Github Action: Updated dictionary term files and term pages

Author: github-actions[bot]

_data/ManifestColumn.csv

@@ -115,7 +115,7 @@ sequencingBatchSizeUnit,The unit of measurement for number of samples in a batch
 sop,"Relevant standard operating procedures. Standard operating procedures used in the assembly and/or annotation of genomes, metagenomes, or environmental sequences. Example - 'http-//press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/its/)'Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 sourceMatID,"Source material identifiers. A unique identifier assigned to a material sample (as defined by http-//rs.tdwg.org/dwc/terms/materialSampleID and as opposed to a particular digital record of a material sample) used for extracting nucleic acids, and subsequent sequencing.The identifier can refer to the original material collected or any derived sub-samples. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 speciesAge,"Age of individual (formatted in months, ex. ""72 months"").note- Uncertainty about the age might require recording age by specifying a lower and upper estimate in months for the age of the animal.",,STRING,ManifestColumn,ManifestColumn
-speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,"Bird,Human,Mammal,Not applicable,Not collected,Not specified,Other,Primate,Rodent,Unknown",STRING,ManifestColumn,ManifestColumn
+speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,"Amphibian,Bird,Fish,Invertebrate,Mammal,Not applicable,Not collected,Not specified,Reptile,Unknown",STRING,ManifestColumn,ManifestColumn
 speciesName,"The scientific name of the species (typically a taxonomic group, ex. ""Eremophila alpestris) the individual belongs to.""""""",,STRING,ManifestColumn,ManifestColumn
 specimenAge,"The subject's age at the time of specimen extraction is the individual's age (since birth) at the time a given specimen was extracted. Measured as age in years. Other, Unknown, Not collected, Not applicable",,STRING,ManifestColumn,ManifestColumn
 specimenSource,Indicate the biological area of the specimen,,STRING,ManifestColumn,ManifestColumn

_data/assay_phenotype_human_template.csv

@@ -1,7 +1,7 @@
 Attribute,Description,Required,columnType,DependsOn,Source,Parent,Valid Values
 diagnosisStatus,"Whether the individual has been diagnosed with a condition or disease (physical and/or cognitive), \True"" indicates the individual has been diagnosed""",True,STRING,,,ManifestColumn,"FALSE,TRUE"
 ethnicGroupCode,"A coded value specifying the self-declared ethnic origination independent of racial origination, provided by the data contributor's data dictionary",False,STRING,,,ManifestColumn,
-speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,True,STRING,,,ManifestColumn,"Bird,Human,Mammal,Not applicable,Not collected,Not specified,Other,Primate,Rodent,Unknown"
+speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,True,STRING,,,ManifestColumn,"Amphibian,Bird,Fish,Invertebrate,Mammal,Not applicable,Not collected,Not specified,Reptile,Unknown"
 Component,,False,,,,,
 Filename,,False,STRING,,,,
 diagnosis,Indicate the disease or condition.,False,STRING,,sage.annotations-experimentalData.diagnosis-0.0.12,ManifestColumn,"AD-DS, Affective Disorder, Alzheimer Disease, Alzheimer disease with psychosis, amyotrophic lateral sclerosis, anxiety, Autism Spectrum Disorder, Bipolar Disorder, Bladder Cancer, Brain Cancer, Breast Cancer, Cervical Cancer, Colon Cancer, control, corticobasal degeneration disorder, CS-DS, dementia, dystonia, essential tremor, Fibrocystic Breast Disease, frontotemporal dementia, gliosis, hypoxia, Juvenile Myelomonocytic Leukemia, Leukemia, Lewy body disease, Longevity, Lung Cancer, Major Depressive Disorder, MCI-DS, mild cognitive impairment, multiple system atrophy, Neurofibromatosis 1, Neurofibromatosis 2, no cognitive impairment, Not Applicable, obesity, obsessive compulsive disorder, Ovary Cancer, Pancreatic Cancer, Parkinson's disease, pathological aging, progressive supranuclear palsy, Prostate Cancer, Schizophrenia, Skin Cancer, Substance Related Disorder, Tourette Syndrome, traumatic brain injury, type 2 diabetes mellitus, vascular dementia, Williams Syndrome"

_data/file_annotation_template.csv

@@ -17,4 +17,4 @@ familyStudyParticipant,Indicates whether or not a file has data from a human par
 assay,The analysis or technology used to generate the data in this file,True,STRING,,sage.annotations-experimentalData.assay-0.0.26,ManifestColumn,"10x multiome, 16SrRNAseq, active avoidance learning behavior, anxiety-related behavior, ATACSeq, atomicForceMicroscopy, autoradiography, Baker Lipidomics, Biocrates Bile Acids, Biocrates p180, Biocrates Q500, bisulfiteSeq, Blood Chemistry Measurement, brightfieldMicroscopy, cellViabilityAssay, ChIPSeq, CITESeq, contextual conditioning behavior, CUT&Tag, DIA, DNA optical mapping, electrochemiluminescence, elevated plus maze test, elevated T maze apparatus method, ELISA, errBisulfiteSeq, exomeSeq, FIA-MSMS, FitBark, frailty assessment, Genotyping, HI-C, HiChIPseq, high content screen, HPLC, HPLC-MSMS, Immunocytochemistry, immunofluorescence, immunohistochemistry, in vivo bioluminescence, ISOSeq, jumpingLibrary, kinesthetic behavior, label free mass spectrometry, Laser Speckle Imaging, LC-MS, LC-MSMS, LC-SRM, Leiden Oxylipins, lentiMPRA, LFP, liquid chromatography-electrochemical detection, lncrnaSeq, locomotor activation behavior, long-read rnaSeq, LTP, MDMS-SL, memory behavior, Metabolon, methylationArray, MIB/MS, microRNAcounts, mirnaArray, mirnaSeq, MRI, mRNAcounts, MudPIT, m6A-rnaSeq, nextGenerationTargetedSequencing, Nightingale NMR, NOMe-Seq, novelty response behavior, open field test, oxBS-Seq, pharmacodynamics, pharmacokinetics, photograph, polymeraseChainReaction, Positron Emission Tomography, proximity extension assay, questionnaire, Rader Lipidomics, Real Time PCR, Ribo-Seq, rotarod performance test, rnaArray, rnaSeq, RPPA, sandwich ELISA, Sanger sequencing, scale, scATACSeq, scCGIseq, scirnaSeq, scrnaSeq, scwholeGenomeSeq, SiMoA, snpArray, snATACSeq, snrnaSeq, spontaneous alternation, STARRSeq, TMT quantitation, tractionForceMicroscopy, UPLC-MSMS, UPLC-ESI-QTOF-MS, UC Davis GCTOF, UCSD Untargeted Metabolomics, Vernier Caliper, von Frey test, westernBlot, wheel running, whole-cell patch clamp, wholeGenomeSeq, Wishart Catecholamines, Wishart High Value Metabolites, Zeno Electronic Walkway, Not collected, Not specified, Not applicable, Other, Unknown"
 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,
 isMultiSpecimen,Boolean flag indicating whether or not a file has data for multiple specimens,True,STRING_LIST,,Sage Bionetworks,ManifestColumn,"true,fasle,Not assigned"
-species,The name of a species (typically a taxonomic group) of organism.,True,STRING_LIST,,Sage Bionetworks,ManifestColumn,"Human,Non Human,Not assigned"
+species,The name of a species (typically a taxonomic group) of organism.,True,STRING_LIST,,Sage Bionetworks,ManifestColumn,"Cross-Species Avian,Cross-Species Mammalian,Human,Mouse"

_data/individual.csv

@@ -8,4 +8,4 @@ hasMMSE,The datafile and/or individualID includes cognitive variables and/or sco
 hasMoCA,The datafile and/or individualID includes cognitive variables and/or scores from the Montreal Cognitive Assessment (MoCA),"Yes, No",STRING,ManifestColumn,individual
 individualID,"Identifying string linked to the individual or animal being studied, provided by the data contributor",,STRING,ManifestColumn,individual
 isMultiSpecimen,Boolean flag indicating whether or not a file has data for multiple specimens,"true,fasle,Not assigned",STRING_LIST,ManifestColumn,individual
-species,The name of a species (typically a taxonomic group) of organism.,"Human,Non Human,Not assigned",STRING_LIST,ManifestColumn,individual
+species,The name of a species (typically a taxonomic group) of organism.,"Cross-Species Avian,Cross-Species Mammalian,Human,Mouse",STRING_LIST,ManifestColumn,individual

_data/individual_human_template.csv

@@ -4,7 +4,7 @@ countryCode,"Indicate the geographic region for the individual (shown as ex. ""8
 diagnosisStatus,"Whether the individual has been diagnosed with a condition or disease (physical and/or cognitive), \True"" indicates the individual has been diagnosed""",True,STRING,,,ManifestColumn,"FALSE,TRUE"
 ethnicGroupCode,"A coded value specifying the self-declared ethnic origination independent of racial origination, provided by the data contributor's data dictionary",False,STRING,,,ManifestColumn,
 fieldCenterCode,Name of the field center,True,STRING,,,ManifestColumn,
-speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,True,STRING,,,ManifestColumn,"Bird,Human,Mammal,Not applicable,Not collected,Not specified,Other,Primate,Rodent,Unknown"
+speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,True,STRING,,,ManifestColumn,"Amphibian,Bird,Fish,Invertebrate,Mammal,Not applicable,Not collected,Not specified,Reptile,Unknown"
 studyCode,"Unique identifier for the study, assigned by the DCC",True,STRING,,,ManifestColumn,"CDCP,ILO,LC,LG,LLFS,Other"
 visitCode,"Indicate which longitudinal visit for the individual the data comes from, provided by the data contributor's data dictionary",True,NUMBER,,,ManifestColumn,
 Component,,False,,,,,

_data/individual_non_human_template.csv

@@ -4,7 +4,7 @@ captivityStatus,"The status of the individual with regard to captivity.note- Wil
 commonName,"The biological species common name the individual belongs to (ex. ""Horned Lark""). note- As a default, the valid scientific name for the species should be indicated.",True,STRING,,,ManifestColumn,
 lifeStage,The life stage of the individual.note- Other values are possible depending on life stage terminology for individual species. Please let the data curation team know.,True,STRING,,,ManifestColumn,"Adult,Juvenile,Post-Juvenile, Not applicable, Not collected, Not specified, Other, Unknown"
 speciesAge,"Age of individual (formatted in months, ex. ""72 months"").note- Uncertainty about the age might require recording age by specifying a lower and upper estimate in months for the age of the animal.",True,STRING,,,ManifestColumn,
-speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,True,STRING,,,ManifestColumn,"Bird,Human,Mammal,Not applicable,Not collected,Not specified,Other,Primate,Rodent,Unknown"
+speciesGroup,The taxonomic ranking including both species and subspecies the individual belongs to.,True,STRING,,,ManifestColumn,"Amphibian,Bird,Fish,Invertebrate,Mammal,Not applicable,Not collected,Not specified,Reptile,Unknown"
 speciesName,"The scientific name of the species (typically a taxonomic group, ex. ""Eremophila alpestris) the individual belongs to.""""""",True,STRING,,,ManifestColumn,
 studyCode,"Unique identifier for the study, assigned by the DCC",True,STRING,,,ManifestColumn,"CDCP,ILO,LC,LG,LLFS,Other"
 taxon,"Taxonomic identifier. The National Center for Biotechnology Information taxon ID (formatted as, ex. ""txid9989"")",True,STRING,,,ManifestColumn,

_data/species.csv

@@ -1,4 +1,5 @@
 Key,Key Description,columnType,Source,Parent
+Cross-Species Avian,,STRING_LIST,,ManifestColumn
+Cross-Species Mammalian,,STRING_LIST,,ManifestColumn
 Human,,STRING_LIST,,ManifestColumn
-Non Human,,STRING_LIST,,ManifestColumn
-Not assigned,,STRING_LIST,,ManifestColumn
+Mouse,,STRING_LIST,,ManifestColumn

_data/speciesGroup.csv

@@ -1,11 +1,11 @@
 Key,Key Description,columnType,Source,Parent
+Amphibian,,STRING,,ManifestColumn
 Bird,,STRING,,ManifestColumn
-Human,,STRING,,ManifestColumn
+Fish,,STRING,,ManifestColumn
+Invertebrate,,STRING,,ManifestColumn
 Mammal,,STRING,,ManifestColumn
 Not applicable,,STRING,,ManifestColumn
 Not collected,,STRING,,ManifestColumn
 Not specified,,STRING,,ManifestColumn
-Other,,STRING,,ManifestColumn
-Primate,,STRING,,ManifestColumn
-Rodent,,STRING,,ManifestColumn
+Reptile,,STRING,,ManifestColumn
 Unknown,,STRING,,ManifestColumn

_data/study_folder_template.csv

@@ -24,4 +24,4 @@ studyMetadata,,False,,,,,
 studyName,,False,,,,,
 studyType,,False,,,,,
 studyWiki,,False,,,,,
-species,The name of a species (typically a taxonomic group) of organism.,True,STRING_LIST,,Sage Bionetworks,ManifestColumn,"Human,Non Human,Not assigned"
+species,The name of a species (typically a taxonomic group) of organism.,True,STRING_LIST,,Sage Bionetworks,ManifestColumn,"Cross-Species Avian,Cross-Species Mammalian,Human,Mouse"