# FEATURE PSI-IDP CV TERMs

<!-- TO DO:
# do we keep synonyms from PSI-MI CV
# do we keep types of synonyms from PSI-MI CV (alternate, short,...)
# do we define subsets similar to PSI-MI CV
# do we copy whole branches or select only terms useful to us from different branches
# header
# copyright statements
# namespace
# complete missing PMIDs
# change all 14755292 to 31824649, and later to PSI-ID pmid
# define PSI-ID specific term ID's
# check definitions
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We need to define a PSI-ID controlled vocabulary, specifically describing aspects of intrinsically disordered proteins and
IDP experiments. This CV will be used to annotate data captured in the PSI-ID XML schema and elements of the schema. Many
terms can be taken from the PSI-MI CV, but as these terms are specific for molecular interactions some of them might need
to be redefined. Also, as the terms of the PSI-MI CV are part of the root term 'molecular interaction', branches of this
CV need to be copied to the PSI-ID CV to make them IDP specific, using an IDP specific root term and namespace.

Branches from the PSI-MI CV we can use:
- alias type (to describe the type of nomenclature used to describe an object or entity in the PSI-ID XML format)
- attribute name (to describe free text stored as attribute value in the PSI-ID XML format)
- cross-reference type (to describe the type of information a cross-reference in the PSI-ID XML format is pointing to)
- database citation (to name databases used to cross-reference IDP-related data in the PSI-ID XML format)
- experimental preparation (to describe experimental treatment and status of experimental constructs analysed in IDP experiments in the PSI-ID XML format)
- feature detection method (will we use this in the schema?) (to describe the method used to determine the features of experimental constructs analysed in IDP experiments in the PSI-ID XML format)
# many methods used for feature detection are present in ECO; we can use these?
- feature range status (to describe the resolution of sequence positions of an experimental construct feature in the PSI-ID XML format)
- feature type (to describe the type of feature of an experimental constructs analysed in IDP experiments in the PSI-ID XML format)
- [interaction] confidence (to describe a measure of confidence in a specific structure state or IDP experiment in the PSI-ID XML format)
- [interactor] type (probably only in a later version of the schema, in which more experimental details might be captured, involving molecules other than proteins) (to describe the type of molecule involved in the experiment)
- parameter type (to describe the type of an experimental variable used in the experiment)
- parameter unit (to describe the unit of an experimental variable used in the experiment)
- [participant] identification method (to describe the method used to determine the molecules/experimental constructs used in the experiment)
# many methods used for molecule identification are present in ECO; we can use these?

Branches from the PSI-MI CV we will probably not use (at least not in a first version of the schema):
- biological role
- causal interaction
- cooperative interaction
- curation content
- curation quality
- experimental role
- interaction detection method (we will need to use methods to determine the structure of a protein or protein region, taken from the ECO CV)
- interaction type (we will need to use terms to describe the structure state of a protein or protein region, taken from the IDPO CV)

-->

<!-- BRANCH FOR FEATURE RANGE STATUS ANNOTATION -->

[Term]
id:
name: feature range status
def: "Describes sequence positions resolution of a given feature of a region or experimental construct. In the PSI-ID schema this CV is associated with the start and end position of a feature range." [PMID:31824649]
synonym: "endStatus" EXACT PSI-ID-alternate []
synonym: "startStatus" EXACT PSI-ID-alternate []
relationship: part_of ID:0000 ! intrinsically disordered protein

[Term]
id:
name: c-terminal position
def: "Term describing the last amino acid of a peptide chain." [PMID:31824649]
comment: Displayed as 'c'.
synonym: "c-term" EXACT PSI-ID-alternate []
synonym: "c-terminal" EXACT PSI-ID-short []
synonym: "c-terminus" EXACT PSI-ID-alternate []
synonym: "carboxy-terminus" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature range status

[Term]
id:
name: certain sequence position
def: "Position within the sequence clearly defined." [PMID:31824649]
synonym: "certain" EXACT PSI-ID-short []
is_a: ??:xxxx ! feature range status

[Term]
id:
name: greater-than
def: "Partially determined sequence position known to be in a location higher than a given position." [PMID:31824649]
comment: Displayed as '>'.
is_a: ??:xxxx ! feature range status

[Term]
id:
name: less-than
def: "Partially determined sequence position known to be in a position lower than a given position." [PMID:31824649]
comment: Displayed as '<'.
is_a: ??:xxxx ! feature range status

[Term]
id:
name: range
def: "Describes a sequence position known to be in a certain range, where the exact position is unclear." [PMID:31824649]
comment: For instance when an amino acid modification is known to be in the region from 5 to 7. Displayed as '..'.
is_a: ??:xxxx ! feature range status

[Term]
id:
name: undetermined sequence position
def: "Term describing a completely unknown or unspecified sequence position." [PMID:31824649]
comment: Displayed as '?'.
synonym: "undetermined" EXACT PSI-ID-short []
is_a: ??:xxxx ! feature range status

[Term]
id:
name: n-terminal position
def: "Term describing the first amino acid of a peptide chain." [PMID:31824649]
comment: Displayed as 'n'.
synonym: "amino-terminus" EXACT PSI-ID-alternate []
synonym: "n-term" EXACT PSI-ID-alternate []
synonym: "n-terminal " EXACT PSI-ID-short []
synonym: "n-terminus" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! feature range status

[Term]
id:
name: ragged n-terminus
def: "Mixture of protein forms where N-terminus has been progressively truncated." [PMID:31824649]
is_a: ??:xxxx ! n-terminal position

[Term]
id:
name: c-terminal range
def: "The C-terminal region of a sequence, exact coordinates not available." [PMID:31824649]
synonym: "c-term range" EXACT PSI-ID-short []
is_a: ??:xxxx ! feature range status

[Term]
id:
name: n-terminal range
def: "The N-terminal region of a sequence, exact coordinates not available." [PMID:31824649]
synonym: "n-term range" EXACT PSI-ID-short []
is_a: ??:xxxx ! feature range status

<!-- BRANCH FOR FEATURE TYPE ANNOTATION -->

[Term]
id:
name: feature type
def: "Property of a subsequence that may interfere with the function and/or structure state of a molecule or molecule region." [PMID:14755292]
relationship: part_of ID:0000 ! intrinsically disordered protein

# biological features - some of the terms below have child terms (not listed here) that specify the effect of the feature on an interaction; these might be adapted to annotate the effect on the structure state or function of a molecule or molecule region

[Term]
id:
name: biological feature
def: "Property of a subsequence that may be involved with or interfere with the function and/or structure state of a molecule or molecule region." [PMID:14755292]
is_a: ??:xxxx ! feature type

[Term]
id:
name: binding-associated region
def: "A region of a molecule or a component of a complex involved in an interaction. This may or may not be a region of the molecule in direct contact with the interacting partner." [PMID:14755292]
synonym: "binding component" RELATED []
synonym: "binding region" EXACT PSI-ID-short []
synonym: "binding site" BROAD []
is_a: ??:xxxx ! biological feature

[Term]
id:
name: mutation
def: "A change in a sequence or structure in comparison to a reference entity due to a insertion, deletion or substitution event." [PMID:14755292]
is_a: ??:xxxx ! biological feature

[Term]
id:
name: polyprotein fragment
def: "Subpart of a polyprotein that is naturally cleaved in vivo." [PMID:14577292]
synonym: "chain" RELATED []
synonym: "polyprotein frag" EXACT PSI-ID-short []
is_a: ??:xxxx ! biological feature

[Term]
id:
name: allosteric post-translational modification
def: "A post-translational modification that elicits an allosteric response upon addition to a target molecule. An allosteric post-translational modification is identified by referring to its feature id." [PMID:18706817]
subset: PSI-MI_slim
synonym: "allosteric ptm" EXACT PSI-MI-short []
is_a: ??:xxxx ! biological feature

[Term]
id:
name: variant
def: "A natural change in a sequence or structure in comparison to a reference entity." []
is_a: ??:xxxx ! biological feature

[Term]
id:
name: DNA chemical modification
def: "Chemical alterations occurring at the nucleotide level in a DNA molecule. The process can involve covalent modifications (i.e. methylations) or other forms of chemical modification." [PMID:14755292]
synonym: "dna chemical modification" EXACT PSI-ID-short []
synonym: "DNA chemical modification" EXACT PSI-ID-alternate []
synonym: "DNA epigenetic modification" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! biological feature

[Term]
id:
name: RNA chemical modification
def: "Chemical alterations occurring at the nucleotide level in an RNA molecule. The process can involve covalent modifications (i.e. 2'-O-methylation) or other forms of chemical modification, such as isomerizations (i.e. pseudouridylation)." [PMID:14755292]
synonym: "post-transcriptional modification" EXACT PSI-ID-alternate []
synonym: "rna chemical modification" EXACT PSI-ID-short []
synonym: "RNA chemical modification" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! biological feature

[Term]
id:
name: carbohydrate chemical modification
def: "Chemical alterations occurring in a carbohydrate molecule. The process can involve covalent modifications (i.e. sulfations) or other forms of chemical modification." [PMID:14755292]
synonym: "carbohydrate chemical modification" EXACT PSI-ID-short []
is_a: ??:xxxx ! biological feature

[Term]
id:
name: attached carbohydrate
def: "Carbohydrate species chemically attached to proteins or protein regions, or other organic molecules." [PMID:14755292]
comment: Specific carbohydrate species can be represented through the MOD ontology and their representation escapes the scope of this CV.
synonym: "attached glycan" EXACT PSI-ID-alternate []
synonym: "glycosylation" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! biological feature

# experimental features - some of the terms below have child terms (not listed here) that specify the type of feature; these might be added as needed

[Term]
id:
name: experimental feature
def: "The form of a molecule or molecule region that was actually used to experimentally demonstrate the structure state (i.e. the experimental construct), that may differ from the sequence described by the identifying accession number." [PMID:14755292]
is_a: ??:xxxx ! feature type

[Term]
id:
name: isotope label
def: "One of several nuclides having the same number of protons in their nuclei and hence having the same atomic number, but differing in the number of neutrons and therefore, in the mass number." [PMID:14755292]
is_a: ??:xxxx ! experimental feature

[Term]
id:
name: radiolabel
def: "A radiolabelled molecule has radio isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule." [PMID:14755292]
synonym: "radiolabeled" EXACT PSI-ID-alternate []
synonym: "radiolabelled" EXACT PSI-ID-short []
is_a: ??:xxxx ! isotope label

[Term]
id:
name: 131i radiolabel
def: "Molecule labelled with 131 radio isotope of iodine atoms." [PMID:14755292]
synonym: "131I" EXACT PSI-ID-alternate []
synonym: "I131" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! radiolabel

[Term]
id:
name: 14c radiolabel
def: "Molecule labelled with the radio isotope 14 of carbon atoms." [PMID:14755292]
synonym: "14C" EXACT PSI-ID-alternate []
synonym: "C14" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! radiolabel

[Term]
id:
name: 32p radiolabel
def: "Molecule labelled with the radio isotope 32 of phosphorus atoms." [PMID:14755292]
synonym: "32P" EXACT PSI-ID-alternate []
synonym: "P32" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! radiolabel

[Term]
id:
name: 33p radiolabel
def: "Molecule labelled with the radio isotope 33 of phosphorus atoms." [PMID:14755292]
synonym: "33P" EXACT PSI-ID-alternate []
synonym: "P33" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! radiolabel

[Term]
id:
name: 3h radiolabel
def: "Molecules labelled with isotope 3 of hydrogen atoms." [PMID:14755292]
synonym: "3H" EXACT PSI-ID-alternate []
synonym: "H3" EXACT PSI-ID-alternate []
synonym: "tritium" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! radiolabel

[Term]
id:
name: 35s radiolabel
def: "Molecule labelled with 35 radio isotope of sulfur. Proteins are often metabolically labelled, usually be growth in 35S labelled culture medium." [PMID:14755292]
synonym: "35S" EXACT PSI-ID-alternate []
synonym: "S35" EXACT PSI-ID-alternate []
synonym: "s35 radiolabelled" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! radiolabel

[Term]
id:
name: 125i radiolabel
def: "Molecule labelled with 125 radio isotope of iodine atoms." [PMID:14755292]
synonym: "125I" EXACT PSI-ID-alternate []
synonym: "I125" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! radiolabel

[Term]
id:
name: rare isotope label
def: "Molecule can be labelled including rare isotopes among its constituent atoms that can be used to identify, localize or quantify the full molecule." [PMID:14577292]
synonym: "rare isotope label" EXACT PSI-ID-short []
is_a: ??:xxxx ! isotope label

[Term]
id:
name: 13c label
def: "Molecules labelled with isotope 13 of carbon atoms." [PMID:14577292]
synonym: "13C" EXACT PSI-ID-alternate []
synonym: "C13" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! rare isotope label

[Term]
id:
name: 15n label
def: "Molecules labelled with isotope 15 of nytrogen atoms." [PMID:14577292]
synonym: "15N" EXACT PSI-ID-alternate []
synonym: "N15" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! rare isotope label

[Term]
id:
name: 2h label
def: "Molecules labelled with isotope 2 of hydrogen atoms." [PMID:14577292]
subset: PSI-MI_slim
synonym: "2H2" EXACT PSI-ID-alternate []
synonym: "D2" EXACT PSI-ID-alternate []
synonym: "deuterium" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! rare isotope label

[Term]
id:
name: dye label
def: "Dye coupled to a molecule allowing its identification isolation and monitoring." [PMID:14577292]
synonym: "dye labelled" EXACT PSI-ID-short []
is_a: ??:xxxx ! experimental feature

# many different types of dye label are listed as child terms (not listed here), and can be added to PSI-ID CV as needed

[Term]
id:
name: tag
def: "Small molecules, peptides or full proteins that can be used as label as they confer some property that facilitates identification, purification and monitoring to the labeled molecule." [PMID:14755292]
is_a: ??:xxxx ! experimental feature

# many different types of tag are listed as child terms (not listed here), and can be added to PSI-ID CV as needed

[Term]
id:
name: identified peptide
def: "Peptide whose sequence is experimentally identified and can lead to a full protein identification." [PMID:14755292]
is_a: ??:xxxx ! experimental feature

[Term]
id:
name: spin label
def: "Paramagnetic fragment, most often a cyclic nitroxide derivative, covalently attached to a molecule of interest." [PMID:10966640]
is_a: ??:xxxx ! experimental feature

# different types of spin label are listed as child terms (not listed here), and can be added to PSI-ID CV as needed

[Term]
id:
name: dna overhang
def: "An overhang is a stretch of unpaired nucleotides in the end of a DNA molecule. These unpaired nucleotides can be in either strand, creating either 3' or 5' overhangs. Longer overhangs are called cohessive ends or sticky ends. They are most often created by restriction endonucleases when they cut DNA. Very often they cut the two DNA strands four base pairs from each other, creating a four-base 3' overhang in the other molecule and a complementary 5' overhang in the other. These ends are called cohessive since they are easily joined back together by a ligase" [PMID:14755292]
synonym: "cohessive ends" EXACT PSI-ID-alternate []
synonym: "sticky ends" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! experimental feature

[Term]
id:
name: 3 prime overhang
def: "An overhang is a stretch of unpaired nucleotides in the end of a 3' strand of a DNA molecule." [PMID:14755292]
subset: PSI-MI_slim
synonym: "3 prime sticky end" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! dna overhang

[Term]
id:
name: 5 prime overhang
def: "An overhang is a stretch of unpaired nucleotides in the end of a 5' strand of a DNA molecule." [PMID:14755292]
synonym: "5 prime sticky end" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! dna overhang

[Term]
id:
name: fluorophore
def: "A fluorophore is a component of a molecule which causes a molecule to be fluorescent. It is a functional group in a molecule which will absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength. The amount and wavelength of the emitted energy depend on both the fluorophore and the chemical environment of the fluorophore." [PMID:14755292]
is_a: ??:xxxx ! experimental feature

# many different types of fluorophore are listed as child terms (not listed here), and can be added to PSI-ID CV as needed

[Term]
id:
name: fluorescent dye label
def: "Dye label containing a fluorophore which absorb energy of a specific wavelength and re-emit energy at a different (but equally specific) wavelength." [PMID:14755292]
synonym: "fluorescent dye" EXACT PSI-ID-short []
is_a: ??:xxxx ! dye label
is_a: ??:xxxx ! fluorophore

# many different types of fluorescent dye label are listed as child terms (not listed here), and can be added to PSI-ID CV as needed

[Term]
id:
name: cross linker
def: "A variety of crosslinkers are used to analyze subunit structure of proteins, protein interactions and various parameters of protein function. Subunit structure is deduced since crosslinkers only bind surface amino residues in relatively close proximity in the native state. Protein interactions are often too weak or transient to be easily detected, but by crosslinking, the interactions can be captured and analyzed." [PMID:14755292]
synonym: "crosslinker" EXACT PSI-ISDalternate []
is_a: ??:xxxx ! experimental feature

[Term]
id:
name: spdp cross linker
def: "N -Succinimidyl 3-(2-pyridyldithio)-propionate, is heterobifunctional, thiol-cleavable \nand membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester \nthat will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond." [PMID:17360572]
synonym: "N -Succinimidyl 3-(2-pyridyldithio)-propionate" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! cross linker

[Term]
id:
name: lc-spdp cross linker
def: "Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate, is an heterobifunctional, thiol-cleavable \nand membrane permeable crosslinkers. It contains an amine-reactive N-hydroxysuccinimide (NHS) ester \nthat will react with lysine residues to form a stable amide bond. The other end of the spacer arm is terminated in the pyridyl disulfide group that will react with sulfhydryls to form a reversible disulfide bond. LC-SPDP is a derivative of the classical SPDP with a longer spacer arm." [PMID:17360572]
synonym: "Succinimidyl 6-(3-[2-pyridyldithio]-propionamido)hexanoate" EXACT PSI-ID-alternate []
is_a: ??:xxxx ! spdp cross linker

[Term]
id:
name: trapping mutant
def: "Permits the identification of substrates of enzymes by mutating residues, usually in the active site such that the enzyme will bind but not act on its substrate." [PMID:9050838]
synonym: "trap-mutant" EXACT PSI-MI-short []
is_a: ??:xxxx ! experimental feature