valuesets 0.3.1__py3-none-any.whl

valuesets/schema/bio/genome_features.yaml

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+name: genome_features
+title: Genome Feature Types
+description: 'Genome feature types from SOFA (Sequence Ontology Feature Annotation),
+
+  the subset of SO used in GFF3 files for genome annotation.
+
+  Organized hierarchically following the Sequence Ontology structure.'
+id: https://w3id.org/linkml/valuesets/bio/genome_features
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  SO: http://purl.obolibrary.org/obo/SO_
+default_prefix: valuesets
+slots:
+  genome_feature:
+    description: Genome feature types from SOFA (Sequence Ontology Feature Annotation)
+    range: GenomeFeatureType
+    multivalued: true
+enums:
+  GenomeFeatureType:
+    description: 'Genome feature types from SOFA (Sequence Ontology Feature Annotation).
+
+      This is the subset of Sequence Ontology terms used in GFF3 files.
+
+      Organized hierarchically following the Sequence Ontology structure.'
+    permissible_values:
+      REGION:
+        description: A sequence feature with an extent greater than zero
+        meaning: SO:0000001
+      BIOLOGICAL_REGION:
+        description: A region defined by its biological properties
+        meaning: SO:0001411
+        is_a: REGION
+      GENE:
+        description: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript
+        meaning: SO:0000704
+        is_a: BIOLOGICAL_REGION
+      TRANSCRIPT:
+        description: An RNA synthesized on a DNA or RNA template by an RNA polymerase
+        meaning: SO:0000673
+        is_a: BIOLOGICAL_REGION
+      PRIMARY_TRANSCRIPT:
+        description: A transcript that has not been processed
+        meaning: SO:0000185
+        is_a: TRANSCRIPT
+      MRNA:
+        description: Messenger RNA; includes 5'UTR, coding sequences and 3'UTR
+        meaning: SO:0000234
+        is_a: TRANSCRIPT
+      EXON:
+        description: A region of the transcript sequence within a gene which is not removed from the primary RNA transcript
+          by RNA splicing
+        meaning: SO:0000147
+        is_a: BIOLOGICAL_REGION
+      CDS:
+        description: Coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein
+        meaning: SO:0000316
+        is_a: BIOLOGICAL_REGION
+      INTRON:
+        description: A region of a primary transcript that is transcribed, but removed from within the transcript by splicing
+        meaning: SO:0000188
+        is_a: BIOLOGICAL_REGION
+      FIVE_PRIME_UTR:
+        description: 5' untranslated region
+        meaning: SO:0000204
+        is_a: BIOLOGICAL_REGION
+      THREE_PRIME_UTR:
+        description: 3' untranslated region
+        meaning: SO:0000205
+        is_a: BIOLOGICAL_REGION
+      NCRNA:
+        description: Non-protein coding RNA
+        meaning: SO:0000655
+        is_a: TRANSCRIPT
+      RRNA:
+        description: Ribosomal RNA
+        meaning: SO:0000252
+        is_a: NCRNA
+        structured_aliases:
+        - literal_form: rRNA
+          source: SO:0000252
+      TRNA:
+        description: Transfer RNA
+        meaning: SO:0000253
+        is_a: NCRNA
+      SNRNA:
+        description: Small nuclear RNA
+        meaning: SO:0000274
+        is_a: NCRNA
+      SNORNA:
+        description: Small nucleolar RNA
+        meaning: SO:0000275
+        is_a: NCRNA
+      MIRNA:
+        description: MicroRNA
+        meaning: SO:0000276
+        is_a: NCRNA
+      LNCRNA:
+        description: Long non-coding RNA
+        meaning: SO:0001877
+        is_a: NCRNA
+      RIBOZYME:
+        description: An RNA with catalytic activity
+        meaning: SO:0000374
+        is_a: NCRNA
+      ANTISENSE_RNA:
+        description: RNA that is complementary to other RNA
+        meaning: SO:0000644
+        is_a: NCRNA
+      PSEUDOGENE:
+        description: A sequence that closely resembles a known functional gene but does not produce a functional product
+        meaning: SO:0000336
+        is_a: BIOLOGICAL_REGION
+      PROCESSED_PSEUDOGENE:
+        description: A pseudogene arising from reverse transcription of mRNA
+        meaning: SO:0000043
+        is_a: PSEUDOGENE
+      REGULATORY_REGION:
+        description: A region involved in the control of the process of gene expression
+        meaning: SO:0005836
+        is_a: BIOLOGICAL_REGION
+      PROMOTER:
+        description: A regulatory region initiating transcription
+        meaning: SO:0000167
+        is_a: REGULATORY_REGION
+      ENHANCER:
+        description: A cis-acting sequence that increases transcription
+        meaning: SO:0000165
+        is_a: REGULATORY_REGION
+      SILENCER:
+        description: A regulatory region which upon binding of transcription factors, suppresses transcription
+        meaning: SO:0000625
+        is_a: REGULATORY_REGION
+      TERMINATOR:
+        description: The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate
+          transcription
+        meaning: SO:0000141
+        is_a: REGULATORY_REGION
+      ATTENUATOR:
+        description: A sequence that causes transcription termination
+        meaning: SO:0000140
+        is_a: REGULATORY_REGION
+      POLYA_SIGNAL_SEQUENCE:
+        description: The recognition sequence for the cleavage and polyadenylation machinery
+        meaning: SO:0000551
+        is_a: REGULATORY_REGION
+      BINDING_SITE:
+        description: A region on a molecule that binds to another molecule
+        meaning: SO:0000409
+        is_a: BIOLOGICAL_REGION
+      TFBS:
+        title: TF_binding_site
+        description: Transcription factor binding site
+        meaning: SO:0000235
+        is_a: BINDING_SITE
+      RIBOSOME_ENTRY_SITE:
+        description: Region where ribosome assembles on mRNA
+        meaning: SO:0000139
+        is_a: BINDING_SITE
+      POLYA_SITE:
+        description: Polyadenylation site
+        meaning: SO:0000553
+        is_a: BIOLOGICAL_REGION
+      REPEAT_REGION:
+        description: A region of sequence containing one or more repeat units
+        meaning: SO:0000657
+        is_a: BIOLOGICAL_REGION
+      DISPERSED_REPEAT:
+        description: A repeat that is interspersed in the genome
+        meaning: SO:0000658
+        is_a: REPEAT_REGION
+      TANDEM_REPEAT:
+        description: A repeat where the same sequence is repeated in the same orientation
+        meaning: SO:0000705
+        is_a: REPEAT_REGION
+      INVERTED_REPEAT:
+        description: A repeat where the sequence is repeated in the opposite orientation
+        meaning: SO:0000294
+        is_a: REPEAT_REGION
+      TRANSPOSABLE_ELEMENT:
+        description: A DNA segment that can change its position within the genome
+        meaning: SO:0000101
+        is_a: BIOLOGICAL_REGION
+      MOBILE_ELEMENT:
+        title: mobile_genetic_element
+        description: A nucleotide region with the ability to move from one place in the genome to another
+        meaning: SO:0001037
+        is_a: BIOLOGICAL_REGION
+      SEQUENCE_ALTERATION:
+        description: A sequence that deviates from the reference sequence
+        meaning: SO:0001059
+        is_a: REGION
+      INSERTION:
+        description: The sequence of one or more nucleotides added between two adjacent nucleotides
+        meaning: SO:0000667
+        is_a: SEQUENCE_ALTERATION
+      DELETION:
+        description: The removal of a sequences of nucleotides from the genome
+        meaning: SO:0000159
+        is_a: SEQUENCE_ALTERATION
+      INVERSION:
+        description: A continuous nucleotide sequence is inverted in the same position
+        meaning: SO:1000036
+        is_a: SEQUENCE_ALTERATION
+      DUPLICATION:
+        description: One or more nucleotides are added between two adjacent nucleotides
+        meaning: SO:1000035
+        is_a: SEQUENCE_ALTERATION
+      SUBSTITUTION:
+        description: A sequence alteration where one nucleotide replaced by another
+        meaning: SO:1000002
+        is_a: SEQUENCE_ALTERATION
+      ORIGIN_OF_REPLICATION:
+        description: The origin of replication; starting site for duplication of a nucleic acid molecule
+        meaning: SO:0000296
+        is_a: BIOLOGICAL_REGION
+      POLYC_TRACT:
+        description: A sequence of Cs
+        is_a: REGION
+      GAP:
+        description: A gap in the sequence
+        meaning: SO:0000730
+        is_a: REGION
+      ASSEMBLY_GAP:
+        title: gap
+        description: A gap between two sequences in an assembly
+        meaning: SO:0000730
+        is_a: GAP
+      CHROMOSOME:
+        description: Structural unit composed of DNA and proteins
+        meaning: SO:0000340
+        is_a: REGION
+      SUPERCONTIG:
+        description: One or more contigs that have been ordered and oriented using end-read information
+        meaning: SO:0000148
+        is_a: REGION
+      CONTIG:
+        description: A contiguous sequence derived from sequence assembly
+        meaning: SO:0000149
+        is_a: REGION
+      SCAFFOLD:
+        title: supercontig
+        description: One or more contigs that have been ordered and oriented
+        meaning: SO:0000148
+        is_a: REGION
+      CLONE:
+        description: A piece of DNA that has been inserted into a vector
+        meaning: SO:0000151
+        is_a: REGION
+      PLASMID:
+        description: A self-replicating circular DNA molecule
+        meaning: SO:0000155
+        is_a: REGION
+      POLYPEPTIDE:
+        description: A sequence of amino acids linked by peptide bonds
+        meaning: SO:0000104
+        is_a: REGION
+      MATURE_PROTEIN_REGION:
+        description: The polypeptide sequence that remains after post-translational processing
+        meaning: SO:0000419
+        is_a: POLYPEPTIDE
+      SIGNAL_PEPTIDE:
+        description: A peptide region that targets a polypeptide to a specific location
+        meaning: SO:0000418
+        is_a: POLYPEPTIDE
+      TRANSIT_PEPTIDE:
+        description: A peptide that directs the transport of a protein to an organelle
+        meaning: SO:0000725
+        is_a: POLYPEPTIDE
+      PROPEPTIDE:
+        title: propeptide
+        description: A peptide region that is cleaved during maturation
+        meaning: SO:0001062
+        is_a: POLYPEPTIDE
+      OPERON:
+        description: A group of contiguous genes transcribed as a single unit
+        meaning: SO:0000178
+        is_a: BIOLOGICAL_REGION
+      STEM_LOOP:
+        description: A double-helical region formed by base-pairing between adjacent sequences
+        meaning: SO:0000313
+        is_a: REGION
+      D_LOOP:
+        description: Displacement loop; a region where DNA is displaced by an invading strand
+        meaning: SO:0000297
+        is_a: REGION
+      MATCH:
+        description: A region of sequence similarity
+        meaning: SO:0000343
+        is_a: REGION
+      CDNA_MATCH:
+        description: A match to a cDNA sequence
+        meaning: SO:0000689
+        is_a: MATCH
+      EST_MATCH:
+        description: A match to an EST sequence
+        meaning: SO:0000668
+        is_a: MATCH
+      PROTEIN_MATCH:
+        description: A match to a protein sequence
+        meaning: SO:0000349
+        is_a: MATCH
+      NUCLEOTIDE_MATCH:
+        description: A match to a nucleotide sequence
+        meaning: SO:0000347
+        is_a: MATCH
+      JUNCTION_FEATURE:
+        title: junction
+        description: A boundary or junction between sequence regions
+        meaning: SO:0000699
+        is_a: BIOLOGICAL_REGION
+      SPLICE_SITE:
+        description: The position where intron is excised
+        meaning: SO:0000162
+        is_a: JUNCTION_FEATURE
+      FIVE_PRIME_SPLICE_SITE:
+        title: five_prime_cis_splice_site
+        description: The 5' splice site (donor site)
+        meaning: SO:0000163
+        is_a: SPLICE_SITE
+      THREE_PRIME_SPLICE_SITE:
+        title: three_prime_cis_splice_site
+        description: The 3' splice site (acceptor site)
+        meaning: SO:0000164
+        is_a: SPLICE_SITE
+      START_CODON:
+        description: The first codon to be translated
+        meaning: SO:0000318
+        is_a: BIOLOGICAL_REGION
+      STOP_CODON:
+        description: The codon that terminates translation
+        meaning: SO:0000319
+        is_a: BIOLOGICAL_REGION
+      CENTROMERE:
+        description: A region where chromatids are held together
+        meaning: SO:0000577
+        is_a: BIOLOGICAL_REGION
+      TELOMERE:
+        description: The terminal region of a linear chromosome
+        meaning: SO:0000624
+        is_a: BIOLOGICAL_REGION

valuesets/schema/bio/genomics.yaml

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+name: genomics
+title: Genomics Value Sets
+description: Value sets related to genomics and sequencing
+id: https://w3id.org/common-value-sets/genomics
+imports:
+- linkml:types
+prefixes:
+  CVS: https://w3id.org/common-value-sets/
+  linkml: https://w3id.org/linkml/
+  mixs: https://genomicsstandardsconsortium.github.io/mixs/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  cds_phase:
+    description: For features of type CDS (coding sequence), the phase indicates where the feature begins with reference to
+      the reading frame
+    range: CdsPhaseType
+  contig_collection:
+    description: The type of the contig set; the type of the 'omics data set
+    range: ContigCollectionType
+  strand:
+    description: The strand that a feature appears on relative to a landmark
+    range: StrandType
+  sequence:
+    description: The type of sequence being represented
+    range: SequenceType
+enums:
+  CdsPhaseType:
+    description: For features of type CDS (coding sequence), the phase indicates where the feature begins with reference to
+      the reading frame. The phase is one of the integers 0, 1, or 2, indicating the number of bases that should be removed
+      from the beginning of this feature to reach the first base of the next codon.
+    permissible_values:
+      PHASE_0:
+        description: Zero bases from reading frame to feature start.
+        title: '0'
+      PHASE_1:
+        description: One base from reading frame to feature start.
+        title: '1'
+      PHASE_2:
+        description: Two bases from reading frame to feature start.
+        title: '2'
+  ContigCollectionType:
+    description: The type of the contig set; the type of the 'omics data set. Terms are taken from the Genomics Standards
+      Consortium where possible. See the GSC checklists at https://genomicsstandardsconsortium.github.io/mixs/ for the controlled
+      vocabularies used.
+    permissible_values:
+      ISOLATE:
+        description: 'Sequences assembled from DNA of isolated organism. Bacteria/Archaea: https://genomicsstandardsconsortium.github.io/mixs/0010003/
+          Euk: https://genomicsstandardsconsortium.github.io/mixs/0010002/ Virus: https://genomicsstandardsconsortium.github.io/mixs/0010005/
+          Organelle: https://genomicsstandardsconsortium.github.io/mixs/0010006/ Plasmid: https://genomicsstandardsconsortium.github.io/mixs/0010004/'
+      MAG:
+        description: Sequences assembled from DNA of mixed community and binned. MAGs are likely to represent a single taxonomic
+          origin. See checkm2 scores for quality assessment.
+        meaning: mixs:0010011
+        title: Metagenome-Assembled Genome
+        aliases:
+        - Mimag
+      METAGENOME:
+        description: Sequences assembled from DNA of mixed community.
+        meaning: mixs:0010007
+        aliases:
+        - Mims
+      METATRANSCRIPTOME:
+        description: Sequences assembled from RNA of mixed community. Currently not represented by GSC.
+      SAG:
+        description: Sequences assembled from DNA of single cell.
+        meaning: mixs:0010010
+        title: Single Amplified Genome
+        aliases:
+        - Misag
+      VIRUS:
+        description: Sequences assembled from uncultivated virus genome (DNA/RNA).
+        meaning: mixs:0010012
+        aliases:
+        - Miuvig
+      MARKER:
+        description: 'Sequences from targeted region of DNA; see protocol for information on targeted region. specimen: https://genomicsstandardsconsortium.github.io/mixs/0010009/
+          survey: https://genomicsstandardsconsortium.github.io/mixs/0010008/'
+  StrandType:
+    description: The strand that a feature appears on relative to a landmark. Also encompasses unknown or irrelevant strandedness.
+    permissible_values:
+      NEGATIVE:
+        description: Represented by "-" in a GFF file; the strand is negative wrt the landmark.
+        title: negative
+      POSITIVE:
+        description: Represented by "+" in a GFF file; the strand is positive with relation to the landmark.
+        title: positive
+      UNKNOWN:
+        description: Represented by "?" in a GFF file. The strandedness is relevant but unknown.
+        title: unknown
+      UNSTRANDED:
+        description: Represented by "." in a GFF file; the feature is not stranded.
+        title: unstranded
+  SequenceType:
+    description: The type of sequence being represented.
+    permissible_values:
+      NUCLEIC_ACID:
+        description: A nucleic acid sequence, as found in an FNA file.
+      AMINO_ACID:
+        description: An amino acid sequence, as would be found in an FAA file.
+default_range: string

valuesets/schema/bio/go_aspect.yaml

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+name: go_aspect
+title: Gene Ontology Aspects
+description: The three main aspects of Gene Ontology - Molecular Function, Biological Process, and Cellular Component
+id: https://w3id.org/linkml/valuesets/bio/go_aspect
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  GO: http://purl.obolibrary.org/obo/GO_
+default_prefix: valuesets
+slots:
+  go_aspect:
+    description: Gene Ontology aspect (namespace) - one of molecular function, biological process, or cellular component
+    range: GOAspect
+enums:
+  GOAspect:
+    description: The three main aspects (namespaces) of Gene Ontology
+    permissible_values:
+      F:
+        title: Molecular Function
+        description: The activities that occur at the molecular level, such as catalysis or binding
+        aliases:
+        - molecular_function
+        - MF
+        meaning: GO:0003674
+      P:
+        title: Biological Process
+        description: The larger processes accomplished by multiple molecular activities
+        aliases:
+        - biological_process
+        - BP
+        meaning: GO:0008150
+      C:
+        title: Cellular Component
+        description: The locations relative to cellular structures in which a gene product performs a function
+        aliases:
+        - cellular_component
+        - CC
+        meaning: GO:0005575

valuesets/schema/bio/go_causality.yaml

@@ -0,0 +1,119 @@
+name: go_causality
+title: Gene Ontology Causality Value Sets
+description: Value sets for GO causal relationships and predicates used in gene ontology annotations and pathway analysis
+id: https://w3id.org/valuesets/bio/go_causality
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  RO: http://purl.obolibrary.org/obo/RO_
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  causal_predicate:
+    description: A term describing the causal relationship between two activities drawn from the Relation Ontology
+    range: CausalPredicateEnum
+enums:
+  CausalPredicateEnum:
+    description: A term describing the causal relationship between two activities. All terms are drawn from
+      the "causally upstream or within" (RO:0002418) branch of the Relation Ontology (RO).
+    permissible_values:
+      CONSTITUTIVELY_UPSTREAM_OF:
+        title: constitutively upstream of
+        meaning: RO:0012009
+      PROVIDES_INPUT_FOR:
+        title: provides input for
+        meaning: RO:0002413
+      REMOVES_INPUT_FOR:
+        title: removes input for
+        meaning: RO:0012010
+      CAUSALLY_UPSTREAM_OF:
+        title: causally upstream of
+        meaning: RO:0002411
+        aliases:
+        - undetermined
+        comments:
+        - Abstract parent class for causal relationships
+      CAUSALLY_UPSTREAM_OF_POSITIVE_EFFECT:
+        title: causally upstream of, positive effect
+        is_a: CAUSALLY_UPSTREAM_OF
+        meaning: RO:0002304
+        annotations:
+          symbol: "+"
+          direction: POSITIVE
+      CAUSALLY_UPSTREAM_OF_NEGATIVE_EFFECT:
+        title: causally upstream of, negative effect
+        is_a: CAUSALLY_UPSTREAM_OF
+        meaning: RO:0002305
+        annotations:
+          symbol: "-"
+          direction: NEGATIVE
+      REGULATES:
+        title: regulates
+        is_a: CAUSALLY_UPSTREAM_OF
+        meaning: RO:0002211
+        annotations:
+          symbol: "R"
+        comments:
+        - Abstract parent class for regulation relationships
+      NEGATIVELY_REGULATES:
+        title: negatively regulates
+        is_a: REGULATES
+        meaning: RO:0002212
+        annotations:
+          symbol: "-R"
+          direction: NEGATIVE
+        comments:
+        - Abstract parent class for negative regulation relationships
+      POSITIVELY_REGULATES:
+        title: positively regulates
+        is_a: REGULATES
+        meaning: RO:0002213
+        annotations:
+          symbol: "+R"
+          direction: POSITIVE
+        comments:
+        - Abstract parent class for positive regulation relationships
+      DIRECTLY_NEGATIVELY_REGULATES:
+        title: directly negatively regulates
+        is_a: NEGATIVELY_REGULATES
+        meaning: RO:0002630
+        annotations:
+          directness: DIRECT
+          direction: NEGATIVE
+      INDIRECTLY_NEGATIVELY_REGULATES:
+        title: indirectly negatively regulates
+        is_a: NEGATIVELY_REGULATES
+        meaning: RO:0002409
+        annotations:
+          directness: INDIRECT
+          direction: NEGATIVE
+      DIRECTLY_POSITIVELY_REGULATES:
+        title: directly positively regulates
+        is_a: POSITIVELY_REGULATES
+        meaning: RO:0002629
+        annotations:
+          directness: DIRECT
+          direction: POSITIVE
+      INDIRECTLY_POSITIVELY_REGULATES:
+        title: indirectly positively regulates
+        is_a: POSITIVELY_REGULATES
+        meaning: RO:0002407
+        annotations:
+          directness: INDIRECT
+          direction: POSITIVE
+      IS_SMALL_MOLECULE_REGULATOR_OF:
+        title: is small molecule regulator of
+        meaning: RO:0012004
+      IS_SMALL_MOLECULE_ACTIVATOR_OF:
+        title: is small molecule activator of
+        is_a: IS_SMALL_MOLECULE_REGULATOR_OF
+        meaning: RO:0012005
+        annotations:
+          direction: POSITIVE
+      IS_SMALL_MOLECULE_INHIBITOR_OF:
+        title: is small molecule inhibitor of
+        is_a: IS_SMALL_MOLECULE_REGULATOR_OF
+        meaning: RO:0012006
+        annotations:
+          direction: NEGATIVE