diff --git a/HTAN.model.csv b/HTAN.model.csv index a4d32b90..d4d6472e 100644 --- a/HTAN.model.csv +++ b/HTAN.model.csv @@ -883,7 +883,7 @@ Publication,An empty parent attribute for publications,,,,FALSE,,,, Publication Manifest,Publication specific attributes.,,"Component,Publication-associated HTAN Parent Data File ID, HTAN Grant ID, HTAN Center ID, Publication Content Type, DOI, Title, Authors, Corresponding Author, Corresponding Author ORCID, Year of Publication, Location of Publication, Publication Abstract, License, PMID, Publication contains HTAN ID, Data Type, Tool, Supporting Link, Supporting Link Description",,FALSE,Publication,,, Publication-associated HTAN Parent Data File ID,HTAN Data File Identifier(s) of the files associated with the content presented/published. Should be comma-separated lists.,,,,TRUE,Publication,,,list like HTAN Grant ID,HTAN grant number(s) (i.e. CA------ format) associated with the content presented/published.,,,,TRUE,Publication,,,list like -HTAN Center ID,List of HTAN Center ID(s) associated with the content presented/published.,"HTA1, HTA2, HTA3, HTA4, HTA5, HTA6, HTA7, HTA8, HTA9, HTA10, HTA11, HTA12, HTA13, HTA14",,,TRUE,Publication,,,list like +HTAN Center ID,List of HTAN Center ID(s) associated with the content presented/published.,"HTA1, HTA2, HTA3, HTA4, HTA5, HTA6, HTA7, HTA8, HTA9, HTA10, HTA11, HTA12, HTA13, HTA14,HTA15,HTA16",,,TRUE,Publication,,,list like Publication Content Type,The type of content presented or published.,"Preprint, Published manuscript, Conference proceedings",,,TRUE,Publication,,, DOI,The digital object identifier (DOI) of the content in the form of https://www.doi.org/{doi} to comply with CrossRef DOI display guidelines.,,,,TRUE,Publication,,https://www.doi.org/,url Corresponding Author,"The name(s) of the corresponding author(s) of the content presented/published. If more than one corresponding author, please list in the order they appear in the author list.",,,,TRUE,Publication,,, @@ -900,6 +900,13 @@ Other Data Type Specified,Other types of data associated with the content.,,,,FA Supporting Link,Relevant external links associated with the content (e.g external datasets used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and/or any other applicable agreement(s). Validated as URL,,,,FALSE,Publication,,,url Supporting Link Description,Description of relevant external links associated with the publication (e.g An external mouse dataset used for validation). Please note: Supporting Links and Supporting Link Descriptions are provided by authors and are not verified by the NIH NCI or the HTAN DCC. This information and any linked data should only be shared by an authorized individual(s) in accordance with the terms of the HTAN data sharing agreements and policies and-or any other applicable agreement(s).,,,,FALSE,Publication,,, Tool,Were any software or computational tools generated for this content,"Yes, No",,,TRUE,Publication,,, +Accessory,An empty parent attribute for accessory ,,,,FALSE,,,, +Accessory Manifest,Accessory specific attributes,,"Component,Accessory Name,Accessory Synapse ID,Accessory Type,Accessory Description,Data Type,HTAN Center ID,Accessory-associated HTAN Parent Data File ID",,FALSE,Accessory,,, +Accessory Name,Name of accessory file or folder,,,,TRUE,Accessory,,, +Accessory Synapse ID,"Synapse ID of accessory file, folder, or dataset",,,,TRUE,Accessory,,,regex match syn\d+ +Accessory Type,"Type of accessory entity (File, Folder, or Dataset)","File,Folder,Dataset",,,TRUE,Accessory,,, +Accessory Description,Free text field containing description of accessory file(s),,,,TRUE,Accessory,,, +Accessory-associated HTAN Parent Data File ID,HTAN Data File Identifier(s) of the files associated with the accessory content. Should be comma-separated lists.,,,,TRUE,Accessory,,,list like MapQ30,Number of reads with Quality >= 30.,,,,FALSE,"scATAC-seq Level 1, NanoString GeoMx DSP ROI DCC Segment Annotation Metadata",,, scATAC-seq Object ID,Orig.Ident or scATAC-seq Object ID,,,,FALSE,scATAC-seq Level 3,,, nCount Peaks,Total number of fragments in peaks,,,,FALSE,scATAC-seq Level 2,,, @@ -1004,4 +1011,4 @@ Tile overlap Y,Percentage of image overlap to allow tile stitching in x directio Barretts Esophagus Goblet Cells Present,Presence or absennce of Barretts esophagus goblet cells.,"Yes, No",,,FALSE,Follow Up,,, Pancreatitis Onset Year,Date of onset of pancreatitis.,,,,FALSE,Follow Up,,,num HTAN Parent Channel Metadata ID,HTAN ID for a level 3 channels table.,,,,TRUE, Imaging Level 4,,, -Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,, +Single Nucleus Capture,Nuclei isolation method,"Plates, 10x, droplet",,,FALSE,scmC-seq Level 1,,, \ No newline at end of file diff --git a/HTAN.model.jsonld b/HTAN.model.jsonld index 69a85956..4117c954 100644 --- a/HTAN.model.jsonld +++ b/HTAN.model.jsonld @@ -958,6 +958,9 @@ "rdfs:comment": "A type of Information Content Entity specific to OS", "rdfs:label": "File", "rdfs:subClassOf": [ + { + "@id": "bts:AccessoryType" + }, { "@id": "bts:InformationContentEntity" } @@ -140932,6 +140935,12 @@ }, { "@id": "bts:HTA14" + }, + { + "@id": "bts:HTA15" + }, + { + "@id": "bts:HTA16" } ], "sms:displayName": "HTAN Center ID", @@ -142515,6 +142524,40 @@ "sms:required": "sms:false", "sms:validationRules": [] }, + { + "@id": "bts:HTA15", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "HTA15", + "rdfs:subClassOf": [ + { + "@id": "bts:HTANCenterID" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTA15", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:HTA16", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "HTA16", + "rdfs:subClassOf": [ + { + "@id": "bts:HTANCenterID" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "HTA16", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Preprint", "@type": "rdfs:Class", @@ -148266,6 +148309,200 @@ "list like" ] }, + { + "@id": "bts:Accessory", + "@type": "rdfs:Class", + "rdfs:comment": "An empty parent attribute for accessory", + "rdfs:label": "Accessory", + "rdfs:subClassOf": [ + { + "@id": "bts:Thing" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Accessory", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:AccessoryManifest", + "@type": "rdfs:Class", + "rdfs:comment": "Accessory specific attributes", + "rdfs:label": "AccessoryManifest", + "rdfs:subClassOf": [ + { + "@id": "bts:Accessory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Accessory Manifest", + "sms:required": "sms:false", + "sms:requiresDependency": [ + { + "@id": "bts:Component" + }, + { + "@id": "bts:AccessoryName" + }, + { + "@id": "bts:AccessorySynapseID" + }, + { + "@id": "bts:AccessoryType" + }, + { + "@id": "bts:AccessoryDescription" + }, + { + "@id": "bts:DataType" + }, + { + "@id": "bts:HTANCenterID" + }, + { + "@id": "bts:Accessory-associatedHTANParentDataFileID" + } + ], + "sms:validationRules": [] + }, + { + "@id": "bts:AccessoryName", + "@type": "rdfs:Class", + "rdfs:comment": "Name of accessory file or folder", + "rdfs:label": "AccessoryName", + "rdfs:subClassOf": [ + { + "@id": "bts:Accessory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Accessory Name", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AccessorySynapseID", + "@type": "rdfs:Class", + "rdfs:comment": "Synapse ID of accessory file, folder, or dataset", + "rdfs:label": "AccessorySynapseID", + "rdfs:subClassOf": [ + { + "@id": "bts:Accessory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Accessory Synapse ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "regex match syn\\d+" + ] + }, + { + "@id": "bts:AccessoryType", + "@type": "rdfs:Class", + "rdfs:comment": "Type of accessory entity (File, Folder, or Dataset)", + "rdfs:label": "AccessoryType", + "rdfs:subClassOf": [ + { + "@id": "bts:Accessory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "schema:rangeIncludes": [ + { + "@id": "bts:File" + }, + { + "@id": "bts:Folder" + }, + { + "@id": "bts:Dataset" + } + ], + "sms:displayName": "Accessory Type", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:AccessoryDescription", + "@type": "rdfs:Class", + "rdfs:comment": "Free text field containing description of accessory file(s)", + "rdfs:label": "AccessoryDescription", + "rdfs:subClassOf": [ + { + "@id": "bts:Accessory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Accessory Description", + "sms:required": "sms:true", + "sms:validationRules": [] + }, + { + "@id": "bts:Accessory-associatedHTANParentDataFileID", + "@type": "rdfs:Class", + "rdfs:comment": "HTAN Data File Identifier(s) of the files associated with the accessory content. Should be comma-separated lists.", + "rdfs:label": "Accessory-associatedHTANParentDataFileID", + "rdfs:subClassOf": [ + { + "@id": "bts:Accessory" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Accessory-associated HTAN Parent Data File ID", + "sms:required": "sms:true", + "sms:validationRules": [ + "list like" + ] + }, + { + "@id": "bts:Folder", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Folder", + "rdfs:subClassOf": [ + { + "@id": "bts:AccessoryType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Folder", + "sms:required": "sms:false", + "sms:validationRules": [] + }, + { + "@id": "bts:Dataset", + "@type": "rdfs:Class", + "rdfs:comment": "TBD", + "rdfs:label": "Dataset", + "rdfs:subClassOf": [ + { + "@id": "bts:AccessoryType" + } + ], + "schema:isPartOf": { + "@id": "http://schema.biothings.io" + }, + "sms:displayName": "Dataset", + "sms:required": "sms:false", + "sms:validationRules": [] + }, { "@id": "bts:Yes-Islowestlevel", "@type": "rdfs:Class",