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genomehubs · Oct 1, 2024 · f24750a · f24750a
2 parents d1a5197 + ab8af44
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diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
 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
@@ -60,7 +60,7 @@ file:
     - TAXON_assembly.types.yaml
   source: INSDC
   source_url_stub: https://www.ncbi.nlm.nih.gov/assembly/
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
 identifiers:
   sample_id:
     header: biosampleAccession

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
 taxonomy:
   taxon:
     header: organismName

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
 identifiers:
   assembly_id:
     header: genbankAccession

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
 identifiers:
   assembly_id:
     header: refseqAccession

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
 identifiers:
   assembly_id:
     index: 0

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
 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
@@ -3,7 +3,7 @@ file:
   header: true
   name: DTOL_Plant_Genome_Size_Estimates.tsv
   source: DTOL Plant Genome Estimates Kew
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
 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
@@ -3,7 +3,7 @@ file:
   header: true
   name: DTOL_assembly_informatics_status_kmer_draft.tsv
   source: Darwin Tree of Life Assembly Team
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   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
@@ -24,7 +24,7 @@ file:
   name: sra.tsv
   needs:
     - ATTR_sra.types.yaml
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
 taxonomy:
   taxon_id:
     header: taxon_id
diff --git a/sources/status-lists/FILE_1kfg_manual_bioprojects_taxon.types.yaml b/sources/status-lists/FILE_1kfg_manual_bioprojects_taxon.types.yaml
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: 1kfg_manual_bioprojects.tsv
   source: Declared Status List in INSDC- 1KFG
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: Declared Status List - 1KFG, JGI GOLD API StudyId Gs000001 with Bioproject IDs on INSDC
 attributes:
   sequencing_status:

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: AtlaSea (France ERGA Partner Branch) Status List, live spreadsheet
   source_contact: "Hugues Roest Crollius, Institut de Biologie de l'ENS (IBENS), France"
   source_url: https://portal.atlasea.fr/home/

diff --git a/sources/status-lists/FILE_Ag100Pest_list.types.yaml b/sources/status-lists/FILE_Ag100Pest_list.types.yaml
@@ -6,7 +6,7 @@ file:
   source: Declared Status List - Ag100Pest
   source_description: Ag100Pest Initiative, USDA, Agricultural Research Service, USA, - static spreadsheet
   source_contact: Anna Childers, Bee Research Laboratory, USDA, Agricultural Research Service, USA
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_url: https://i5k.github.io/ag100pest
 attributes:
   long_list:

diff --git a/sources/status-lists/FILE_Aus_Genome_status_Bioplatforms.types.yaml b/sources/status-lists/FILE_Aus_Genome_status_Bioplatforms.types.yaml
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: Aus_Genome_status_Bioplatforms.tsv
   source: Declared Status Lists - Bioplatforms Australia
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: Australian Genomes live Spreadsheet - Aus_Genome_status - Bioplatforms
   source_url: https://data.bioplatforms.com/
 attributes:

diff --git a/sources/status-lists/FILE_B10K_expanded_2022-04-19.types.yaml b/sources/status-lists/FILE_B10K_expanded_2022-04-19.types.yaml
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: B10K_expanded_2022-04-19.tsv
   source: Declared Status List - B10K
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: B10K static spreadsheet - B10K Samples 2021
   source_url: https://b10k.genomics.cn/species.html
 attributes:

diff --git a/sources/status-lists/FILE_BAT1K.types.yaml b/sources/status-lists/FILE_BAT1K.types.yaml
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: BAT1K_expanded.tsv
   source: Declared Status List - BAT1K
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: Declared Status Lists -BAT1K - static spreadsheet - ALL Bats
   source_contact: Meike Mei - https://bat1k.com/contact-us/
   source_url: https://bat1k.com/species-database/

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
   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
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: CBP_expanded.tsv
   source: Declared Status List - CBP
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   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_CGP.types.yaml b/sources/status-lists/FILE_CGP.types.yaml
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: CGP_expanded.tsv
   source: Declared Target List - CGP
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: Declared Target List - Cetaceans Genomes Project - live spreadsheet
   source_contact: Phillip Morin, Southwest Fisheries Science Center, USA
 attributes:

diff --git a/sources/status-lists/FILE_California_Conservation_Genomes_list.types.yaml b/sources/status-lists/FILE_California_Conservation_Genomes_list.types.yaml
@@ -5,7 +5,7 @@ file:
   name: CCGP_expanded.tsv
   source: Declared Status List - CCGP
   source_description: California Conservation Genomics Project live spreadsheet synced with CCGP tracking system - https://www.ccgproject.org/reference-genomes-tracking
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_contact: Courtney Miller & Erin Toffelmier, University of California, Los Angeles - UCLA
   source_url: https://www.ccgproject.org/reference-genomes-tracking
 attributes:

diff --git a/sources/status-lists/FILE_CanadaBP.types.yaml b/sources/status-lists/FILE_CanadaBP.types.yaml
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: CANBP_expanded.tsv
   source: Declared Status List - CanBP
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: Declared Status List - Canadian Biogenome Project - Live spreadsheet - CanadianBioGenomeProject_species_all
   source_contact: Samantha Jones, Genome Sciences Centre, BC Cancer Research Centre, Canada
   source_url: https://earthbiogenome.ca/project-status-and-data.mhtml

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
 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
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: sts.tsv
   source: Declared Status Lists - DTOL STS
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   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
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: DTOL_chordata_collected.tsv
   source: DTOL Chordata Collections List
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   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
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: EBPN_expanded.tsv
   source: Declared Status Lists - EBPN
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   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.types.yaml b/sources/status-lists/FILE_ERGA-BGE.types.yaml
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: ERGA-BGE_expanded.tsv
   source: Declared Status List - ERGA-BGE
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: ERGA-BGE Target and Status List, live spreadsheet
   source_contact: Tyler Alioto, CNAG, Barcelona, Spain
   source_url: https://genomes.cnag.cat/erga-stream/goat/

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
   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
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: SLOVENIA-HSP_expanded.tsv
   source: Declared Status List - ERGA-BGE Hotspots - Slovenia
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   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
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: SPAIN-HSP_expanded.tsv
   source: Declared Status List - ERGA-BGE Hotspots - Spain
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   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
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: ERGA-CH_expanded.tsv
   source: Declared Status List - ERGA-CH
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   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_GAGA.types.yaml b/sources/status-lists/FILE_GAGA.types.yaml
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: GAGA_expanded.tsv
   source: Declared Status List - GAGA
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: Declared Status List - Global Ant Genomics Alliance, Live spreadsheet - GAGA_all_species_list_v2
   source_contact: Guojie Zhang, University of Copenhagen, Denmark
 attributes:

diff --git a/sources/status-lists/FILE_GIGA_targets_status.types.yaml b/sources/status-lists/FILE_GIGA_targets_status.types.yaml
@@ -5,7 +5,7 @@ file:
   name: GIGA_expanded.tsv
   source: Declared Status List - GIGA
   source_description: Declared Status List - Global Invertebrate Genomics Alliance (GIGA), Static file - GIGA-phylumlist_withClass
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_contact: Jeff Robinson, UMBC
 attributes:
   long_list:

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
   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
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: OTHER_expanded.tsv
   source: Declared Status List - Other Projects
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   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_Polar_genomes.types.yaml b/sources/status-lists/FILE_Polar_genomes.types.yaml
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: PGP_expanded.tsv
   source: Declared Status List - PGP
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: Declared Status List - Polar Genomes Project, live spreadsheet - Polar_Genomes_Project_goat
   source_contact: Seunghyun Kang, Korea Polar Research Institute (KOPRI)
 attributes:

diff --git a/sources/status-lists/FILE_Psyche_targets.types.yaml b/sources/status-lists/FILE_Psyche_targets.types.yaml
@@ -6,7 +6,7 @@ file:
   source: Declared Target List - Psyche
   source_description: Original Target List for Project Psyche from Jan 2023, static spreadsheet - "Lepiforum's Checklist of European Lepidoptera"
   source_contact: "Charlotte Wright, Wellcome Sanger Institute"
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_url: https://lepiforum.org/wiki/page/Downloads
 attributes:
   long_list:

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
   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
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: jgi_1kfg.tsv
   source: Declared Status List - 1KFG
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   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_squalomix.types.yaml b/sources/status-lists/FILE_squalomix.types.yaml
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: SQUALOMIX_expanded.tsv
   source: Declared Status List - SQUALOMIX
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: Declared Status List - SQUALOMIX, shark and ray genomics and beyond, static spreadsheet - Squalomix_BySKuraku_all
   source_contact: Shigehiro Kuraku nig.ac.jp
 attributes:

diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
   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
@@ -4,7 +4,7 @@ file:
   comment: "#"
   name: YGG_expanded.tsv
   source: Declared Status List - yggdrasil
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
   source_description: Declared Status List - yggdrasil, live tsv
   source_contact: Sergei Kliver
 attributes:

diff --git a/sources/tolids/name b/sources/tolids/name
@@ -1,2 +1,2 @@
 file:
-  source_date: "2024-09-30"
+  source_date: "2024-10-01"
diff --git 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: "2024-09-30"
+  source_date: "2024-10-01"
 taxon_names:
   tolid_prefix:
     index: 0