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Github Action: Updated dictionary term files and term pages
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14 files changed

+386
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‎_data/DataModel.csv‎

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@@ -190,6 +190,11 @@ controlType,"Control samples suitable for normalization and batch correction.Pos
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platformLocation,"The name of the laboratory, facility, vendor, company, or location where the data generation platform was located, provided by the data contributor. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",STRING,sage.annotations-experimentalData.platformLocation-0.0.2,experimentalData
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age,"Age of the individual (age in years of the individual at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.)",STRING,,individual
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cohort,Name of the cohort the individual belongs to,STRING,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",individual
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hasADLs,The datafile and/or individualID includes cognitive variables and/or scores from the Activities of daily living (ADLs),STRING,,individual
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hasCASI,The datafile and/or individualID includes cognitive variables and/or scores from the Cognitive Abilities Screening Instrument (CASI),STRING,,individual
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hasCDR,The datafile and/or individualID includes cognitive variables and/or scores from the The Clinical Dementia Rating (CDR),STRING,,individual
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hasMMSE,The datafile and/or individualID includes cognitive variables and/or scores from the Mini-Mental State Examination (MMSE),STRING,,individual
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hasMoCA,The datafile and/or individualID includes cognitive variables and/or scores from the Montreal Cognitive Assessment (MoCA),STRING,,individual
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individualID,"Identifying string linked to the individual or animal being studied, provided by the data contributor",STRING,sage.annotations-experimentalData.individualID-0.0.2,individual
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species,The name of a species (typically a taxonomic group) of organism.,STRING_LIST,Sage Bionetworks,individual
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spectrometerFrequency,The frequency at which a spectrometer causes hydrogen atoms to resonate (in MHz),NUMBER,sage.annotations-experimentalData.spectrometerFrequency-0.0.2,mass spectrometry

‎_data/hasADLs.csv‎

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Key,Key Description,columnType,Source,Parent
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Yes,,STRING,,ManifestColumn
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No,,STRING,,ManifestColumn

‎_data/hasCASI.csv‎

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Key,Key Description,columnType,Source,Parent
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Yes,,STRING,,ManifestColumn
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No,,STRING,,ManifestColumn

‎_data/hasCDR.csv‎

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Key,Key Description,columnType,Source,Parent
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Yes,,STRING,,ManifestColumn
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No,,STRING,,ManifestColumn

‎_data/hasMMSE.csv‎

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Key,Key Description,columnType,Source,Parent
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Yes,,STRING,,ManifestColumn
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No,,STRING,,ManifestColumn

‎_data/hasMoCA.csv‎

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Key,Key Description,columnType,Source,Parent
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Yes,,STRING,,ManifestColumn
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No,,STRING,,ManifestColumn

‎_data/individual.csv‎

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Key,Key Description,Valid Values,columnType,Parent,module
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age,"Age of the individual (age in years of the individual at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.)",,STRING,ManifestColumn,individual
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cohort,Name of the cohort the individual belongs to,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB,CHS, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HABC, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, MrOS, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, SOF, UK Biobank, UPBB, UPenn, UW ADRC,ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP",STRING,ManifestColumn,individual
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hasADLs,The datafile and/or individualID includes cognitive variables and/or scores from the Activities of daily living (ADLs),"Yes, No",STRING,ManifestColumn,individual
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hasCASI,The datafile and/or individualID includes cognitive variables and/or scores from the Cognitive Abilities Screening Instrument (CASI),"Yes, No",STRING,ManifestColumn,individual
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hasCDR,The datafile and/or individualID includes cognitive variables and/or scores from the The Clinical Dementia Rating (CDR),"Yes, No",STRING,ManifestColumn,individual
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hasMMSE,The datafile and/or individualID includes cognitive variables and/or scores from the Mini-Mental State Examination (MMSE),"Yes, No",STRING,ManifestColumn,individual
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hasMoCA,The datafile and/or individualID includes cognitive variables and/or scores from the Montreal Cognitive Assessment (MoCA),"Yes, No",STRING,ManifestColumn,individual
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individualID,"Identifying string linked to the individual or animal being studied, provided by the data contributor",,STRING,ManifestColumn,individual
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species,The name of a species (typically a taxonomic group) of organism.,"Human,Mouse",STRING_LIST,ManifestColumn,individual

‎_data/individual_human_template.csv‎

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@@ -15,4 +15,9 @@ race,Race of individual,True,STRING,,sage.annotations-demographics.race-0.0.2,Ma
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sex,The biological sex of the individual,True,STRING,,sage.annotations-experimentalData.sex-0.0.2,ManifestColumn,"Female,Male,Not applicable,Not collected,Not specified,Other,Unknown"
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age,"Age of the individual (age in years of the individual at first recorded study event (enrollment, visit, observation, sample collection, survey completion, etc.)",True,STRING,,,ManifestColumn,
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cohort,Name of the cohort the individual belongs to,False,STRING,,"http://purl.obolibrary.org/obo/NCIT_C61512,http://purl.obolibrary.org/obo/STATO_0000203",ManifestColumn,"ABC-DS, ACT, ADNI, Banner, BEB-Miller, BLSA, CHDWB,CHS, CLINCOR, DiCAD, EHBS, Emory ADRC, Framingham, HABC, HBTRC, HPGP, HUP, LBP, MARS, MAYO, MC, MCJ, MCR, MSBB, MrOS, NYBB, Pitt ADRC, RADC, ROSMAP, SMRI, SOF, UK Biobank, UPBB, UPenn, UW ADRC,ABC-DS,ACT,ADNI,Banner,BEB-Miller,Biggs Institute Brain Bank,BLSA,CHDWB,CLINCOR,Columbia ADRC,DiCAD,EFIGA,EHBS,Emory ADRC,FBS,Framingham,HBCC,HBTRC,HPGP,HUP,LBP,MARS,Mayo Clinic,MC,MCJ,MCR,MSBB,NYBB,Pitt ADRC,RADC,ROSMAP,SMRI,UFL,UK Biobank,UPBB,UPenn,UW ADRC,WHICAP"
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hasADLs,The datafile and/or individualID includes cognitive variables and/or scores from the Activities of daily living (ADLs),False,STRING,,,ManifestColumn,"Yes, No"
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hasCASI,The datafile and/or individualID includes cognitive variables and/or scores from the Cognitive Abilities Screening Instrument (CASI),False,STRING,,,ManifestColumn,"Yes, No"
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hasCDR,The datafile and/or individualID includes cognitive variables and/or scores from the The Clinical Dementia Rating (CDR),False,STRING,,,ManifestColumn,"Yes, No"
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hasMMSE,The datafile and/or individualID includes cognitive variables and/or scores from the Mini-Mental State Examination (MMSE),False,STRING,,,ManifestColumn,"Yes, No"
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hasMoCA,The datafile and/or individualID includes cognitive variables and/or scores from the Montreal Cognitive Assessment (MoCA),False,STRING,,,ManifestColumn,"Yes, No"
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individualID,"Identifying string linked to the individual or animal being studied, provided by the data contributor",True,STRING,,sage.annotations-experimentalData.individualID-0.0.2,ManifestColumn,

‎docs/modules/individual/hasADLs.md‎

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---
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datatable: true
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layout: page
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parent: individual
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title: hasADLs
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---
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{% assign mydata=site.data.hasADLs %}
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{: .note-title }
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>hasADLs
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>
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>The datafile and/or individualID includes cognitive variables and/or scores from the Activities of daily living (ADLs) [[Source]](nan)
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<table id="myTable" class="display" style="width:100%">
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<thead>
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{% for column in mydata[0] %}
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<th>{{ column[0] }}</th>
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{% endfor %}
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</thead>
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<tbody>
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{% for row in mydata %}
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<tr>
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{% for cell in row %}
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<td>{{ cell[1] }}</td>
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{% endfor %}
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</tr>
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{% endfor %}
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</tbody>
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</table>
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<script type="text/javascript">
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$('#myTable').DataTable({
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responsive: {
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details: {
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display: $.fn.dataTable.Responsive.display.modal( {
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header: function ( row ) {
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var data = row.data();
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return 'Details for '+data[0];
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}
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} ),
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renderer: $.fn.dataTable.Responsive.renderer.tableAll({
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tableClass: "table"
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})
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}
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},
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"deferRender": true,
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"columnDefs": [
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{
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targets: [4],
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render : function(data, type, row, meta){
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if(type === 'display' & data != 'Sage Bionetworks'){
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return $('<a>')
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.attr('href', data)
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.text(data)
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.wrap('<div></div>')
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.parent()
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.html();}
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if(type === 'display' & data == 'Sage Bionetworks'){
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return $('<a>')
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.attr('href', 'https://sagebionetworks.org/')
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.text(data)
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.wrap('<div></div>')
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.parent()
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.html();
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} else {
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return data;
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}
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}
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}
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]
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});
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</script>

‎docs/modules/individual/hasCASI.md‎

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---
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datatable: true
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layout: page
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parent: individual
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title: hasCASI
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---
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{% assign mydata=site.data.hasCASI %}
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{: .note-title }
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>hasCASI
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>
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>The datafile and/or individualID includes cognitive variables and/or scores from the Cognitive Abilities Screening Instrument (CASI) [[Source]](nan)
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<table id="myTable" class="display" style="width:100%">
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<thead>
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{% for column in mydata[0] %}
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<th>{{ column[0] }}</th>
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{% endfor %}
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</thead>
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<tbody>
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{% for row in mydata %}
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<tr>
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{% for cell in row %}
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<td>{{ cell[1] }}</td>
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{% endfor %}
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</tr>
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{% endfor %}
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</tbody>
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</table>
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<script type="text/javascript">
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$('#myTable').DataTable({
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responsive: {
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details: {
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display: $.fn.dataTable.Responsive.display.modal( {
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header: function ( row ) {
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var data = row.data();
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return 'Details for '+data[0];
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}
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} ),
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renderer: $.fn.dataTable.Responsive.renderer.tableAll({
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tableClass: "table"
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})
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}
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},
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"deferRender": true,
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"columnDefs": [
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{
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targets: [4],
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render : function(data, type, row, meta){
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if(type === 'display' & data != 'Sage Bionetworks'){
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return $('<a>')
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.attr('href', data)
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.text(data)
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.wrap('<div></div>')
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.parent()
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.html();}
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if(type === 'display' & data == 'Sage Bionetworks'){
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return $('<a>')
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.attr('href', 'https://sagebionetworks.org/')
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.text(data)
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.wrap('<div></div>')
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.parent()
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.html();
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} else {
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return data;
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}
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}
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}
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]
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});
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</script>

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