format-version: 1.2
subsetdef: Alliance_of_Genome_Resources "Alliance of Genome Resources Gene Biotype Slim"
subsetdef: biosapiens "biosapiens protein feature ontology"
subsetdef: DBVAR "database of genomic structural variation"
subsetdef: SOFA "SO feature annotation"
synonymtypedef: aa1 "amino acid 1 letter code"
synonymtypedef: aa3 "amino acid 3 letter code"
synonymtypedef: AAMOD "amino acid modification"
synonymtypedef: AGR "Alliance of Genome Resources"
synonymtypedef: BS "biosapiens"
synonymtypedef: dbsnp "dbsnp variant terms"
synonymtypedef: dbvar "DBVAR"
synonymtypedef: ebi_variants "ensembl variant terms"
synonymtypedef: RNAMOD "RNA modification" EXACT
synonymtypedef: VAR "variant annotation term"
ontology: so/subsets/biosapiens

[Term]
id: SO:0000409
name: binding_site
namespace: sequence
alt_id: BS:00033
def: "A biological_region of sequence that, in the molecule, interacts selectively and non-covalently with other molecules. A region on the surface of a molecule that may interact with another molecule. When applied to polypeptides: Amino acids involved in binding or interactions. It can also apply to an amino acid bond which is represented by the positions of the two flanking amino acids." [EBIBS:GAR, SO:ke]
comment: See GO:0005488 : binding.
subset: biosapiens
subset: SOFA
synonym: "binding site" EXACT []
synonym: "binding_or_interaction_site" EXACT []
synonym: "INSDC_feature:misc_binding" EXACT []
synonym: "site" RELATED []
xref: http://en.wikipedia.org/wiki/Binding_site "wiki"

[Term]
id: SO:0000417
name: polypeptide_domain
namespace: sequence
alt_id: BS:00012
alt_id: BS:00134
alt_id: SO:0001069
def: "A structurally or functionally defined protein region. In proteins with multiple domains, the combination of the domains determines the function of the protein. A region which has been shown to recur throughout evolution." [EBIBS:GAR]
comment: Range. Old definition from before biosapiens: A region of a single polypeptide chain that folds into an independent unit and exhibits biological activity. A polypeptide chain may have multiple domains.
subset: biosapiens
synonym: "domain" BROAD BS [uniprot:feature_type]
synonym: "polypeptide domain" EXACT []
synonym: "polypeptide_structural_domain" EXACT BS []
synonym: "structural domain" BROAD BS []
is_a: SO:0001070 ! polypeptide_structural_region
is_a: SO:0100021 ! polypeptide_conserved_region

[Term]
id: SO:0000418
name: signal_peptide
namespace: sequence
alt_id: BS:00159
def: "The signal_peptide is a short region of the peptide located at the N-terminus that directs the protein to be secreted or part of membrane components." [http://www.insdc.org/files/feature_table.html]
comment: Old def before biosapiens:The sequence for an N-terminal domain of a secreted protein; this domain is involved in attaching nascent polypeptide to the membrane leader sequence.
subset: biosapiens
subset: SOFA
synonym: "INSDC_feature:sig_peptide" EXACT []
synonym: "signal" RELATED [uniprot:feature_type]
synonym: "signal peptide" EXACT []
synonym: "signal peptide coding sequence" EXACT []
xref: http://en.wikipedia.org/wiki/Signal_peptide "wiki"
is_a: SO:0000839 ! polypeptide_region
relationship: part_of SO:0001062 ! propeptide

[Term]
id: SO:0000419
name: mature_protein_region
namespace: sequence
alt_id: BS:00149
def: "The polypeptide sequence that remains when the cleaved peptide regions have been cleaved from the immature peptide." [EBIBS:GAR, http://www.insdc.org/files/feature_table.html, SO:cb]
comment: This term mature peptide, merged with the biosapiens term mature protein region and took that to be the new name. Old def: The coding sequence for the mature or final peptide or protein product following post-translational modification.
subset: biosapiens
subset: SOFA
synonym: "chain" RELATED [uniprot:feature_type]
synonym: "INSDC_feature:mat_peptide" EXACT []
synonym: "mature peptide" RELATED []
synonym: "mature protein region" EXACT []
is_a: SO:0000839 ! polypeptide_region
relationship: part_of SO:0001063 ! immature_peptide_region

[Term]
id: SO:0000691
name: cleaved_initiator_methionine
namespace: sequence
alt_id: BS:00067
def: "The initiator methionine that has been cleaved from a mature polypeptide sequence." [EBIBS:GAR]
subset: biosapiens
synonym: "cleaved initiator methionine" EXACT []
synonym: "init_met" RELATED [uniprot:feature_type]
synonym: "initiator methionine" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region

[Term]
id: SO:0000725
name: transit_peptide
namespace: sequence
alt_id: BS:00055
def: "The transit_peptide is a short region at the N-terminus of the peptide that directs the protein to an organelle (chloroplast, mitochondrion, microbody or cyanelle)." [http://www.insdc.org/files/feature_table.html]
comment: Added to bring SO inline with the EMBL, DDBJ, GenBank feature table. Old definition before biosapiens: The coding sequence for an N-terminal domain of a nuclear-encoded organellar protein. This domain is involved in post translational import of the protein into the organelle.
subset: biosapiens
subset: SOFA
synonym: "INSDC_feature:transit_peptide" EXACT []
synonym: "signal" RELATED []
synonym: "transit" RELATED [uniprot:feature_type]
synonym: "transit peptide" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0000839
name: polypeptide_region
namespace: sequence
alt_id: BS:00124
alt_id: BS:00331
def: "Biological sequence region that can be assigned to a specific subsequence of a polypeptide." [SO:GAR, SO:ke]
comment: Added to allow the polypeptide regions to have is_a paths back to the root.
subset: biosapiens
subset: SOFA
synonym: "positional" RELATED []
synonym: "positional polypeptide feature" RELATED []
synonym: "region" NARROW [uniprot:feature_type]
synonym: "region or site annotation" RELATED []
synonym: "site" NARROW [uniprot:feature_type]

[Term]
id: SO:0000912
name: asx_turn
namespace: sequence
alt_id: BS:00203
def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Aspartate or Asparagine (Asx), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif

[Term]
id: SO:0001061
name: propeptide_cleavage_site
namespace: sequence
alt_id: BS:00063
def: "The propeptide_cleavage_site is the arginine/lysine boundary on a propeptide where cleavage occurs." [EBIBS:GAR]
comment: Discrete.
subset: biosapiens
synonym: "propeptide cleavage site" EXACT []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0001062 ! propeptide

[Term]
id: SO:0001062
name: propeptide
namespace: sequence
alt_id: BS:00077
def: "Part of a peptide chain which is cleaved off during the formation of the mature protein." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "INSDC_feature:propeptide" EXACT []
synonym: "propep" RELATED [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Propeptide "wiki"
is_a: SO:0100011 ! cleaved_peptide_region

[Term]
id: SO:0001063
name: immature_peptide_region
namespace: sequence
alt_id: BS:00129
def: "An immature_peptide_region is the extent of the peptide after it has been translated and before any processing occurs." [EBIBS:GAR]
comment: Range.
subset: biosapiens
subset: SOFA
synonym: "immature peptide region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001064
name: active_peptide
namespace: sequence
alt_id: BS:00076
def: "Active peptides are proteins which are biologically active, released from a precursor molecule." [EBIBS:GAR, UniProt:curation_manual]
comment: Hormones, neuropeptides, antimicrobial peptides, are active peptides. They are typically short (<40 amino acids) in length.
subset: biosapiens
synonym: "active peptide" EXACT []
synonym: "peptide" BROAD [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Peptide "wiki"
is_a: SO:0000419 ! mature_protein_region

[Term]
id: SO:0001066
name: compositionally_biased_region_of_peptide
namespace: sequence
alt_id: BS:00068
def: "Polypeptide region that is rich in a particular amino acid or homopolymeric and greater than three residues in length." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "compbias" RELATED [uniprot:feature_type]
synonym: "compositional bias" RELATED []
synonym: "compositionally biased" RELATED []
synonym: "compositionally biased region of peptide" RELATED []
synonym: "compositionally_biased_region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001067
name: polypeptide_motif
namespace: sequence
alt_id: BS:00032
def: "A sequence motif is a short (up to 20 amino acids) region of biological interest. Such motifs, although they are too short to constitute functional domains, share sequence similarities and are conserved in different proteins. They display a common function (protein-binding, subcellular location etc.)." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "motif" BROAD [uniprot:feature_type]
synonym: "polypeptide motif" EXACT []
is_a: SO:0100021 ! polypeptide_conserved_region

[Term]
id: SO:0001068
name: polypeptide_repeat
namespace: sequence
alt_id: BS:00070
def: "A polypeptide_repeat is a single copy of an internal sequence repetition." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "polypeptide repeat" EXACT []
synonym: "repeat" RELATED [uniprot:feature_type]
is_a: SO:0100021 ! polypeptide_conserved_region

[Term]
id: SO:0001070
name: polypeptide_structural_region
namespace: sequence
alt_id: BS:00337
def: "Region of polypeptide with a given structural property." [EBIBS:GAR, SO:cb]
comment: Range.
subset: biosapiens
synonym: "polypeptide structural region" EXACT []
synonym: "structural_region" RELATED []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001071
name: membrane_structure
namespace: sequence
alt_id: BS:00128
def: "Arrangement of the polypeptide with respect to the lipid bilayer." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "membrane structure" EXACT []
is_a: SO:0001070 ! polypeptide_structural_region

[Term]
id: SO:0001072
name: extramembrane_polypeptide_region
namespace: sequence
alt_id: BS:00154
def: "Polypeptide region that is localized outside of a lipid bilayer." [EBIBS:GAR, SO:cb]
comment: Range.
subset: biosapiens
synonym: "extramembrane" RELATED BS []
synonym: "extramembrane polypeptide region" EXACT []
synonym: "extramembrane_region" RELATED BS []
synonym: "topo_dom" RELATED BS [uniprot:feature_type]
is_a: SO:0001070 ! polypeptide_structural_region
relationship: part_of SO:0001071 ! membrane_structure

[Term]
id: SO:0001073
name: cytoplasmic_polypeptide_region
namespace: sequence
alt_id: BS:00145
def: "Polypeptide region that is localized inside the cytoplasm." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "cytoplasm_location" EXACT BS []
synonym: "cytoplasmic polypeptide region" EXACT []
synonym: "inside" RELATED BS []
is_a: SO:0001072 ! extramembrane_polypeptide_region

[Term]
id: SO:0001074
name: non_cytoplasmic_polypeptide_region
namespace: sequence
alt_id: BS:00144
def: "Polypeptide region that is localized outside of a lipid bilayer and outside of the cytoplasm." [EBIBS:GAR, SO:cb]
comment: This could be inside an organelle within the cell.
subset: biosapiens
synonym: "non cytoplasmic polypeptide region" EXACT []
synonym: "non_cytoplasm_location" EXACT BS []
synonym: "outside" RELATED BS []
is_a: SO:0001072 ! extramembrane_polypeptide_region

[Term]
id: SO:0001075
name: intramembrane_polypeptide_region
namespace: sequence
alt_id: BS:00156
def: "Polypeptide region present in the lipid bilayer." [EBIBS:GAR]
subset: biosapiens
synonym: "intramembrane" RELATED BS []
synonym: "intramembrane polypeptide region" EXACT []
is_a: SO:0001070 ! polypeptide_structural_region
relationship: part_of SO:0001071 ! membrane_structure

[Term]
id: SO:0001076
name: membrane_peptide_loop
namespace: sequence
alt_id: BS:00155
def: "Polypeptide region localized within the lipid bilayer where both ends traverse the same membrane." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "membrane peptide loop" EXACT []
synonym: "membrane_loop" RELATED BS []
is_a: SO:0001075 ! intramembrane_polypeptide_region

[Term]
id: SO:0001077
name: transmembrane_polypeptide_region
namespace: sequence
alt_id: BS:00158
def: "Polypeptide region traversing the lipid bilayer." [EBIBS:GAR, UniProt:curator_manual]
subset: biosapiens
synonym: "transmem" RELATED BS [uniprot:feature_type]
synonym: "transmembrane" RELATED BS []
synonym: "transmembrane polypeptide region" EXACT []
is_a: SO:0001075 ! intramembrane_polypeptide_region

[Term]
id: SO:0001078
name: polypeptide_secondary_structure
namespace: sequence
alt_id: BS:00003
def: "A region of peptide with secondary structure has hydrogen bonding along the peptide chain that causes a defined conformation of the chain." [EBIBS:GAR]
comment: Biosapien term was secondary_structure.
subset: biosapiens
synonym: "2nary structure" RELATED BS []
synonym: "polypeptide secondary structure" EXACT []
synonym: "secondary structure" RELATED BS []
synonym: "secondary structure region" RELATED BS []
synonym: "secondary_structure" RELATED BS []
xref: http://en.wikipedia.org/wiki/Secondary_structure "wiki"
is_a: SO:0001070 ! polypeptide_structural_region

[Term]
id: SO:0001079
name: polypeptide_structural_motif
namespace: sequence
alt_id: BS:0000338
def: "Motif is a three-dimensional structural element within the chain, which appears also in a variety of other molecules. Unlike a domain, a motif does not need to form a stable globular unit." [EBIBS:GAR]
subset: biosapiens
synonym: "polypeptide structural motif" RELATED []
synonym: "structural_motif" RELATED BS []
xref: http://en.wikipedia.org/wiki/Structural_motif "wiki"
is_a: SO:0001070 ! polypeptide_structural_region

[Term]
id: SO:0001080
name: coiled_coil
namespace: sequence
alt_id: BS:00041
def: "A coiled coil is a structural motif in proteins, in which alpha-helices are coiled together like the strands of a rope." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "coiled" RELATED BS [uniprot:feature_type]
synonym: "coiled coil" EXACT []
xref: http://en.wikipedia.org/wiki/Coiled_coil "wiki"
is_a: SO:0001079 ! polypeptide_structural_motif

[Term]
id: SO:0001081
name: helix_turn_helix
namespace: sequence
alt_id: BS:00147
def: "A motif comprising two helices separated by a turn." [EBIBS:GAR]
subset: biosapiens
synonym: "helix turn helix" EXACT []
synonym: "helix-turn-helix" EXACT []
synonym: "HTH" RELATED BS []
is_a: SO:0001079 ! polypeptide_structural_motif
relationship: has_part SO:0001114 ! peptide_helix
relationship: has_part SO:0001128 ! polypeptide_turn_motif

[Term]
id: SO:0001082
name: polypeptide_sequencing_information
namespace: sequence
alt_id: BS:00125
def: "Incompatibility in the sequence due to some experimental problem." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "sequencing_information" EXACT []

[Term]
id: SO:0001083
name: non_adjacent_residues
namespace: sequence
alt_id: BS:00182
def: "Indicates that two consecutive residues in a fragment sequence are not consecutive in the full-length protein and that there are a number of unsequenced residues between them." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "non consecutive" EXACT []
synonym: "non_cons" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001084
name: non_terminal_residue
namespace: sequence
alt_id: BS:00072
def: "The residue at an extremity of the sequence is not the terminal residue." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "non terminal" EXACT []
synonym: "non_ter" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001085
name: sequence_conflict
namespace: sequence
alt_id: BS:00069
def: "Different sources report differing sequences." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "conflict" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001086
name: sequence_uncertainty
namespace: sequence
alt_id: BS:00181
def: "Describes the positions in a sequence where the authors are unsure about the sequence assignment." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "INSDC_feature:unsure" EXACT []
synonym: "unsure" EXACT [uniprot:feature_type]
is_a: SO:0001082 ! polypeptide_sequencing_information

[Term]
id: SO:0001087
name: cross_link
namespace: sequence
alt_id: BS:00178
def: "Posttranslationally formed amino acid bonds." [EBIBS:GAR, UniProt:curation_manual]
subset: biosapiens
synonym: "cross link" EXACT []
synonym: "crosslink" RELATED []
is_obsolete: true

[Term]
id: SO:0001088
name: disulfide_bond
namespace: sequence
alt_id: BS:00028
def: "The covalent bond between sulfur atoms that binds two peptide chains or different parts of one peptide chain and is a structural determinant in many protein molecules." [EBIBS:GAR, UniProt:curation_manual]
comment: 2 discreet & joined.
subset: biosapiens
synonym: "disulfid" RELATED []
synonym: "disulfide" RELATED []
synonym: "disulfide bond" RELATED []
synonym: "disulphide" EXACT []
synonym: "disulphide bond" RELATED []
is_obsolete: true

[Term]
id: SO:0001089
name: post_translationally_modified_region
namespace: sequence
alt_id: BS:00052
def: "A region where a transformation occurs in a protein after it has been synthesized. This which may regulate, stabilize, crosslink or introduce new chemical functionalities in the protein." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "mod_res" EXACT [uniprot:feature_type]
synonym: "modified residue" EXACT []
synonym: "post_translational_modification" EXACT []
xref: http://en.wikipedia.org/wiki/Post_translational_modification "wiki"
is_a: SO:0100001 ! biochemical_region_of_peptide

[Term]
id: SO:0001090
name: covalent_binding_site
namespace: sequence
alt_id: BS:00246
def: "Binding involving a covalent bond." [EBIBS:GAR]
subset: biosapiens
synonym: "covalent binding site" EXACT []
is_obsolete: true

[Term]
id: SO:0001091
name: non_covalent_binding_site
namespace: sequence
alt_id: BS:00029
def: "Binding site for any chemical group (co-enzyme, prosthetic group, etc.)." [EBIBS:GAR]
comment: Discrete.
subset: biosapiens
synonym: "binding" RELATED [uniprot:curation]
synonym: "binding site" RELATED []
synonym: "non covalent binding site" EXACT []
is_obsolete: true

[Term]
id: SO:0001092
name: polypeptide_metal_contact
namespace: sequence
alt_id: BS:00027
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with metal ions." [EBIBS:GAR, SO:cb, UniProt:curation_manual]
comment: Residue is part of a binding site for a metal ion.
subset: biosapiens
synonym: "metal_binding" RELATED []
is_a: SO:0000409 ! binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0001093
name: protein_protein_contact
namespace: sequence
alt_id: BS:00131
def: "A binding site that, in the protein molecule, interacts selectively and non-covalently with polypeptide residues." [EBIBS:GAR, UniProt:Curation_manual]
subset: biosapiens
synonym: "protein protein contact" EXACT []
synonym: "protein protein contact site" EXACT []
synonym: "protein_protein_interaction" RELATED []
xref: http://en.wikipedia.org/wiki/Protein_protein_interaction "wiki"
is_a: SO:0000409 ! binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0001094
name: polypeptide_calcium_ion_contact_site
namespace: sequence
alt_id: BS:00186
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with calcium ions." [EBIBS:GAR]
comment: Residue involved in contact with calcium.
subset: biosapiens
synonym: "ca bind" RELATED []
synonym: "ca_bind" EXACT BS [uniprot:feature_type]
synonym: "Ca_contact_site" EXACT []
synonym: "polypeptide calcium ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001095
name: polypeptide_cobalt_ion_contact_site
namespace: sequence
alt_id: BS:00136
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with cobalt ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Co_contact_site" EXACT []
synonym: "polypeptide cobalt ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001096
name: polypeptide_copper_ion_contact_site
namespace: sequence
alt_id: BS:00146
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with copper ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Cu_contact_site" EXACT []
synonym: "polypeptide copper ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001097
name: polypeptide_iron_ion_contact_site
namespace: sequence
alt_id: BS:00137
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with iron ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Fe_contact_site" EXACT []
synonym: "polypeptide iron ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001098
name: polypeptide_magnesium_ion_contact_site
namespace: sequence
alt_id: BS:00187
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with magnesium ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Mg_contact_site" EXACT []
synonym: "polypeptide magnesium ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001099
name: polypeptide_manganese_ion_contact_site
namespace: sequence
alt_id: BS:00140
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with manganese ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Mn_contact_site" EXACT []
synonym: "polypeptide manganese ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001100
name: polypeptide_molybdenum_ion_contact_site
namespace: sequence
alt_id: BS:00141
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with molybdenum ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "Mo_contact_site" EXACT []
synonym: "polypeptide molybdenum ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001101
name: polypeptide_nickel_ion_contact_site
namespace: sequence
alt_id: BS:00142
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with nickel ions." [EBIBS:GAR]
subset: biosapiens
synonym: "Ni_contact_site" EXACT []
synonym: "polypeptide nickel ion contact site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001102
name: polypeptide_tungsten_ion_contact_site
namespace: sequence
alt_id: BS:00143
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with tungsten ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "polypeptide tungsten ion contact site" EXACT []
synonym: "W_contact_site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001103
name: polypeptide_zinc_ion_contact_site
namespace: sequence
alt_id: BS:00185
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with zinc ions." [EBIBS:GAR, SO:cb]
subset: biosapiens
synonym: "polypeptide zinc ion contact site" EXACT []
synonym: "Zn_contact_site" EXACT []
is_a: SO:0001092 ! polypeptide_metal_contact

[Term]
id: SO:0001104
name: catalytic_residue
namespace: sequence
alt_id: BS:00026
def: "Amino acid involved in the activity of an enzyme." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "act_site" RELATED [uniprot:feature_type]
synonym: "active site residue" EXACT []
synonym: "catalytic residue" EXACT []
relationship: part_of SO:0100019 ! polypeptide_catalytic_motif

[Term]
id: SO:0001105
name: polypeptide_ligand_contact
namespace: sequence
alt_id: BS:00157
def: "Residues which interact with a ligand." [EBIBS:GAR]
subset: biosapiens
synonym: "polypeptide ligand contact" EXACT []
synonym: "protein-ligand interaction" RELATED []
is_a: SO:0000409 ! binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0001106
name: asx_motif
namespace: sequence
alt_id: BS:00202
def: "A motif of five consecutive residues and two H-bonds in which: Residue(i) is Aspartate or Asparagine (Asx), side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3), main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001107
name: beta_bulge
namespace: sequence
alt_id: BS:00208
def: "A motif of three residues within a beta-sheet in which the main chains of two consecutive residues are H-bonded to that of the third, and in which the dihedral angles are as follows: Residue(i): -140 degrees < phi(l) -20 degrees , -90 degrees < psi(l) < 40 degrees. Residue (i+1): -180 degrees < phi < -25 degrees or +120 degrees < phi < +180 degrees, +40 degrees < psi < +180 degrees or -180 degrees < psi < -120 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge" EXACT []
xref: http://en.wikipedia.org/wiki/Beta_bulge "wiki"
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001108
name: beta_bulge_loop
namespace: sequence
alt_id: BS:00209
def: "A motif of three residues within a beta-sheet consisting of two H-bonds. Beta bulge loops often occur at the loop ends of beta-hairpins." [EBIBS:GAR, Http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge loop" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001109
name: beta_bulge_loop_five
namespace: sequence
alt_id: BS:00210
def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+4), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+3), these loops have an RL nest at residues i+2 and i+3." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge loop five" EXACT []
is_a: SO:0001108 ! beta_bulge_loop

[Term]
id: SO:0001110
name: beta_bulge_loop_six
namespace: sequence
alt_id: BS:00211
def: "A motif of three residues within a beta-sheet consisting of two H-bonds in which: the main-chain NH of residue(i) is H-bonded to the main-chain CO of residue(i+5), the main-chain CO of residue i is H-bonded to the main-chain NH of residue(i+4), these loops have an RL nest at residues i+3 and i+4." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta bulge loop six" EXACT []
is_a: SO:0001108 ! beta_bulge_loop

[Term]
id: SO:0001111
name: beta_strand
namespace: sequence
alt_id: BS:00042
def: "A beta strand describes a single length of polypeptide chain that forms part of a beta sheet. A single continuous stretch of amino acids adopting an extended conformation of hydrogen bonds between the N-O and the C=O of another part of the peptide. This forms a secondary protein structure in which two or more extended polypeptide regions are hydrogen-bonded to one another in a planar array." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "strand" RELATED BS [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Beta_sheet "wiki"
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001112
name: antiparallel_beta_strand
namespace: sequence
alt_id: BS:0000341
def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (one running N-terminal to C-terminal and one running C-terminal to N-terminal). Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i) and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they form two mutual backbone hydrogen bonds to each other's flanking peptide groups; this is known as a close pair of hydrogen bonds. The peptide backbone dihedral angles (phi, psi) are about (-140 degrees, 135 degrees) in antiparallel sheets." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "antiparallel beta strand" EXACT []
is_a: SO:0001111 ! beta_strand

[Term]
id: SO:0001113
name: parallel_beta_strand
namespace: sequence
alt_id: BS:00151
def: "A peptide region which hydrogen bonded to another region of peptide running in the oposite direction (both running N-terminal to C-terminal). This orientation is slightly less stable because it introduces nonplanarity in the inter-strand hydrogen bonding pattern. Hydrogen bonding occurs between every other C=O from one strand to every other N-H on the adjacent strand. In this case, if two atoms C-alpha (i)and C-alpha (j) are adjacent in two hydrogen-bonded beta strands, then they do not hydrogen bond to each other; rather, one residue forms hydrogen bonds to the residues that flank the other (but not vice versa). For example, residue i may form hydrogen bonds to residues j - 1 and j + 1; this is known as a wide pair of hydrogen bonds. By contrast, residue j may hydrogen-bond to different residues altogether, or to none at all. The dihedral angles (phi, psi) are about (-120 degrees, 115 degrees) in parallel sheets." [EBIBS:GAR, UniProt:curation_manual]
comment: Range.
subset: biosapiens
synonym: "parallel beta strand" EXACT []
is_a: SO:0001111 ! beta_strand

[Term]
id: SO:0001114
name: peptide_helix
namespace: sequence
alt_id: BS:00152
def: "A helix is a secondary_structure conformation where the peptide backbone forms a coil." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "helix" RELATED BS []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001115
name: left_handed_peptide_helix
namespace: sequence
alt_id: BS:00222
def: "A left handed helix is a region of peptide where the coiled conformation turns in an anticlockwise, left handed screw." [EBIBS:GAR]
subset: biosapiens
synonym: "helix-l" RELATED []
synonym: "left handed helix" EXACT []
is_a: SO:0001114 ! peptide_helix

[Term]
id: SO:0001116
name: right_handed_peptide_helix
namespace: sequence
alt_id: BS:0000339
def: "A right handed helix is a region of peptide where the coiled conformation turns in a clockwise, right handed screw." [EBIBS:GAR]
subset: biosapiens
synonym: "helix" RELATED BS []
synonym: "right handed helix" EXACT []
is_a: SO:0001114 ! peptide_helix

[Term]
id: SO:0001117
name: alpha_helix
namespace: sequence
alt_id: BS:00040
def: "The helix has 3.6 residues per turn which corresponds to a translation of 1.5 angstroms (= 0.15 nm) along the helical axis. Every backbone N-H group donates a hydrogen bond to the backbone C=O group of the amino acid four residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "a-helix" RELATED BS []
synonym: "helix" RELATED BS [uniprot:feature_type]
xref: http://en.wikipedia.org/wiki/Alpha_helix "wiki"
is_a: SO:0001116 ! right_handed_peptide_helix

[Term]
id: SO:0001118
name: pi_helix
namespace: sequence
alt_id: BS:00153
def: "The pi helix has 4.1 residues per turn and a translation of 1.15 (=0.115 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid five residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "pi helix" EXACT []
xref: http://en.wikipedia.org/wiki/Pi_helix "wiki"
is_a: SO:0001116 ! right_handed_peptide_helix

[Term]
id: SO:0001119
name: three_ten_helix
namespace: sequence
alt_id: BS:0000340
def: "The 3-10 helix has 3 residues per turn with a translation of 2.0 angstroms (=0.2 nm) along the helical axis. The N-H group of an amino acid forms a hydrogen bond with the C=O group of the amino acid three residues earlier." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "3(10) helix" EXACT []
synonym: "3-10 helix" EXACT []
synonym: "310 helix" EXACT []
synonym: "three ten helix" EXACT []
xref: http://en.wikipedia.org/wiki/310_helix "wiki"
is_a: SO:0001116 ! right_handed_peptide_helix

[Term]
id: SO:0001120
name: polypeptide_nest_motif
namespace: sequence
alt_id: BS:00223
def: "A motif of two consecutive residues with dihedral angles. Nest should not have Proline as any residue. Nests frequently occur as parts of other motifs such as Schellman loops." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest" RELATED BS []
synonym: "nest_motif" EXACT []
synonym: "polypeptide nest motif" RELATED []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001121
name: polypeptide_nest_left_right_motif
namespace: sequence
alt_id: BS:00224
def: "A motif of two consecutive residues with dihedral angles: Residue(i): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest_left_right" EXACT []
synonym: "nest_lr" EXACT []
synonym: "polypeptide nest left right motif" EXACT []
is_a: SO:0001120 ! polypeptide_nest_motif

[Term]
id: SO:0001122
name: polypeptide_nest_right_left_motif
namespace: sequence
alt_id: BS:00225
def: "A motif of two consecutive residues with dihedral angles: Residue(i): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "nest_right_left" EXACT []
synonym: "nest_rl" EXACT []
synonym: "polypeptide nest right left motif" EXACT []
is_a: SO:0001120 ! polypeptide_nest_motif

[Term]
id: SO:0001123
name: schellmann_loop
namespace: sequence
alt_id: BS:00226
def: "A motif of six or seven consecutive residues that contains two H-bonds." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "paperclip" RELATED BS []
synonym: "paperclip loop" RELATED []
synonym: "schellmann loop" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001124
name: schellmann_loop_seven
namespace: sequence
alt_id: BS:00228
def: "Wild type: A motif of seven consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+6), the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+5)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "schellmann loop seven" EXACT []
synonym: "seven-residue schellmann loop" EXACT []
is_a: SO:0001123 ! schellmann_loop

[Term]
id: SO:0001125
name: schellmann_loop_six
namespace: sequence
alt_id: BS:00227
def: "Common Type: A motif of six consecutive residues that contains two H-bonds in which: the main-chain CO of residue(i) is H-bonded to the main-chain NH of residue(i+5) the main-chain CO of residue(i+1) is H-bonded to the main-chain NH of residue(i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "schellmann loop six" EXACT []
synonym: "six-residue schellmann loop" EXACT []
is_a: SO:0001123 ! schellmann_loop

[Term]
id: SO:0001126
name: serine_threonine_motif
namespace: sequence
alt_id: BS:00229
def: "A motif of five consecutive residues and two hydrogen bonds in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2) or (i+3) , the main-chain CO group of residue(i) is H-bonded to the main-chain NH of residue(i+3) or (i+4)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "serine/threonine motif" EXACT []
synonym: "st motif" EXACT []
synonym: "st_motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001127
name: serine_threonine_staple_motif
namespace: sequence
alt_id: BS:00230
def: "A motif of four or five consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain OH of residue(i) is H-bonded to the main-chain CO of residue(i3) or (i4), Phi angles of residues(i1), (i2) and (i3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "serine threonine staple motif" EXACT []
synonym: "st_staple" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001128
name: polypeptide_turn_motif
namespace: sequence
alt_id: BS:00148
def: "A reversal in the direction of the backbone of a protein that is stabilized by hydrogen bond between backbone NH and CO groups, involving no more than 4 amino acid residues." [EBIBS:GAR, uniprot:feature_type]
comment: Range.
subset: biosapiens
synonym: "turn" RELATED BS []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0001129
name: asx_turn_left_handed_type_one
namespace: sequence
alt_id: BS:00206
def: "Left handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn left handed type one" EXACT []
synonym: "asx_turn_il" RELATED []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001130
name: asx_turn_left_handed_type_two
namespace: sequence
alt_id: BS:00204
def: "Left handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn left handed type two" EXACT []
synonym: "asx_turn_iil" EXACT []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001131
name: asx_turn_right_handed_type_two
namespace: sequence
alt_id: BS:00205
def: "Right handed type II (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, +80 degrees < psi +120 degrees < +180 degrees. Residue(i+1): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn right handed type two" EXACT []
synonym: "asx_turn_iir" EXACT []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001132
name: asx_turn_right_handed_type_one
namespace: sequence
alt_id: BS:00207
def: "Right handed type I (dihedral angles):- Residue(i): -140 degrees < chi (1) -120 degrees < -20 degrees, -90 degrees < psi +120 degrees < +40 degrees. Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "asx turn type right handed type one" EXACT []
synonym: "asx_turn_ir" EXACT []
is_a: SO:0000912 ! asx_turn

[Term]
id: SO:0001133
name: beta_turn
namespace: sequence
alt_id: BS:00212
def: "A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles of the second and third residues, which are the basis for sub-categorization." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif

[Term]
id: SO:0001134
name: beta_turn_left_handed_type_one
namespace: sequence
alt_id: BS:00215
def: "Left handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles:- Residue(i+1): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees. Residue(i+2): -140 degrees > phi > -20 degrees, -90 degrees > psi > +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn left handed type one" EXACT []
synonym: "beta_turn_il" EXACT []
synonym: "type I' beta turn" EXACT []
synonym: "type I' turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001135
name: beta_turn_left_handed_type_two
namespace: sequence
alt_id: BS:00213
def: "Left handed type II: A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees > phi > -20 degrees, +80 degrees > psi > +180 degrees. Residue(i+2): +20 degrees > phi > +140 degrees, -40 degrees > psi > +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn left handed type two" EXACT []
synonym: "beta_turn_iil" EXACT []
synonym: "type II' beta turn" EXACT []
synonym: "type II' turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001136
name: beta_turn_right_handed_type_one
namespace: sequence
alt_id: BS:00216
def: "Right handed type I:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees. Residue(i+2): -140 degrees < phi < -20 degrees, -90 degrees < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn right handed type one" EXACT []
synonym: "beta_turn_ir" EXACT []
synonym: "type I beta turn" EXACT []
synonym: "type I turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001137
name: beta_turn_right_handed_type_two
namespace: sequence
alt_id: BS:00214
def: "Right handed type II:A motif of four consecutive residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth. It is characterized by the dihedral angles: Residue(i+1): -140 degrees < phi < -20 degrees, +80 degrees < psi < +180 degrees. Residue(i+2): +20 degrees < phi < +140 degrees, -40 degrees < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "beta turn right handed type two" EXACT []
synonym: "beta_turn_iir" EXACT []
synonym: "type II beta turn" EXACT []
synonym: "type II turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001138
name: gamma_turn
namespace: sequence
alt_id: BS:00219
def: "Gamma turns, defined for 3 residues i,( i+1),( i+2) if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "gamma turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif

[Term]
id: SO:0001139
name: gamma_turn_classic
namespace: sequence
alt_id: BS:00220
def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=75.0 - psi(i+1)=-64.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "classic gamma turn" EXACT []
synonym: "gamma turn classic" EXACT []
is_a: SO:0001138 ! gamma_turn

[Term]
id: SO:0001140
name: gamma_turn_inverse
namespace: sequence
alt_id: BS:00221
def: "Gamma turns, defined for 3 residues i, i+1, i+2 if a hydrogen bond exists between residues i and i+2 and the phi and psi angles of residue i+1 fall within 40 degrees: phi(i+1)=-79.0 - psi(i+1)=69.0." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "gamma turn inverse" EXACT []
is_a: SO:0001138 ! gamma_turn

[Term]
id: SO:0001141
name: serine_threonine_turn
namespace: sequence
alt_id: BS:00231
def: "A motif of three consecutive residues and one H-bond in which: residue(i) is Serine (S) or Threonine (T), the side-chain O of residue(i) is H-bonded to the main-chain NH of residue(i+2)." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "serine/threonine turn" EXACT []
synonym: "st_turn" EXACT []
is_a: SO:0001128 ! polypeptide_turn_motif

[Term]
id: SO:0001142
name: st_turn_left_handed_type_one
namespace: sequence
alt_id: BS:00234
def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn left handed type one" EXACT []
synonym: "st_turn_il" EXACT []
is_a: SO:0001141 ! serine_threonine_turn

[Term]
id: SO:0001143
name: st_turn_left_handed_type_two
namespace: sequence
alt_id: BS:00232
def: "The peptide twists in an anticlockwise, left handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn left handed type two" EXACT []
synonym: "st_turn_iil" EXACT []
is_a: SO:0001141 ! serine_threonine_turn

[Term]
id: SO:0001144
name: st_turn_right_handed_type_one
namespace: sequence
alt_id: BS:00235
def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, -90 degrees psi +120 degrees < +40 degrees, residue(i+1): -140 degrees < phi < -20 degrees, -90 < psi < +40 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn right handed type one" EXACT []
synonym: "st_turn_ir" EXACT []
is_a: SO:0001141 ! serine_threonine_turn

[Term]
id: SO:0001145
name: st_turn_right_handed_type_two
namespace: sequence
alt_id: BS:00233
def: "The peptide twists in an clockwise, right handed manner. The dihedral angles for this turn are: Residue(i): -140 degrees < chi(1) -120 degrees < -20 degrees, +80 degrees psi +120 degrees < +180 degrees, residue(i+1): +20 degrees < phi < +140 degrees, -40 < psi < +90 degrees." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "st turn right handed type two" EXACT []
synonym: "st_turn_iir" EXACT []
is_a: SO:0001141 ! serine_threonine_turn

[Term]
id: SO:0001146
name: polypeptide_variation_site
namespace: sequence
alt_id: BS:00336
def: "A site of sequence variation (alteration). Alternative sequence due to naturally occurring events such as polymorphisms and alternative splicing or experimental methods such as site directed mutagenesis." [EBIBS:GAR, SO:ke]
comment: For example, was a substitution natural or mutated as part of an experiment? This term is added to merge the biosapiens term sequence_variations.
subset: biosapiens
synonym: "sequence_variations" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0001147
name: natural_variant_site
namespace: sequence
alt_id: BS:00071
def: "Describes the natural sequence variants due to polymorphisms, disease-associated mutations, RNA editing and variations between strains, isolates or cultivars." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "natural_variant" BROAD []
synonym: "sequence variation" BROAD []
synonym: "variant" BROAD [uniprot:feature_type]
is_a: SO:0001146 ! polypeptide_variation_site

[Term]
id: SO:0001148
name: mutated_variant_site
namespace: sequence
alt_id: BS:00036
def: "Site which has been experimentally altered." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "mutagen" EXACT BS [uniprot:feature_type]
synonym: "mutagenesis" EXACT []
synonym: "mutated_site" EXACT []
is_a: SO:0001146 ! polypeptide_variation_site

[Term]
id: SO:0001149
name: alternate_sequence_site
namespace: sequence
alt_id: BS:00073
alt_id: SO:0001065
def: "Description of sequence variants produced by alternative splicing, alternative promoter usage, alternative initiation and ribosomal frameshifting." [EBIBS:GAR, UniProt:curation_manual]
comment: Discrete.
subset: biosapiens
synonym: "alternative_sequence" EXACT []
synonym: "isoform" NARROW []
synonym: "sequence variation" NARROW []
synonym: "var_seq" EXACT [uniprot:feature_type]
synonym: "varsplic" NARROW []
is_a: SO:0001146 ! polypeptide_variation_site

[Term]
id: SO:0001150
name: beta_turn_type_six
namespace: sequence
def: "A motif of four consecutive peptide resides of type VIa or type VIb and where the i+2 residue is cis-proline." [SO:cb]
subset: biosapiens
synonym: "beta turn type six" EXACT []
synonym: "cis-proline loop" EXACT []
synonym: "type VI beta turn" EXACT []
synonym: "type VI turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0001151
name: beta_turn_type_six_a
namespace: sequence
def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -90 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]
subset: biosapiens
synonym: "beta turn type six a" EXACT []
synonym: "type VIa beta turn" EXACT []
synonym: "type VIa turn" EXACT []
is_a: SO:0001150 ! beta_turn_type_six

[Term]
id: SO:0001152
name: beta_turn_type_six_a_one
namespace: sequence
def: "A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -60 degrees, psi-2 = 120 degrees, phi-3 = -90 degrees, psi-3 = 0 degrees." [PMID:27428516]
subset: biosapiens
synonym: "beta turn type six a one" EXACT []
synonym: "type VIa1 beta turn" EXACT []
synonym: "type VIa1 turn" EXACT []
is_a: SO:0001151 ! beta_turn_type_six_a

[Term]
id: SO:0001153
name: beta_turn_type_six_a_two
namespace: sequence
def: "A type VIa beta turn with the following phi and psi sngles on amino acid residues 2 and 3: phi-2 = -120 degrees, psi-2 = 120 degrees, phi-3 = -60 degrees, psi-3 = 0 degrees." [PMID:27428516]
subset: biosapiens
synonym: "beta turn type six a two" EXACT []
synonym: "type VIa2 beta turn" EXACT []
synonym: "type VIa2 turn" EXACT []
is_a: SO:0001151 ! beta_turn_type_six_a

[Term]
id: SO:0001154
name: beta_turn_type_six_b
namespace: sequence
def: "A motif of four consecutive peptide residues, of which the i+2 residue is proline, and that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -120 degrees, psi ~ 120 degrees. Residue(i+2): phi ~ -60 degrees, psi ~ 0 degrees." [PMID:2371257, SO:cb]
subset: biosapiens
synonym: "beta turn type six b" EXACT []
synonym: "type VIb beta turn" EXACT []
synonym: "type VIb turn" EXACT []
is_a: SO:0001150 ! beta_turn_type_six

[Term]
id: SO:0001155
name: beta_turn_type_eight
namespace: sequence
def: "A motif of four consecutive peptide residues that may contain one H-bond, which, if present, is between the main-chain CO of the first residue and the main-chain NH of the fourth and is characterized by the dihedral angles: Residue(i+1): phi ~ -60 degrees, psi ~ -30 degrees. Residue(i+2): phi ~ -120 degrees, psi ~ 120 degrees." [PMID:2371257, SO:cb]
subset: biosapiens
synonym: "beta turn type eight" EXACT []
synonym: "type VIII beta turn" EXACT []
synonym: "type VIII turn" EXACT []
is_a: SO:0001133 ! beta_turn

[Term]
id: SO:0100001
name: biochemical_region_of_peptide
namespace: sequence
def: "A region of a peptide that is involved in a biochemical function." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "biochemical motif" EXACT []
synonym: "biochemical region of peptide" EXACT []
synonym: "biochemical_region" RELATED []
is_a: SO:0001067 ! polypeptide_motif

[Term]
id: SO:0100002
name: molecular_contact_region
namespace: sequence
def: "A region that is involved a contact with another molecule." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "molecular contact region" RELATED []
is_a: SO:0100001 ! biochemical_region_of_peptide

[Term]
id: SO:0100003
name: intrinsically_unstructured_polypeptide_region
namespace: sequence
def: "A region of polypeptide chain with high conformational flexibility." [EBIBS:GAR]
subset: biosapiens
synonym: "disordered region" RELATED BS []
synonym: "intrinsically unstructured polypeptide region" EXACT []
is_a: SO:0001070 ! polypeptide_structural_region

[Term]
id: SO:0100004
name: catmat_left_handed_three
namespace: sequence
def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-3l" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100005
name: catmat_left_handed_four
namespace: sequence
def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-4l" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100006
name: catmat_right_handed_three
namespace: sequence
def: "A motif of 3 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -75 bounds -100 to -50, res i+1: psi 140 bounds 110 to 170. An extra restriction of the length of the O to O distance would be useful, that it be less than 5 Angstrom. More precisely these two oxygens are the main chain carbonyl oxygen atoms of residues i-1 and i+1." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-3r" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100007
name: catmat_right_handed_four
namespace: sequence
def: "A motif of 4 consecutive residues with dihedral angles as follows: res i: phi -90 bounds -120 to -60, res i: psi -10 bounds -50 to 30, res i+1: phi -90 bounds -120 to -60, res i+1: psi -10 bounds -50 to 30, res i+2: phi -75 bounds -100 to -50, res i+2: psi 140 bounds 110 to 170. The extra restriction of the length of the O to O distance is similar, that it be less than 5 Angstrom. In this case these two Oxygen atoms are the main chain carbonyl oxygen atoms of residues i-1 and i+2." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "catmat-4r" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100008
name: alpha_beta_motif
namespace: sequence
def: "A motif of five consecutive residues and two H-bonds in which: H-bond between CO of residue(i) and NH of residue(i+4), H-bond between CO of residue(i) and NH of residue(i+3),Phi angles of residues(i+1), (i+2) and (i+3) are negative." [EBIBS:GAR, http://www.ebi.ac.uk/msd-srv/msdmotif/]
subset: biosapiens
synonym: "alpha beta motif" EXACT []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100009
name: lipoprotein_signal_peptide
namespace: sequence
def: "A peptide that acts as a signal for both membrane translocation and lipid attachment in prokaryotes." [EBIBS:GAR]
subset: biosapiens
synonym: "lipoprotein signal peptide" EXACT []
synonym: "prokaryotic membrane lipoprotein lipid attachment site" EXACT []
is_a: SO:0100011 ! cleaved_peptide_region

[Term]
id: SO:0100010
name: no_output
namespace: sequence
def: "An experimental region wherean analysis has been run and not produced any annotation." [EBIBS:GAR]
subset: biosapiens
synonym: "no output" EXACT BS []

[Term]
id: SO:0100011
name: cleaved_peptide_region
namespace: sequence
def: "The cleaved_peptide_region is the region of a peptide sequence that is cleaved during maturation." [EBIBS:GAR]
comment: Range.
subset: biosapiens
subset: SOFA
synonym: "cleaved peptide region" EXACT []
is_a: SO:0000839 ! polypeptide_region
relationship: part_of SO:0001063 ! immature_peptide_region

[Term]
id: SO:0100012
name: peptide_coil
namespace: sequence
def: "Irregular, unstructured regions of a protein's backbone, as distinct from the regular region (namely alpha helix and beta strand - characterised by specific patterns of main-chain hydrogen bonds)." [EBIBS:GAR]
subset: biosapiens
synonym: "coil" RELATED BS []
synonym: "peptide coil" EXACT []
synonym: "random coil" RELATED BS []
is_a: SO:0001078 ! polypeptide_secondary_structure

[Term]
id: SO:0100013
name: hydrophobic_region_of_peptide
namespace: sequence
def: "Hydrophobic regions are regions with a low affinity for water." [EBIBS:GAR]
comment: Range.
subset: biosapiens
synonym: "hydropathic" RELATED []
synonym: "hydrophobic region of peptide" RELATED []
synonym: "hydrophobic_region" EXACT []
synonym: "hydrophobicity" RELATED []
is_a: SO:0000839 ! polypeptide_region

[Term]
id: SO:0100014
name: n_terminal_region
namespace: sequence
def: "The amino-terminal positively-charged region of a signal peptide (approx 1-5 aa)." [EBIBS:GAR]
subset: biosapiens
synonym: "N-region" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0000418 ! signal_peptide

[Term]
id: SO:0100015
name: c_terminal_region
namespace: sequence
def: "The more polar, carboxy-terminal region of the signal peptide (approx 3-7 aa)." [EBIBS:GAR]
subset: biosapiens
synonym: "C-region" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0000418 ! signal_peptide

[Term]
id: SO:0100016
name: central_hydrophobic_region_of_signal_peptide
namespace: sequence
def: "The central, hydrophobic region of the signal peptide (approx 7-15 aa)." [EBIBS:GAR]
subset: biosapiens
synonym: "central hydrophobic region of signal peptide" EXACT []
synonym: "central_hydrophobic_region" RELATED []
synonym: "H-region" RELATED []
is_a: SO:0100011 ! cleaved_peptide_region
relationship: part_of SO:0000418 ! signal_peptide

[Term]
id: SO:0100017
name: polypeptide_conserved_motif
namespace: sequence
def: "A conserved motif is a short (up to 20 amino acids) region of biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]
subset: biosapiens
synonym: "motif" RELATED []
is_a: SO:0001067 ! polypeptide_motif

[Term]
id: SO:0100018
name: polypeptide_binding_motif
namespace: sequence
def: "A polypeptide binding motif is a short (up to 20 amino acids) polypeptide region of biological interest that contains one or more amino acids experimentally shown to bind to a ligand." [EBIBS:GAR]
subset: biosapiens
synonym: "binding" RELATED [uniprot:feature_type]
synonym: "polypeptide binding motif" EXACT []
is_a: SO:0100001 ! biochemical_region_of_peptide

[Term]
id: SO:0100019
name: polypeptide_catalytic_motif
namespace: sequence
def: "A polypeptide catalytic motif is a short (up to 20 amino acids) polypeptide region that contains one or more active site residues." [EBIBS:GAR]
subset: biosapiens
synonym: "catalytic_motif" RELATED []
synonym: "polypeptide catalytic motif" EXACT []
is_a: SO:0100001 ! biochemical_region_of_peptide

[Term]
id: SO:0100020
name: polypeptide_DNA_contact
namespace: sequence
def: "A binding site that, in the polypeptide molecule, interacts selectively and non-covalently with DNA." [EBIBS:GAR, SO:ke]
subset: biosapiens
synonym: "DNA_bind" EXACT BS [uniprot:feature]
synonym: "polypeptide DNA contact" EXACT []
is_a: SO:0000409 ! binding_site
is_a: SO:0100002 ! molecular_contact_region

[Term]
id: SO:0100021
name: polypeptide_conserved_region
namespace: sequence
def: "A subsection of sequence with biological interest that is conserved in different proteins. They may or may not have functional or structural significance within the proteins in which they are found." [EBIBS:GAR]
subset: biosapiens
synonym: "polypeptide conserved region" EXACT []
is_a: SO:0000839 ! polypeptide_region

[Typedef]
id: adjacent_to
name: adjacent_to
namespace: sequence
def: "A geometric operator, specified in Egenhofer 1989. Two features meet if they share a junction on the sequence. X adjacent_to Y iff X and Y share a boundary but do not overlap." [PMID:20226267, SO:ke]
subset: SOFA

[Typedef]
id: associated_with
name: associated_with
namespace: sequence
comment: This relationship is vague and up for discussion.

[Typedef]
id: complete_evidence_for_feature
name: complete_evidence_for_feature
namespace: sequence
def: "B is complete_evidence_for_feature A if the extent (5' and 3' boundaries) and internal boundaries of B fully support the extent and internal boundaries of A." [SO:ke]
comment: If A is a feature with multiple regions such as a multi exon transcript, the supporting EST evidence is complete if each of the regions is supported by an equivalent region in B. Also there must be no extra regions in B that are not represented in A. This relationship was requested by jeltje on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
is_transitive: true
is_a: evidence_for_feature ! evidence_for_feature

[Typedef]
id: connects_on
name: connects_on
namespace: sequence
def: "X connects_on Y, Z, R iff whenever Z is on a R, X is adjacent to a Y and adjacent to a Z." [PMID:20226267]
comment: Example: A splice_junction connects_on exon, exon, mature_transcript.
created_by: kareneilbeck
creation_date: 2010-10-14T01:38:51Z

[Typedef]
id: contained_by
name: contained_by
namespace: sequence
def: "X contained_by Y iff X starts after start of Y and X ends before end of Y." [PMID:20226267]
comment: The inverse is contains. Example: intein contained_by immature_peptide_region.
is_transitive: true
created_by: kareneilbeck
creation_date: 2010-10-14T01:26:16Z

[Typedef]
id: contains
name: contains
namespace: sequence
def: "The inverse of contained_by." [PMID:20226267]
comment: Example: pre_miRNA contains miRNA_loop.
is_transitive: true
created_by: kareneilbeck
creation_date: 2010-10-14T01:32:15Z

[Typedef]
id: derives_from
name: derives_from
namespace: sequence
subset: SOFA
is_transitive: true

[Typedef]
id: disconnected_from
name: disconnected_from
namespace: sequence
def: "X is disconnected_from Y iff it is not the case that X overlaps Y." [PMID:20226267]
created_by: kareneilbeck
creation_date: 2010-10-14T01:42:10Z

[Typedef]
id: edited_from
name: edited_from
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:19:45Z

[Typedef]
id: edited_to
name: edited_to
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:19:11Z

[Typedef]
id: evidence_for_feature
name: evidence_for_feature
namespace: sequence
def: "B is evidence_for_feature A, if an instance of B supports the existence of A." [SO:ke]
comment: This relationship was requested by nlw on the SO term tracker. The thread for the discussion is available can be accessed via tracker ID:1917222.
is_transitive: true

[Typedef]
id: exemplar_of
name: exemplar_of
namespace: sequence
def: "X is exemplar of Y if X is the best evidence for Y." [SO:ke]
comment: Tracker id: 2594157.

[Typedef]
id: finished_by
name: finished_by
namespace: sequence
def: "Xy is finished_by Y if Y part of X, and X and Y share a 3' boundary." [PMID:20226267]
comment: Example CDS finished_by stop_codon.
created_by: kareneilbeck
creation_date: 2010-10-14T01:45:45Z

[Typedef]
id: finishes
name: finishes
namespace: sequence
def: "X finishes Y if X is part_of Y and X and Y share a 3' or C terminal boundary." [PMID:20226267]
comment: Example: stop_codon finishes CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T02:17:53Z

[Typedef]
id: gained
name: gained
namespace: sequence
def: "X gained Y if X is a variant_of X' and Y part of X but not X'." [SO:ke]
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may gain a stop codon not present in the reference sequence.
created_by: kareneilbeck
creation_date: 2011-06-28T12:51:10Z

[Typedef]
id: genome_of
name: genome_of
namespace: sequence

[Typedef]
id: guided_by
name: guided_by
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:27:04Z

[Typedef]
id: guides
name: guides
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:27:24Z

[Typedef]
id: has_integral_part
name: has_integral_part
namespace: sequence
def: "X has_integral_part Y if and only if: X has_part Y and Y part_of X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: mRNA has_integral_part CDS.
is_a: has_part ! has_part
created_by: kareneilbeck
creation_date: 2009-08-19T12:01:46Z

[Typedef]
id: has_origin
name: has_origin
namespace: sequence

[Typedef]
id: has_part
name: has_part
namespace: sequence
def: "Inverse of part_of." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: operon has_part gene.

[Typedef]
id: has_quality
name: has_quality
namespace: sequence
comment: The relationship between a feature and an attribute.

[Typedef]
id: homologous_to
name: homologous_to
namespace: sequence
subset: SOFA
is_symmetric: true
is_a: similar_to ! similar_to

[Typedef]
id: integral_part_of
name: integral_part_of
namespace: sequence
def: "X integral_part_of Y if and only if: X part_of Y and Y has_part X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: exon integral_part_of transcript.
is_a: part_of ! part_of
created_by: kareneilbeck
creation_date: 2009-08-19T12:03:28Z

[Typedef]
id: is_consecutive_sequence_of
name: is_consecutive_sequence_of
namespace: sequence
def: "R is_consecutive_sequence_of R iff every instance of R is equivalent to a collection of instances of U:u1, u2, un, such that no pair of ux uy is overlapping and for all ux, it is adjacent to ux-1 and ux+1, with the exception of the initial and terminal u1,and un (which may be identical)." [PMID:20226267]
comment: Example: region is consecutive_sequence of base.
created_by: kareneilbeck
creation_date: 2010-10-14T02:19:48Z

[Typedef]
id: lost
name: lost
namespace: sequence
def: "X lost Y if X is a variant_of X' and Y part of X' but not X." [SO:ke]
comment: A relation with which to annotate the changes in a variant sequence with respect to a reference.\nFor example a variant transcript may have lost a stop codon present in the reference sequence.
created_by: kareneilbeck
creation_date: 2011-06-28T12:53:16Z

[Typedef]
id: maximally_overlaps
name: maximally_overlaps
namespace: sequence
def: "A maximally_overlaps X iff all parts of A (including A itself) overlap both A and Y." [PMID:20226267]
comment: Example: non_coding_region_of_exon maximally_overlaps the intersections of exon and UTR.
created_by: kareneilbeck
creation_date: 2010-10-14T01:34:48Z

[Typedef]
id: member_of
name: member_of
namespace: sequence
comment: A subtype of part_of. Inverse is collection_of. Winston, M, Chaffin, R, Herrmann: A taxonomy of part-whole relations. Cognitive Science 1987, 11:417-444.
subset: SOFA
is_transitive: true
is_a: part_of ! part_of

[Typedef]
id: non_functional_homolog_of
name: non_functional_homolog_of
namespace: sequence
def: "A relationship between a pseudogenic feature and its functional ancestor." [SO:ke]
subset: SOFA
is_a: homologous_to ! homologous_to

[Typedef]
id: orthologous_to
name: orthologous_to
namespace: sequence
subset: SOFA
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: overlaps
name: overlaps
namespace: sequence
def: "X overlaps Y iff there exists some Z such that Z contained_by X and Z contained_by Y." [PMID:20226267]
comment: Example: coding_exon overlaps CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T01:33:15Z

[Typedef]
id: paralogous_to
name: paralogous_to
namespace: sequence
subset: SOFA
is_symmetric: true
is_a: homologous_to ! homologous_to

[Typedef]
id: part_of
name: part_of
namespace: sequence
def: "X part_of Y if X is a subregion of Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: amino_acid part_of polypeptide.
subset: SOFA
is_transitive: true

[Typedef]
id: partial_evidence_for_feature
name: partial_evidence_for_feature
namespace: sequence
def: "B is partial_evidence_for_feature A if the extent of B supports part_of but not all of A." [SO:ke]
is_a: evidence_for_feature ! evidence_for_feature

[Typedef]
id: position_of
name: position_of
namespace: sequence

[Typedef]
id: processed_from
name: processed_from
namespace: sequence
def: "Inverse of processed_into." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: miRNA processed_from miRNA_primary_transcript.
created_by: kareneilbeck
creation_date: 2009-08-19T12:14:00Z

[Typedef]
id: processed_into
name: processed_into
namespace: sequence
def: "X is processed_into Y if a region X is modified to create Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: miRNA_primary_transcript processed into miRNA.
created_by: kareneilbeck
creation_date: 2009-08-19T12:15:02Z

[Typedef]
id: recombined_from
name: recombined_from
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:21:03Z

[Typedef]
id: recombined_to
name: recombined_to
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:20:07Z

[Typedef]
id: sequence_of
name: sequence_of
namespace: sequence

[Typedef]
id: similar_to
name: similar_to
namespace: sequence
subset: SOFA
is_symmetric: true

[Typedef]
id: started_by
name: started_by
namespace: sequence
def: "X is strted_by Y if Y is part_of X and X and Y share a 5' boundary." [PMID:20226267]
comment: Example: CDS started_by start_codon.
created_by: kareneilbeck
creation_date: 2010-10-14T01:43:55Z

[Typedef]
id: starts
name: starts
namespace: sequence
def: "X starts Y if X is part of Y, and A and Y share a 5' or N-terminal boundary." [PMID:20226267]
comment: Example: start_codon starts CDS.
created_by: kareneilbeck
creation_date: 2010-10-14T01:47:53Z

[Typedef]
id: trans_spliced_from
name: trans_spliced_from
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:22:14Z

[Typedef]
id: trans_spliced_to
name: trans_spliced_to
namespace: sequence
created_by: kareneilbeck
creation_date: 2009-08-19T02:22:00Z

[Typedef]
id: transcribed_from
name: transcribed_from
namespace: sequence
def: "X is transcribed_from Y if X is synthesized from template Y." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: primary_transcript transcribed_from gene.
created_by: kareneilbeck
creation_date: 2009-08-19T12:05:39Z

[Typedef]
id: transcribed_to
name: transcribed_to
namespace: sequence
def: "Inverse of transcribed_from." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: gene transcribed_to primary_transcript.
created_by: kareneilbeck
creation_date: 2009-08-19T12:08:24Z

[Typedef]
id: translates_to
name: translates_to
namespace: sequence
def: "Inverse of translation _of." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: codon translates_to amino_acid.
created_by: kareneilbeck
creation_date: 2009-08-19T12:11:53Z

[Typedef]
id: translation_of
name: translation_of
namespace: sequence
def: "X is translation of Y if Y is translated by ribosome to create X." [http://precedings.nature.com/documents/3495/version/1]
comment: Example: Polypeptide translation_of CDS.
created_by: kareneilbeck
creation_date: 2009-08-19T12:09:59Z

[Typedef]
id: variant_of
name: variant_of
namespace: sequence
def: "A' is a variant (mutation) of A = definition every instance of A' is either an immediate mutation of some instance of A, or there is a chain of immediate mutation processes linking A' to some instance of A." [SO:immuno_workshop]
comment: Added to SO during the immunology workshop, June 2007. This relationship was approved by Barry Smith.