Github Action: Updated dictionary term files and term pages

Author: github-actions[bot]

_data/DataModel.csv

@@ -32,6 +32,7 @@ countryCode,"Indicate the geographic region for the individual (shown as ex. ""8
 dataFile,"Name of additional file(s) accompanying the data. The file(s) provide, for example, the name of any raw files generated by the instrument, generated reports from a vendor, an Rscript, or an instructions document. The files can be instrument raw files, converted peak lists such as mzML, MGF, or result files like mzIdentML. The files can be additional documentation submitted alongside the data needed for reuse and sharing purposes. Provide the file names of any additional files submitted alongside the data (ex., an ADAT file). Multiple file names can be separated by (;)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",STRING,,ManifestColumn
 dataModelVersion,Version of the data model,,,ManifestColumn
 dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata",STRING_LIST,Sage Bionetworks,ManifestColumn
+dataType,,STRING,Sage Bionetworks,ManifestColumn
 dataTypeAll,,STRING_LIST,Sage Bionetworks,ManifestColumn
 databaseLibrary,"The name(s) of the associated database library. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",STRING,,ManifestColumn
 databaseName,"The name of the search database (nr, SwissProt or est_human, and/or mass spectral library). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",STRING,,ManifestColumn

_data/ManifestColumn.csv

@@ -29,7 +29,8 @@ countryCode,"Indicate the geographic region for the individual (shown as ex. ""8
 dataFile,"Name of additional file(s) accompanying the data. The file(s) provide, for example, the name of any raw files generated by the instrument, generated reports from a vendor, an Rscript, or an instructions document. The files can be instrument raw files, converted peak lists such as mzML, MGF, or result files like mzIdentML. The files can be additional documentation submitted alongside the data needed for reuse and sharing purposes. Provide the file names of any additional files submitted alongside the data (ex., an ADAT file). Multiple file names can be separated by (;)Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 dataModelVersion,Version of the data model,,,,ManifestColumn
 dataSubtype,"Further qualification of dataType, which may be used to indicate the state of processing of the data, aggregation of the data, or presence of metadata","raw,processed,results,normalized,metadata, Not assigned",STRING_LIST,ManifestColumn,ManifestColumn
-dataTypeAll,,,STRING_LIST,ManifestColumn,ManifestColumn
+dataType,,"clinical,drugScreen,electrophysiology,epigenetics,geneExpression,genomeAssembly,genomicVariants,imaging,lipidomics,metabolomics,metagenomics,Not applicable,Not collected,Not specified,Other,phenotype,proteomics,Unknown,wearableData",STRING,ManifestColumn,ManifestColumn
+dataTypeAll,,"clinical,drugScreen,electrophysiology,epigenetics,geneExpression,genomeAssembly,genomicVariants,imaging,lipidomics,metabolomics,metagenomics,Not applicable,Not collected,Not specified,Other,phenotype,proteomics,Unknown,wearableData",STRING_LIST,ManifestColumn,ManifestColumn
 databaseLibrary,"The name(s) of the associated database library. Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 databaseName,"The name of the search database (nr, SwissProt or est_human, and/or mass spectral library). Provide a value OR provide one of these values - Unknown Not collected, Not applicable, Not specified",,STRING,ManifestColumn,ManifestColumn
 databaseSource,"The name of the organization, project, or laboratory from where the database is obtained (UniProt, NCBI, EBI, other).",,STRING,ManifestColumn,ManifestColumn
@@ -116,7 +117,7 @@ sop,"Relevant standard operating procedures. Standard operating procedures used
 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.,"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
+speciesName,"The scientific name of the species (typically a taxonomic group, ex. ""Eremophila alpestris) the individual belongs to.""""""","Acomys cahirinus, Acomys russatus, Accipiter cooperii, Actitis macularius, Aix sponsa, Anas acuta, Anas carolinensis, Anas platyrhynchos, Antigone canadensis, Archilochus colubris, Artibeus jamaicensis, Baeolophus bicolor, Balaena mysticetus, Blarina brevicauda, Bombycilla cedrorum, Bonasa umbellus, Bos taurus, Branta canadensis, Bubo virginianus, Buteo jamaicensis, Buteo lineatus, Canis latrans, Cardinalis cardinalis, Castor canadensis, Cavia porcellus, Charadrius vociferus, Chinchilla lanigera, Columba livia, Condylura cristata, Corvus brachyrhynchos, Cricetomys ansorgei, Cricetulus barabensis, Cricetulus griseus, Cryptomys damarensis, Cuniculus paca, Cyanocitta cristata, Cygnus olor, Dryobates pubescens, Dumetella carolinensis, Ellobius lutescens, Ellobius talpinus, Eonycteris spelaea, Eptesicus fuscus, Equus caballus, Eremophila alpestris, Fukomys damarensis, Haemorhous mexicanus, Heterocephalus glaber, Hirundo rustica, Homo sapiens, Hydrochoerus hydrochaeris, Hydroprogne caspia, Hylocichla mustelina, Icteria virens, Larus argentatus, Larus delawarensis, Macaca fascicularis, Macaca mulatta, Mareca strepera, Marmota monax, Melanerpes carolinus, Meleagris gallopavo, Melospiza melodia, Meriones unguiculatus, Mesocricetus auratus, Microtus pennsylvanicus, Mimus polyglottos, Molothrus ater, Multi-species, Mus musculus, Myocastor coypus, Myotis lucifugus, Nannospalax galili, Neosciurus carolinensis, Neotoma cinerea, Neotoma floridana, Not applicable, Not collected, Not provided, Not specified, Octodon degus, Odocoileus virginianus, Ondatra zibethicus, Other, Pan troglodytes, Papio anubis, Passer domesticus, Passerina caerulea, Passerina cyanea, Peromyscus gossypinus, Peromyscus leucopus, Peromyscus maniculatus, Phalacrocorax auritus, Phasianus colchicus, Picoides villosus, Pipilo erythrophthalmus, Poecile carolinensis, Quiscalus quiscula, Rattus norvegicus, Rattus rattus, Regulus calendula, Saimiri boliviensis, Sayornis phoebe, Scalopus aquaticus, Sciurus carolinensis, Sciurus niger, Sciurus vulgaris, Scolopax minor, Setophaga citrina, Setophaga coronata, Setophaga dominica, Setophaga petechia, Setophaga pinus, Sialia sialis, Sigmodon hispidus, Sitta carolinensis, Spatula clypeata, Spinus tristis, Spizella passerina, Spizella pusilla, Spizelloides arborea, Struthio camelus, Sturnus vulgaris, Sus scrofa, Sylvilagus floridanus, Tachycineta bicolor, Tamias striatus, Tamiasciurus hudsonicus, Thryothorus ludovicianus, Toxostoma rufum, Troglodytes aedon, Turdus migratorius, Tursiops truncatus, Vicugna pacos, Vireo griseus, Vireo olivaceus, Zalophus californianus, Zenaida macroura, Zonotrichia albicollis, Unknown",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
 specimenType,Type of biological material comprising the Specimen,"blood,Cerebrospinal Fluid (CSF),Not applicable,Not collected,Not specified,organoid,plasma,saliva,serum,sputum,stool,swabs,tissue,Unknown,urine",STRING,ManifestColumn,ManifestColumn

_data/analysis_results_metadata_template.csv

@@ -1,4 +1,4 @@
 Attribute,Description,Required,columnType,DependsOn,Source,Parent,Valid Values
 analysisType,Type of analysis,False,STRING_LIST,,Sage Bionetworks,ManifestColumn,"ANOVA,batch effect correction,clustering,data normalization,de-novo assembly,dose response study,enrichment analysis,genome-wide association,mendelian randomization analysis,network analysis,polygenic risk scores, Not assigned"
-dataTypeAll,,True,STRING_LIST,,Sage Bionetworks,ManifestColumn,
+dataTypeAll,,True,STRING_LIST,,Sage Bionetworks,ManifestColumn,"clinical,drugScreen,electrophysiology,epigenetics,geneExpression,genomeAssembly,genomicVariants,imaging,lipidomics,metabolomics,metagenomics,Not applicable,Not collected,Not specified,Other,phenotype,proteomics,Unknown,wearableData"
 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"

_data/dataType.csv

@@ -0,0 +1,20 @@
+Key,Key Description,columnType,Source,Parent
+clinical,,STRING,,ManifestColumn
+drugScreen,,STRING,,ManifestColumn
+electrophysiology,,STRING,,ManifestColumn
+epigenetics,,STRING,,ManifestColumn
+geneExpression,,STRING,,ManifestColumn
+genomeAssembly,,STRING,,ManifestColumn
+genomicVariants,,STRING,,ManifestColumn
+imaging,,STRING,,ManifestColumn
+lipidomics,,STRING,,ManifestColumn
+metabolomics,,STRING,,ManifestColumn
+metagenomics,,STRING,,ManifestColumn
+Not applicable,,STRING,,ManifestColumn
+Not collected,,STRING,,ManifestColumn
+Not specified,,STRING,,ManifestColumn
+Other,,STRING,,ManifestColumn
+phenotype,,STRING,,ManifestColumn
+proteomics,,STRING,,ManifestColumn
+Unknown,,STRING,,ManifestColumn
+wearableData,,STRING,,ManifestColumn

_data/dataTypeAll.csv

@@ -0,0 +1,20 @@
+Key,Key Description,columnType,Source,Parent
+clinical,,STRING_LIST,,ManifestColumn
+drugScreen,,STRING_LIST,,ManifestColumn
+electrophysiology,,STRING_LIST,,ManifestColumn
+epigenetics,,STRING_LIST,,ManifestColumn
+geneExpression,,STRING_LIST,,ManifestColumn
+genomeAssembly,,STRING_LIST,,ManifestColumn
+genomicVariants,,STRING_LIST,,ManifestColumn
+imaging,,STRING_LIST,,ManifestColumn
+lipidomics,,STRING_LIST,,ManifestColumn
+metabolomics,,STRING_LIST,,ManifestColumn
+metagenomics,,STRING_LIST,,ManifestColumn
+Not applicable,,STRING_LIST,,ManifestColumn
+Not collected,,STRING_LIST,,ManifestColumn
+Not specified,,STRING_LIST,,ManifestColumn
+Other,,STRING_LIST,,ManifestColumn
+phenotype,,STRING_LIST,,ManifestColumn
+proteomics,,STRING_LIST,,ManifestColumn
+Unknown,,STRING_LIST,,ManifestColumn
+wearableData,,STRING_LIST,,ManifestColumn