build bioschemas on Sun May 5 01:01:17 UTC 2024

research-software-ecosystem · May 5, 2024 · 150873a · 150873a
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diff --git a/data/1000genomes/1000genomes.bioschemas.jsonld b/data/1000genomes/1000genomes.bioschemas.jsonld
@@ -36,15 +36,7 @@
   },
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-      "@type": "sc:CreativeWork"
-    },
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-      "@id": "https://doi.org/10.1038/nature15393",
+      "@id": "https://doi.org/10.1038/nature11632",
       "@type": "sc:CreativeWork"
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@@ -53,61 +45,61 @@
       "biotools:primaryContact": "Auton A",
       "dcterms:conformsTo": "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT",
       "sc:additionalType": [
-        "Web application",
-        "Database portal"
+        "Database portal",
+        "Web application"
       ],
       "sc:applicationSubCategory": [
         {
           "@id": "edam:topic_3365"
         },
         {
-          "@id": "edam:topic_0622"
+          "@id": "edam:topic_0199"
         },
         {
-          "@id": "edam:topic_3325"
+          "@id": "edam:topic_0622"
         },
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-          "@id": "edam:topic_0199"
+          "@id": "edam:topic_0625"
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-          "@id": "edam:topic_3473"
+          "@id": "edam:topic_3325"
         },
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-          "@id": "edam:topic_0625"
+          "@id": "edam:topic_3473"
         }
       ],
       "sc:citation": [
-        "pubmed:26432246",
         "pmcid:PMC3498066",
-        "pubmed:23128226",
+        "pubmed:20981092",
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-          "@id": "https://doi.org/10.1038/nature09534"
+          "@id": "https://doi.org/10.1038/nature15394"
         },
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           "@id": "https://doi.org/10.1038/nature11632"
         },
-        "pmcid:PMC4617611",
+        "pmcid:PMC3042601",
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           "@id": "https://doi.org/10.1038/nature15393"
         },
-        "pmcid:PMC4750478",
-        "pmcid:PMC3042601",
-        "pubmed:26432245",
-        "pubmed:20981092",
         {
-          "@id": "https://doi.org/10.1038/nature15394"
-        }
+          "@id": "https://doi.org/10.1038/nature09534"
+        },
+        "pubmed:23128226",
+        "pmcid:PMC4617611",
+        "pmcid:PMC4750478",
+        "pubmed:26432246",
+        "pubmed:26432245"
       ],
       "sc:description": "The 1000 Genomes Project ran between 2008 and 2015, creating a deep catalogue of human genetic variation. The International Genome Sample Resource (IGSR) was set up to ensure the future usability and accessibility of this data.",
       "sc:featureList": [
         {
           "@id": "edam:operation_0306"
         },
         {
-          "@id": "edam:operation_3431"
+          "@id": "edam:operation_3196"
         },
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-          "@id": "edam:operation_3196"
+          "@id": "edam:operation_3431"
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         {
           "@id": "edam:operation_3202"
@@ -116,17 +108,25 @@
       "sc:isAccessibleForFree": true,
       "sc:name": "1000Genomes",
       "sc:operatingSystem": [
-        "Linux",
+        "Mac",
         "Windows",
-        "Mac"
+        "Linux"
       ],
       "sc:softwareHelp": {
         "@id": "http://www.internationalgenome.org/about"
       },
       "sc:url": "http://www.internationalgenome.org"
     },
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-      "@id": "https://doi.org/10.1038/nature11632",
+      "@id": "https://doi.org/10.1038/nature15394",
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diff --git a/data/1000genomes_assembly_converter/1000genomes_assembly_converter.bioschemas.jsonld b/data/1000genomes_assembly_converter/1000genomes_assembly_converter.bioschemas.jsonld
@@ -40,7 +40,7 @@
       "@type": "sc:SoftwareApplication",
       "biotools:primaryContact": "Ensembl Genomes webteam",
       "bsc:input": {
-        "@id": "_:N6a544c3a96db45519e0bc44630f51dfd"
+        "@id": "_:N745fba8ef3bc47219618730c9f32648b"
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       "dcterms:conformsTo": "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT",
       "sc:additionalType": "Web application",
@@ -54,8 +54,8 @@
       },
       "sc:name": "1000Genomes assembly converter",
       "sc:operatingSystem": [
-        "Windows",
         "Linux",
+        "Windows",
         "Mac"
       ],
       "sc:provider": "EMBL-EBI",
@@ -71,23 +71,23 @@
       "sc:url": "http://browser.1000genomes.org/tools.html"
     },
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-      "@id": "_:N6a544c3a96db45519e0bc44630f51dfd",
+      "@id": "_:N745fba8ef3bc47219618730c9f32648b",
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-          "@id": "edam:format_2305"
+          "@id": "edam:format_2306"
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+          "@id": "edam:format_3003"
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+          "@id": "edam:format_2305"
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-          "@id": "edam:format_3003"
+          "@id": "edam:format_3007"
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       ],
       "sc:name": "Nucleic acid features"

diff --git a/data/1000genomes_data_slicer/1000genomes_data_slicer.bioschemas.jsonld b/data/1000genomes_data_slicer/1000genomes_data_slicer.bioschemas.jsonld
@@ -40,7 +40,7 @@
       "@type": "sc:SoftwareApplication",
       "biotools:primaryContact": "Ensembl Genomes webteam",
       "bsc:input": {
-        "@id": "_:Nd1c3cd385e7e4568adf70ad2c0b4687e"
+        "@id": "_:Nb271065183b94a95b986dc5245c830e6"
       },
       "dcterms:conformsTo": "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT",
       "sc:additionalType": "Web application",
@@ -57,34 +57,34 @@
       },
       "sc:name": "1000Genomes data slicer",
       "sc:operatingSystem": [
-        "Mac",
         "Linux",
+        "Mac",
         "Windows"
       ],
       "sc:provider": "EMBL-EBI",
       "sc:softwareHelp": [
         {
-          "@id": "http://browser.1000genomes.org/tools.html"
+          "@id": "http://www.ebi.ac.uk/about/terms-of-use"
         },
         {
-          "@id": "http://www.ebi.ac.uk/about/terms-of-use"
+          "@id": "http://browser.1000genomes.org/tools.html"
         }
       ],
       "sc:softwareVersion": "1",
       "sc:url": "http://browser.1000genomes.org/tools.html"
     },
     {
-      "@id": "_:Nd1c3cd385e7e4568adf70ad2c0b4687e",
+      "@id": "_:Nb271065183b94a95b986dc5245c830e6",
       "@type": "bsct:FormalParameter",
       "sc:additionalType": {
         "@id": "edam:data_2012"
       },
       "sc:encodingFormat": [
         {
-          "@id": "edam:format_3016"
+          "@id": "edam:format_2572"
         },
         {
-          "@id": "edam:format_2572"
+          "@id": "edam:format_3016"
         }
       ],
       "sc:name": "Sequence coordinates"

diff --git a/data/1000genomes_id_history_converter/1000genomes_id_history_converter.bioschemas.jsonld b/data/1000genomes_id_history_converter/1000genomes_id_history_converter.bioschemas.jsonld
@@ -35,19 +35,15 @@
     "xsd": "http://www.w3.org/2001/XMLSchema#"
   },
   "@graph": [
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-      "@type": "sc:CreativeWork"
-    },
     {
       "@id": "https://bio.tools/1000genomes_id_history_converter",
       "@type": "sc:SoftwareApplication",
       "biotools:primaryContact": "Ensembl Genomes webteam",
       "bsc:input": {
-        "@id": "_:N67881a87fed349eeaf004b282bc3c691"
+        "@id": "_:Nbeb8a373faea47d2817f7314ed4488d2"
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       "bsc:output": {
-        "@id": "_:N5b6a5963ce5e491ebe39d4d87f0aa918"
+        "@id": "_:N6bdfb30c6d274b6c85911efa42ce07b5"
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       "dcterms:conformsTo": "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT",
       "sc:additionalType": "Web application",
@@ -64,9 +60,9 @@
       },
       "sc:name": "1000Genomes ID history converter",
       "sc:operatingSystem": [
+        "Mac",
         "Windows",
-        "Linux",
-        "Mac"
+        "Linux"
       ],
       "sc:provider": "EMBL-EBI",
       "sc:softwareHelp": [
@@ -81,20 +77,24 @@
       "sc:url": "http://browser.1000genomes.org/tools.html"
     },
     {
-      "@id": "_:N5b6a5963ce5e491ebe39d4d87f0aa918",
+      "@id": "_:N6bdfb30c6d274b6c85911efa42ce07b5",
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       "sc:additionalType": {
         "@id": "edam:data_2610"
       },
       "sc:name": "Ensembl ID"
     },
     {
-      "@id": "_:N67881a87fed349eeaf004b282bc3c691",
+      "@id": "_:Nbeb8a373faea47d2817f7314ed4488d2",
       "@type": "bsct:FormalParameter",
       "sc:additionalType": {
         "@id": "edam:data_2610"
       },
       "sc:name": "Ensembl ID"
+    },
+    {
+      "@id": "https://doi.org/10.1002/9781118782392.ch27",
+      "@type": "sc:CreativeWork"
     }
   ]
 }
diff --git a/...00genomes_variation_pattern_finder/1000genomes_variation_pattern_finder.bioschemas.jsonld b/...00genomes_variation_pattern_finder/1000genomes_variation_pattern_finder.bioschemas.jsonld
@@ -44,7 +44,7 @@
       "@type": "sc:SoftwareApplication",
       "biotools:primaryContact": "Ensembl Genomes webteam",
       "bsc:input": {
-        "@id": "_:N699a887989124091b259cdbd6b34379a"
+        "@id": "_:Nee05e840f301476aa093ef353ddba32a"
       },
       "dcterms:conformsTo": "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT",
       "sc:additionalType": "Web application",
@@ -65,8 +65,8 @@
       },
       "sc:name": "1000Genomes Variation Pattern Finder",
       "sc:operatingSystem": [
-        "Windows",
         "Linux",
+        "Windows",
         "Mac"
       ],
       "sc:provider": "EMBL-EBI",
@@ -82,7 +82,7 @@
       "sc:url": "http://browser.1000genomes.org/tools.html"
     },
     {
-      "@id": "_:N699a887989124091b259cdbd6b34379a",
+      "@id": "_:Nee05e840f301476aa093ef353ddba32a",
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       "sc:additionalType": {
         "@id": "edam:data_3498"

diff --git a/data/1000genomes_vcf2ped/1000genomes_vcf2ped.bioschemas.jsonld b/data/1000genomes_vcf2ped/1000genomes_vcf2ped.bioschemas.jsonld
@@ -40,7 +40,7 @@
       "@type": "sc:SoftwareApplication",
       "biotools:primaryContact": "Ensembl Genomes webteam",
       "bsc:input": {
-        "@id": "_:N137889fbf5f54948b034efc87e807ed9"
+        "@id": "_:Ndf167cc6d6f142a89468d914efcd53a0"
       },
       "dcterms:conformsTo": "https://bioschemas.org/profiles/ComputationalTool/0.6-DRAFT",
       "sc:additionalType": "Web application",
@@ -53,8 +53,8 @@
         }
       ],
       "sc:author": [
-        "Resequencing Informatics",
-        "Ensembl Genomes team"
+        "Ensembl Genomes team",
+        "Resequencing Informatics"
       ],
       "sc:contributor": "Resequencing Informatics",
       "sc:description": "Convert a VCF file into a linkage pedigree file (ped) and a marker information file, which together may be loaded into ld visualization tools like Haploview.",
@@ -75,7 +75,7 @@
       "sc:url": "http://browser.1000genomes.org/tools.html"
     },
     {
-      "@id": "_:N137889fbf5f54948b034efc87e807ed9",
+      "@id": "_:Ndf167cc6d6f142a89468d914efcd53a0",
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       "sc:additionalType": {
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diff --git a/data/13check_rna/13check_rna.bioschemas.jsonld b/data/13check_rna/13check_rna.bioschemas.jsonld
@@ -35,10 +35,6 @@
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-      "@type": "sc:CreativeWork"
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       "@id": "https://bio.tools/13Check_RNA",
       "@type": "sc:SoftwareApplication",
@@ -50,13 +46,13 @@
       "sc:additionalType": "Library",
       "sc:applicationSubCategory": [
         {
-          "@id": "edam:topic_0749"
+          "@id": "edam:topic_0593"
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+          "@id": "edam:topic_0749"
         },
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-          "@id": "edam:topic_0593"
+          "@id": "edam:topic_0099"
         }
       ],
       "sc:citation": {
@@ -70,14 +66,18 @@
       "sc:license": "MIT",
       "sc:name": "13Check_RNA",
       "sc:operatingSystem": [
-        "Linux",
         "Windows",
-        "Mac"
+        "Mac",
+        "Linux"
       ],
       "sc:softwareHelp": {
         "@id": "https://github.com/BIOS-IMASL/13Check_RNA/blob/master/README.md"
       },
       "sc:url": "https://github.com/BIOS-IMASL/13Check_RNA"
+    },
+    {
+      "@id": "https://doi.org/10.1093/bioinformatics/bty470",
+      "@type": "sc:CreativeWork"
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 }