Use absolute paths and add missing string types (Sage-Bionetworks#851)

* Use absolute paths in $id field

* Increment version numbers

* Increment and update bindingDensity, sourceCell

Co-authored-by: Kara Woo <[email protected]>

CONTRIBUTING.md

@@ -14,7 +14,7 @@ examples, but the general format for a new term should be like this:
 ```json
 {
   "$schema": "http://json-schema.org/draft-07/schema#",
-  "$id": "sage.annotations-<MODULENAME>.<KEY>-0.0.1",
+  "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-<MODULENAME>.<KEY>-0.0.1",
   "description": "<DESCRIPTION OF THE KEY>",
   "anyOf": [
     {

README.md

@@ -16,7 +16,7 @@ that are valid JSON Schema, such as the following:
 ```
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-experimentalData.specimenID-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-experimentalData.specimenID-0.0.1",
     "description": "Identifying string linked to a particular sample or specimen",
     "type": "string"
 }

schemas/testschema.json

@@ -1,6 +1,6 @@
 {
   "$schema": "http://json-schema.org/draft-07/schema#",
-  "$id":"sage.annotations-testschema.json-0.0.2",
+  "$id":"https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-testschema.json-0.0.3",
   "properties": {
     "resourceType": {
       "$ref": "sage.annotations-sageCommunity.resourceType-0.0.1"

term-templates/template-boolean.json

@@ -1,6 +1,6 @@
 {
   "$schema": "http://json-schema.org/draft-07/schema#",
-  "$id": "sage.annotations-<MODULENAME>.<KEY>-0.0.1",
+  "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-<MODULENAME>.<KEY>-0.0.1",
   "description": "<DESCRIPTION OF THE KEY>",
   "type": "boolean"
 }

term-templates/template-enum.json

@@ -1,6 +1,6 @@
 {
   "$schema": "http://json-schema.org/draft-07/schema#",
-  "$id": "sage.annotations-<MODULENAME>.<KEY>-0.0.1",
+  "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-<MODULENAME>.<KEY>-0.0.1",
   "description": "<DESCRIPTION OF THE KEY>",
   "anyOf": [
     {

term-templates/template-number.json

@@ -1,6 +1,6 @@
 {
   "$schema": "http://json-schema.org/draft-07/schema#",
-  "$id": "sage.annotations-<MODULENAME>.<KEY>-0.0.1",
+  "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-<MODULENAME>.<KEY>-0.0.1",
   "description": "<DESCRIPTION OF THE KEY>",
   "type": "number"
 }

term-templates/template-string.json

@@ -1,6 +1,6 @@
 {
   "$schema": "http://json-schema.org/draft-07/schema#",
-  "$id": "sage.annotations-<MODULENAME>.<KEY>-0.0.1",
+  "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-<MODULENAME>.<KEY>-0.0.1",
   "description": "<DESCRIPTION OF THE KEY>",
   "type": "string",
   "minLength": 1,

terms/PsychENCODESpecific/grant.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id":"sage.annotations-PsychENCODESpecific.grant-0.0.1",
+    "$id":"https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-PsychENCODESpecific.grant-0.0.2",
     "description": "Grant number including activity code, institute code, and serial number (e.g. U01MH103392)",
     "type": "string",
     "anyOf": [

terms/PsychENCODESpecific/study.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id":"sage.annotations-PsychENCODESpecific.study-0.0.4",
+    "$id":"https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-PsychENCODESpecific.study-0.0.5",
     "description": "Study",
     "type": "string",
     "anyOf": [

terms/analysis/alignmentMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.alignmentMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.alignmentMethod-0.0.2",
     "description": "DNA or RNA sequence alignment method",
+    "type": "string",
     "anyOf": [
         {
             "const": "Burrows-Wheeler technique",

terms/analysis/analysisType.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.analysisType-0.0.8",
-    "description": "",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.analysisType-0.0.9",
+    "description": "Type of analysis",
+    "type": "string",
     "anyOf": [
         {
             "const": "ANOVA",

terms/analysis/assemblyMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.assemblyMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.assemblyMethod-0.0.2",
     "description": "Algorithm used to build a reference genome from short read sequencing data.",
+    "type": "string",
     "anyOf": [
         {
             "const": "Velvet",

terms/analysis/batchEffectCorrectionMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.batchEffectCorrectionMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.batchEffectCorrectionMethod-0.0.2",
     "description": "Methods for identifying or correcting potential confounding variables in regression analyses.",
+    "type": "string",
     "anyOf": [
         {
             "const": "COMBAT",

terms/analysis/clusteringMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.clusteringMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.clusteringMethod-0.0.2",
     "description": "A method to identify groups of similar variables based on their data distribution.",
+    "type": "string",
     "anyOf": [
         {
             "const": "hierarchical clustering",

terms/analysis/differentialExpressionMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.differentialExpressionMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.differentialExpressionMethod-0.0.2",
     "description": "Method used to test for differentially expressed genes or isoforms.",
+    "type": "string",
     "anyOf": [
         {
             "const": "limma",

terms/analysis/enrichmentMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.enrichmentMethod-0.0.1",
-    "description": "",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.enrichmentMethod-0.0.2",
+    "description": "Enrichment method.",
+    "type": "string",
     "anyOf": [
         {
             "const": "Fisher's exact test",

terms/analysis/fdr.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.fdr-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.fdr-0.0.2",
     "type": "number",
     "description": "False discovery rate"
 }

terms/analysis/multipleTestingAdjustmentMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.multipleTestingAdjustmentMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.multipleTestingAdjustmentMethod-0.0.2",
     "description": "Method used to control either family wise error rate, false discovery rate, or other measures of burden of false positives and false negatives when performing multiple statistical tests.",
+    "type": "string",
     "anyOf": [
         {
             "const": "Benjamini Hochberg",

terms/analysis/peakCallingMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.peakCallingMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.peakCallingMethod-0.0.2",
     "description": "The algorithm used to identify protein-binding regions in a genome sequence from the data generated from a ChIP-sequencing or ChIP-chip experiment.",
+    "type": "string",
     "anyOf": [
         {
             "const": "MACS",

terms/analysis/somaticMutationCallingMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.somaticMutationCallingMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.somaticMutationCallingMethod-0.0.2",
     "description": "Algorithm to call somatic mutations.",
+    "type": "string",
     "anyOf": [
         {
             "const": "VarDict",

terms/analysis/statisticalNetworkReconstructionMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.statisticalNetworkReconstructionMethod-0.0.1",
-    "description": "",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.statisticalNetworkReconstructionMethod-0.0.2",
+    "description": "Statistical network reconstruction method.",
+    "type": "string",
     "anyOf": [
         {
             "const": "Weighted correlation network analysis",

terms/analysis/supervisedLearningMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.supervisedLearningMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.supervisedLearningMethod-0.0.2",
     "description": "An algorithm to fit a model to make predictions of future outcomes based past data.",
+    "type": "string",
     "anyOf": [
         {
             "const": "penalized regression",

terms/analysis/transcriptQuantificationMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.transcriptQuantificationMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.transcriptQuantificationMethod-0.0.2",
     "description": "Method for quantifying abundance of transcript expression.",
+    "type": "string",
     "anyOf": [
         {
             "const": "kallisto",

terms/analysis/validationMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.validationMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.validationMethod-0.0.2",
     "description": "Method to test targeted sequence level hypothesis.",
+    "type": "string",
     "anyOf": [
         {
             "const": "CRISPR-Cas9",

terms/analysis/visualizationMethod.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-analysis.visualizationMethod-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-analysis.visualizationMethod-0.0.2",
     "description": "The format in which data is visually displayed.",
+    "type": "string",
     "anyOf": [
         {
             "const": "scatter plot",

terms/array/channel.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-array.channel-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-array.channel-0.0.2",
     "description": "Fluorescent color labeling for an array",
+    "type": "string",
     "anyOf": [
         {
             "const": "Cy5",

terms/batch/arrayBatch.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "sage.annotations-batch.arrayBatch-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-batch.arrayBatch-0.0.2",
     "type": "string",
     "description": "The hybridization batch the sample was in"
 }

terms/batch/batch.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-batch.batch-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-batch.batch-0.0.2",
     "description": "Batch specimen was processed in",
     "type": "string"
 }

terms/batch/batchChannel.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "sage.annotations-batch.batchChannel-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-batch.batchChannel-0.0.2",
     "type": "string",
     "description": "TMT channel the sample is labeled with"
 }

terms/batch/dnaBatch.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "sage.annotations-batch.dnaBatch-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-batch.dnaBatch-0.0.2",
     "type": "string",
     "description": "DNA isolation batch"
 }

terms/batch/libraryBatch.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "sage.annotations-batch.libraryBatch-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-batch.libraryBatch-0.0.2",
     "type": "string",
     "description": "Batch library was prepared in"
 }

terms/batch/nanostringBatch.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "sage.annotations-batch.nanostringBatch-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-batch.nanostringBatch-0.0.2",
     "type": "string",
     "description": "The batch of samples run on a nanostring panel. Twelve samples can be processed together at once on a machine."
 }

terms/batch/rnaBatch.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "sage.annotations-batch.rnaBatch-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-batch.rnaBatch-0.0.2",
     "type": "string",
     "description": "Batch in which RNA sample was isolated"
 }

terms/batch/sequencingBatch.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "sage.annotations-batch.sequencingBatch-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-batch.sequencingBatch-0.0.2",
     "type": "string",
     "description": "Batch library was sequenced in"
 }

terms/batch/transposaseBatch.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema",
-    "$id": "sage.annotations-batch.transposaseBatch-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-batch.transposaseBatch-0.0.2",
     "type": "string",
     "description": "Transposition reaction batch"
 }

terms/cancer/cellSubType.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-cancer.cellSubType-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-cancer.cellSubType-0.0.2",
     "description": "This term is to be used when cell type is not specific enough, such as certain classes of T cells",
     "type": "string"
 }

terms/cancer/experimentalCondition.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-cancer.experimentalCondition-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-cancer.experimentalCondition-0.0.2",
     "description": "This describes the condition under which the data were collected, designed to be free form, extra things that do not fit in pre-defined terms",
     "type": "string"
 }

terms/cancer/experimentalTimePoint.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-cancer.experimentalTimePoint-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-cancer.experimentalTimePoint-0.0.2",
     "description": "Number describing time point at which data was collected",
     "type": "string"
 }

terms/cancer/genePerturbationTechnology.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-cancer.genePerturbationTechnology-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-cancer.genePerturbationTechnology-0.0.2",
     "description": "Technology used to perform gene perturbation",
+    "type": "string",
     "anyOf": [
         {
             "const": "RNAi",

terms/cancer/genePerturbationType.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-cancer.genePerturbationType-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-cancer.genePerturbationType-0.0.2",
     "description": "Specific way in which a single gene was perturbed in a sample",
+    "type": "string",
     "anyOf": [
         {
             "const": "overexpression",

terms/cancer/genePerturbed.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-cancer.genePerturbed-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-cancer.genePerturbed-0.0.2",
     "description": "In the case of gene modulation, this describes the gene or genes that were modulated",
     "type": "string"
 }

terms/cancer/timePointUnit.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-cancer.timePointUnit-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-cancer.timePointUnit-0.0.2",
     "description": "For timed experiments this represents the unit of time measured",
+    "type": "string",
     "anyOf": [
         {
             "const": "hours",

terms/cancer/transplantationDonorTissue.json

@@ -1,6 +1,6 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-cancer.transplantationDonorTissue-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-cancer.transplantationDonorTissue-0.0.2",
     "description": "",
     "type": "string"
 }

terms/cancer/transplantationRecipientSpecies.json

@@ -1,7 +1,8 @@
 {
     "$schema": "http://json-schema.org/draft-07/schema#",
-    "$id": "sage.annotations-cancer.transplantationRecipientSpecies-0.0.1",
+    "$id": "https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/sage.annotations-cancer.transplantationRecipientSpecies-0.0.2",
     "description": "Species into which donor tissue was grown",
+    "type": "string",
     "anyOf": [
         {
             "const": "Human",