VISDATA - Brazil Unified Social Assistance System

PiperOrigin-RevId: 659430677

biomedical_schema/biological_taxonomy.mcf

@@ -16,6 +16,14 @@ typeOf: schema:Class
 subClassOf: dcs:BiologicalEntity
 definition: "A set of organisms asserted to represent a natural cohesive biological unit."
 
+Node: dcid:biologicalIsolate
+name: "biologicalIsolate"
+typeOf: schema:Property
+domainIncludes: dcs:BiologicalEntity
+rangeIncludes: schema:Text
+description: "The individual isolate from which the sequences in the genome assembly were derived."
+descriptionUrl: "https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt"
+
 Node: dcid:biologicalTaxonomyGroup
 name: "biologicalTaxonomyGroup"
 typeOf: schema:Property
@@ -38,6 +46,14 @@ rangeIncludes: schema:Text
 description: "The individual isolate from which the sequences in the genome assembly were derived."
 descriptionUrl: "https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt"
 
+Node: dcid:breed
+name: "breed"
+typeOf: schema:Property
+domainIncludes: dcs:BiologicalEntity
+rangeIncludes: schema:Text
+description: "A breed is a specific group of domestic animals having homogeneous appearance (phenotype), homogeneous behavior, and/or other characteristics that distinguish it from other organisms of the same species. In literature, there exist several slightly deviating definitions. Breeds are formed through genetic isolation and either natural adaptation to the environment or selective breeding, or a combination of the two."
+descriptionUrl: "https://en.wikipedia.org/wiki/Breed"
+
 Node: dcid:commonName
 name: "commonName"
 typeOf: schema:Property
@@ -46,6 +62,22 @@ rangeIncludes: schema:Text
 description: "In biology, a common name of a taxon or organism (also known as a vernacular name, English name, colloquial name, country name, popular name, or farmer's name) is a name that is based on the normal language of everyday life; and is often contrasted with the scientific name for the same organism, which is often based in Latin. A common name is sometimes frequently used, but that is not always the case."
 descriptionUrl: "https://en.wikipedia.org/wiki/Common_name"
 
+Node: dcid:cultivar
+name: "cultivar"
+typeOf: schema:Property
+domainIncludes: dcs:BiologicalEntity
+rangeIncludes: schema:Text
+description: "A cultivar is a kind of cultivated plant that people have selected for desired traits and which retains those traits when propagated. Methods used to propagate cultivars include division, root and stem cuttings, offsets, grafting, tissue culture, or carefully controlled seed production. Most cultivars arise from deliberate human manipulation, but some originate from wild plants that have distinctive characteristics. Cultivar names are chosen according to rules of the International Code of Nomenclature for Cultivated Plants (ICNCP), and not all cultivated plants qualify as cultivars. Horticulturists generally believe the word cultivar was coined as a term meaning 'cultivated variety'."
+descriptionUrl: "https://en.wikipedia.org/wiki/Cultivar"
+
+Node: dcid:ecotype
+name: "ecotype"
+typeOf: schema:Property
+domainIncludes: dcs:BiologicalEntity
+rangeIncludes: schema:Text
+description: "In evolutionary ecology, an ecotype, sometimes called ecospecies, describes a genetically distinct geographic variety, population, or race within a species, which is genotypically adapted to specific environmental conditions. Typically, though ecotypes exhibit phenotypic differences (such as in morphology or physiology) stemming from environmental heterogeneity, they are capable of interbreeding with other geographically adjacent ecotypes without loss of fertility or vigor."
+descriptionUrl: "https://en.wikipedia.org/wiki/Ecotype"
+
 Node: dcid:genBankName
 name: "genBankName"
 typeOf: schema:Property
@@ -68,6 +100,13 @@ rangeIncludes: schema:Text
 description: "The scientific name for any taxon below the rank of species. This may also be referred to as an infraspecific taxon or infraspecies."
 descriptionUrl: "https://en.wikipedia.org/wiki/Infraspecific_name"
 
+Node: dcid:isLatestVersion
+name: "isLatestVersion"
+typeOf: schema:Property
+domainIncludes: schema:Thing
+rangeIncludes: schema:Boolean
+description: "This is the latest version of the CreativeWork embodied by a specified resource."
+
 Node: dcid:ncbiBlastName
 name: "ncbiBlastName"
 typeOf: schema:Property
@@ -104,6 +143,14 @@ rangeIncludes: schema:Text
 domainIncludes: dcs:Taxon
 description: "The scientific name of a species."
 
+Node: dcid:strain
+name: "strain"
+typeOf: schema:Property
+domainIncludes: dcs:BiologicalEntity
+rangeIncludes: schema:Text
+description: "A strain is a genetic variant, a subtype or a culture within a biological species. Strains are often seen as inherently artificial concepts, characterized by a specific intent for genetic isolation."
+descriptionUrl: "https://en.wikipedia.org/wiki/Strain_(biology)"
+
 Node: dcid:taxonDivision
 name: "taxonDivision"
 typeOf: schema:Property

biomedical_schema/genome_annotation.mcf

@@ -277,6 +277,14 @@ domainIncludes: schema:Thing
 rangeIncludes: schema:Text
 description: "The level of confidence that a given result is accurate."
 
+Node: dcid:contigCount
+name: "contigCount"
+typeOf: schema:Property
+domainIncludes: dcs:GenomeAssembly
+rangeIncludes: schema:Text
+description: "The number of contigs in the primary assembly."
+descriptionUrl: "https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt"
+
 Node: dcid:dbSNPBuildID
 name: "dbSNPBuildID"
 typeOf: schema:Property
@@ -374,20 +382,6 @@ rangeIncludes: schema:Quantity
 description: "Percent of nitrogenous bases (guanine or cytosine) in DNA submitted for the assembly, rounded to the nearest 0.5%."
 descriptionUrl: "https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt"
 
-Node: dcid:geneCount
-name: "geneCount"
-typeOf: schema:Property
-domainIncludes dcs:GenomeAnnotation
-rangeIncludes: schema:Number
-description: "The total number of genes (both protein coding and non-coding genes) within a consensus region of DNA."
-
-Node: dcid:geneticScaffoldingCount
-name: "geneticScaffoldingCount"
-typeOf: schema:Property
-domainIncludes dcs:GenomeAnnotation
-rangeIncludes: schema:Number
-description: "The number of overlapping DNA segments that represent a consensus region of DNA."
-
 Node: dcid:genBankAssemblyAccession
 name: "genBankAssemblyAccession"
 typeOf: schema:Property
@@ -403,6 +397,13 @@ rangeIncludes: schema:Text
 description: "WGS-master: the GenBank Nucleotide accession and version for the master record of the Whole Genome Shotgun (WGS) project for the genome assembly. The master record can be retrieved from the NCBI Nucleotide resource: https://www.ncbi.nlm.nih.gov/nuccore. Genome assemblies that are complete genomes, and those that are clone-based, do not have WGS-master records. GenBank uses a different format for accessions of sequences that are a part of the WGS project."
 descriptionUrl: "https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt"
 
+Node: dcid:geneCount
+name: "geneCount"
+typeOf: schema:Property
+domainIncludes: dcs:GenomeAnnotation
+rangeIncludes: schema:Number
+description: "The total number of genes (both protein coding and non-coding genes) within a consensus region of DNA."
+
 Node: dcid:geneID
 name: "geneID"
 typeOf: schema:Property
@@ -433,8 +434,8 @@ domainIncludes: dcs:GeneticVariant
 description: "GeneReviews, an international point-of-care resource for busy clinicians, provides clinically relevant and medically actionable information for inherited conditions in a standardized journal-style format, covering diagnosis, management, and genetic counseling for patients and their families. Each chapter in GeneReviews is written by one or more experts on the specific condition or disease and goes through a rigorous editing and peer review process before being published online."
 descriptionUrl: "https://www.ncbi.nlm.nih.gov/books/NBK1116/"
 
-Node: dcid:geneticScaffoldingCount
-name: "geneticScaffoldingCount"
+Node: dcid:geneticScaffoldCount
+name: "geneticScaffoldCount"
 typeOf: schema:Property
 domainIncludes dcs:GenomeAssembly
 rangeIncludes: schema:Number

biomedical_schema/genome_annotation_enum.mcf

@@ -21,6 +21,77 @@ name: "Text Mining"
 description: "An association between two things was made through automated text mining of the scientific literature."
 
 
+# BiologicalTaxonomyGroupEnum
+Node: dcid:BiologicalTaxonomyGroupEnum
+name: "BiologicalTaxonomyGroupEnum"
+typeOf: schema:Class
+subClassOf: schema:Enumeration
+description: "Commonly used organism groups."
+
+Node: dcid:BiologicalTaxonomyGroupArchaea
+name: "Archaea"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+description: "Archaea is a domain of single-celled organisms. These microorganisms lack cell nuclei and are therefore prokaryotes."
+descriptionUrl: "https://en.wikipedia.org/wiki/Archaea"
+
+Node: dcid:BiologicalTaxonomyGroupBacteria
+name: "Bacteria"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+description: "Bacteria are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. "
+descriptionUrl: "https://en.wikipedia.org/wiki/Bacteria"
+
+Node: dcid:BiologicalTaxonomyGroupFungi
+name: "Fungi"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+description: "A fungus is any member of the group of eukaryotic organisms that includes microorganisms such as yeasts and molds, as well as the more familiar mushrooms. These organisms are classified as one of the traditional eukaryotic kingdoms, along with Animalia, Plantae and either Protista or Protozoa and Chromista."
+descriptionUrl: "https://en.wikipedia.org/wiki/Fungus"
+
+Node: dcid:BiologicalTaxonomyGroupInvertebrate
+name: "Invertebrate"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+description: "Invertebrates an umbrella term describing animals that neither develop nor retain a vertebral column (commonly known as a spine or backbone), which evolved from the notochord. It is a paraphyletic grouping including all animals excluding the chordate subphylum Vertebrata, i.e. vertebrates."
+descriptionUrl: "https://en.wikipedia.org/wiki/Invertebrate"
+
+Node: dcid:BiologicalTaxonomyGroupMetagenomes
+name: "Metagenomes"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+description: "Metagenome is a sequence that comes from genetic material recovered directly from environmental or clinical samples."
+
+Node: dcid:BiologicalTaxonomyGroupOther
+name: "Other"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+
+Node: dcid:BiologicalTaxonomyGroupPlant
+name: "Plant"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+description: "Plants are the eukaryotes that form the kingdom Plantae; they are predominantly photosynthetic. This means that they obtain their energy from sunlight, using chloroplasts derived from endosymbiosis with cyanobacteria to produce sugars from carbon dioxide and water, using the green pigment chlorophyll. Exceptions are parasitic plants that have lost the genes for chlorophyll and photosynthesis, and obtain their energy from other plants or fungi."
+descriptionUrl: "https://en.wikipedia.org/wiki/Plant"
+
+Node: dcid:BiologicalTaxonomyGroupProtozoa
+name: "Protozoa"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+description: "Protozoa are a polyphyletic group of single-celled eukaryotes, either free-living or parasitic, that feed on organic matter such as other microorganisms or organic debris."
+descriptionUrl: "https://en.wikipedia.org/wiki/Protozoa"
+
+Node: dcid:BiologicalTaxonomyGroupVertebrateMammalian
+name: "Vertebrate, Mammalian"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+description: "A mammal (from Latin mamma 'breast') is a vertebrate animal of the class Mammalia (/məˈmeɪli.ə/). Mammals are characterized by the presence of milk-producing mammary glands for feeding their young, a neocortex region of the brain, fur or hair, and three middle ear bones."
+descriptionUrl: "https://en.wikipedia.org/wiki/Mammal"
+
+Node: dcid:BiologicalTaxonomyGroupVertebrateOther
+name: "Vertebrate, Other"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+description: "Vertebrates (/ˈvɜːrtəbrɪts, -ˌbreɪts/) are deuterostomal animals with bony or cartilaginous axial endoskeleton — known as the vertebral column, spine or backbone — around and along the spinal cord. This group specifically refers to all vertebrates except for the subgroup mammals."
+descriptionUrl: "https://en.wikipedia.org/wiki/Vertebrate"
+
+Node: dcid:BiologicalTaxonomyGroupViral
+name: "viral"
+typeOf: dcs:BiologicalTaxonomyGroupEnum
+description: "A virus is a submicroscopic infectious agent that replicates only inside the living cells of an organism. Viruses infect all life forms, from animals and plants to microorganisms, including bacteria and archaea."
+descriptionUrl: "https://en.wikipedia.org/wiki/Virus"
+
+
 # ClinSigEnum
 Node: dcid:ClinSigEnum
 name: "ClinSigEnum"
@@ -747,48 +818,48 @@ subClassOf: schema:Enumeration
 description: "Denotes the relation of the genome assembly with the type material from which it was derived."
 
 Node: dcid:GenomeAssemblyDerivedFromTypeMaterial
-name: “assembly from type material”
+name: “Assembly From Type Material”
 typeOf: dcs:GenomeAssemblyDerivedFromEnum
 description: “The sequences in the genome assembly were derived from type material.”
 descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”
 
 Node: dcid:GenomeAssemblyDerivedFromSynonymTypeMaterial
-name: “assembly from synonym type material”
+name: “Assembly From Synonym Type Material”
 typeOf: dcs:GenomeAssemblyDerivedFromEnum
 description: “The sequences in the genome assembly were derived from synonym type material.”
 descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”
 
 Node: dcid:GenomeAssemblyDerivedFromPathotypeMaterial
-name: “assembly from pathotype material”
+name: “Assembly From Pathotype Material”
 typeOf: dcs:GenomeAssemblyDerivedFromEnum
 description: “The sequences in the genome assembly were derived from pathovar material.”
 descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”
 
 Node: dcid:GenomeAssemblyDerivedFromCladeExemplar
-name: “assembly designated as clade exemplar”
+name: “Assembly Designated As Clade Exemplar”
 typeOf: dcs:GenomeAssemblyDerivedFromEnum
 description: “The sequences in the genome assembly were derived from clade exemplar material.”
 
 Node: dcid:GenomeAssemblyDerivedFromNeotype
-name: “assembly designated as neotype”
+name: “Assembly Designated As Neotype”
 typeOf: dcs:GenomeAssemblyDerivedFromEnum
 description: “The sequences in the genome assembly were derived from neotype material.”
 descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”
 
 Node: dcid:GenomeAssemblyDerivedFromReftype
-name: “assembly designated as reftype”
+name: “Assembly Designated As Reftype”
 typeOf: dcs:GenomeAssemblyDerivedFromEnum
 description: “The sequences in the genome assembly were derived from reference material where type material never was available and is not likely to ever be available.”
 descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”
 
 Node: dcid:GenomeAssemblyDerivedFromIctvSpeciesExemplar
-name: “ICTV species exemplar”
+name: “ICTV Species Exemplar”
 typeOf: dcs:GenomeAssemblyDerivedFromEnum
 description: “ The International Committee on Taxonomy of Viruses (ICTV) designated the genome assembly as the exemplar for the virus species.”
 descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”
 
 Node: dcid:GenomeAssemblyDerivedFromIctvAdditionalIsolate
-name: “ICTV additional isolate”
+name: “ICTV Additional Isolate”
 typeOf: dcs:GenomeAssemblyDerivedFromEnum
 description: “ The International Committee on Taxonomy of Viruses (ICTV) designated the genome assembly an additional isolate for the virus species.”
 descriptionUrl: “https://ftp.ncbi.nlm.nih.gov/genomes/README_assembly_summary.txt”
@@ -815,7 +886,7 @@ descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/#level"
 description: "There is sequence for one or more chromosomes. This could be a completely sequenced chromosome without gaps or a chromosome containing scaffolds or contigs with gaps between them. There may also be unplaced or unlocalized scaffolds."
 
 Node: dcid:GenomeAssemblyLevelScaffold
-name: " caffold"
+name: "Scaffold"
 typeOf: dcs:GenomeAssemblyLevelEnum
 descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/#level"
 description: "Some sequence contigs have been connected across gaps to create scaffolds, but the scaffolds are all unplaced or unlocalized."
@@ -1099,13 +1170,13 @@ descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"
 
 Node: dcid:RefSeqCategoryReferenceGenome
 name: "Reference Genome"
-typeOf: dcs:GenomeAssemblyLevelEnum
+typeOf: dcs:RefSeqCategoryEnum
 descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"
 description: "A manually selected high quality genome assembly that NCBI and the community have identified as being important as a standard against which other data are compared."
 
-Node: dcid:RefSeqCategoryRepresentationGenome
-name: "Representation Genome"
-typeOf: dcs:GenomeAssemblyLevelEnum
+Node: dcid:RefSeqCategoryRepresentativeGenome
+name: "Representative Genome"
+typeOf: dcs:RefSeqCategoryEnum
 descriptionUrl: "https://www.ncbi.nlm.nih.gov/assembly/help/"
 description: "A genome computationally or manually selected as a representative from among the best genomes available for a species or clade that does not have a designated reference genome."