Skip to content

Commit

Permalink
Merge pull request #346 from ncihtan/add-accessory
Browse files Browse the repository at this point in the history 
Create accessory component
  • Loading branch information
@adamjtaylor
adamjtaylor authored Feb 19, 2024
2 parents bb798b5 + 76e92d1 commit 39460c8
Show file tree
Hide file tree
Showing 2 changed files with 246 additions and 2 deletions.
11 changes: 9 additions & 2 deletions HTAN.model.csv
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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,,,
Expand All @@ -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,,,
Expand Down Expand Up @@ -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,,,
237 changes: 237 additions & 0 deletions HTAN.model.jsonld
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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"
}
Expand Down Expand Up @@ -140932,6 +140935,12 @@
},
{
"@id": "bts:HTA14"
},
{
"@id": "bts:HTA15"
},
{
"@id": "bts:HTA16"
}
],
"sms:displayName": "HTAN Center ID",
Expand Down Expand Up @@ -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",
Expand Down Expand Up @@ -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",
Expand Down

0 comments on commit 39460c8

Please sign in to comment.