON_assembly.types.yaml - source_date: "2024-07-20" + source_date: "2024-07-22" identifiers: assembly_alias: header: alias diff --git a/sources/genomesize-karyotype/FILE_DTOL_Plant_Genome_Size_Estimates.types.yaml b/sources/genomesize-karyotype/FILE_DTOL_Plant_Genome_Size_Estimates.types.yaml index b6a28fe9b..3e2669639 100644 --- a/sources/genomesize-karyotype/FILE_DTOL_Plant_Genome_Size_Estimates.types.yaml +++ b/sources/genomesize-karyotype/FILE_DTOL_Plant_Genome_Size_Estimates.types.yaml @@ -3,7 +3,7 @@ file: header: true name: DTOL_Plant_Genome_Size_Estimates.tsv source: DTOL Plant Genome Estimates Kew - source_date: "2024-07-20" + source_date: "2024-07-22" attributes: genome_size: type: long diff --git a/sources/genomesize-karyotype/FILE_DTOL_assembly_informatics_status_kmer_draft.types.yaml b/sources/genomesize-karyotype/FILE_DTOL_assembly_informatics_status_kmer_draft.types.yaml index 5bb0d71fc..7b6cd5a81 100644 --- a/sources/genomesize-karyotype/FILE_DTOL_assembly_informatics_status_kmer_draft.types.yaml +++ b/sources/genomesize-karyotype/FILE_DTOL_assembly_informatics_status_kmer_draft.types.yaml @@ -3,7 +3,7 @@ file: header: true name: DTOL_assembly_informatics_status_kmer_draft.tsv source: Darwin Tree of Life Assembly Team - source_date: "2024-07-20" + source_date: "2024-07-22" source_url: https://qc.tol.sanger.ac.uk/ attributes: genome_size_kmer: diff --git a/sources/sra/sra.types.yaml b/sources/sra/sra.types.yaml index b91818ef6..fa3b39545 100644 --- a/sources/sra/sra.types.yaml +++ b/sources/sra/sra.types.yaml @@ -24,7 +24,7 @@ file: name: sra.tsv needs: - ATTR_sra.types.yaml - source_date: "2024-07-20" + source_date: "2024-07-22" taxonomy: taxon_id: header: taxon_id diff --git a/sources/status-lists/FILE_ATLASEA.types.yaml b/sources/status-lists/FILE_ATLASEA.types.yaml index 1dacc448a..523f3b71e 100644 --- a/sources/status-lists/FILE_ATLASEA.types.yaml +++ b/sources/status-lists/FILE_ATLASEA.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: ATLASEA_expanded.tsv source: Declared Status List - ATLASEA - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: AtlaSea (France ERGA Partner Branch) Status List, live spreadsheet source_contact: "Hugues Roest Crollius, Institut de Biologie de l'ENS (IBENS), France" attributes: diff --git a/sources/status-lists/FILE_BEENOME100.types.yaml b/sources/status-lists/FILE_BEENOME100.types.yaml index 9fb5dbeb7..34040c566 100644 --- a/sources/status-lists/FILE_BEENOME100.types.yaml +++ b/sources/status-lists/FILE_BEENOME100.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: BEENOME100_expanded.tsv source: Declared Status List - Beenome100 - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: Declared Status Lists - Beenome 100 - live spreadsheet source_contact: Michael Branstetter attributes: diff --git a/sources/status-lists/FILE_CBP_expanded.types.yaml b/sources/status-lists/FILE_CBP_expanded.types.yaml index 89a9223db..269acea63 100644 --- a/sources/status-lists/FILE_CBP_expanded.types.yaml +++ b/sources/status-lists/FILE_CBP_expanded.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: CBP_expanded.tsv source: Declared Status List - CBP - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: CBP Status List - Live Spreadsheet - CBP_GOAT source_contact: Montserrat Corominas source_link: https://dades.biogenoma.cat diff --git a/sources/status-lists/FILE_DTOL_nhm.types.yaml b/sources/status-lists/FILE_DTOL_nhm.types.yaml index 8282c65f7..f5ff725a4 100644 --- a/sources/status-lists/FILE_DTOL_nhm.types.yaml +++ b/sources/status-lists/FILE_DTOL_nhm.types.yaml @@ -3,7 +3,7 @@ file: header: true comment: "#" name: nhm.tsv - source_date: "2024-07-20" + source_date: "2024-07-22" metadata: source_slug: header: otherCatalogNumbers diff --git a/sources/status-lists/FILE_DTOL_sts.types.yaml b/sources/status-lists/FILE_DTOL_sts.types.yaml index afe446a6c..af0db0343 100644 --- a/sources/status-lists/FILE_DTOL_sts.types.yaml +++ b/sources/status-lists/FILE_DTOL_sts.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: sts.tsv source: Declared Status Lists - DTOL STS - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: Declared Status Lists - DTOL Samples Tracking System #source_contact: https://sts.tol.sanger.ac.uk source_url: https://sts.tol.sanger.ac.uk/api/v1/swagger diff --git a/sources/status-lists/FILE_DToL_chordata_collected.types.yaml b/sources/status-lists/FILE_DToL_chordata_collected.types.yaml index 600e9d6b8..830f0e289 100644 --- a/sources/status-lists/FILE_DToL_chordata_collected.types.yaml +++ b/sources/status-lists/FILE_DToL_chordata_collected.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: DTOL_chordata_collected.tsv source: DTOL Chordata Collections List - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: DTOL Chordata Working Group, Live Spreadsheet source_contact: DTOL Chordates SWG attributes: diff --git a/sources/status-lists/FILE_EBP_Nor_long_list.types.yaml b/sources/status-lists/FILE_EBP_Nor_long_list.types.yaml index fdeb2beaa..c012f09b8 100644 --- a/sources/status-lists/FILE_EBP_Nor_long_list.types.yaml +++ b/sources/status-lists/FILE_EBP_Nor_long_list.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: EBPN_expanded.tsv source: Declared Status Lists - EBPN - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: Declared Status Lists - Earth Biogenome Project Norway (EBP-Nor) - live spreadsheet - EBP-Nor_all_goat source_contact: Ole K. Tørresen - University of Oslo attributes: diff --git a/sources/status-lists/FILE_ERGA-BGE_Community.types.yaml b/sources/status-lists/FILE_ERGA-BGE_Community.types.yaml index 9fb4dc8ea..b056e638d 100644 --- a/sources/status-lists/FILE_ERGA-BGE_Community.types.yaml +++ b/sources/status-lists/FILE_ERGA-BGE_Community.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: BGE_expanded.tsv source: Declared Status List - ERGA-BGE Community Sampling - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: ERGA-BGE Community Sampling Status List, live spreadsheet source_contact: Thomas Marcussen, University of Oslo, Norway attributes: diff --git a/sources/status-lists/FILE_ERGA-BGE_Greece-Hsp.types.yaml b/sources/status-lists/FILE_ERGA-BGE_Greece-Hsp.types.yaml index b2093dbc7..9f463d67b 100644 --- a/sources/status-lists/FILE_ERGA-BGE_Greece-Hsp.types.yaml +++ b/sources/status-lists/FILE_ERGA-BGE_Greece-Hsp.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: GREECE-HSP_expanded.tsv source: Declared Status List - ERGA-BGE Hotspots - Greece - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: ERGA-BGE Hotspots - Greece Status List, live spreadsheet source_contact: Javier Palma, Instituto de Biologia Evolutiva - CSIC, Barcelona, Spain attributes: diff --git a/sources/status-lists/FILE_ERGA-BGE_Slovenia-Hsp.types.yaml b/sources/status-lists/FILE_ERGA-BGE_Slovenia-Hsp.types.yaml index b2b42d469..07c9024ca 100644 --- a/sources/status-lists/FILE_ERGA-BGE_Slovenia-Hsp.types.yaml +++ b/sources/status-lists/FILE_ERGA-BGE_Slovenia-Hsp.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: SLOVENIA-HSP_expanded.tsv source: Declared Status List - ERGA-BGE Hotspots - Slovenia - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: ERGA-BGE Hotspots - Slovenia Status List, live spreadsheet source_contact: Javier Palma, Instituto de Biologia Evolutiva - CSIC, Barcelona, Spain attributes: diff --git a/sources/status-lists/FILE_ERGA-BGE_Spain-Hsp.types.yaml b/sources/status-lists/FILE_ERGA-BGE_Spain-Hsp.types.yaml index fb2b6f62d..b063981bc 100644 --- a/sources/status-lists/FILE_ERGA-BGE_Spain-Hsp.types.yaml +++ b/sources/status-lists/FILE_ERGA-BGE_Spain-Hsp.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: SPAIN-HSP_expanded.tsv source: Declared Status List - ERGA-BGE Hotspots - Spain - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: ERGA-BGE Hotspots - Spain Status List, live spreadsheet source_contact: Javier Palma, Instituto de Biologia Evolutiva - CSIC, Barcelona, Spain attributes: diff --git a/sources/status-lists/FILE_ERGA-CH.types.yaml b/sources/status-lists/FILE_ERGA-CH.types.yaml index 31a5b3fd5..9b17708a7 100644 --- a/sources/status-lists/FILE_ERGA-CH.types.yaml +++ b/sources/status-lists/FILE_ERGA-CH.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: ERGA-CH_expanded.tsv source: Declared Status List - ERGA-CH - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: ERGA Switzerland Branch Status List, live spreadsheet source_contact: Robert Waterhouse, University of Lausanne and Swiss Institute of Bioinformatics, Switzerland attributes: diff --git a/sources/status-lists/FILE_LOEWE-TBG.types.yaml b/sources/status-lists/FILE_LOEWE-TBG.types.yaml index 9aa59b867..a88bcfd35 100644 --- a/sources/status-lists/FILE_LOEWE-TBG.types.yaml +++ b/sources/status-lists/FILE_LOEWE-TBG.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: LOEWE-TBG_expanded.tsv source: Declared Status List - LOEWE-TBG - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: Declared Status List - The LOEWE Centre for Translational Biodiversity Genomics, live spreadsheet - LOEWE-TBG_GoaT source_contact: Prof Dr. Michael Hiller, Prof Dr. Miklós Bálint, Senckenberg, Frankfurt, Germany attributes: diff --git a/sources/status-lists/FILE_OTHER_status.types.yaml b/sources/status-lists/FILE_OTHER_status.types.yaml index 14cf72294..daf660bbc 100644 --- a/sources/status-lists/FILE_OTHER_status.types.yaml +++ b/sources/status-lists/FILE_OTHER_status.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: OTHER_expanded.tsv source: Declared Status List - Other Projects - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: Declared Status List - Other Projects, Multiple Contributing Labs, live spreadsheet - GoaT_OTHER_projects_subprojects source_contact: Individual contributors - see https://docs.google.com/spreadsheets/d/1yOzTrQy231afNA1CVCA9dH0SjB5VyvX12hdiotKPvhY/edit#gid=586527579 source_url: https://goat.cog.sanger.ac.uk/?shared=sources/status-lists/ diff --git a/sources/status-lists/FILE_eurofish.types.yaml b/sources/status-lists/FILE_eurofish.types.yaml index 58c65ec2c..c5f1a877e 100644 --- a/sources/status-lists/FILE_eurofish.types.yaml +++ b/sources/status-lists/FILE_eurofish.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: EUROFISH_expanded.tsv source: Declared Status Lists - EUROFISH - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: Declared Status List - EUROFISH, live spreadsheet - eurofish_all.tsv source_contact: Gene Myers, mpi-cbg.de attributes: diff --git a/sources/status-lists/FILE_jgi1kfg_status.types.yaml b/sources/status-lists/FILE_jgi1kfg_status.types.yaml index a56f2d5b1..2129feab7 100644 --- a/sources/status-lists/FILE_jgi1kfg_status.types.yaml +++ b/sources/status-lists/FILE_jgi1kfg_status.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: jgi_1kfg.tsv source: Declared Status List - 1KFG - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: Declared Status List - 1KFG, JGI GOLD API StudyId Gs000001 source_url: https://gold.jgi.doe.gov/projects?page=1&Study.GOLD+Study+ID=Gs0000001&Project.Sequencing+Strategy=Whole+Genome+Sequencing attributes: diff --git a/sources/status-lists/FILE_vgp_table_tracker.types.yaml b/sources/status-lists/FILE_vgp_table_tracker.types.yaml index 46c648c02..c5f90d499 100644 --- a/sources/status-lists/FILE_vgp_table_tracker.types.yaml +++ b/sources/status-lists/FILE_vgp_table_tracker.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: vgp.tsv source: Declared Status List - VGP - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: Declared Status List - VGP Project tracker yaml file in github/vgl-hub/genome-portal # source_contact: source_url: https://github.com/vgl-hub/genome-portal/blob/master/_data/table_tracker.yml diff --git a/sources/status-lists/FILE_yggdrasil.types.yaml b/sources/status-lists/FILE_yggdrasil.types.yaml index b85c2ec14..c5322488e 100644 --- a/sources/status-lists/FILE_yggdrasil.types.yaml +++ b/sources/status-lists/FILE_yggdrasil.types.yaml @@ -4,7 +4,7 @@ file: comment: "#" name: YGG_expanded.tsv source: Declared Status List - yggdrasil - source_date: "2024-07-20" + source_date: "2024-07-22" source_description: Declared Status List - yggdrasil, live tsv source_contact: Sergei Kliver attributes: diff --git a/sources/tolids/name b/sources/tolids/name index 3bcb2daac..4dd774d36 100644 --- a/sources/tolids/name +++ b/sources/tolids/name @@ -1,2 +1,2 @@ file: - source_date: "2024-07-20" + source_date: "2024-07-22" diff --git a/sources/tolids/tolids.names.yaml b/sources/tolids/tolids.names.yaml index 233f3df74..3ad7745fb 100644 --- a/sources/tolids/tolids.names.yaml +++ b/sources/tolids/tolids.names.yaml @@ -4,7 +4,7 @@ file: name: tolids.tsv.gz source: dToL sample naming source_url: https://id.tol.sanger.ac.uk/ - source_date: "2024-07-20" + source_date: "2024-07-22" taxon_names: tolid_prefix: index: 0