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Expand metadata tokenisation #57

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merged 5 commits into from
Apr 19, 2024
Merged

Expand metadata tokenisation #57

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77f2f48
Update Metadata references
LibraChris Mar 21, 2024
ebce217
Update ReferenceObjects.fs
LibraChris Mar 22, 2024
600fc31
Update testing
LibraChris Mar 22, 2024
8a444fe
Update FileSystemTokenization Test
LibraChris Apr 9, 2024
b035f0c
Adapt ARCMock to allow for empty fields to be deleted
LibraChris Apr 16, 2024
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495 changes: 278 additions & 217 deletions src/ARCTokenization/ARCMock.fs
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30 changes: 18 additions & 12 deletions src/ARCTokenization/structural_ontologies/ASSMSO.fs
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Original file line number Diff line number Diff line change
Expand Up @@ -13,20 +13,26 @@ module ASSMSO =

module ``ASSAY`` =
let key = CvTerm.create("ASSMSO:00000002","ASSAY","ASSMSO")

let ``Assay Measurement Type`` = CvTerm.create("ASSMSO:00000004","Assay Measurement Type","ASSMSO")
let ``Assay Measurement Type Term Accession Number`` = CvTerm.create("ASSMSO:00000006","Assay Measurement Type Term Accession Number","ASSMSO")
let ``Assay Measurement Type Term Source REF`` = CvTerm.create("ASSMSO:00000008","Assay Measurement Type Term Source REF","ASSMSO")
let ``Assay Technology Type`` = CvTerm.create("ASSMSO:00000011","Assay Technology Type","ASSMSO")
let ``Assay Technology Type Term Accession Number`` = CvTerm.create("ASSMSO:00000013","Assay Technology Type Term Accession Number","ASSMSO")
let ``Assay Technology Type Term Source REF`` =CvTerm.create("ASSMSO:00000015","Assay Technology Type Term Source REF","ASSMSO")
let ``Assay Technology Platform`` = CvTerm.create("ASSMSO:00000017","Assay Technology Platform","ASSMSO")
let ``Assay File Name`` = CvTerm.create("ASSMSO:00000019","Assay File Name","ASSMSO")

module ``ASSAY PERFORMERS`` =
let key = CvTerm.create("ASSMSO:00000020","ASSAY PERFORMERS","ASSMSO")

let ``Assay Performer Last Name`` = CvTerm.create("ASSMSO:00000021","Assay Performer Last Name","ASSMSO")
let ``Assay Performer First Name`` = CvTerm.create("ASSMSO:00000023","Assay Performer First Name","ASSMSO")
let ``Assay Performer Mid Initials`` = CvTerm.create("ASSMSO:00000025","Assay Performer Mid Initials","ASSMSO")
let ``Assay Performer Email`` = CvTerm.create("ASSMSO:00000027","Assay Performer Email","ASSMSO")
let ``Assay Performer Phone`` = CvTerm.create("ASSMSO:00000029","Assay Performer Phone","ASSMSO")
let ``Assay Performer Fax`` = CvTerm.create("ASSMSO:00000031","Assay Performer Fax","ASSMSO")
let ``Assay Performer Address`` = CvTerm.create("ASSMSO:00000033","Assay Performer Address","ASSMSO")
let ``Assay Performer Affiliation`` = CvTerm.create("ASSMSO:00000035","Assay Performer Affiliation","ASSMSO")
let ``Assay Performer Roles`` = CvTerm.create("ASSMSO:00000037","Assay Performer Roles","ASSMSO")
let ``Assay Performer Roles Term Accession Number`` = CvTerm.create("ASSMSO:00000039","Assay Performer Roles Term Accession Number","ASSMSO")
let ``Assay Performer Roles Term Source REF`` = CvTerm.create("ASSMSO:00000041","Assay Performer Roles Term Source REF","ASSMSO")
let ``Assay Person Last Name`` = CvTerm.create("ASSMSO:00000021","Assay Person Last Name","ASSMSO")
let ``Assay Person First Name`` = CvTerm.create("ASSMSO:00000023","Assay Person First Name","ASSMSO")
let ``Assay Person Mid Initials`` = CvTerm.create("ASSMSO:00000025","Assay Person Mid Initials","ASSMSO")
let ``Assay Person Email`` = CvTerm.create("ASSMSO:00000027","Assay Person Email","ASSMSO")
let ``Assay Person Phone`` = CvTerm.create("ASSMSO:00000029","Assay Person Phone","ASSMSO")
let ``Assay Person Fax`` = CvTerm.create("ASSMSO:00000031","Assay Person Fax","ASSMSO")
let ``Assay Person Address`` = CvTerm.create("ASSMSO:00000033","Assay Person Address","ASSMSO")
let ``Assay Person Affiliation`` = CvTerm.create("ASSMSO:00000035","Assay Person Affiliation","ASSMSO")
let ``Assay Person Roles`` = CvTerm.create("ASSMSO:00000037","Assay Person Roles","ASSMSO")
let ``Assay Person Roles Term Accession Number`` = CvTerm.create("ASSMSO:00000039","Assay Person Roles Term Accession Number","ASSMSO")
let ``Assay Person Roles Term Source REF`` = CvTerm.create("ASSMSO:00000041","Assay Person Roles Term Source REF","ASSMSO")
92 changes: 74 additions & 18 deletions src/ARCTokenization/structural_ontologies/INVMSO.fs
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Expand Up @@ -12,23 +12,33 @@ module INVMSO =
let key = CvTerm.create("INVMSO:00000001","Investigation Metadata","INVMSO")

module ``ONTOLOGY SOURCE REFERENCE`` =
let key = CvTerm.create("INVMSO:00000002","ONTOLOGY SOURCE REFERENCE","INVMSO")

let key = CvTerm.create("INVMSO:00000002","ONTOLOGY SOURCE REFERENCE","INVMSO")
let ``Term Source Name`` = CvTerm.create("INVMSO:00000003","Term Source Name","INVMSO")
let ``Term Source File`` = CvTerm.create("INVMSO:00000004","Term Source File","INVMSO")
let ``Term Source Version`` = CvTerm.create("INVMSO:00000005","Term Source Version","INVMSO")
let ``Term Source Description`` = CvTerm.create("INVMSO:00000006","Term Source Description","INVMSO")

module ``INVESTIGATION`` =
let key = CvTerm.create("INVMSO:00000007","INVESTIGATION","INVMSO")

let ``Investigation Identifier`` = CvTerm.create("INVMSO:00000008","Investigation Identifier","INVMSO")
let ``Investigation Title`` = CvTerm.create("INVMSO:00000009","Investigation Title","INVMSO")
let ``Investigation Description`` = CvTerm.create("INVMSO:00000010","Investigation Description","INVMSO")
let ``Investigation Submission Date`` = CvTerm.create("INVMSO:00000011","Investigation Submission Date","INVMSO")
let ``Investigation Public Release Date`` = CvTerm.create("INVMSO:00000012","Investigation Public Release Date","INVMSO")

module ``INVESTIGATION PUBLICATIONS`` =
let key = CvTerm.create("INVMSO:00000013","INVESTIGATION PUBLICATIONS","INVMSO")
module ``INVESTIGATION PUBLICATIONS`` =
let key = CvTerm.create("INVMSO:00000013","INVESTIGATION PUBLICATIONS","INVMSO")
let ``Investigation Publication PubMed ID`` = CvTerm.create("INVMSO:00000014","Investigation Publication PubMed ID","INVMSO")
let ``Investigation Publication DOI`` = CvTerm.create("INVMSO:00000015","Investigation Publication DOI","INVMSO")
let ``Investigation Publication Author List`` = CvTerm.create("INVMSO:00000016","Investigation Publication Author List","INVMSO")
let ``Investigation Publication Title`` = CvTerm.create("INVMSO:00000017","Investigation Publication Title","INVMSO")
let ``Investigation Publication Status`` = CvTerm.create("INVMSO:00000018","Investigation Publication Status","INVMSO")
let ``Investigation Publication Status Term Accession Number`` = CvTerm.create("INVMSO:00000019","Investigation Publication Status Term Accession Number","INVMSO")
let ``Investigation Publication Status Term Source REF`` = CvTerm.create("INVMSO:00000020","Investigation Publication Status Term Source REF","INVMSO")

module ``INVESTIGATION CONTACTS`` =
let key = CvTerm.create("INVMSO:00000021","INVESTIGATION CONTACTS","INVMSO")

let ``Investigation Person Last Name`` = CvTerm.create("INVMSO:00000022","Investigation Person Last Name","INVMSO")
let ``Investigation Person First Name`` = CvTerm.create("INVMSO:00000023","Investigation Person First Name","INVMSO")
let ``Investigation Person Mid Initials`` = CvTerm.create("INVMSO:00000024","Investigation Person Mid Initials","INVMSO")
Expand All @@ -39,37 +49,83 @@ module INVMSO =
let ``Investigation Person Affiliation`` = CvTerm.create("INVMSO:00000029","Investigation Person Affiliation","INVMSO")
let ``Investigation Person Roles`` = CvTerm.create("INVMSO:00000030","Investigation Person Roles","INVMSO")
let ``Investigation Person Roles Term Accession Number`` = CvTerm.create("INVMSO:00000031","Investigation Person Roles Term Accession Number","INVMSO")
let ``Investigation Person Roles Term Source REF`` = CvTerm.create("INVMSO:000000","Investigation Person Roles Term Source REF","INVMSO")
let ``Investigation Person Roles Term Source REF`` = CvTerm.create("INVMSO:00000032","Investigation Person Roles Term Source REF","INVMSO")
let ``Comment[<Investigation Person ORCID>]`` = CvTerm.create("INVMSO:00000093","Comment[<Investigation Person ORCID>]","INVMSO")
let ``Comment[Investigation Person ORCID]`` = CvTerm.create("INVMSO:00000094","Comment[Investigation Person ORCID]","INVMSO")
let ``Comment[ORCID]`` = CvTerm.create("INVMSO:00000095","Comment[ORCID]","INVMSO")

module ``STUDY`` =
let key = CvTerm.create("INVMSO:00000033","STUDY","INVMSO")

let ``Study Identifier`` = CvTerm.create("INVMSO:00000034","Study Identifier","INVMSO")
let ``Study Title`` = CvTerm.create("INVMSO:00000035","Study Title","INVMSO")
let ``Study Description`` = CvTerm.create("INVMSO:00000036","Study Description","INVMSO")
let ``Study Submission Date`` = CvTerm.create("INVMSO:00000037","Study Submission Date","INVMSO")
let ``Study Public Release Date`` = CvTerm.create("INVMSO:00000038","Study Public Release Date","INVMSO")
let ``Study File Name`` = CvTerm.create("INVMSO:00000039","Study File Name","INVMSO")

module ``STUDY DESIGN DESCRIPTORS`` =
module ``STUDY DESIGN DESCRIPTORS`` =
let key = CvTerm.create("INVMSO:00000040","STUDY DESIGN DESCRIPTORS","INVMSO")

module ``STUDY PUBLICATIONS`` =
let ``Study Design Type`` = CvTerm.create("INVMSO:00000041","Study Design Type","INVMSO")
let ``Study Design Type Term Accession Number`` = CvTerm.create("INVMSO:00000042","Study Design Type Term Accession Number","INVMSO")
let ``Study Design Type Term Source REF`` = CvTerm.create("INVMSO:00000043","Study Design Type Term Source REF","INVMSO")

module ``STUDY PUBLICATIONS`` =
let key = CvTerm.create("INVMSO:00000044","STUDY PUBLICATIONS","INVMSO")

module ``STUDY FACTORS`` =
let ``Study Publication PubMed ID`` = CvTerm.create("INVMSO:00000045","Study Publication PubMed ID","INVMSO")
let ``Study Publication DOI`` = CvTerm.create("INVMSO:00000046","Study Publication DOI","INVMSO")
let ``Study Publication Author List`` = CvTerm.create("INVMSO:00000047","Study Publication Author List","INVMSO")
let ``Study Publication Title`` = CvTerm.create("INVMSO:00000048","Study Publication Title","INVMSO")
let ``Study Publication Status`` = CvTerm.create("INVMSO:00000049","Study Publication Status","INVMSO")
let ``Study Publication Status Term Accession Number`` = CvTerm.create("INVMSO:00000050","Study Publication Status Term Accession Number","INVMSO")
let ``Study Publication Status Term Source REF`` = CvTerm.create("INVMSO:00000051","Study Publication Status Term Source REF","INVMSO")

module ``STUDY FACTORS`` =
let key = CvTerm.create("INVMSO:00000052","STUDY FACTORS","INVMSO")
let ``Study Factor Name`` = CvTerm.create("INVMSO:00000053","Study Factor Name","INVMSO")
let ``Study Factor Type`` = CvTerm.create("INVMSO:00000054","Study Factor Type","INVMSO")
let ``Study Factor Type Term Accession Number`` = CvTerm.create("INVMSO:00000055","Study Factor Type Term Accession Number","INVMSO")
let ``Study Factor Type Term Source REF`` = CvTerm.create("INVMSO:00000056","Study Factor Type Term Source REF","INVMSO")

module ``STUDY ASSAYS`` =
let key = CvTerm.create("INVMSO:00000057","STUDY ASSAYS","INVMSO")

let ``Study Assay File Name`` = CvTerm.create("INVMSO:00000065","Study Assay File Namee","INVMSO")

module ``STUDY PROTOCOLS`` =
let ``Study Assay Measurement Type`` = CvTerm.create("INVMSO:00000058","Study Assay Measurement Type","INVMSO")
let ``Study Assay Measurement Type Term Accession Number`` = CvTerm.create("INVMSO:00000059","Study Assay Measurement Type Term Accession Number","INVMSO")
let ``Study Assay Measurement Type Term Source REF`` = CvTerm.create("INVMSO:00000060","Study Assay Measurement Type Term Source REF","INVMSO")
let ``Study Assay Technology Type`` = CvTerm.create("INVMSO:00000061","Study Assay Technology Type","INVMSO")
let ``Study Assay Technology Type Term Accession Number`` = CvTerm.create("INVMSO:00000062","Study Assay Technology Type Term Accession Number","INVMSO")
let ``Study Assay Technology Type Term Source REF`` = CvTerm.create("INVMSO:00000063","Study Assay Technology Type Term Source REF","INVMSO")
let ``Study Assay Technology Platform`` = CvTerm.create("INVMSO:00000064","Study Assay Technology Platform","INVMSO")
let ``Study Assay File Name`` = CvTerm.create("INVMSO:00000065","Study Assay File Name","INVMSO")

module ``STUDY PROTOCOLS`` =
let key = CvTerm.create("INVMSO:00000066","STUDY PROTOCOLS","INVMSO")

module ``STUDY CONTACTS`` =
let ``Study Protocol Name`` = CvTerm.create("INVMSO:00000067","Study Protocol Name","INVMSO")
let ``Study Protocol Type`` = CvTerm.create("INVMSO:00000068","Study Protocol Type","INVMSO")
let ``Study Protocol Type Term Accession Number`` = CvTerm.create("INVMSO:00000069","Study Protocol Type Term Accession Number","INVMSO")
let ``Study Protocol Type Term Source REF`` = CvTerm.create("INVMSO:00000070","Study Protocol Type Term Source REF","INVMSO")
let ``Study Protocol Description`` = CvTerm.create("INVMSO:00000071","Study Protocol Description","INVMSO")
let ``Study Protocol URI`` = CvTerm.create("INVMSO:00000072","Study Protocol URI","INVMSO")
let ``Study Protocol Version`` = CvTerm.create("INVMSO:00000073","Study Protocol Version","INVMSO")
let ``Study Protocol Parameters Name`` = CvTerm.create("INVMSO:00000074","Study Protocol Parameters Name","INVMSO")
let ``Study Protocol Parameters Term Accession Number`` = CvTerm.create("INVMSO:00000075","Study Protocol Parameters Term Accession Number","INVMSO")
let ``Study Protocol Parameters Term Source REF`` = CvTerm.create("INVMSO:00000076","Study Protocol Parameters Term Source REF","INVMSO")
let ``Study Protocol Components Name`` = CvTerm.create("INVMSO:00000077","Study Protocol Components Name","INVMSO")
let ``Study Protocol Components Type`` = CvTerm.create("INVMSO:00000078","Study Protocol Components Type","INVMSO")
let ``Study Protocol Components Type Term Accession Number`` = CvTerm.create("INVMSO:00000079","Study Protocol Components Type Term Accession Number","INVMSO")
let ``Study Protocol Components Type Term Source REF`` = CvTerm.create("INVMSO:00000080","Study Protocol Components Type Term Source REF","INVMSO")

module ``STUDY CONTACTS`` =
let key = CvTerm.create("INVMSO:00000081","STUDY CONTACTS","INVMSO")
let ``Study Person Last Name`` = CvTerm.create("INVMSO:00000082","Study Person Last Name","INVMSO")
let ``Study Person First Name`` = CvTerm.create("INVMSO:00000083","Study Person First Name","INVMSO")
let ``Study Person Mid Initials`` = CvTerm.create("INVMSO:00000084","Study Person Mid Initials","INVMSO")
let ``Study Person Email`` = CvTerm.create("INVMSO:00000085","Study Person Email","INVMSO")
let ``Study Person Phone`` = CvTerm.create("INVMSO:00000086","Study Person Phone","INVMSO")
let ``Study Person Fax`` = CvTerm.create("INVMSO:00000087","Study Person Fax","INVMSO")
let ``Study Person Address`` = CvTerm.create("INVMSO:00000088","Study Person Address","INVMSO")
let ``Study Person Affiliation`` = CvTerm.create("INVMSO:00000089","Study Person Affiliation","INVMSO")
let ``Study Person Roles`` = CvTerm.create("INVMSO:00000090","Study Person Roles","INVMSO")
let ``Study Person Roles Term Accession Number`` = CvTerm.create("INVMSO:00000091","Study Person Roles Term Accession Number","INVMSO")
let ``Study Person Roles Term Source REF`` = CvTerm.create("INVMSO:00000092","Study Person Roles Term Source REF","INVMSO")


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